Rice promoters for regulation of plant expression

REFERENCE TO MATERIAL SUBMITTED ON COMPACT DISC

[0002] The sequence listing accompanying this application is contained on compact disc. The material on the CD-ROM (filed in duplicate herewith), on CD volume labeled “COPY 1” and “COPY 2”, each containing a text file named “6011 1-NP_SEQ_LST.txt” created Sep. 26, 2002, having a size of 8.81 MB, is hereby incorporated by reference in its entirety pursuant to 37 C.F.R. §1.52(e)(5).

FIELD OF THE INVENTION

[0003] The present invention relates generally to the field of plant molecular biology. More specifically, it relates to the regulation of gene expression in plants such as monocots.

BACKGROUND OF THE INVENTION

[0004] Manipulation of crop plants to alter and/or improve phenotypic characteristics (such as productivity or quality) requires the expression of heterologous genes in plant tissues. Such genetic manipulation relies on the availability of a means to drive and to control gene expression as required. For example, genetic manipulation relies on the availability and use of suitable promoters which are effective in plants and which regulate gene expression so as to give the desired effect(s) in the transgenic plant. It is advantageous to have the choice of a variety of different promoters so that the most suitable promoter may be selected for a particular gene, construct, cell, tissue, plant or environment. Moreover, the increasing interest in cotransforming plants with multiple plant transcription units (PTU) and the potential problems associated with using common regulatory sequences for these purposes merit having a variety of promoter sequences available. There is, therefore, a great need in the art for the identification of novel sequences that can be used for expression of selected transgenes in economically important plants. More specifically, there is a need for the systematic identification of genes that are expressed in a particular manner, e.g., using microarray technology.

SUMMARY OF THE INVENTION

[0005] The present invention provides an isolated nucleic acid molecule (polynucleotide) having a plant nucleotide sequence that directs tissue-specific or tissue-preferential, or constitutive, transcription of a linked nucleic acid segment in a plant or plant cell, e.g., a linked plant DNA comprising an open reading frame for a structural or regulatory gene.

[0006] In one embodiment of the invention, the nucleotide sequence of the invention directs tissue-specific (or tissue-preferential), or constitutive, transcription of a linked nucleic acid segment in a plant or plant cell and is preferably obtained or obtainable from plant genomic DNA having a gene comprising an open reading frame (ORF) encoding a polypeptide which is substantially similar, and preferably has at least 70% or more, e.g., between 71% and 89%, and even 90% or more, e.g., between 91% and 99%, amino acid sequence identity, to a polypeptide encoded by an Orgza, e.g., Oryza sativa, gene, with each individual number within this range of between 71% and 89% and 91% and 99% also being part of the invention, wherein said gene comprises any one of:

[0007] (i) SEQ ID NOs:2275-2672, 5959, 5972, 5973, 5977-5990 and 6001 (e.g., including a promoter obtained or obtainable from any one of SEQ ID NOs:2275-2672, 5959, 5972, 5973, 5977-5990 and 6001) which directs seed-specific (or seed-preferential) transcription of a linked nucleic acid segment;

[0008] (ii) SEQ ID NOs:2144-2274 (e.g., including a promoter obtained or obtainable from any one of SEQ ID NOs:2144-2274) which directs root-specific (or root-preferential) transcription of a linked nucleic acid segment;

[0009] (iii) SEQ ID NOs:1886-1918 (e.g., including a promoter obtained or obtainable from any one of SEQ ID NOs:1886-1918) which directs green tissue (leaf and stem)-specific (or green tissue-preferential) transcription of a linked nucleic acid segment;

[0010] (iv) SEQ ID NOs:1919-2085 (e.g., including a promoter obtained or obtainable from any one of SEQ ID NOs:1919-2085) which directs panicle-specific (or panicle-preferential) transcription of a linked nucleic acid segment;

[0011] (v) SEQ ID NOs:2086-2143 (e.g., including a promoter obtained or obtainable from any one of SEQ ID NOs:2086-2143) which directs pollen-specific (or pollen-preferential) transcription of a linked nucleic acid segment;

[0012] (vi) SEQ ID NOs: 1598-1885 and 5960-5971 (e.g., including a promoter obtained or obtainable from any one of SEQ ID NOs: 1598-1885 and 5960-5971, respectively) which directs constitutive transcription of a linked nucleic acid segment;

[0013] or

[0014] (a) a fragment (portion) thereof which has substantially the same promoter activity as the corresponding promoter listed in SEQ ID NOs:2275-2672, 5959, 5972, 5973, 5977-5990 and 6001, SEQ ID NOs:2144-2274, SEQ ID NOs:1886-1918, SEQ ID NOs:1919-2085, or SEQ ID NOs: 1598-1885 and 5960-5971;

[0015] (b) a nucleotide sequence having substantial similarity to a promoter sequence listed in SEQ ID NOs:2275-2672, 5959, 5972, 5973, 5977-5990 and 6001, SEQ ID NOs:2144-2274, SEQ ID NOs:1886-1918, SEQ ID NOs:1919-2085, or SEQ ID NOs: 1598-1885 and 5960-5971;

[0016] (c) a nucleotide sequence capable of hybridizing to a promoter sequence listed in SEQ ID NOs:2275-2672, 5959, 5972, 5973, 5977-5990 and 6001, SEQ ID NOs:2144-2274, SEQ ID NOs:1886-1918, SEQ ID NOs:1919-2085, or SEQ ID NOs: 1598-1885 and 5960-5971;

[0017] (d) a nucleotide sequence capable of hybridizing to a nucleic acid comprising 50 to 200 or more consecutive nucleotides of a nucleotide sequence listed in SEQ ID NOs:2275-2672, 5959, 5972, 5973, 5977-5990 and 6001, SEQ ID NOs:2144-2274, SEQ ID NOs:1886-1918, SEQ ID NOs:1919-2085, or SEQ ID NOs: 1598-1885 and 5960-5971 or the complement thereof;

[0018] (e) a nucleotide sequence which is the complement or reverse complement of any of the previously mentioned nucleotide sequences.

[0019] For example, in one embodiment, a plant nucleotide sequence is the promoter sequence for a gene, and preferably is obtained or obtainable from a gene, comprising an ORF encoding a polypeptide which is substantially similar, and preferably has at least 70% or more, e.g., between 71% and 89%, and even 90% or more, e.g., between 91% and 99%, amino acid sequence identity, to a polypeptide encoded by an Oryza, e.g., Oryza sativa, gene, with each individual number within this range of between 71% and 89% and 91% and 99% also being part of the invention, wherein said gene comprises an ORF comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1-398 and 5928-5939 (constitutively expressed ORFs), SEQ ID NOs:399-464 (green-specific ORFs); SEQ ID NOs:465-720 (panicle-specific ORFs), SEQ ID NOs:721-800 (pollen-specific ORFs), SEQ ID NOs:801-1019 (root-specific ORFs), SEQ ID NOs:1020-1597, 5927, 5940, 5941, 5945-5958 (seed-specific ORFs), and a fragment (portion) thereof which encodes a polypeptide which has substantially the same activity as the corresponding polypeptide encoded by an ORF listed in SEQ ID NOs: 1-398 and 5928-5939; SEQ ID NOs: 399-464, SEQ ID NOs:465-720, SEQ ID NOs:721-800, SEQ ID NOs:801-1019, and SEQ ID NOs:1020-1597, 5927, 5940, 5941, 5945-5958.

[0020] In another embodiment, a plant nucleotide sequence is the promoter sequence for a gene, and preferably is obtained or obtainable from a gene, which is substantially similar, and preferably has at least 70%, or more, e.g., between 71% and 89%, and even 90% or more, e.g., between 91% and 99%, nucleic acid sequence identity to an Oryza gene, with each individual number within this range of between 71% and 89% and 91% and 99% also being part of the invention, wherein said gene comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOs:2275-2672, 5959, 5972, 5973, 5977-5990 and 6001, SEQ ID NOs:2144-2274, SEQ ID NOs:1886-1918, SEQ ID NOs:1919-2085, SEQ ID NOs:2086-2143, SEQ ID NOs: 1598-1885 and 5960-5971, and a fragment (portion) thereof which has substantially the same promoter activity as the corresponding promoter listed in SEQ ID NOs:2275-2672, 5959, 5972, 5973, 5977-5990 and 6001, SEQ ID NOs:2144-2274, SEQ ID NOs:1886-1918, SEQ ID NOs:1919-2085, SEQ ID NOs:2086-2143, and SEQ ID NOs: 1598-1885 and 5960-5971.

[0021] In another embodiment the invention relates to a nucleotide sequence for a promoter, which is preferably obtained or obtainable from plant genomic DNA, from a gene comprising an ORF which is substantially similar, and preferably has at least 70% or more, e.g., between 71% and 89%, and even 90% or more, e.g., between 91% and 99%,, nucleic acid sequence identity, to an Oryza gene, with each individual number within this range of between 71% and 89% and 91% and 99% also being part of the invention, wherein said gene comprises an ORF comprising one of the sequences selected from the group consisting of SEQ ID NOs: 1-398 and 5928-5939; SEQ ID NOs: 399-464, SEQ ID NOs:465-720, SEQ ID NOs:721-800, SEQ ID NOs:801-1019, SEQ ID NOs:1020-1597, 5927, 5940, 5941, 5945-5958, and a fragment (portion) thereof which encodes a polypeptide which has substantially the same activity as the corresponding polypeptide encoded by an ORF listed in SEQ ID NOs: 1-398; SEQ ID NOs: 399-464, SEQ ID NOs:465-720, SEQ ID NOs:721-800, SEQ ID NOs:801-1019, and SEQ ID NOs:1020-1597, 5927, 5940, 5941, 5945-5958.

[0022] Hence, the isolated nucleic acid molecules of the invention include the orthologs of the Oryza sequences disclosed herein, i.e., the corresponding nucleotide sequences in organisms other than Oryza, including, but not limited to, plants other than Oryza, preferably cereal plants, e.g., corn, wheat, rye, turfgrass, sorghum, millet, sugarcane, barley and banana, but also non-cereal plants, e.g., alfalfa, sunflower, canola, soybean, cotton, peanut, tobacco or sugarbeet. An orthologous gene is a gene from a different species that encodes a product having the same or similar function, e.g., catalyzing the same reaction as a product encoded by a gene from a reference organism. Thus, an ortholog includes polypeptides having less than, e.g., 65% amino acid sequence identity, but which ortholog encodes a polypeptide having the same or similar function. Databases such GenBank may be employed to identify sequences related to the Oryza sequences, e.g., orthologs in cereal crops such as wheat and other cereals. Alternatively, recombinant DNA techniques such as hybridization or PCR may be employed to identify sequences related to the Oryza sequences or to clone the equivalent sequences from different Oryza DNAs. For example, SEQ ID NOs:2673-4708, SEQ ID NOs: 4768-5229, and SEQ ID NOs:5230-5926, which represent wheat, banana and maize orthologs of some of the rice sequences disclosed herein. The encoded ortholog products likely have at least 70% sequence identity to each other. Hence, the invention includes an isolated nucleic acid molecule comprising a nucleotide sequence from a gene that encodes a polypeptide having at least 70% identity to a polypeptide encoded by a gene having one or more of the Oryza sequences disclosed herein. For example, promoter sequences within the scope of the invention are those which direct expression of an open reading frame which encodes a polypeptide that is substantially similar to an Oryza polypeptide encoded by a gene having a promoter selected from the group consisting of SEQ ID NOs:1598-2672, 5959, 5972, 5973, 5977-5990 and 6001.

[0023] Preferably, the promoters of the invention include a consecutive stretch of about 25 to 2000, including 50 to 500 or 100 to 250, and up to 1000 or 1500, contiguous nucleotides, e.g., 40 to about 743, 60 to about 743, 125 to about 743, 250 to about 743, 400 to about 743, 600 to about 743, of any one of SEQ ID NOs:1598-2672, 5959, 5972, 5973, 5977-5990 and 6001, or the promoter orthologs thereof, which include the minimal promoter region.

[0024] In a particular embodiment of the invention said consecutive stretch of about 25 to 2000, including 50 to 500 or 100 to 250, and up to 1000 or 1500, contiguous nucleotides, e.g., 40 to about 743, 60 to about 743, 125 to about 743, 250 to about 743, 400 to about 743, 600 to about 743, has at least 75%, preferably 80%, more preferably 90% and most preferably 95%, nucleic acid sequence identity with a corresponding consecutive stretch of about 25 to 2000, including 50 to 500 or 100 to 250, and up to 1000 or 1500, contiguous nucleotides, e.g., 40 to about 743, 60 to about 743, 125 to about 743, 250 to about 743, 400 to about 743, 600 to about 743, of any one of SEQ ID NOs: 1598-2672, 5959, 5972, 5973, 5977-5990 and 6001, or the promoter orthologs thereof, which include the minimal promoter region. The above defined stretch of contiguous nucleotides preferably comprises one or more promoter motifs selected from the group consisting of TATA box, GC-box, CAAT-box and a transcription start site.

[0025] In case of promoters directing tissue-specific transcription of a linked nucleic acid segment in a plant or plant cell such as, for example, a promoter directing root-specific, green tissue (leaf and stem)-specific, seed-specific, panicle-specific, pollen-specific, etc., transcription, it is further preferred that previously defined stretch of contiguous nucleotides comprises further motifs that participate in the tissue specificity of said stretch(es) of nucleotides, e.g., for seed-specific promoters, motifs selected from the group consisting of the P box and GCNA elements, including but not limited to TGTAAAG and TGA(G/C)TCA.

[0026] The invention also provides an isolated nucleic acid molecule, e.g., DNA or RNA, comprising a plant nucleotide sequence comprising an open reading frame that is preferentially expressed in a specific plant tissue, i.e., in seeds, roots, green tissue (leaf and stem), panicle or pollen, or is expressed constitutively.

[0027] One embodiment the invention provides

[0028] (a) an isolated nucleic acid molecule, e.g., DNA or RNA, comprising a plant nucleotide sequence comprising an ORF that is constitutively expressed or preferentially expressed in a specific plant tissue, i.e., in seeds, roots, green tissue (leaf and stem), panicle or pollen and which is capable of hybridizing and thus substantially similar, and preferably has at least 70% or more, e.g., between 71% and 89%, and even 90% or more, e.g., between 91% and 99%,nucleic acid sequence identity, to an ORF expressed in a constitutive (e.g., an ORF comprising one of SEQ ID NOs:1-398 and 5928-5939) or in a tissue-specific or tissue-preferential manner, for example, in a seed-specific (or seed-preferential) manner, e.g., an ORF comprising one of SEQ ID NOs:1020-1597; 5927, 5940, 5941, 5945-5958

[0029] (i) a root-specific (or root-preferential) manner, e.g., an ORF comprising one of SEQ ID NOs:801-1019;

[0030] (ii) a green tissue (leaf and stem)-specific (or green tissue (leaf and stem)-preferential) manner, e.g., an ORF comprising one of SEQ ID NOs:399-464;

[0031] (iii) a panicle-specific (or panicle-preferential) manner, e.g., an ORF comprising one of SEQ ID NOs:465-720; or

[0032] (iv) a pollen-specific (or pollen-preferential) manner, e.g., an ORF comprising one of SEQ ID NOs:721-800; or

[0033] (b) a part thereof still encoding a partial-length polypeptide having substantially the same activity as the full-length polypeptide encoded by an ORF listed in SEQ ID NOs.1-398, and 5928-5939 and 399-1597, 5927, 5940, 5941, 5945-5958., e.g., at least 50%, more preferably at least 80%, even more preferably at least 90% to 95% the activity of the full-length polypeptide;

[0034] (c) the complement or reverse complement thereof

[0035] The invention also provides

[0036] (a) an isolated nucleic acid molecule, e.g., DNA or RNA, comprising a plant nucleotide sequence comprising an ORF that is constitutively expressed or preferentially expressed in a specific plant tissue, i.e., in seeds, roots, green tissue (leaf and stem), panicles or pollen and which encodes a polypeptide that is capable of hybridising and thus substantially similar, and preferably has at least 70% or more, e.g., between 71% and 89%, and even 90% or more, e.g., between 91% and 99%,, amino acid sequence identity, to a polypeptide encoded by an Oryza gene with each individual number within this range of between 71% and 89% and 91% and 99% also being part of the invention, wherein said gene comprises an ORF comprising any one of the sequences selected from the group consisting of SEQ ID NOs: 1-398, and 5928-5939 (constitutiv); SEQ ID NOs: 399-464 (green-tissue), SEQ ID NOs:465-720 (specific); SEQ ID NOs:721-800 (pollen); SEQ ID NOs:801-1019 (root); and SEQ ID NOs:1026-1597, 5927, 5940, 5941, 5945-5958 (seed),

[0037] (b) the complement or reverse complement thereof, and

[0038] (c) a fragment thereof still encoding a partial-length polypeptide having substantially the same activity as the full-length polypeptide encoded by an ORF listed in SEQ ID NOs.1-398 and 5928-5939 and 399-1597, 5927, 5940, 5941, 5945-5958, e.g., at least 50%, more preferably at least 80%, even more preferably at least 90% to 95% the activity of the full-length polypeptide

[0039] The invention also provides

[0040] (b) an isolated nucleic acid molecule, e.g., DNA or RNA, comprising a plant nucleotide sequence comprising an ORF that is constitutively expressed or preferentially expressed in a specific plant tissue, i.e., in seeds, roots, green tissue (leaf and stem), panicles or pollen and which encodes a polypeptide that is capable of hybridizing and thus substantially similar, and preferably has at least 70% or more, e.g., between 71% and 89%, and even 90% or more, e.g., between 91% and 99%, amino acid sequence identity, to a polypeptide encoded by an Oryza gene with each individual number within this range of between 71% and 89% and 91% and 99% also being part of the invention, wherein said gene comprises a promoter sequence as given in any one of the sequences selected from the group consisting of SEQ ID NOs: 1598-1885 and 5960-5971, SEQ ID NOs: 1886-1918, SEQ ID NOs:1919-2085, SEQ ID NOs:2086-2143, SEQ ID NOs:2144-2274, and SEQ ID NOs:2275-2672, 5959, 5972, 5973, 5977-5990 and 6001

[0041] (c) the complement or reverse complement thereof, and

[0042] (d) a fragment thereof having substantially the same activity as the corresponding promoter listed in SEQ ID NOs: SEQ ID NOs: 1598-1885, 5960-5971 and 1886-2672, 5959, 5972, 5973, 5977-5990 and 6001 respectively, e.g., at least 50%, more preferably at least 80%, even more preferably at least 90% to 95% of the activity.

[0043] The invention also provides

[0044] (a) an isolated nucleic acid molecule, e.g., DNA or RNA, comprising a plant nucleotide sequence comprising an ORF that is constitutively or preferentially expressed in a specific plant tissue, i.e., in seeds, roots, green tissue (leaf and stem), panicles or pollen and which is capable of hybridizing and thus substantially similar, and preferably has at least 70% or more, e.g., between 71% and 89%, and even 90% or more, e.g., between 91% and 99%, nucleic acid sequence identity, to an Oryza gene with each individual number within this range of between 71% and 89% and 91% and 99% also being part of the invention, wherein said gene is an ORF expressed in a constitutive or a tissue-specific or tissue-preferential manner and comprises a promoter as given in any one of the sequences selected from the group consisting of SEQ ID NOs: 1598-1885 and 5960-5971; SEQ ID NOs: 1886-1918, SEQ ID NOs:1919-2085; SEQ ID NOs:2086-2143; SEQ ID NOs:2144-2274; and SEQ ID NOs:2275-2672, 5959, 5972, 5973, 5977-5990 and 6001

[0045] (b) the complement or reverse complement thereof, and

[0046] (c) and a fragment thereof having substantially the same activity as the corresponding promoter listed in SEQ ID NOs: 1598-1885, 5960-5971 and SEQ ID NOs:1886-2672, 5959, 5972, 5973, 5977-5990 and 6001 respectively, , e.g., at least 50%, more preferably at least 80%, even more preferably at least 90% to 95% of the activity.

[0047] ORFs which are expressed in a constitutive or in tissue-specific or -preferential manner, may be useful to prepare plants that over- or under-express the encoded polypeptide product or to prepare knockout plants.

[0048] The promoters and open reading frames of the invention can be identified by employing an array of nucleic acid samples, e.g., each sample having a plurality of oligonucleotides, and each plurality corresponding to a different plant gene, on a solid substrate, e.g., a DNA chip, and probes corresponding to nucleic acid expressed in, for example, one or more plant tissues and/or at one or more developmental stages, e.g., probes corresponding to nucleic acid expressed in seed of a plant relative to control nucleic acid from sources other than seed. Thus, genes that are upregulated or downregulated in the majority of tissues at a majority of developmental stages, or upregulated or downregulated in one tissue such as in seed, can be systematically identified.

[0049] As described herein, GeneChip® technology was utilized to discover rice genes that are preferentially (or exclusively) expressed in seed, pollen, specific, root or green tissue, as well as those that are constitutively expressed. Specifically, labeled rice cRNA probes were hybridized to the rice DNA array, expression levels were determined by laser scanning and then rice genes were identified that had a particular expression pattern. The rice oligonucleotide probe array consists of probes from over 18,000 unique rice genes, which covers approximately 40-50% of the genome. This genome array permits a broader, more complete and less biased analysis of gene expression. Using this approach, 812 genes were identified, the expression of which was altered, e.g., specifically elevated, in seed tissues and 367 genes were identified that were preferentially expressed in endosperm, 91 genes were identified that were preferentially expressed in embryo, and 137 genes were identified that were preferentially expressed in aleurone; 618 genes were identified that were constitutively expressed; 335 genes were identified that were specifically or preferentially expressed in panicle; 265 genes were identified that were specifically or preferentially expressed in root tissue, 80 genes were identified that were specifically or preferentially expressed in pollen; and 90 genes were identified that were specifically or preferentially expressed in leaf and/or stem tissue.

[0050] Generally, the promoters of the invention may be employed to express a nucleic acid segment that is operably linked to said promoter such as, for example, an open reading frame, or a portion thereof, an anti-sense sequence, or a transgene in plants. The open reading frame may be obtained from an insect resistance gene, a disease resistance gene such as, for example, a bacterial disease resistance gene, a fungal disease resistance gene, a viral disease resistance gene, a nematode disease resistance gene, a herbicide resistance gene, a gene affecting grain composition or quality, a nutrient utilization gene, a mycotoxin reduction gene, a male sterility gene, a selectable marker gene, a screenable marker gene, a negative selectable marker, a positive selectable marker, a gene affecting plant agronomic characteristics, i.e., yield, standability, and the like, or an environment or stress resistance gene, i.e., one or more genes that confer herbicide resistance or tolerance, insect resistance or tolerance, disease resistance or tolerance (viral, bacterial, fungal, oomycete, or nematode), stress tolerance or resistance (as exemplified by resistance or tolerance to drought, heat, chilling, freezing, excessive moisture, salt stress, or oxidative stress), increased yields, food content and makeup, physical appearance, male sterility, drydown, standability, prolificacy, starch properties or quantity, oil quantity and quality, amino acid or protein composition, and the like. By “resistant” is meant a plant which exhibits substantially no phenotypic changes as a consequence of agent administration, infection with a pathogen, or exposure to stress. By “tolerant” is meant a plant which, although it may exhibit some phenotypic changes as a consequence of infection, does not have a substantially decreased reproductive capacity or substantially altered metabolism.

[0051] In particular, seed-specific promoters may be useful for expressing genes as well as for producing large quantities of protein, for expressing oils or proteins of interest, e.g., antibodies, genes for increasing the nutritional value of the seed and the like. Panicle-specific, root-specific, and pollen-specific promoters may be useful for expressing genes that confer pathogen-resistance, e.g., insect resistance, to those tissues, or to silence other genes that are expressed in those tissues.

[0052] For instance, pollen-specific promoters may be employed to introduce genes into pollen for the purpose of arresting pollen development thereby rendering a plant male sterile.

[0053] Such genes may include those coding for proteins toxic to pollen. It is also contemplated that chimeric plasmids may be constructed which allow the expression of antisense mRNAs which are capable of inhibiting expression of genes which play a role in pollen development. It is also contemplated that expression cassettes or vectors of the present invention which comprise a pollen-specific promoter may be useful for the introduction of one or more useful phenotypic characteristics into pollen including but not limited to pesticide resistance, resistance to insect pests or toxicity to insect pests, or which optimize other pollen functions. One embodiment the invention comprises genetic manipulation of plants to potentiate the effects of gibberellin or other hormones involved in initiation of fruit set. The invention comprises the temporal expression of a structural gene which encodes a plant hormone such as a gibberellin or cytokine, or proteins associated with the production of such hormones (i.e,. enzymes, biosynthetic intermediates and the like.) which are associated with initiation of fruit set. The structural gene is placed under the control of a pollen microspore- or megaspore-specific promoter such that the expression of the hormone is timed to occur just prior to pollination so that fruit development and maturation is induced without the need for fertilization.

[0054] Root-specific promoters may be useful for expressing genes including but not limited to defense-related genes, including genes conferring insecticidal resistance and stress tolerance, e.g., salt, cold or drought tolerance, genes for altering nutrient uptake and genes that are involved with specific morphological traits that allow for increased water absorption, uptake or extraction from soil, e.g., soil of low moisture content. For example, introduction and expression of genes that alter root characteristics may enhance water uptake. Additionally, the use of root-specific promoters in transgenic plants can provide beneficial traits that are localized in the consumable (by animals and humans) roots of plants such as carrots, parsnips, and beets. However, other parts of the plants, including stalks, husks, vegetative parts, and the like, may also be desirable, including use as part of animal silage or for ornamental purposes. Often chemical constituents (e.g., oils or starches) of maize and other crops are extracted for foods or industrial use and transgenic plants may be created which have enhanced or modified levels of such components.

[0055] Green tissue-specific promoters may be useful for expressing genes including but not limited to genes involved in photosynthetic pathways, and for those which are leaf-specific, for producing large quantities of protein, and for expressing oils or proteins of interest, genes for increasing the nutritional value of a plant, and defense-related genes (e.g., against pathogens such as a virus or fungus), including genes encoding insecticidal polypeptides.

[0056] Panicle-specific promoters may be useful for expressing genes including but not limited to genes involved in flower development and flowering such as MADS-box genes that, when expressed in transgenic plants, result in such phenotypes as, for example, reduced apical dominance or dwarfism and early flowering.

[0057] Constitutive promoters are useful for expressing a wide variety of genes including those which alter metabolic pathways, confer disease resistance, for protein production, e.g., antibody production, or to improve nutrient uptake and the like. Constitutive promoters may be modified so as to be regulatable, e.g., inducible. The genes and promoters described hereinabove can be used to identify orthologous genes and their promoters which are also likely expressed in a particular tissue and/or development manner. Moreover, the orthologous promoters are useful to express linked open reading frames. In addition, by aligning the promoters of these orthologs, novel cis elements can be identified that are useful to generate synthetic promoters.

[0058] The present invention further provides a composition, an expression cassette or a recombinant vector containing the nucleic acid molecule of the invention, and host cells comprising the expression cassette or vector, e.g., comprising a plasmid. In particular, the present invention provides an expression cassette or a recombinant vector comprising a promoter of the invention linked to a nucleic acid segment which, when present in a plant, plant cell or plant tissue, results in transcription of the linked nucleic acid segment. The invention also provides an expression cassette or a recombinant vector comprising a plant nucleotide sequence comprising an open reading frame of the invention which, when present in a plant, plant cell or plant tissue, results in expression of the product encoded by the open reading frame. Further, the invention provides isolated polypeptides encoded by any one of the open reading frames comprising SEQ ID NOs:1-1597, 5927, 5940, 5941, 5945-5958, a fragment thereof which encodes a polypeptide which has substantially the same activity as the corresponding polypeptide encoded by an ORF listed in SEQ ID NOs:1-1597, 5927, 5940, 5941, 5945-5958, or the orthologs thereof.

[0059] The invention also provides sense and anti-sense nucleic acid molecules corresponding to the open reading frames identified in SEQ ID NOs:1-1597, 5927, 5940, 5941, 5945-5958 as well as their orthologs. Also provided are compositions, expression cassettes, e.g., recombinant vectors, and host cells, comprising a nucleic acid molecule which comprises a nucleic acid segment which is preferentially expressed in seeds (e.g., SEQ ID NOs:1020-1597, 5927, 5940, 5941, 5945-5958), root (SEQ ID NOs:801-1019), pollen (SEQ ID NOs:721-800), specific (SEQ ID NOs:465-720), or green tissue (SEQ ID NOs:399-464), or constitutively expressed (SEQ ID NOs:1-398 and 5928-5939), in either sense or antisense orientation.

[0060] In one embodiment, the invention provides an expression cassette or vector containing an isolated nucleic acid molecule having a nucleotide sequence that directs tissue-specific, tissue-preferential or constitutive transcription of a linked nucleic acid segment in a cell, which nucleotide sequence is from a gene which encodes a polypeptide having at least 70% identity to an Oryza polypeptide encoded by a gene having one of the promoters listed in SEQ ID NOs:1598-2672, 5959, 5972, 5973, 5977-5990 and 6001, and which nucleotide sequence is optionally operably linked to other suitable regulatory sequences, e.g., a transcription terminator sequence, operator, repressor binding site, transcription factor binding site and/or an enhancer. This expression cassette or vector may be contained in a host cell. The expression cassette or vector may augment the genome of a transformed plant or may be maintained extrachromosomally. The expression cassette may be operatively linked to a structural gene, the open reading frame thereof, or a portion thereof. The expression cassette may further comprise a Ti plasmid and be contained in an Agrobacterium tumefaciens cell; it may be carried on a microparticle, wherein the microparticle is suitable for ballistic transformation of a plant cell; or it may be contained in a plant cell or protoplast. Further, the expression cassette or vector can be contained in a transformed plant or cells thereof, and the plant may be a dicot or a monocot. In particular, the plant may be a cereal plant.

[0061] The present invention further provides a method of augmenting a plant genome by contacting plant cells with a nucleic acid molecule of the invention, e.g., one having a nucleotide sequence that directs tissue-specific, tissue-preferential or constitutive transcription of a linked nucleic acid segment isolatable or obtained from a plant gene encoding a polypeptide that is substantially similar to a polypeptide encoded by the an Oryza gene having a sequence according to any one of SEQ ID NOs:1-2672, 5959, 5972, 5973, 5977-5990 and 6001 so as to yield transformed plant cells; and regenerating the transformed plant cells to provide a differentiated transformed plant, wherein the differentiated transformed plant expresses the nucleic acid molecule in the cells of the plant. The nucleic acid molecule may be present in the nucleus, chloroplast, mitochondria and/or plastid of the cells of the plant. The present invention also provides a transgenic plant prepared by this method, a seed from such a plant and progeny plants from such a plant including hybrids and inbreds. Preferred transgenic plants are transgenic maize, soybean, barley, alfalfa, sunflower, canola, soybean, cotton, peanut, sorghum, tobacco, sugarbeet, rice, wheat, rye, turfgrass, millet, sugarcane, tomato, or potato.

[0062] A transformed (transgenic) plant of the invention includes plants, the genome of which is augmented by a nucleic acid molecule of the invention, or in which the corresponding gene has been disrupted, e.g., to result in a loss, a decrease or an alteration, in the function of the product encoded by the gene, which plant may also have increased yields and/or produce a better-quality product than the corresponding wild-type plant. The nucleic acid molecules of the invention are thus useful for targeted gene disruption, as well as markers and probes.

[0063] The invention also provides a method of plant breeding, e.g., to prepare a crossed fertile transgenic plant. The method comprises crossing a fertile transgenic plant comprising a particular nucleic acid molecule of the invention with itself or with a second plant, e.g., one lacking the particular nucleic acid molecule, to prepare the seed of a crossed fertile transgenic plant comprising the particular nucleic acid molecule. The seed is then planted to obtain a crossed fertile transgenic plant. The plant may be a monocot or a dicot. In a particular embodiment, the plant is a cereal plant.

[0064] The crossed fertile transgenic plant may have the particular nucleic acid molecule inherited through a female parent or through a male parent. The second plant may be an inbred plant. The crossed fertile transgenic may be a hybrid. Also included within the present invention are seeds of any of these crossed fertile transgenic plants.

[0065] The present invention also provides a method to identify a nucleotide sequence that directs tissue-specific or tissue-preferential transcription of linked nucleic acid in the genome of a plant cell by contacting a probe of plant nucleic acid, e.g., cRNA from rice, isolated from various tissues of a plant, with a plurality of isolated nucleic acid samples on one or more, i.e., a plurality of, solid substrates so as to form a complex between at least a portion of the probe and a nucleic acid sample(s) having sequences that are structurally related to the sequences in the probe. Each sample comprises one or a plurality of oligonucleotides corresponding to at least a portion of a plant gene. Then complex formation is compared between samples contacted with a particular tissue, e.g., a seed-specific, probe and samples contacted with a different tissue, e.g., a non-seed specific probe, so as to determine which RNAs are expressed in the particular tissue of the plant. The probe and/or samples may be nucleic acid from a dicot or from a monocot.

[0066] The present invention also provides a method to identify a nucleotide sequence that directs constitutive transcription of nucleic acid in the genome of a plant cell by contacting a probe of plant nucleic acid, e.g., cRNA from rice, isolated from various tissues of a plant and at various developmental stages with a plurality of isolated nucleic acid samples on one or more, i.e., a plurality of, solid substrates so as to form a complex between at least a portion of the probe and a nucleic acid sample(s) having sequences that are structurally related to the sequences in the probe. Each sample comprises one or a plurality of oligonucleotides corresponding to at least a portion of a plant gene. Complex formation is then compared to determine which RNAs are present in a majority of, preferably in substantially all, tissues, in a majority of, preferably at substantially all, developmental stages of the plant. The probe and/or samples may be nucleic acid from a dicot or from a monocot.

[0067] The compositions of the invention include plant nucleic acid molecules, and the amino acid sequences for the polypeptides or partial-length polypeptides encoded by the nucleic acid molecule which comprises an open reading frame. These sequences can be employed to alter expression of a particular gene corresponding to the open reading frame by decreasing or eliminating expression of that plant gene or by overexpressing a particular gene product. Methods of this embodiment of the invention include stably transforming a plant with the nucleic acid molecule which includes an open reading frame operably linked to a promoter capable of driving expression of that open reading frame (sense or antisense) in a plant cell. By “portion” or “fragment”, as it relates to a nucleic acid molecule which comprises an open reading frame or a fragment thereof encoding a partial-length polypeptide having the activity of the full length polypeptide, is meant a sequence having at least 80 nucleotides, more preferably at least 150 nucleotides, and still more preferably at least 400 nucleotides. If not employed for expressing, a “portion” or “fragment” means at least 9, preferably 12, more preferably 15, even more preferably at least 20, consecutive nucleotides, e.g., probes and primers,(oligonucleotides), corresponding to the nucleotide sequence of the nucleic acid molecules of the invention. Thus, to express a particular gene product, the method comprises introducing to a plant, plant cell, or plant tissue an expression cassette comprising a promoter linked to an open reading frame so as to yield a transformed differentiated plant, transformed cell or transformed tissue. Transformed cells or tissue can be regenerated to provide a transformed differentiated plant. The transformed differentiated plant or cells thereof preferably expresses the open reading frame in an amount that alters the amount of the gene product in the plant or cells thereof, which product is encoded by the open reading frame. The present invention also provides a transformed plant prepared by the method, progeny and seed thereof.

[0068] The invention further includes a nucleotide sequence which is complementary to one (hereinafter “test” sequence) which hybridizes under stringent conditions with a nucleic acid molecule of the invention as well as RNA which is transcribed from the nucleic acid molecule. When the hybridization is performed under stringent conditions, either the test or nucleic acid molecule of invention is preferably supported, e.g., on a membrane or DNA chip. Thus, either a denatured test or nucleic acid molecule of the invention is preferably first bound to a support and hybridization is effected for a specified period of time at a temperature of, e.g., between 55 and 70° C., in double strength citrate buffered saline (SC) containing 0.1% SDS followed by rinsing of the support at the same temperature but with a buffer having a reduced SC concentration. Depending upon the degree of stringency required such reduced concentration buffers are typically single strength SC containing 0.1% SDS, half strength SC containing 0.1% SDS and one-tenth strength SC containing 0.1% SDS.

[0069] A computer readable medium containing one or more of the nucleotide sequences of the invention as well as methods of use for the computer readable medium are provided. This medium allows a nucleotide sequence corresponding to at least one of SEQ ID NOs:1598-2672, 5959, 5972, 5973, 5977-5990 and 6001 (promoters), SEQ ID NOs: 1-1597, 5927, 5940, 5941, 5945-5958 and 2673-5926 (orthologous open reading frames of wheat, banana and maizeor fragments thereof), to be used as a reference sequence to search against a database. This medium also allows for computer-based manipulation of a nucleotide sequence corresponding to at least one of SEQ ID NOs:1-60001.

BRIEF DESCRIPTION OF THE TABLES

[0070] Table 1 provides the SEQ ID NOs and corresponding description for Oryza genes which are expressed in a constitutive manner and further the SEQ ID NOs for the corresponding homologous sequences found in wheat, banana and maize.

[0071] * identifies a first subset of genes.

[0072] *″ identifies a 2nd subset of genes.

[0073] Three subgroups of constitutively expressed genes can be distinguished based on the expression level of those genes. The levels are ranked from highest (1) to lowest (3). For example, promoters with the highest level of constitutive expression include those having an open reading frame corresponding to SEQ ID NOs:1-24, the next highest include those having an open reading frame corresponding to SEQ ID NOs:25-142, the next highest include those having an open reading frame corresponding to SEQ ID NOs:143-293, and the lowest include those having an open reading frame corresponding to SEQ ID NOs:294-398 and 5928-5939.

[0074] Table 2 provides the SEQ ID NOs: and corresponding description for Oryza genes which are expressed in a seed-specific manner and further the SEQ ID NOs for the corresponding homologous sequences found in wheat, banana and maize.

[0075] Six subgroups of seed-specific genes can be distinguished based on the expression level of those genes. The levels are ranked from highest (1) to lowest (6). For example, promoters with the highest level of seed-specific expression include those from a gene having an open reading frame corresponding to SEQ ID NOs:1020-1021, the next highest include those from a gene having an open reading frame corresponding to SEQ ID NOs:1022-1025, the next highest include those from a gene having an open reading, frame corresponding to SEQ ID NOs:1026-1030, the next highest include those from a gene having an open reading frame corresponding to SEQ ID NOs:1031-1048, the next highest include those from a gene having an open reading frame corresponding to SEQ ID NOs:1049-1165 and the lowest include those from a gene having an open reading frame corresponding to SEQ ID NOs:1166-1597, 5927, 5940, 5941, 5945-5958.

[0076] Table 3 provides the SEQ ID NOs: and corresponding description for Oryza genes which are expressed in an aleurone-specific manner and further the SEQ ID NOs for the corresponding homologous sequences found in wheat, banana and maize.

[0077] Table 4 provides the SEQ ID NOs: and corresponding description for Oryza genes which are expressed in an endosperm-specific manner and further the SEQ ID NOs for the corresponding homologous sequences found in wheat, banana and maize.

[0078] Table 5 provides the SEQ ID NOs: and corresponding description for Oryza genes which are expressed in an embryo-specific manner and further the SEQ ID NOs for the corresponding homologous sequences found in wheat, banana and maize.

[0079] Table 6 provides the SEQ ID NOs: and corresponding description for Oryza genes which are expressed in a leaf- and stem-specific manner and further the SEQ ID NOs for the corresponding homologous sequences found in wheat, banana and maize.

[0080] Four subgroups of leaf- and stem-specific genes can be distinguished based on the expression level of those genes. The levels are ranked from highest (1) to lowest (4). For example, promoters with the highest level of leaf and stem-specific expression include those from a gene having an open reading frame corresponding to SEQ ID NOs:399-404, the next highest include those from a gene having an open reading frame corresponding to SEQ ID NOs:405-416, the next highest include those from a gene having an open reading frame corresponding to SEQ ID NOs:417-456, and the lowest include those from a gene having an open reading frame corresponding to SEQ ID NOs:457-464.

[0081] Table 7 provides the SEQ ID NOs: and corresponding description for Oryza genes which are expressed in a panicle-specific manner and further the SEQ ID NOs for the corresponding homologous sequences found in wheat, banana and maize.

[0082] Three subgroups of panicle-specific genes can be distinguished based on the expression level of those genes. The levels are ranked from highest (1) to lowest (3). For example, promoters with the highest level of panicle-specific expression include those from a gene having an open reading frame corresponding to SEQ ID NOs:465-469, the next highest include those from a gene having an open reading frame corresponding to SEQ ID NOs:470-535, and the lowest include those from a gene having an open reading frame corresponding to SEQ ID NOs:536-720.

[0083] Table 8 provides the SEQ ID NOs: and corresponding description for Oryza genes which are expressed in a root-specific manner and further the SEQ ID NOs for the corresponding homologous sequences found in wheat, banana and maize.

[0084] Four subgroups of root-specific genes can be distinguished based on the expression level of those genes. The levels are ranked from highest (1) to lowest (4). For example, promoters with the highest level of root-specific expression include those from a gene having an open reading frame corresponding to SEQ ID NOs:801-809, the next highest include those from a gene having an open reading frame corresponding to SEQ ID NOs:810-846, the next highest include those from a gene having an open reading frame corresponding to SEQ ID NOs:847-885, and the lowest include those from a gene having an open reading frame corresponding to SEQ ID NOs:886-1019.

[0085] Table 9 provides the SEQ ID NOs: and corresponding description for Oryza genes which are express in a pollen-specific manner and further the SEQ ID NOs for the corresponding homologous sequences found in wheat, banana and maize.

[0086] Three subgroups of pollen-specific genes can be distinguished based on the expression level of those genes. The levels are ranked from highest (1) to lowest (3). For example, promoters with the highest level of pollen-specific expression include those from a gene having an open reading frame corresponding to SEQ ID NOs:721-728, the next highest include those from a gene having an open reading frame corresponding to SEQ ID NOs:729-743, and the lowest include those from a gene having an open reading frame corresponding to SEQ ID NOs:744-800.

[0087] Table 10 identifies the start and end point and the nucleotide sequences of tri-nucleotide repeat units in the coding sequence of selected ORFs.

[0088] Table 11 provides Swiss Prot information.

[0089] Table 12 illustrates the promoter designation, probe set or gene, gene description, PCR product size for a promoter containing PCR product and primers employed to amplify promoter sequences, for exemplary constitutively expressed promoters.

DETAILED DESCRIPTION OF THE INVENTION

[0090] In accordance with the present invention, nucleic acid constructs are provided that allow initiation of transcription in a “tissue-specific”, i.e., seed-, root-, green tissue (leaf and stem)-, panicle-, or pollen-specific, or in a constitutive manner. Constructs of the invention comprise regulated transcription initiation regions associated with protein translation elongation, and the compositions of the present invention are drawn to novel nucleotide sequences for tissue-specific as well as constitutive expression. The present invention thus provides for isolated nucleic acid molecules comprising a plant nucleotide sequence that directs tissue-specific, i.e., seed-, root-, green tissue (leaf and stem)-, panicle-, or pollen-specific, transcription of a linked nucleic acid segment in a plant cell. Preferably, nucleotide sequence is obtained or obtainable from plant genomic DNA from a gene encoding a polypeptide which is substantially similar and preferably has at least 70% amino acid sequence identity to a polypeptide encoded by an Oryza gene comprising any one of SEQ ID NOs:2275-2672, 5959, 5972, 5973, 5977-5990 and 6001 (seed-specific promoters) and SEQ ID NOs:1020-1597, 5927, 5940, 5941, 5945-5958 (seed-specific ORFs); SEQ ID NOs:2144-2274 (root-specific promoters) and SEQ ID NOs:801-1019 (root-specific ORFs); SEQ ID NOs:1886-1918 (green-tissue specific promoters) and SEQ ID NOs:399-464 (green tissue-specific ORFs); SEQ ID NOs:1919-2085 (panicle-specific promoters) and SEQ ID NOs:465-720 (panicle-specific promoters); or SEQ ID NOs:2086-2143 (pollen-specific promoters) and SEQ ID NOs:721-800 (pollen-specific ORFs) which directs tissue-specific expression. Thus, these nucleotide sequences exhibit promoter activity in a seed-, root-, green tissue (leaf and stem)-, panicle-, or pollen-specific manner.

[0091] Also in accordance with the present invention, nucleic acid constructs are provided that allow initiation of transcription in a “tissue-independent,” “tissue general,” or “constitutive” manner. Constructs of this embodiment invention comprise regulated transcription initiation regions associated with protein translation elongation and the compositions of this embodiment of the present invention are drawn to novel nucleotide sequences for tissue-independent, tissue-general, or,constitutive plant promoters. By “tissue-independent,” “tissue-general,” or “constitutive” is intended expression in the cells throughout a plant at most times and in most tissues. As with other promoters classified as “constitutive” (e.g., ubiquitin), some variation in absolute levels of expression can exist among different tissues or stages. However, constitutive promoters generally are expressed at high or moderate levels in most, and preferably all, tissues and most, and preferably all, developmental stages.

[0092] The present invention thus provides for isolated nucleic acid molecules comprising a plant nucleotide sequence that directs constitutive transcription of a linked nucleic acid fragment in a plant cell. Preferably, the nucleotide sequence is obtained or obtainable from plant genomic DNA from a gene encoding a polypeptide which is substantially similar and preferably has at least 70% amino acid sequence identity to a polypeptide encoded by an Oryza gene comprising any one of SEQ ID NOs:1598-1885 and 5960-5971, respectively (corresponding to a gene comprising an ORF comprising one of SEQ ID NOs:1-398 and 5928-5939 ) or a fragment thereof which exhibits promoter activity in a constitutive fashion (i.e., at most times and in most tissues). Tissue-specific, i.e., seed-, root-, green tissue (leaf and stem)-, panicle-, or pollen-specific, and constitutive promoter sequences may be obtained from other plant species by using the tissue-specific and constitutive Oryza promoter sequences or corresponding genes described herein as probes to screen for homologous structural genes in other plants by hybridization under low, moderate or stringent hybridization conditions. Regions of the tissue-specific and constitutive promoter sequences of the present invention which are conserved among species could also be used as PCR primers to amplify a segment from a species other than Oryza, and that segment used as a hybridization probe (the latter approach permitting higher stringency screening) or in a transcription assay to determine promoter activity. Moreover, the tissue-specific and constitutive promoter sequences could be employed to identify structurally related sequences in a database using computer algorithms.

[0093] These tissue-specific and constitutive promoters are capable of driving the expression of a coding sequence in a target cell, particularly in a plant cell. The promoter sequences and methods disclosed herein are useful in regulating tissue-specific and constitutive expression, respectively, of any heterologous nucleotide sequence in a host plant in order to vary the phenotype of that plant. These promoters can be used with combinations of enhancer, upstream elements, and/or activating sequences from the 5′ flanking regions of plant expressible structural genes. Similarly the upstream element can be used in combination with various plant promoter sequences. In one embodiment the promoter and upstream element are used together to obtain at least 10-fold higher expression of an introduced gene in monocot transgenic plants than is obtained with the maize ubiquitin 1 promoter.

[0094] In particular, all of the promoters of the invention are useful to modify the phenotype of a plant. Various changes in the phenotype of a transgenic plant are desirable, i.e., modifying the fatty acid composition in a plant, altering the amino acid content of a plant, altering a plant's pathogen defense mechanism, and the like. These results can be achieved by providing expression of heterologous products or increased expression of endogenous products in plants. Alternatively, the results can be achieved by providing for a reduction of expression of one or more endogenous products, particularly enzymes or cofactors in the plant. These changes result in an alteration in the phenotype of the transformed plant.

[0095] I. Definitions

[0096] The term “gene” is used broadly to refer to any segment of nucleic acid associated with a biological function. Thus, genes include coding sequences and/or the regulatory sequences required for their expression. For example, gene refers to a nucleic acid fragment that expresses mRNA or functional RNA, or encodes a specific protein, and which includes regulatory sequences. Genes also include nonexpressed DNA segments that, for example, form recognition sequences for other proteins. Genes can be obtained from a variety of sources, including cloning from a source of interest or synthesizing from known or predicted sequence information, and may include sequences designed to have desired parameters.

[0097] The term “native” or “wild type” gene refers to a gene that is present in the genome of an untransformed cell, i.e., a cell not having a known mutation.

[0098] A “marker gene” encodes a selectable or screenable trait.

[0099] The term “chimeric gene” refers to any gene that contains 1) DNA sequences, including regulatory and coding sequences, that are not found together in nature, or 2) sequences encoding parts of proteins not naturally adjoined, or 3) parts of promoters that are not naturally adjoined. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or comprise regulatory sequences. and coding sequences derived from the same source, but arranged in a manner different from that found in nature.

[0100] A “transgene” refers to a gene that has been introduced into the genome by transformation and is stably maintained. Transgenes may include, for example, genes that are either heterologous or homologous to the genes of a particular plant to be transformed. Additionally, transgenes may comprise native genes inserted into a non-native organism, or chimeric genes. The term “endogenous gene” refers to a native gene in its natural location in the genome of an organism. A “foreign” gene refers to a gene not normally found in the host organism but that is introduced by gene transfer.

[0101] An “oligonucleotide” corresponding to a nucleotide sequence of the invention, e.g., for use in probing or amplification reactions, may be about 30 or fewer nucleotides in length (e.g., 9, 12, 15, 18, 20, 21 or 24, or any number between 9 and 30). Generally specific primers are upwards of 14 nucleotides in length. For optimum specificity and cost effectiveness, primers of 16 to 24 nucleotides in length may be preferred. Those skilled in the art are well versed in the design of primers for use processes such as PCR. If required, probing can be done with entire restriction fragments of the gene disclosed herein which may be 100's or even 1000's of nucleotides in length.

[0102] The terms “protein,” “peptide” and “polypeptide” are used interchangeably herein.

[0103] The nucleotide sequences of the invention can be introduced into any plant. The genes to be introduced can be conveniently used in expression cassettes for introduction and expression in any plant of interest. Such expression cassettes will comprise the transcriptional initiation region of the invention linked to a nucleotide sequence of interest. Preferred promoters include constitutive, tissue-specific, developmental-specific, inducible and/or viral promoters. Such an expression cassette is provided with a plurality of restriction sites for insertion of the gene of interest to be under the transcriptional regulation of the regulatory regions. The expression cassette may additionally contain selectable marker genes. The cassette will include in the 5′-3′ direction of transcription, a transcriptional and translational initiation region, a DNA sequence of interest, and a transcriptional and translational termination region functional in plants. The termination region may be native with the transcriptional initiation region, may be native with the DNA sequence of interest, or may be derived from another source. Convenient termination regions are available from the Ti-plasmid of A. tumefaciens, such, as the octopine synthase and nopaline synthase termination regions. See also, Guerineau et al., 1991; Proudfoot, 1991; Sanfacon et al., 1991; Mogen et al., 1990; Munroe et al., 1990; Ballas et al., 1989; Joshi et al., 1987.

[0104] “Coding sequence” refers to a DNA or RNA sequence that codes for a specific amino acid sequence and excludes the non-coding sequences. It may constitute an “uninterrupted coding sequence”, i.e., lacking an intron, such as in a cDNA or it may include one or more introns bounded by appropriate splice junctions. An “intron” is a sequence of RNA which is contained in the primary transcript but which is removed through cleavage and re-ligation of the RNA within the cell to create the mature mRNA that can be translated into a protein.

[0105] The terms “open reading frame” and “ORF” refer to the amino acid sequence encoded between translation initiation and termination codons of a coding sequence. The terms “initiation codon” and “termination codon” refer to a unit of three adjacent nucleotides (‘codon’) in a coding sequence that specifies initiation and chain termination, respectively, of protein synthesis (mRNA translation).

[0106] A “functional RNA” refers to an antisense RNA, ribozyme, or other RNA that is not translated.

[0107] The term “RNA transcript” refers to the product resulting from RNA polymerase catalyzed transcription of a DNA sequence. When the RNA transcript is a perfect complementary copy of the DNA sequence, it is referred to as the primary transcript or it may be a RNA sequence derived from posttranscriptional processing of the primary transcript and is referred to as the mature RNA. “Messenger RNA” (mRNA) refers to the RNA that is without introns and that can be translated into protein by the cell. “cDNA” refers to a single- or a double-stranded DNA that is complementary to and derived from mRNA.

[0108] “Regulatory sequences” and “suitable regulatory sequences” each refer to nucleotide sequences located upstream (5′ non-coding sequences), within, or downstream (3′ non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences include enhancers, promoters, translation leader sequences, introns, and polyadenylation signal sequences. They include natural and synthetic sequences as well as sequences which may be a combination of synthetic and natural sequences. As is noted above, the term “suitable regulatory sequences” is not limited to promoters.

[0109] “5′ non-coding sequence” refers to a nucleotide sequence located 5′ (upstream) to the coding sequence. It is present in the fully processed mRNA upstream of the initiation codon and may affect processing of the primary transcript to mRNA, mRNA stability or translation efficiency (Turner et al., 1995).

[0110] “3′ non-coding sequence” refers to nucleotide sequences located 3′ (downstream) to a coding sequence and include polyadenylation signal sequences and other sequences encoding regulatory signals capable of affecting mRNA processing or gene expression. The polyadenylation signal is usually characterized by affecting the addition of polyadenylic acid tracts to the 3′ end of the mRNA precursor. The use of different 3′ non-coding sequences is exemplified by Ingelbrecht et al., 1989.

[0111] The term “translation leader sequence” refers to that DNA sequence portion of a gene between the promoter and coding sequence that is transcribed into RNA and is present in the fully processed mRNA upstream (5′) of the translation start codon. The translation leader sequence may affect processing of the primary transcript to mRNA, mRNA stability or translation efficiency.

[0112] “Signal peptide” refers to the amino terminal extension of a polypeptide, which is translated in conjunction with the polypeptide forming a precursor peptide and which is required for its entrance into the secretory pathway. The term “signal sequence” refers to a nucleotide sequence that encodes the signal peptide.

[0113] “Promoter” refers to a nucleotide sequence, usually upstream (5′) to its coding sequence, which controls the expression of the coding sequence by providing the recognition for RNA polymerase and other factors required for proper transcription. “Promoter” includes a minimal promoter that is a short DNA sequence comprised of a TATA box and other sequences that serve to specify the site of transcription initiation, to which regulatory elements are added for control of expression. “Promoter” also refers to a nucleotide sequence that includes a minimal promoter plus regulatory elements that is capable of controlling the expression of a coding sequence or functional RNA. This type of promoter sequence consists of proximal and more distal upstream elements, the latter elements often referred to as enhancers. Accordingly, an “enhancer” is a DNA sequence which can stimulate promoter activity and may be an innate element of the promoter or a heterologous element inserted to enhance the level or tissue specificity of a promoter. It is capable of operating in both orientations (normal or flipped), and is capable of functioning even when moved either upstream or downstream from the promoter. Both enhancers and other upstream promoter elements bind sequence-specific DNA-binding proteins that mediate their effects. Promoters may be derived in their entirety from a native gene, or be composed of different elements, derived from different promoters found in nature, or even be comprised of synthetic DNA segments. A promoter may also contain DNA sequences that are involved in the binding of protein factors which control the effectiveness of transcription initiation in response to physiological or developmental conditions.

[0114] The “initiation site” is the position surrounding the first nucleotide that is part of the transcribed sequence, which is also defined as position +1. With respect to this site all other sequences of the gene and its controlling regions are numbered. Downstream sequences (i.e., further protein encoding sequences in the 3′ direction) are denominated positive, while upstream sequences (mostly of the controlling regions in the 5′ direction) are denominated negative.

[0115] Promoter elements, particularly a TATA element, that are inactive or that have greatly reduced promoter activity in the absence of upstream activation are referred to as “minimal or core promoters.” In the presence of a suitable transcription factor, the minimal promoter functions to permit transcription. A “minimal or core promoter” thus consists only of all basal elements needed for transcription initiation, e.g., a TATA box and/or an initiator.

[0116] “Constitutive expression” refers to expression using a constitutive or regulated promoter. “Conditional” and “regulated expression” refer to expression controlled by a regulated promoter.

[0117] “Constitutive promoter” refers to a promoter that is able to express the open reading frame (ORF) that it controls in all or nearly all of the plant tissues during all or nearly all developmental stages of the plant. Each of the transcription-activating elements do not exhibit an absolute tissue-specificity, but mediate transcriptional activation in most plant parts at a level of ≧1% of the level reached in the part of the plant in which transcription is most active.

[0118] “Regulated promoter” refers to promoters that direct gene expression not constitutively, but in a temporally- and/or spatially-regulated manner, and includes both tissue-specific and inducible promoters. It includes natural and synthetic sequences as well as sequences which may be a combination of synthetic and natural sequences. Different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental conditions. New promoters of various types useful in plant cells are constantly being discovered, numerous examples may be found in the compilation by Okamuro et al. (1989). Typical regulated promoters useful in plants include but are not limited to safener-inducible promoters, promoters derived from the tetracycline-inducible system, promoters derived from salicylate-inducible systems, promoters derived from alcohol-inducible systems, promoters derived from glucocorticoid-inducible system, promoters derived from pathogen-inducible systems, and promoters derived from ecdysome-inducible systems.

[0119] “Tissue-specific promoter” refers to regulated promoters that are not expressed in all plant cells but only in one or more cell types in specific organs (such as leaves or seeds), specific tissues (such as embryo or cotyledon), or specific cell types (such as leaf parenchyma or seed storage cells). These also include promoters that are temporally regulated, such as in early or late embryogenesis, during fruit ripening in developing seeds or fruit, in fully differentiated leaf, or at the onset of senescence.

[0120] “Inducible promoter” refers to those regulated promoters that can be turned on in one or more cell types by an external stimulus, such as a chemical, light, hormone, stress, or a pathogen.

[0121] “Operably-linked” refers to the association of nucleic acid sequences on single nucleic acid fragment so that the function of one is affected by the other. For example, a regulatory DNA sequence is said to be “operably linked to” or “associated with” a DNA sequence that codes for an RNA or a polypeptide if the two sequences are situated such that the regulatory DNA sequence affects expression of the coding DNA sequence (i.e., that the coding sequence or functional RNA is under the transcriptional control of the promoter). Coding sequences can be operably-linked to regulatory sequences in sense or antisense orientation.

[0122] “Expression” refers to the transcription and/or translation of an endogenous gene, ORF or portion thereof, or a transgene in plants. For example, in the case of antisense constructs, expression may refer to the transcription of the antisense DNA only. In addition, expression refers to the transcription and stable accumulation of sense (mRNA) or functional RNA. Expression may also refer to the production of protein.

[0123] “Specific expression” is the expression of gene products which is limited to one or a few plant tissues (spatial limitation) and/or to one or a few plant developmental stages (temporal limitation). It is acknowledged that hardly a true specificity exists: promoters seem to be preferably switch on in some tissues, while in other tissues there can be no or only little activity. This phenomenon is known as leaky expression. However, with specific expression in this invention is meant preferable expression in one or a few plant tissues.

[0124] The “expression pattern” of a promoter (with or without enhancer) is the pattern of expression levels which shows where in the plant and in what developmental stage transcription is initiated by said promoter. Expression patterns of a set of promoters are said to be complementary when the expression pattern of one promoter shows little overlap with the expression pattern of the other promoter. The level of expression of a promoter can be determined by measuring the ‘steady state’ concentration of a standard transcribed reporter mRNA. This measurement is indirect since the concentration of the reporter mRNA is dependent not only on its synthesis rate, but also on the rate with which the mRNA is degraded. Therefore, the steady state level is the product of synthesis rates and degradation rates.

[0125] The rate of degradation can however be considered to proceed at a fixed rate when the transcribed sequences are identical, and thus this value can serve as a measure of synthesis rates. When promoters are compared in this way techniques available to those skilled in the art are hybridization S1-RNAse analysis, northern blots and competitive RT-PCR. This list of techniques in no way represents all available techniques, but rather describes commonly used procedures used to analyze transcription activity and expression levels of mRNA.

[0126] The analysis of transcription start points in practically all promoters has revealed that there is usually no single base at which transcription starts, but rather a more or less clustered set of initiation sites, each of which accounts for some start points of the mRNA. Since this distribution varies from promoter to promoter the sequences of the reporter mRNA in each of the populations would differ from each other. Since each mRNA species is more or less prone to degradation, no single degradation rate can be expected for different reporter mRNAs. It has been shown for various eukaryotic promoter sequences that the sequence surrounding the initiation site (‘initiator’) plays an important role in determining the level of RNA expression directed by that specific promoter. This includes also part of the transcribed sequences. The direct fusion of promoter to reporter sequences would therefore lead to suboptimal levels of transcription.

[0127] A commonly used procedure to analyze expression patterns and levels is through determination of the ‘steady state’ level of protein accumulation in a cell. Commonly used candidates for the reporter gene, known to those skilled in the art are beta-glucuronidase (GUS), chloramphenicol acetyl transferase (CAT) and proteins with fluorescent properties, such as green fluorescent protein (GFP) from Aequora victoria. In principle, however, many more proteins are suitable for this purpose, provided the protein does not interfere with essential plant functions. For quantification and determination of localization a number of tools are suited. Detection systems can readily be created or are available which are based on, e.g., immunochemical, enzymatic, fluorescent detection and quantification. Protein levels can be determined in plant tissue extracts or in intact tissue using in situ analysis of protein expression.

[0128] Generally, individual transformed lines with one chimeric promoter reporter construct will vary in their levels of expression of the reporter gene. Also frequently observed is the phenomenon that such transformants do not express any detectable product (RNA or protein). The variability in expression is commonly ascribed to ‘position effects’, although the molecular mechanisms underlying this inactivity are usually not clear.

[0129] “Overexpression” refers to the level of expression in transgenic cells or organisms that exceeds levels of expression in normal or untransformed (nontransgenic) cells or organisms.

[0130] “Antisense inhibition” refers to the production of antisense RNA transcripts capable of suppressing the expression of protein from an endogenous gene or a transgene.

[0131] “Gene silencing” refers to homology-dependent suppression of viral genes, transgenes, or endogenous nuclear genes. Gene silencing may be transcriptional, when the suppression is due to decreased transcription of the affected genes, or post-transcriptional, when the suppression is due to increased turnover (degradation) of RNA species homologous to the affected genes (English et al., 1996). Gene silencing includes virus-induced gene silencing (Ruiz et al. 1998).

[0132] The terms “heterologous DNA sequence,” “exogenous DNA segment” or “heterologous nucleic acid,” as used herein, each refer to a sequence that originates from a source foreign to the particular host cell or, if from the same source, is modified from its original form. Thus, a heterologous gene in a host cell includes a gene that is endogenous to the particular host cell but has been modified through, for example, the use of DNA shuffling. The terms also include non-naturally occurring multiple copies of a naturally occurring DNA sequence. Thus, the terms refer to a DNA segment that is foreign or heterologous to the cell, or homologous to the cell but in a position within the host cell nucleic acid in which the element is not ordinarily found. Exogenous DNA segments are expressed to yield exogenous polypeptides. A “homologous” DNA sequence is a DNA sequence that is naturally associated with a host cell into which it is introduced.

[0133] “Homologous to” in the context of nucleotide sequence identity refers to the similarity between the nucleotide sequence of two nucleic acid molecules or between the amino acid sequences of two protein molecules. Estimates of such homology are provided by either DNA-DNA or DNA-RNA hybridization under conditions of stringency as is well understood by those skilled in the art (as described in Haines and Higgins (eds.), Nucleic Acid Hybridization, IRL Press, Oxford, U.K.), or by the comparison of sequence similarity between two nucleic acids or proteins.

[0134] The term “substantially similar” refers to nucleotide and amino acid sequences that represent functional and/or structural equivalents of Oryza sequences disclosed herein.

[0135] In its broadest sense, the term “substantially similar” when used herein with respect to a nucleotide sequence means that the nucleotide sequence is part of a gene which encodes a polypeptide having substantially the same structure and function as a polypeptide encoded by a gene for the reference nucleotide sequence, e.g., the nucleotide sequence comprises a promoter from a gene that is the ortholog of the gene corresponding to the reference nucleotide sequence, as well as promoter sequences that are structurally related the promoter sequences particularly exemplified herein, i.e., the substantially similar promoter sequences hybridize to the complement of the promoter sequences exemplified herein under high or very high stringency conditions. For example, altered nucleotide sequences which simply reflect the degeneracy of the genetic code but nonetheless encode amino acid sequences that are identical to a particular amino acid sequence are substantially similar to the particular sequences. The term “substantially similar” also includes nucleotide sequences wherein the sequence has been modified, for example, to optimize expression in particular cells, as well as nucleotide sequences encoding a variant polypeptide having one or more amino acid substitutions relative to the (unmodified) polypeptide encoded by the reference sequence, which substitution(s) does not alter the activity of the variant polypeptide relative to the unmodified polypeptide.

[0136] In its broadest sense, the term “substantially similar” when used herein with respect to polypeptide means that the polypeptide has substantially the same structure and function as the reference polypeptide. In addition, amino acid sequences that are substantially similar to a particular sequence are those wherein overall amino acid identity is at least 65% or greater to the instant sequences. Modifications that result in equivalent nucleotide or amino acid sequences are well within the routine skill in the art. The percentage of amino acid sequence identity between the substantially similar and the reference polypeptide is at least 65%, 66%, 67%, 68%, 69%, 70%, e.g., 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, and even 90% or more, e.g., 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, up to at least 99%, wherein the reference polypeptide is an Oryza polypeptide encoded by a gene with a promoter having any one of SEQ ID NOs:1-350 and 1051-1551, e.g., a nucleotide sequence comprising an open reading frame having any one of SEQ ID NOs:351-700 or 1552-2052 which encodes one of SEQ ID Nos:701-1050 or 2053-2553. One indication that two polypeptides are substantially similar to each other, besides having substantially the same function, is that an agent, e.g., an antibody, which specifically binds to one of the polypeptides, specifically binds to the other.

[0137] Sequence comparisons maybe carried out using a Smith-Waterman sequence alignment algorithm (see e.g., Waterman (1995) or http://www hto.usc.edu/software/seqaln/index.html). The localS program, version 1.16, is preferably used with following parameters: match: 1, mismatch penalty: 0.33, open-gap penalty: 2, extended-gap penalty: 2.

[0138] Moreover, a nucleotide sequence that is “substantially similar” to a reference nucleotide sequence is said to be “equivalent” to the reference nucleotide sequence. The skilled artisan recognizes that equivalent nucleotide sequences encompassed by this invention can also be defined by their ability to hybridize, under low, moderate and/or stringent conditions (e.g., 0.1×SSC, 0.1% SDS, 65° C.), with the nucleotide sequences that are within the literal scope of the instant claims.

[0139] What is meant by “substantially the same activity” when used in reference to a polynucleotide or polypeptide fragment is that the fragment has at least 65%, 66%, 67%, 68%, 69%, 70%, e.g., 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, and even 90% or more, e.g., 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, up to at least 99% of the activity of the full length polynucleotide or full length polypeptide.

[0140] “Target gene” refers to a gene on the replicon that expresses the desired target coding sequence, functional RNA, or protein. The target gene is not essential for replicon replication. Additionally, target genes may comprise native non-viral genes inserted into a non-native organism, or chimeric genes, and will be under the control of suitable regulatory sequences. Thus, the regulatory sequences in the target gene may come from any source, including the virus. Target genes may include coding sequences that are either heterologous or homologous to the genes of a particular plant to be transformed. However, target genes do not include native viral genes. Typical target genes include, but are not limited to genes encoding a structural protein, a seed storage protein, a protein that conveys herbicide resistance, and a protein that conveys insect resistance. Proteins encoded by target genes are known as “foreign proteins”. The expression of a target gene in a plant will typically produce an altered plant trait.

[0141] The term “altered plant trait” means any phenotypic or genotypic change in a transgenic plant relative to the wild-type or non-transgenic plant host.

[0142] “Replication gene” refers to a gene encoding a viral replication protein. In addition to the ORF of the replication protein, the replication gene may also contain other overlapping or non-overlapping ORF(s), as are found in viral sequences in nature. While not essential for replication, these additional ORFs may enhance replication and/or viral DNA accumulation. Examples of such additional ORFs are AC3 and AL3 in ACMV and TGMV geminiviruses, respectively.

[0143] “Chimeric trans-acting replication gene” refers either to a replication gene in which the coding sequence of a replication protein is under the control of a regulated plant promoter other than that in the native viral replication gene, or a modified native viral replication gene, for example, in which a site specific sequence(s) is inserted in the 5′ transcribed but untranslated region. Such chimeric genes also include insertion of the known sites of replication protein binding between the promoter and the transcription start site that attenuate transcription of viral replication protein gene.

[0144] “Chromosomally-integrated” refers to the integration of a foreign gene or DNA construct into the host DNA by covalent bonds. Where genes are not “chromosomally integrated” they may be “transiently expressed.” Transient expression of a gene refers to the expression of a gene that is not integrated into the host chromosome but functions independently, either as part of an autonomously replicating plasmid or expression cassette, for example, or as part of another biological system such as a virus.

[0145] The term “transformation” refers to the transfer of a nucleic acid fragment into the genome of a host cell, resulting in genetically stable inheritance. Host cells containing the transformed nucleic acid fragments are referred to as “transgenic” cells, and organisms comprising transgenic cells are referred to as “transgenic organisms”. Examples of methods of transformation of plants and plant cells include Agrobacterium-mediated transformation (De Blaere et al., 1987) and particle bombardment technology (Klein et al. 1987; U.S. Pat. No. 4,945,050). Whole plants may be regenerated from transgenic cells by methods well known to the skilled artisan (see, for example, Fromm et al., 1990).

[0146] “Transformed,” “transgenic,” and “recombinant” refer to a host organism such as a bacterium or a plant into which a heterologous nucleic acid molecule has been introduced. The nucleic acid molecule can be stably integrated into the genome generally known in the art and are disclosed in Sambrook et al., 1989. See also Innis et al., 1995 and Gelfand, 1995; and Innis and Gelfand, 1999. Known methods of PCR include, but are not limited to, methods using paired primers, nested primers, single specific primers, degenerate primers, gene-specific primers, vector-specific primers, partially mismatched primers, and the like. For example, “transformed,” “transformant,” and “transgenic” plants or calli have been through the transformation process and contain a foreign gene integrated into their chromosome. The term “untransformed” refers to normal plants that have not been through the transformation process.

[0147] “Transiently transformed” refers to cells in which transgenes and foreign DNA have been introduced (for example, by such methods as Agrobacterium-mediated transformation or biolistic bombardment), but not selected for stable maintenance.

[0148] “Stably transformed” refers to cells that have been selected and regenerated on a selection media following transformation.

[0149] “Transient expression” refers to expression in cells in which a virus or a transgene is introduced by viral infection or by such methods as Agrobacterium-mediated transformation, electroporation, or biolistic bombardment, but not selected for its stable maintenance.

[0150] “Genetically stable” and “heritable” refer to chromosomally-integrated genetic elements that are stably maintained in the plant and stably inherited by progeny through successive generations.

[0151] “Primary transformant” and “T0 generation” refer to transgenic plants that are of the same genetic generation as the tissue which was initially transformed (i.e., not having gone through meiosis and fertilization since transformation).

[0152] “Secondary transformants” and the “T1, T2, T3, etc. generations” refer to transgenic plants derived from primary transformants through one or more meiotic and fertilization cycles. They may be derived by self-fertilization of primary or secondary transformants or crosses of primary or secondary transformants with other transformed or untransformed plants.

[0153] “Wild-type” refers to a virus or organism found in nature without any known mutation.

[0154] “Genome” refers to the complete genetic material of an organism.

[0155] The term “nucleic acid” refers to deoxyribonucleotides or ribonucleotides and polymers thereof in either single- or double-stranded form, composed of monomers (nucleotides) containing a sugar, phosphate and a base which is either a purine or pyrimidine. Unless specifically limited, the term encompasses nucleic acids containing known analogs of natural nucleotides which have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions) and complementary sequences as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., 1991; Ohtsuka et al., 1985; Rossolini et al. 1994). A “nucleic acid fragment” is a fraction of a given nucleic acid molecule. In higher plants, deoxyribonucleic acid (DNA) is the genetic material while ribonucleic acid (RNA) is involved in the transfer of information contained within DNA into proteins. The term “nucleotide sequence” refers to a polymer of DNA or RNA which can be single- or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases capable of incorporation into DNA or RNA polymers. The terms “nucleic acid” or “nucleic acid sequence” may also be used interchangeably with gene, cDNA, DNA and RNA encoded by a gene.

[0156] The invention encompasses isolated or substantially purified nucleic acid or protein compositions. In the context of the present invention, an “isolated” or “purified” DNA molecule or an “isolated” or “purified” polypeptide is a DNA molecule or polypeptide that, by the hand of man, exists apart from its native environment and is therefore not a product of nature. An isolated DNA molecule or polypeptide may exist in a purified form or may exist in a non-native environment such as, for example, a transgenic host cell. For example, an “isolated” or “purified” nucleic acid molecule or protein, or biologically active portion thereof, is substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized. Preferably, an “isolated” nucleic acid is free of sequences (preferably protein encoding sequences) that naturally flank the nucleic acid (i.e., sequences located at the 5′ and 3′ ends of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived. For example, in various embodiments, the isolated nucleic acid molecule can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb, or 0.1 kb of nucleotide sequences that naturally flank the nucleic acid molecule in genomic DNA of the cell from which the nucleic acid is derived. A protein that is substantially free of cellular material includes preparations of protein or polypeptide having less than about 30%, 20%, 10%, 5%, (by dry weight) of contaminating protein. When the protein of the invention, or biologically active portion thereof, is recombinantly produced, preferably culture medium represents less than about 30%, 20%, 10%, or 5% (by dry weight) of chemical precursors or non-protein of interest chemicals.

[0157] The nucleotide sequences of the invention include both the naturally occurring sequences as well as mutant (variant) forms. Such variants will continue to possess the desired activity, i.e., either promoter activity or the activity of the product encoded by the open reading frame of the non-variant nucleotide sequence.

[0158] Thus, by “variants” is intended substantially similar sequences. For nucleotide sequences comprising an open reading frame, variants include those sequences that, because of the degeneracy of the genetic code, encode the identical amino acid sequence of the native protein. Naturally occurring allelic variants such as these can be identified with the use of well-known molecular biology techniques, as, for example, with polymerase chain reaction (PCR) and hybridization techniques. Variant nucleotide sequences also include synthetically derived nucleotide sequences, such as those generated, for example, by using site-directed mutagenesis and for open reading frames, encode the native protein, as well as those that encode a polypeptide having amino acid substitutions relative to the native protein. Generally, nucleotide sequence variants of the invention will have at least 40, 50, 60, to 70%, e.g., preferably 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, to 79%, generally at least 80%, e.g., 81%-84%, at least 85%, e.g., 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, to 98% and 99% nucleotide sequence identity to the native (wild type or endogenous) nucleotide sequence.

[0159] “Conservatively modified variations” of a particular nucleic acid sequence refers to those nucleic acid sequences that encode identical or essentially identical amino acid sequences, or where the nucleic acid sequence does not encode an amino acid sequence, to essentially identical sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given polypeptide. For instance the codons CGT, CGC, CGA, CGG, AGA, and AGG all encode the amino acid arginine. Thus, at every position where an arginine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded protein. Such nucleic acid variations are “silent variations” which are one species of “conservatively modified variations.” Every nucleic acid sequence described herein which encodes a polypeptide also describes every possible silent variation, except where otherwise noted. One of skill will recognize that each codon in a nucleic acid (except ATG, which is ordinarily the only codon for methionine) can be modified to yield a functionally identical molecule by standard techniques. Accordingly, each “silent variation” of a nucleic acid which encodes a polypeptide is implicit in each described sequence.

[0160] The nucleic acid molecules of the invention can be “optimized” for enhanced expression in plants of interest. See, for example, EPA 035472; WO 91/16432; Perlak et al., 1991; and Murray et al., 1989. In this manner, the open reading frames in genes or gene fragments can be synthesized utilizing plant-preferred codons. See, for example, Campbell and Gowri, 1990 for a discussion of host-preferred codon usage. Thus, the nucleotide sequences can be optimized for expression in any plant. It is recognized that all or any part of the gene sequence may be optimized or synthetic. That is, synthetic or partially optimized sequences may also be used. Variant nucleotide sequences and proteins also encompass, sequences and protein derived from a mutagenic and recombinogenic procedure such as DNA shuffling. With such a procedure, one or more different coding sequences can be manipulated to create a new polypeptide possessing the desired properties. In this manner, libraries of recombinant polynucleotides are generated from a population of related sequence polynucleotides comprising sequence regions that have substantial sequence identity and can be homologously recombined in vitro or in vivo. Strategies for such DNA shuffling are known in the art. See, for example, Stemmer, 1994; Stemmer, 1994; Crameri et al., 1997; Moore et al., 1997; Zhang et al., 1997; Crameri et al., 1998; and U.S. Pat. Nos. 5,605,793 and 5,837,458.

[0161] By “variant” polypeptide is intended a polypeptide derived from the native protein by deletion (so-called truncation) or addition of one or more amino acids to the N-terminal and/or C-terminal end of the native protein; deletion or addition of one or more amino acids at one or more sites in the native protein; or substitution of one or more amino acids at one or more sites in the native protein. Such variants may result from, for example, genetic polymorphism or from human manipulation. Methods for such manipulations are generally known in the art.

[0162] Thus, the polypeptides may be altered in various ways including amino acid substitutions, deletions, truncations, and insertions. Methods for such manipulations are generally known in the art. For example, amino acid sequence variants of the polypeptides can be prepared by mutations in the DNA. Methods for mutagenesis and nucleotide sequence alterations are well known in the art. See, for example, Kunkel, 1985; Kunkel et al., 1987; U.S. Pat. No. 4,873,192; Walker and Gaastra, 1983 and the references cited therein. Guidance as to appropriate amino acid substitutions that do not affect biological activity of the protein of interest may be found in the model of Dayhoff et al. (1978). Conservative substitutions, such as exchanging one amino acid with another having similar properties, are preferred.

[0163] Individual substitutions deletions or additions that alter, add or delete a single amino acid or a small percentage of amino acids (typically less than 5%, more typically less than 1%) in an encoded sequence are “conservatively modified variations,” where the alterations result in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art. The following five groups each contain amino acids that are conservative substitutions for one another: Aliphatic: Glycine (G), Alanine (A), Valine (V), Leucine (L), Isoleucine (I); Aromatic: Phenylalanine (F), Tyrosine (Y), Tryptophan (W); Sulfur-containing: Methionine (M), Cysteine (C); Basic: Arginine I, Lysine (K), Histidine (H); Acidic: Aspartic acid (D), Glutamic acid (E), Asparagine (N), Glutamine (Q). See also, Creighton, 1984. In addition, individual substitutions, deletions or additions which alter, add or delete a single amino acid or a small percentage of amino acids in an encoded sequence are also “conservatively modified variations.”

[0164] “Expression cassette” as used herein means a DNA sequence capable of directing expression of a particular nucleotide sequence in an appropriate host cell, comprising a promoter operably linked to the nucleotide sequence of interest which is operably linked to termination signals. It also typically comprises sequences required for proper translation of the nucleotide sequence. The coding region usually codes for a protein of interest but may also code for a functional RNA of interest, for example antisense RNA or a nontranslated RNA, in the sense or antisense direction. The expression cassette comprising the nucleotide sequence of interest may be chimeric, meaning that at least one of its components is heterologous with respect to at least one of its other components. The expression cassette may also be one which is naturally occurring but has been obtained in a recombinant form useful for heterologous expression. The expression of the nucleotide sequence in the expression cassette may be under the control of a constitutive promoter or of an inducible promoter which initiates transcription only when the host cell is exposed to some particular external stimulus. In the case of a multicellular organism, the promoter can also be specific to a particular tissue or organ or stage of development.

[0165] “Vector” is defined to include, inter alia, any plasmid, cosmid, phage or Agrobacterium binary vector in double or single stranded linear or circular form which may or may not be self transmissible or mobilizable, and which can transform prokaryotic or eukaryotic host either by integration into the cellular genome or exist extrachromosomally (e.g. autonomous replicating plasmid with an origin of replication).

[0166] Specifically included are shuttle vectors by which is meant a DNA vehicle capable, naturally or by design, of replication in two different host organisms, which may be selected from actinomycetes and related species, bacteria and eukaryotic (e.g. higher plant, mammalian, yeast or fungal cells).

[0167] Preferably the nucleic acid in the vector is under the control of, and operably linked to, an appropriate promoter or other regulatory elements for transcription in a host cell such as a microbial, e.g. bacterial, or plant cell. The vector may be a bi-functional expression vector which functions in multiple hosts. In the case of genomic DNA, this may contain its own promoter or other regulatory elements and in the case of cDNA this may be under the control of an appropriate promoter or other regulatory elements for expression in the host cell.

[0168] “Cloning vectors” typically contain one or a small number of restriction endonuclease recognition sites at which foreign DNA sequences can be inserted in a determinable fashion without loss of essential biological function of the vector, as well as a marker gene that is suitable for use in the identification and selection of cells transformed with the cloning vector. Marker genes typically include genes that provide tetracycline resistance, hygromycin resistance or ampicillin resistance.

[0169] A “transgenic plant” is a plant having one or more plant cells that contain an expression vector.

[0170] “Plant tissue” includes differentiated and undifferentiated tissues or plants, including but not limited to roots, stems, shoots, leaves, pollen, seeds, tumor tissue and various forms of cells and culture such as single cells, protoplast, embryos, and callus tissue. The plant tissue may be in plants or in organ, tissue or cell culture.

[0171] The following terms are used to describe the sequence relationships between two or more nucleic acids or polynucleotides: (a) “reference sequence”, (b) “comparison window”, (c) “sequence identity”, (d) “percentage of sequence identity”, and (e) “substantial identity”.

[0172] (a) As used herein, “reference sequence” is a defined sequence used as a basis for sequence comparison. A reference sequence may be a subset or the entirety of a specified sequence; for example, as a segment of a full length cDNA or gene sequence, or the complete cDNA or gene sequence.

[0173] (b) As used herein, “comparison window” makes reference to a contiguous and specified segment of a polynucleotide sequence, wherein the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. Generally, the comparison window is at least 20 contiguous nucleotides in length, and optionally can be 30, 40, 50, 100, or longer. Those of skill in the art understand that to avoid a high similarity to a reference sequence due to inclusion of gaps in the polynucleotide sequence a gap penalty is typically introduced and is subtracted from the number of matches.

[0174] Methods of alignment of sequences for comparison are well known in the art. Thus, the determination of percent identity between any two sequences can be accomplished using a mathematical algorithm. Preferred, non-limiting examples of such mathematical algorithms are the algorithm of Myers and Miller, 1988; the local homology algorithm of Smith et al. 1981; the homology alignment algorithm of Needleman and Wunsch 1970; the search-for-similarity-method of Pearson and Lipman 1988; the algorithm of Karlin and Altschul, 1990, modified as in Karlin and Altschul, 1993.

[0175] Computer implementations of these mathematical algorithms can be utilized for comparison of sequences to determine sequence identity. Such implementations include, but are not limited to: CLUSTAL in the PC/Gene program (available from Intelligenetics, Mountain View, Calif.); the ALIGN program (Version 2.0) and GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Version 8 (available from Genetics Computer Group (GCG), 575 Science Drive, Madison, Wis., USA). Alignments using these programs can be performed using the default parameters. The CLUSTAL program is well described by Higgins et al. 1988; Higgins et al. 1989; Corpet et al. 1988; Huang et al. 1992; and Pearson et al. 1994. The ALIGN program is based on the algorithm of Myers and Miller, supra. The BLAST programs of Altschul et al., 1990, are based on the algorithm of Karlin and Altschul supra.

[0176] Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., 1990). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when the cumulative alignment score falls off by the quantity X from its maximum achieved value, the cumulative score goes to zero or below due to the accumulation of one or more negative-scoring residue alignments, or the end of either sequence is reached.

[0177] In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul (1993). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a test nucleic acid sequence is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid sequence to the reference nucleic acid sequence is less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.

[0178] To obtain gapped alignments for comparison purposes, Gapped BLAST (in BLAST 2.0) can be utilized as described in Altschul et al. 1997. Alternatively, PSI-BLAST (in BLAST 2.0) can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al., supra. When utilizing BLAST, Gapped BLAST, PSI-BLAST, the default parameters of the respective programs (e.g. BLASTN for nucleotide sequences, BLASTX for proteins) can be used. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, a cutoff of 100, M=5, N=−4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, 1989). See http://www.ncbi.nlm.nih.gov. Alignment may also be performed manually by inspection.

[0179] For purposes of the present invention, comparison of nucleotide sequences for determination of percent sequence identity to the promoter sequences disclosed herein is preferably made using the BlastN program (version 1.4.7 or later) with its default parameters or any equivalent program. By “equivalent program” is intended any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide or amino acid residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by the preferred program.

[0180] (c) As used herein, “sequence identity” or “identity” in the context of two nucleic acid or polypeptide sequences makes reference to the residues in the two sequences that are the same when aligned for maximum correspondence over a specified comparison window. When percentage of sequence identity is used in reference to proteins it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule. When sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Sequences that differ by such conservative substitutions are said to have “sequence similarity” or “similarity.” Means for making this adjustment are well known to those of skill in the art. Typically this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated, e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, Calif.).

[0181] (d) As used herein, “percentage of sequence identity” means the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison, and multiplying the result by 100 to yield the percentage of sequence identity.

[0182] (e)(i) The term “substantial identity” of polynucleotide sequences means that a polynucleotide comprises a sequence that has at least 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, or 79%, preferably at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, or 89%, more preferably at least 90%, 91%, 92%, 93%, or 94%, and most preferably at least 95%, 96%, 97%, 98%, or 99% sequence identity, compared to a reference sequence using one of the alignment programs described using standard parameters. One of skill in the art will recognize that these values can be appropriately adjusted to determine corresponding identity of proteins encoded by two nucleotide sequences by taking into account codon degeneracy, amino acid similarity, reading frame positioning, and the like. Substantial identity of amino acid sequences for these purposes normally means sequence identity of at least 70%, more preferably at least 80%, 90%, and most preferably at least 95%.

[0183] Another indication that nucleotide sequences are substantially identical is if two molecules hybridize to each other under stringent conditions (see below). Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. However, stringent conditions encompass temperatures in the range of about 1° C. to about 20° C., depending upon the desired degree of stringency as otherwise qualified herein. Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides they encode are substantially identical. This may occur, e.g., when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code. One indication that two nucleic acid sequences are substantially identical is when the polypeptide encoded by the first nucleic acid is immunologically cross reactive with the polypeptide encoded by the second nucleic acid.

[0184] (e)(ii) The term “substantial identity” in the context of a peptide indicates that a peptide comprises a sequence with at least 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, or 79%, preferably 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, or 89%, more preferably at least 90%, 91%, 92%, 93%, or 94%, or even more preferably, 95%, 96%, 97%, 98% or 99%, sequence identity to the reference sequence over a specified comparison window. Preferably, optimal alignment is conducted using the homology alignment algorithm of Needleman and Wunsch (1970). An indication that two peptide sequences are substantially identical is that one peptide is immunologically reactive with antibodies raised against the second peptide. Thus, a peptide is substantially identical to a second peptide, for example, where the two peptides differ only by a conservative substitution.

[0185] For sequence comparison, typically one sequence acts as a reference sequence to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are input into a computer, subsequence coordinates are designated if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.

[0186] As noted above, another indication that two nucleic acid sequences are substantially identical is that the two molecules hybridize to each other under stringent conditions. The phrase “hybridizing specifically to” refers to the binding, duplexing, or hybridizing of a molecule only to a particular nucleotide sequence under stringent conditions when that sequence is present in a complex mixture (e.g., total cellular) DNA or RNA. “Bind(s) substantially” refers to complementary hybridization between a probe nucleic acid and a target nucleic acid and embraces minor mismatches that can be accommodated by reducing the stringency of the hybridization media to achieve the desired detection of the target nucleic acid sequence.

[0187] “Stringent hybridization conditions” and “stringent hybridization wash conditions” in the context of nucleic acid hybridization experiments such as Southern and Northern hybridization are sequence dependent, and are different under different environmental parameters. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Specificity is typically the function of post-hybridization washes, the critical factors being the ionic strength and temperature of the final wash solution. For DNA-DNA hybrids, the Tm can be approximated from the equation of Meinkoth and Wahl, 1984; Tm 81.5° C.+16.6 (log M)+0.41 (%GC)−0.61 (% form)−500/L; where M is the molarity of monovalent cations, %GC is the percentage of guanosine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs. Tm is reduced by about 1° C. for each 1% of mismatching; thus, Tm, hybridization, and/or wash conditions can be adjusted to hybridize to sequences of the desired identity. For example, if sequences with >90% identity are sought, the Tm can be decreased 10° C. Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point I for the specific sequence and its complement at a defined ionic strength and pH. However, severely stringent conditions can utilize a hybridization and/or wash at 1, 2, 3, or 4° C. lower than the thermal melting point I; moderately stringent conditions can utilize a hybridization and/or wash at 6, 7, 8, 9, or 10° C. lower than the thermal melting point I; low stringency conditions can utilize a hybridization and/or wash at 11, 12, 13, 14, 15, or 20° C. lower than the thermal melting point I. Using the equation, hybridization and wash compositions, and desired T, those of ordinary skill will understand that variations in the stringency of hybridization and/or wash solutions are inherently described. If the desired degree of mismatching results in a T of less than 45° C. (aqueous solution) or 32° C. (formamide solution), it is preferred to increase the SSC concentration so that a higher temperature can be used. An extensive guide to the hybridization of nucleic acids is found in Tijssen, 1993. Generally, highly stringent hybridization and wash conditions are selected to be about 5° C. lower than the thermal melting point Tm for the specific sequence at a defined ionic strength and pH.

[0188] An example of highly stringent wash conditions is 0.15 M NaCl at 72° C. for about 15 minutes. An example of stringent wash conditions is a 0.2×SSC wash at 65° C. for 15 minutes (see, Sambrook, infra, for a description of SSC buffer). Often, a high stringency wash is preceded by a low stringency wash to remove background probe signal. An example medium stringency wash for a duplex of, e.g., more than 100 nucleotides, is 1×SSC at 45° C. for 15 minutes. An example low stringency wash for a duplex of, e.g., more than 100 nucleotides, is 4-6×SSC at 40° C. for 15 minutes. For short probes (e.g., about 10 to 50 nucleotides), stringent conditions typically involve salt concentrations of less than about 1.5 M, more preferably about 0.01 to 1.0 M, Na ion concentration (or other salts) at pH 7.0 to 8.3, and the temperature is typically at least about 30° C. and at least about 60° C. for long robes (e.g., >50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. In general, a signal to noise ratio of 2× (or higher) than that observed for an unrelated probe in the particular hybridization assay indicates detection of a specific hybridization. Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the proteins that they encode are substantially identical. This occurs, e.g., when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code.

[0189] Very stringent conditions are selected to be equal to the Tm for a particular probe. An example of stringent conditions for hybridization of complementary nucleic acids which have more than 100 complementary residues on a filter in a Southern or Northern blot is 50% formamide, e.g., hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 0.1×SSC at 60 to 65° C. Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37° C., and a wash in 1× to 2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at 50 to 55° C. Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37° C., and a wash in 0.5× to 1×SSC at 55 to 60° C.

[0190] The following are examples of sets of hybridization/wash conditions that may be used to clone orthologous nucleotide sequences that are substantially identical to reference nucleotide sequences of the present invention: a reference nucleotide sequence preferably hybridizes to the reference nucleotide sequence in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO4, 1 mM EDTA at 50° C. with washing in 2×SSC, 0. 1% SDS at 50° C., more desirably in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO4, 1 mM EDTA at 50° C. with washing in 1×SSC, 0.1% SDS at 50° C., more desirably still in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO4, 1 mM EDTA at 50° C. with washing in 0.5×SSC, 0. 1% SDS at 50° C., preferably in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO4, 1 mM EDTA at 50° C. with washing in 0.1×SSC, 0.1% SDS at 50° C., more preferably in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO4, 1 mM EDTA at 50° C. with washing in 0.1×SSC, 0.1% SDS at 65° C.

[0191] “DNA shuffling” is a method to introduce mutations or rearrangements, preferably randomly, in a DNA molecule or to generate exchanges of DNA sequences between two or more DNA molecules, preferably randomly. The DNA molecule resulting from DNA shuffling is a shuffled DNA molecule that is a non-naturally occurring DNA molecule derived from at least one template DNA molecule. The shuffled DNA preferably encodes a variant polypeptide modified with respect to the polypeptide encoded by the template DNA, and may have an altered biological activity with respect to the polypeptide encoded by the template DNA.

[0192] “Recombinant DNA molecule’ is a combination of DNA sequences that are joined together using recombinant DNA technology and procedures used to join together DNA sequences as described, for example, in Sambrook et al., 1989.

[0193] The word “plant” refers to any plant, particularly to seed plant, and “plant cell” is a structural and physiological unit of the plant, which comprises a cell wall but may also refer to a protoplast. The plant cell may be in form of an isolated single cell or a cultured cell, or as a part of higher organized unit such as, for example, a plant tissue, or a plant organ.

[0194] “Significant increase” is an increase that is larger than the margin of error inherent in the measurement technique, preferably an increase by about 2-fold or greater.

[0195] “Significantly less” means that the decrease is larger than the margin of error inherent in the measurement technique, preferably a decrease by about 2-fold or greater.

[0196] II. Nucleic Acid Molecules of the Invention

[0197] The invention relates to an isolated plant, e.g., Oryza, nucleic acid molecule which directs the expression of linked nucleic acid segment in a plant, e.g., in a particular tissue or constitutively, as well as the corresponding open reading frame and encoded product. The nucleic acid molecule, e.g., one which comprises a promoter, can be used to overexpress a linked nucleic acid segment so as to express a product in a constitutive, tissue-specific or tissue-preferential manner, or to alter the expression of the product, e.g., via the use of antisense vectors or by “knocking out” the expression of at least one genomic copy of the gene.

[0198] The nucleic acid molecules of the invention can be obtained or isolated from any plant or non-plant source, or produced synthetically by purley chemical means. Preferred sources include, but are not limited to, corn (Zea mays), Brassica sp. (e.g., B. napus, B. rapa, B. juncea), particularly those Brassica species useful as sources of seed oil, alfalfa (Medicago sativa), rice (Oryza sativa), rye (Secale cereale), sorghum (Sorghum bicolor, Sorghum vulgare), millet (e.g., pearl millet (Pennisetum glaucum), proso millet (Panicum miliaceum), foxtail millet (Setaria italica), finger millet (Eleusine coracana)), sunflower (Helianthus annuus), safflower (Carthamus tinctorius), wheat (Triticum aestivum), soybean (Glycine max), tobacco (Nicotiana tabacum), potato (Solanum tuberosum), peanuts (Arachis hypogaea), cotton (Gossypium barbadense, Gossypium hirsutum), sweet potato (Ipomoea batatus), cassava (Manihot esculenta), coffee (Cofea spp.), coconut (Cocos nucifera), pineapple (Ananas comosus), citrus trees (Citrus spp.), cocoa (Theobroma cacao), tea (Camellia sinensis), banana (Musa spp.), avocado (Persea ultilane), fig (Ficus casica), guava (Psidium guajava), mango (Mangifera indica), olive (Olea europaea), papaya (Carica papaya), cashew (Anacardium occidentale), macadamia (Macadamia integrifolia), almond (Prunus amygdalus), sugar beets (Beta vulgaris), sugarcane (Saccharum spp.), oats, duckweed (Lemna), barley, vegetables, ornamentals, and conifers.

[0199] Duckweed (Lemna, see WO 00/07210) includes members of the family Lemnaceae. There are known four genera and 34 species of duckweed as follows: genus Lemna (L. aequinoctialis, L. disperma, L. ecuadoriensis, L. gibba, L. japonica, L. minor, L. miniscula, L. obscura, L. perpusilla, L. tenera, L. trisulca, L. turionifera, L. valdiviana); genus Spirodela (S. intermedia, S. polyrrhiza, S. punctata); genus Woffia (Wa. Angusta, Wa. Arrhiza, Wa. Australina, Wa. Borealis, Wa. Brasiliensis, Wa. Columbiana, Wa. Elongata, Wa. Globosa, Wa. Microscopica, Wa. Neglecta) and genus Wofiella (W1. ultila, W1. ultilane n, W1. gladiata, W1. ultila, W1. lingulata, W1. repunda, W1. rotunda, and W1. neotropica). Any other genera or species of Lemnaceae, if they exist, are also aspects of the present invention. Lemna gibba, Lemna minor, and Lemna miniscula are preferred, with Lemna minor and Lemna miniscula being most preferred. Lemna species can be classified using the taxonomic scheme described by Landolt, Biosystematic Investigation on the Family of Duckweeds: The family of Lemnaceae—A Monograph Study. Geobatanischen Institut ETH, Stiftung Rubel, Zurich (1986)).

[0200] Vegetables from which to obtain or isolate the nucleic acid molecules of the invention include, but are not limited to, tomatoes (Lycopersicon esculentum), lettuce (e.g., Lactuca sativa), green beans (Phaseolus vulgaris), lima beans (Phaseolus limensis), peas (Lathyrus spp.), and members of the genus Cucumis such as cucumber (C. sativus), cantaloupe (C. cantalupensis), and musk melon (C. melo). Ornamentals from which to obtain or isolate the nucleic acid molecules of the invention include, but are not limited to, azalea (Rhododendron spp.), hydrangea (Macrophylla hydrangea), hibiscus (Hibiscus rosasanensis), roses (Rosa spp.), tulips (Tulipa spp.), daffodils (Narcissus spp.), petunias (Petunia hybrida), carnation (Dianthus caryophyllus), poinsettia (Euphorbia pulcherrima), and chrysanthemum. Conifers that may be employed in practicing the present invention include, for example, pines such as loblolly pine (Pinus taeda), slash pine (Pinus elliotii), ponderosa pine (Pinus ponderosa), lodgepole pine (Pinus contorta), and Monterey pine (Pinus radiata), Douglas-fir (Pseudotsuga menziesii); Western hemlock (Tsuga ultilane); Sitka spruce (Picea glauca); redwood (Sequoia sempervirens); true firs such as silver fir (Abies amabilis) and balsam fir (Abies balsamea); and cedars such as Western red cedar (Thuja plicata) and Alaska yellow-cedar (Chamaecyparis nootkatensis). Leguminous plants from which the nucleic acid molecules of the invention can be isolated or obtained include, but are not limited to, beans and peas. Beans include guar, locust bean, fenugreek, soybean, garden beans, cowpea, mungbean, lima bean, fava bean, lentils, chickpea, and the like. Legumes include, but are not limited to, Arachis, e.g., peanuts, Vicia, e.g., crown vetch, hairy vetch, adzuki bean, mung bean, and chickpea, Lupinus, e.g., lupine, trifolium, Phaseolus, e.g., common bean and lima bean, Pisum, e.g., field bean, Melilotus, e.g., clover, Medicago, e.g., alfalfa, Lotus, e.g., trefoil, lens, e.g., lentil, and false indigo. Preferred forage and turf grass from which the nucleic acid molecules of the invention can be isolated or obtained for use in the methods of the invention include, but are not limited to, alfalfa, orchard grass, tall fescue, perennial ryegrass, creeping bent grass, and redtop.

[0201] Other preferred sources of the nucleic acid molecules of the invention include Acacia, aneth, artichoke, arugula, blackberry, canola, cilantro, clementines, escarole, eucalyptus, fennel, grapefruit, honey dew, jicama, kiwifruit, lemon, lime, mushroom, nut, okra, orange, parsley, persimmon, plantain, pomegranate, poplar, radiata pine, radicchio, Southern pine, sweetgum, tangerine, triticale, vine, yams, apple, pear, quince, cherry, apricot, melon, hemp, buckwheat, grape, raspberry, chenopodium, blueberry, nectarine, peach, plum, strawberry, watermelon, eggplant, pepper, cauliflower, Brassica, e.g., broccoli, cabbage, ultilan sprouts, onion, carrot, leek, beet, broad bean, celery, radish, pumpkin, endive, gourd, garlic, snapbean, spinach, squash, turnip, ultilane, and zucchini.

[0202] Yet other sources of nucleic acid molecules are ornamental plants including, but not limited to, impatiens, Begonia, Pelargonium, Viola, Cyclamen, Verbena, Vinca, Tagetes, Primula, Saint Paulia, Agertum, Amaranthus, Antihirrhinum, Aquilegia, Cineraria, Clover, Cosmo, Cowpea, Dahlia, Datura, Delphinium, Gerbera, Gladiolus, Gloxinia, Hippeastrum, Mesembryanthemum, Salpiglossos, and Zinnia, and plants such as those shown in Table 1.

1TABLE 1LATINCOMMONMAP REFERENCESFAMILYNAMENAMERESOURCESLINKSCucurbitaceaeCucumisCucumberhttp://sativuswww.cucurbit.org/CucumisMelonhttp://melogenome.cornell.edu/cgc/CitrullusWatermelonlanatusCucurbitaSquash -peposummerCucurbitaSquash -maximawinterCucurbitaPumpkin/moschatabutternutTotalhttp://www.nal.usda.gov/pgdic/Map_proj/SolanaceaeLycopersiconTomato15x BAC on varietygenome.esculentumHeinz 1706 order fromcornell.Clemson Genome centeredu/solgenes(www.genome.clemson.edu)http://11.6x BAC of L.ars-genome.cheesmanii (originatescornell.edu/from J. Giovannoni)cgi-bin/WebAce/available from Clemsonwebace?genome centerdb = solgenes(www.genome.clemson.edu)http://EST collection fromgenome.TIGRcornell.(www.tigr.org/tdb/lgi/index.html)edu/tgc/EST collection fromhttp://Clemsom Genometgrc.Centerucdavis.edu/(www.genome.clemson.edu)TAG 99: 254-271, 1999(esculentum x pennelli)TAG 89: 1007-1013,1994 (peruvianum)Plant Cell Reports12: 293-297, 1993(RAPDs)Genetics 132: 1141-1160,1992 (potato x tomato)Genetics 120: 1095-1105,1988 (RFLP potato andtomato)Genetics 115: 387-393,1986 (esculentum xpennelli isozyme andcDNAs)CapsicumPepperhttp://annuumneptune.netimages.com./˜chile/science.htmlCapsicumChile pepperfrutescensSolanumEggplantmelongena(Nicotiana(Tobacco)tabacum)(Solanum(Potato)tuberosum)(Petunia x(Petunia)4x BAC of Petunia hybridahybrida7984 available fromhort. Ex E.Clemson genome centerVilm.)(www.genome.clemson.edu)Totalhttp://www.nal.usda.gov/pgdic/Map_proj/BrassicaceaeBrassicaBroccolihttp://oleracea L.res.agr.ca/var. italicaecorc/cwmt/crucifer/traits/index.htmhttp://geneous.cit.cornell.edu/cabbage/aboutcab.htmlBrassicaCabbageoleracea L.var. capitataBrassicaChineserapaCabbageBrassicaCaulifloweroleracea L.var. botrytisRaphanusDaikonsativus var.niger(Brassica(Oilseedhttp://napus)rape)ars-genome.cornell.edu/cgi-bin/WebAce/webace?db = brassicadbArabidopsis12x and 6x BACs onhttp://Columbia strain availablears-genome.from Clemson genomecornell.edu/centercgi-bin/(www.genome.clemson.edu)WebAce/webace?db = agrTotalhttp://www.nal.usda.gov/pgdic/Map_proj/UmbelliferaeDaucusCarrotcarotaCompositaeLactucaLettucesativaHelianthus(Sunflower)annuusTotalChenopodiaceaeSpinaciaSpinacholeracea(Beta(Sugar Beet)vulgaris)TotalLeguminosaePhaseolusBean4.3x BAC available fromhttp://vulgarisClemson genome centerars-genome.(www.genome.clemson.edu)cornell.edu/cgi-bin/WebAce/webace?db = beangenesPisumPeasativum(Glycine(Soybean)7.5x and 7.9x BACshttp://max)available from Clemsonars-genome.genome centercornell.edu/(www.genome.clemson.edu)cgi-bin/WebAce/webace?db = soybaseTotalhttp://www.nal.usda.gov/pgdic/Map_proj/GramineaeZea maysSweet CornNovartis BACs for Mo17and B73 have been donatedto Clemson Genome Center(www.genome.clemson.edu)(Zea mays)(Field Corn)http://www.agron.missouri.edu/mnl/Totalhttp://www.nal.usda.gov/pgdic/Map_proj/LiliaceaeAllium cepaOnionLeek(Garlic)(Asparagus)Totalhttp://www.nal.usda.gov/pgdic/Map_proj/

[0203] Yet other preferred sources include, but are not limited to, crop plants and in particular cereals (for example, corn, alfalfa, sunflower, Brassica, canola, soybean, barley, soybean, sugarbeet, cotton, safflower, peanut, sorghum, wheat, millet, tobacco, and the like), and even more preferably corn, wheat and soybean.

[0204] According to one embodiment, the present invention is directed to a nucleic acid molecule comprising a nucleotide sequence isolated or obtained from any plant which encodes a polypeptide having at least 70% amino acid sequence identity to a polypeptide encoded by a gene comprising any one of SEQ ID NOs:1-2672, 5959, 5972, 5973, 5977-5990 and 6001. Based on the Oryza nucleic acid sequences of the present invention, orthologs may be identified or isolated from the genome of any desired organism, preferably from another plant, according to well known techniques based on their sequence similarity to the Oryza nucleic acid sequences, e.g., hybridization, PCR or computer generated sequence comparisons. For example, all or a portion of a particular Oryza nucleic acid sequence is used as a probe that selectively hybridizes to other gene sequences present in a population of cloned genomic DNA fragments or cDNA fragments (i.e., genomic or cDNA libraries) from a chosen source organism. Further, suitable genomic and cDNA libraries may be prepared from any cell or tissue of an organism. Such techniques include hybridization screening of plated DNA libraries (either plaques or colonies; see, e.g., Sambrook et al., 1989) and amplification by PCR using oligonucleotide primers preferably corresponding to sequence domains conserved among related polypeptide or subsequences of the nucleotide sequences provided herein (see, e.g., Innis et al., 1990). These methods are particularly well suited to the isolation of gene sequences from organisms closely related to the organism from which the probe sequence is derived. The application of these methods using the Oryza sequences as probes is well suited for the isolation of gene sequences from any source organism, preferably other plant species. In a PCR approach, oligonucleotide primers can be designed for use in PCR reactions to amplify corresponding DNA sequences from cDNA or genomic DNA extracted from any plant of interest. Methods for designing PCR primers and PCR cloning are generally known in the art.

[0205] In hybridization techniques, all or part of a known nucleotide sequence is used as a probe that selectively hybridizes to other corresponding nucleotide sequences present in a population of cloned genomic DNA fragments or cDNA fragments (i.e., genomic or cDNA libraries) from a chosen organism. The hybridization probes may be genomic DNA fragments, cDNA fragments, RNA fragments, or other oligonucleotides, and may be labeled with a detectable group such as 32P, or any other detectable marker. Thus, for example, probes for hybridization can be made by labeling synthetic oligonucleotides based on the sequence of the invention. Methods for preparation of probes for hybridization and for construction of cDNA and genomic libraries are generally known in the art and are disclosed in Sambrook et al. (1989). In general, sequences that hybridize to the sequences disclosed herein will have at least 40% to 50%, about 60% to 70% and even about 80% 85%, 90%, 95% to 98% or more identity with the disclosed sequences. That is, the sequence similarity of sequences may range, sharing at least about 40% to 50%, about 60% to 70%, and even about 80%, 85%, 90%, 95% to 98% sequence similarity.

[0206] The nucleic acid molecules of the invention can also be identified by, for example, a search of known databases for genes encoding polypeptides having a specified amino acid sequence identity or DNA having a specified nucleotide sequence identity. Methods of alignment of sequences for comparison are well known in the art and are described hereinabove.

[0207] Virtually any DNA composition may be used for delivery to recipient plant cells, e.g., monocotyledonous cells, to ultimately produce fertile transgenic plants in accordance with the present invention. For example, DNA segments or fragments in the form of vectors and plasmids, or linear DNA segments or fragments, in some instances containing only the DNA element to be expressed in the plant, and the like, may be employed. The construction of vectors which may be employed in conjunction with the present invention will be known to those of skill of the art in light of the present disclosure (see, e.g., Sambrook et al., 1989; Gelvin et al., 1990).

[0208] Vectors, plasmids, cosmids, YACs (yeast artificial chromosomes), BACs (bacterial artificial chromosomes) and DNA segments for use in transforming such cells will, of course, generally comprise the cDNA, gene or genes which one desires to introduce into the cells. These DNA constructs can further include structures such as promoters, enhancers, polylinkers, or even regulatory genes as desired. The DNA segment, fragment or gene chosen for cellular introduction will often encode a protein which will be expressed in the resultant recombinant cells, such as will result in a screenable or selectable trait and/or which will impart an improved phenotype to the regenerated plant. However, this may not always be the case, and the present invention also encompasses transgenic plants incorporating non-expressed transgenes.

[0209] In certain embodiments, it is contemplated that one may wish to employ replication-competent viral vectors in monocot transformation. Such vectors include, for example, wheat dwarf virus (WDV) “shuttle” vectors, such as pW1-11 and PW1-GUS (Ugaki et al., 1991). These vectors are capable of autonomous replication in maize cells as well as E. coli, and as such may provide increased sensitivity for detecting DNA delivered to transgenic cells. A replicating vector may also be useful for delivery of genes flanked by DNA sequences from transposable elements such as Ac, Ds, or Mu. It has been proposed (Laufs et al., 1990) that transposition of these elements within the maize genome requires DNA replication. It is also contemplated that transposable elements would be useful for introducing DNA segments or fragments lacking elements necessary for selection and maintenance of the plasmid vector in bacteria, e.g., antibiotic resistance genes and origins of DNA replication. It is also proposed that use of a transposable element such as Ac, Ds, or Mu would actively promote integration of the desired DNA and hence increase the frequency of stably transformed cells. The use of a transposable element such as Ac, Ds, or Mu may actively promote integration of the DNA of interest and hence increase the frequency of stably transformed cells. Transposable elements may be useful to allow separation of genes of interest from elements necessary for selection and maintenance of a plasmid vector in bacteria or selection of a transformant. By use of a transposable element, desirable and undesirable DNA sequences may be transposed apart from each other in the genome, such that through genetic segregation in progeny, one may identify plants with either the desirable undesirable DNA sequences.

[0210] It is one of the objects of the present invention to provide recombinant DNA molecules comprising a nucleotide sequence which directs transcription according to the invention operably linked to a nucleic acid segment or sequence of interest. The nucleic acid segment of interest can, for example, code for a ribosomal RNA, an antisense RNA or any other type of RNA that is not translated into protein. In another preferred embodiment of the invention, the nucleic acid segment of interest is translated into a protein product. The nucleotide sequence which directs transcription and/or the nucleic acid segment may be of homologous or heterologous origin with respect to the plant to be transformed. A recombinant DNA molecule useful for introduction into plant cells includes that which has been derived or isolated from any source, that may be subsequently characterized as to structure, size and/or function, chemically altered, and later introduced into plants. An example of a nucleotide sequence or segment of interest “derived” from a source, would be a nucleotide sequence or segment that is identified as a useful fragment within a given organism, and which is then chemically synthesized in essentially pure form. An example of such a nucleotide sequence or segment of interest “isolated” from a source, would be nucleotide sequence or segment that is excised or removed from said source by chemical means, e.g., by the use of restriction endonucleases, so that it can be further manipulated, e.g., amplified, for use in the invention, by the methodology of genetic engineering. Such a nucleotide sequence or segment is commonly referred to as “recombinant.”

[0211] Therefore a useful nucleotide sequence, segment or fragment of interest includes completely synthetic DNA, semi-synthetic DNA, DNA isolated from biological sources, and DNA derived from introduced RNA. Generally, the introduced DNA is not originally resident in the plant genotype which is the recipient of the DNA, but it is within the scope of the invention to isolate a gene from a given plant genotype, and to subsequently introduce multiple copies of the gene into the same genotype, e.g., to enhance production of a given gene product such as a storage protein or a protein that confers tolerance or resistance to water deficit.

[0212] The introduced recombinant DNA molecule includes but is not limited to, DNA from plant genes, and non-plant genes such as those from bacteria, yeasts, animals or viruses. The introduced DNA can include modified genes, portions of genes, or chimeric genes, including genes from the same or different genotype. The term “chimeric gene” or “chimeric DNA” is defined as a gene or DNA sequence or segment comprising at least two DNA sequences or segments from species which do not combine DNA under natural conditions, or which DNA sequences or segments are positioned or linked in a manner which does not normally occur in the native genome of untransformed plant.

[0213] The introduced recombinant DNA molecule used for transformation herein may be circular or linear, double-stranded or single-stranded. Generally, the DNA is in the form of chimeric DNA, such as plasmid DNA, that can also contain coding regions flanked by regulatory sequences which promote the expression of the recombinant DNA present in the resultant plant.

[0214] Generally, the introduced recombinant DNA molecule will be relatively small, i.e., less than about 30 kb to minimize any susceptibility to physical, chemical, or enzymatic degradation which is known to increase as the size of the nucleotide molecule increases. As noted above, the number of proteins, RNA transcripts or mixtures thereof which is introduced into the plant genome is preferably preselected and defined, e.g., from one to about 5-10 such products of the introduced DNA may be formed.

[0215] Two principal methods for the control of expression are known, viz.: overexpression and underexpression. Overexpression can be achieved by insertion of one or more than one extra copy of the selected gene. It is, however, not unknown for plants or their progeny, originally transformed with one or more than one extra copy of a nucleotide sequence, to exhibit the effects of underexpression as well as overexpression. For underexpression there are two principle methods which are commonly referred to in the art as “antisense downregulation” and “sense downregulation” (sense downregulation is also referred to as “cosuppression”). Generically these processes are referred to as “gene silencing”. Both of these methods lead to an inhibition of expression of the target gene.

[0216] Obtaining sufficient levels of transgene expression in the appropriate plant tissues is an important aspect in the production of genetically engineered crops. Expression of heterologous DNA sequences in a plant host is dependent upon the presence of an operably linked promoter that is functional within the plant host. Choice of the promoter sequence will determine when and where within the organism the heterologous DNA sequence is expressed.

[0217] It is specifically contemplated by the inventors that one could mutagenize a promoter to potentially improve the utility of the elements for the expression of transgenes in plants. The mutagenesis of these elements can be carried out at random and the mutagenized promoter sequences screened for activity in a trial-by-error procedure.

[0218] Alternatively, particular sequences which provide the promoter with desirable expression characteristics, or the promoter with expression enhancement activity, could be identified and these or similar sequences introduced into the sequences via mutation. It is further contemplated that one could mutagenize these sequences in order to enhance their expression of transgenes in a particular species.

[0219] The means for mutagenizing a DNA segment encoding a promoter sequence of the current invention are well-known to those of skill in the art. As indicated, modifications to promoter or other regulatory element may be made by random, or site-specific mutagenesis procedures. The promoter and other regulatory element may be modified by altering their structure through the addition or deletion of one or more nucleotides from the sequence which encodes the corresponding unmodified sequences.

[0220] Mutagenesis may be performed in accordance with any of the techniques known in the art, such as, and not limited to, synthesizing an oligonucleotide having one or more mutations within the sequence of a particular regulatory region. In particular, site-specific mutagenesis is a technique useful in the preparation of promoter mutants, through specific mutagenesis of the underlying DNA. The technique further provides a ready ability to prepare and test sequence variants, for example, incorporating one or more of the foregoing considerations, by introducing one or more nucleotide sequence changes into the DNA. Site-specific mutagenesis allows the production of mutants through the use of specific oligonucleotide sequences which encode the DNA sequence of the desired mutation, as well as a sufficient number of adjacent nucleotides, to provide a primer sequence of sufficient size and sequence complexity to form a stable duplex on both sides of the deletion junction being traversed. Typically, a primer of about 17 to about 75 nucleotides or more in length is preferred, with about 10 to about 25 or more residues on both sides of the junction of the sequence being altered.

[0221] In general, the technique of site-specific mutagenesis is well known in the art, as exemplified by various publications. As will be appreciated, the technique typically employs a phage vector which exists in both a single stranded and double stranded form. Typical vectors useful in site-directed mutagenesis include vectors such as the M13 phage. These phage are readily commercially available and their use is generally well known to those skilled in the art.

[0222] Double stranded plasmids also are routinely employed in site directed mutagenesis which eliminates the step of transferring the gene of interest from a plasmid to a phage.

[0223] In general, site-directed mutagenesis in accordance herewith is performed by first obtaining a single-stranded vector or melting apart of two strands of a double stranded vector which includes within its sequence a DNA sequence which encodes the promoter. An oligonucleotide primer bearing the desired mutated sequence is prepared, generally synthetically. This primer is then annealed with the single-stranded vector, and subjected to DNA polymerizing enzymes such as E. coli polymerase I Klenow fragment, in order to complete the synthesis of the mutation-bearing strand. Thus, a heteroduplex is formed wherein one strand encodes the original non-mutated sequence and the second strand bears the desired mutation.

[0224] This heteroduplex vector is then used to transform or transfect appropriate cells, such as E. coli cells, and cells are selected which include recombinant vectors bearing the mutated sequence arrangement. Vector DNA can then be isolated from these cells and used for plant transformation. A genetic selection scheme was devised by Kunkel et al. (1987) to enrich for clones incorporating mutagenic oligonucleotides. Alternatively, the use of PCR with commercially available thermostable enzymes such as Taq polymerase may be used to incorporate a mutagenic oligonucleotide primer into an amplified DNA fragment that can then be cloned into an appropriate cloning or expression vector. The PCR-mediated mutagenesis procedures of Tomic et al. (1990) and Upender et al. (1995) provide two examples of such protocols. A PCR employing a thermostable ligase in addition to a thermostable polymerase also may be used to incorporate a phosphorylated mutagenic oligonucleotide into an amplified DNA fragment that may then be cloned into an appropriate cloning or expression vector. The mutagenesis procedure described by Michael (1994) provides an example of one such protocol.

[0225] The preparation of sequence variants of the selected promoter-encoding DNA segments using site-directed mutagenesis is provided as a means of producing potentially useful species and is not meant to be limiting as there are other ways in which sequence variants of DNA sequences may be obtained. For example, recombinant vectors encoding the desired promoter sequence may be treated with mutagenic agents, such as hydroxylamine, to obtain sequence variants.

[0226] As used herein; the term “oligonucleotide directed mutagenesis procedure” refers to template-dependent processes and vector-mediated propagation which result in an increase in the concentration of a specific nucleic acid molecule relative to its initial concentration, or in an increase in the concentration of a detectable signal, such as amplification. As used herein, the term “oligonucleotide directed mutagenesis procedure” also is intended to refer to a process that involves the template-dependent extension of a primer molecule. The term template-dependent process refers to nucleic acid synthesis of an RNA or a DNA molecule wherein the sequence of the newly synthesized strand of nucleic acid is dictated by the well-known rules of complementary base pairing (see, for example, Watson and Rarnstad, 1987). Typically, vector mediated methodologies involve the introduction of the nucleic acid fragment into a DNA or RNA vector, the clonal amplification of the vector, and the recovery of the amplified nucleic acid fragment. Examples of such methodologies are provided by U.S. Pat. No. 4,237,224. A number of template dependent processes are available to amplify the target sequences of interest present in a sample, such methods being well known in the art and specifically disclosed herein below.

[0227] Where a clone comprising a promoter has been isolated in accordance with the instant invention, one may wish to delimit the essential promoter regions within the clone. One efficient, targeted means for preparing mutagenizing promoters relies upon the identification of putative regulatory elements within the promoter sequence. This can be initiated by comparison with promoter sequences known to be expressed in similar tissue-specific or developmentally unique manner. Sequences which are shared among promoters with similar expression patterns are likely candidates for the binding of transcription factors and are thus likely elements which confer expression patterns. Confirmation of these putative regulatory elements can be achieved by deletion analysis of each putative regulatory region followed by functional analysis of each deletion construct by assay of a reporter gene which is functionally attached to each construct. As such, once a starting promoter sequence is provided, any of a number of different deletion mutants of the starting promoter could be readily prepared.

[0228] As indicated above, deletion mutants, deletion mutants of the promoter of the invention also could be randomly prepared and then assayed. With this strategy, a series of constructs are prepared, each containing a different portion of the clone (a subclone), and these constructs are then screened for activity. A suitable means for screening for activity is to attach a deleted promoter or intron construct which contains a deleted segment to a selectable or screenable marker, and to isolate only those cells expressing the marker gene. In this way, a number of different, deleted promoter constructs are identified which still retain the desired, or even enhanced, activity. The smallest segment which is required for activity is thereby identified through comparison of the selected constructs. This segment may then be used for the construction of vectors for the expression of exogenous genes.

[0229] Furthermore, it is contemplated that promoters combining elements from more than one promoter may be useful. For example, U.S. Pat. No. 5,491,288 discloses combining a Cauliflower Mosaic Virus promoter with a histone promoter. Thus, the elements from the promoters disclosed herein may be combined with elements from other promoters.

[0230] Promoters which are useful for plant transgene expression include those that are inducible, viral, synthetic, constitutive (Odell et al., 1985), temporally regulated, spatially regulated, tissue-specific, and spatio-temporally regulated.

[0231] Where expression in specific tissues or organs is desired, tissue-specific promoters may be used. In contrast, where gene expression in response to a stimulus is desired, inducible promoters are the regulatory elements of choice. Where continuous expression is desired throughout the cells of a plant, constitutive promoters are utilized. Additional regulatory sequences upstream and/or downstream from the core promoter sequence may be included in expression constructs of transformation vectors to bring about varying levels of expression of heterologous nucleotide sequences in a transgenic plant.

[0232] A variety of 5N and 3N transcriptional regulatory sequences are available for use in the present invention. Transcriptional terminators are responsible for the termination of transcription and correct mRNA polyadenylation. The 3N nontranslated regulatory DNA sequence preferably includes from about 50 to about 1,000, more preferably about 100 to about 1,000, nucleotide base pairs and contains plant transcriptional and translational termination sequences. Appropriate transcriptional terminators and those which are known to function in plants include the CaMV 35S terminator, the tml terminator, the nopaline synthase terminator, the pea rbcS E9 terminator, the terminator for the T7 transcript from the octopine synthase gene of Agrobacterium tumefaciens, and the 3N end of the protease inhibitor I or II genes from potato or tomato, although other 3N elements known to those of skill in the art can also be employed. Alternatively, one also could use a gamma coixin, oleosin 3 or other terminator from the genus Coix.

[0233] Preferred 3N elements include those from the nopaline synthase gene of Agrobacterium tumefaciens (Bevan et al., 1983), the terminator for the T7 transcript from the octopine synthase gene of Agrobacterium tumefaciens, and the 3′ end of the protease inhibitor I or II genes from potato or tomato.

[0234] As the DNA sequence between the transcription initiation site and the start of the coding sequence, i.e., the untranslated leader sequence, can influence gene expression, one may also wish to employ a particular leader sequence. Preferred leader sequences are contemplated to include those which include sequences predicted to direct optimum expression of the attached gene, i.e., to include a preferred consensus leader sequence which may increase or maintain mRNA stability and prevent inappropriate initiation of translation. The choice of such sequences will be known to those of skill in the art in light of the present disclosure. Sequences that are derived from genes that are highly expressed in plants will be most preferred.

[0235] Other sequences that have been found to enhance gene expression in transgenic plants include intron sequences (e.g., from Adh1, bronze1, actin1, actin 2 (WO 00/760067), or the sucrose synthase intron) and viral leader sequences (e.g., from TMV, MCMV and AMV). For example, a number of non-translated leader sequences derived from viruses are known to enhance expression. Specifically, leader sequences from Tobacco Mosaic Virus (TMV), Maize Chlorotic Mottle Virus (MCMV), and Alfalfa Mosaic Virus (AMV) have been shown to be effective in enhancing expression (e.g., Gallie et al., 1987; Skuzeski et al., 1990). Other leaders known in the art include but are not limited to: Picornavirus leaders, for example, EMCV leader (Encephalomyocarditis 5 noncoding region) (Elroy-Stein et al., 1989); Potyvirus leaders, for example, TEV leader (Tobacco Etch Virus); MDMV leader (Maize Dwarf Mosaic Virus); Human immunoglobulin heavy-chain binding protein (BiP) leader, (Macejak et al., 1991); Untranslated leader from the coat protein mRNA of alfalfa mosaic virus (AMV RNA 4), (Jobling et al., 1987; Tobacco mosaic virus leader (TMV), (Gallie et al., 1989; and Maize Chlorotic Mottle Virus leader (MCMV) (Lommel et al., 1991. See also, Della-Cioppa et al., 1987.

[0236] Regulatory elements such as Adh intron 1 (Callis et al., 1987), sucrose synthase intron (Vasil et al., 1989) or TMV omega element (Gallie, et al., 1989), may further be included where desired.

[0237] Examples of enhancers include elements from the CaMV 35S promoter, octopine synthase genes (Ellis el al., 1987), the rice actin I gene, the maize alcohol dehydrogenase gene (Callis et al., 1987), the maize shrunken I gene (Vasil et al., 1989), TMV Omega element (Gallie et al., 1989) and promoters from non-plant eukaryotes (e.g. yeast; Ma et al., 1988).

[0238] Vectors for use in accordance with the present invention may be constructed to include the ocs enhancer element. This element was first identified as a 16 bp palindromic enhancer from the octopine synthase (ocs) gene of ultilane (Ellis et al., 1987), and is present in at least 10 other promoters (Bouchez et al., 1989). The use of an enhancer element, such as the ocs elements and particularly multiple copies of the element, will act to increase the level of transcription from adjacent promoters when applied in the context of monocot transformation.

[0239] Ultimately, the most desirable DNA segments for introduction into, for example, a monocot genome, may be homologous genes or gene families which encode a desired trait (e.g., increased yield per acre) and which are introduced under the control of novel promoters or enhancers, etc., or perhaps even homologous or tissue specific (e.g., root-, collar/sheath-, whorl-, stalk-, earshank-, kernel- or leaf-specific) promoters or control elements. Indeed, it is envisioned that a particular use of the present invention will be the expression of a gene in a constitutive or a seed-specific manner.

[0240] Vectors for use in tissue-specific targeting of genes in transgenic plants will typically include tissue-specific promoters and may also include other tissue-specific control elements such as enhancer sequences. Promoters which direct specific or enhanced expression in certain plant tissues will be known to those of skill in the art in light of the present disclosure. These include, for example, the rbcS promoter, specific for green tissue; the ocs, nos and mas promoters which have higher activity in roots or wounded leaf tissue; a truncated (−90 to +8) 35S promoter which directs enhanced expression in roots, an alpha-tubulin gene that directs expression in roots and promoters derived from zein storage protein genes which direct expression in endosperm. It is particularly contemplated that one may advantageously use the 16 bp ocs enhancer element from the octopine synthase (ocs) gene (Ellis et al., 1987; Bouchez et al., 1989), especially when present in multiple copies, to achieve enhanced expression in, roots.

[0241] Tissue specific expression may be functionally accomplished by introducing a constitutively expressed gene (all tissues) in combination with an antisense gene that is expressed only in those tissues where the gene product is not desired. For example, a gene coding for the crystal toxin protein from B. thuringiensis (Bt) may be introduced such that it is expressed in all tissues using the 35S promoter from Cauliflower Mosaic Virus. Expression of an antisense transcript of the Bt gene in a maize kernel, using for example a zein promoter, would prevent accumulation of the Bt protein in seed. Hence the protein encoded by the introduced gene would be present in all tissues except the kernel.

[0242] Expression of some genes in transgenic plants will be desired only under specified conditions. For example, it is proposed that expression of certain genes that confer resistance to environmental stress factors such as drought will be desired only under actual stress conditions. It is contemplated that expression of such genes throughout a plants development may have detrimental effects. It is known that a large number of genes exist that respond to the environment. For example, expression of some genes such as rbcS, encoding the small subunit of ribulose bisphosphate carboxylase, is regulated by light as mediated through phytochrome. Other genes are induced by secondary stimuli. For example, synthesis of abscisic acid (ABA) is induced by certain environmental factors, including but not limited to water stress. A number of genes have been shown to be induced by ABA (Skriver and Mundy, 1990). It is also anticipated that expression of genes conferring resistance to insect predation would be desired only under conditions of actual insect infestation. Therefore, for some desired traits inducible expression of genes in transgenic plants will be desired.

[0243] Expression of a gene in a transgenic plant will be desired only in a certain time period during the development of the plant. Developmental timing is frequently correlated with tissue specific gene expression. For example, expression of zein storage proteins is initiated in the endosperm about 15 days after pollination.

[0244] Additionally, vectors may be constructed and employed in the intracellular targeting of a specific gene product within the cells of a transgenic plant or in directing a protein to the extracellular environment. This will generally be achieved by joining a DNA sequence encoding a transit or signal peptide sequence to the coding sequence of a particular gene. The resultant transit, or signal, peptide will transport the protein to a particular intracellular, or extracellular destination, respectively, and will then be post-translationally removed. Transit or signal peptides act by facilitating the transport of proteins through intracellular membranes, e.g., vacuole, vesicle, plastid and mitochondrial membranes, whereas signal peptides direct proteins through the extracellular membrane.

[0245] A particular example of such a use concerns the direction of a herbicide resistance gene, such as the EPSPS gene, to a particular organelle such as the chloroplast rather than to the cytoplasm. This is exemplified by the use of the rbcs transit peptide which confers plastid-specific targeting of proteins. In addition, it is proposed that it may be desirable to target certain genes responsible for male sterility to the mitochondria, or to target certain genes for resistance to phytopathogenic organisms to the extracellular spaces, or to target proteins to the vacuole.

[0246] By facilitating the transport of the protein into compartments inside and outside the cell, these sequences may increase the accumulation of gene product protecting them from proteolytic degradation. These sequences also allow for additional mRNA sequences from highly expressed genes to be attached to the coding sequence of the genes. Since mRNA being translated by ribosomes is more stable than naked mRNA, the presence of translatable mRNA in front of the gene may increase the overall stability of the mRNA transcript from the gene and thereby increase synthesis of the gene product. Since transit and signal sequences are usually post-translationally removed from the initial translation product, the use of these sequences allows for the addition of extra translated sequences that may not appear on the final polypeptide. Targeting of certain proteins may be desirable in order to enhance the stability of the protein (U.S. Pat. No. 5,545,818).

[0247] It may be useful to target DNA itself within a cell. For example, it may be useful to target introduced DNA to the nucleus as this may increase the frequency of transformation. Within the nucleus itself it would be useful to target a gene in order to achieve site specific integration. For example, it would be useful to have an gene introduced through transformation replace an existing gene in the cell.

[0248] Other elements include those that can be regulated by endogenous or exogenous agents, e.g., by zinc finger proteins, including naturally occurring zinc finger proteins or chimeric zinc finger proteins (see, e.g., U.S. Pat. No. 5,789,538, WO 99/48909; WO 99/45132; WO 98/53060; WO 98/53057; WO 98/53058; WO 00/23464; WO 95/19431; and WO 98/54311) or myb-like transcription factors. For example, a chimeric zinc finger protein may include amino acid sequences which bind to a specific DNA sequence (the zinc finger) and amino acid sequences that activate (e.g., GAL 4 sequences) or repress the transcription of the sequences linked to the specific DNA sequence.

[0249] It is one of the objects of the present invention to provide recombinant DNA molecules comprising a nucleotide sequence according to the invention operably linked to a nucleotide segment of interest.

[0250] A nucleotide segment of interest is reflective of the commercial markets and interests of those involved in the development of the crop. Crops and markets of interest changes, and as developing nations open up world markets, new crops and technologies will also emerge. In addition, as the understanding of agronomic traits and characteristics such as yield and heterosis increase, the choice of genes for transformation will change accordingly. General categories of nucleotides of interest include, for example, genes involved in information, such as zinc fingers, those involved in communication, such as kinases, and those involved in housekeeping, such as heat shock proteins. More specific categories of transgenes, for example, include genes encoding important traits for agronomics, insect resistance, disease resistance, herbicide resistance, sterility, grain characteristics, and commercial products. Genes of interest include, generally, those involved in starch, oil, carbohydrate, or nutrient metabolism, as well as those affecting kernel size, sucrose loading, zinc finger proteins, see, e.g., U.S. Pat. No. 5,789,538, WO 99/48909; WO 99/45132; WO 98/53060; WO 98/53057; WO 98/53058; WO 00/23464; WO 95/19431; and WO 98/54311, and the like.

[0251] One skilled in the art recognizes that the expression level and regulation of a transgene in a plant can vary significantly from line to line. Thus, one has to test several lines to find one with the desired expression level and regulation. Once a line is identified with the desired regulation specificity of a chimeric Cre transgene, it can be crossed with lines carrying different inactive replicons or inactive transgene for activation.

[0252] Other sequences which may be linked to the gene of interest which encodes a polypeptide are those which can target to a specific organelle, e.g., to the mitochondria, nucleus, or plastid, within the plant cell. Targeting can be achieved by providing the polypeptide with an appropriate targeting peptide sequence, such as a secretory signal peptide (for secretion or cell wall or membrane targeting, a plastid transit peptide, a chloroplast transit peptide, e.g., the chlorophyll a/b binding protein, a mitochondrial target peptide, a vacuole targeting peptide, or a nuclear targeting peptide, and the like. For example, the small subunit of ribulose bisphosphate carboxylase transit peptide, the EPSPS transit peptide or the dihydrodipicolinic acid synthase transit peptide may be used. For examples of plastid organelle targeting sequences (see WO 00/12732). Plastids are a class of plant organelles derived from proplastids and include chloroplasts, leucoplasts, aravloplasts, and chromoplasts. The plastids are major sites of biosynthesis in plants. In addition to photosynthesis in the chloroplast, plastids are also sites of lipid biosynthesis, nitrate reduction to ammonium, and starch storage. And while plastids contain their own circular, genome, most of the proteins localized to the plastids are encoded by the nuclear genome and are imported into the organelle from the cytoplasm.

[0253] Transgenes used with the present invention will often be genes that direct the expression of a particular protein or polypeptide product, but they may also be non-expressible DNA segments, e.g., transposons such as Ds that do no direct their own transposition. As used herein, an “expressible gene” is any gene that is capable of being transcribed into RNA (e.g., mRNA, antisense RNA, etc.) or translated into a protein, expressed as a trait of interest, or the like, etc., and is not limited to selectable, screenable or non-selectable marker genes. The invention also contemplates that, where both an expressible gene that is not necessarily a marker gene is employed in combination with a marker gene, one may employ the separate genes on either the same or different DNA segments for transformation. In the latter case, the different vectors are delivered concurrently to recipient cells to maximize cotransformation.

[0254] The choice of the particular DNA segments to be delivered to the recipient cells will often depend on the purpose of the transformation. One of the major purposes of transformation of crop plants is to add some commercially desirable, agronomically important traits to the plant. Such traits include, but are not limited to, herbicide resistance or tolerance; insect resistance or tolerance; disease resistance or tolerance (viral, bacterial, fungal, nematode); stress tolerance and/or resistance, as exemplified by resistance or tolerance to drought, heat, chilling, freezing, excessive moisture, salt stress; oxidative stress; increased yields; food content and makeup; physical appearance; male sterility; drydown; standability; prolificacy; starch properties; oil quantity and quality; and the like. One may desire to incorporate one or more genes conferring any such desirable trait or traits, such as, for example, a gene or genes encoding pathogen resistance.

[0255] In certain embodiments, the present invention contemplates the transformation of a recipient cell with more than one advantageous transgene. Two or more transgenes can be supplied in a single transformation event using either distinct transgene-encoding vectors, or using a single vector incorporating two or more gene coding sequences. For example, plasmids bearing the bar and aroA expression units in either convergent, divergent, or colinear orientation, are considered to be particularly useful. Further preferred combinations are those of an insect resistance gene, such as a Bt gene, along with a protease inhibitor gene such as pinII, or the use of bar in combination with either of the above genes. Of course, any two or more transgenes of any description, such as those conferring herbicide, insect, disease (viral, bacterial, fungal, nematode) or drought resistance, male sterility, drydown, standability, prolificacy, starch properties, oil quantity and quality, or those increasing yield or nutritional quality may be employed as desired.

[0256] A. Exemplary Transgenes

[0257] 1. Herbicide Resistance

[0258] The genes encoding phosphinothricin acetyltransferase (bar and pat), glyphosate tolerant EPSP synthase genes, the glyphosate degradative enzyme gene gox encoding glyphosate oxidoreductase, deh (encoding a dehalogenase enzyme that inactivates dalapon), herbicide resistant (e.g., sulfonylurea and imidazolinone) acetolactate synthase, and bxn genes (encoding a nitrilase enzyme that degrades bromoxynil) are good examples of herbicide resistant genes for use in transformation. The bar and pat genes code for an enzyme, phosphinothricin acetyltransferase (PAT), which inactivates the herbicide phosphinothricin and prevents this compound from inhibiting glutamine synthetase enzymes. The enzyme 5-enolpyruvylshikimate 3-phosphate synthase (EPSP Synthase), is normally inhibited by the herbicide N-(phosphonomethyl)glycine (glyphosate). However, genes are known that encode glyphosate-resistant EPSP Synthase enzymes.

[0259] These genes are particularly contemplated for use in monocot transformation. The deh gene encodes the enzyme dalapon dehalogenase and confers resistance to the herbicide dalapon. The bxn gene codes for a specific nitrilase enzyme that converts bromoxynil to a non-herbicidal degradation product.

[0260] 2. Insect Resistance

[0261] An important aspect of the present invention concerns the introduction of insect resistance-conferring genes into plants. Potential insect resistance genes which can be introduced include Bacillus thuringiensis crystal toxin genes or Bt genes (Watrud et al., 1985). Bt genes may provide resistance to lepidopteran or coleopteran pests such as European Corn Borer (ECB) and corn rootworm (CRW). Preferred Bt toxin genes for use in such embodiments include the CryIA(b) and CryIA(c) genes. Endotoxin genes from other species of B. thuringiensis which affect insect growth or development may also be employed in this regard.

[0262] The poor expression of Bt toxin genes in plants is a well-documented phenomenon, and the use of different promoters, fusion proteins, and leader sequences has not led to ;significant increases in Bt protein expression (Vaeck et al., 1989; Barton et al., 1987). It is therefore contemplated that the most advantageous Bt genes for use in the transformation protocols disclosed herein will be those in which the coding sequence has been modified to effect increased expression in plants, and more particularly, those in which maize preferred codons have been used. Examples of such modified Bt toxin genes include the variant Bt CryIA(b) gene termed Iab6 (Perlak et al., 1991) and the synthetic CryIA(c) genes termed 1800a and 1800b.

[0263] Protease inhibitors may also provide insect resistance (Johnson et al., 1989), and will thus have utility in plant transformation. The use of a protease inhibitor II gene, pinII, from tomato or potato is envisioned to be particularly useful. Even more advantageous is the use of a pinII gene in combination with a Bt toxin gene, the combined effect of which has been discovered by the present inventors to produce synergistic insecticidal activity. Other genes which encode inhibitors of the insects' digestive system, or those that encode enzymes or co-factors that facilitate the production of inhibitors, may also be useful. This group may be exemplified by oryzacystatin and amylase inhibitors, such as those from wheat and barley.

[0264] Also, genes encoding lectins may confer additional or alternative insecticide properties. Lectins (originally termed phytohemagglutinins) are multivalent carbohydrate-binding proteins which have the ability to agglutinate red blood cells from a range of species. Lectins have been identified recently as insecticidal agents with activity against weevils, ECB and rootworm (Murdock et al., 1990; Czapla and Lang, 1990). Lectin genes contemplated to be useful include, for example, barley and wheat germ agglutinin (WGA) and rice lectins (Gatehouse et al., 1984), with WGA being preferred.

[0265] Genes controlling the production of large or small polypeptides active against insects when introduced into the insect pests, such as, e.g., lytic peptides, peptide hormones and toxins and venoms, form another aspect of the invention. For example, it is contemplated, that the expression of juvenile hormone esterase, directed towards specific insect pests, may also result in insecticidal activity, or perhaps cause cessation of metamorphosis (Hammock et al., 1990).

[0266] Transgenic plants expressing genes which encode enzymes that affect the integrity of the insect cuticle form yet another aspect of the invention. Such genes include those encoding, e.g., chitinase, proteases, lipases and also genes for the production of nikkomycin, a compound that inhibits chitin synthesis, the introduction of any of which is contemplated to produce insect resistant maize plants. Genes that code for activities that affect insect molting, such those affecting the production of ecdysteroid UDP-glucosyl transferase, also fall within the scope of the useful transgenes of the present invention.

[0267] Genes that code for enzymes that facilitate the production of compounds that reduce the nutritional quality of the host plant to insect pests are also encompassed by the present invention. It may be possible, for instance, to confer insecticidal activity on a plant by altering its sterol composition. Sterols are obtained by insects from their diet and are used for hormone synthesis and membrane stability. Therefore alterations in plant sterol composition by expression of novel genes, e.g., those that directly promote the production of undesirable sterols or those that convert desirable sterols into undesirable forms, could have a negative effect on insect growth and/or development and hence endow the plant with insecticidal activity. Lipoxygenases are naturally occurring plant enzymes that have been shown to exhibit anti-nutritional effects on insects and to reduce the nutritional quality of their diet. Therefore, further embodiments of the invention concern transgenic plants with enhanced lipoxygenase activity which may be resistant to insect feeding.

[0268] The present invention also provides methods and compositions by which to achieve qualitative or quantitative changes in plant secondary metabolites. One example concerns transforming plants to produce DIMBOA which, it is contemplated, will confer resistance to European corn borer, rootworm and several other maize insect pests. Candidate genes that are particularly considered for use in this regard include those genes at the bx locus known to be involved in the synthetic DIMBOA pathway (Dunn et al., 1981). The introduction of genes that can regulate the production of maysin, and genes involved in the production of dhurrin in sorghum, is also contemplated to be of use in facilitating resistance to earworm and rootworm, respectively.

[0269]

Tripsacum dactyloides
is a species of grass that is resistant to certain insects, including corn root worm. It is anticipated that genes encoding proteins that are toxic to insects or are involved in the biosynthesis of compounds toxic to insects will be isolated from Tripsacum and that these novel genes will be useful in conferring resistance to insects. It is known that the basis of insect resistance in Tripsacum is genetic, because said resistance has been transferred to Zea mays via sexual crosses (Branson and Guss, 1972).

[0270] Further genes encoding proteins characterized as having potential insecticidal activity may also be used as transgenes in accordance herewith. Such genes include, for example, the cowpea trypsin inhibitor (CpTI; Hilder et al., 1987) which may be used as a rootworm deterrent; genes encoding avermectin (Campbell, 1989; Ikeda et al., 1987) which may prove particularly useful as a corn rootworm deterrent; ribosome inactivating protein genes; and even genes that regulate plant structures. Transgenic maize including anti-insect antibody genes and genes that code for enzymes that can covert a non-toxic insecticide (pro-insecticide) applied to the outside of the plant into an insecticide inside the plant are also contemplated.

[0271] 3. Environment or Stress Resistance

[0272] Improvement of a plant's ability to tolerate various environmental stresses such as, but not limited to, drought, excess moisture, chilling, freezing, high temperature, salt, and oxidative stress, can also be effected through expression of heterologous, or overexpression of homologous genes. Benefits may be realized in terms of increased resistance to freezing temperatures through the introduction of an “antifreeze” protein such as that of the Winter Flounder (Cutler et al., 1989) or synthetic gene derivatives thereof. Improved chilling tolerance may also be conferred through increased expression of glycerol-3-phosphate acetyltransferase in chloroplasts (Murata et al., 1992; Wolter et al., 1992). Resistance to oxidative stress (often exacerbated by conditions such as chilling temperatures in combination with high light intensities) can be conferred by expression of superoxide dismutase (Gupta et al., 1993), and may be improved by glutathione reductase (Bowler et al., 1992). Such strategies may allow for tolerance to freezing in newly emerged fields as well as extending later maturity higher yielding varieties to earlier relative maturity zones.

[0273] Expression of novel genes that favorably effect plant water content, total water potential, osmotic potential, and turgor can enhance the ability of the plant to tolerate drought. As used herein, the terms “drought resistance” and “drought tolerance” are used to refer to a plants increased resistance or tolerance to stress induced by a reduction in water availability, as compared to normal circumstances, and the ability of the plant to function and survive in lower-water environments, and perform in a relatively superior manner. In this aspect of the invention it is proposed, for example, that the expression of a gene encoding the biosynthesis of osmotically-active solutes can impart protection against drought. Within this class of genes are DNAs encoding mannitol dehydrogenase (Lee and Saier, 1982) and trehalose-6-phosphate synthase (Kaasen et al., 1992). Through the subsequent action of native phosphatases in the cell or by the introduction and coexpression of a specific phosphatase, these introduced genes will result in the accumulation of either mannitol or trehalose, respectively, both of which have been well documented as protective compounds able to mitigate the effects of stress. Mannitol accumulation in transgenic tobacco has been verified and preliminary results indicate that plants expressing high levels of this metabolite are able to tolerate an applied osmotic stress (Tarczynski et al., 1992).

[0274] Similarly, the efficacy of other metabolites in protecting either enzyme function (e.g. alanopine or propionic acid) or membrane integrity (e.g., alanopine) has been documented (Loomis et al., 1989), and therefore expression of gene encoding the biosynthesis of these compounds can confer drought resistance in a manner similar to or complimentary to mannitol. Other examples of naturally occurring metabolites that are osmotically active and/or provide some direct protective effect during drought and/or desiccation include sugars and sugar derivatives such as fructose, erythritol (Coxson et al., 1992), sorbitol, dulcitol (Karsten et al., 1992), glucosylglycerol (Reed et al., 1984; Erdmann et al., 1992), sucrose, stachyose (Koster and Leopold, 1988; Blackman et al., 1992), ononitol and pinitol (Vernon and Bohnert, 1992), and raffinose (Bernal-Lugo and Leopold, 1992). Other osmotically active solutes which are not sugars include, but are not limited to, proline and glycine-betaine (Wyn-Jones and Storey, 1981). Continued canopy growth and increased reproductive fitness during times of stress can be augmented by introduction and expression of genes such as those controlling the osmotically active compounds discussed above and other such compounds, as represented in one exemplary embodiment by the enzyme myoinositol 0-methyltransferase.

[0275] It is contemplated that the expression of specific proteins may also increase drought tolerance. Three classes of Late Embryogenic Proteins have been assigned based on structural similarities (see Dure et al., 1989). All three classes of these proteins have been demonstrated in maturing (i.e., desiccating) seeds. Within these 3 types of proteins, the Type-II (dehydrin-type) have generally been implicated in drought and/or desiccation tolerance in vegetative plant parts (i.e. Mundy and Chua, 1988; Piatkowski et al., 1990; Yamaguchi-Shinozaki et al., 1992). Recently, expression of a Type-III LEA (HVA-1) in tobacco was found to influence plant height, maturity and drought tolerance (Fitzpatrick, 1993). Expression of structural genes from all three groups may therefore confer drought tolerance. Other types of proteins induced during water stress include thiol proteases, aldolases and transmembrane transporters (Guerrero et al., 1990), which may confer various protective and/or repair-type functions during drought stress. The expression of a gene that effects lipid biosynthesis and hence membrane composition can also be useful in conferring drought resistance on the plant.

[0276] Many genes that improve drought resistance have complementary modes of action. Thus, combinations of these genes might have additive and/or synergistic effects in improving drought resistance in maize. Many of these genes also improve freezing tolerance (or resistance); the physical stresses incurred during freezing and drought are similar in nature and may be mitigated in similar fashion. Benefit may be conferred via constitutive expression of these genes, but the preferred means of expressing these novel genes may be through the use of a turgor-induced promoter (such as the promoters for the turgor-induced genes described in Guerrero et al. 1990 and Shagan et al., 1993). Spatial and temporal expression patterns of these genes may enable maize to better withstand stress.

[0277] Expression of genes that are involved with specific morphological traits that allow for increased water extractions from drying soil would be of benefit. For example, introduction and expression of genes that alter root characteristics may enhance water uptake. Expression of genes that enhance reproductive fitness during times of stress would be of significant value. For example, expression of DNAs that improve the synchrony of pollen shed and receptiveness of the female flower parts, i.e., silks, would be of benefit. In addition, expression of genes that minimize kernel abortion during times of stress would increase the amount of grain to be harvested and hence be of value. Regulation of cytokinin levels in monocots, such as maize, by introduction and expression of an isopentenyl transferase gene with appropriate regulatory sequences can improve monocot stress resistance and yield (Gan et al., Science, 270:1986 (1995)).

[0278] Given the overall role of water in determining yield, it is contemplated that enabling plants to utilize water more efficiently, through the introduction and expression of novel genes, will improve overall performance even when soil water availability is not limiting. By introducing genes that improve the ability of plants to maximize water usage across a full range of stresses relating to water availability, yield stability or consistency of yield performance may be realized.

[0279] 4. Disease Resistance

[0280] It is proposed that increased resistance to diseases may be realized through introduction of genes into plants period. It is possible to produce resistance to diseases caused, by viruses, bacteria, fungi, root pathogens, insects and nematodes. It is also contemplated that control of mycotoxin producing organisms may be realized through expression of introduced genes.

[0281] Resistance to viruses may be produced through expression of novel genes. For example, it has been demonstrated that expression of a viral coat protein in a transgenic plant can impart resistance to infection of the plant by that virus and perhaps other closely related viruses (Cuozzo et al., 1988, Hemenway et al., 1988, Abel et al., 1986). It is contemplated that expression of antisense genes targeted at essential viral functions may impart resistance to said virus. For example, an antisense gene targeted at the gene responsible for replication of viral nucleic acid may inhibit said replication and lead to resistance to the virus. It is believed that interference with other viral functions through the use of antisense genes may also increase resistance to viruses. Further it is proposed that it may be possible to achieve resistance to viruses through other approaches, including, but not limited to the use of satellite viruses.

[0282] It is proposed that increased resistance to diseases caused by bacteria and fungi may be realized through introduction of novel genes. It is contemplated that genes encoding so-called “peptide antibiotics,” pathogenesis related (PR) proteins, toxin resistance, and proteins affecting host-pathogen interactions such as morphological characteristics will be useful. Peptide antibiotics are polypeptide sequences which are inhibitory to growth of bacteria and other microorganisms. For example, the classes of peptides referred to as cecropins and magainins inhibit growth of many species of bacteria and fungi. It is proposed that expression of PR proteins in plants may be useful in conferring resistance to bacterial disease. These genes are induced following pathogen attack on a host plant and have been divided into at least five classes of proteins (Bol et al., 1990). Included amongst the PR proteins are beta-1,3-glucanases, chitinases, and osmotin and other proteins that are believed to function in plant resistance to disease organisms. Other genes have been identified that have antifungal properties, e.g., UDA (stinging nettle lectin) and hevein (Broakgert et al., 1989; Barkai-Golan et al., 1978). It is known that certain plant diseases are caused by the production of phytotoxins. Resistance to these diseases could be achieved through expression of a novel gene that encodes an enzyme capable of degrading or otherwise inactivating the phytotoxin. Expression novel genes that alter the interactions between the host plant and pathogen may be useful in reducing the ability the disease organism to invade the tissues of the host plant, e.g., an increase in the waxiness of the leaf cuticle or other morphological characteristics.

[0283] Plant parasitic nematodes are a cause of disease in many plants. It is proposed that it would be possible to make the plant resistant to these organisms through the expression of novel genes. It is anticipated that control of nematode infestations would be accomplished by altering the ability of the nematode to recognize or attach to a host plant and/or enabling the plant to produce nematicidal compounds, including but not limited to proteins.

[0284] 5. Mycotoxin Reduction/Elimination

[0285] Production of mycotoxins, including aflatoxin and fumonisin, by fungi associated with plants is a significant factor in rendering the grain not useful. These fungal organisms do not cause disease symptoms and/or interfere with the growth of the plant, but they produce chemicals (mycotoxins) that are toxic to animals. Inhibition of the growth of these fungi would reduce the synthesis of these toxic substances and, therefore, reduce grain losses due to mycotoxin contamination. Novel genes may be introduced into plants that would inhibit synthesis of the mycotoxin without interfering with fungal growth. Expression of a novel gene which encodes an enzyme capable of rendering the mycotoxin nontoxic would be useful in order to achieve reduced mycotoxin contamination of grain. The result of any of the above mechanisms would be a reduced presence of mycotoxins on grain.

[0286] 6. Grain Composition or Quality

[0287] Genes may be introduced into plants, particularly commercially important cereals such as maize, wheat or rice, to improve the grain for which the cereal is primarily grown. A wide range of novel transgenic plants produced in this manner may be envisioned depending on the particular end use of the grain.

[0288] For example, the largest use of maize,grain is for feed or food. Introduction of genes that alter the composition of the grain may greatly enhance the feed or food value. The primary components of maize grain are starch, protein, and oil. Each of these primary components of maize grain may be improved by altering its level or composition. Several examples may be mentioned for illustrative purposes but in no way provide an exhaustive list of possibilities.

[0289] The protein of many cereal grains is suboptimal for feed and food purposes especially when fed to pigs, poultry, and humans. The protein is deficient in several amino acids that are essential in the diet of these species, requiring the addition of supplements to the grain. Limiting essential amino acids may include lysine, methionine, tryptophan, threonine, valine, arginine, and histidine. Some amino acids become limiting only after the grain is supplemented with other inputs for feed formulations. For example, when the grain is supplemented with soybean meal to meet lysine requirements, methionine becomes limiting. The levels of these essential amino acids in seeds and grain may be elevated by mechanisms which include, but are not limited to, the introduction of genes to increase the biosynthesis of the amino acids, decrease the degradation of the amino acids, increase the storage of the amino acids in proteins, or increase transport of the amino acids to the seeds or grain.

[0290] One mechanism for increasing the biosynthesis of the amino acids is to introduce genes that deregulate the amino acid biosynthetic pathways such that the plant can no longer adequately control the levels that are produced. This may be done by deregulating or bypassing steps in the amino acid biosynthetic pathway which are normally regulated by levels of the amino acid end product of the pathway. Examples include the introduction of genes that encode deregulated versions of the enzymes aspartokinase or dihydrodipicolinic acid (DHDP)-synthase for increasing lysine and threonine production, and anthranilate synthase for increasing tryptophan production. Reduction of the catabolism of the amino acids may be accomplished by introduction of DNA sequences that reduce or eliminate the expression of genes encoding enzymes that catalyse steps in the catabolic pathways such as the enzyme lysine-ketoglutarate reductase.

[0291] The protein composition of the grain may be altered to improve the balance of amino acids in a variety of ways including elevating expression of native proteins, decreasing expression of those with poor composition, changing the composition of native proteins, or introducing genes encoding entirely new proteins possessing superior composition. DNA may be introduced that decreases the expression of members of the zein family of storage proteins. This DNA may encode ribozymes or antisense sequences directed to impairing expression of zein proteins or expression of regulators of zein expression such as the opaque-2 gene product. The protein composition of the grain may be modified through the phenomenon of cosuppression, i.e., inhibition of expression of an endogenous gene through the expression of an identical structural gene or gene fragment introduced through transformation (Goring-et al., 1991). Additionally, the introduced DNA may encode enzymes which degrade seines. The decreases in zein expression that are achieved may be accompanied by increases in proteins with more desirable amino acid composition or increases in other major seed constituents such as starch. Alternatively, a chimeric gene may be introduced that comprises a coding sequence for a native protein of adequate amino acid composition such as for one of the globulin proteins or 10 kD zein of maize and a promoter or other regulatory sequence designed to elevate expression of said protein. The coding sequence of said gene may include additional or replacement codons for essential amino acids. Further, a coding sequence obtained from another species, or, a partially or completely synthetic sequence encoding a completely unique peptide sequence designed to enhance the amino acid composition of the seed may be employed.

[0292] The introduction of genes that alter the oil content of the grain may be of value. Increases in oil content may result in increases in metabolizable energy content and density of the seeds for uses in feed and food. The introduced genes may encode enzymes that remove or reduce rate-limitations or regulated steps in fatty acid or lipid biosynthesis. Such genes may include, but are not limited to, those that encode acetyl-CoA carboxylase, ACP-acyltransferase, beta-ketoacyl-ACP synthase, plus other well known fatty acid biosynthetic activities. Other possibilities are genes that encode proteins that do not possess enzymatic activity such as acyl carrier protein. Additional examples include 2-acetyltransferase, oleosin pyruvate dehydrogenase complex, acetyl CoA synthetase, ATP citrate lyase, ADP-glucose pyrophosphorylase and genes of the carnitine-CoA-acetyl-CoA shuttles. It is anticipated that expression of genes related to oil biosynthesis will be targeted to the plastid, using a plastid transit peptide sequence and preferably expressed in the seed embryo. Genes may be introduced that alter the balance of fatty acids present in the oil providing a more healthful or nutritive feedstuff. The introduced DNA may also encode sequences that block expression of enzymes involved in fatty acid biosynthesis, altering the proportions of fatty acids present in the grain such as described below.

[0293] Genes may be introduced that enhance the nutritive value of the starch component of the grain, for example by increasing the degree of branching, resulting in improved utilization of the starch in cows by delaying its metabolism.

[0294] Besides affecting the major constituents of the grain, genes may be introduced that affect a variety of other nutritive, processing, or other quality aspects of the grain as used for feed or food. For example, pigmentation of the grain may be increased or decreased. Enhancement and stability of yellow pigmentation is desirable in some animal feeds and may be achieved by introduction of genes that result in enhanced production of xanthophylls and carotenes by eliminating rate-limiting steps in their production. Such genes may encode altered forms of the enzymes phytoene synthase, phytoene desaturase, or lycopene synthase. Alternatively, unpigmented white corn is desirable for production of many food products and may be produced by the introduction of DNA which blocks or eliminates steps in pigment production pathways.

[0295] Feed or food comprising some cereal grains possesses insufficient quantities of vitamins and must be supplemented to provide adequate nutritive value. Introduction of genes that enhance vitamin biosynthesis in seeds may be envisioned including, for example, vitamins A, E, B12, choline, and the like. For example, maize grain also does not possess sufficient mineral content for optimal nutritive value. Genes that affect the accumulation or availability of compounds containing phosphorus, sulfur, calcium, manganese, zinc, and iron among others would be valuable. An example may be the introduction of a gene that reduced phytic acid production or encoded the enzyme phytase which enhances phytic acid breakdown. These genes would increase levels of available phosphate in the diet, reducing the need for supplementation with mineral phosphate.

[0296] Numerous other examples of improvement of cereals for feed and food purposes might be described. The improvements may not even necessarily involve the grain, but may, for example, improve the value of the grain for silage. Introduction of DNA to accomplish this might include sequences that alter lignin production such as those that result in the “brown midrib” phenotype associated with superior feed value for cattle.

[0297] In addition to direct improvements in feed or food value, genes may also be introduced which improve the processing of grain and improve the value of the products resulting from the processing. The primary method of processing certain grains such as maize is via wetmilling. Maize may be improved though the expression of novel genes that increase the efficiency and reduce the cost of processing such as by decreasing steeping time.

[0298] Improving the value of wetmilling products may include altering the quantity or quality of starch, oil, corn gluten meal, or the components of corn gluten feed. Elevation of starch may be achieved through the identification and elimination of rate limiting steps in starch biosynthesis or by decreasing levels of the other components of the grain resulting in proportional increases in starch. An example of the former may be the introduction of genes encoding ADP-glucose pyrophosphorylase enzymes with altered regulatory activity or which are expressed at higher level. Examples of the latter may include selective inhibitors of, for example, protein or oil biosynthesis expressed during later stages of kernel development.

[0299] The properties of starch may be beneficially altered by changing the ratio of amylose to amylopectin, the size of the starch molecules, or their branching pattern. Through these changes a broad range of properties may be modified which include, but are not limited to, changes in gelatinization temperature, heat of gelatinization, clarity of films and pastes, Theological properties, and the like. To accomplish these changes in properties, genes that encode granule-bound or soluble starch synthase activity or branching enzyme activity may be introduced alone or combination. DNA such as antisense constructs may also be used to decrease levels of endogenous activity of these enzymes. The introduced genes or constructs may possess regulatory sequences that time their expression to specific intervals in starch biosynthesis and starch granule development. Furthermore, it may be advisable to introduce and express genes that result in the in vivo derivatization, or other modification, of the glucose moieties of the starch molecule. The covalent attachment of any molecule may be envisioned, limited only by the existence of enzymes that catalyze the derivatizations and the accessibility of appropriate substrates in the starch granule. Examples of important derivations may include the addition of functional groups such as amines, carboxyls, or phosphate groups which provide sites for subsequent in vitro derivatizations or affect starch properties through the introduction of ionic charges. Examples of other modifications may include direct changes of the glucose units such as loss of hydroxyl groups or their oxidation to aldehyde or carboxyl groups.

[0300] Oil is another product of wetmilling of corn and other grains, the value of which may be improved by introduction and expression of genes. The quantity of oil that can be extracted by wetmilling may be elevated by approaches as described for feed and food above. Oil properties may also be altered to improve its performance in the production and use of cooking oil, shortenings, lubricants or other oil-derived products or improvement of its health attributes when used in the food-related applications. Novel fatty acids may also be synthesized which upon extraction can serve as starting materials for chemical syntheses. The changes in oil properties may be achieved by altering the type, level, or lipid arrangement of the fatty acids present in the oil. This in turn may be accomplished by the addition of genes that encode enzymes that catalyze the synthesis of novel fatty acids and the lipids possessing them or by increasing levels of native fatty acids while possibly reducing levels of precursors. Alternatively DNA sequences may be introduced which slow or block steps in fatty acid biosynthesis resulting in the increase in precursor fatty acid intermediates. Genes that might be added include desaturases, epoxidases, hydratases, dehydratases, and other enzymes that catalyze reactions involving fatty acid intermediates. Representative examples of catalytic steps that might be blocked include the desaturations from stearic to oleic acid and oleic to linolenic acid resulting in the respective accumulations of stearic and oleic acids.

[0301] Improvements in the other major cereal wetmilling products, gluten meal and gluten feed, may also be achieved by the introduction of genes to obtain novel plants. Representative possibilities include but are not limited to those described above for improvement of food and feed value.

[0302] In addition it may further be considered that the plant be used for the production or manufacturing of useful biological compounds that were either not produced at all, or not produced at the same level, in the plant previously. The novel plants producing these compounds are made possible by the introduction and expression of genes by transformation methods. The possibilities include, but are not limited to, any biological compound which is presently produced by any organism such as proteins, nucleic acids, primary and intermediary metabolites, carbohydrate polymers, etc. The compounds may be produced by the plant, extracted upon harvest and/or processing, and used for any presently recognized useful purpose such as pharmaceuticals, fragrances, industrial enzymes to name a few.

[0303] Further possibilities to exemplify the range of grain traits or properties potentially encoded by introduced genes in transgenic plants include grain with less breakage susceptibility for export purposes or larger grit size when processed by dry milling through introduction of genes that enhance gamma-zein synthesis, popcorn with improved popping, quality and expansion volume through genes that increase pericarp thickness, corn with whiter grain for food uses though introduction of genes that effectively block expression of enzymes involved in pigment production pathways, and improved quality of alcoholic beverages or sweet corn through introduction of genes which affect flavor such as the shrunken gene (encoding sucrose synthase) for sweet corn.

[0304] 7. Plant Agronomic Characteristics

[0305] Two of the factors determining where plants can be grown are the average daily temperature during the growing season and the length of time between frosts. Within the areas where it is possible to grow a particular plant, there are varying limitations on the maximal time it is allowed to grow to maturity and be harvested. The plant to be grown in a particular area is selected for its ability to mature and dry down to harvestable moisture content within the required period of time with maximum possible yield. Therefore, plant of varying maturities are developed for different growing locations. Apart from the need to dry down sufficiently to permit harvest is the desirability of having maximal drying take place in the field to minimize the amount of energy required for additional drying post-harvest. Also the more readily the grain can dry down, the more time there is available for growth and kernel fill. Genes that influence maturity and/or dry down can be identified and introduced into plant lines using transformation techniques to create new varieties adapted to different growing locations or the same growing location but having improved yield to moisture ratio at harvest. Expression of genes that are involved in regulation of plant development may be especially useful, e.g., the liguleless and rough sheath genes that have been identified in plants.

[0306] Genes may be introduced into plants that would improve standability and other plant growth characteristics. For example, expression of novel genes which confer stronger stalks, improved root systems, or prevent or reduce ear droppage would be of great value to the corn farmer. Introduction and expression of genes that increase the total amount of photoassimilate available by, for example, increasing light distribution and/or interception would be advantageous. In addition the expression of genes that increase the efficiency of photosynthesis and/or the leaf canopy would further increase gains in productivity. Such approaches would allow for increased plant populations in the field.

[0307] Delay of late season vegetative senescence would increase the flow of assimilate into the grain and thus increase yield. Overexpression of genes within plants that are associated with “stay green” or the expression of any gene that delays senescence would achieve be advantageous. For example, a non-yellowing mutant has been identified in Festuca pratensis (Davies et al., 1990). Expression of this gene as well as others may prevent premature breakdown of chlorophyll and thus maintain canopy function.

[0308] 8. Nutrient Utilization

[0309] The ability to utilize available nutrients and minerals may be a limiting factor in growth of many plants. It is proposed that it would be possible to alter nutrient uptake, tolerate pH extremes, mobilization through the plant, storage pools, and availability for metabolic activities by the introduction of novel genes. These modifications would allow a plant to more efficiently utilize available nutrients. It is contemplated that an increase in the activity of, for example, an enzyme that is normally present in the plant and involved in nutrient utilization would increase the availability of a nutrient. An example of such an enzyme would be phytase. It is also contemplated that expression of a novel gene may make a nutrient source available that was previously not accessible, e.g., an enzyme that releases a component of nutrient value from a more complex molecule, perhaps a macromolecule.

[0310] 9. Male Sterility

[0311] Male sterility is useful in the production of hybrid seed. It is proposed that male sterility may be produced through expression of novel genes. For example, it has been shown that expression of genes that encode proteins that interfere with development of the male inflorescence and/or gametophyte result in male sterility. Chimeric ribonuclease genes that express in the anthers of transgenic tobacco and oilseed rape have been demonstrated to lead to male sterility (Mariani et al, 1990).

[0312] For example, a number of mutations were discovered in maize that confer cytoplasmic male sterility. One mutation in particular, referred to as T cytoplasm, also correlates with sensitivity to Southern corn leaf blight. A DNA sequence, designated TURF-13 (Levings, 1990), was identified that correlates with T cytoplasm. It would be possible through the introduction of TURF-13 via transformation to separate male sterility from disease sensitivity. As it is necessary to be able to restore male fertility for breeding purposes and for grain production, it is proposed that genes encoding restoration of male fertility may also be introduced.

[0313] 10. Negative Selectable Markers

[0314] Introduction of genes encoding traits that can be selected against may be useful for eliminating undesirable linked genes. When two or more genes are introduced together by cotransformation, the genes will be linked together on the host chromosome. For example, a gene encoding a Bt gene that confers insect resistance on the plant may be introduced into a plant together with a bar gene that is useful as a selectable marker and confers resistance to the herbicide Ignite® on the plant. However, it may not be desirable to have an insect resistant plant that is also resistant to the herbicide Ignite®. It is proposed that one could also introduce an antisense bar gene that is expressed in those tissues where one does not want expression of the bar gene, e.g., in whole plant parts. Hence, although the bar gene is expressed and is useful as a selectable marker, it is not useful to confer herbicide resistance on the whole plant. The bar antisense gene is a negative selectable marker.

[0315] Negative selection is necessary in order to screen a population of transformants for rare homologous recombinants generated through gene targeting. For example, a homologous recombinant may be identified through the inactivation of a gene that was previously expressed in that cell. The antisense gene to neomycin phosphotransferase II (nptII) has been investigated as a negative selectable marker in tobacco (Nicotiana tabacum) and Arabidopsis thaliana (Xiang and Guerra, 1993). In this example both sense and antisense nptII genes are introduced into a plant through transformation and the resultant plants are sensitive to the antibiotic kanamycin. An introduced gene that integrates into the host cell chromosome at the site of the antisense nptII gene, and inactivates the antisense gene, will make the plant resistant to kanamycin and other aminoglycoside antibiotics. Therefore, rare site specific recombinants may be identified by screening for antibiotic resistance. Similarly, any gene, native to the plant or introduced through transformation, that when inactivated confers resistance to a compound, may be useful as a negative selectable marker.

[0316] It is contemplated that negative selectable markers may also be useful in other ways. One application is to construct transgenic lines in which one could select for transposition to unlinked sites. In the process of tagging it is most common for the transposable element to move to a genetically linked site on the same chromosome. A selectable marker for recovery of rare plants in which transposition has occurred to an unlinked locus would be useful. For example, the enzyme cytosine deaminase may be useful for this purpose (Stouggard, 1993). In the presence of this enzyme the compound 5-fluorocytosine is converted to 5-fluoruracil which is toxic to plant and animal cells. If a transposable element is linked to the gene for the enzyme cytosine deaminase, one may select for transposition to unlinked sites by selecting for transposition events in which the resultant plant is now resistant to 5-fluorocytosine. The parental plants and plants containing transpositions to linked sites will remain sensitive to 5-fluorocytosine. Resistance to 5-fluorocytosine is due to loss of the cytosine deaminase gene through genetic segregation of the transposable element and the cytosine deaminase gene. Other genes that encode proteins that render the plant sensitive to a certain compound will also be useful in this context. For example, T-DNA gene 2 from Agrobacterium tumefaciens encodes a protein that catalyzes the conversion of alpha-naphthalene acetamide (NAM) to alpha-napthalene acetic acid (NAA) renders plant cells sensitive to high concentrations of NAM (Depicker et al., 1988).

[0317] It is also contemplated that negative selectable markers may be useful in the construction of transposon tagging lines. For example, by marking an autonomous transposable element such as Ac, Master Mu, or En/Spn with a negative selectable marker, one could select for transformants in which the autonomous element is not stably integrated into the genome. This would be desirable, for example, when transient expression of the autonomous element is desired to activate in trans the transposition of a defective transposable element, such as Ds, but stable integration of the autonomous element is not desired. The presence of the autonomous element may not be desired in order to stabilize the defective element, i.e., prevent it from further transposing. However, it is proposed that if stable integration of an autonomous transposable element is desired in a plant the presence of a negative selectable marker may make it possible to eliminate the autonomous element during the breeding process.

[0318] 11. Non-Protein-Expressing Sequences

[0319] a. RNA-Expressing

[0320] DNA may be introduced into plants for the purpose of expressing RNA transcripts that function to affect plant phenotype yet are not translated into protein. Two examples are antisense RNA and RNA with ribozyme activity. Both may serve possible functions in reducing or eliminating expression of native or introduced plant genes.

[0321] Genes may be constructed or isolated, which when transcribed, produce antisense RNA that is complementary to all or part(s) of a targeted messenger RNA(s). The antisense RNA reduces production of the polypeptide product of the messenger RNA. The polypeptide product may be any protein encoded by the plant genome. The aforementioned genes will be referred to as antisense genes. An antisense gene may thus be introduced into a plant by transformation methods to produce a novel transgenic plant with reduced expression of a selected protein of interest. For example, the protein may be an enzyme that catalyzes a reaction in the plant. Reduction of the enzyme activity may reduce or eliminate products of the reaction which include any enzymatically synthesized compound in the plant such as fatty acids, amino acids, carbohydrates, nucleic acids and the like. Alternatively, the protein may be a storage protein, such as a zein, or a structural protein, the decreased expression of which may lead to changes in seed amino acid composition or plant morphological changes respectively. The possibilities cited above are provided only by way of example and do not represent the full range of applications.

[0322] Genes may also be constructed or isolated, which when transcribed produce RNA enzymes, or ribozymes, which can act as endoribonucleases and catalyze the cleavage of RNA molecules with selected sequences. The cleavage of selected messenger RNA's can result in the reduced production of their encoded polypeptide products. These genes may be used to prepare novel transgenic plants which possess them. The transgenic plants may possess reduced levels of polypeptides including but not limited to the polypeptides cited above that may be affected by antisense RNA.

[0323] It is also possible that genes may be introduced to produce novel transgenic plants which have reduced expression of a native gene product by a mechanism of cosuppression. It has been demonstrated in tobacco, tomato, and petunia (Goring et al, 1991; Smith et al., 1990; Napoli et al., 1990; van der Krol et al.,, 1990) that expression of the sense transcript of a native gene will reduce or eliminate expression of the native gene in a manner similar to that observed for antisense genes. The introduced gene may encode all or part of the targeted native protein but its translation may not be required for reduction of levels of that native protein.

[0324] b. Non-RNA-Expressing

[0325] For example, DNA elements including those of transposable elements such as Ds, Ac, or Mu, may be, inserted into a gene and cause mutations. These DNA elements may be inserted in order to inactivate (or activate) a gene and thereby “tag” a particular trait. In this instance the transposable element does not cause instability of the tagged mutation, because the utility of the element does not depend on its ability to move in the genome. Once a desired trait is tagged, the introduced DNA sequence may be used to clone the corresponding gene, e.g., using the introduced DNA sequence as a PCR primer together with PCR gene cloning techniques (Shapiro, 1983; Dellaporta et al., 1988). Once identified, the entire gene(s) for the particular trait, including control or regulatory regions where desired may be isolated, cloned and manipulated as desired. The utility of DNA elements introduced into an organism for purposed of gene tagging is independent of the DNA sequence and does not depend on any biological activity of the DNA sequence, i.e., transcription into RNA or translation into protein. The sole function of the DNA element is to disrupt the DNA sequence of a gene.

[0326] It is contemplated that unexpressed DNA sequences, including novel synthetic sequences could be introduced into cells as proprietary “labels” of those cells and plants and seeds thereof. It would not be necessary for a label DNA element to disrupt the function of a gene endogenous to the host organism, as the sole function of this DNA would be to identify the origin of the organism. For example, one could introduce a unique DNA sequence into a plant and this DNA element would identify all cells, plants, and progeny of these cells as having arisen from that labeled source. It is proposed that inclusion of label DNAs would enable one to distinguish proprietary germplasm or germplasm derived from such, from unlabelled germplasm.

[0327] Another possible element which may be introduced is a matrix attachment region element (MAR), such as the chicken lysozyme A element (Stief et al., 1989), which can be positioned around an expressible gene of interest to effect an increase in overall expression of the gene and diminish position dependant effects upon incorporation into the plant genome (Stief et al., 1989; Phi-Van et al., 1990).

[0328] Further nucleotide sequences of interest that may be contemplated for use within the scope of the present invention in operable linkage with the promoter sequences according to the invention are isolated nucleic acid molecules, e.g., DNA or RNA, comprising a plant nucleotide sequence according to the invention comprising an open reading frame that is preferentially expressed in a specific tissue, i.e., seed-, root, green tissue (leaf and stem), panicle-, or pollen, or is expressed constitutively.

[0329] B. Marker Genes

[0330] In order to improve the ability to identify transformants, one may desire to employ a selectable or screenable marker gene as, or in addition to, the expressible gene of interest. “Marker genes” are genes that impart a distinct phenotype to cells expressing the marker gene and thus allow such transformed cells to be distinguished from cells that do not have the marker. Such genes may encode either a selectable or screenable marker, depending on whether the marker confers a trait which one can ‘select’ for by chemical means, i.e., through the use of a selective agent (e.g., a herbicide, antibiotic, or the like), or whether it is simply a trait that one can identify through observation or testing, i.e., by ‘screening’ (e.g., the R-locus trait, the green fluorescent protein (GFP)). Of course, many examples of suitable marker genes are known to the art and can be employed in the practice of the invention.

[0331] Included within the terms selectable or screenable marker genes are also genes which encode a “secretable marker” whose secretion can be detected as a means of identifying or selecting for transformed cells. Examples include markers which encode a secretable antigen that can be identified by antibody interaction, or even secretable enzymes which can be detected by their catalytic activity. Secretable proteins fall into a number of classes, including small, diffusible proteins detectable, e.g., by ELISA; small active enzymes detectable in extracellular solution (e.g., alpha-amylase, beta-lactamase, phosphinothricin acetyltransferase); and proteins that are inserted or trapped in the cell wall (e.g., proteins that include a leader sequence such as that found in the expression unit of extensin or tobacco PR-S).

[0332] With regard to selectable secretable markers, the use of a gene that encodes a protein that becomes sequestered in the cell wall, and which protein includes a unique epitope is considered to be particularly advantageous. Such a secreted antigen marker would ideally employ an epitope sequence that would provide low background in plant tissue, a promoter-leader sequence that would impart efficient expression and targeting across the plasma membrane, and would produce protein that is bound in the cell wall and yet accessible to antibodies. A normally secreted wall protein modified to include a unique epitope would satisfy all such requirements.

[0333] One example of a protein suitable for modification in this manner is extensin, or hydroxyproline rich glycoprotein (HPRG). For example, the maize HPRG (Steifel et al., 1990) molecule is well characterized in terms of molecular biology, expression and protein structure. However, any one of a variety of ultilane and/or glycine-rich wall proteins (Keller et al., 1989) could be modified by the addition of an antigenic site to create a screenable marker.

[0334] One exemplary embodiment of a secretable screenable marker concerns the use of a maize sequence encoding the wall protein HPRG, modified to include a 15 residue epitope from the pro-region of murine interleukin, however, virtually any detectable epitope may be employed in such embodiments, as selected from the extremely wide variety of antigen-antibody combinations known to those of skill in the art. The unique extracellular epitope can then be straightforwardly detected using antibody labeling in conjunction with chromogenic or fluorescent adjuncts.

[0335] Elements of the present disclosure may be exemplified in detail through the use of the bar and/or GUS genes, and also through the use of various other markers. Of course, in light of this disclosure, numerous other possible selectable and/or screenable marker genes will be apparent to those of skill in the art in addition to the one set forth hereinbelow. Therefore, it will be understood that the following discussion is exemplary rather than exhaustive. In light of the techniques disclosed herein and the general recombinant techniques which are known in the art, the present invention renders possible the introduction of any gene, including marker genes, into a recipient cell to generate a transformed plant.

[0336] 1. Selectable Markers

[0337] Possible selectable markers for use in connection with the present invention include, but are not limited to, a neo gene (Potrykus et al., 1985) which codes for kanamycin resistance and can be selected for using kanamycin, G418, paromomycin, and the like; a bar gene which codes for bialaphos or phosphinothricin resistance; a gene which encodes an altered EPSP synthase protein (Hinchee et al., 1988) thus conferring glyphosate resistance; a nitrilase gene such as bxn from Klebsiella ozaenae which confers resistance to bromoxynil (Stalker et al., 1988); a mutant acetolactate synthase gene (ALS) which confers resistance to imidazolinone, sulfonylurea or other ALS-inhibiting chemicals (European Patent Application 154,204, 1985); a methotrexate-resistant DHFR gene (Thillet et al., 1988); a dalapon dehalogenase gene that confers resistance to the herbicide dalapon; a mutated anthranilate synthase gene that confers resistance to 5-methyl tryptophan. Preferred selectable marker genes encode phosphinothricin acetyltransferase; glyphosate resistant EPSPS, aminoglycoside phosphotransferase; hygromycin phosphotransferase, or neomycin phosphotransferase. Where a mutant EPSP synthase gene is employed, additional benefit may be realized through the incorporation of a suitable chloroplast transit peptide, CTP (European Patent Application 0,218,571, 1987).

[0338] An illustrative embodiment of a selectable marker gene capable of being used in systems to select transformants is the genes that encode the enzyme phosphinothricin acetyltransferase, such as the bar gene from Streptomyces hygroscopicus or the pat gene from Streptomyces viridochromogenes. The enzyme phosphinothricin acetyl transferase (PAT) inactivates the active ingredient in the herbicide bialaphos, phosphinothricin (PPT). PPT inhibits glutamine synthetase, (Murakami et al., 1986; Twell et al., 1989) causing rapid accumulation of ammonia and cell death. The success in using this selective system in conjunction with monocots was particularly surprising because of the major difficulties which have been reported in transformation of cereals (Potrykus, 1989).

[0339] Where one desires to employ a bialaphos resistance gene in the practice of the invention, a particularly useful gene for this purpose is the bar or pat genes obtainable from species of Streptomyces (e.g., ATCC No. 21,705). The cloning of the bar gene has been described (Murakami et al., 1986; Thompson et al., 1987) as has the use of the bar gene in, the context of plants other than monocots (De Block et al., 1987; De Block et al., 1989).

[0340] 2. Screenable Markers

[0341] Screenable markers that may be employed include, but are not limited to, a beta-glucuronidase (GUS) or uidA gene which encodes an enzyme for which various chromogenic substrates are known; an R-locus gene, which encodes a product that regulates the production of anthocyanin pigments (red color) in plant tissues (Dellaporta et al., 1988); a beta-lactamase gene (Sutcliffe, 1978), which encodes an enzyme for which various chromogenic substrates are known (e.g., PADAC, a chromogenic cephalosporin); a xylE gene (Zukowsky et al., 1983) which encodes a catechol dioxygenase that can convert chromogenic catechols; an ∀-amylase gene (Ikuta et al., 1990); a tyrosinase gene (Katz et al., 1983) which encodes an enzyme capable of oxidizing tyrosine to DOPA and dopaquinone which in turn condenses to form the easily detectable compound melanin; a ∃-galactosidase gene, which encodes an enzyme for which there are chromogenic substrates; a luciferase (lux) gene (Ow et al., 1986), which allows for bioluminescence detection; or even an aequorin gene (Prasher et al., 1985), which may be employed in calcium-sensitive bioluminescence detection, or a green fluorescent protein gene (Niedz et al., 1995).

[0342] Genes from the maize R gene complex are contemplated to be particularly useful as screenable markers. The R gene complex in maize encodes a protein that acts to regulate the production of anthocyanin pigments in most seed and plant tissue. A gene from the R gene complex was applied to maize transformation, because the expression of this gene in transformed cells does not harm the cells. Thus, an R gene introduced into such cells will cause the expression of a red pigment and, if stably incorporated, can be visually scored as a red sector. If a maize line is carries dominant □ultila for genes encoding the enzymatic intermediates in the anthocyanin biosynthetic pathway (C2, A1, A2, Bz1 and Bz2), but carries a recessive allele at the R locus, transformation of any cell from that line with R will result in red pigment formation. Exemplary lines include Wisconsin 22 which contains the rg-Stadler allele and TR112, a K55 derivative which is r-g, b, P1. Alternatively any genotype of maize can be utilized if the C1 and R alleles are introduced together.

[0343] It is further proposed that R gene regulatory regions may be employed in chimeric constructs in order to provide mechanisms for controlling the expression of chimeric genes. More diversity of phenotypic expression is known at the R locus than at any other locus (Coe et al., 1988). It is contemplated that regulatory regions obtained from regions 5′ to the structural R gene would be valuable in directing the expression of genes, e.g., insect resistance, drought resistance, herbicide tolerance or other protein coding regions. For the purposes of the present invention, it is believed that any of the various R gene family members may be successfully employed (e.g., P, S, Lc, etc.). However, the most preferred will generally be Sn (particularly Sn:bol3). Sn is a dominant member of the R gene complex and is functionally similar to the R and B loci in that Sn controls the tissue specific deposition of anthocyanin pigments in certain seedling and plant cells, therefore, its phenotype is similar to R.

[0344] A further screenable marker contemplated for use in the present invention is firefly luciferase, encoded by the lux gene. The presence of the lux gene in transformed cells may be detected using, for example, X-ray film, scintillation counting, fluorescent spectrophotometry, low-light video cameras, photon counting cameras or multiwell luminometry. It is also envisioned that this system may be developed for populational screening for bioluminescence, such as on tissue culture plates, or even for whole plant screening. Where use of a screenable marker gene such as lux or GFP is desired, benefit may be realized by creating a gene fusion between the screenable marker gene and a selectable marker gene, for example, a GFP-NPTII gene fusion. This could allow, for example, selection of transformed cells followed by screening of transgenic plants or seeds.

[0345] 1. C. Exemplary DNA Molecules

[0346] The invention provides an isolated nucleic acid molecule, e.g., DNA or RNA, comprising a plant nucleotide sequence comprising an open reading frame that is preferentially expressed in a specific plant tissue, i.e., in seeds, roots, green tissue (leaf and stem), panicles or pollen, or is expressed constitutively, or a promoter thereof.

[0347] In one specific embodiment the invention provides an isolated nucleic acid molecule, e.g., DNA or RNA, comprising a plant nucleotide sequence comprising an open reading frame that is preferentially expressed in a specific plant tissue, i.e., in seeds, roots, green tissue (leaf and stem), panicles or pollen and which is substantially similar, and preferably has at least 70%, e.g., 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, and even 90% or more, e.g., 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, and 99%, nucleic acid sequence identity, to an open reading frame expressed in

[0348] (i) a seed-specific manner, e.g., one of SEQ ID NOs:1020-1597, 5927, 5940, 5941, 5945-5958;

[0349] (ii) a root-specific manner, e.g., one of SEQ ID NOs:801-1019;

[0350] (iii) a green tissue (leaf and stem)-specific manner, e.g., one of SEQ ID NOs:399-464;

[0351] (iv) a panicle-specific manner, e.g., one of SEQ ID NOs:465-720; or

[0352] (v) a pollen-specific manner, e.g., one of SEQ ID NOs:721-800;

[0353] or the complement thereof.

[0354] In another embodiment the invention provides an isolated nucleic acid molecule, e.g., DNA or RNA, comprising a plant nucleotide sequence comprising an open reading frame that is constitutively expressed and which is substantially similar, and preferably has at least 70%, e.g., 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, and even 90% or more, e.g., 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, and 99%, nucleic acid sequence identity, to a constitutively expressed open reading frame, which comprises one of SEQ ID NOs:1-398 and 5928 -5939 or the complement thereof.

[0355] In another embodiment, the invention provides an isolated nucleic acid molecule comprising a promoter which is preferentially expressed in a specific plant tissue, i.e., in seeds, roots, green tissue (leaf and stem), panicles or pollen and which is substantially similar, and preferably has at least 70%, e.g., 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, and even 90% or more, e.g., 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, and 99%, nucleic acid sequence identity, to a gene comprising a promoter listed in

[0356] (i) SEQ ID NOs:2275-2672, 5959, 5972, 5973, 5977-5990 and 6001 (e.g., including a promoter obtained or obtainable from any one of SEQ ID NOs:2275-2672, 5959, 5972, 5973, 5977-5990 and 6001) which directs seed-specific transcription of a linked nucleic acid segment;

[0357] (ii) SEQ ID NOs:2144-2274 (e.g., including a promoter obtained or obtainable from any one of SEQ ID NOs:2144-2274) which directs root-specific transcription of a linked nucleic acid segment;

[0358] (iii) SEQ ID NOs:1886-1918 (e.g., including a promoter obtained or obtainable from any one of SEQ ID NOs:1886-1918) which directs green tissue (leaf and stem)-specific transcription of a linked nucleic acid segment;

[0359] (iv) SEQ ID NOs:1919-2085 (e.g., including a promoter obtained or obtainable from any one of SEQ ID NOs:1919-2085) which directs panicle-specific transcription of a linked nucleic acid segment;

[0360] (v) SEQ ID NOs:2086-2143 (e.g., including a promoter obtained or obtainable from any one of SEQ ID NOs:2086-2143) which directs pollen-specific transcription of a linked nucleic acid segment.

[0361] In yet another embodiment, the invention provides an isolated nucleic acid molecule comprising a promoter constitutively expressed and which is substantially similar, and preferably has at least 70%, e.g., 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, and even 90% or more, e.g., 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, and 99%, nucleic acid sequence identity, to a gene comprising a promoter listed in

[0362] (vi) SEQ ID NOs:1598-1885 and 5960-5971 (e.g., including a promoter obtained or obtainable from anyone of SEQ ID NOs:1598-1885 and 5960-5971, respectively) which directs constitutve transcription of a linked nucleic acid segment.

[0363] The present invention further provides a composition, an expression cassette or a recombinant vector containing the nucleic acid molecule of the invention, and host cells comprising the expression cassette or vector, e.g., comprising a plasmid. In particular, the present invention provides an expression cassette or a recombinant vector comprising a promoter linked to a nucleic acid segment comprising an open reading frame according to the invention which, when present in a plant, plant cell or plant tissue, results in transcription of the linked nucleic acid segment. Further, the invention provides isolated polypeptides encoded by any one of the open reading frames comprising SEQ ID NOs:1-1597, 5927, 5940, 5941, 5945-5958, or the orthologs thereof, e.g., an open reading frame comprising one of SEQ ID NOs:2673-5926.

[0364] The choice of promoter directing expression of a nucleic acid segment comprising an open reading frame according to the invention will vary depending on the temporal and spatial requirements for expression, and also depending on the target species. In some cases, expression in multiple tissues is desirable. While in others, tissue-specific, e.g., seed-specific, expression is desirable. Although many promoters from dicotyledons have been shown to be operational in monocotyledons and vice versa, ideally dicotyledonous promoters are selected for expression in dicotyledons, and monocotyledonous promoters for expression in monocotyledons. However, there is no restriction to the provenance of selected promoters; it is sufficient that they are operational in driving the expression of the nucleotide sequences in the desired cell.

[0365] These promoters include, but are not limited to, constitutive, inducible, temporally regulated, developmentally regulated, spatially-regulated, chemically regulated, stress-responsive, tissue-specific, viral and synthetic promoters. Promoter sequences are known to be strong or weak. A strong promoter provides for a high level of gene expression, whereas a weak promoter provides for a very low level of gene expression. An inducible promoter is a promoter that provides for the turning on and off of gene expression in response to an exogenously added agent, or to an environmental or developmental stimulus. A bacterial promoter such as the Ptac promoter can be induced to varying levels of gene expression depending on the level of isothiopropylgalactoside added to the transformed bacterial cells. An isolated promoter sequence that is a strong promoter for heterologous nucleic acid is advantageous because it provides for a sufficient level of gene expression to allow for easy detection and selection of transformed cells and provides for a high level of gene expression when desired.

[0366] Within a plant promoter region there are several domains that are necessary for full function of the promoter. The first of these domains lies immediately upstream of the structural gene and forms the “core promoter region” containing consensus sequences, normally 70 base pairs immediately upstream of the gene. The core promoter region contains the characteristic CAAT and TATA boxes plus surrounding sequences, and represents a transcription initiation sequence that defines the transcription start point for the structural gene.

[0367] The presence of the core promoter region defines a sequence as being a promoter: if the region is absent, the promoter is non-functional. Furthermore, the core promoter region is insufficient to provide full promoter activity. A series of regulatory sequences upstream of the core constitute the remainder of the promoter. The regulatory sequences determine expression level, the spatial and temporal pattern of expression and, for an important subset of promoters, expression under inductive conditions (regulation by external factors such as light, temperature, chemicals, hormones).

[0368] A range of naturally-occurring promoters are known to be operative in plants and have been used to drive the expression of heterologous (both foreign and endogenous) genes in plants: for example, the constitutive 35S cauliflower mosaic virus (CaMV) promoter, the ripening-enhanced tomato polygalacturonase promoter (Bird et al., 1988), the E8 promoter (Diekman & Fischer, 1988) and the fruit specific 2A1 promoter (Pear et al., 1989) and many others, e.g., U2 and U5 snRNA promoters from maize, the promoter from alcohol dehydrogenase, the Z4 promoter from a gene encoding the Z4 22 kD zein protein, the Z10 promoter from a gene encoding a 10 kD zein protein, a Z27 promoter from a gene encoding a 27 kD zein protein, the A20 promoter from the gene encoding a 19 kD-zein protein, inducible promoters, such as the light inducible promoter derived from the pea rbcS gene and the actin promoter from rice, e.g., the actin 2 promoter (WO 00/70067); seed specific promoters, such as the phaseolin promoter from beans, may also be used. The nucleotide sequences of this invention can also be expressed under the regulation of promoters that are chemically regulated. This enables the nucleic acid sequence or encoded polypeptide to be synthesized only when the crop plants are treated with the inducing chemicals. Chemical induction of gene expression is detailed in EP 0 332 104 (to Ciba-Geigy) and U.S. Pat. No. 5,614,395. A preferred promoter for chemical induction is the tobacco PR-1a promoter.

[0369] Examples of some constitutive promoters which have been described include the rice actin 1 (Wang et al., 1992; U.S. Pat. No. 5,641,876), CaMV 35S (Odell et al., 1985), CaMV 19S (Lawton et al., 1987), nos, Adh, sucrose synthase; and the ubiquitin promoters.

[0370] Examples of tissue specific promoters which have been described include the lectin (Vodkin, 1983; Lindstrom et al., 1990) corn alcohol dehydrogenase 1 (Vogel et al., 1989; Dennis et al., 1984), corn light harvesting complex (Simpson, 1986; Bansal et al., 1992), corn heat shock protein (Odell et al., 1985), pea small subunit RuBP carboxylase (Poulsen et al., 1986), Ti plasmid mannopine synthase (Langridge et al., 1989), Ti plasmid nopaline synthase (Langridge et al., 1989), petunia chalcone isomerase (vanTunen et al., 1988), bean glycine rich protein 1 (Keller et al., 1989), truncated CaMV 35s (Odell et al., 1985), potato patatin (Wenzler et al., 1989), root cell (Yamamoto et al., 1990), maize zein (Reina et al., 1990; Kriz et al., 1987; Wandelt et al., 1989; Langridge et al., 1983; Reina et al., 1990), globulin-1 (Belanger et al., 1991), α-tubulin, cab (Sullivan et al., 1989), PEPCase (Hudspeth & Grula, 1989), R gene complex-associated promoters (Chandler et al., 1989), histone, and chalcone synthase promoters (Franken et al., 1991). Tissue specific enhancers are described in Fromm et al. (1989).

[0371] Inducible promoters that have been described include the ABA- and turgor-inducible promoters, the promoter of the auxin-binding protein gene (Schwob et al., 1993), the UDP glucose flavonoid glycosyl-transferase gene promoter (Ralston et al., 1988), the MPI proteinase inhibitor promoter (Cordero et al., 1994), and the glyceraldehyde-3-phosphate dehydrogenase gene promoter (Kohler et al., 1995; Quigley et al., 1989; Martinez et al., 1989).

[0372] Several other tissue-specific regulated genes and/or promoters have been reported in plants. These include genes encoding the seed storage proteins (such as napin, cruciferin, beta-conglycinin, and phaseolin) zein or oil body proteins (such as oleosin), or genes involved in fatty acid biosynthesis (including acyl carrier protein, stearoyl-ACP desaturase. And fatty acid desaturases (fad 2-1)), and other genes expressed during embryo development (such as Bce4, see, for example, EP 255378 and Kridl et al., 1991). Particularly useful for seed-specific expression is the pea vicilin promoter (Czako et al., 1992). (See also U.S. Pat. No. 5,625,136, herein incorporated by reference.) Other useful promoters for expression in mature leaves are those that are switched on at the onset of senescence, such as the SAG promoter from Arabidopsis (Gan et al., 1995).

[0373] A class of fruit-specific promoters expressed at or during antithesis through fruit development, at least until the beginning of ripening, is discussed in U.S. Pat. No. 4,943,674. cDNA clones that are preferentially expressed in cotton fiber have been isolated (John et al., 1992). cDNA clones from tomato displaying differential expression during fruit development have been isolated and characterized (Mansson et al., 1985, Slater et al., 1985). The promoter for polygalacturonase gene is active in fruit ripening. The polygalacturonase gene is described in U.S. Pat. No. 4,535,060, U.S. Pat. No. 4,769,061, U.S. Pat. No. 4,801,590, and U.S. Pat. No. 5,107,065, which disclosures are incorporated herein by reference.

[0374] Other examples of tissue-specific promoters include those that direct expression in leaf cells following damage to the leaf (for example, from chewing insects), in tubers (for example, patatin gene promoter), and in fiber cells (an example of a developmentally-regulated fiber cell protein is E6 (John et al., 1992). The E6 gene is most active in fiber, although low levels of transcripts are found in leaf, ovule and flower.

[0375] The tissue-specificity of some “tissue-specific” promoters may not be absolute and may be tested by one skilled in the art using the diphtheria toxin sequence. One can also achieve tissue-specific expression with “leaky” expression by a combination of different tissue-specific promoters (Beals et al., 1997). Other tissue-specific promoters can be isolated by one skilled in the art (see U.S. Pat. No. 5,589,379). Several inducible promoters (“gene switches”) have been reported. Many are described in the review by Gatz (1996) and Gatz (1997). These include tetracycline repressor system, Lac repressor system, copper-inducible systems, salicylate-inducible systems (such as the PR1a system), glucocorticoid-(Aoyama et al., 1997) and ecdysome-inducible systems. Also included are the benzene sulphonamide-(U.S. Pat. No. 5,364,780) and alcohol-(WO 97/06269 and WO 97/06268) inducible systems and glutathione S-transferase promoters. Other studies have focused on genes inducibly regulated in response to environmental stress or stimuli such as increased salinity. Drought, pathogen and wounding. (Graham et al., 1985; Graham et al., 1985, Smith et al., 1986). Accumulation of metallocarboxypeptidase-inhibitor protein has been reported in leaves of wounded potato plants (Graham et al., 1981). Other plant genes have been reported to be induced methyl jasmonate, elicitors, heat-shock, anaerobic stress, or herbicide safeners.

[0376] Regulated expression of the chimeric transacting viral replication protein can be further regulated by other genetic strategies. For example, Cre-mediated gene activation as described by Odell et al. 1990. Thus, a DNA fragment containing 3′ regulatory sequence bound by lox sites between the promoter and the replication protein coding sequence that blocks the expression of a chimeric replication gene from the promoter can be removed by Cre-mediated excision and result in the expression of the trans-acting replication gene. In this case, the chimeric Cre gene, the chimeric trans-acting replication gene, or both can be under the control of tissue- and developmental-specific or inducible promoters. An alternate genetic strategy is the use of tRNA suppressor gene. For example, the regulated expression of a tRNA suppressor gene can conditionally control expression of a trans-acting replication protein coding sequence containing an appropriate termination codon as described by Ulmasov et al. 1997. Again, either the chimeric tRNA suppressor gene, the chimeric transacting replication gene, or both can be under the control of tissue- and developmental-specific or inducible promoters.

[0377] Frequently it is desirable to have continuous or inducible expression of a DNA sequence throughout the cells of an organism in a tissue-independent manner. For example, increased resistance of a plant t6 infection by soil- and airborne-pathogens might be accomplished by genetic manipulation of the plant's genome to comprise a continuous promoter operably linked to a heterologous pathogen-resistance gene such that pathogen-resistance proteins are continuously expressed throughout the plant's tissues.

[0378] Alternatively, it might be desirable to inhibit expression of a native DNA sequence within a plant's tissues to achieve a desired phenotype. In this case, such inhibition might be accomplished with transformation of the plant to comprise a constitutive, tissue-independent promoter operably linked to an antisense nucleotide sequence, such that constitutive expression of the antisense sequence produces an RNA transcript that interferes with translation of the mRNA of the native DNA sequence.

[0379] To define a minimal promoter region, a DNA segment representing the promoter region is removed from the 5′ region of the gene of interest and operably linked to the coding sequence of a marker (reporter) gene by recombinant DNA techniques well known to the art. The reporter gene is operably linked downstream of the promoter, so that transcripts initiating at the promoter proceed through the reporter gene. Reporter genes generally encode proteins which are easily measured, including, but not limited to, chloramphenicol acetyl transferase (CAT), beta-glucuronidase (GUS), green fluorescent protein (GFP), beta-galactosidase (beta-GAL), and luciferase.

[0380] The construct containing the reporter gene under the control of the promoter is then introduced into an appropriate cell type by transfection techniques well known to the art. To assay for the reporter protein, cell lysates are prepared and appropriate assays, which are well known in the art, for the reporter protein are performed. For example, if CAT were the reporter gene of choice, the lysates from cells transfected with constructs containing CAT under the control of a promoter under study are mixed with isotopically labeled chloramphenicol and acetyl-coenzyme A (acetyl-CoA). The CAT enzyme transfers the acetyl group from acetyl-CoA to the 2- or 3-position of chloramphenicol. The reaction is monitored by thin-layer chromatography, which separates acetylated chloramphenicol from unreacted material. The reaction products are then visualized by autoradiography.

[0381] The level of enzyme activity corresponds to the amount of enzyme that was made, which in turn reveals the level of expression from the promoter of interest. This level of expression can be compared to other promoters to determine the relative strength of the promoter under study. In order to be sure that the level of expression is determined by the promoter, rather than by the stability of the mRNA, the level of the reporter mRNA can be measured directly, such as by Northern blot analysis.

[0382] Once activity is detected, mutational and/or deletional analyses may be employed to determine the minimal region and/or sequences required to initiate transcription. Thus, sequences can be deleted at the 5′ end of the promoter region and/or at the 3′ end of the promoter region, and nucleotide substitutions introduced. These constructs are then introduced to cells and their activity determined.

[0383] In one embodiment, the promoter may be a gamma zein promoter, an oleosin ole16 promoter, a globulins promoter, an actin I promoter, an actin cl promoter, a sucrose synthetase promoter, an INOPS promoter, an EXM5 promoter, a globulin2 promoter, a b-32, ADPG-pyrophosphorylase promoter, an LtpI promoter, an Ltp2 promoter, an oleosin ole17 promoter, an oleosin ole18 promoter, an actin 2 promoter, a pollen-specific protein promoter, a pollen-specific pectate lyase promoter, an anther-specific protein promoter, an anther-specific gene RTS2 promoter, a pollen-specific gene promoter, a tapeturn-specific gene promoter, tapeturn-specific gene RAB24 promoter, a anthranilate synthase alpha subunit promoter, an alpha zein promoter, an anthranilate synthase beta subunit promoter, a dihydrodipicolinate synthase promoter, a Thil promoter, an alcohol dehydrogenase promoter, a cab binding protein promoter, an H3C4 promoter, a RUBISCO SS starch branching enzyme promoter, an ACCase promoter, an actin3 promoter, an actin7 promoter, a regulatory protein GF14-12 promoter, a ribosomal protein L9 promoter, a cellulose biosynthetic enzyme promoter, an S-adenosyl-L-homocysteine hydrolase promoter, a superoxide dismutase promoter, a C-kinase receptor promoter, a phosphoglycerate mutase promoter, a root-specific RCc3 mRNA promoter, a glucose-6 phosphate isomerase promoter, a pyrophosphate-fructose 6-phosphatelphosphotransferase promoter, an ubiquitin promoter, a beta-ketoacyl-ACP synthase promoter, a 33 kDa photosystem 11 promoter, an oxygen evolving protein promoter, a 69 kDa vacuolar ATPase subunit promoter, a metallothionein-like protein promoter, a glyceraldehyde-3-phosphate dehydrogenase promoter, an ABA- and ripening-inducible-like protein promoter, a phenylalanine ammonia lyase promoter, an adenosine triphosphatase S-adenosyl-L-homocysteine hydrolase promoter, an a-tubulin promoter, a cab promoter, a PEPCase promoter, an R gene promoter, a lectin promoter, a light harvesting complex promoter, a heat shock protein promoter, a chalcone synthase promoter, a zein promoter, a globulin-1 promoter, an ABA promoter, an auxin-binding protein promoter, a UDP glucose flavonoid glycosyl-transferase gene promoter, an NTI promoter, an actin promoter, an opaque 2 promoter, a b70 promoter, an oleosin promoter, a CaMV 35S promoter, a CaMV 19S promoter, a histone promoter, a turgor-inducible promoter, a pea small subunit RuBP carboxylase promoter, a Ti plasmid mannopine synthase promoter, Ti plasmid nopaline synthase promoter, a petunia chalcone isomerase promoter, a bean glycine rich protein I promoter, a CaMV 35S transcript promoter, a potato patatin promoter, or a S-E9 small subunit RuBP carboxylase promoter.

(a) III. Transformed (Transgenic) Plants of the Invention and Methods of Preparation

[0384] Plant species may be transformed with the DNA construct of the present invention by the DNA-mediated transformation of plant cell protoplasts and subsequent regeneration of the plant from the transformed protoplasts in accordance with procedures well known in the art.

[0385] Any plant tissue capable of subsequent clonal propagation, whether by organogenesis or embryogenesis, may be transformed with a vector of the present invention. The term “organogenesis,” as used herein, means a process by which shoots and roots are developed sequentially from meristematic centers; the term “embryogenesis,” as used herein, means a process by which shoots and roots develop together in a concerted fashion (not sequentially), whether from somatic cells or gametes. The particular tissue chosen will vary depending on the clonal propagation systems available for, and best suited to, the particular species being transformed. Exemplary tissue targets include leaf disks, pollen, embryos, cotyledons, hypocotyls, megagametophytes, callus tissue, existing meristematic tissue (e.g., apical meristems, axillary buds, and root meristems), and induced meristem tissue (e.g., cotyledon meristem and ultilane meristem).

[0386] Plants of the present invention may take a variety of forms. The plants may be chimeras of transformed cells and non-transformed cells; the plants may be clonal transformants (e.g., all cells transformed to contain the expression cassette); the plants may comprise grafts of transformed and untransformed tissues (e.g., a transformed root stock grafted to an untransformed scion in citrus species). The transformed plants may be propagated by a variety of means, such as by clonal propagation or classical breeding techniques. For example, first generation (or T1) transformed plants may be selfed to give homozygous second generation (or T2) transformed plants, and the T2 plants further propagated through classical breeding techniques. A dominant selectable marker (such as npt II) can be associated with the expression cassette to assist in breeding.

[0387] Thus, the present invention provides a transformed (transgenic) plant cell, in planta or ex planta, including a transformed plastid or other organelle, e.g., nucleus, mitochondria or chloroplast. The present invention may be used for transformation of any plant species, including, but not limited to, cells from corn (Zea mays), Brassica sp. (e.g., B. napus, B. rapa, B. juncea), particularly those Brassica species useful as sources of seed oil, alfalfa (Medicago sativa), rice (Oryza sativa), rye (Secale cereale), sorghum (Sorghum bicolor, Sorghum vulgare), millet (e.g., pearl millet (Pennisetum glaucum), proso millet (Panicum miliaceum), foxtail millet (Setaria italica), finger millet (Eleusine coracana)), sunflower (Helianthus annuus), safflower (Carthamus tinctorius), wheat (Triticum aestivum), soybean (Glycine max), tobacco (Nicotiana tabacum), potato (Solanum tuberosum), peanuts (Arachis hypogaea), cotton (Gossypium barbadense, Gossypium hirsutum), sweet potato (Ipomoea batatus), cassava (Manihot esculenta), coffee (Cofea spp.), coconut (Cocos nucifera), pineapple (Ananas comosus), citrus trees (Citrus spp.), cocoa (Theobroma cacao), tea (Camellia sinensis), banana (Musa spp.), avocado (Persea ultilane), fig (Ficus casica), guava (Psidium guajava), mango (Mangifera indica), olive (Olea europaea), papaya (Carica papaya),, cashew (Anacardium occidentale), macadamia (Macadamia integrifolia), almond (Prunus amygdalus), sugar beets (Beta vulgaris), sugarcane (Saccharum spp.), oats, duckweed (Lemna), barley, vegetables, ornamentals, and conifers.

[0388] Duckweed (Lemna, see WO 00/07210) includes members of the family Lemnaceae. There are known four genera and 34 species of duckweed as follows: genus Lemna (L. aequinoctialis, L. disperma, L. ecuadoriensis, L. gibba, L. japonica, L. minor, L. miniscula, L. obscura, L. perpusilla, L. tenera, L. trisulca, L. turionifera, L. valdiviana); genus Spirodela (S. intermedia, S. polyrrhiza, S. punctata); genus Woffia (Wa. Angusta, Wa. Arrhiza, Wa. Australina, Wa. Borealis, Wa. Brasiliensis, Wa. Columbiana, Wa. Elongata, Wa. Globosa, Wa. Microscopica, Wa. Neglecta) and genus Wofiella (Wl. ultila, Wl. ultilanen, Wl. gladiata, Wl. ultila, Wl. lingulata, Wl. repunda, Wl. rotunda, and Wl. neotropica). Any other genera or species of Lemnaceae, if they exist, are also aspects of the present invention. Lemna gibba, Lemna minor, and Lemna miniscula are preferred, with Lemna minor and Lemna miniscula being most preferred. Lemna species can be classified using the taxonomic scheme described by Landolt, Biosystematic Investigation on the Family of Duckweeds: The family of Lemnaceae—A Monograph Study. Geobatanischen Institut ETH, Stiftung Rubel, Zurich (1986)).

[0389] Vegetables within the scope of the invention include tomatoes (Lycopersicon esculentum), lettuce (e.g., Lactuca sativa), green beans (Phaseolus vulgaris), lima beans (Phaseolus limensis), peas (Lathyrus spp.), and members of the genus Cucumis such as cucumber (C. sativus), cantaloupe (C. cantalupensis), and musk melon (C. melo). Ornamentals include azalea (Rhododendron spp.), hydrangea (Macrophylla hydrangea), hibiscus (Hibiscus rosasanensis), roses (Rosa spp.), tulips (Tulipa spp.), daffodils (Narcissus spp.), petunias (Petunia hybrida), carnation (Dianthus caryophyllus), poinsettia (Euphorbia pulcherrima), and chrysanthemum. Conifers that may be employed in practicing the present invention include, for example, pines such as loblolly pine (Pinus taeda), slash pine (Pinus elliotii), ponderosa pine (Pinus ponderosa), lodgepole pine (Pinus contorta), and Monterey pine (Pinus radiata), Douglas-fir (Pseudotsuga menziesii); Western hemlock (Tsuga ultilane); Sitka spruce (Picea glauca); redwood (Sequoia sempervirens); true firs such as silver fir (Abies amabilis) and balsam fir (Abies balsamea); and cedars such as Western red cedar (Thuja plicata) and Alaska yellow-cedar (Chamaecyparis nootkatensis). Leguminous plants include beans and peas. Beans include guar, locust bean, fenugreek, soybean, garden beans, cowpea, mungbean, lima bean, fava bean, lentils, chickpea, etc. Legumes include, but are not limited to, Arachis, e.g., peanuts, Vicia, e.g., crown vetch, hairy vetch, adzuki bean, mung bean, and chickpea, Lupinus, e.g., lupine, trifolium, Phaseolus, e.g., common bean and lima bean, Pisum, e.g., field bean, Melilotus, e.g., clover, Medicago, e.g., alfalfa, Lotus, e.g., trefoil, lens, e.g., lentil, and false indigo. Preferred forage and turf grass for use in the methods of the invention include alfalfa, orchard grass, tall fescue, perennial ryegrass, creeping bent grass, and redtop.

[0390] Other plants within the scope of the invention include Acacia, aneth, artichoke, arugula, blackberry, canola, cilantro, clementines, escarole, eucalyptus, fennel, grapefruit, honey dew, jicama, kiwifruit, lemon, lime, mushroom, nut, okra, orange, parsley, persimmon, plantain, pomegranate, poplar, radiata pine, radicchio, Southern pine, sweetgum, tangerine, triticale, vine, yams, apple, pear, quince, cherry, apricot, melon, hemp, buckwheat, grape, raspberry, chenopodium, blueberry, nectarine, peach, plum, strawberry, watermelon, eggplant, pepper, cauliflower, Brassica, e.g., broccoli, cabbage, ultilan sprouts, onion, carrot, leek, beet, broad bean, celery, radish, pumpkin, endive, gourd, garlic, snapbean, spinach, squash, turnip, ultilane, and zucchini.

[0391] Ornamental plants within the scope of the invention include impatiens, Begonia, Pelargonium, Viola, Cyclamen, Verbena, Vinca, Tagetes, Primula, Saint Paulia, Agertum, Amaranthus, Antihirrhinum, Aquilegia, Cineraria, Clover, Cosmo, Cowpea, Dahlia, Datura, Delphinium, Gerbera, Gladiolus, Gloxinia, Hippeastrum, Mesembryanthemum, Salpiglossos, and Zinnia. Other plants within the scope of the invention are shown in Table 1 (above).

[0392] Preferably, transgenic plants of the present invention are crop plants and in particular cereals (for example, corn, alfalfa, sunflower, rice, Brassica, canola, soybean, barley, soybean, sugarbeet, cotton, safflower, peanut, sorghum, wheat, millet, tobacco, etc.), and even more preferably corn, rice and soybean.

[0393] Transformation of plants can be undertaken with a single DNA molecule or multiple DNA molecules (i.e., co-transformation), and both these techniques are suitable for use with the expression cassettes of the present invention. Numerous transformation vectors are available for plant transformation, and the expression cassettes of this invention can be used in conjunction with any such vectors. The selection of vector will depend upon the preferred transformation technique and the target species for transformation.

[0394] A variety of techniques are available and known to those skilled in the art for introduction of constructs into a plant cell host. These techniques generally include transformation with DNA employing A. tumefaciens or A. rhizogenes as the transforming agent, liposomes, PEG precipitation, electroporation, DNA injection, direct DNA uptake, microprojectile bombardment, particle acceleration, and the like (See, for example, EP 295959 and EP 138341) (see below). However, cells other than plant cells may be transformed with the expression cassettes of the invention. The general descriptions of plant expression vectors and reporter genes, and Agrobacterium and Agrobacterium-mediated gene transfer, can be found in Gruber et al. (1993).

[0395] Expression vectors containing genomic or synthetic fragments can be introduced into protoplasts or into intact tissues or isolated cells. Preferably expression vectors are introduced into intact tissue. General methods of culturing plant tissues are provided for example by Maki et al., (1993); and by Phillips et al. (1988). Preferably, expression vectors are introduced into maize or other plant tissues using a direct gene transfer method such as microprojectile-mediated delivery, DNA injection, electroporation and the like. More preferably expression vectors are introduced into plant tissues using the microprojectile media delivery with the biolistic device. See, for example, Tomes et al. (1995). The vectors of the invention can not only be used for expression of structural genes but may also be used in exon-trap cloning, or promoter trap procedures to detect differential gene expression in varieties of tissues, (Lindsey et al., 1993; Auch & Reth et al.).

[0396] It is particularly preferred to use the binary type vectors of Ti and Ri plasmids of Agrobacterium spp. Ti-derived vectors transform a wide variety of higher plants, including monocotyledonous and dicotyledonous plants, such as soybean, cotton, rape, tobacco, and rice (Pacciotti et al., 1985: Byrne et al., 1987; Sukhapinda et al., 1987; Lorz et al., 1985; Potrykus, 1985; Park et al., 1985: Hiei et al., 1994). The use of T-DNA to transform plant cells has received extensive study and is amply described (EP 120516; Hoekema, 1985; Knauf, et al., 1983; and An et al., 1985). For introduction into plants, the chimeric genes of the invention can be inserted into binary vectors as described in the examples.

[0397] Other transformation methods are available to those skilled in the art, such as direct uptake of foreign DNA constructs (see EP 295959), techniques of electroporation (Fromm et al., 1986) or high velocity ballistic bombardment with metal particles coated with the nucleic acid constructs (Kline et al., 1987, and U.S. Pat. No. 4,945,050). Once transformed, the cells can be regenerated by those skilled in the art. Of particular relevance are the recently described methods to transform foreign genes into commercially important crops, such as rapeseed (De Block et al., 1989), sunflower (Everett et al., 1987), soybean (McCabe et al., 1988; Hinchee et al., 1988; Chee et al., 1989; Christou et al., 1989; EP 301749), rice (Hiei et al., 1994), and corn (Gordon Kamm et al., 1990; Fromm et al., 1990).

[0398] Those skilled in the art will appreciate that the choice of method might depend on the type of plant, i.e., monocotyledonous or dicotyledonous, targeted for transformation. Suitable methods of transforming plant cells include, but are not limited to, microinjection (Crossway et al., 1986), electroporation (Riggs et al., 1986), Agrobacterium-mediated transformation (Hinchee et al., 1988), direct gene transfer (Paszkowski et al., 1984), and ballistic particle acceleration using devices available from Agracetus, Inc., Madison, Wis. And BioRad, Hercules, Calif. (see, for example, Sanford et al., U.S. Pat. No. 4,945,050; and McCabe et al., 1988). Also see, Weissinger et al., 1988; Sanford et al., 1987 (onion); Christou et al., 1988 (soybean); McCabe et al., 1988 (soybean); Datta et al., 1990 (rice); Klein et al., 1988 (maize); Klein et al., 1988 (maize); Klein et al., 1988 (maize); Fromm et al., 1990 (maize); and Gordon-Kamm et al., 1990 (maize); Svab et al., 1990 (tobacco chloroplast); Koziel et al., 1993 (maize); Shimamoto et al., 1989 (rice); Christou et al., 1991 (rice); European Patent Application EP 0 332 581 (orchardgrass and other Pooideae); Vasil et al., 1993 (wheat); Weeks et al., 1993 (wheat). In one embodiment, the protoplast transformation method for maize is employed (European Patent Application EP 0 292 435, U.S. Pat. No. 5,350,689).

[0399] In another embodiment, a nucleotide sequence of the present invention is directly transformed into the plastid genome. Plastid transformation technology is extensively described in U.S. Pat. Nos. 5,451,513, 5,545,817, and 5,545,818, in PCT application no. WO 95/16783, and in McBride et al., 1994. The basic technique for chloroplast transformation involves introducing regions of cloned plastid DNA flanking a selectable marker together with the gene of interest into a suitable target tissue, e.g., using biolistics or protoplast transformation (e.g., calcium chloride or PEG mediated transformation). The 1 to 1.5 kb flanking regions, termed targeting sequences, facilitate orthologous recombination with the plastid genome and thus allow the replacement or modification of specific regions of the plastome. Initially, point mutations in the chloroplast 16S rRNA and rps12 genes conferring resistance to spectinomycin and/or streptomycin are utilized as selectable markers for transformation (Svab et al., 1990; Staub et al., 1992). This resulted in stable homoplasmic transformants at a frequency of approximately one per 100 bombardments of target leaves. The presence of cloning sites between these markers allowed creation of a plastid targeting vector for introduction of foreign genes (Staub et al., 1993). Substantial increases in transformation frequency are obtained by replacement of the recessive rRNA or r-protein antibiotic resistance genes with a dominant selectable marker, the bacterial aadA gene encoding the spectinomycin-detoxifying enzyme aminoglycoside-3N-adenyltransferase (Svab et al., 1993). Other selectable markers useful for plastid transformation are known in the art and encompassed within the scope of the invention. Typically, approximately 15-20 cell division cycles following transformation are required to reach a homoplastidic state. Plastid expression, in which genes are inserted by orthologous recombination into all of the several thousand copies of the circular plastid genome present in each plant cell, takes advantage of the enormous copy number advantage over nuclear-expressed genes to permit expression levels that can readily exceed 10% of the total soluble plant protein. In a preferred embodiment, a nucleotide sequence of the present invention is inserted into a plastid targeting vector and transformed into the plastid genome of a desired plant host. Plants homoplastic for plastid genomes containing a nucleotide sequence of the present invention are obtained, and are preferentially capable of high expression of the nucleotide sequence.

[0400]

Agrobacterium tumefaciens
cells containing a vector comprising an expression cassette of the present invention, wherein the vector comprises a Ti plasmid, are useful in methods of making transformed plants. Plant cells are infected with an Agrobacterium tumefaciens as described above to produce a transformed plant cell, and then a plant is regenerated from the transformed plant cell. Numerous Agrobacterium vector systems useful in carrying out the present invention are known.

[0401] For example, vectors are available for transformation using Agrobacterium tumefaciens. These typically carry at least one T-DNA border sequence and include vectors such as pBIN19 (Bevan, 1984). In one preferred embodiment, the expression cassettes of the present invention may be inserted into either of the binary vectors pCIB200 and pCIB2001 for use with Agrobacterium. These vector cassettes for Agrobacterium-mediated transformation wear constructed in the following manner. PTJS75kan was created by NarI digestion of pTJS75 (Schmidhauser & Helinski, 1985) allowing excision of the tetracycline-resistance gene, followed by insertion of an AccI fragment from pUC4K carrying an NPTII (Messing & Vierra, 1982; Bevan et al., 1983; McBride et al., 1990). XhoI linkers were ligated to the EcoRV fragment of pCIB7 which contains the left and right T-DNA borders, a plant selectable nos/nptII chimeric gene and the pUC polylinker (Rothstein et al., 1987), and the XhoI-digested fragment was cloned into SalI-digested pTJS75kan to create pCIB200 (see also EP 0 332 104, example 19). pCIB200 contains the following unique polylinker restriction sites: EcoRI, SstI, KpnI, BglII, XbaI, and SalI. The plasmid pCIB2001 is a derivative of pCIB200 which was created by the insertion into the polylinker of additional restriction sites. Unique restriction sites in the polylinker of pCIB2001 are EcoRI, SstI, KpnI, BglII, XbaI, SalI, MluI, BclI, AvrII, ApaI, HpaI, and StuI. PCIB2001, in addition to containing these unique restriction sites also has plant and bacterial kanamycin selection, left and right T-DNA borders for Agrobacterium-mediated transformation, the RK2-derived trfA function for mobilization between E. coli and other hosts, and the OriT and OriV functions also from RK2. The pCIB2001 polylinker is suitable for the cloning of plant expression cassettes containing their own regulatory signals.

[0402] An additional vector useful for Agrobacterium-mediated transformation is the binary vector pCIB 10, which contains a gene encoding kanamycin resistance for selection in plants, T-DNA right and left border sequences and incorporates sequences from the wide host-range plasmid pRK252 allowing it to replicate in both E. coli and Agrobacterium. Its construction is described by Rothstein et al., 1987. Various derivatives of pCIB10 have been constructed which incorporate the gene for hygromycin B phosphotransferase described by Gritz et al., 1983. These derivatives enable selection of transgenic plant cells on hygromycin only (pCIB743), or hygromycin and kanamycin (pCIB715, pCIB717).

[0403] Methods using either a form of direct gene transfer or Agrobacterium-mediated transfer usually, but not necessarily, are undertaken with a selectable marker which may provide resistance to an antibiotic (e.g., kanamycin, hygromycin or methotrexate) or a herbicide (e.g., phosphinothricin). The choice of selectable marker for plant transformation is not, however, critical to the invention.

[0404] For certain plant species, different antibiotic or herbicide selection markers may be preferred. Selection markers used routinely in transformation include the nptII gene which confers resistance to kanamycin and related antibiotics (Messing & Vierra, 1982; Bevan et al., 1983), the bar gene which confers resistance to the herbicide phosphinothricin (White et al., 1990, Spencer et al., 1990), the hph gene which confers resistance to the antibiotic hygromycin (Blochinger & Diggelmann), and the dhfr gene, which confers resistance to methotrexate (Bourouis et al., 1983).

[0405] One such vector useful for direct gene transfer techniques in combination with selection by the herbicide Basta (or phosphinothricin) is pCIB3064. This vector is based on the plasmid pCIB246, which comprises the CaMV 35S promoter in operational fusion to the E. coli GUS gene and the CaMV 35S transcriptional terminator and is described in the PCT published application WO 93/07278, herein incorporated by reference. One gene useful for conferring resistance to phosphinothricin is the bar gene from Streptomyces viridochromogenes (Thompson et al., 1987). This vector is suitable for the cloning of plant expression cassettes containing their own regulatory signals.

[0406] An additional transformation vector is pSOG35 which utilizes the E. coli gene dihydrofolate reductase (DHFR) as a selectable marker conferring resistance to methotrexate. PCR was used to amplify the 35S promoter (about 800 bp), intron 6 from the maize Adh1 gene (about 550 bp) and 18 bp of the GUS untranslated leader sequence from pSOG10. A 250 bp fragment encoding the E. coli dihydrofolate reductase type II gene was also amplified by PCR and these two PCR fragments were assembled with a SacI-PstI fragment from pBI221 (Clontech) which comprised the pUC19 vector backbone and the nopaline synthase terminator. Assembly of these fragments generated pSOG19 which contains the 35S promoter in fusion with the intron 6 sequence, the GUS leader, the DHFR gene and the nopaline synthase terminator. Replacement of the GUS leader in pSOG 19 with the leader sequence from Maize Chlorotic Mottle Virus check (MCMV) generated the vector pSOG35. pSOG19 and pSOG35 carry the pUC-derived gene for ampicillin resistance and have HindIII, SphI, PstI and EcoRI sites available for the cloning of foreign sequences.

(b) IV. Production and Characterization of Stably Transformed Plants

[0407] Transgenic plant cells are then placed in an appropriate selective medium for selection of transgenic cells which are then grown to callus. Shoots are grown from callus and plantlets generated from the shoot by growing in rooting medium. The various constructs normally will be joined to a marker for selection in plant cells. Conveniently, the marker may be resistance to a biocide (particularly an antibiotic, such as kanamycin, G418, bleomycin, hygromycin, chloramphenicol, herbicide, or the like). The particular marker used will allow for selection of transformed cells as compared to cells lacking the DNA which has been introduced. Components of DNA constructs including transcription cassettes of this invention may be prepared from sequences which are native (endogenous) or foreign (exogenous) to the host. By “foreign” it is meant that the sequence is not found in the wild-type host into which the construct is introduced. Heterologous constructs will contain at least one region which is not native to the gene from which the transcription-initiation-region is derived.

[0408] To confirm the presence of the transgenes in transgenic cells and plants, a variety of assays may be performed. Such assays include, for example, “molecular biological” assays well known to those of skill in the art, such as Southern and Northern blotting, in situ hybridization and nucleic acid-based amplification methods such as PCR or RT-PCR; “biochemical” assays, such as detecting the presence of a protein product, e.g., by immunological means (ELISAs and Western blots) or by enzymatic function; plant part assays, such as seed assays; and also, by analyzing the phenotype of the whole regenerated plant, e.g., for disease or pest resistance.

[0409] DNA may be isolated from cell lines or any plant parts to determine the presence of the preselected nucleic acid segment through the use of techniques well known to those skilled in the art. Note that intact sequences will not always be present, presumably due to rearrangement or deletion of sequences in the cell.

[0410] The presence of nucleic acid elements introduced through the methods of this invention may be determined by polymerase chain reaction (PCR). Using this technique discreet fragments of nucleic acid are amplified and detected by gel electrophoresis. This type of analysis permits one to determine whether a preselected nucleic acid segment is present in a stable transformant, but does not prove integration of the introduced preselected nucleic acid segment into the host cell genome. In addition, it is not possible using PCR techniques to determine whether transformants have exogenous genes introduced into different sites in the, genome, i.e., whether transformants are of independent origin. It is contemplated that using PCR techniques it would be possible to clone fragments of the host genomic DNA adjacent to an introduced preselected DNA segment.

[0411] Positive proof of DNA integration into the host genome and the independent identities of transformants may be determined using the technique of Southern hybridization. Using this technique specific DNA sequences that were introduced into the host genome and flanking host DNA sequences can be identified. Hence the Southern hybridization pattern of a given transformant serves as an identifying characteristic of that transformant. In addition it is possible through Southern hybridization to demonstrate the presence of introduced preselected DNA segments in high molecular weight DNA, i.e., confirm that the introduced preselected, DNA segment has been integrated into the host cell genome. The technique of Southern hybridization provides information that is obtained using PCR, e.g., the presence of a preselected DNA segment, but also demonstrates integration into the genome and characterizes each individual transformant.

[0412] It is contemplated that using the techniques of dot or slot blot hybridization which are modifications of Southern hybridization techniques one could obtain the same information that is derived from PCR, e.g., the presence of a preselected DNA segment.

[0413] Both PCR and Southern hybridization techniques can be used to demonstrate transmission of a preselected DNA segment to progeny. In most instances the characteristic Southern hybridization pattern for a given transformant will segregate in progeny as one or more Mendelian genes (Spencer et al., 1992); Laursen et al., 1994) indicating stable inheritance of the gene. The nonchimeric nature of the callus and the parental transformants (R0) was suggested by germline transmission and the identical Southern blot hybridization patterns and intensities of the transforming DNA in callus, R0 plants and R1 progeny that segregated for the transformed gene.

[0414] Whereas DNA analysis techniques may be conducted using DNA isolated from any part of a plant, RNA may only be expressed in particular cells or tissue types and hence it will be necessary to prepare RNA for analysis from these tissues. PCR techniques may also be used for detection and quantitation of RNA produced from introduced preselected DNA segments. In this application of PCR it is first necessary to reverse transcribe RNA into DNA, using enzymes such as reverse transcriptase, and then through the use of conventional PCR techniques amplify the DNA. In most instances PCR techniques, while useful, will not demonstrate integrity of the RNA product. Further information about the nature of the RNA product may be obtained by Northern blotting. This technique will demonstrate the presence of an RNA species and give information about the integrity of that RNA. The presence or absence of an RNA species can also be determined using dot or slot blot Northern hybridizations. These techniques are modifications of Northern blotting and will only demonstrate the presence or absence of an RNA species.

[0415] While Southern blotting and PCR may be used to detect the preselected DNA segment in question, they do not provide information as to whether the preselected DNA segment is being expressed. Expression may be evaluated by specifically identifying the protein products of the introduced preselected DNA segments or evaluating the phenotypic changes brought about by their expression.

[0416] Assays for the production and identification of specific proteins may make use of physical-chemical, structural, functional, or other properties of the proteins. Unique physical-chemical or structural properties allow the proteins to be separated and identified by electrophoretic procedures, such as native or denaturing gel electrophoresis or isoelectric focusing, or by chromatographic techniques such as ion exchange or gel exclusion chromatography. The unique structures of individual proteins offer opportunities for use of specific antibodies to detect their presence in formats such as an ELISA assay. Combinations of approaches may be employed with even greater specificity such as Western blotting in which antibodies are used to locate individual gene products that have been separated by electrophoretic techniques. Additional techniques may be employed to absolutely confirm the identity of the product of interest such as evaluation by amino acid sequencing following purification. Although these are among the most commonly employed, other procedures may be additionally used.

[0417] Assay procedures may also be used to identify the expression of proteins by their functionality, especially the ability of enzymes to catalyze specific chemical reactions involving specific substrates and products. These reactions may be followed by providing and quantifying the loss of substrates or the generation of products of the reactions by physical or chemical procedures. Examples are as varied as the enzyme to be analyzed.

[0418] Very frequently the expression of a gene product is determined by evaluating the phenotypic results of its expression. These assays also may take many forms including but not limited to analyzing changes in the chemical composition, morphology, or physiological properties of the plant. Morphological changes may include greater stature or thicker stalks. Most often changes in response of plants or plant parts to imposed treatments are evaluated under carefully controlled conditions termed bioassays.

(c) V. Uses of Transgenic Plants

[0419] Once an expression cassette of the invention has been transformed into a particular plant species, it may be propagated in that species or moved into other varieties of the same species, particularly including commercial varieties, using traditional breeding techniques. Particularly preferred plants of the invention include the agronomically important crops listed above. The genetic properties engineered into the transgenic seeds and plants described above are passed on by sexual reproduction and can thus be maintained and propagated in progeny plants. The present invention also relates to a transgenic plant cell, tissue, organ, seed or plant part obtained from the transgenic plant. Also included within the invention are transgenic descendants of the plant as well as transgenic plant cells, tissues, organs, seeds and plant parts obtained from the descendants.

[0420] Preferably, the expression cassette in the transgenic plant is sexually transmitted. In one preferred embodiment, the coding sequence is sexually transmitted through a complete normal sexual cycle of the R0 plant to the R1 generation. Additionally preferred, the expression cassette is expressed in the cells, tissues, seeds or plant of a transgenic plant in an amount that is different than the amount in the cells, tissues, seeds or plant of a plant which only differs in that the expression cassette is absent.

[0421] The transgenic plants produced herein are thus expected to be useful for a variety of commercial and research purposes. Transgenic plants can be created for use in traditional agriculture to possess traits beneficial to the grower (e.g., agronomic traits such as resistance to water deficit, pest resistance, herbicide resistance or increased yield), beneficial to the consumer of the grain harvested from the plant (e.g., improved nutritive content in human food or animal feed; increased vitamin, amino acid, and antioxidant content; the production of antibodies (passive immunization) and nutriceuticals), or beneficial to the food processor (e.g., improved processing traits). In such uses, the plants are generally grown for the use of their grain in human or animal foods. Additionally, the use of root-specific promoters in transgenic plants can provide beneficial traits that are localized in the consumable (by animals and humans) roots of plants such as carrots, parsnips, and beets. However, other parts of the plants, including stalks, husks, vegetative parts, and the like, may also have utility, including use as part of animal silage or for ornamental purposes. Often, chemical constituents (e.g., oils or starches) of maize and other crops are extracted for foods or industrial use and transgenic plants may be created which have enhanced or modified levels of such components.

[0422] Transgenic plants may also find use in the commercial manufacture of proteins or other molecules, where the molecule of interest is extracted or purified from plant parts, seeds, and the like. Cells or tissue from the plants may also be cultured, grown in vitro, or fermented to manufacture such molecules.

[0423] The transgenic plants may also be used in commercial breeding programs, or may be crossed or bred to plants of related crop species. Improvements encoded by the expression cassette may be transferred, e.g., from maize cells to cells of other species, e.g., by protoplast fusion.

[0424] The transgenic plants may have many uses in research or breeding, including creation of new mutant plants through insertional mutagenesis, in order to identify beneficial mutants that might later be created by traditional mutation and selection. An example would be the introduction of a recombinant DNA sequence encoding a transposable element that may be used for generating genetic variation. The methods of the invention may also be used to create plants having unique “signature sequences” or other marker sequences which can be used to identify proprietary lines or varieties.

[0425] Thus, the transgenic plants and seeds according to the invention can be used in plant breeding which aims at the development of plants with improved properties conferred by the expression cassette, such as tolerance of drought, disease, or other stresses. The various breeding steps are characterized by well-defined human intervention such as selecting the lines to be crossed, directing pollination of the parental lines, or selecting appropriate descendant plants. Depending on the desired properties different breeding measures are taken. The relevant techniques are well known in the art and include but are not limited to hybridization, inbreeding, backcross breeding, ultilane breeding, variety blend, interspecific hybridization, aneuploid techniques, etc. Hybridization techniques also include the sterilization of plants to yield male or female sterile plants by mechanical, chemical or biochemical means. Cross pollination of a male sterile plant with pollen of a different line assures that the genome of the male sterile but female fertile plant will uniformly obtain properties of both parental lines. Thus, the transgenic seeds and plants according to the invention can be used for the breeding of improved plant lines which for example increase the effectiveness of conventional methods such as herbicide or pesticide treatment or allow to dispense with said methods due to their modified genetic properties. Alternatively new crops with improved stress tolerance can be obtained which, due to their optimized genetic “equipment”, yield harvested product of better quality than products which were not able to tolerate comparable adverse developmental conditions.

[0426] Polynucleotides derived from nucleotide sequences of the present invention having any of the nucleotide sequences of SEQ ID NOs: 1 to SEQ ID NO: 1597, 5927, 5940, 5941, 5945-5958 are useful to detect the presence in a test sample of at least one copy of a nucleotide sequence containing the same or substantially the same sequence, or a fragment, complement, or variant thereof. The sequence of the probes and/or primers of the instant invention need not be identical to those provided in the Sequence Listing or the complements thereof. Some variation in probe or primer sequence and/or length can allow additional family members to be detected, as well as orthologous genes and more taxonomically distant related sequences. Similarly probes and/or primers of the invention can include additional nucleotides that serve as a label for detecting duplexes, for isolation of duplexed polynucleotides, or for cloning purposes.

[0427] Preferred probes and primers of the invention include isolated, purified, or recombinant polynucleotides containing a contiguous span of between at least 12 to at least 1000 nucleotides of any nucleotid sequence which is substantially similar, and preferably has at least between 70% and 99% sequence identity to any one of SEQ ID NOs: 1 to 1597, 5927, 5940, 5941, 5945-5958 and further of any nucleotide sequence which is substantially similar, and preferably has at least between 70% and 99% sequence identity to any one of SEQ ID NO: 1598 to 2672, 5959, 5972, 5973, 5977-5990 and 6001 representing promoter sequences, or the complements thereof, with each individual number of nucleotides within this range also being part of the invention. Preferred are isolated, purified, or recombinant polynucleotides containing a contiguous span of at least 12, 15, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 750, or 1000 nucleotides of any nucleotide sequence which is substantially similar, and preferably has at least between 70% and 99% sequence identity to any one of SEQ ID NOs: 1 to 1597, 5927, 5940, 5941, 5945-5958 and further of any nucleotide sequence which is substantially similar, and preferably has at least between 70% and 99% sequence identity to any one of SEQ ID NO: 1598 to 2672, 5959, 5972, 5973, 5977-5990 and 6001 representing promoter sequences, or the complements thereof. The appropriate length for primers and probes will vary depending on the application. For use as PCR primers, probes are 12-40 nucleotides, preferably 18-30 nucleotides long. For use in mapping, probes are 50 to 500 nucleotides, preferably 100-250 nucleotides long. For use in Southern hybridizations, probes as long as several kilobases can be used. The appropriate length for primers and probes under a particular set of assay conditions may be empirically determined by one of skill in the art.

[0428] The primers and probes can be prepared by any suitable method, including, for example, cloning and restriction of appropriate sequences and direct chemical synthesis by a method such as the phosphodiester method of Narang et al. (Meth Enzymol 68: 90 (1979)), the diethylphosphoramidite method, the triester method of Matteucci et al. (J Am Chem Soc 103: 3185 (1981)), or according to Urdea et al. (Proc Natl Acad 80: 7461 (1981)), the solid support method described in EP 0 707 592, or using commercially available automated oligonucleotide synthesizers.

[0429] Detection probes are generally nucleotide sequences or uncharged nucleotide analogs such as, for example peptide nucleotides which are disclosed in International Patent Application WO 92/20702, morpholino analogs which are described in U.S. Pat. Nos. 5,185,444, 5,034,506 and 5,142,047. The probe may have to be rendered “non-extendable” such that additional dNTPs cannot be added to the probe. Analogs are usually non-extendable, and nucleotide probes can be rendered non-extendable by modifying the 3′ end of the probe such that the hydroxyl group is no longer capable of participating in elongation. For example, the 3′ end of the probe can be functionalized with the capture or detection label to thereby consume or otherwise block the hydroxyl group. Alternatively, the 3′ hydroxyl group simply can be cleaved, replaced or modified so as to render the probe non-extendable.

[0430] Any of the polynucleotides of the present invention can be labeled, if desired, by incorporating a label detectable by spectroscopic, photochemical, biochemical, immunochemical, or chemical means. For example, useful labels include radioactive substances (32P, 35S, 3H, 125I), fluorescent dyes (5-bromodesoxyuridine, fluorescein, acetylaminofluorene, digoxigenin) or biotin. Preferably, polynucleotides are labeled at their 3′ and 5′ ends. Examples of non-radioactive labeling of nucleotide fragments are described in the French patent No. FR-7810975 and by Urdea et al. (Nuc Acids Res 16:4937 (1988)). In addition, the probes according to the present invention may have structural characteristics such that they allow the signal amplification, such structural characteristics being, for example, branched DNA probes as described in EP 0 225 807.

[0431] A label can also be used to capture the primer so as to facilitate the immobilization of either the primer or a primer extension product, such as amplified DNA, on a solid support. A capture label is attached to the primers or probes and can be a specific binding member that forms a binding pair with the solid's phase reagent's specific binding member, for example biotin and streptavidin. Therefore depending upon the type of label carried by a polynucleotide or a probe, it may be employed to capture or to detect the target DNA. Further, it will be understood that the polynucleotides, primers or probes provided herein, may, themselves, serve as the capture label. For example, in the case where a solid phase reagent's binding member is a nucleotide sequence, it may be selected such that it binds a complementary portion of a primer or probe to thereby immobilize the primer or probe to the solid phase. In cases where a polynucleotide probe itself serves as the binding member, those skilled in the art will recognize that the probe will contain a sequence or “tail” that is not complementary to the target. In the case where a polynucleotide primer itself serves as the capture label, at least a portion of the primer will be free to hybridize with a nucleotide on a solid phase. DNA labeling techniques are well known in the art.

[0432] Any of the polynucleotides, primers and probes of the present invention can be conveniently immobilized on a solid support. Solid supports are known to those skilled in the art and include the walls of wells of a reaction tray, test tubes, polystyrene beads, magnetic beads, nitrocellulose strips, membranes, microparticles such as latex particles, sheep (or other animal) red blood cells, duracytes and others. The solid support is not critical and can be selected by one skilled in the art. Thus, latex particles, microparticles, magnetic or non-magnetic beads, membranes, plastic tubes, walls of microtiter wells, glass or silicon chips, sheep (or other suitable animal's) red blood cells and duracytes are all suitable examples. Suitable methods for immobilizing nucleotides on solid phases include ionic, hydrophobic, covalent interactions and the like. A solid support, as used herein, refers to any material that is insoluble, or can be made insoluble by a subsequent reaction. The solid support can be chosen for its intrinsic ability to attract and immobilize the capture reagent. Alternatively, the solid phase can retain an additional receptor that has the ability to attract and immobilize the capture reagent. The additional receptor can include a charged substance that is oppositely charged with respect to the capture reagent itself or to a charged substance conjugated to the capture reagent. As yet another alternative, the receptor molecule can be any specific binding member which is immobilized upon (attached to) the solid support and which has the ability to immobilize the capture reagent through a specific binding reaction. The receptor molecule enables the indirect binding of the capture reagent to a solid support material before the performance of the assay or during the performance of the assay. The solid phase thus can be a plastic, derivatized plastic, magnetic or non-magnetic metal, glass or silicon surface of a test tube, microtiter well, sheet, bead, microparticle, chip, sheep (or other suitable animal's) red blood cells, duracytes and other configurations known to those of ordinary skill in the art. The polynucleotides of the invention can be attached to or immobilized on a solid support individually or in groups of at least 2, 5, 8, 10, 12, 15, 20, or 25 distinct polynucleotides of the invention to a single solid support. hi addition, polynucleotides other than those of the invention may be attached to the same solid support as one or more polynucleotides of the invention.

[0433] The polynucleotides of the invention that are expressed or repressed in response to environmental stimuli such as, for example, stress or treatment with chemicals or pathogens or at different developmental stages can be identified by employing an array of nucleic acid samples, e.g., each sample having a plurality of oligonucleotides, and each plurality corresponding to a different plant gene, on a solid substrate, e.g., a DNA chip, and probes corresponding to nucleic acid expressed in, for example, one or more plant tissues and/or at one or more developmental stages, e.g., probes corresponding to nucleic acid expressed in seed of a plant relative to control nucleic acid from sources other than seed. Thus, genes that are upregulated or downregulated in the majority of tissues at a majority of developmental stages, or upregulated or downregulated in one tissue such as in seed, can be systematically identified. The probes may also correspond to nucleic acid expressed in respone to a defined treatment such as, for example, a treatment with a variety of plant hormones or the exposure to specific environmental conditions involving, for example, an abiotic stress or exposure to light.

[0434] Specifically, labeled rice cRNA probes were hybridized to the rice DNA array, expression levels were determined by laser scanning and then rice genes were identified that had a particular expression pattern. The rice oligonucleotide probe array consists of probes from over 18,000 unique rice genes, which covers approximately 40-50% of the genome. This genome array permits a broader, more complete and less biased analysis of gene expression.

[0435] Consequently, the invention also deals with a method for detecting the presence of a polynucleotide including a nucleotide sequence which is substantially similar to a nucleotide sequence given in SEQ ID NOs: 1 to SEQ ID NO: 6001, or a fragment or a variant thereof, or a complementary sequence thereto, in a sample, the method including the following steps of:

[0436] (a) bringing into contact a nucleotide probe or a plurality of nucleotide probes which can hybridize with a polynucleotide having a nucleotide sequence which is substantially similar to a nucleotide sequence given in SEQ ID NOs: 1 to SEQ ID NO: 6001, a fragment or a variant thereof, or a complementary sequence thereto and the sample to be assayed.

[0437] (b) detecting the hybrid complex formed between the probe and a nucleotide in the sample.

[0438] The invention further concerns a kit for detecting the presence of a polynucleotide including a nucleotide sequence which is substantially similar to a nucleotide sequence given in SEQ ID NOs: 1 to SEQ ID NO: 6001, a fragment or a variant thereof, or a complementary sequence thereto, in a sample, the kit including a nucleotide probe or a plurality of nucleotide probes which can hybridize with a nucleotide sequence included in a polynucleotide, which nucleotide sequence is substantially similar to a nucleotide sequence given in of SEQ ID NOs: 1 to SEQ ID NO: 6001, a fragment or a variant thereof, or a complementary sequence thereto and, optionally, the reagents necessary for performing the hybridization reaction.

[0439] In a first preferred embodiment of this detection method and kit, the nucleotide probe or the plurality of nucleotide probes are labeled with a detectable molecule. In a second preferred embodiment of the method and kit, the nucleotide probe or the plurality of nucleotide probes has been immobilized on a substrate.

[0440] The isolated polynucleotides of the invention can be used to create various types of genetic and physical maps of the genome of rice or other plants. Such maps are used to devise positional cloning strategies for isolating novel genes from the mapped crop species. The sequences of the present invention are also useful for chromosome mapping, chromosome identification, tagging of genes which are tissue-specifically expressed.

[0441] The isolated polynucleotides of the invention can further be used as probes for identifying polymorphisms associated with phenotypes of interest. Briefly, total DNA is isolated from an individual or isogenic line, cleaved with one or more restriction enzymes, separated according to mass, transferred to a solid support, and hybridized with a probe molecule according to the invention. The pattern of fragments hybridizing to a probe molecule is compared for DNA from different individuals or lines, where differences in fragment size signals a polymorphism associated with a particular nucleotide sequence according to the present invention. After identification of polymorphic sequences, linkage studies can be conducted. After identification of many polymorphisms using a nucleotide sequence according to the invention, linkage studies can be conducted by using the individuals showing polymorphisms as parents in crossing programs. Recombinants, F2 progeny recombinants or recombinant inbreds, can then be analyzed using the same restriction enzyme/hybridization procedure. The order of DNA polymorphisms along the chromosomes can be inferred based on the frequency with which they are inherited together versus inherited independently. The closer together two polymorphisms occur in a chromosome, the higher the probability that they are inherited together. Integration of the relative positions of polymorphisms and associated marker sequences produces a genetic map of the species, where the distances between markers reflect the recombination frequencies in that chromosome segment. Preferably, the polymorphisms and marker sequences are sufficiently numerous to produce a genetic map of sufficiently high resolution to locate one or more loci of interest.

[0442] The use of recombinant inbred lines for such genetic mapping is described for rice (Oh et al., Mol Cells 8:175 (1998); Nandi et al., Mol Gen Genet 255:1 (1997); Wang et al., Genetics 136:1421 (1994)), sorghum (Subudhi et al., Genome 43:240 (2000)), maize (Burr et al., Genetics 118:519 (1998); Gardiner et al., Genetics 134:917 (1993)), and Arabidopsis (Methods in Molecular Biology, Martinez-Zapater and Salinas, eds., 82:137-146, (1998)). However, this procedure is not limited to plants and can be used for other organisms such as yeast or other fungi, or for oomycetes or other protistans.

[0443] The nucleotide sequences of the present invention can also be used for simple sequence repeat identification, also known as single sequence repeat, (SSR) mapping. SSR mapping in rice has been described by Miyao et al. (DNA Res 3:233 (1996)) and Yang et al. (Mol Gen Genet 245:187 (1994)), and in maize by Ahn et al. (Mol Gen Genet 241:483 (1993)). SSR mapping can be achieved using various methods. In one instance, polymorphisms are identified when sequence specific probes flanking an SSR contained within an sequence of the invention are made and used in polymerase chain reaction (PCR) assays with template DNA from two or more individuals or, in plants, near isogenic lines. A change in the number of tandem repeats between the SSR-flanking sequence produces differently sized fragments (U.S. Pat. No. 5,766,847). Alternatively, polymorphisms can be identified by using the PCR fragment produced from the SSR-flanking sequence specific primer reaction as a probe against Southern blots representing different individuals (Refseth et al., Electrophoresis 18:1519 (1997)). Rice SSRs were used to map a molecular marker closely linked to a nuclear restorer gene for fertility in rice as described by Akagi et al. (Genome 39:205 (1996)).

[0444] The nucleotide sequences of the present invention can be used to identify and develop a variety of microsatellite markers, including the SSRs described above, as genetic markers for comparative analysis and mapping of genomes. The nucleotide sequences of the present invention can be used in a variation of the SSR technique known as inter-SSR (ISSR); which uses microsatellite oligonucleotides as primers to amplify genomic segments different from the repeat region itself (Zietkiewicz et al., Genomics 20:176 (1994)). ISSR employs oligonucleotides based on a simple sequence repeat anchored or not at their 5′- or 3′-end by two to four arbitrarily chosen nucleotides, which triggers site-specific annealing and initiates PCR amplification of genomic segments which are flanked by inversely orientated and closely spaced repeat sequences. In one embodiment of the present invention, microsatellite markers derived from the nucleotide sequences disclosed in the Sequence Listing, or substantially similar sequences or allelic variants thereof, may be used to detect the appearance or disappearance of markers indicating genomic instability as described by Leroy et al. (Electron. J Biotechnol, 3(2), at http://www.ejb.org (2000)), where alteration of a fingerprinting pattern indicated loss of a marker corresponding to a part of a gene involved in the regulation of cell proliferation. Microsatellite markers derived from nucleotide sequences as provided in the Sequence Listing will be useful for detecting genomic alterations such as the change observed by Leroy et al. (Electron. J Biotechnol, 3(2), supra (2000)) which appeared to be the consequence of microsatellite instability at the primer binding site or modification of the region between the microsatellites, and illustrated somaclonal variation leading to genomic instability. Consequently, the nucleotide sequences of the present invention are useful for detecting genomic alterations involved in somaclonal variation, which is an important source of new phenotypes.

[0445] In addition, because the genomes of closely related species are largely syntenic (that is, they display the same ordering of genes within the genome), these maps can be used to isolate novel alleles from wild relatives of crop species by positional cloning strategies. This shared synteny is very powerful for using genetic maps from one species to map genes in another. For example, a gene mapped in rice provides information for the gene location in maize and wheat.

[0446] The various types of maps discussed above can be used with the nucleotide sequences of the invention to identify Quantitative Trait Loci (QTLs) for a variety of uses, including marker-assisted breeding. Many important crop traits are quantitative traits and result from the combined interactions of several genes. These genes reside at different loci in the genome, often on different chromosomes, and generally exhibit multiple alleles at each locus. Developing markers, tools, and methods to identify and isolate the QTLs enables marker-assisted breeding to enhance traits of interest or suppress undesirable traits that interfere with a desired effect. The nucleotide sequences as provided in the Sequence Listing can be used to generate markers, including single-sequence repeats (SSRs) and microsatellite markers for QTLs of interest to assist marker-assisted breeding. The nucleotide sequences of the invention can be used to identify QTLs and isolate alleles as described by Li et al. in a study of QTLs involved in resistance to a pathogen of rice. (Li et al., Mol Gen Genet 261:58 (1999)). In addition to isolating QTL alleles in rice, other cereals, and other monocot and dicot crop species, the nucleotide sequences of the invention can also be used to isolate alleles from the corresponding QTL(s) of wild relatives. Transgenic plants having various combinations of QTL alleles can then be created and the effects of the combinations measured. Once an ideal allele combination has been identified, crop improvement can be accomplished either through biotechnological means or by directed conventional breeding programs. (Flowers et al., J Exp Bot 51:99 (2000); Tanksley and McCouch, Science 277:1063 (1997)).

[0447] In another embodiment the nucleotide sequences of the invention can be used to help create physical maps of the genome of maize, Arabidopsis and related species. Where the nucleotide sequences of the invention have been ordered on a genetic map, as described above, then the nucleotide sequences of the invention can be used as probes to discover which clones in large libraries of plant DNA fragments in YACs, PACs, etc. contain the same nucleotide sequences of the invention or similar sequences, thereby facilitating the assignment of the large DNA fragments to chromosomal positions. Subsequently, the large BACs, YACs, etc. can be ordered unambiguously by more detailed studies of their sequence composition and by using their end or other sequence to find the identical sequences in other cloned DNA fragments (Mozo et al., Nat Genet 22:271 (1999)). Overlapping DNA sequences in this way allows assembly of large sequence contigs that, when sufficiently extended, provide a complete physical map of a chromosome. The nucleotide sequences of the invention themselves may provide the means of joining cloned sequences into a contig, and are useful for constructing physical maps.

[0448] In another embodiment, the nucleotide sequences of the present invention may be useful in mapping and characterizing the genomes of other cereals. Rice has been proposed as a model for cereal genome analysis (Havukkala, Curr Opin Genet Devel 6:711 (1996)), based largely on its smaller genome size and higher gene density, combined with the considerable conserved gene order among cereal genomes (Ahn et al., Mol Gen Genet 241:483 (1993)). The cereals demonstrate both general conservation of gene order (synteny) and considerable sequence homology among various cereal gene families. This suggests that studies on the functions of genes or proteins from rice that are tissue-specifically expressed could lead to the identification of orthologous genes or proteins in other cereals, including maize, wheat, secale, sorghum, barley, millet, teff, milo, triticale, flax, gramma grass, Tripsacum sp., and teosinte. The nucleotide sequences according to the invention can also be used to physically characterize homologous chromosomes in other cereals, as described by Sarma et al. (Genome 43:191 (2000)), and their use can be extended to non-cereal monocots such as sugarcane, grasses, and lilies.

[0449] Given the synteny between rice and other cereal genomes, the nucleotide sequences of the present invention can be used to obtain molecular markers for mapping and, potentially, for positional cloning. Kilian et al. described the use of probes from the rice genomic region of interest to isolate a saturating number of polymorphic markers in barley, which were shown to map to syntenic regions in rice and barley, suggesting that the nucleotide sequences of the, invention derived from the rice genome would be useful in positional cloning of syntenic genes of interest from other cereal species. (Kilian, et al, Nucl Acids Res 23:2729 (1995); Kilian, et al., Plant Mol Biol 35:187 (1997)). Synteny between rice and barley has recently been reported in the area of the carrying malting quality QTLs (Han, et al., Genome 41:373 (1998)), and use of synteny between cereals for positional cloning efforts is likely to add considerable value to rice genome analysis. Likewise, mapping of the ligules region of sorghum was facilitated using molecular markers from a syntenic region of the rice genome. (Zwick, et al., Genetics 148:1983 (1998)).

[0450] Rice marker technology utilizing the nucleotide sequences of the present invention can also be used to identify QTL alleles for a trait of interest from a wild relative of cultivated rice, for example as described by Xiao, et al. (Genetics 150:899 (1998)). Wild relatives of domesticated plants represent untapped pools of genetic resources for abiotic and biotic stress resistance, apomixis and other breeding strategies, plant architecture, determinants of yield, secondary metabolites, and other valuable traits. In rice, Xiao et al. (supra) used molecular markers to introduce an average of approximately 5% of the genome of a wild relative, and the resulting plants were scored for phenotypes such as plant height, panicle length and 1000-grain weight. Trait-improving alleles were found for all phenotypes except plant height, where any change is considered negative. Of the 35 trait-improving alleles, Xiao et al. found that 19 had no effect on other phenotypes whereas 16 had deleterious effects on other traits. The nucleotide sequences of the invention such as those provided in the Sequence Listing can be employed as molecular markers to identify QTL alleles for trait of interest from a wild relative, by which these valuable traits can be introgressed from wild relatives using methods including, but not limited to, that described by Xiao et al. ((1998) supra). Accordingly, the nucleotide sequences of the invention can be employed in a variety of molecular marker technologies for yield improvement.

[0451] Following the procedures described above to identify polymorphisms, and using a plurality of the nucleotide sequences of the invention, any individual (or line) can be genotyped. Genotyping a large number of DNA polymorphisms such as single nucleotide polymorphisms (SNPs), in breeding lines makes it possible to find associations between certain polymorphisms or groups of polymorphisms, and certain phenotypes. In addition to sequence polymorphisms, length polymorphisms such as triplet repeats are studied to find associations between polymorphism and phenotype. Genotypes can be used for the identification of particular cultivars, varieties, lines, ecotypes, and genetically modified plants or can serve as tools for subsequent genetic studies of complex traits involving multiple phenotypes.

[0452] The patent publication WO95/35505 and U.S. Pat. Nos. 5,445,943 and 5,410,270 describe scanning multiple alleles of a plurality of loci using hybridization to arrays of oligonucleotides. The nucleotide sequences of the invention are suitable for use in genotyping techniques useful for each of the types of mapping discussed above.

[0453] In a preferred embodiment, the nucleotide sequences of the invention are useful for identifying and isolating a least one unique stretch of protein-encoding nucleotide sequence. The nucleotide sequences of the invention are compared with other coding sequences having sequence similarity with the sequences provided in the Sequence Listing, using a program such as BLAST. Comparison of the nucleotide sequences of the invention with other similar coding sequences permits the identification of one or more unique stretches of coding sequences encoding proteins that are tissue-specifically expressed and that are not identical to the corresponding coding sequence being screened. Preferably, a unique stretch of coding sequence of about 25 base pairs (bp) long is identified, more preferably 25 bp, or even more preferably 22 bp, or 20 bp, or yet even more preferably 18 bp or 16 bp or 14 bp. In one embodiment, a plurality of nucleotide sequences is screened to identify unique coding sequences accroding to the invention. In one embodiment, one or more unique coding sequences accroding to the invention can be applied to a chip as part of an array, or used in a non-chip array system. In a further embodiment, a plurality of unique coding sequences accroding to the invention is used in a screening array. In another embodiment, one or more unique coding sequences accroding to the invention can be used as immobilized or as probes in solution. In yet another embodiment, one or more unique coding sequences accroding to the invention can be used as primers for PCR. In a further embodiment, one or more unique coding sequences accroding to the invention can be used as organism-specific primers for PCR in a solution containing DNA from a plurality of sources.

[0454] In another embodiment unique stretches of nucleotide sequences according to the invention are identified that are preferably about 30 bp, more preferably 50 bp or 75 bp, yet more preferably 100 bp, 150 bp, 200 bp, 250, 500 bp, 750 bp, or 1000 bp. The length of an unique coding sequence may be chosen by one of skill in the art depending on its intended use and on the characteristics of the nucleotide sequence being used. In one embodiment, unique coding sequences accroding to the invention may be used as probes to screen libraries to find homologs, orthologs, or paralogs. In another embodiment, unique coding sequences accroding to the invention may be used as probes to screen genomic DNA or cDNA to find homologs, orthologs, or paralogs. In yet another embodiment, unique coding sequences according to the invention may be used to study gene evolution and genome evolution.

[0455] The invention also provides a computer readable medium having stored thereon a data structure containing nucleic acid sequences having at least 70% sequence identity to a nucleic acid sequence selected from those listed in SEQ ID Nos: 1-6001, as well as complementary, ortholog, and variant sequences thereof Storage and use of nucleic acid sequences on a computer readable medium is well known in the art. See for example U.S. Pat. Nos. 6,023,659; 5,867,402; 5,795,716. Examples of such medium include, but are not limited to, magnetic tape, optical disk, CD-ROM, random access memory, volatile memory, non-volatile memory and bubble memory. Accordingly, the nucleic acid sequences contained on the computer readable medium may be compared through use of a module that receives the sequence information and compares it to other sequence information. Examples of other sequences to which the nucleic acid sequences of the invention may be compared include those maintained by the National Center for Biotechnology Information (NCBI)(http://www.ncbi.nlm.nih.gov/) and the Swiss Protein Data Bank. A computer is an example of such a module that can read and compare nucleic acid sequence information. Accordingly, the invention also provides the method of comparing a nucleic acid sequence of the invention to another sequence. For example, a sequence of the invention may be submitted to the NCBI for a Blast search as described herein where the sequence is compared to sequence information contained within the NCBI database and a comparison is returned. The invention also provides nucleic acid sequence information in a computer readable medium that allows the encoded polypeptide to be optimized for a desired property. Examples of such properties include, but are not limited to, increased or decreased: thermal stability, chemical stability, hydrophylicity, hydrophobicity, and the like. Methods for the use of computers to model polypeptides and polynucleotides having altered activities are well known in the art and have been reviewed. (Lesyng et al., 1993; Surles et al., 1994; Koehl et al., 1996; Rossi et al., 2001).

EXAMPLE 1

GeneChip® Standard Protocol

[0456] 1.1 Quantitation of Total RNA

[0457] Total RNA from plant tissue is extracted and quantified.

[0458] 30 Quantify total RNA using GeneQuant

[0459] 1OD260=40 mg RNA/ml; A260/A280=1.9 to about 2.1

[0460] 2. Run gel to check the integrity and purity of the extracted RNA

[0461] 1.2 Synthesis of Double-stranded cDNA

[0462] Gibco/BRL SuperScript Choice System for cDNA Synthesis (Cat#1B090-019) was employed to prepare cDNAs. T7-(dT)24 oligonucleotides were prepared and purified by HPLC. (5′-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24-3′; SEQ ID NO:4709).

[0463] 1.2.1 Step 1. Primer hybridization:

[0464] Incubate at 70° C. for 10 minutes

[0465] Quick spin and put on ice briefly

[0466] 1.2.2 Step 2. Temperature adjustment:

[0467] Incubate at 42° C. for 2 minutes

[0468] 1.2.3 Step 3. First strand synthesis:

[0469] DEPC-water-1:1

[0470] RNA (10:g final)-10:1

[0471] T7=(dT)24 Primer (100 pmol final)-1:1 pmol

[0472] 5×1st strand cDNA buffer-4:1

[0473] 0.1M DTT (10 mM final)-2:1

[0474] 10 mM dNTP mix (500:M final)-1:1

[0475] Superscript II RT 200 U/:1-1:1

[0476] Total of 20:1

[0477] Mix well

[0478] Incubate at 42° C. for 1 hour

[0479] 1.2.4 Step 4. Second strand synthesis:

[0480] Place reactions on ice, quick spin

[0481] DEPC-water-91:1

[0482] 5×2nd strand cDNA buffer-30:1

[0483] 10 mM dNTP mix (250 mM final)-3:1

[0484]

E. coli
DNA ligase (10 U/:1)-1:1

[0485]

E. coli
DNA polymerase 1-10 U/:1-4:1

[0486] RnaseH 2U/:1-1:1

[0487] T4 DNA polymerase 5 U/:1-2:1

[0488]

0
.5 M EDTA (0.5 M final)-10:1

[0489] Total 162:1

[0490] Mix/spin down/incubate 16° C. for 2 hours

[0491] 1.2.5 Step 5. Completing the reaction:

[0492] Incubate at 16° C. for 5 minutes

[0493] 1.3 Purification of Double Stranded cDNA

[0494] 1. Centrifuge PLG (Phase Lock Gel, Eppendorf 5 Prime Inc., pI-188233) at 14,000×, transfer 162:1 of cDNA to PLG

[0495] 2. Add 162:1 of Phenol:Chloroform:Isoamyl alcohol (pH 8.0), centrifuge 2 minutes

[0496] 3. Transfer the supernatant to a fresh 1.5 ml tube, add

[0497] Glycogen (5 mg/ml) 2

[0498] 0.5 M NH4OAC (0.75×Vol) 120

[0499] ETOH (2.5×Vol, −20° C.) 400

[0500] 4. Mix well and centrifuge at 14,000× for 20 minutes

[0501] 5. Remove supernatant, add 0.5 ml 80% EtOH (−20° C.)

[0502] 6. Centrifuge for 5 minutes, air dry or by speed vac for 5-10 minutes

[0503] 7. Add 44:1 DEPC H2O

[0504] Analyze of quantity and size distribution of cDNA

[0505] Run a gel using 1:1 of the double-stranded synthesis product

[0506] 1.4 Synthesis of Biotinylated cRNA

[0507] (use Enzo BioArray High Yield RNA Transcript Labeling Kit Cat#900182)

2Purified cDNA22:1 10X Hy buffer4:110X biotin ribonucleotides4:110X DTT4:110X Rnase inhibitor mix4:120X T7 RNA polymerase2:1Total40:1

[0508] Centrifuge 5 seconds, and incubate for 4 hours at 37° C.

[0509] Gently mix every 30-45 minutes

[0510] 1.5 Purification and Quantification of cRNA

[0511] (use Qiagen Rneasy Mini kit Cat# 74103)

3cRNA 40:1DEPC H2O 60:1RLT buffer350:1mix by vortexingEtOH250:1mix by pipettingTotal700:1Wait 1 minute or more for the RNA to stickCentrifuge at 2000 rpm for 5 minutesRPE buffer500:1Centrifuge at 10,000 rpm for 1 minuteRPE buffer500:1Centrifuge at 10,000 rpm for 1 minuteCentrifuge at 10,000 rpm for 1 minute to dry the columnDEPC H2O 30:1Wait for 1 minute, then elute cRNA from by centrifugation, 10 K 1 minuteDEPC H2O 30:1

[0512] Repeat previous step

[0513] Determine concentration and dilute to 1:g/:1 concentration

41.6 Fragmentation of cRNAcRNA (1:g/:1)15:1 5X Fragmentation Buffer*6:1DEPC H2O9:130:1 *5x Fragmentation Buffer1M Tris (pH8.1) 4.0 mlMgOAc0.64 g KOAC0.98 g DEPC H2OTotal 20 mlFilter Sterilize

[0514] 1.7 Array Wash and Staining

[0515] Stringent Wash Buffer**

[0516] Non-Stringent Wash Buffer***

[0517] SAPE Stain****

[0518] Antibody Stain*****

[0519] Wash on fluidics station using the appropriate antibody amplification protocol

[0520] **Stringent Buffer: 12×MES 83.3 ml, 5 M NaCl 5.2 ml, 10% Tween 1.0 ml, H2O 910 ml, Filter Sterilize

[0521] ***Non-Stringent Buffer: 20×SSPE 300 ml, 10% Tween 1.0 ml, H2O 698 ml, Filter Sterilize, Antifoam 1.0.

[0522] ****SAPE stain: 2×Stain Buffer 600:1, BSA 48:1, SAPE 12:1, H2O 540:1.

[0523] *****Antibody Stain: 2×Stain Buffer 300:1, H2O 266.4:1, BSA 24:1, Goat IgG 6:1, Biotinylated Ab 3.6:1

EXAMPLE 2

Characterization of Gene Expression Profiles During Oryza Plant Development

[0524] A rice gene array (proprietary to Affymetrix) and probes derived from rice RNA extracted from different tissues and developmental stages were used to identify the expression profile of genes on the chip. The rice array contains over 23,000 genes (approximately 18,000 unique genes) or roughly 50% of the rice genome and is similar to the Arabidopsis GeneChip® (Affymetrix) with the exception that the 16 oligonucleotide probe sets do not contain mismatch probe sets. The level of expression is therefore determined by internal software that analyzes the intensity level of the 16 probe sets for each gene. The highest and lowest probes are removed if they do not fit into a set of predefined statistical criteria and the remaining sets are averaged to give an expression value. The final expression values are normalized by software, as described below. The advantages of a gene chip in such an analysis include a global gene expression analysis, quantitative results, a highly reproducible system, and a higher sensitivity than Northern blot analyses.

[0525] Total RNA was isolated from 29 samples at different developmental stages (see Table 2).

5TABLE 2germgerminating seed rootgerminating seed leaf3-4 leaf arialroot tilleringleaf tilleringarial tilleringpanicle 1-3panicle 4-7panicle 8-14panicle 15-20Panicle panicle emergenceleaf bootingarial bootingroot bootingroot panicle emergencestem panicle emergenceInflorescencestem matureroot matureleaf maturestem senescenceleaf senescenceEmbryoEndospermseed coatAleuroneseed milkseed softseed hard

Example 2.1

Preparation of RNA

[0526] Total RNA is prepared from the frozen samples using Qiagen RNeasy columns (Valencia, Calif.) and precipitated overnight at −20° C. after the addition of 0.25 volumes of 10M LiCl2. Pellets are washed with 70% EtOH, air dried and resuspended in RNase-free water.

[0527] Alternatively, total RNA is prepared using the “Pine Tree method” (Chang et al., 1993) where 1 gram of the ground frozen sample is added to 5 ml of extraction buffer (2% hexadectltrimethylamminium bromide, 2% polyvilylpyrrolidone K 30, 100 mM Tris-HCl (pH 8.0), 25 mM EDTA, 2.0 M NaCl, 0.5 g/L spermidine and 2% beta-mercaptoethanol, previously warmed to 65° C.) and mixed by inversion and vortexing. The solution is extracted two times with an equal volume of chloroform:isoamyl alcohol and precipitated overnight at −20° C. after the addition of 0.25 volumes of 10M LiCl2. Pellets are washed with 70% EtOH, air dried and resuspended in RNase-free water.

Example 2.2

Preparation of cDNA

[0528] Total RNA (5 μg) from each sample is reverse transcribed. First strand cDNA synthesis is accomplished at 42° C. for one hour using 5 μg of total RNA from Arabidopsis tissue, 100 pmol of an oligo dT(24) primer containing a 5′ T7 RNA polymerase promoter sequence [5′-GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24-3′; SEQ ID NO:4710] synthesized by Genosys, and SuperScript II reverse transcriptase (RT) (Gibco/BRL).

[0529] First strand cDNA synthesis reactions performed with SuperScript II RT are carried out according to the manufacturer's recommendations using 50 mM Tris-HCl (pH 8.3), 75 mM KCl, 3 mM MgCl2, 10 mM dithiotreitol (DTT), 0.5 mM dNTPs, and 200 units of RT enzyme.

[0530] The second cDNA strand is synthesized using 40 units of E. coli DNA polymerase I, 10 units of E. coli DNA ligase, and 2 units of RNase H in a reaction containing 25 mM Tris-HCl (pH 7.5), 100 mM KCl, 5 mM MgCl2, 10 mM (NH4)SO4, 0.15 mM β-NAD+, 1 mM dNTPs, and 1.2 mM DTT. The reaction proceeded at 16° C. for 2 hours and is terminated using EDTA. Double-stranded cDNA products are purified by phenol/chloroform extraction and ethanol precipitation.

Example 2.3

Preparation of Biotinylated cRNA Probes

[0531] Synthesized cDNAs (approximately 0.1 μg) are used as templates to produce biotinylated cRNA probes by in vitro transcription using T7 RNA Polymerase (ENZO BioArray High Yield RNA Transcript Labeling Kit). Labeled cRNAs are purified using affinity resin (Qiagen RNeasy Spin Columns) and randomly fragmented to produce molecules of approximately 35 to 200 bases. Fragmentation is achieved by incubation at 94° C. for 35 minutes in a buffer containing 40 mM Tris-acetate, pH 8.1, 100 mM potassium acetate, and 30 mM magnesium acetate.

Example 2.4

Array Hybridization

[0532] The labeled samples are mixed with 0.1 mg/mL sonicated herring sperm DNA in a hybridization buffer containing 100 mM 2-N-Morpholino-ethane-sulfonic acid (MES), 1 M NaCl, 20 mM EDTA, 0.01% Tween 20, denatured at 99° C. for 5 min, and equilibrated at 45° C. for 5 min before hybridization. The hybridization mix is then transferred to the Arabidopsis GeneChip genome array (Affymetrix) cartridge and hybridized at 45° C. for 16 h on a rotisserie at 60 rpm.

[0533] The hybridized arrays are then rinsed and stained in a fluidics station (Affymetrix). They are first rinsed with wash buffer A (6×SSPE (0.9 M NaCl, 0.06 M NaH2PO4, 0.006 M EDTA), 0.01% Tween 20, 0.005% Antifoam) at 25° C. for 10 min and incubated with wash buffer B (100 mM MES, 0.1 M NaCl, 0.01% Tween 20) at 50° C. for 20 min, then stained with Streptavidin Phycoerythrin (SAPE) (100 mM MES, 1 M NaCl, 0.05% Tween 20, 0.005% Antifoam, 10 mg/mL SAPE 2 mg/mL BSA) at 25° C. for 10 min, washed with wash buffer A at 25° C. for 20 min and stained with biotinylated anti-streptavidin antibody at 25° C. for 10 min. After staining, arrays are stained with SAPE at 25° C. for 10 min and washed with wash buffer A at 30° C. for 30 min. The probe arrays are scanned twice and the intensities are averaged with a Hewlett-Packard GeneArray Scanner.

[0534] GeneSpring software was used to analyze relative expression levels and compare tissue-specificity of gene expression.

Example 2.5

Data Analysis

[0535] GeneChip Suite 3.2 (Affymetrix) is used for data normalization. The overall intensity of all probe sets of each array is scaled to 100 so hybridization intensity of all arrays is equivalent. False positives are defined based on experiments in which samples are split, hybridized to GeneChip expression arrays and the results compared. A false positive is indicated if a probe set is scored qualitatively as an “Increase” or “Decrease” and quantitatively as changing by at least two fold and average difference is greater than 25. A significant change is defined as 2-fold change or above with an expression baseline of 25, which is determined as the threshold level according to the scaling.

[0536] The expression data of selected genes are then normalized. Briefly, the median of the expression level within each chip is calculated, and the difference between the average difference and median average difference is used as new value to measure the gene expression level. The expression data are also adjusted across different chip experiments according to the calculated medium. Normalized data (genes and arrays) are analysed by the self organization map (SOM) method (Tamayo et al., P.N.A.S., 96:2907 (1999), and then subject to heirachy cluster analysis (Eisen et al., P.N.A.S., 95:14863 (1998). By the cluster analysis, genes and chip experiments are clustered according to the expression levels.

[0537] 2.5.1. Promoter Analysis

[0538] Generally, a database with rice contigs and Perl scripts were employed to determine which rice contig contained sequences from the identified genes. Five gene prediction programs were analyzed on these contigs and the rice sequence was blasted to these predictions. The prediction that contained the entire rice sequence within an exon was used to find the promoter that was adjacent to the first exon.

[0539] For Oryza genes that were constitutively expressed, a cut off value of 250 in all samples was used to screen for genes that were expressed in all tissues (range of 250-8638). The background level (gene not expressed) was 50. This analysis resulted in the identification of 618 genes that were constitutively expressed (Table 1A). The ORFs for 398 of those genes are listed in SEQ ID NOs:1-398 and the promoters for some of those genes in SEQ ID NOs:1598-1885 and 5960-5971, respectively. Based on expression analysis, 150 genes were selected (Table 1B) and 120 genes of those considered for further analysis (Table 1C). Primers were prepared to isolate 38 promoters from the 120 genes (Table 12). Preferred constitutively expressed genes include but are not limited to those having SEQ ID NOs:7, 10, 12, 14, 22, 53, 54, 63, 84, 102, 103, 123, 128, and 136, and orthologs thereof, e.g., promoters having SEQ ID NOs:1647, 1634, 1606, 1684, 1631, 1662, 1691, 1630, 1603, 1663, 1604, or an ortholog thereof. Further preferred constitutively expressed genes include but are not limited to those having SEQ ID NOs: 5928, 5929, 5930, 5931, 5932, 5933, 5934, 5935, 5936, 5937, 5938, and 5939, and orthologs thereof, e.g., promoters having SEQ ID NOs: 5960, 5961, 5962, 5963, 5964, 5965, 5966, 5967, 5968, 5969, 5970, and 5971, or an ortholog thereof.

[0540] For Oryza genes expressed primarily in seed tissue, all genes that were expressed at 50 or above in at least one of the 29 tissues (about 13,450 genes) were filtered to be expressed less than 50 in all non-seed related samples, not including aleurone, seed coat, embryo, endosperm and seed milk, soft dough and hard dough. These analyses resulted in the identification of 812 genes that were preferentially expressed in seed tissue (Table 2A). The ORFs for 578 of those genes are listed in SEQ ID NOs: 1020-1567 and the promoters for some of those in SEQ ID NOs:2275-2672. Preferred seed-specific promoters are those from genes having SEQ ID NOs:1021-1023, 1028, 1044, 1033, 1068, 1403, 1081, 1048, 1046, 1097, 1309, 1147, 1038, 1107, 1161, 1162, 1505, and 1026 and the orthologs thereof, e.g., promoters having SEQ ID NOs:2275-2277, 2279, 2289, 2283, 2317, 2293, 2291, 2464, 2364, 2286, 2325, 2376, 2377, and 2586, and an ortholog thereof. Further preferred are those from genes having SEQ ID NOs: 5927, 5940, 5941, and 5945-5958 and the orthologs thereof, e.g., promoters having SEQ ID NOs: , 5959, 5972, 5973, 5977-5990 and 6001, and an ortholog thereof.

[0541] For seed-specific genes that were expressed only in a particular part of a seed, e.g., embryo, endosperm, aleurone, genes that were expressed at 50 or above in the particular sample but less than 50 in all other samples absent that particular tissue sample were selected. Thus, embryo-specific, endosperm-specific and aleurone-specific genes were identified (Tables 3-5). Preferred aleurone-specific promoters are those from genes having SEQ ID NOs:1045, 1165, 1324, 1150, 1547, 1373, and 5927 and the orthologs thereof, e.g., promoters having SEQ ID NOs:2290, 2380, 2366, 2627 and 5959, or an ortholog thereof. Preferred embryo-specific promoters are from genes having SEQ ID NOs:1294, 1346, 1325, 1412, 1079 and the orthologs thereof, e.g., a promoter having SEQ ID NO:2315 or an ortholog thereof. Further preferred embryo-specific promoters are from genes having SEQ ID NOs: 5940 and 5941 and the orthologs thereof, e.g., a promoter having SEQ ID NO: 5972 and 5973, or an ortholog thereof. Preferred endosperm-specific promoters are from genes having SEQ ID NOs:1043 and 1215 and the orthologs thereof, e.g., a promoter having SEQ ID NO:2411 or an ortholog thereof.

[0542] A cut off value of less than 50 in all non-root samples was used to screen for Oryza genes that were expressed in a root-specific manner. The background level (gene not expressed) was 50. Genes that were expressed at greater than 50 in one or more of all root samples were selected. This analysis resulted in the identification of 265 genes that were expressed primarily in root tissue (Table 8A). The ORFs for 219 of these genes is shown in SEQ ID NOs:801-1019 and some of the promoters in SEQ ID NOs:2144-2274.

[0543] For Oryza genes expressed primarily in Oryza panicle tissue (flower and pollen), all genes that were expressed at 50 or above on at least one of the rice panicle chips (about 10,597 genes) were filtered to be expressed less than 50 in (i) leaf samples at germinating seed, tillering, mature and senescence stages; (ii) root samples at germinating seed, tillering, booting, mature and panicle emergence stages; (iii) stem samples at panicle emergence and senescence stages; and (iv) seed hard dough and aleurone samples. These analyses resulted in the identification of 335 genes that were preferentially expressed in panicle tissue (Table 7A). The ORFs for 256 of those genes is listed in SEQ ID NOs:465-720 and some of the promoters in SEQ ID NOs:1919-2085 (for panicle). Preferred panicle-specific promoters are those from genes having SEQ ID NOs:689, 511, 482, 467 and 468, and the orthologs thereof, e.g., promoters having SEQ ID NOs:1920-1921, 2054, or an ortholog thereof.

[0544] Eighty pollen-specific Oryza genes were identified (Table 9A and SEQ ID NOs:721-800) as well some pollen-specific promoters (SEQ ID NOs:2086-2143 Preferred pollen-specific promoter are those from genes having SEQ ID NOs:723-726 and 728 and the orthologs thereof, e.g., promoters having SEQ ID NOs:2088-2090, or an ortholog thereof.

[0545] For Oryza genes expressed primarily in leaf and stem, i.e., green tissue, all genes that were expressed at 50 or above in at least three of the tissues (about 12,563 genes) were filtered to be expressed more than 50 in arial 3-4 leaf stage samples; less than 50 in all seed samples (day 0-19); and less than 50 in aleurone, embryo, endosperm and pollen samples. Analysis revealed 90 genes expressed in arial tissue at tillering stages that were expressed 2 fold greater than in root tissue at tillering stage (Table 6A). The ORFs for 66 of those genes are shown in SEQ ID NOs:399-464 and some of the promoters for those genes in SEQ ID NOs:1886-1918. Preferred green tissue-specific promoters are those from genes having SEQ ID NOs:401, 405, 408, 410, 416, 417, 419, 433, 438, 447 and 454 and orthologs thereof, e.g., promoters having SEQ ID NOs:1903, 1910, 1897, 1890, 1891, or an ortholog thereof.

[0546] Leaf-specific but not fruit-specific genes were determined by filtering the genes as follows: relative expression of less than 50 in all of the seed samples, and greater than 50 in the leaf at tillering stage sample. This analysis resulted in the identification of five rice sequences: 5942/5991 (RF1; OS009452.1), OS012592.1, OS019946, OS001669.1, and OS002989.1. The promoter for one such gene is shown in SEQ ID NOs: 5974 and 5996, respectively.. The promoter sequence for two leaf-specific but not pollen-specific genes is shown in Table 15B.

EXAMPLE 3

Promoter Analysis

[0547] The gene chip experiment described above are designed to uncover genes that are constitutively or tissue specifically (tissue-preferentially) expressed. Candidate promoters are identified based upon the expression profiles of the associated transcripts representatives of which are provided in SEQ ID NOs: 1598-1885 and SEQ ID NOs: 1886-2672, respectively and further in SEQ ID Nos: 5960-5971, 5972-5990, and 5996 -6001.

[0548] Candidate promoters are obtained by PCR and fused to a GUS reporter gene containing an intron. Both histochemical and fluormetric GUS assays are carried out on stably transformed rice and maize plants and GUS activity is detected in the transformants.

[0549] Further, transient assays with the promoter::GUS constructs are carried out in rice embryogenic callus and GUS activity is detected by histochemical staining according the protocol described below (see Example 12).

Example 3.1

Construction of Binary Promoter::Reporter Plasmids

[0550] To construct a binary promoter::reporter plasmid for rice transformation a vector containing a candidate promoter of interest (i.e., the DNA sequence 5′ of the initiation codon for the gene of interest) is used, which results from recombination in a BP reaction between a PCR product using the promoter of interest as a template and pDONR201™, producing an entry vector. The regulatory/promoter sequence is fused to the GUS reporter gene (Jefferson et al, 1987) by recombination using GATEWAY™ Technology according to manufacturers protocol as described in the Instruction Manual (GATEWAY™ Cloning Technology, GIBCO BRL, Rockville, Md. http://www.lifetech.com/).

[0551] Briefly, the Gateway Gus-intron-Gus (GIG)/NOS expression cassette is ligated into pNOV2117 binary vector in 5′ to 3′ orientation. The 4.1 kB expression cassette is ligated into the Kpn-I site of pNOV2117, then clones are screened for orientation to obtain pNOV2346, a GATEWAY™ adapted binary destination vector.

[0552] The promoter fragment in the entry vector is recombined via the LR reaction with the binary destination vector containing the GUS coding region with an intron that has an attR site 5′ to the GUS reporter, producing a binary vector with a promoter fused to the GUS reporter (pNOVCANDProm). The orientation of the inserted fragment is maintained by the att sequences and the final construct is verified by sequencing. The construct is then transformed into Agrobacterium tumefaciens strains by electroporation as described herein below.

Example 3.2

Transient Expression Analysis of Candidate Promoters in Rice Embryogenic Callus

[0553] 3.2.1 Materials

[0554] Embryogenic rice callus (Kaybonett cultivar)

[0555] LBA 4404 Agrobacterium strains

[0556] KCMS liquid media for re-suspending bacterial pellet

[0557] 200 mM stock (40mg/ml) Acetosyringone

[0558] Sterile filter paper discs (8.5 mm in diameter)

[0559] LB spec liquid culture

[0560] MS-CIM media plates

[0561] MS-AS plates (co-cultivation plates)

[0562] MS-Tim plates (recovery plates)

[0563] Gus staining solution

[0564] 3.2.2 Methods

[0565] 3.2.2.1 Induction of Embryogenic Callus

[0566] 1. Sterilize mature Kaybonett rice seeds in 40% ultra Clorox, 1 drop Tween 20, for 40 min.

[0567] 2. Rinse with sterile water and plate on MS-CIM media (12 seeds/plate)

[0568] 3. Grow in dark for four weeks.

[0569] 4. Isolate embryogenic calli from scutellum to MS-CIM

[0570] 5. Let grow in dark 8 days before use for transformation

[0571] 3.2.2.2 Agrobacterium Preparation and Induction

[0572] 1. Start 6 mL shaking cultures of LBA4404 Agrobacterium strains harboring rice promoter binary plasmids.

[0573] 2. Grow the cultures at room temperature for 48 hrs in the rotary shaker.

[0574] 3. Spin down the cultures at 8,000 rpm at 4° C. and re-suspend bacterial pellets in 10 ml of KCMS media supplemented with 100 □M Acetosyringone.

[0575] 4. Place in the shaker at room temp for 1 hr for induction of Agrobacterium virulence genes.

[0576] 5. In a sterile hood dilute Agrobacterium cultures 1:3 in KSMS media and transfer diluted cultures into deep petri dishes.

[0577] 3.2.2.3 Inoculation of Plant Material and Staining

[0578] 6. In a sterile hood transfer embryogenic callus into diluted Agrobacerium solution and incubate for 30 minutes.

[0579] 7. In a sterile hood blot callus tissue on sterile filter paper and transfer on MS-AS plates.

[0580] 8. Co-culture plates in 22° C. growth chamber in the dark for two days.

[0581] 9. In a sterile hood transfer callus tissue to MS-Tim plates for the tissue recovery (the presence of Timentin will prevent Agrobacterium growth).

[0582] 10. Incubate tissue on MS-Tim media for two days at 22° C. in the dark.

[0583] 11. Remove callus tissue from the plates and stain for 48 hrs. in GUS staining solution.

[0584] 12. De-stain tissue in 70% EtOH for 24 hours.

[0585] 3.2.2.4 Recipies

[0586] KCMS media (liquid), pH to 5.5

[0587] 100 ml/l MS Major Salts, 10 ml/l MS Minor Salts, 5 ml/l MS iron stock, 0.5M K2HPO4, 0.1 mg/ml Myo-Inositol,

[0588] 1.3 μg/ml Thiamine, 0.2 g/ml 2,4-D (1 mg/ml), 0.1 g/ml Kinetin, 3% Sucrose, 100 □M Acetosyringone

[0589] MS-CIM media, pH 5.8

[0590] MS Basal salt (4.3 g/L), B5 Vitamins (200×) (5 m/L), 2% Sucrose (20 g/L), Proline (500 mg/L), Glutamine (500 mg/L), Casein Hydrolysate (300 mg/L), 2 □g/ml 2,4-D, Phytagel (3 g/L)

[0591] MS-As Medium, pH 5.8

[0592] MS Basal salt (4.3 g/L), B5 Vitamins (200×) (5 m/L), 2% Sucrose (20 g/L), Proline (500 mg/L), Glutamine (500 mg/L), Casein Hydrolysate (300 mg/L), 2 □g/ml 2,4-D, Phytagel (3 g/L), 200 □M Acetosyringone

[0593] MS-Tim media, pH 5.8

[0594] MS Basal salt (4.3 g/L), B5 Vitamins (200×) (5 m/L), 2% Sucrose (20 g/L), Proline (500 mg/L), Glutamine (500 mg/L), Casein Hydrolysate (300 mg/L), 2□g/ml 2,4-D, Phytagel (3 g/L), 400 mg/l Timentin

[0595] Gus staining solution, pH 7

[0596] 0.3M Mannitol; 0.02M EDTA, pH=7.0; 0.04 NaH2PO4; 1 mM x-gluc

[0597] The binary Promoter::Reporter Plasmids described in Example 3 above can also be used for stable transformation of rice and maize plants according to the protocols provided in Examples 10.1 and 10.2, respectively.

6Pro-moterSEQBinaryleafleaf-2rootroot-2flowerseedantherpollenRiceNameIDVectory leafo leafstemroothuskkernelsilkpollencommentsMaizeRC11pNOV6043−−+−−RiceRC11pNOV6043−+−+baz,−−Maizee, sRC25963pNOV6030−/++++++RiceRC25963pNOV6030−−−/+−+baz−−!′MaizeRC265966pNOV6046−+−+−−RiceRC265966pNOV6046−++−+baz−−!MaizeRC335968pNOV6044−+−/++−−RiceRC335968pNOV6044−+−+baz,−−!Maizes, pRF15974pNOV6045−+−+−−RiceRF15974pNOV6045−+−+baz−−MaizeRS105977pNOV6034−−/+−/+−++RiceRS105977pNOV6034−+−++ e−−!SeedMaizespecificrootback-groundRS186001pNOV6035−/+−/+−/+−/+−/++/−RiceRS186001pNOV6035−−/+MaizeRS32275pNOV6031−−/+−+++++RiceRS32275pNOV6031−+−+baz−“−!”SeedMaizespecificRS42276pNOV6032−−/+−/+−−/++++RiceRS42276pNOV6032−−−+++ ec−−!SeedMaizespecificRS82283pNOV6033+/−−/+−−/+−/++++++−RiceRS82283pNOV6033−−/+−++ e, p−−SeedMaizespecificZmUpNOV6048+++++++++PositiveRiceBIin-ControltronZmUpNOV6048++++++++++++++++PositiveMaizeBIin-ControltronGUS staining scores: + = staining observed ++ = strong staining +++ = very strong staining − = no staining “−!” = some pollen grains stained, probably contamination +/− = some lines showed staining, but not all −/+ = staining faint or seen in only 1 or 2 lines blank = not analyzed yet Note: many RS seem to stain in kernel and root Key: baz − black abscission zone s - scutellum p - pedicel e = endosperm or embryo sc - seed coat

EXAMPLE 4

Rice Orthologs of Arabidopsis Tissue-specifically Expressed Genes Identified by Reverse Genetics

[0598] Understanding the function of every gene is the major challenge in the age of completely sequenced eukaryotic genomes. Sequence homology can be helpful in identifying possible functions of many genes. However, reverse genetics, the process of identifying the function of a gene by obtaining and studying the phenotype of an individual containing a mutation in that gene, is another approach to identify the function of a gene.

[0599] Reverse genetics in Arabidopsis has been aided by the establishment of large publicly available collections of insertion mutants (Krysan et al., (1999) Plant Cell 11, 2283-2290; Tisser et al., (1999) Plant Cell 11, 1841 -1852; Speulman et al., (1999). Plant Cell 11, 1853-1866; Parinov et al., (1999). Plant Cell 11, 2263-2270; Parinov and Sundaresan, 2000; Biotechnology 11, 157-161). Mutations in genes of interest are identified by screening the population by PCR amplification using primers derived from sequences near the insert border and the gene of interest to screen through large pools of individuals. Pools producing PCR products are confirmed by Southern hybridization and further deconvoluted into subpools until the individual is identified (Sussman et al., (2000) Plant Physiology 124, 1465-1467).

[0600] Recently, some groups have begun the process of sequencing insertion site flanking regions from individual plants in large insertion mutant populations, in effect prescreening a subset of lines for genomic insertion sites (Parinov et al., (1999) . Plant Cell 11, 2263-2270; Tisser et al., (1999) . Plant Cell 11, 1841-1852). The advantage to this approach is that the laborious and time-consuming process of PCR-based screening and deconvolution of pools is avoided.

[0601] A large database of insertion site flanking sequences from approximately 100,000 T-DNA mutagenized Arabidopsis plants of the Columbia ecotype (GARLIC lines) is prepared. T-DNA left border sequences from individual plants are amplified using a modified thermal asymmetric interlaced-polymerase chain reaction (TAIL-PCR) protocol (Liu et al., (1995) . Plant J. 8, 457-463). Left border TAIL-PCR products are sequenced and assembled into a database that associates sequence tags with each of the approximately 100,000 plants in the mutant collection. Screening the collection for insertions in genes of interest involves a simple gene name or sequence BLAST query of the insertion site flanking sequence database, and search results point to individual lines. Insertions are confirmed using PCR.

[0602] Analysis of the GARLIC insert lines suggests that there are 76,856 insertions that localize to a subset of the genome representing coding regions and promoters of 22,880 genes. Of these, 49,231 insertions lie in the promoters of over 18,572 genes, and an additional 27,625 insertions are located within the coding regions of 13,612 genes. Approximately 25,000 T-DNA left border mTAIL-PCR products (25% of the total 102,765) do not have significant matches to the subset of the genome representing promoters and coding regions, and are therefore presumed to lie in noncoding and/or repetitive regions of the genome.

[0603] The Arabidopsis T-DNA GARLIC insertion collection is used to investigate the roles of certain genes, which are expressed in specific plant tissues. Target genes are chosen using a variety of criteria, including public reports of mutant phenotypes, RNA profiling experiments, and sequence similarity to tissue-specific genes. Plant lines with insertions in genes of interest are then identified. Each T-DNA insertion line is represented by a seed lot collected from a plant that is hemizygous for a particular T-DNA insertion. Plants homozygous for insertions of interest are identified using a PCR assay. The seed produced by these plants is homozygous for the T-DNA insertion mutation of interest.

[0604] Homozygous mutant plants are tested for altered grain composition. The genes interrupted in these mutants contribute to the observed phenotype.

[0605] Rice orthologs of the Arabidopsis genes are identified by similarity searching of a rice database using the Double-Affine Smith-Waterman algorithm (BLASP with e values better than −10).

EXAMPLE 5

Cloning and Sequencing of Nucleic Acid Molecules from Rice

[0606] 5.1 Genomic DNA. Plant genomic DNA samples are isolated from a collection of tissues which are listed in Table 1. Individual tissues are collected from a minimum of five plants and pooled. DNA can be isolated according to one of the three procedures, e.g., standard procedures described by Ausubel et al. (1995), a quick leaf prep described by Klimyuk et al. (1993), or using FTA paper (Life Technologies).

[0607] For the latter procedure, a piece of plant tissue such as, for example, leaf tissue is excised from the plant, placed on top of the FTA paper and covered with a small piece of parafilm that serves as a barrier material to prevent contamination of the crushing device. In order to drive the sap and cells from the plant tissue into the FTA paper matrix for effective cell lysis and nucleic acid entrapment, a crushing device is used to mash the tissue into the FTA paper. The FTA paper is air dried for an hour. For analysis of DNA, the samples can be archived on the paper until analysis. Two mm punches are removed from the specimen area on the FTA paper using a 2 mm Harris Micro Punch™ and placed into PCR tubes. Two hundred (200) microliters of FTA purification reagent is added to the tube containing the punch and vortexed at low speed for 2 seconds. The tube is then incubated at room temperature for 5 minutes. The solution is removed with a pipette so as to repeat the wash one more time. Two hundred (200) microliters of TE (10 mM Tris, 0.1 mM EDTA, pH 8.0) is added and the wash is repeated two more times. The PCR mix is added directly to the punch for subsequent PCR reactions.

[0608] 5.2 Cloning of Candidate cDNA: A candidate cDNA is amplified from total RNA isolated from rice tissue after reverse transcription using primers designed against the computationally predicted cDNA. Primers designed based on the genomic sequence can be used to PCR amplify the full-length cDNA (start to stop codon) from first strand cDNA prepared from rice cultivar Nipponbare tissue.

[0609] The Qiagen RNeasy kit (Qiagen, Hilden, Germany) is used for extraction of total RNA. The Superscript II kit (Invitrogen, Carlsbad, USA) is used for the reverse transcription reaction. PCR amplification of the candidate cDNA is carried out using the reverse primer sequence located at the translation start of the candidate gene in 5′-3′ direction. This is performed with high-fidelity Taq polymerase (Invitrogen, Carlsbad, USA).

[0610] The PCR fragment is then cloned into pCR2.1-TOPO (Invitrogen) or the pGEM-T easy vector (Promega Corporation, Madison, Wis., USA) per the manufacturer's instructions, and several individual clones are subjected to sequencing analysis.

[0611] 5.3 DNA sequencing: DNA preps for 2-4 independent clones are miniprepped following the manufacturer's instructions (Qiagen). DNA is subjected to sequencing analysis using the BigDye™ Terminator Kit according to manufacturer's instructions (ABI). Sequencing makes use of primers designed to both strands of the predicted gene of interest. DNA sequencing is performed using standard dye-terminator sequencing procedures and automated sequencers (models 373 and 377; Applied Biosystems, Foster City, Calif.). All sequencing data are analyzed and assembled using the Phred/Phrap/Consed software package (University of Washington) to an error ratio equal to or less than 10−4 at the consensus sequence level.

[0612] The consensus sequence from the sequencing analysis is then to be validated as being intact and the correct gene in several ways. The coding region is checked for being full length (predicted start and stop codons present) and uninterrupted (no internal stop codons). Alignment with the gene prediction and BLAST analysis is used to ascertain that this is intact the right gene.

[0613] The clones are sequenced to verify their correct amplification.

EXAMPLE 6

Functional Analysis in Plants

[0614] A plant complementation assay can be used for the functional characterization of the tissue-specifically expressed genes according to the invention.

[0615] Rice and Arabidopsis putative orthologue pairs are identified using BLAST comparisons, TFASTXY comparisons, and Double-Affine Smith-Waterman similarity searches. Constructs containing a rice cDNA or genomic clone inserted between the promoter and terminator of the Arabidopsis orthologue are generated using overlap PCR (Gene 77, 61-68 (1989)) and GATEWAY cloning (Life Technologies Invitrogen). For ease of cloning, rice cDNA clones are preferred to rice genomic clones. A three stage PCR strategy is used to make these constructs.

[0616] (1) In the first stage, primers are used to PCR amplify: (i) 2 Kb upstream of the translation start site of the Arabidopsis orthologue, (ii) the coding region or cDNA of the rice orthologue, and (iii) the 500 bp immediately downstream of the Arabidopsis orthogue's translation stop site. Primers are designed to incorporate onto their 5′ ends at least 16 bases of the 3′ end of the adjacent fragment, except in the case of the most distal primers which flank the gene construct (the forward primer of the promoter and the reverse primer of the terminator). The forward primer of the promoters contains on their 5′ ends partial AttB 1 sites, and the reverse primer of the terminators contains on their 5′ ends partial AttB2 sites, for Gateway cloning.

[0617] (2) In the second stage, overlap PCR is used to join either the promoter and the coding region, or the coding region and the terminator.

[0618] (3) In the third stage either the promoter-coding region product can be joined to the terminator or the coding region-terminator product can be joined to the promoter, using overlap PCR and amplification with full Att site-containing primers, to link all three fragments, and put full Att sites at the construct termini.

[0619] The fused three-fragment piece flanked by Gateway cloning sites are introduced into the LTI donor vector pDONR201 using the BP clonase reaction, for confirmation by sequencing. Confirmed sequenced constructs are introduced into a binary vector containing Gateway cloning sites, using the LR clonase reaction such as, for example, pAS200.

[0620] The pAS200 vector was created by inserting the Gateway cloning cassette RfA into the Acc651 site of pNOV3510.

[0621] pNOV3510 was created by ligation of inverted pNOV2114 VSI binary into pNOV3507, a vector containing a PTX5′ Arab Protox promoter driving the PPO gene with the Nos terminator.

[0622] pNOV2 114 was created by insertion of virGN54D (Pazour et al. 1992, J. Bacteriol. 174:4169-4174) from pAD1289 (Hansen et al. 1994, PNAS 91:7603-7607) into pHiNK085.

[0623] pHiNK085 was created by deleting the 35S:PMI cassette and M13 ori in pVictorHiNK.

[0624] pPVictorHiNK was created by modifying the T-DNA of pVictor (described in WO 97/04112) to delete M13 derived sequences and to improve its cloning versatility by introducing the BIGLINK polylinker.

[0625] The sequence of the pVictor HiNK vector is disclosed in SEQ ID NO: 5 in WO 00/6837, which is incorporated herein by reference. The pVictorHiNK vector contains the following constituents that are of functional importance:

[0626] The origin of replication (ORI) functional in Agrobacterium is derived from the Pseudomonas aeruginosa plasmid pVS1 (Itoh et al. 1984. Plasmid 11: 206-220; Itoh and Haas, 1985. Gene 36: 27-36). The pVS1 ORI is only functional in Agrobacterium and can be mobilised by the helper plasmid pRK2013 from E.coli into A. tumefaciens by means of a triparental mating procedure (Ditta et al., 1980. Proc. Natl. Acad. Sci USA 77: 7347-7351).

[0627] The ColE1 origin of replication functional in E. coli is derived from pUC 19 (Yannisch-Perron et al., 1985. Gene 33: 103-119).

[0628] The bacterial resistance to spectinomycin and streptomycin encoded by a 0.93 kb fragment from transposon Tn7 (Fling et al., 1985. Nucl. Acids Res. 13: 7095) functions as selectable marker for maintenance of the vector in E. coli and Agrobacterium The gene is fused to the tac promoter for efficient bacterial expression (Amman et al., 1983. Gene 25: 167-178).

[0629] The right and left T-DNA border fragments of 1.9 kb and 0.9 kb that comprise the 24 bp border repeats, have been derived from the Ti-plasmid of the nopaline type Agrobacterium tumefaciens strains pTiT37 (Yadav et al., 1982. Proc. Natl. Acad. Sci. USA. 79: 6322-6326).

[0630] The plasmid is introduced into Agrobacterium tumefaciens GV3101 pMP90 by electroporation. The positive bacterial transformants are selected on LB medium containing 50 μg/μl kanamycin and 25 μg/μl gentamycin. Plants are transformed by standard methodology (e.g., by dipping flowers into a solution containing the Agrobacterium) except that 0.02% Silwet-77 (Lehle Seeds, Round Rock, Tex.) is added to the bacterial suspension and the vacuum step omitted. Five hundred (500) mg of seeds are planted per 2 ft2 flat of soil and and progeny seeds are selected for transformants using PPO selection.

[0631] Primary transformants are analyzed for complementation. Primary transformants are genotyped for the Arabidopsis mutation and presence of the transgene. When possible, >50 mutants harboring the transgene should be phenotyped to observe variation due to transgene copy number and expression.

EXAMPLE 7

Vector Construction for Overexpression and Gene “Knockout” Experiments

[0632] 7.1 Overexpression

[0633] Vectors used for expression of full-length “candidate genes” of interest in plants (overexpression) are designed to overexpress the protein of interest and are of two general types, biolistic and binary, depending on the plant transformation method to be used.

[0634] For biolistic transformation (biolistic vectors), the requirements are as follows:

[0635] 1. a backbone with a bacterial selectable marker (typically, an antibiotic resistance gene) and origin of replication functional in Escherichia coli (E. coli ; eg. ColE1), and

[0636] 2. a plant-specific portion consisting of:

[0637] a. a gene expression cassette consisting of a promoter (eg. ZmUBIint MOD), the gene of interest (typically, a full-length cDNA) and a transcriptional terminator (eg. Agrobacterium tumefaciens nos terminator);

[0638] b. a plant selectable marker cassette, consisting of a promoter (eg. rice Act1D-BV MOD), selectable marker gene (eg. phosphomannose isomerase, PMI) and transcriptional terminator (eg. CaMV terminator).

[0639] Vectors designed for transformation by Agrobacterium tumefaciens (A. tumefaciens; binary vectors) consist of:

[0640] 1. a backbone with a bacterial selectable marker functional in both E. coli and A. tumefaciens (eg. spectinomycin resistance mediated by the aadA gene) and two origins of replication, functional in each of aforementioned bacterial hosts, plus the A. tumefaciens virG gene;

[0641] 2. a plant-specific portion as described for biolistic vectors above, except in this instance this portion is flanked by A. tumefaciens right and left border sequences which mediate transfer of the DNA flanked by these two sequences to the plant.

[0642] 7.2 Knock Out Vectors

[0643] Vectors designed for reducing or abolishing expression of a single gene or of a family or related genes (knockout vectors) are also of two general types corresponding to the methodology used to downregulate gene expression: antisense or double-stranded RNA interference (dsRNAi).

[0644] (a) Anti-sense

[0645] For antisense vectors, a full-length or partial gene fragment (typically, a portion of the cDNA) can be used in the same vectors described for full-length expression, as part of the gene expression cassette. For antisense-mediated down-regulation of gene expression, the coding region of the gene or gene fragment will be in the opposite orientation relative to the promoter; thus, mRNA will be made from the non-coding (antisense) strand in planta.

[0646] (b) dsRNAi

[0647] For dsRNAi vectors, a partial gene fragment (typically, 300 to 500 basepairs long) is used in the gene expression cassette, and is expressed in both the sense and antisense orientations, separated by a spacer region (typically, a plant intron, eg. the OsSH1 intron 1, or a selectable marker, eg. conferring kanamycin resistance). Vectors of this type are designed to form a double-stranded mRNA stem, resulting from the basepairing of the two complementary gene fragments in planta.

[0648] Biolistic or binary vectors designed for overexpression or knockout can vary in a number of different ways, including eg. the selectable markers used in plant and bacteria, the transcriptional terminators used in the gene expression and plant selectable marker cassettes, and the methodologies used for cloning in gene or gene fragments of interest (typically, conventional restriction enzyme-mediated or Gateway™ recombinase-based cloning). An important variant is the nature of the gene expression cassette promoter driving expression of the gene or gene fragment of interest in most tissues of the plants (constitutive, eg. ZmUBIint MOD), in specific plant tissues (eg. maize ADP-gpp for endosperm-specific expression), or in an inducible fashion (eg. GAL4bsBz1 for estradiol-inducible expression in lines constitutively expressing the cognate transcriptional activator for this promoter).

EXAMPLE 8

Insertion of a “Candidate Gene” into Expression Vector

[0649] A validated rice cDNA clone in pCR2.1-TOPO or the pGEM-T easy vector is subcloned using conventional restriction enzyme-based cloning into a vector, downstream of the maize ubiquitin promoter and intron, and upstream of the Agrobacterium tumefaciens nos 3′ end transcriptional terminator. The resultant gene expression cassette (promoter, “candidate gene” and terminator) is further subcloned, using conventional restriction enzyme-based cloning, into the pNOV2117 binary vector (Negrotto et al (2000) Plant Cell Reports 19, 798-803; plasmid pNOV117 disclosed in this article corresponds to pNOV2117 described herein), generating pNOVCAND.

[0650] The pNOVCAND binary vector is designed for transformation and over-expression of the “candidate gene” in monocots. It consists of a binary backbone containing the sequences necessary for selection and growth in Escherichia coli DH-5α (Invitrogen) and Agrobacterium tumefaciens LBA4404 (pAL4404; pSB1), including the bacterial spectinomycin antibiotic resistance aadA gene from E. coli transposon Tn7, origins of replication for E. coli (ColE1) and A. tumefaciens (VS1), and the A. tumefaciens virG gene. In addition to the binary backbone, which is identical to that of pNOV2114 described herein previously (see Example 5 above), pNOV2117 contains the T-DNA portion flanked by the right and left border sequences, and including the Positech™ (Syngenta) plant selectable marker (WO 94/20627) and the “candidate gene” gene expression cassette. The Positech™ plant selectable marker confers resistance to mannose and in this instance consists of the maize ubiquitin promoter driving expression of the PMI (phosphomannose isomerase) gene, followed by the cauliflower mosaic virus transcriptional terminator.

[0651] Plasmid pNOV2117 is introduced into Agrobacterium tumefaciens LBA4404 (pAL4404; pSB1) by electroporation. Plasmid pAL4404 is a disarmed helper plasmid (Ooms et al (1982) Plasmid 7, 15-29). Plasmid pSB1 is a plasmid with a wide host range that contains a region of homology to pNOV2117 and a 15.2 kb KpnI fragment from the virulence region of pTiBo542 (Ishida et al (1996) Nat Biotechnol 14, 745-750). Introduction of plasmid pNOV2117 into Agrobacterium strain LBA4404 results in a co-integration of pNOV2117 and pSB1.

[0652] Alternatively, plasmid pCIB7613, which contains the hygromycin phosphotransferase (hpt) gene (Gritz and Davies, Gene 25, 179-188, 1983) as a selectable marker, may be employed for transformation.

[0653] Plasmid pCIB7613 (see WO 98/06860, incorporated herein by reference in its entirety) is selected for rice transformation. In pCIB7613, the transcription of the nucleic acid sequence coding hygromycin-phosphotransferase (HYG gene) is driven by the corn ubiquitin promoter (ZmUbi) and enhanced by corn ubiquitin intron 1. The 3′polyadenylation signal is provided by NOS 3′ nontranslated region.

[0654] Other useful plasmids include pNADII002 (GAL4-ER-VP16) which contains the yeast GAL4 DNA Binding domain (Keegan et al., Science, 231:699 (1986)), the mammalian estrogen receptor ligand binding domain (Greene et al., Science, 231 :1150 (1986)) and the transcriptional activation domain of the HSV VP16 protein (Triezenberg et al.,1988). Both hpt and GAL4-ER-VP16 are constitutively expressed using the maize Ubiquitin promoter, and pSGCDL1 (GAL4BS Bz1 Luciferase), which carries the firefly luciferase reporter gene under control of a minimal maize Bronze1 (Bz1) promoter with 10 upstream synthetic GAL4 binding sites. All constructs use termination signals from the nopaline synthase gene.

EXAMPLE 9

Plant Transformation

Example 9.1

Rice Transformation

[0655] pNOVCAND is transformed into a rice cultivar (Kaybonnet) using Agrobacterium-mediated transformation, and mannose-resistant calli are selected and regenerated.

[0656] Agrobacterium is grown on YPC solid plates for 2-3 days prior to experiment initiation. Agrobacterial colonies are suspended in liquid MS media to an OD of 0.2 at λ600 nm. Acetosyringone is added to the agrobacterial suspension to a concentration of 200 μM and agro is induced for 30 min.

[0657] Three-week-old calli which are induced from the scutellum of mature seeds in the N6 medium (Chu, C. C. et al., Sci, Sin., 18, 659-668(1975)) are incubated in the agrobacterium solution in a 100×25 petri plate for 30 minutes with occasional shaking. The solution is then, removed with a pipet and the callus transfered to a MSAs medium which is overlayed with sterile filter paper.

[0658] Co-Cultivation is continued for 2 days in the dark at 22° C.

[0659] Calli are then placed on MS-Timetin plates for 1 week. After that they are tranfered to PAA+ mannose selection media for 3 weeks.

[0660] Growing calli (putative events) are picked and transfered to PAA+ mannose media and cultivated for 2 weeks in light.

[0661] Colonies are tranfered to MS20SorbKinTim regeneration media in plates for 2 weeks in light. Small plantlets are transferred to MS20SorbKinTim regeneration media in GA7 containers. When they reach the lid, they are transfered to soil in the greenhouse.

[0662] Expression of the “candidate gene” in transgenic To plants is analyzed. Additional rice cultivars, such as but not limited to, Nipponbare, Taipei 309 and Fuzisaka 2 are also transformed and assayed for expression of the “candidate gene” product and enhanced protein expression.

Example 9.2

Maize Transformation

[0663] Transformation of immature maize embryos is performed essentially as described in Negrotto et al., (2000) Plant Cell Reports 19: 798-803. For this example, all media constituents are as described in Negrotto et al., supra. However, various media constituents described in the literature may be substituted.

[0664] 9.2.1. Transformation Plasmids and Selectable Marker

[0665] The genes used for transformation are cloned into a vector suitable for maize transformation as described in Example 17. Vectors used contain the phosphomannose isomerase (PMI) gene (Negrotto et al. (2000) Plant Cell Reports 19: 798-803).

[0666] 9.2.2. Preparation of Agrobacterium tumefaciens

[0667] Agrobacterium strain LBA4404 (pSB1) containing the plant transformation plasmid is grown on YEP (yeast extract (5 g/L), peptone (10 g/L), NaCl (5 g/L),15 g/l agar, pH 6.8) solid medium for 2 to 4 days at 28° C. Approximately 0.8×109 Agrobacteria are suspended in LS-inf media supplemented with 100 □M, acetosyringone (As) (Negrotto et al.,(2000) Plant Cell Rep 19: 798-803). Bacteria are pre-induced in this medium for 30-60 minutes.

[0668] 9.2.3. Inoculation

[0669] Immature embryos from A188 or other suitable maize genotypes are excised from 8-12 day old ears into liquid LS-inf+100 □M As. Embryos are rinsed once with fresh infection medium. Agrobacterium solution is then added and embryos are vortexed for 30 seconds and allowed to settle with the bacteria for 5 minutes. The embryos are then transferred scutellum side up to LSAs medium and cultured in the dark for two to three days. Subsequently, between 20 and 25 embryos per petri plate are transferred to LSDc medium supplemented with cefotaxime (250 mg/l) and silver nitrate (1.6 mg/l) and cultured in the dark for 28° C. for 10 days.

[0670] 9.2.4. Selection of Transformed Cells and Regeneration of Transformed Plants

[0671] Immature embryos producing embryogenic callus are transferred to LSD1M0.5S medium. The cultures are selected on this medium for 6 weeks with a subculture step at 3 weeks. Surviving calli are transferred either to LSD1M0.5S medium to be bulked-up or to Reg1 medium. Following culturing in the light (16 hour light/8 hour dark regiment), green tissues are then transferred to Reg2 medium without growth regulators and incubated for 1-2 weeks. Plantlets are transferred to Magenta GA-7 boxes (Magenta Corp, Chicago Ill.) containing Reg3 medium and grown in the light. Plants that are PCR positive for the promoter-reporter cassette are transferred to soil and grown in the greenhouse.

EXAMPLE 10

Chromosomal Markers to Identify the Location of a Nucleic Acid Sequence

[0672] The sequences of the present invention can also be used for SSR mapping. SSR mapping in rice has been described by Miyao et al. (DNA Res 3:233 (1996)) and Yang et al. (Mol Gen Genet 245:187 (1994)), and in maize by Ahn et al. (Mol Gen Genet 241:483 (1993)). SSR mapping can be achieved using various methods. In one instance, polymorphisms are identified when sequence specific probes flanking an SSR contained within a sequence are made and used in polymerase chain reaction (PCR) assays with template DNA from two or more individuals or, in plants, near isogenic lines. A change in the number of tandem repeats between the SSR-flanking sequence produces differently sized fragments (U.S. Pat. No. 5,766,847). Alternatively, polymorphisms can be identified by using the PCR fragment produced from the SSR-flanking sequence specific primer reaction as a probe against Southern blots representing different individuals (Refseth et al., Electrophoresis 18:1519 (1997)). Rice SSRs can be used to map a molecular marker closely linked to functional gene, as described by Akagi et al. (Genome 39:205 (1996)).

[0673] The sequences of the present invention can be used to identify and develop a variety of microsatellite markers, including the SSRs described above, as genetic markers for comparative analysis and mapping of genomes.

[0674] Many of the polynucleotides listed in Tables 2 to 11 contain at least 3 consecutive di-, tri- or tetranucleotide repeat units in their coding region that can potentially be developed into SSR markers. Trinucleotide motifs that can be commonly found in the coding regions of said polynucleotides and easily identified by screening the polynucleotides sequences for said motifs are, for example: CGG; GCC, CGC, GGC, etc. Once such a repeat unit has been found, primers can be designed which are complementary to the region flanking the repeat unit and used in any of the methods described below.

[0675] Sequences of the present invention can also be used in a variation of the SSR technique known as inter-SSR (ISSR), which uses microsatellite oligonucleotides as primers to amplify genomic segments different from the repeat region itself (Zietkiewicz et al., Genomics 20:176 (1994)). ISSR employs oligonucleotides based on a simple sequence repeat anchored or not at their 5′- or 3′-end by two to four arbitrarily chosen nucleotides, which triggers site-specific annealing and initiates PCR amplification of genomic segments which are flanked by inversely orientated and closely spaced repeat sequences. In one embodiment of the present invention, microsatellite markers as disclosed herein, or substantially similar sequences or allelic variants thereof, may be used to detect the appearance or disappearance of markers indicating genomic instability as described by Leroy et al. (Electron. J Biotechnol, 3(2), at http://www.ejb.org (2000)), where alteration of a fingerprinting pattern indicated loss of a marker corresponding to a part of a gene involved in the regulation of cell proliferation. Microsatellite markers are useful for detecting genomic alterations such as the change observed by Leroy et al. (Electron. J Biotechnol, 3(2), supra (2000)) which appeared to be the consequence of microsatellite instability at the primer binding site or modification of the region between the microsatellites, and illustrated somaclonal variation leading to genomic instability. Consequently, sequences of the present invention are useful for detecting genomic alterations involved in somaclonal variation, which is an important source of new phenotypes.

[0676] In addition, because the genomes of closely related species are largely syntenic (that is, they display the same ordering of genes within the genome), these maps can be used to isolate novel alleles from wild relatives of crop species by positional cloning strategies. This shared synteny is very powerful for using genetic maps from one species to map genes in another. For example, a gene mapped in rice provides information for the gene location in maize and wheat.

EXAMPLE 11

Quantitative Trait Linked Breeding

[0677] Various types of maps can be used with the sequences of the invention to identify Quantitative Trait Loci (QTLs) for a variety of uses, including marker-assisted breeding. Many important crop traits are quantitative traits and result from the combined interactions of several genes. These genes reside at different loci in the genome, often on different chromosomes, and generally exhibit multiple alleles at each locus. Developing markers, tools, and methods to identify and isolate the QTLs involved in a trait, enables marker-assisted breeding to enhance desirable traits or suppress undesirable traits. The sequences disclosed herein can be used as markers for QTLs to assist marker-assisted breeding. The sequences of the invention can be used to identify QTLs and isolate alleles as described by Li et al. in a study of QTLs involved in resistance to a pathogen of rice. (Li et al., Mol Gen Genet 261:58 (1999)). In addition to isolating QTL alleles in rice, other cereals, and other monocot and dicot crop species, the sequences of the invention can also be used to isolate alleles from the corresponding QTL(s) of wild relatives. Transgenic plants having various combinations of QTL alleles can then be created and the effects of the combinations measured. Once an ideal allele combination has been identified, crop improvement can be accomplished either through biotechnological means or by directed conventional breeding programs. (Flowers et al., J Exp Bot 51:99 (2000); Tanksley and McCouch, Science 277:1063 (1997)).

EXAMPLE 12

Marker-Assisted Breeding

[0678] Markers or genes associated with specific desirable or undesirable traits are known and used in marker assisted breeding programs. It is particularly beneficial to be able to screen large numbers of markers and large numbers of candidate parental plants or progeny plants. The methods of the invention allow high volume, multiplex screening for numerous markers from numerous individuals simultaneously.

[0679] Markers or genes associated with specific desirable or undesirable traits are known and used in marker assisted breeding programs. It is particularly beneficial to be able to screen large numbers of markers and large numbers of candidate parental plants or progeny plants. The methods of the invention allow high volume, multiplex screening for numerous markers from numerous individuals simultaneously.

[0680] A multiplex assay is designed providing SSRs specific to each of the markers of interest. The SSRs are linked to different classes of beads. All of the relevant markers may be expressed genes, so RNA or cDNA techniques are appropriate. RNA is extracted from root tissue of 1000 different individual plants and hybridized in parallel reactions with the different classes of beads. Each class of beads is analyzed for each sample using a microfluidics analyzer. For the classes of beads corresponding to qualitative traits, qualitative measures of presence or absence of the target gene are recorded. For the classes of beads corresponding to quantitative traits, quantitative measures of gene activity are recorded. Individuals showing activity of all of the qualitative genes and highest expression levels of the quantitative traits are selected for further breeding steps. In procedures wherein no individuals have desirable results for all the measured genes, individuals having the most desirable, and fewest undesirable, results are selected for further breeding steps. In either case, progeny are screened to further select for homozygotes with high quantitative levels of expression of the quantitative traits.

EXAMPLE 13

Method of Modifying the Gene Frequency

[0681] The invention further provides a method of modifying the frequency of a gene in a plant population, including the steps of: identifying an SSR within a coding region of a gene; screening a plurality of plants using the SSR as a marker to determine the presence or absence of the gene in an individual plant; selecting at least one individual plant for breeding based on the presence or absence of the gene; and breeding at least one plant thus selected to produce a population of plants having a modified frequency of the gene. The identification of the SSR within the coding region of a gene can be accomplished based on sequence similarity between the nucleic acid molecules of the invention and the region within the gene of interest flanking the SSR.

7TABLE 1SEQ ID NOs and corresponding description for Oryza genes which are expressed in a constitutive mannerand further SEQ ID NOs for the corresponding homologous sequences found in wheat, banana and maize.ORFPromoWheatBanaMaize(SEQ(SEQ(SEQ(SEQ(SEQID)ID)DescriptionID)ID)ID)Constitutively Expressed 3*Similar to gi|1136122|emb|CAA62917.1|alfa-tubulin3336, 4234,50165557[Oryza sativa]4233, 2877,4232, 3760,4228, 4229,3144, 3143,3335, 4230,3145, 3215,4231, 2974 6*1601Similar to YER4_YEAST P40057SACCHAROMYCES CEREVISIAE (BAKER SYEAST). HYPOTHETICAL 14.3 KD PROTEIN INPTP3-ILV1 INTERGENIC REGION. 8*Similar to V7K_BYDVP P09517 BARLEY YELLOWDWARF VIRUS (ISOLATE PAV) (BYDV). 6.7 KDPROTEIN (ORF 5).23* 1613Similar to UL51_HSV11 P10235 HERPES SIMPLEX5666VIRUS (TYPE 1/STRAIN 17). PROTEIN UL51.19* 1610Similar to DUAL CHICK Q90830 GALLUS5735GALLUS (CHICKEN). DUALIN.15* 1607Open Reading Frame containing a Sage tag sequence5731near 3 end OS_ORF007907 ST(F) HTC047420-A01.R.21 FRAME: −1 ORF: 2 LEN: 55517* 1608Similar to ICP0_PRVIF P29129 PSEUDORABIESVIRUS (STRAIN INDIANA-FUNKHAUSER /BECKER) (PRV). TRANS-ACTINGTRANSCRIPTIONAL PROTEIN ICP0 (EARLYPROTEIN 0) (EP0). 9*1602Similar to TCTP_MEDSA P28014 Q403703404, 310451575388MEDICAGO SATIVA (ALFALFA).TRANSLATIONALLY CONTROLLED TUMORPROTEIN HOMOLOG (TCTP).22*″ Open Reading Frame OS_ORF001266 HTC007198-A01.6 FRAME: −2 ORF: 1 LEN: 66913* 1605Similar to gi|166742|gb|AAA32811.1|histone H44225, 4189,520656544129, 4224,3756, 4274,3725, 3735,3776, 3739,4268, 3743,4242, 4281,4278, 4243,3728, 4279,3748, 3753,4130, 4183,4244, 3750,4261, 4216,4203, 3774,4201, 4245,3746, 3759,3757, 3714,4260, 4250,4280, 4182,4037, 3761,4217, 4202,4190, 4140,4263, 3765,3752, 4096,3737, 3742 5*Similar to EF1A_MAIZE Q41803 ZEA MAYS3850, 3858,50235610(MAIZE). ELONGATION FACTOR 1-ALPHA (EF-1-3852, 3832,ALPHA).3859, 3857,3856, 3853,3855, 3830,3851, 3854,3846, 3860,2963, 3835,3836, 2939,3847, 3845,383118* 1609Similar to gi|8778551|gb|AAF79559.1|AC022464_175632F22G5.35 [Arabidopsis thaliana] 1*1598Similar to gi|2145360|emb|CAA70105.1|Hsc70-G83311, 2923,51505609protein [Arabidopsis thaliana]3808, 3806,3494, 3804,3598, 3807,2874, 3805,3596, 3602,2873, 3600,4240, 3439,3597, 4239,3593, 4241,3438, 3592,3459, 3594,3590, 2975,2989 7*″Open Reading Frame containing a Sage tag sequence5840near 3 end OS_ORF014602 ST(F) HTC094277-A01.F.15 FRAME: 3 ORF: 1 LEN: 54616*″ Similar to VGLI_HSVBS Q08102 BOVINE5364HERPESVIRUS TYPE 1.2 (STRAIN ST).GLYCOPROTEIN I.12*″ 1604Similar to STRR_STRGR P08076 STREPTOMYCESGRISEUS. STREPTOMYCIN BIOSYNTHESISOPERON POSSIBLE REGULATORY PROTEIN.14*″ 1606Open Reading Frame OS_ORF010093 ST(R)50905493HTC060970-A01.F.4 FRAME: 1 ORF: 2 LEN: 89121*″ 1612Similar to ULC5_HCMVA P16835 HUMANCYTOMEGALOVIRUS (STRAIN AD169).HYPOTHETICAL PROTEIN UL125.24*″ 1614Similar to UL33_HSVEB P28953 EQUINEHERPESVIRUS TYPE 1 (STRAIN AB4P) (EHV-1).GENE 27 PROTEIN. 4*″1600Similar to gi|303857|dbj|BAA02154.1|52115480ubiquitin/ribosomal polyprotein [Oryza sativa]11*″ Open Reading Frame containing a Sage tag sequencenear 3 end OS_ORF019788 ST(F) HTC133660-A01.F.18 FRAME: −3 ORF: 3 LEN: 54320*″ 1611Similar to gi|5103822|gb|AAD39652.1|AC007591_1749545522ESTs gb|R30529, gb|Z48463, gb|Z48467,gb|AA597369 and gb|AA394772 come from this gene.[Arabidopsis thaliana] 2*″1599Similar to gi|4646220|gb|AAD26886.1|AC007290_55834hypothetical protein [Arabidopsis thaliana]75*″ Similar to H3_ENCAL P08903 ENCEPHALARTOS3582, 3564,49785672ALTENSTEINII (ALTENSTEIN S BREAD TREE)3560, 3563,(CYCAD). HISTONE H3.3552, 3569,3583, 3578,3580, 3577,3511, 3529,3562, 3515,3585, 3579,3525, 3587,3574, 3567,3544, 3532,3570, 3531,3528, 3559,3588, 3571,3540, 3565,3533, 3573,3572, 3575,3535, 3566,3589, 3584,3576, 3512,3530, 3520,3536, 3568,3521, 3513,3516, 3534,3581, 353762*″ Similar to SGF3_BOMMO Q17237 BOMBYX MORI(SILK MOTH). SILK GLAND FACTOR 3 (POUDOMAIN PROTEIN M1).128*″1684Similar to gi|3406035|gb|AAC29139.1|TINY5786[Arabidopsis thaliana]121*″1678Open Reading Frame OS_ORF017490 HTC116385-5616A01.F.8 FRAME: −3 ORF: 1 LEN: 67592*″ 1652Similar to gi|4584540|emb|CAB40770.1|putativeprotein [Arabidopsis thaliana]136*″1691Open Reading Frame OS_ORF013948 HTC089691-A01.R.17 FRAME: 2 ORF: 4 LEN: 73877*″ 1644Similar to RS23_FRAAN P46297 FRAGARIA3792, 3791,5181ANANASSA (STRAWBERRY). 40 S RIBOSOMAL3793PROTEIN S23 (S12).28*″ 1617Similar to gi|829283|emb|CAA78738.1|heat shock4697, 4262,50005677protein hsp82 [Oryza sativa]3885, 3886,3179, 3733,4219, 4218,4220, 4208,2743, 420710*″ 1603Similar to gi|974605|gb|AAA75104.1|single-stranded4253, 3887,5892nucleic acid binding protein4248, 3795,3889, 3794110*″Similar to gi|2252633|gb|AAB65496.1|hypotheticalprotein [Arabidopsis thaliana]47*″ Similar to YS88_CAEEL Q0938449435622CAENORHABDITIS ELEGANS. HYPOTHETICAL12.3 KD PROTEIN ZK945.8 IN CHROMOSOME II.53*″ 1630Similar to gi|5006851|gb|AAD37696.1|AF145727_15668homeodomain leucine zipper protein [Oryza sativa]54*″ 1631Similar to gi|8096630|dbj|BAA96201.1|hypotheticalprotein [Oryza sativa]83*″ Similar to POU2_BRARE Q90270 Q9048349165410BRACHYDANIO RERIO (ZEBRAFISH) (ZEBRADANIO). POU DOMAIN PROTEIN 2.124*″1680Similar to BIOH_ECOLI P13001 ESCHERICHIA28305281COLI. BIOH PROTEIN.87*″ 1648Similar to gi|7629994|emb|CAB88336.1|60 S52185442RIBOSOMAL PROTEIN L36 homolog [Arabidopsisthaliana]138*″1692Open Reading Frame OS_ORF012152 HTC075887-A01.26 FRAME: −1 ORF: 4 LEN: 83142*″ 1625Similar to gi|755187|gb|AAB07758.1|glyceraldehyde506654573-phosphate dehydrogenase81*″ Similar to VP3_CAV26 P54095 CHICKEN ANEMIAVIRUS (USA ISOLATE 26P4) (CAV). APOPTIN(VP3).25*″ Similar to gi|1100217|gb|AAA82697.1|sucrose3447, 3486,48075661synthase3155, 3154,4386, 3156,3437, 2840,3485, 3111,3249, 298498*″ 1658Open Reading Frame OS_ORF021766 HTC148742-A01.R.37 FRAME: −2 ORF: 6 LEN: 66360*″ Similar to gi|169793|gb|AAA33907.1|histone 33563, 3569,497756723515, 3528,3570, 3511,3532, 3584,3580, 3559,3560, 3562,3565, 3583,3552, 3533,3525, 3529,3585, 3579,3582, 3564,3571, 3576,3577, 3578,3574, 3572,3573, 3567,3544, 3531,3587, 3540,3588, 3575,3535, 3536,3530, 3589,3568, 3566,3537, 3513,3521, 3516,3520, 3581,3561, 3512103*″1663Similar to gi|3080441|emb|CAA18758.1|putative296649385690protein [Arabidopsis thaliana]99*″ 1659Open Reading Frame containing a Sage tag sequencenear 3 end OS_ORF019581 ST(F) HTC132137-A01.F.12 FRAME: 3 ORF: 1 LEN: 561119*″1677Similar to gi|4262212|gb|AAD14506.1|En/Spm-liketransposon protein [Arabidopsis thaliana]112*″1670Open Reading Frame OS_ORF011158 HTC068757-A01.F.17 FRAME: −3 ORF: 1 LEN: 1224111*″1669Similar to V18K_MLVAB P03400 ABELSONMURINE LEUKEMIA VIRUS. 18 KD PROTEIN.102*″1662Open Reading Frame OS_ORF001938 HTC011169-5532A01.13 FRAME: 1 ORF: 2 LEN: 1011141*″1695Similar to NPT2_RAT Q06496 RATTUSNORVEGICUS (RAT). RENAL SODIUM-DEPENDENT PHOSPHATE TRANSPORTPROTEIN 2(SODIUM/PHOSPHATECOTRANSPORTER 2)(NA(+)/PI COTRANSPORTER 2) (RENALSODIUM-PHOSPHATETRANSPORT PROTEIN 2)(RENAL NA+-DEPENDENT PHOSPHATECOTRANSPORTER46*″ 1627Similar to gi|7435060|pir∥T01316 epoxide hydrolase3770, 37215861homolog T14P8.15 - Arabidopsis thaliana101*″1661Open Reading Frame OS_ORF001719 HTC009782-A01.9 FRAME: 2 ORF: 1 LEN: 675123*″Open Reading Frame OS_ORF013133 HTC083102-A01.R.9 FRAME: −3 ORF: 2 LEN: 68457*″ Similar to gi|5730136|emb|CAB52470.1|putativeprotein [Arabidopsis thaliana]64*″ 1635Similar to gi|435944|gb|AAC49557.1|DNA-bindingfactor of bZIP class76*″ 1643Similar to gi|1107487|emb|CAA63025.1|60 S3838, 3840,51535606ribosomal protein L27a [Arabidopsis thaliana]3841, 384250*″ 1629Similar to RS2_DROME P31009 DROSOPHILA3661, 3671,52145884MELANOGASTER (FRUIT FLY). 40 S RIBOSOMAL3662, 3670,PROTEIN S2 (STRINGS OF PEARLS PROTEIN).3669, 3658,308431*″ Similar to gi|1136120|emb|CAA62916.1|alpha-tubulin3336, 4229,50165557[Oryza sativa]4234, 4233,3760, 4232,2877, 3144,4228, 3143,3335, 4230,3145, 3215,4231109*″1668Open Reading Frame OS_ORF020205 HTC136407-5360A01.F.19 FRAME: 2 ORF: 6 LEN: 87397*″ 1657Similar to NEU1_RAT PO1179 RATTUSNORVEGICUS (RAT). OXYTOCIN-NEUROPHYSIN 1 PRECURSOR (OCYTOCIN-NEUROPHYSIN 1).140*″1694Open Reading Frame OS_ORF014808 ST(R)HTC096028-A01.R.22 FRAME: −1 ORF: 48 LEN: 52278*″ Similar to gi|6682246|gb|AAF23298.1|AC016661_233792, 3791,4903putative 40 S ribosomal protein S23 [Arabidopsis3793thaliana]106*″Similar to gi|4539355|emb|CAB40049.1|putative48005883protein [Arabidopsis thaliana]33*″ Similar to gi|6691220|gb|AAF24558.1|AC007508_21F1K23.3 [Arabidopsis thaliana]63*″ 1634Similar to gi|8099126|dbj|BAA90498.1|rice ESTs51705558AA754121, AW155454, D48581 correspond to aregion of the predicated gene; unknown protein [Oryzasativa]100*″1660Similar to YLL2_EBVA8 Q07285 EPSTEIN-BARRVIRUS (STRAIN AG876) (HUMAN HERPESVIRUS4), AND EPSTEIN-BARR VIRUS (STRAIN P3HR-1)(HUMAN HERPESVIRUS 4). HYPOTHETICALBLLF2 PROTEIN.55*″ Open Reading Frame OS_ORF002688 HTC015682-A01.33 FRAME: −2 ORF: 8 LEN: 76227*″ 1616Similar to MYOD_PIG P49811 SUS SCROFA (PIG).MYOBLAST DETERMINATION PROTEIN 1.94*″ 1654Open Reading Frame OS_ORF020521 HTC138332-A01.F.30 FRAME: −1 ORF: 2 LEN: 894126*″1682Similar to gi|3746060|gb|AAC63835.1|unknown381950885407protein [Arabidopsis thaliana]132*″1687Open Reading Frame OS_ORF003818 ST(R)HTC022168-A01.43 FRAME: 2 ORF: 13 LEN: 627131*″Similar to Y140_NPVAC P41699 AUTOGRAPHACALIFORNICA NUCLEAR POLYHEDROSISVIRUS (ACMNPV). HYPOTHETICAL 7.1 KDPROTEIN IN ME53-IE0 INTERGENIC REGION.59*″ 1633Similar to gi|4966370|gb|AAD34701.1|AC006341_29>F3O9.30 [Arabidopsis thaliana]134*″1689Similar to gi|928896|emb|CAA60523.1|protein kinase3801, 3549,50225367catalytic domain (fragment) [Arabidopsis thaliana]3543, 4438,354884*″ 1647Similar to gi|3461812|gb|AAC32906.1|putative basic51045755blue protein (plantacyanin) [Arabidopsis thaliana]89*″ 1649Similar to gi|6735331|emb|CAB68157.1|putative50435248protein [Arabidopsis thaliana]291618Similar to LCM_LOCMI P80060 P80058 LOCUSTA5436MIGRATORIA (MIGRATORY LOCUST).PROTEASE INHIBITORS PRECURSOR(CONTAINS: PROTEASE INHIBITOR LCMII (PARS INTERCEREBRALIS MAJOR PEPTIDE D2)(PMP-D2); PROTEASE INHIBITOR LCMI II (PARSINTERCEREBRALIS MAJOR PEPTIDE C)7″Similar to gi|5852178|emb|CAB55416.1|zhb0008.1[Oryza sativa]1301686Open Reading Frame OS_ORF009113 HTC054673-A01.R.12 FRAME: 1 ORE: 6 LEN: 807137Similar to gi|2829868|gb|AAC00576.1|Unknownprotein [Arabidopsis thaliana]901650Similar to LIG4_PHACH P11542 P14153PHANEROCHAETE CHRYSOSPORIUM.LIGNINASE H2 PRECURSOR (EC 1.11.1.-) (LIGNINPEROXIDASE) (LG4).1051665Similar to ITA3_MOUSE Q62470 Q08441 Q08442MUS MUSCULUS (MOUSE). INTEGRIN ALPHA-3PRECURSOR (GALACTOPROTEIN B3) (GAPB3)(VLA-3 ALPHACHAIN) (CD49C).441626Similar to gi|3618312|dbj|BAA33202.1|zinc finger5788protein [Oryza sativa]661637Similar to gi|218210|dbj|BAA00539.1|small subunit of50195718ribulose-1,5-bisphosphate carboxylase (RuBPC) [Oryzasativa]1041664Similar to gi|3668085|gb|AAC61817.1|hypothetical5329protein [Arabidopsis thaliana]951655Similar to LFE4_CHICK Q90839 GALLUS GALLUS(CHICKEN). UNKNOWN LENS FIBER PROTEINCLFEST4 PRECURSOR.120Similar to gi|2827560|emb|CAA16568.1|predictedprotein [Arabidopsis thaliana]68Similar to gi|2293568|gb|AAB65433.1|HvB12D49475739homolog [Oryza sativa]741642Similar to gi|394736|emb|CAA40596.1|basic/leucine3262, 4300,49615769zipper protein [Oryza sativa]4299, 42981131671Similar to NT4_RAT P34131 RATTUS5470NORVEGICUS (RAT). NEUROTROPHIN-4PRECURSOR (NT-4) (NEUROTROPHIN-5) (NT-5).52Similar to gi|6006381|dbj|BAA84811.1|hypotheticalprotein [Oryza sativa]1331688Similar to gi|3193310|gb|AAC19293.1|contains4258, 3732,5857similarity to Nicotiana tabacum hin1 (GB: Y07563)4264, 3768,[Arabidopsis thaliana]4265, 4266,4257, 3747,3718, 37781271683Open Reading Frame OS_ORF005639 HTC033693-A01.R.7 FRAME: 2 ORF: 1 LEN: 669801646Similar to RS26_ORYSA P49216 ORYZA SATIVA3821, 3822,49595812(RICE). 40 S RIBOSOMAL PROTEIN S26 (S31).3820931653Similar to NIDO_RAT P08460 RATTUSNORVEGICUS (RAT). NIDOGEN (ENTACTIN)(FRAGMENT).38Similar to TBB_TRYCR P08562 TRYPANOSOMA3823, 3834,49825546CRUZI. TUBULIN BETA CHAIN (FRAGMENT).3618, 3006,4598, 3824,3619, 3826,3827, 3609,3606, 3616,3829, 3610,3608, 3607,3620, 3614,3828, 3612,3613, 3605,3604, 3825,3615, 3611,3617, 3833,45971291685Similar to GVPO_HALME Q02240HALOBACTERIUM MEDITERRANEI(HALOFERAX MEDITERRANEI). GVPO PROTEIN.35Similar to ACH4_RAT P09483 RATTUS3119, 3361,5413NORVEGICUS (RAT). NEURONAL3362ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-4 CHAIN PRECURSOR.911651Similar to ACH2_HUMAN Q15822 HOMOSAPIENS (HUMAN). NEURONALACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-2 CHAIN PRECURSOR.88Similar to RS21_ORYSA P35687 ORYZA SATIVA49685909(RICE). 40 S RIBOSOMAL PROTEIN S21.1151673Similar to CLUS_MESAU P14683 MESOCRICETUSAURATUS (GOLDEN HAMSTER). CLUSTERIN(SULFATED GLYCOPROTEIN 2) (SGP-2)(FRAGMENT).61Similar to RS9_TOBAC P49214 NICOTIANA3972, 3971,49675621TABACUM (COMMON TOBACCO). 40 S3970, 3965,RIBOSOMAL PROTEIN S9 (S4) (FRAGMENT).396440Similar to UL56_HSV2H P28282 HERPES SIMPLEXVIRUS (TYPE 2/STRAIN HG52). PROTEIN UL56.481628Similar to YT55_STRFR P20190 STREPTOMYCESFRADIAE. HYPOTHETICAL PROTEIN INTRANSPOSON TN4556 (FRAGMENT).69Similar to VE2_HPV29 P50772 HUMANPAPILLOMA VIRUS TYPE 29. REGULATORYPROTEIN E2.261615Similar to YRM5_CAEEL Q09601CAENORHABDITIS ELEGANS. HYPOTHETICAL40.4 KD PROTEIN R06F6.5 IN CHROMOSOME II.86Similar to gi|9229502|dbj|BAB00007.1|gene_id: MIL23.14˜unknown protein [Arabidopsisthaliana]321620Similar to gi|6466964|gb|AAF13099.1|AC009176_263368, 3366,5414putative RNA-binding protein, 3 partial [Arabidopsis3367, 3248thaliana]1071666Similar to CASK RAT P04468 RATTUSNORVEGICUS (RAT). KAPPA CASEINPRECURSOR.1161674Similar to gi|3063713|emb|CAA18604.1|putativeprotein [Arabidopsis thaliana]1141672Similar to E1BS_ADE12 P04492 HUMANADENOVIRUS TYPE 12. E1B PROTEIN, SMALL T-ANTIGEN (E1B 19K).1171675Similar to VGLL_HSV11 P10185 HERPES SIMPLEXVIRUS (TYPE 1/STRAIN 17). GLYCOPROTEIN LPRECURSOR.361622Similar to YRS5_CAEEL Q093495923CAENORHABDITIS ELEGANS. HYPOTHETICAL113.2 KD PROTEIN T05H10.5 IN CHROMOSOMEII.1221679Similar to YFX2_RHILE P14311 RHIZOBIUMLEGUMINOSARUM. HYPOTHETICAL 8.8 KDPROTEIN IN FIXW 5 REGION.711639Similar to gi|967985|gb|AAA74960.1|ribosomal51855539protein-linked ubiquitin651636Similar to gi|2580438|dbj|BAA23142.1|PCF1 [Oryza5405sativa]82Similar to gi|2668748|gb|AAB88619.1|ribosomal50865900protein L17 [Zea mays]721640Similar to gi|445612|prf∥1909359A ribosomal protein48375438S19 [Solanum tuberosum]49Similar to gi|1709498|sp|P50700|OSL3_ARATH3136, 3135,51825297OSMOTIN-LIKE PROTEIN OSM34 PRECURSOR4067, 406158Similar to gi|2570507|gb|AAB82139.1|ribosomal4272, 4273,48425915protein [Oryza sativa]4271, 4254,4255791645Similar to gi|7340694|emb|CAB82993.1|hypotheticalprotein [Arabidopsis thaliana]391624Similar to gi|9295726|gb|AAF87032.1|AC006535_105595T24P13.16 [Arabidopsis thaliana]561632Similar to gi|3738291|gb|AAC63633.1|unknown3848, 3849,5423protein [Arabidopsis thaliana]3599961656Similar to gi|3608141|gb|AAC36174.1|unknown4633, 463248905781protein [Arabidopsis thaliana]85Similar to gi|7413650|emb|CAB85998.1|ribosomal51905400protein L35-like [Arabidopsis thaliana]43Similar to gi|1293784|gb|AAA98698.1|similar to3378, 3379,4775human QM protein, a putative tumor supressor, and to3171, 2851,maize ubiquinol-cytochrome C reductase complex3172, 2949subunit VI requiring protein SC34731641Similar to gi|2995277|emb|CAA06224.1|51865673ubiquitin/ribosomal fusion protein [Lycopersiconesculentum]671638Similar to gi|6513935|gb|AAF14839.1|AC011664_21hypothetical protein [Arabidopsis thaliana]1421696Similar to RS25_CAEEL P528214912CAENORHABDITIS ELEGANS. PROBABLE 40 SRIBOSOMAL PROTEIN S25.1081667Similar to CHRD_RAT Q63148 RATTUSNORVEGICUS (RAT). CHORDIN (FRAGMENT).301619Similar to gi|5817301|gb|AAD52695.1|AF087818_151385464auxin transport protein [Arabidopsis thaliana]45Similar to GALE_BRELA Q452912710, 2711,50475517BREVIBACTERIUM LACTOFERMENTUM. UDP-2709, 3106,GLUCOSE 4-EPIMERASE (EC 5.1.3.2)2782(GALACTOWALDENASE) (UDP-GALACTOSE 4-EPIMERASE).1351690Similar to gi|8954065|gb|AAF82238.1|AC069143_145257Contains similarity to an AP2 domain containingprotein RAP2.10 mRNA from Arabidopsis thalianagb|AF003103 and contains an AP2 PF|00847 domain.EST gb|AI996763 comes from this gene.371623Similar to EF2_CHLKE P28996 CHLORELLA3657, 3656,4882KESSLERI. ELONGATION FACTOR 2 (EF-2).3654, 3647,3652, 3644,3650, 3651,3653, 365541Similar to gi|8467991|dbj|BAA96592.1|hypothetical5878protein [Oryza sativa]341621Similar to CIKA_HUMAN Q14721 HOMO SAPIENS2812(HUMAN). VOLTAGE-GATED POTASSIUMCHANNEL PROTEIN KV2.1 (DHK1).1181676Similar to Y116_ADE02 P03287 HUMANADENOVIRUS TYPE 2. HYPOTHETICAL 11.6 KDEARLY PROTEIN.1391693Similar to gi|8953729|dbj|BAA98092.1|emb|CAA71173.1˜gene_id: F6N7.23˜similar tounknown protein [Arabidopsis thaliana]1251681Similar to gi|3915825|sp|P49227|RL5_ARATH 60 S5719RIBOSOMAL PROTEIN L551Similar to gi|20238|emb|CAA36190.1|GOS2 [Oryza4070, 4072,4835sativa]4071, 2747,2746, 2748,3409286Similar to ATP4_IPOBA Q40089 IPOMOEA3346, 3345,5608BATATAS (SWEET POTATO) (BATATE). ATP3347SYNTHASE DELTA CHAIN, MITOCHONDRIALPRECURSOR (EC 3.6.1.34).1751718Similar to gi|4884522|dbj|BAA77779.1|class III30385454chitinase homologue (OsChib3H-g) [Oryza sativa]2251751Similar to VE2_HPV2A P25482 HUMAN5397PAPILLOMA VIRUS TYPE 2A. REGULATORYPROTEIN E2.2351760Similar to YFIP_ECOLI Q47319 ESCHERICHIACOLI. HYPOTHETICAL 27.0 KD PROTEIN INUNG-PSSA INTERGENIC REGION.147Similar to gi|7417426|gb|AAF62555.1|AF249880_14012, 401151555792UDP-glucose pyrophosphorylase [Oryza sativa subsp.indica]2831801Similar to VG12_BPPF1 P25132 BACTERIOPHAGEPF1. 12.0 KD PROTEIN (ORF 110).2111740Similar to RS17_HUMAN P08708 HOMO SAPIENS3175, 3173,49015345(HUMAN). 40 S RIBOSOMAL PROTEIN S17.31742411766Similar to ERFK_ECOLI P39176 ESCHERICHIA5894COLI. PROTEIN ERFK/SRFK PRECURSOR.1721717Similar to gi|6002799|gb|AAF00148.1|AF149815_151215639unknown [Oryza sativa]2401765Open Reading Frame OS_ORF021481 ST(R)HTC146509-A01.F.1 FRAME: 2 ORF: 2 LEN: 516255Open Reading Frame OS_ORF019240 HTC129282-5443A01.F.45 FRAME: 1 ORF: 1 LEN: 7951591706Open Reading Frame OS_ORF008660 HTC051956-A01.F.25 FRAME: −2 ORF: 1 LEN: 9032691787Similar to CASK SHEEP P02669 OVIS ARIES(SHEEP). KAPPA CASEIN PRECURSOR.2631781Similar to Y14K_PMV P20955 PAPAYA MOSAICPOTEXVIRUS (PMV). HYPOTHETICAL 14.1 KDPROTEIN IN ORF1 CODING STRAND.2321757Similar to PBP2_ECOLI P08150 ESCHERICHIACOLI. PENICILLIN-BINDING PROTEIN 2 (PBP-2).2931810Similar to C551_AZOVI P00104 AZOTOBACTER5167VINELANDII. CYTOCHROME C-551 (C551).2921809Similar to EST1_PSEFL Q51758 PSEUDOMONASFLUORESCENS. CARBOXYLESTERASE 1 (EC3.1.1.1) (ESTERASE I).2761794Similar to gi|7529288|emb|CAB86640.1|putative51405716protein [Arabidopsis thaliana]2781796Similar to gi|6573781|gb|AAF17701.1|AC009243_28F28K19.4 [Arabidopsis thaliana]213Similar to gi|6069647|dbj|BAA85423.1|hypothetical5450protein [Oryza sativa]204Similar to ATF4_MOUSE Q06507 MUS MUSCULUS(MOUSE). CYCLIC-AMP-DEPENDENTTRANSCRIPTION FACTOR ATF-4 (C/EBP-RELATED ATF)(C/ATF).254Open Reading Frame OS_ORF018238 HTC121584-A01.F.11 FRAME: −2 ORF: 10 LEN: 6632601778Similar to ATF6_HUMAN P18850 HOMO SAPIENS50495528(HUMAN). CYCLIC-AMP-DEPENDENTTRANSCRIPTION FACTOR ATF-6 (FRAGMENT).2801798Similar to gi|7801657|emb|CAB91578.1|putative5821protein [Arabidopsis thaliana]2501773Similar to VE7_HPV31 P17387 HUMANPAPILLOMA VIRUS TYPE 31. E7 PROTEIN.214Similar to gi|2244789|emb|CAB10211.1|ribosomal4188, 4187,48045315protein [Arabidopsis thaliana]3888, 3890,38912061737Similar to H2BT_RAT Q00729 RATTUS4123, 3744,51895575NORVEGICUS (RAT). HISTONE H2B, TESTIS.3771, 4120,4119, 4110,4277, 3772,4066, 4269,4117, 4118,4155, 4105,3754, 3720,3749, 4031,4138, 4109,3773, 3767,4276, 4084,3738, 4206,3736, 3726,4122, 4267,3777, 4192,4170, 4121,4191, 4065,3775, 3769,3712, 4145,3758, 4270,4275, 3723,3763, 4174,3722, 4064,4124, 4146186Similar to gi|8778567|gb|AAF79575.1|AC022464_335637F22G5.15 [Arabidopsis thaliana]2021735Similar to IF51_CAEEL P34563 CAENORHABDITIS51955389ELEGANS. PROBABLE INITIATION FACTOR 5A(EIF-5A) (EIF-4D).189Similar to RDH1_HUMAN Q92781 HOMO SAPIENS4661, 44415582(HUMAN). 11-CIS RETINOL DEHYDROGENASE(EC 1.1.1.105) (11-CIS RDH).2301756Similar to gi|4106388|gb|AAD02829.1|unknown[Arabidopsis thaliana]1541704Similar to MENE_BACSU P23971 BACILLUS3996, 3993,50925594SUBTILIS. O-SUCCINYLBENZOIC ACID--COA3995, 3994LIGASE (EC 6.2.1.26) (OSB-COASYNTHETASE) (O-SUCCINYLBENZOATE-COASYNTHASE).188Similar to HMZ1_DROSU Q24648 DROSOPHILA48255866SUBOBSCURA (FRUIT FLY). ZERKNUELLTPROTEIN.2081738Similar to gi|4104058|gb|AAD10251.1|blue copper-52155692binding protein homolog [Triticum aestivum]2841802Similar to THIO_CLOSG P81108 CLOSTRIDIUM4563, 45645675SPOROGENES. THIOREDOXIN (FRAGMENT).185Similar to gi|1710495|sp|P49690|RL23_ARATH 60 S3502, 3501,52245651RIBOSOMAL PROTEIN L232841, 32191871724Similar to IM17_HUMAN Q99595 HOMO SAPIENS5369(HUMAN). MITOCHONDRIAL IMPORT INNERMEMBRANE TRANSLOCASE SUBUNIT TIM17HOMOLOG.1441698Similar to gi|4432862|gb|AAD20710.1|unknown3527, 3526,51145629protein [Arabidopsis thaliana]3522, 3524,3523156Similar to OST4_PIG Q29381 SUS SCROFA (PIG).423550335764DOLICHYL-DIPHOSPHOOLIGOSACCHARIDE-PROTEIN GLYCOSYLTRANSFERASE 48KDSUBUNIT (EC 2.4.1.119) (OLIGOSACCHARYLTRANSFERASE 48 KD SUBUNIT)(DDOST 48 KDSUBUNIT) (FRAGMENT).155Similar to GS17_XENLA P07733 XENOPUS LAEVIS(AFRICAN CLAWED FROG). GASTRULA-SPECIFIC PROTEIN 17.1771720Similar to gi|7573627|dbj|BAA94536.1|hypothetical5749protein [Oryza sativa]1651710Similar to ALF_ORYSA P17784 ORYZA SATIVA3871, 3872,51085819(RICE). FRUCTOSE-BISPHOSPHATE ALDOLASE3867, 3873(EC 4.1.2.13).218Similar to BCL2_MOUSE P10417 P10418 MUSMUSCULUS (MOUSE). APOPTOSIS REGULATORBCL-2.201Similar to gi|5931784|emb|CAB56630.1|SBP-domain51035416protein 4 [Zea mays]2211747Similar to gi|9295712|gb|AAF87018.1|AC005292_275387F26F24.11 [Arabidopsis thaliana]2151742Similar to gi|1668773|emb|CAA67922.1|ubiquitin-like5149protein [Oryza sativa]2821800Similar to gi|4582451|gb|AAD24835.1|AC007071_748895262unknown protein [Arabidopsis thaliana]2621780Similar to NEU3_CATCO P17668 CATOSTOMUS5295COMMERSONI (WHITE SUCKER). VASOTOCIN-NEUROPHYSIN VT 1 PRECURSOR (VT).251Open Reading Frame OS_ORF018254 HTC121717-A01.F.7 FRAME: −3 ORF: 1 LEN: 6602591777Similar to gi|8885623|dbj|BAA97553.1|2758, 2756,5763gb|AAF32471.1˜gene_id: F24C7.9˜similar to unknown2757, 2915protein [Arabidopsis thaliana]2711789Similar to gi|9279763|dbj|BAB01389.1|emb|CAB45833.1˜gene_id: MZN24.24˜similar tounknown protein [Arabidopsis thaliana]1661711Similar to YA14_SCHPO Q09686398950855920SCHIZOSACCHAROMYCES POMBE (FISSIONYEAST). HYPOTHETICAL 28.0 KD PROTEINC13C5.04 IN CHROMOSOME I.258Similar to RL32_THETH P80339 O05480 THERMUSAQUATICUS (SUBSP. THERMOPHILUS). 50 SRIBOSOMAL PROTEIN L32.2441768Similar to ACM1_PIG P04761 SUS SCROFA (PIG).5687MUSCARINIC ACETYLCHOLINE RECEPTOR M1(BRAIN).2231749Similar to gi|3927834|gb|AAC79591.1|unknownprotein [Arabidopsis thaliana]1991733Similar to gi|857574|gb|AAA68 175.1|H+-ATPase3487, 4197,516555414198, 3488,41962461770Similar to gi|9280304|dbj|BAB01759.1|5871emb|CAB38961.1˜gene_id: MRP15.18˜similar tounknown protein [Arabidopsis thaliana]2391764Similar to gi|3980377|gb|AAC95180.1|unknown3925, 3910,5340protein [Arabidopsis thaliana]3924, 39231611707Similar to LEM3_HUMAN P16109 HOMO SAPIENS(HUMAN). P-SELECTIN PRECURSOR (GRANULEMEMBRANE PROTEIN 140) (GMP-140)(PADGEM) (CD62P) (LEUKOCYTE-ENDOTHELIALCELL ADHESION MOLECULE 3) (LECAM3).2201746Similar to gi|6579207|gb|AAF18250.1|AC011438_122765, 2764,50995429T23G18.10 [Arabidopsis thaliana]29671521703Similar to gi|9294350|dbj|BAB02247.1|gb|AAD03575.1˜gene_id: F3H11.10˜similar tounknown protein [Arabidopsis thaliana]2281754Open Reading Frame OS_ORF021536 HTC147061-A01.R.7 FRAME: −1 ORF: 1 LEN: 6812641782Open Reading Frame OS_ORF010347 HTC062980-3880, 3881,A01.R.9 FRAME: −2 ORF: 4 LEN: 6783879207Similar to RL23_TOBAC Q07760 NICOTIANA3502, 3501,5224TABACUM (COMMON TOBACCO). 60 S2841, 3219RIBOSOMAL PROTEIN L23.2871804Similar to gi|6382501|gb|AAF07787.1|AC010704_125847unknown protein [Arabidopsis thaliana]2421767Similar to gi|4586030|gb|AAD25648.1|AC007109_6unknown protein [Arabidopsis thaliana]2291755Similar to HXB9_MOUSE P20615 MUS MUSCULUS(MOUSE). HOMEOBOX PROTEIN HOX-B9 (HOX-2.5).2671785Similar to PNTA_ECOLI P07001 P7688832445780ESCHERICHIA COLI. NAD(P)TRANSHYDROGENASE SUBUNIT ALPHA (EC1.6.1.1) (PYRIDINENUCLEOTIDETRANSHYDROGENASE SUBUNIT ALPHA)(NICOTINAMIDENUCLEOTIDETRANSHYDROGENASE SUBUNITALPHA).257Similar to gi|3434971|dbj|BAA32420.1|ethylene5638responsive element binding factor 3 [Arabidopsisthaliana]182Similar to gi|8467950|dbj|BAA96574.1|Similar to5352Arabidopsis thaliana chromosome 4 BAC T15B16;hypothetical protein (AF104919) [Oryza sativa]243Similar to TR11_HUMAN Q15643 HOMO SAPIENS(HUMAN). THYROID RECEPTOR INTERACTINGPROTEIN 11 (TRIP11) (FRAGMENT).1711716Similar to PRSD_ECOLI P42183 ESCHERICHIACOLI. CHAPERONE PROTEIN PRSD(FRAGMENT).2741792Similar to YT44_STRFR P20188 STREPTOMYCES5649FRADIAE. HYPOTHETICAL 44.4 KD PROTEIN INTRANSPOSON TN4556.1951729Similar to GSHC_SCHMA Q00277 SCHISTOSOMA5200MANSONI (BLOOD FLUKE). GLUTATHIONEPEROXIDASE (EC 1.11.1.9) (GPX).1461700Similar to gi|224389|prf∥110321.8A glycinin A5[Glycine max]2261752Open Reading Frame OS_ORF007080 HTC042461-A01.R.20 FRAME: −1 ORF: 1 LEN: 11221641709Open Reading Frame OS_ORF011196 HTC069008-5816A01.F.9 FRAME: 2 ORF: 1 LEN: 7472221748Open Reading Frame containing a Sage tag sequencenear 3 end OS_ORF010241 ST(F) HTC062062-A01.F.8 FRAME: −3 ORF: 13 LEN: 6332881805Similar to gi|6728996|gb|AAF26993.1|AC016827_449415406hypothetical protein [Arabidopsis thaliana]2481772Similar to AMYG_ASPSH P22832 ASPERGILLUSSHIROUSAMI. GLUCOAMYLASE PRECURSOR(EC 3.2.1.3) (GLUCAN 1,4-ALPHA-GLUCOSIDASE) (1,4-ALPHA-D-GLUCANGLUCOHYDROLASE).2271753Similar to PM17_BOVIN Q06154 BOS TAURUS(BOVINE). MELANOCYTE PROTEIN PMEL 17(RETINAL PIGMENT EPITHELIAL-SPECIFIC PROTEIN) (FRAGMENT).1571705Similar to gi|3249078|gb|AAC24062.1|Contains5738similarity to CONSTANS protein gb|2244883 from A.thaliana. [Arabidopsis thaliana]249Similar to gi|6729517|emb|CAB67673.1|putative5489protein [Arabidopsis thaliana]2191745Similar to gi|7543914|emb|CAB87154.1|putativeprotein [Arabidopsis thaliana]2901807Similar to YD87_SCHPO Q10412SCHIZOSACCHAROMYCES POMBE (FISSIONYEAST). HYPOTHETICAL 44.6 KD PROTEINC1F3.07C IN CHROMOSOME I.153Similar to gi|6539579|dbj|BAA88195.1|Similar to3005, 30045372human dimethylaniline monooxygenase (AC002376)[Oryza sativa]1691714Similar to gi|4514635|dbj|BAA75476.1|root capprotein 1 [Zea mays]2161743Similar to gi|903689|gb|AAB96840.1|acyl carrier5161protein precursor [Arabidopsis thaliana]2531775Similar to EFA1_XENLA P52794 XENOPUS5332LAEVIS (AFRICAN CLAWED FROG). EPHRIN-A1PRECURSOR (EPH-RELATED RECEPTORTYROSINE KINASE LIGAND 1) (LERK-1) (XELF).2371762Similar to COBL_PSEDE P21921 PSEUDOMONASDENITRIFICANS. PRECORRIN-6Y C5,15-METHYLTRANSFERASE (DECARBOXYLATING)(EC 2.1.1.132) (PRECORRIN-6METHYLTRANSFERASE) (PRECORRIN-6YMETHYLASE).205Similar to gi|6069651|dbj|BAA85427.1|hypotheticalprotein [Oryza sativa]2891806Similar to gi|4417269|gb|AAD20394.1|hypotheticalprotein [Arabidopsis thaliana]183Similar to gi|4582468|gb|AAD24852.1|AC007071_242976518340 S ribosomal protein; contains C-terminal domain[Arabidopsis thaliana]2731791Similar to LSHB_CANFA P18842 CANISFAMILIARIS (DOG). LUTROPIN BETA CHAINPRECURSOR (LUTEINIZING HORMONE) (LSH-B)(LH-B)(FRAGMENT).1921726Similar to CXA3_RAT P29414 RATTUSNORVEGICUS (RAT). GAP JUNCTION ALPHA-3PROTEIN (CONNEXIN 46) (CX46).2721790Similar to STCI_EMENI Q00675 EMERICELLA5653NIDULANS (ASPERGILLUS NIDULANS).PUTATIVE STERIGMATOCYSTINBIOSYNTHESIS LIPASE/ESTERASE STCI.2521774Similar to BPHD_PSES1 P17548 PSEUDOMONAS4068, 4069SP. (STRAIN KKS102). 2-HYDROXY-6-OXO-6-PHENYLHEXA-2,4-DIENOATE HYDROLASE (EC3.7.1.-).180Similar to gi|1388080|gb|AAC49354.1|thioredoxin h5754173Similar to gi|8777392|dbj|BAA96982.1|11-beta-5864hydroxysteroid dehydrogenase-like [Arabidopsisthaliana]2911808Open Reading Frame OS_ORF006689 HTC040175-5506A01.F.19 FRAME: 2 ORF: 7 LEN: 801148Similar to gi|7267933|emb|CAB78275.1|cytochrome4089, 4088,52175733P450 homolog [Arabidopsis thaliana]30861451699Open Reading Frame containing a Sage tag sequence5301near 3 end OS_ORF011358 ST(F) HTC070113-A01.F.8 FRAME: 2 ORF: 1 LEN: 534174Similar to gi|166924|gb|AAA32903.1|ubiquitin carrier49325665protein2341759Similar to YUES_CAEEL P90859 P90852343550985695CAENORHABDITIS ELEGANS. HYPOTHETICAL64.7 KD PROTEIN F26E4.11 IN CHROMOSOME I.160Similar to gi|246250|gb|AAB21538.1|GmPK4 = protein3949, 394849225655kinase [Glycine max L. = soybeans, Peptide, 101 aa]1621708Similar to gi|4678920|emb|CAB41311.1|putative heat2880, 3220,5279shock transcription factor [Arabidopsis thaliana]3690, 3689,3926, 36881981732Similar to gi|8099125|dbj|BAA90497.1|rice EST5558C27893 corresponds to a region of the predicated gene;unknown protein [Oryza sativa]2361761Similar to gi|8953758|dbj|BAA98113.1|gene_id: K15C23.4˜unknown protein [Arabidopsisthaliana]1961730Open Reading Frame OS_ORF004409 HTC025875-A01.9 FRAME: −1 ORF: 4 LEN: 813181Similar to gi|6478924|gb|AAF14029.1|AC011436_3unknown protein [Arabidopsis thaliana]2241750Similar to gi|7413567|emb|CAB86046.1|putativeprotein [Arabidopsis thaliana]1431697Similar to YAGT_ECOLI P77165 ESCHERICHIACOLI. HYPOTHETICAL 24.3 KD PROTEIN ININTF-EAEH INTERGENIC REGION.1761719Similar to gi|6983878|dbj|BAA90813.1|hypothetical5489protein [Oryza sativa]2561776Similar to gi|8096645|dbj|BAA96216.1|hypotheticalprotein [Oryza sativa]1791722Similar to gi|7268425|emb|CAB78717.1|apetala25786domain TINY like protein [Arabidopsis thaliana]1841723Similar to gi|3293561|gb|AAC25778.1|germin-like4116, 4075,52045760protein 8 [Oryza sativa]4115, 4073,4593, 4074,4592, 4076,4575, 4596,45762471771Open Reading Frame OS_ORF007879 HTC047180-A01.F.9 FRAME: −1 ORF: 3 LEN: 7022851803Similar to gi|7329661|emb|CAB82758.1|putative5290protein [Arabidopsis thaliana]2681786Similar to YOAC_MYCTU Q507425584MYCOBACTERIUM TUBERCULOSIS.HYPOTHETICAL 13.9 KD PROTEIN CY9C4.12.2121741Similar to gi|168540|gb|AAA18549.1|putative, similar49255910to ribosomal protein S222451769Open Reading Frame OS_ORF010851 ST(R)HTC066685-A01.R.44 FRAME: −2 ORF: 2 LEN: 7382171744Similar to gi|3201971|gb|AAC19376.1|hypotheticalsecretory protein SH27A precursor [Oryza sativa]2031736Similar to gi|1815662|gb|AAC78393.1|low molecular3668, 3677,49275663mass heat shock protein Oshsp18.0 [Oryza sativa]3679, 3678,3675, 3676,4029, 3302209Open Reading Frame OS_ORF020474 HTC137976-A01.R.9 FRAME: −1 ORF: 1 LEN: 7441911725Similar to gi|3702333|gb|AAC62890.1|hypothetical4674protein [Arabidopsis thaliana]163Similar to TPM4_DROME P49455 DROSOPHILAMELANOGASTER (FRUIT FLY). TROPOMYOSIN1, FUSION PROTEIN 33.1971731Similar to gi|7630036|emb|CAB88330.1|putativeprotein [Arabidopsis thaliana]2381763Similar to FRA_DROME P21525 DROSOPHILAMELANOGASTER (FRUIT FLY).TRANSCRIPTION FACTOR DFRA (FOS-RELATEDANTIGEN) (AP-1).1941728Similar to gi|5596483|emb|CAB51421.1|RING-H25727finger protein RHA1a-like protein [Arabidopsisthaliana]1701715Similar to gi|2586127|gb|AAB82766.1|b-keto acyl4701, 4700,4867reductase [Hordeum vulgare]4702231Similar to AMPH_HUMAN P49418 HOMO SAPIENS(HUMAN). AMPHIPHYSIN.2331758Similar to DSVB_DESGI P94694 DESULFOVIBRIOGIGAS. SULFITE REDUCTASE, DISSIMILATORY-TYPE BETA SUBUNIT (EC1.8.99.3) (DESULFOVIRIDIN BETA SUBUNIT)(HYDROGENSULFITE REDUCTASEBETASUBUNIT) (FRAGMENT).2701788Open Reading Frame containing a Sage tag sequence5907near 3 end OS_ORF017300 ST(F) HTC115342-A01.R.10 FRAME: 1 ORF: 6 LEN: 525190Open Reading Frame OS_ORF012115 HTC075620-A01.F.7 FRAME: 2 ORF: 8 LEN: 675150Similar to gi|579225|emb|CAA01514.1|unnamed49045448protein product [Triticum aestivum]1681713Similar to gi|6751704|gb|AAF27686.1|AC018848_329225479hypothetical protein [Arabidopsis thaliana]2791797Similar to SUT1_YEAST P530325562SACCHAROMYCES CEREVISIAE (BAKER SYEAST). PROBABLE STEROL CARRIER.1931727Similar to gi|6730712|gb|AAF27107.1|AC011809_164449, 44484820Unknown protein [Arabidopsis thaliana]1491701Similar to CRTI_STRSE P54971 STREPTOMYCES4602, 2919,5393SETONII. PHYTOENE DEHYDROGENASE (EC4601, 27891.3.-.-) (PHYTOENE DESATURASE).2771795Similar to CILA_ECOLI P75726 P77102ESCHERICHIA COLI. CITRATE LYASE ALPHACHAIN (EC 4.1.3.6) (CITRASE).2611779Similar to MYOD_HUMAN P15172 HOMO30915570SAPIENS (HUMAN). MYOBLASTDETERMINATION PROTEIN 1 (MYOGENICFACTOR MYF-3).158Similar to gi|4432834|gb|AAD20683.1|unknown50615356protein [Arabidopsis thaliana]1671712Similar to gi|9294462|dbj|BAB02681.1|1-asparaginase3909, 3907,50505600(1-asparagine amidohydrolase) [Arabidopsis thaliana]3908, 3064,3906, 2901,39052101739Similar to gi|3157922|gb|AAC17605.1|Contains51215488similarity to proline-rich protein, gb|S68113 fromBrassica napus. [Arabidopsis thaliana]2661784Open Reading Frame OS_ORF009294 HTC055735-2916, 4437,A01.16 FRAME: −2 ORF: 8 LEN: 88528201511702Similar to gi|4416306|gb|AAD20311.1|hypothetical4338, 2689,51295624protein [Zea mays]2688, 26902001734Similar to gi|7340678|emb|CAB82977.1|putative51245309protein [Arabidopsis thaliana]2751793Similar to gi|7459220|pir∥T08447 hypothetical proteinF22O6.100 - Arabidopsis thaliana1781721Similar to gi|7340871|dbj|BAA92961.1|hypothetical4771protein [Oryza sativa]2651783Similar to Y4VG_RHISN Q53215 RHIZOBIUM SP.44455825(STRAIN NGR234). PROBABLE CYTOCHROMEP450 Y4VG (EC 1.14.14.-).2811799Similar to gi|7488315|pir∥T00933 RNA-binding protein5871homolog T24P15.15 - Arabidopsis thaliana3611853Similar to ACRO_RAT P29293 RATTUSNORVEGICUS (RAT). ACROSIN PRECURSOR (EC 3.4.21.10).3461840Similar to gi|7267617|emb|CAB80929.1|hypotheticalprotein [Arabidopsis thaliana]3781869Similar to VP3_CAVCI P54094 CHICKEN ANEMIAVIRUS (USA ISOLATE CIA-1) (CAV). APOPTIN(VP3).3841873Similar to gi|6957718|gb|AAF32462.1|unknown5851protein [Arabidopsis thaliana]321Similar to VIC2_AGRRA P13460AGROBACTERIUM RHIZOGENES. VIRC2PROTEIN.3081817Similar to PGKH_CHLFU P36232 CHLORELLA50945249FUSCA. PHOSPHOGLYCERATE KINASE,CHLOROPLAST (EC 2.7.2.3) (PERIODCLOCK PROTEIN) (FRAGMENT).337Similar to gi|1352427|sp|P47815|IF1A_WHEAT3884, 3882,52095324EUKARYOTIC TRANSLATION INITIATION3883FACTOR 1A (EIF-1A) (EIF-4C)3861875Similar to RBS_OLILU P14961 OLISTHODISCUS5019LUTEUS (HETEROSIGMA AKASHIWO).RIBULOSE BISPHOSPHATE CARBOXYLASESMALL CHAIN (EC 4.1.1.39).3701862Similar to gi|2760330|gb|AAB95243.1|F1N21.153920, 3918,50455507[Arabidopsis thaliana]3917, 3916,3919, 39213581851Open Reading Frame containing a Sage tag sequencenear 3 end OS_ORF001736 ST(F) HTC009976-A01.7FRAME: −3 ORF: 1 LEN: 5223401834Similar to YOO3_CAEEL P34635CAENORHABDITIS ELEGANS. HYPOTHETICAL25.2 KD PROTEIN ZK507.3 IN CHROMOSOME III.3191825Similar to gi|4262229|gb|AAD14522.1|unknown5107protein [Arabidopsis thaliana]3481842Open Reading Frame OS_ORF018077 HTC120520-A01.R.35 FRAME: 3 ORF: 1 LEN: 987302Similar to YCS0_YEAST P2562345105207SACCHAROMYCES CEREVISIAE (BAKER SYEAST). HYPOTHETICAL 72.7 KD PROTEIN INRIM1-CRY1 INTERGENIC REGION.3851874Similar to RELX_DASSA P81191 DASYATISSABINA (ATLANTIC STINGRAY). RELAXIN-LIKEPROTEIN AGF.3351831Open Reading Frame OS_ORF016871 HTC111915-A01.R.5 FRAME: −3 ORF: 1 LEN: 6363391833Open Reading Frame OS_ORF005335 HTC031718-A01.F.21 FRAME: 2 ORF: 18 LEN: 7413381832Similar to gi|3193326|gb|AAC19308.1|contains50605642similarity to transcriptional activators such as Ra-likeand myc-like regulatory R proteins [Arabidopsisthaliana]3331830Similar to RL26_HUMAN Q02877 HOMO SAPIENS3951, 3952,4898(HUMAN), AND MUS MUSCULUS (MOUSE). 60 S3950RIBOSOMAL PROTEIN L26.310Similar to gi|7486247|pir∥T01293 hypothetical protein5830F27F23.25 - Arabidopsis thaliana303Similar to LACS_TRAVE Q12717 TRAMETES3180, 29425255VERSICOLOR (WHITE-ROT FUNGUS). LACCASEPRECURSOR (EC 1.10.3.2)(BENZENEDIOL: OXYGENOXIDOREDUCTASE) (URISHIOL OXIDASE)(DIPHENOL OXIDASE) (LACCASE IV).3501844Similar to SCAD_HUMAN P51172 HOMO SAPIENS(HUMAN). AMILORIDE-SENSITIVE SODIUMCHANNEL DELTA-SUBUNIT (EPITHELIALNA+ CHANNEL DELTA SUBUNIT) (DELTA ENAC)(NONVOLTAGE-GATED SODIUM CHANNEL 1DELTA SUBUNIT) (SCNED) (DELTA NACH).3451839Similar to gi|4587548|gb|AAD25779.1|AC006577_1551525751Contains similarity to gb|U93273 putative auxin-repressed protein from Prunus armenica. ESTgb|Z26668 comes from this gene. [Arabidopsisthaliana]3671859Similar to gi|8843817|dbj|BAA973.65.1|contains4252, 42515618similarity to unknownprotein˜gene_id: MUL3.10˜pir∥T08554 [Arabidopsisthaliana]3471841Similar to COXD_HUMAN Q02221 O00761 HOMOSAPIENS (HUMAN). CYTOCHROME C OXIDASEPOLYPEPTIDE VIA-HEART PRECURSOR (EC1.9.3.1) (COXVIAH).3571850Similar to LSHB_BALAC P33088 BALAENOPTERA5871ACUTOROSTRATA (MINKE WHALE) (LESSERRORQUAL). LUTROPIN BETA CHAIN(LUTEINIZING HORMONE) (LSH-B) (LH-B).3131821Similar to gi|8778280|gb|AAF79289.1|AC068602_12450748805702F14D16.19 [Arabidopsis thaliana]3521846Similar to gi|7594528|emb|CAB88053.1|putative5230protein [Arabidopsis thaliana]3111819Similar to gi|3777436|emb|CAA04440.1|DNA binding5461protein [Hordeum vulgare]322Similar to YI3C_MYCTU P19773MYCOBACTERIUM TUBERCULOSIS. INSERTIONELEMENT IS986 HYPOTHETICAL 13 KDPROTEIN (ORFC).2981813Similar to gi|21481|emb|CAA78034.1|70-kD heat3311, 2923,51505753shock protein [Solanum tuberosum]3808, 3494,3804, 3806,3598, 3807,2874, 4240,4239, 3439,3596, 2873,3602, 3805,3600, 3597,3593, 3601,4241, 3438,3590, 3592,3459, 3594,2975, 29893231826Similar to ULC9_HCMVA P16838 HUMAN5637CYTOMEGALOVIRUS (STRAIN AD169).HYPOTHETICAL PROTEIN UL129.2991814Similar to gi|6633856|gb|AAF19715.1|AC008047_22F2K11.8 [Arabidopsis thaliana]3931881Similar to gi|3738331|gb|AAC63672.1|unknown5841protein [Arabidopsis thaliana]3691861Similar to gi|4063754|gb|AAC98462.1|putativechloroplast nucleoid DNA-binding protein[Arabidopsis thaliana]314Similar to gi|2832700|emb|CAA16798.1|unknown4557, 45565319protein [Arabidopsis thaliana]3601852Open Reading Frame OS_ORF001954 ST(R)HTC011269-A01.9 FRAME: 1 ORF: 7 LEN: 513320Similar to gi|6520161|dbj|BAA87939.1|ZF145855[Arabidopsis thaliana]3421836Similar to E75C_DROME P13055 DROSOPHILA5809MELANOGASTER (FRUIT FLY). ECDYSONE-INDUCIBLE PROTEIN E75-C.328Open Reading Frame OS_ORF006350 HTC038039-A01.R.19 FRAME: 2 ORF: 7 LEN: 7953981885Similar to gi|140171|sp|P03936|YAC9_MAIZE5456TRANSPOSABLE ELEMENT ACTIVATORHYPOTHETICAL 23 KD PROTEIN (AC 23 KDPROTEIN)3971884Similar to gi|8843749|dbj|BAA97297.1|404952105398emb|CAB61744.1˜gene_id: MXK3.7˜similar tounknown protein [Arabidopsis thaliana]3961883Similar to gi|6642674|gb|AAF20254.1|AC015450_155478hypothetical protein [Arabidopsis thaliana]3241827Similar to PRF1_LYCES Q00451 LYCOPERSICON4302, 3959,50445593ESCULENTUM (TOMATO). 36.4 KD PROLINE-3958RICH PROTEIN.300Open Reading Frame OS_ORF010018 HTC060592-3051A01.F.33 FRAME: −2 ORF: 1 LEN: 696306Similar to gi|2780740|dbj|BAA24356.1|trans-ciinamate3876, 4611,502856034-hydroxylase [Arabidopsis thaliana]3874, 3868,3875, 3869,3870381Similar to gi|5823341|gb|AAD53109.1|AF176004_14610, 46095437putative transcription factor [Arabidopsis thaliana]3721863Open Reading Frame OS_ORF019338 HTC129955-A01.8 FRAME: −2 ORF: 3 LEN: 6633641856Similar to DAP1_HUMAN P51397 HOMO SAPIENS5386(HUMAN). DEATH-ASSOCIATED PROTEIN 1(DAP-1).3791870Similar to INTR_STRAM P1543 5 STREPTOMYCES457949875730AMBOFACIENS. INTEGRASE.3041816Similar to RNT1_TRIHA P26875 TRICHODERMA5714HARZIANUM. GUANYL-SPECIFICRIBONUCLEASE TH1 (EC 3.1.27.3).3531847Similar to gi|7459596|pir∥T01153 hypothetical proteinF26B6.29 - Arabidopsis thaliana394Similar to Y4HN_RHISN P55481 RHIZOBIUM SP.(STRAIN NGR234). HYPOTHETICAL 16.0 KDPROTEIN Y4HN.3921880Similar to gi|4539010|emb|CAB39631.1|putative49695351DNA-directed RNA polymerase [Arabidopsis thaliana]3091818Similar to HV58_MOUSE P18529 MUS MUSCULUS5822(MOUSE). IG HEAVY CHAIN PRECURSOR VREGION (5-76).331Similar to gi|6041842|gb|AAF02151.1|AC009853_114336, 2899unknown protein [Arabidopsis thaliana]315Similar to gi|9279738|dbj|BAB01328.1|3894, 3892,5256gene_id: MWL2.24˜unknown protein [Arabidopsis4150thaliana]3651857Similar to gi|3608146|gb|AAC36179.1|unknown5535protein [Arabidopsis thaliana]3491843Similar to gi|5262197|emb|CAB45794.1|hypothetical28485173protein [Arabidopsis thaliana]382Similar to gi|3776562|gb|AAC64879.1|Similar togb|X80472 STS15 gene from Solanum tuberosum.[Arabidopsis thaliana]3801871Similar to gi|245409|gb|AAB21424.1|ATPase subunit6 [corn, C male-sterile cytoplasm, Peptide Partial, 184aa]327Similar to gi|4455218|emb|CAB36541.1|putative51105511protein [Arabidopsis thaliana]3291829Similar to gi|5281018|emb|CAB45991.1|OBP33pep5815like protein [Arabidopsis thaliana]3741865Similar to VE2_HPV18 P06790 HUMANPAPILLOMA VIRUS TYPE 18. REGULATORYPROTEIN E2.3761867Open Reading Frame OS_ORF005044 HTC029791-A01.F.6 FRAME: 1 ORF: 1 LEN: 729371Similar to gi|4966371|gb|AAD34702.1|AC006341_305579Similar to gb|D14414 Indole-3-acetic acid inducedprotein from Vigna radiata. ESTs gb|AA712892 andgb|Z17613 come from this gene. [Arabidopsis thaliana]3251828Similar to YKU7_YEAST P360394935SACCHAROMYCES CEREVISIAE (BAKER SYEAST). HYPOTHETICAL 29.4 KD PROTEIN INSTE6-LOS1 INTERGENIC REGION.2951811Open Reading Frame OS_ORF017345 HTC115523-3114, 31155305A01.F.13 FRAME: 1 ORF: 22 LEN: 10893751866Open Reading Frame OS_ORF001416 HTC008104-A01.7 FRAME: 3 ORF: 1 LEN: 7653511845Similar to CASK_PIG P11841 SUS SCROFA (PIG).KAPPA CASEIN PRECURSOR.307Open Reading Frame OS_ORF010317 HTC062709-A01.25 FRAME: −2 ORF: 11 LEN: 6993181824Similar to gi|8096605|dbj|BAA96177.1|hypotheticalprotein [Oryza sativa]305Similar to NRM1_SHEEP P49280 OVIS ARIES4647, 464648925534(SHEEP). NATURAL RESISTANCE-ASSOCIATEDMACROPHAGE PROTEIN 1 (NRAMP1) (FRAGMENT).3551849Open Reading Frame OS_ORF015774 HTC103176-A01.R.26 FRAME: −2 ORF: 19 LEN: 675359Open Reading Frame OS_ORF011279 HTC069461-A01.F.14 FRAME: −2 ORF: 21 LEN: 7293661858Similar to VE2_HPV45 P36794 HUMANPAPILLOMA VIRUS TYPE 45. REGULATORYPROTEIN E2.332Similar to gi|5042444|gb|AAD38281.1|AC007789_748605708putative low molecular early light-inducible protein[Oryza sativa]3621854Similar to gi|7248410|dbj|BAA92733.1|hypotheticalprotein [Oryza sativa]3681860Similar to PST MOUSE Q64692 MUS MUSCULUS2838, 283752035823(MOUSE). ALPHA-2,8-POLYSIALYLTRANSFERASE (EC 2.4.99.-)(ST8SIAIV) (CMP-N-ACETYLNEURAMINATE-POLY-ALPHA-2,8-SIALYL TRANSFERASE).3831872Similar to gi|8809685|dbj|BAA97226.1|contains50355848similarity to probable DNA binding proteinPCF1˜gene_id: MJM18.6 [Arabidopsis thaliana]3411835Similar to ICLN_RAT Q04753 RATTUS4537NORVEGICUS (RAT). CHLORIDECONDUCTANCE REGULATORY PROTEIN ICLN.3161822Similar to YOE2_STRAT Q53684 STREPTOMYCES48715756ANTIBIOTICUS. HYPOTHETICAL 48.5 KDPROTEIN IN OLED 5 REGION PRECURSOR(ORF2).3891878Similar to gi|3927839|gb|AAC79596.1|hypothetical5349protein [Arabidopsis thaliana]3171823Similar to DMPD_PSESP P19076 PSEUDOMONAS3352, 335351605725SP. (STRAIN CF600). 2-HYDROXYMUCONICSEMIALDEHYDE HYDROLASE (EC 3.1.1.-)(HMSH).3011815Similar to BEL1_SFV1 P29169 SIMIAN FOAMY5476VIRUS (TYPE 1) (SFV-1). BEL-1 PROTEIN.330Similar to ST12_KLULA Q08400KLUYVEROMYCES LACTIS (YEAST). STE12PROTEIN.2961812Similar to BEL1_SFV3L P27402 SIMIAN FOAMYVIRUS (TYPE 3/STRAIN LK3) (SFV-3). BEL-1PROTEIN.3541848Similar to gi|6561967|emb|CAB62433.1|putative5266protein [Arabidopsis thaliana]334Open Reading Frame OS_ORF004707 HTC027672-A01.R.12 FRAME: −3 ORF: 1 LEN: 1401294Similar to A2AB_ELEMA O19014 ELEPHASMAXIMUS (INDIAN ELEPHANT). ALPHA-2BADRENERGIC RECEPTOR (ALPHA-2BADRENOCEPTOR) (FRAGMENT).3881877Similar to gi|6560766|gb|AAF16766.1|AC010155_19F3M18.10 [Arabidopsis thaliana]3431837Similar to YNA8_YEAST P539834451, 4454,5474SACCHAROMYCES CEREVISIAE (BAKER S4450YEAST). HYPOTHETICAL 76.7 KD PROTEIN INSPO1-SIS1 INTERGENIC REGION.336Similar to gi|3445197|gb|AAC32427.1|homeodomain48255866transcription factor (HAT9) [Arabidopsis thaliana]3121820Open Reading Frame OS_ORF007081 HTC042461-A01.R.20 FRAME: −2 ORF: 1 LEN: 1086356Similar to gi|3776565|gb|AAC64882.1|T22H22.8[Arabidopsis thaliana]3771868Similar to gi|9280693|gb|AAF86562.1|AC069252_215385F2E2.8 [Arabidopsis thaliana]3871876Similar to gi|9229979|dbj|BAB00670.1|gene_id: MGD8.19˜similar to unknown protein(gb|AAD32889.1) [Arabidopsis thaliana]297Open Reading Frame OS_ORF015837 HTC103626-A01.R.22 FRAME: −1 ORF: 37 LEN: 11643441838Similar to V17_BPT3 P07719 BACTERIOPHAGE T3.GENE 1.7 PROTEIN.3911879Similar to gi|6980074|gb|AAF34713.1|AF224762_151935314SigA binding protein [Arabidopsis thaliana]3951882Similar to gi|8978280|dbj|BAA98171.1|5647gene_id: K21L13.2˜unknownprotein [Arabidopsisthaliana]390Similar to gi|2388568|gb|AAB71449.1|YUP8H12.1052225611Arabidopsis thaliana]3731864Similar to gi|7671465|emb|CAB89405.1|putative3591, 36035826protein [Arabidopsis thaliana]326Similar to gi|3582330|gb|AAC35227.1|putative5386monooxygenase [Arabidopsis thaliana]3631855Similar to gi|4417302|gb|AAD20426.1|hypothetical(protein [Arabidopsis thaliana]

[0682]

8

TABLE 2

SEQ ID NOs. and corresponding descriptions for Oryza genes which are

expressed in a seed-specific manner and further the SEQ ID NOs for

corresponding homologous sequences found in wheat, banana and maize.

ORF
Promo

Bana
Maize

(SEQ
(SEQ

Wheat
(SEQ
(SEQ

ID)
ID)
Description
(SEQ ID)
ID)
ID)

seed

1020

Similar to gi|20208|emb|CAA38211.1|glutelin [Oryza
4346, 2794,

sativa
]
4348, 4347

1021
2275
Similar to gi|7209261|emb|CAB76962.1|alpha-gliadin

[Triticum aestivum]

1022
2276
Similar to gi|226227|prf||1502200A prolamin [Avena
4347, 4348

sativa
]

1023
2277
Similar to gi|4138581|emb|CAA67107.1|mitochondrial
3974, 3975,
5164
5581

energy transfer protein [Solanum tuberosum]
3973, 3967,

3968, 3969,

2898

1045
2290
Similar to gi|3549657|emb|CAA20568.1|putative

protein [Arabidopsis thaliana]

1027

Similar to gi|4584507|emb|CAB40745.1|starch
3410, 3480

5563

branching enzyme II [Solanum tuberosum]

1030
2281
Similar to gi|5803247|dbj|BAA83557.1|Similar to

OsENOD93a gene for early nodulin (AB018375)

[Oryza sativa]

1028
2279
Similar to gi|3093462|gb|AAC15247.1|ADP-glucose

5817

pyrophosphorylase large subunit [Oryza sativa]

1026

Open Reading Frame OS_ORF005803 ST(R)
3037, 3291

5765

HTC034709-A01.26 FRAME: 3 ORF: 12 LEN: 840

1024
2278
Similar to gi|4105681|gb|AAD02494.1|unknown

5627

[Oryza sativa]

1048
2293
Open Reading Frame OS_ORF019202 ST(R)

5011

HTC128990-A01.R.16 FRAME: −1 ORF: 22 LEN: 660

1025

Similar to gi|218199|dbj|BAA01999.1|allergenic

protein [Oryza sativa]

1032
2282
Similar to PULA_KLEPN P07206 KLEBSIELLA
3049

PNEUMONIAE. PULLULANASE PRECURSOR (EC

3.2.1.41) (ALPHA-DEXTRIN ENDO-1,6-ALPHA-

GLUCOSIDASE) (PULLULAN 6-

GLUCANOHYDROLASE).

1029
2280
Similar to gi|944830|emb|CAA43183.1|soybean 24 kDa
4642

5420

oleosin isoform [Glycine max]

1036

Similar to gi|169759|gb|AAA33890.1|ADP-glucose
4612, 3211
5001
5817

pyrophosphorylase 51 kD subunit (EC 2.7.7.27)

1162
2377
Similar to gi|5042333|emb|CAB44664.1|BETL4

protein [Zea mays]

1033
2283
Similar to gi|4416304|gb|AAD20309.1|hypothetical

protein [Zea mays]

1165
2380
Similar to gi|924624|gb|AAA80496.1|flower-specific

gamma-thionin-like protein/acidic protein precursor

1044
2289
Similar to gi|8439904|gb|AAF75090.1|AC007583_26

ESTs gb|Z27026 and gb|29860 come from this gene.

[Arabidopsis thaliana]

1088

Similar to gi|4539346|emb|CAB37494.1|putative

protein [Arabidopsis thaliana]

1034
2284
Open Reading Frame OS_ORF006108 HTC036556-
4323, 4015,

A01.F.16 FRAME: −1 ORF: 1 LEN: 765
4322, 4324,

4016

1040

Similar to gi|4996644|dbj|BAA78574.1|Dof zinc finger

protein [Oryza sativa]

1031

Similar to gi|2252843|gb|AAB62842.1|A_IG005I10.24

gene product [Arabidopsis thaliana]

1068

Similar to gi|6016705|gb|AAF01531.1|AC009325_1

5067

unknown protein [Arabidopsis thaliana]

1095
2322
Similar to gi|6721166|gb|AAF26794.1|AC016829_18
3253

germin-like protein [Arabidopsis thaliana]

1390
2497
Similar to gi|1345528|emb|CAA54682.1|ES43
3896, 3898,

[Hordeum vulgare]
3897, 3895

1324

Similar to gi|5915837|sp|O81974|C7D8_SOYBN

5724

CYTOCHROME P450 71D8 (P450 CP7)

1206

Similar to gi|3142298|gb|AAC16749.1|Strong

5491

similarity to protein SBT1 gb|X98929 from

Lycopersicum esculentum. [Arabidopsis thaliana]

1133
2350
Similar to ISP_BACSP P29140 BACILLUS SP.
3023, 3022,

5484

(STRAIN 221). INTRACELLULAR ALKALINE
3101

PROTEASE (EC 3.4.21.—).

1229
2420
Similar to gi|8778384|gb|AAF79392.1|AC068197_2
3432, 2879,

F16A14.2 [Arabidopsis thaliana]
4588, 3301,

3446

1563
2642
Similar to gi|6539566|dbj|BAA88183.1|Similar to
4551, 4552

phosphoribosyl-ATP pyrophosphohydrolase

(AB006082) [Oryza sativa]

1087

Similar to YG3L_YEAST P48236
2875, 4422

5827

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). HYPOTHETICAL 51.6 KD PROTEIN IN

RPL30B-RSR1 INTERGENIC REGION.

1047
2292
Open Reading Frame OS_ORF003518 HTC020469-

A01.7 FRAME: −1 ORF: 3 LEN: 657

1041
2288
Similar to gi|6729036|gb|AAF27032.1|AC009177_22
4659, 4660

5371

putative glucose and ribitol dehydrogenase homolog

[Arabidopsis thaliana]

1414

Similar to gi|7769863|gb|AAF69541.1|AC008007_16

5015

F12M16.29 [Arabidopsis thaliana]

1155

Similar to YHJD_ECOLI P37642 ESCHERICHIA

COLI
. HYPOTHETICAL 37.9 KD PROTEIN IN

TREF-KDGK INTERGENIC REGION (O337).

1108
2326
Open Reading Frame OS_ORF011610 HTC072062-

A01.F.11 FRAME: 2 ORF: 5 LEN: 738

1594

Similar to gi|4337176|gb|AAD18097.1|T31J12.4
4653, 2811,

[Arabidopsis thaliana]
4654

1082

Similar to gi|4586037|gb|AAD25655.1|AC007109_13
4048, 4549,

5796

putative heat shock protein [Arabidopsis thaliana]
4550, 3403,

4548, 3402,

4043

1141
2358
Open Reading Frame OS_ORF002232 HTC012937-

5770

A01.25 FRAME: −2 ORF: 24 LEN: 855

1126

Similar to YP99_CAEEL Q09477

CAENORHABDITIS ELEGANS
. HYPOTHETICAL

22.7 KD PROTEIN C28H8.9 IN CHROMOSOME III.

1125
2343
Similar to ABP1_YEAST P15891

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). ACTIN BINDING PROTEIN.

1119
2337
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF008102 ST(F) HTC048468-

A01.F.25 FRAME: 1 ORF: 13 LEN: 546

1408

Similar to gi|7269842|emb|CAB79701.1|ribosomal

5011

protein S15a homolog [Arabidopsis thaliana]

1131
2348
Open Reading Frame OS_ORF019613 HTC132417-
3648, 3649,

A01.32 FRAME: 3 ORF: 16 LEN: 780
2819

1161
2376
Similar to gi|9081787|dbj|BAA99526.1|hypothetical

protein [Oryza sativa]

1148
2365
Similar to gi|3941456|gb|AAC83604.1|putative
3692, 3694,
4970
5874

transcription factor [Arabidopsis thaliana]
2904, 3915,

4427, 3693

1042

Similar to gi|4097100|gb|AAD10374.1|globulin-like

5543

protein [Oryza sativa]

1461
2551
Similar to gi|2245101|emb|CAB10523.1|hypothetical

4896

protein [Arabidopsis thaliana]

1145
2362
Similar to gi|7485867|pir||T00960 hypothetical protein
4622

5828

F20D22.10 - Arabidopsis thaliana

1134
2351
Open Reading Frame OS_ORF019604 HTC132357-

A01.R.27 FRAME: 1 ORF: 7 LEN: 639

1104

Similar to YC06_KLEPN Q48452 KLEBSIELLA

PNEUMONIAE. HYPOTHETICAL 80.4 KD

PROTEIN IN CPS REGION (ORF6).

1345

Similar to gi|7269851|emb|CAB79710.1|putative

5487

protein [Arabidopsis thaliana]

1460
2550
Similar to gi|4220484|gb|AAD12707.1|hypothetical
4439, 4440

protein [Arabidopsis thaliana]

1403

Similar to gi|6957714|gb|AAF32458.1|hypothetical
3490, 3489
4960
5520

protein [Arabidopsis thaliana]

1072
2309
Similar to gi|6466941|gb|AAF13076.1|AC009176_3

unknown protein [Arabidopsis thaliana]

1316
2469
Similar to gi|8778754|gb|AAF79762.1|AC009317_21
4550, 4048,

5644

T30E16.34 [Arabidopsis thaliana]
4549, 4043,

4548, 4044,

2718, 3403,

3402

1038
2286
Similar to gi|5295941|dbj|BAA81842.1|ESTs
2788
5052
5704

AU075322(C11109), D22430(C11109) correspond to a

region of the predicted gene.; Similar to Medicago

sativa
early nodule-specific protein (ENOD8) gene,

complete cds.(L18899) [Oryza sativa]

1469
2558
Similar to gi|4204311|gb|AAD10692.1|lcl|prt_seq No

5876

definition line found

1067
2305
Similar to gi|6714358|gb|AAF26048.1|AC012562_3
2994, 2992,
5123

hypothetical protein [Arabidopsis thaliana]
4349

1441
2533
Similar to ELI1_PHYCR P41802 PHYTOPHTHORA

CRYPTOGEA. ACIDIC ELICITIN A1 PRECURSOR.

1100

Similar to YAYF_SCHPO Q10222

SCHIZOSACCHAROMYCES POMBE
(FISSION

YEAST). HYPOTHETICAL PROTEIN C4H3.15C IN

CHROMOSOME I (FRAGMENT).

1261
2440
Open Reading Frame OS_ORF011947 ST(R)

5722

HTC074509-A01.R.21 FRAME: 3 ORF: 3 LEN: 528

1142
2359
Similar to VNFG_AZOCH P15333 AZOTOBACTER

CHROOCOCCUM MCD 1. NITROGENASE

VANADIUM-IRON PROTEIN DELTA CHAIN (EC

1.18.6.1)(NITROGENASE COMPONENT I)

(DINITROGENASE).

1150
2366
Similar to gi|1346724|sp|P48007|PIST_ARATH
3321

5530

FLORAL HOMEOTIC PROTEIN PISTILLATA

1287
2453
Open Reading Frame OS_ORF003469 HTC020152-

5693

A01.25 FRAME: −2 ORF: 16 LEN: 1140

1066
2304
Open Reading Frame OS_ORF011792 HTC073334-

4778
5485

A01.F.37 FRAME: −1 ORF: 16 LEN: 966

1369
2488
Similar to gi|6721107|gb|AAF26761.1|AC007396_10

5188
5238

T4O12.17 [Arabidopsis thaliana]

1591
2667
Similar to gi|4309727|gb|AAD15497.1|putative
3755, 3766,
5177
5458

ribosomal protein L6 [Arabidopsis thaliana]
3745, 3741,

3713

1049
2294
Similar to PGS1_RAT P47853 RATTUS
2903
4917
5300

NORVEGICUS
(RAT). BONE/CARTILAGE

PROTEOGLYCAN I PRECURSOR (BIGLYCAN)

(PG-S1).

1111
2329
Open Reading Frame OS_ORF018782 HTC125558-

A01.F.12 FRAME: −3 ORF: 4 LEN: 729

1109
2327
Similar to gi|18583|emb|CAA48907.1|nodulin

[Glycine max]

1326

Similar to gi|4895230|gb|AAD32816.1|AC007660_17
3464

5897

unknown protein [Arabidopsis thaliana]

1350

Similar to MLO2_SCHPO Q09329
3341, 3342
5194
5425

SCHIZOSACCHAROMYCES POMBE
(FISSION

YEAST). MLO2 PROTEIN.

1054

Open Reading Frame OS_ORF004775 HTC028124-
3087

A01.F.22 FRAME: −1 ORF: 27 LEN: 1044

1157
2372
Open Reading Frame OS_ORF001203 HTC006819-

5588

A01.28 FRAME: −3 ORF: 1 LEN: 777

1243
2430
Similar to gi|8778718|gb|AAF79726.1|AC005106_7
4318, 4317,
5135

T25N20.15 [Arabidopsis thaliana]
4689

1037
2285
Similar to gi|228454|prf||1804333B Gln synthetase

4980
5656

[Arabidopsis thaliana]

1425
2518
Similar to VE1_HPV63 Q07847 HUMAN

PAPILLOMA VIRUS TYPE 63. REPLICATION

PROTEIN E1.

1094

Open Reading Frame OS_ORF019404 HTC130656-

4940

A01.F.12 FRAME: −2 ORF: 1 LEN: 678

1335

Similar to gi|8671775|gb|AAF78381.1|AC069551_14

T10O22.22 [Arabidopsis thaliana]

1260

Similar to gi|5881963|gb|AAD55139.1|AF066079_1

5395

dihydrolipoamide S-acetyltransferase [Arabidopsis

thaliana
]

1147
2364
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF000613 ST(F) HTC003481-

A01.18 FRAME: 1 ORF: 34 LEN: 762

1062

Open Reading Frame OS_ORF002475 HTC014377-
2786, 4649,

5241

A01.16 FRAME: −3 ORF: 18 LEN: 693
4629, 4648,

2882, 4589,

4628

1065
2303
Similar to gi|995619|emb|CAA62665.1|lectin like
3303, 3232,

protein [Arabidopsis thaliana]
4027

1504
2585
Similar to YPPG_BACSU P50835 BACILLUS

SUBTILIS
. HYPOTHETICAL 14.5 KD PROTEIN IN

PONA-COTD INTERGENIC REGION.

1256
2438
Similar to gi|6682631|gb|AAF23352.1|AC016163_26
2729
5199

unknown protein [Arabidopsis thaliana]

1079
2315
Similar to NEPU_THEVU Q08751
3665, 4214,
4791
5521

THERMOACTINOMYCES VULGARIS
.
3702, 3704,

NEOPULLULANASE (EC 3.2.1.135) (ALPHA-
3663, 3695,

AMYLASE II).
3701, 3673,

3705, 3700,

3667, 3703,

3698, 3672,

3680, 3697,

3699, 4215,

3682, 3674,

3664, 3681,

3666, 2978,

3181

1135
2352
Similar to gi|416490|emb|CAA51289.1|GT-2 factor
2912

5239

[Arabidopsis thaliana]

1053

Similar to gi|7573384|emb|CAB87688.1|putative
3444
4957

protein [Arabidopsis thaliana]

1241
2428
Similar to gi|5295948|dbj|BAA81849.1|hypothetical

protein [Oryza sativa]

1558
2637
Similar to YQJL_BACSU P54549 BACILLUS

SUBTILIS
. HYPOTHETICAL 28.2 KD PROTEIN IN

GLNQ-ANSR INTERGENIC REGION.

1093

Similar to gi|2605714|gb|AAB84183.1|beta-tonoplast
4143, 4144,
4984
5572

intrinsic protein [Arabidopsis thaliana]
4179, 4141,

4425, 4178,

4423, 4177,

4424

1083

Open Reading Frame OS_ORF017793 HTC118665-
3167
5202
5559

A01.F.5 FRAME: −1 ORF: 2 LEN: 780

1432
2525
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF004912 ST(F) HTC028900-

A01.F.8 FRAME: −1 ORF: 1 LEN: 1140

1143
2360
Open Reading Frame OS_ORF018659 HTC124609-

A01.F.4 FRAME: −3 ORF: 9 LEN: 705

Similar to YNZ3_CAEEL P45963

CAENORHABDITIS ELEGANS
. HYPOTHETICAL

ACETYLCHOLINE RECEPTOR LIKE PROTEIN

T09A5.3 INCHROMOSOME III.

1294

Similar to gi|804946|emb|CAA85389.1|acyl-(acyl
3468, 3467
4966
5824

carrier protein) thioesterase [Arabidopsis thaliana]

1364

Open Reading Frame OS_ORF009128 HTC054783-

5899

A01.F.13 FRAME: −1 ORF: 8 LEN: 633

1549
2629
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF010160 ST(F) HTC061531-

A01.F.19 FRAME: −1 ORF: 1 LEN: 1017

1211

Similar to gi|4406810|gb|AAD20118.1|unknown

5465

protein [Arabidopsis thaliana]

1159
2374
Open Reading Frame OS_ORF011119 ST(R)

5363

HTC068485-A01.R.10 FRAME: −3 ORF: 1 LEN: 573

1596
2671
Similar to 7B2_XENLA P18844 XENOPUS LAEVIS

(AFRICAN CLAWED FROG). NEUROENDOCRINE

PROTEIN 7B2 (SECRETOGRANIN V)

(FRAGMENT).

1510
2591
Open Reading Frame OS_ORF018745 HTC125312-

A01.R.20 FRAME: −3 ORF: 28 LEN: 795

1373

Similar to gi|4490708|emb|CAB38842.1|putative

5168
5776

protein [Arabidopsis thaliana]

1291
2456
Similar to YNU6_CAEEL P50444

4780

CAENORHABDITIS ELEGANS
. HYPOTHETICAL

42.9 KD PROTEIN R74.6 IN CHROMOSOME III.

1163
2378
Similar to gi|9294354|dbj|BAB02251.1|
4614, 4613

5427

gb|AAF25994.1˜gene_id: MMF12.4˜similar to

unknown protein [Arabidopsis thaliana]

1063
2302
Similar to HPI2_ECTVA P38524

ECTOTHIORHODOSPIRA VACUOLATA. HIGH

POTENTIAL IRON-SULFUR PROTEIN, ISOZYME

2 (HIPIP 2).

1252

Similar to gi|7413593|emb|CAB86083.1|putative
3990, 3991
4832

protein [Arabidopsis thaliana]

1238
2426
Similar to gi|7716575|gb|AAF68437.1|putative DNA
3138, 2887,

5852

cytosine methyltransferase MET3 [Zea mays]
3137, 2886,

3238, 2950,

3128

1338
2477
Similar to gi|3894216|dbj|BAA34599.1|elongation
4134, 4135,

5550

factor 1 beta 2 [Oryza sativa]
4133

1582
2659
Open Reading Frame OS_ORF008474 HTC051016-

A01.R.13 FRAME: 2 ORF: 12 LEN: 681

1436
2528
Open Reading Frame OS_ORF016926 HTC112251-

5191
5863

A01.14 FRAME: 1 ORF: 10 LEN: 654

1375
2491
Similar to gi|7340854|dbj|BAA92944.1|hypothetical

protein [Oryza sativa]

1332

Similar to gi|6017106|gb|AAF01589.1|AC009895_10
4039, 4038
4797
5633

hypothetical protein [Arabidopsis thaliana]

1139
2356
Open Reading Frame OS_ORF006860 HTC041127-

A01.23 FRAME: 1 ORF: 4 LEN: 852

1092

Similar to CC22_PEA P28567 PISUM SATIVUM
3035, 3092,

5926

(GARDEN PEA). CELL DIVISION CONTROL
3431, 3288,

PROTEIN 2 HOMOLOG 2 (EC 2.7.1.—)
4153

(FRAGMENT).

1208
2407
Open Reading Frame OS_ORF011285 HTC069506-
3303, 4027,

A01.R.4 FRAME: −2 ORF: 3 LEN: 786
2712, 4028,

3232

1351

Similar to NXL2_ASTST P01381 ASTROTIA

5607

STOKESI (STOKES S SEA SNAKE) (DISTEIRA

STOKESI). LONG NEUROTOXIN 2 (TOXIN C).

1355

Open Reading Frame OS_ORF017900 ST(R)

5667

HTC119232-A01.40 FRAME: 2 ORF: 14 LEN: 759

1140
2357
Open Reading Frame OS_ORF000732 ST(R)

HTC004214-A01.47 FRAME: −1 ORF: 6 LEN: 813

1295

Similar to gi|7488260|pir|T00673 protein kinase

homolog F6E13.6 - Arabidopsis thaliana

1099
2324
Similar to gi|7270031|emb|CAB79847.1|predicted

5565

protein [Arabidopsis thaliana]

1589
2666
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF021256 ST(F) HTC144712-

A01.R.2 FRAME: 2 ORF: 7 LEN: 528

1545
2625
Open Reading Frame OS_ORF014969 HTC097200-

A01.R.41 FRAME: −1 ORF: 13 LEN: 876

1186
2396
Similar to CLCB_BOVIN P04975 BOS TAURUS

(BOVINE). CLATHRIN LIGHT CHAIN B (BRAIN

AND LYMPHOCYTE LCB).

1463
2552
Similar to CLCB_HUMAN P09497 HOMO SAPIENS

(HUMAN). CLATHRIN LIGHT CHAIN B (BRAIN

AND LYMPHOCYTE LCB).

1296
2458
Similar to gi|9294401|dbj|BAB02482.1|
4380

gene_id: MOE17.5˜unknown protein [Arabidopsis

thaliana
]

1144
2361
Similar to gi|9294687|dbj|BAB03053.1|

gene_id: MHC9.8˜unknown protein [Arabidopsis

thaliana
]

1230
2421
Open Reading Frame OS_ORF006541 HTC039204-

A01.F.15 FRAME: 2 ORF: 7 LEN: 681

1232

Open Reading Frame OS_ORF002127 HTC012268-

A01.50 FRAME: 1 ORF: 28 LEN: 891

1077
2313
Similar to COAT_ICMV Q08583 INDIAN CASSAVA

5253

MOSAIC VIRUS (ICMV). COAT PROTEIN.

1537
2618
Similar to PDI_CHICK P09102 Q90969 GALLUS
3507, 3506,
4911
5311

GALLUS
(CHICKEN). PROTEIN DISULFIDE
3499, 3498

ISOMERASE (PDI) (EC 5.3.4.1)/PROLYL 4-

HYDROXYLASEBETA SUBUNIT (EC 1.14.11.2)/

CELLULAR THYROID HORMONE

BINDINGPROTEIN.

1138
2355
Similar to gi|82583|pir||E22364 alpha/beta-gliadin

precursor (clone A1235) - wheat

1592
2668
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF014275 ST(F) HTC091876-

A01.49 FRAME: −1 ORF: 42 LEN: 795

1496
2578
Similar to WAP_CAMDR P09837 CAMELUS
2815, 2968

DROMEDARIUS
(DROMEDARY) (ARABIAN

CAMEL). WHEY ACIDIC PROTEIN (WAP).

1105

Similar to DPB2_YEAST P24482 Q06622
2817

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). DNA POLYMERASE EPSILON, SUBUNIT

B (EC 2.7.7.7) (DNA POLYMERASE IISUBUNIT B).

1340

Open Reading Frame OS_ORF006899 HTC041396-

5327

A01.41 Frame: 2 ORF: 2 LEN: 849

1529
2610
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF020346 ST(F) HTC137170-

A01.19 FRAME: −2 ORF: 3 LEN: 1437

1249

Similar to gi|8099244|gb|AAF72092.1|AC025098_26

Conserved hypothetical protein, similar to rice

hypothetical protein AAF34431 [Oryza sativa]

1129
2346
Similar to CASK_ODOHE Q95225 Q95226

ODOCOILEUS HEMIONUS (MULE DEER)

(BLACK-TAILED DEER). KAPPA CASEIN

(FRAGMENT).

1314

Open Reading Frame OS_ORF004164 ST(R)
3473

5906

HTC024228-A01.36 FRAME: 1 ORF: 7 LEN: 549

1476

Similar to YXEP_BACSU P54955 BACILLUS

SUBTILIS
. HYPOTHETICAL 41.6 KD PROTEIN IN

IDH-DEOR INTERGENIC REGION.

1101

Similar to gi|2961389|emb|CAA18136.1|purple acid
4062, 4063
5112
5835

phosphatase like protein [Arabidopsis thaliana]

1151
2367
Open Reading Frame OS_ORF002273 HTC013181-

4975
5674

A01.21 FRAME: −2 ORF: 16 LEN: 675

1380

Similar to gi|6289052|gb|AAF06789.1|AF192975_1
4351, 3043,
4829

unknown [Oryza sativa]
4350, 3044,

3042

1081
2317
Similar to gi|4510349|gb|AAD21438.1|putative bZIP
3933, 3935,

5583

transcription factor [Arabidopsis thaliana]
3934

1386

Similar to gi|4185501|gb|AAD09105.1|fertilization-
2870, 2869

independent seed 2 protein [Arabidopsis thaliana]

1231
2422
Open Reading Frame OS_ORF014200 HTC091206-

A01.F.14 FRAME: −2 ORF: 5 LEN: 906

1114
2332
Similar to YEGX_ECOLI P76421 O08480

ESCHERICHIA COLI
. HYPOTHETICAL 32.0 KD

PROTEIN IN DHNA-THID INTERGENIC REGION.

1517
2598
Similar to gi|8843783|dbj|BAA97331.1|

gb|AAC80581.1˜gene_id: MZN1.7˜similar to unknown

protein [Arabidopsis thaliana]

1498
2579
Open Reading Frame OS_ORF013608 HTC087069-

5322

A01.R.4 FRAME: 1 ORF: 4 LEN: 663

1534
2615
Similar to gi|4140257|emb|CAA10352.1|LEA-like

5805

protein [Arabidopsis thaliana]

1259

Open Reading Frame containing a Sage tag sequence
2895, 3493

near 3 end OS_ORF006433 ST(F) HTC038577-

A01.35 FRAME: −3 ORF: 29 LEN: 675

1055
2297
Similar to AMIA_ECOLI P36548 ESCHERICHIA
3557, 3819,
5026
5846

COLI
. PROBABLE N-ACETYLMURAMOYL-L-
3554, 3818,

ALANINE AMIDASE AMIA PRECURSOR(EC
3550

3.5.1.28).

1539
2620
Open Reading Frame OS_ORF012379 ST(R)

HTC077361-A01.R.25 FRAME: −1 ORF: 6 LEN: 1119

1127
2344
Similar to UK14_RAT P52759 RATTUS
2991, 3277
5062
5246

NORVEGICUS
(RAT). 14.5 KD TRANSLATIONAL

INHIBITOR PROTEIN (PERCHROLIC ACID

SOLUBLEPROTEIN).

1396
2502
Open Reading Frame OS_ORF007652 HTC045616-

5267

A01.R.24 FRAME: 2 ORF: 20 LEN: 684

1123
2341
Open Reading Frame OS_ORF010912 HTC067127-

A01.F.24 FRAME: 1 ORF: 17 LEN: 675

1121
2339
Open Reading Frame OS_ORF014277 HTC091891-

A01.F.5 FRAME: 1 ORF: 4 LEN: 669

1480

Similar to YIA7_YEAST P40555
2693

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). HYPOTHETICAL 24.8 KD PROTEIN IN

FAA3-BET1 INTERGENIC REGION.

1417
2510
Open Reading Frame OS_ORF000206 HTC001182-

A01.25 FRAME: −3 ORF: 23 LEN: 915

1477
2563
Open Reading Frame OS_ORF006071 HTC036306-

A01.27 FRAME: 1 ORF: 7 LEN: 1761

1312
2466
Similar to gi|6063552|dbj|BAA85412.1|ESTs
4545

5540

AU065232(E60855), C23624(S1554),

AU078241(E60855) correspond to a region of the

predicted gene.; similar to putative adenylate kinase.

(AC005896) [Oryza sativa]

1359

Similar to AEFA_ECOLI P77338 ESCHERICHIA

COLI
. AEFA PROTEIN.

1073
2310
Similar to gi|5803244|dbj|BAA83554.1|Similar to
3323, 4292,
4789
5617

hexose carrier protein HEX6 &RCCHCP_1 (Q07423)
3324

[Oryza sativa]

1146
2363
Similar to UL06_HCMVA P16720 HUMAN

5864

CYTOMEGALOVIRUS (STRAIN AD169).

HYPOTHETICAL PROTEIN UL6.

1218
2414
Similar to gi|2828295|emb|CAA16709.1|putative
4604, 3397,
5038

protein [Arabidopsis thaliana]
2920, 4605

1164
2379
Open Reading Frame OS_ORF022040 HTC151019-

5361

A01.R.15 FRAME: 2 ORF: 7 LEN: 606

1486
2570
Similar to E321_ADE1P P35770 HUMAN

ADENOVIRUS TYPE 11 (AD11P) (STRAIN

SLOBISKI). EARLY E3 20.6 KD GLYCOPROTEIN.

1533
2614
Open Reading Frame OS_ORF002013 HTC011543-

A01.21 FRAME: 1 ORF: 6 LEN: 1566

1571
2649
Similar to IM23_YEAST P32897

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). MITOCHONDRIAL IMPORT INNER

MEMBRANE TRANSLOCASE SUBUNIT

TIM23(MITOCHONDRIAL PROTEIN IMPORT

PROTEIN 3) (MITOCHONDRIAL PROTEIN

IMPORTPROTEIN MAS6) (MEMBRANE IMPORT

MACHINERY PROTEIN MIM2

1090

Similar to gi|6721556|dbj|BAA89586. 1|hypothetical

5542

protein [Oryza sativa]

1124
2342
Open Reading Frame OS_ORF010827 HTC066509-

A01.F.19 FRAME: 2 ORF: 28 LEN: 675

1190
2398
Similar to UBPT_CAEEL Q17361

CAENORHABDITIS ELEGANS
. QUEUINE TRNA-

RIBOSYLTRANSFERASE (EC 2.4.2.29) (TRNA-

GUANINETRANSGLYCOSYLASE) (GUANINE

INSERTION ENZYME).

1365

Similar to gi|3249086|gb|AAC24070.1|Contains
3963, 3960,
4907

similarity to 21 KD subunit of the Arp2/3 protein
3962, 3961

complex (ARC21) gb|AF006086 from Homo sapiens.

EST gb|Z37222 comes [Arabidopsis thaliana]

1051

Open Reading Frame OS_ORF016166 HTC106341-

A01.R.18 FRAME: −3 ORF: 4 LEN: 861

1521
2602
Similar to gi|9280680|gb|AAF86549.1|AC069252_8
3370, 3408,
5064
5802

F2E2.12 [Arabidopsis thaliana]
3372, 3371

1492
2575
Similar to YD57_SCHPO Q10311

SCHIZOSACCHAROMYCES POMBE
(FISSION

YEAST). HYPOTHETICAL 25.9 KD PROTEIN

C6C3.07 IN CHROMOSOME I.

1450

Similar to YAJO_ECOLI P77735 ESCHERICHIA

COLI
. HYPOTHETICAL OXIDOREDUCTASE IN

PGPA-ISPA INTERGENIC REGION.

1154
2370
Similar to gi|6581058|gb|AAF18438.1|AF192467_1

5519

Sgt1 [Oryza sativa]

1447
2538
Similar to gi|7487883|pir||T00987 hypothetical protein

4803

T9J22.21 - Arabidopsis thaliana

1551
2631
Open Reading Frame OS_ORF013836 HTC088733-

A01.F.19 FRAME: 1 ORF: 19 LEN: 1476

1046
2291
Similar to gi|5802240|gb|AAD51623.1|AF169020_1

seed maturation protein PM35 [Glycine max]

1546
2626
Open Reading Frame OS_ORF013277 HTC084148-

A01.5 FRAME: 3 ORF: 1 LEN: 735

1160
2375
Similar to YJEQ_ECOLI P39286 ESCHERICHIA

COLI
. HYPOTHETICAL 37.7 KD PROTEIN IN PSD-

AMIB INTERGENIC REGION (F337).

1481
2566
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF013162 ST(F) HTC083361-

A01.F.40 FRAME: −2 ORE: 1 LEN: 696

1358
2483
Similar to gi|7670024|dbj|BAA94978.1|contains

5473

similarity to similar to ubiquitin conjugating

enzyme˜gene_id: K14A17.7 [Arabidopsis thaliana]

1153
2369
Similar to MYBH_DICDI P34127 DICTYOSTELIUM
4609, 4610

5437

DISCOIDEUM (SLIME MOLD). MYB-LIKE

PROTEIN (FRAGMENT).

1059
2300
Open Reading Frame OS_ORF001606 HTC009227-

A01.48 FRAME: 2 ORF: 25 LEN: 1299

1419
2512
Similar to YV23_MYCLE P54580

5408

MYCOBACTERIUM LEPRAE. HYPOTHETICAL

27.9 KD PROTEIN B2168_C2_209.

1334

Open Reading Frame OS_ORF004663 HTC027383-

5757

A01.F.15 FRAME: 1 ORF: 3 LEN: 663

1339

Open Reading Frame OS_ORF013226 ST(R)

5569

HTC083788-A01.R.7 FRAME: 3 ORF: 2 LEN: 813

1547
2627
Similar to gi|8778731|gb|AAF79739.1|AC005106_20

T25N20.6 [Arabidopsis thaliana]

1177
2390
Open Reading Frame containing a Sage tag sequence
3365, 4159,
4989

near 3 end OS_ORF001044 ST(F) HTC005847-
2769, 3364,

A01.28 FRAME: −2 ORF: 3 LEN: 783
4496, 4497,

2768, 2809,

4158, 3271,

3109, 4530,

2932, 3269,

3295, 2707

1385
2495
Similar to gi|2911041|emb|CAA17551.1|kinetochore

5187
5238

(SKP1p)-like protein [Arabidopsis thaliana]

1300
2461
Similar to gi|4582787|emb|CAB40376.1|adenosine
4033, 4034,
4806
5804

kinase [Zea mays]
4035

1451
2541
Similar to gi|8843778|dbj|BAA97326.1|

5380

emb|CAB85555.1˜gene_id: MZN1.2˜similar to

unknown protein [Arabidopsis thaliana]

1120
2338
Open Reading Frame OS_ORF010615 HTC065139-

A01.R.9 FRAME: −2 ORF: 2 LEN: 660

1433
2526
Similar to gi|6453867|gb|AAF09051.1|AC011717_18

hypothetical protein [Arabidopsis thaliana]

1467
2556
Similar to gi|3790581|gb|AAC69853.1|RING-H2
4303, 4304
4857

finger protein RHB1a [Arabidopsis thaliana]

1074
2311
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF021691 ST(F) HTC148178-

A01.14 FRAME: −2 ORF: 1 LEN: 681

1258

Similar to gi|4733993|gb|AAD28672.1|AC007188_2

5075
5362

unknown protein [Arabidopsis thaliana]

1228

Similar to gi|1839244|gb|AAB46988.1|EGF receptor
2855, 2854,
4910
5869

like protein [Arabidopsis thaliana]
3691, 2959

1445
2536
Open Reading Frame OS_ORF011257 HTC069347-

A01.F.8 FRAME: −1 ORF: 1 LEN: 786

1527
2608
Open Reading Frame OS_ORF013101 HTC082889-

A01.R.9 FRAME: −1 ORF: 7 LEN: 690

1279
2450
Similar to gi|2245022|emb|CAB10442.1|hypothetical

5862

protein [Arabidopsis thaliana]

1284

Similar to HIS8_MYCSM P28735

MYCOBACTERIUM SMEGMATIS. HISTIDINOL-

PHOSPHATE AMINOTRANSFERASE (EC 2.6.1.9)

(IMIDAZOLE ACETOL-PHOSPHATE

TRANSAMINASE) (FRAGMENT).

1137
2354
Similar to LECG_ARAHY P02872 ARACHIS

HYPOGAEA (PEANUT). GALACTOSE-BINDING

LECTIN PRECURSOR (AGGLUTININ) (PNA).

1176
2389
Similar to gi|3757521|gb|AAC64223.1|putative
3134, 3133,

ubiquitin-conjugating enzyme [Arabidopsis thaliana]
3284

1171
2384
Similar to gi|9293951|dbj|BAB01854.1|DNA-directed
2884, 3900,

RNA polymerase, subunit B [Arabidopsis thaliana]
3904

1110
2328
Open Reading Frame OS_ORF000534 HTC002946-

5858

A01.10 FRAME: −3 ORF: 1 LEN: 657

1511
2592
Similar to gi|3152568|gb|AAC17049.1|Similar to
3235, 4493
5025

hypothetical protein product gb|Z97337 from A.

thaliana
. EST gb|H76597 comes from this gene.

[Arabidopsis thaliana]

1560
2639
Similar to PHS_PSEAE P43335 PSEUDOMONAS
3504, 3505,
4822

AERUGINOSA. PTERIN-4-ALPHA-
3503, 3500,

CARBINOLAMINE DEHYDRATASE (EC 4.2.1.96)
3508

(PHS)(4-ALPHA-HYDROXY-

TETRAHYDROPTERIN DEHYDRATASE)

(PHENYLALANINEHYDROXYLASE-

STIMULATING PROTEIN) (PCD).

1509
2590
Similar to gi|6553925|gb|AAF16590.1|AC012329_14

hypothetical protein [Arabidopsis thaliana]

1353

Open Reading Frame OS_ORF008479 HTC051059-
3493

A01.11 FRAME: 3 ORF: 6 LEN: 933

1513
2594
Similar to gi|9294219|dbj|BAB02121.1|

4834

gb|AAF01563.1˜gene_id: K17E12. 8˜similar to

unknown protein [Arabidopsis thaliana]

1180
2392
Open Reading Frame OS_ORF007418 HTC044323-
2953, 3955,

5761

A01.R.10 FRAME: 1 ORF: 1 LEN: 705
3954, 3953

1437
2529
Open Reading Frame OS_ORF020518 HTC138308-

5896

A01.F.6 FRAME: −2 ORF: 4 LEN: 1080

1424
2517
Similar to gi|4337197|gb|AAD18111.1|AIG2-like
4699
4946

protein [Arabidopsis thaliana]

1315
2468
Similar to gi|6899895|emb|CAB71904.1|RAV-like

5588

protein [Arabidopsis thaliana]

1466
2555
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF001178 ST(F) HTC006675-A01.9

FRAME: 3 ORF: 10 LEN: 588

1057

Open Reading Frame OS_ORF008654 ST(R)
3141, 3121,

5872

HTC051926-A01.R.21 FRAME: 3 ORF: 16 LEN: 597
2918

1470

Similar to gi|482709|pir||A61062 NADH

5058

dehydrogenase (ubiquinone) (EC 1.6.5.3) chain 4 —

soybean mitochondrion (fragment)

1242
2429
Similar to gi|6466961|gb|AAF13096.1|AC009176_23
2850, 2849
4919
5486

hypothetical protein [Arabidopsis thaliana]

1096
2323
Open Reading Frame OS_ORF013567 HTC086832-
3731

5548

A01.R.10 FRAME: −2 ORF: 6 LEN: 651

1233

Similar to YDB3_SCHPO Q10356
4321, 4320

5347

SCHIZOSACCHAROMYCES POMBE
(FISSION

YEAST). HYPOTHETICAL 21.1 KD PROTEIN

C22E12.03C IN CHROMOSOME I.

1130
2347
Open Reading Frame OS_ORF009250 ST(R)

5536

HTC055587-A01.R.20 FRAME: −2 ORF: 18 LEN: 609

1107
2325
Similar to gi|6069672|dbj|BAA85448.1|hypothetical
2993

protein [Oryza sativa]

1454
2544
Similar to KR62_SHEEP P02448 OVIS ARIES

(SHEEP). KERATIN, HIGH-TYROSINE MATRIX

PROTEIN (COMPONENT 0.62).

1538
2619
Open Reading Frame OS_ORF012452 HTC077995-

5815

A01.R.13 FRAME: 3 ORF: 12 LEN: 666

1347
2479
Similar to gi|9294416|dbj|BAB02497.1|
2750, 2749,
5074
5435

gene_id: MOE17.21˜ref|NP_002083.1˜similar to
2751

unknown protein [Arabidopsis thaliana]

1289
2455
Similar to gi|556902|emb|CAA84288.1|54-kD signal
4083, 3716,

recognition particle (SRP) specific protein
4085, 4086

[Lycopersicon esculentum]

1268
2444
Open Reading Frame containing a Sage tag sequence

5334

near 3 end OS_ORF010085 ST(F) HTC060921-A01.3

FRAME: −2 ORF: 7 LEN: 582

1464
2553
Similar to gi|8096408|dbj|BAA95878.1|EST

AU062706(C30225) corresponds to a region of the

predicted gene.˜hypothetical protein [Oryza sativa]

1512
2593
Similar to gi|6714422|gb|AAF26110.1|AC012328_13
2965, 3280

hypothetical protein [Arabidopsis thaliana]

1235
2423
Open Reading Frame containing a Sage tag sequence

5285

near 3 end OS_ORF003649 ST(F) HTC021208-

A01.22 FRAME: −3 ORF: 14 LEN: 1257

1213
2409
Similar to gi|6562257|emb|CAB62627.1|putative
4453, 4452
4914
5390

protein [Arabidopsis thaliana]

1468
2557
Open Reading Frame OS_ORF006107 HTC036528-

A01.30 FRAME: −2 ORF: 28 LEN: 795

1561
2640
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF001814 ST(F) HTC010532-.

A01.14 FRAME: 3 ORF: 17 LEN: 948

1203

Open Reading Frame OS_ORF017107 HTC113682-

A01.F.39 FRAME: 1 ORF: 16 LEN: 741

1578
2655
Similar to gi|8843728|dbj|BAA97276.1|homeodomain

5148
5670

transcription factor-like [Arabidopsis thaliana]

1381

Open Reading Frame OS_ORF004338 HTC025425-

5583

A01.19 FRAME: 3 ORF: 4 LEN: 657

1236
2424
Open Reading Frame OS_ORF003108 HTC018151-
3255, 4619,
5065
5726

A01.14 FRAME: −3 ORF: 3 LEN: 909
4618, 3287

1278
2449
Similar to gi|7485274|pir||T08864 hypothetical protein
3348, 3011,
5117

A_TM017A05.2 - Arabidopsis thaliana
4378, 2698,

3012, 2699,

3349

1323

Similar to DAPF_HAEIN P44859 HAEMOPHILUS
4147

INFLUENZAE. DIAMINOPIMELATE EPIMERASE

(EC 5.1.1.7).

1429
2522
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF010917 ST(F) HTC067133-

A01.F.25 FRAME: −1 ORF: 36 LEN: 543

1443
2534
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF015365 ST(F) HTC100104-

A01.R.5 FRAME: −3 ORF: 2 LEN: 633

1039
2287
Similar to CS66_WHEAT P46526 TRITICUM
3625

5549

AESTIVUM
(WHEAT). COLD SHOCK PROTEIN

CS66.

1113
2331
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF016057 ST(F) HTC105401-

A01.F.20 FRAME: 1 ORF: 20 LEN: 834

1407
2506
Similar to gi|7630235|dbj|BAA94768.1|hypothetical

protein [Oryza sativa]

1220
2416
Open Reading Frame OS_ORF017123 HTC113816-
3009, 2951

5741

A01.28 FRAME: −1 ORF: 4 LEN: 828

1431
2524
Similar to gi|6562304|emb|CAB62602.1|putative

4848

protein [Arabidopsis thaliana]

1522
2603
Similar to gi|5734723|gb|AAD49988.1|AC007259_1

receptor-like protein kinase [Arabidopsis thaliana]

1084
2318
Similar to gi|7573432|emb|CAB87748.1|putative
4534, 4535,

protein [Arabidopsis thaliana]
4533

1085
2319
Similar to gi|8467993|dbj|BAA96594.1|ESTs
4337, 3166,
4986

AU082600(C11471), C26010(C11471) correspond to a
3134

region of the predicted gene.˜Similar to Arabidopsis

thaliana
chromosome 2 BAC clone F12A24; putative

ubiquitin-conjugating enzyme. (AC005167) [Oryza

sativa
]

1475
2562
Similar to NODB_AZOCA Q07740

AZORHIZOBIUM CAULINODANS.

CHITOOLIGOSACCHARIDE DEACETYLASE (EC

3.5.1.—) (NODULATION PROTEIN B).

1288
2454
Open Reading Frame containing a Sage tag sequence
2814, 2813

5355

near 3 end OS_ORF008809 ST(F) HTC052791-

A01.R.20 FRAME: −2 ORF: 10 LEN: 759

1183

Similar to gi|9294228|dbj|BAB02130.1|
2795, 3168,

5252

gb|AAD39565.1˜gene_id: MLD15.4˜similar to
3169, 2796

unknown protein [Arabidopsis thaliana]

1174
2387
Similar to gi|7267302|emb|CAB81084.1|UV-damaged
2881, 4402,
4893

DNA binding factor-like protein [Arabidopsis thaliana]
4403, 4401,

2798, 4282

1272

Similar to gi|168640|gb|AAA66268.1|mosaic protein

5142

1406

Similar to gi|7076784|emb|CAB75899.1|2-

oxoglutarate dehydrogenase, E1 subunit-like protein

[Arabidopsis thaliana]

1391
2498
Similar to gi|7248391|dbj|BAA92714.1|hypothetical

protein [Oryza sativa]

1399

Similar to ABP4_MAIZE P33488 ZEA MAYS

5445

(MAIZE). AUXIN-BINDING PROTEIN 4

PRECURSOR (ABP).

1227
2419
Open Reading Frame OS_ORF014096 HTC090622-
3291, 3330,
4847
5509

A01.F.4 FRAME: 1 ORF: 2 LEN: 663
4055, 3292,

2964

1427
2520
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF000879 ST(F) HTC004954-A01.4

FRAME: −2 ORF: 1 LEN: 501

1444
2535
Similar to CY2_RHOTE P00098 RHODOCYCLUS

TENUIS (RHODOSPIRILLUM TENUE).

CYTOCHROME C2.

1520
2601
Similar to gi|2828289|emb|CAA16703.1|hypothetical
4483, 2863

5901

protein [Arabidopsis thaliana]

1292
2457
Similar to BZTA_RHOCA Q52663 RHODOBACTER

CAPSULATUS (RHODOPSEUDOMONAS

CAPSULATA).

GLUTAMATE/GLUTAMINE/ASPARTATE/ASPAR

AGINE-BINDING PROTEIN PRECURSORBZTA.

1557
2636
Open Reading Frame OS_ORF021175 HTC144175-
4019

5355

A01.R.30 FRAME: 3 ORF: 14 LEN: 1191

1112
2330
Similar to gi|4510366|gb|AAD21454.1|hypothetical

5012
5902

protein [Arabidopsis thaliana]

1361

Similar to gi|6520227|dbj|BAA87955.1|ZCW7

[Arabidopsis thaliana]

1384
2494
Similar to gi|1345585|emb|CAA50062.1|B

transcriptional activator [Zea mays]

1544
2624
Similar to gi|2244832|emb|CAB10254.1|hypothetical

4828
5856

protein [Arabidopsis thaliana]

1374

Similar to gi|1402891|emb|CAA66823.1|unknown

[Arabidopsis thaliana]

1595
2670
Open Reading Frame containing a Sage tag sequence

5885

near 3 end OS_ORF007923 ST(F) HTC047502-

A01.R.12 FRAME: −2 ORF: 12 LEN: 567

1152
2368
Similar to gi|8926755|emb|CAB96548.1|putative rice
2872, 2871

bicoid protein [Oryza sativa subsp. japonica]

1370
2489
Open Reading Frame OS_ORF018320 HTC122173-

A01.11 FRAME: 1 ORF: 9 LEN: 846

1058
2299
Similar to COMI_DICDI Q03380 DICTYOSTELIUM
3256, 2682

DISCOIDEUM (SLIME MOLD). COMITIN (CABP1-

RELATED PROTEIN P24) (24 KD ACTIN-BINDING

PROTEIN).

1264

Open Reading Frame OS_ORF020840 HTC141053-

5515

A01.F.10 FRAME: −2 ORF: 1 LEN: 789

1204
2406
Similar to CLPB_SYNY3 P74361 SYNECHOCYSTIS
2859, 2933,

5799

SP. (STRAIN PCC 6803). CLPB PROTEIN.
4641, 2858,

2857, 2971

1050
2295
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF002649 ST(F) HTC015461-

A01.45 FRAME: 1 ORF: 4 LEN: 897

1455
2545
Open Reading Frame OS_ORF004035 HTC023345-

A01.22 FRAME: 3 ORF: 3 LEN: 852

1515
2596
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF013547 ST(F) HTC086635-

A01.R.5 FRAME: −3 ORF: 2 LEN: 738

1309
2464
Similar to gi|5302773|emb|CAB46061.1|heat shock

5508

protein like [Arabidopsis thaliana]

1580
2657
Similar to gi|2982457|emb|CAA18221.1|hypothetical

5844

protein [Arabidopsis thaliana]

1280

Open Reading Frame OS_ORF016729 ST(R)

5891

HTC110880-A01.F.12 FRAME: 3 ORF: 15 LEN: 510

1061

Similar to gi|6437533|gb|AAF08565.1|AC012193_14
2852
4793

hypothetical protein [Arabidopsis thaliana]

1382

Similar to gi|8778307|gb|AAF79316.1|AC002304_9

F14J16.15 [Arabidopsis thaliana]

1507
2588
Open Reading Frame OS_ORF014728 HTC095231-
3268, 3245

A01.R.21 FRAME: −2 ORF: 18 LEN: 1038

1398
2504
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF008116 ST(F) HTC048551-

A01.42 FRAME: 1 ORF: 4 LEN: 567

1435
2527
Similar to gi|4883606|gb|AAD31575.1|AC006922_7
4003
4965
5396

putative cis-Golgi SNARE protein [Arabidopsis

thaliana
]

1086

Similar to YRBB_ECOLI P45389 ESCHERICHIA

COLI
. HYPOTHETICAL 14.4 KD PROTEIN IN

MURA-RPON INTERGENIC REGION (F129).

1540
2621
Similar to gi|685234|emb|CAA56426.1|H1

[Arabidopsis thaliana]

1305

Similar to YNT1_ANASP Q05067 ANABAENA SP.

(STRAIN PCC 7120). HYPOTHETICAL ABC

TRANSPORTER ATP-BINDING PROTEIN IN

NTCA/BIFA 3 REGION(ORF1) (FRAGMENT).

1377
2492
Similar to gi|3941414|gb|AAC83583.1|putative

5136
5303

transcription factor [Arabidopsis thaliana]

1576
2653
Similar to P30_TOXGO P13664 TOXOPLASMA

GONDII. MAJOR SURFACE ANTIGEN P30

PRECURSOR.

1193

Similar to gi|3600048|gb|AAC35535.1|similar to

hypothetical proteins in Schizosaccharomyces pombe

(GB: Z98533) and C. elegans (GB: Z48334 and Z78419)

[Arabidopsis thaliana]

1523
2604
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF004361 ST(F) HTC025646-A01.5

FRAME: −1 ORF: 3 LEN: 648

1448
2539
Open Reading Frame OS_ORF007167 HTC042869-

A01.R.21 FRAME: 3 ORF: 21 LEN: 651

1411

Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF012877 ST(F) HTC080961-

A01.F.19 FRAME: 2 ORF: 1 LEN: 537

1205

Open Reading Frame OS_ORF012677 HTC079731-

A01.5 FRAME: −2 ORF: 2 LEN: 855

1076

Similar to gi|4512702|gb|AAD21755.1|putative WD-
3377, 3376

40 repeat protein [Arabidopsis thaliana]

1356

Similar to gi|4768996|gb|AAD29711.1|AF140498_1

hypothetical protein [Oryza sativa]

1056
2298
Open Reading Frame OS_ORF014992 ST(R)
3090, 3148,

5908

HTC097367-A01.F.13 FRAME: −3 ORF: 6 LEN: 642
3147, 3146

1456
2546
Similar to gi|6041852|gb|AAF02161.1|AC009853_21
3360

5426

unknown protein, 3 partial [Arabidopsis thaliana]

1530
2611
Similar to gi|3335347|gb|AAC27149.1|Contains

5426

similarity to ARI, RING finger protein gb|X98309 from

Drosophila melanogaster
. ESTs gb|T44383,

gb|W43120, gb|N65868, gb|H36013, gb|AA042241,

gb|T76869 and gb|AA042359 come from this gene.

[Arabidopsis thalia]

1559
2638
Similar to gi|3738091|gb|AAC63588.1|putative bHLH

transcription factor [Arabidopsis thaliana]

1367
2486
Similar to gi|435946|gb|AAC49558.1|DNA-binding

factor of bZIP class

1550
2630
Similar to gi|8843759|dbj|BAA97307.1|
3624, 3796,

emb|CAB62602.1˜gene_id: MXK3.18˜similar to
3623, 3621,

unknown protein [Arabidopsis thaliana]
4666, 3622

1069
2306
Similar to gi|7406405|emb|CAB85515.1|putative

5068
5411

protein [Arabidopsis thaliana]

1115
2333
Open Reading Frame OS_ORF002824 HTC016383-

A01.16 FRAME: 3 ORF: 18 LEN: 744

1368
2487
Open Reading Frame OS_ORF013471 HTC085904-

5631

A01.R.22 FRAME: 2 ORF: 1 LEN: 657

1585
2662
Similar to UL34_HCMVA P16812 HUMAN

CYTOMEGALOVIRUS (STRAIN AD169).

HYPOTHETICAL PROTEIN UL34.

1078
2314
Open Reading Frame OS_ORF004236 HTC024771-

5478

A01.7 FRAME: −1 ORF: 1 LEN: 759

1394

Similar to ADX_CHICK P13216 GALLUS GALLUS

4815
5357

(CHICKEN). ADRENODOXIN PRECURSOR

(ADRENAL FERREDOXIN) (FRAGMENT).

1330
2475
Similar to gi|9280689|gb|AAF86558.1|AC069252_17
4502

F2E2.17 [Arabidopsis thaliana]

1506
2587
Similar to I131_MOUSE O09030 MUS MUSCULUS

(MOUSE). INTERLEUKIN-13 RECEPTOR ALPHA-

1 CHAIN PRECURSOR (IL-13R-ALPHA-1) (IL-

13RA-1) (INTERLEUKIN-13 BINDING PROTEIN)

(NR4).

1331
2476
Open Reading Frame OS_ORF013279 HTC084207-

A01.F.22 FRAME: 3 ORF: 19 LEN: 930

1484
2569
Open Reading Frame OS_ORF010749 HTC066005-

5859

A01.12 FRAME: 1 ORF: 13 LEN: 651

1179

Similar to gi|4467146|emb|CAB37515.1|galactosidase
4284

like protein [Arabidopsis thaliana]

1485

Similar to 5HT1_APLCA Q16950 APLYSIA

CALIFORNICA
(CALIFORNIA SEA HARE). 5-

HYDROXYTRYPTAMINE 1 RECEPTOR (5-HTB1)

(SEROTONIN RECEPTOR 1).

1265
2442
Similar to CCB2_RABIT P54288 ORYCTOLAGUS
4082, 4081,

CUNICULUS
(RABBIT). DIHYDROPYRIDINE-
2941, 4056

SENSITIVE L-TYPE, CALCIUM CHANNEL BETA-

2 SUBUNIT(CAB2).

1519
2600
Open Reading Frame OS_ORF002845 HTC016551-

A01.21 FRAME: −2 ORF: 9 LEN: 1677

1214
2410
Open Reading Frame containing a Sage tag sequence
3708

near 3 end OS_ORF013972 ST(F) HTC089849-

A01.22 FRAME: 2 ORF: 16 LEN: 537

1389
2496
Similar to gi|3941526|gb|AAC83639.1|putative
3692, 3694,
4886
5531

transcription factor [Arabidopsis thaliana]
2904, 4427,

3915, 4428,

3693

1240

Similar to gi|1086540|gb|AAC49219.1|Ra

1478
2564
Open Reading Frame OS_ORF018918 ST(R)

HTC126528-A01.F.14 FRAME: 3 ORF: 17 LEN: 513

1362

Similar to YIHI_ECOLI P32130 ESCHERICHIA

COLI
. HYPOTHETICAL 19.1 KD PROTEIN IN

POLA-HEMN INTERGENIC REGION (O169).

1132
2349
Similar to gi|7406435|emb|CAB85544.1|putative

protein [Arabidopsis thaliana]

1317

Open Reading Frame OS_ORF013506 HTC086076-

A01.R.18 FRAME: −2 ORF: 10 LEN: 753

1195
2400
Similar to gi|4455283|emb|CAB36819.1|L1 specific
2972
4821
5359

homeobox gene ATML1/ovule-specific homeobox

protein A20 [Arabidopsis thaliana]

1052
2296
Similar to K1CS_RAT Q63279 RATTUS

NORVEGICUS
(RAT). KERATIN, TYPE I

CYTOSKELETAL 19 (CYTOKERATIN 19) (K19)

(CK 19)(FRAGMENT).

1526
2607
Open Reading Frame OS_ORF014719 HTC095181-

A01.R.17 FRAME: 1 ORF: 6 LEN: 930

1321
2472
Similar to gi|4895195|gb|AAD32782.1|AC007661_19
2781
4790
5843

putative mitochondrial carrier protein [Arabidopsis

thaliana
]

1181
2393
Similar to gi|7485913|pir||T00906 hypothetical protein
4560, 3029,
4995
5829

F21B7.20 - Arabidopsis thaliana
4559, 4607,

4606

1548
2628
Similar to gi|6996252|emb|CAB75478.1|putative

protein [Arabidopsis thaliana]

1239
2427
Similar to gi|7362762|emb|CAB83132.1|putative
3161, 3160,

5318

protein [Arabidopsis thaliana]
3936, 3938,

3937, 2956

1583
2660
Similar to gi|4388823|gb|AAD19778.1|hypothetical

protein [Arabidopsis thaliana]

1404

Similar to gi|7268671|emb|CAB78879.1|myb-like

protein [Arabidopsis thaliana]

1299
2460
Similar to YR02_CAEEL Q10015

CAENORHABDITIS ELEGANS
. HYPOTHETICAL

45.2 KD PROTEIN T25E4.2 IN CHROMOSOME II.

1500
2581
Similar to gi|7488434|pir||T06699 zinc finger protein
3190, 3100,

T29H11.50 - Arabidopsis thaliana
3893

1106

Open Reading Frame OS_ORF013978 HTC089902-

A01.R.17 FRAME: −2 ORF: 15 LEN: 846

1363
2484
Similar to gi|1695698|dbj|BAA13181.1|C-type cyclin

[Oryza sativa]

1579
2656
Similar to GREA_MYCLE P46808

MYCOBACTERIUM LEPRAE. TRANSCRIPTION

ELONGATION FACTOR GREA (TRANSCRIPT

CLEAVAGE FACTORGREA).

1570

Open Reading Frame OS_ORF021360 HTC145470-

A01.R.8 FRAME: 2 ORF: 9 LEN: 660

1416
2509
Open Reading Frame OS_ORF001739 HTC010017-

A01.13 FRAME: 1 ORF: 1 LEN: 1221

1514
2595
Open Reading Frame containing a Sage tag sequence
3877, 4379,

near 3 end OS_ORF019284 ST(F) HTC129613-
3406, 3407,

A01.R.5 FRAME: −3 ORF: 2 LEN: 534
3405

1372

Similar to gi|7288033|emb|CAB81795.1|putative

5803

protein [Arabidopsis thaliana]

1525
2606
Open Reading Frame OS_ORF014843 HTC096188-

A01.R.23 FRAME: 3 ORF: 4 LEN: 942

1225

Similar to gi|3927830|gb|AAC79587.1|hypothetical
4474, 4473

5258

protein [Arabidopsis thaliana]

1136
2353
Open Reading Frame OS_ORF006047 HTC036097-

A01.R.9 FRAME: 3 ORF: 3 LEN: 771

1342

Similar to gi|6137251|sp|O22757|YML2_ARATH

HYPOTHETICAL MLO-LIKE PROTEIN F5J6.23

1401

Similar to LAMC_DROME Q03427 DROSOPHILA

MELANOGASTER
(FRUIT FLY). LAMIN C (PG-IF).

1207

Similar to gi|6692109|gb|AAF24574.1|AC007764_16

4844
5614

F22C12.18 [Arabidopsis thaliana]

1188
2397
Open Reading Frame containing a Sage tag sequence
3790, 3331,

near 3 end OS_ORF013981 ST(F) HTC089945-
2943

A01.R.1 FRAME: 1 ORF: 1 LEN: 540

1473

Similar to UL55_HSVEB P28963 EQUINE

HERPESVIRUS TYPE 1 (STRAIN AB4P) (EHV-1),

AND EQUINEHERPESVIRUS TYPE 1 (STRAIN

KENTUCKY A) (EHV-1). GENE 4 PROTEIN (ORF

L2).

1173
2386
Similar to gi|2982442|emb|CAA18250.1|hypothetical

protein [Arabidopsis thaliana]

1393
2500
Similar to MERC_THIFE P22905 THIO BACILLUS

FERROOXIDANS. MERCURIC RESISTANCE

PROTEIN MERC.

1593
2669
Similar to gi|9294053|dbj|BAB02010.1|

gb|AAD03575.1˜gene_id: MOB24.16˜similar to

unknown protein [Arabidopsis thaliana]

1459
2549
Open Reading Frame OS_ORF011248 HTC069298-

A01.F.24 FRAME: −1 ORF: 7 LEN: 720

1168

Similar to gi|4733891|gb|AAD17931.2|unconventional
3462, 3267,

myosin heavy chain [Zea mays]
3079

1508
2589
Open Reading Frame OS_ORF006474 HTC038851-

A01.R.16 FRAME: 2 ORF: 9 LEN: 696

1542
2623
Open Reading Frame OS_ORF009690 ST(R)
4113, 4114

HTC058211-A01.F.15 FRAME: −2 ORF: 2 LEN: 975

1479
2565
Open Reading Frame OS_ORF016333 HTC107775-

A01.R.12 FRAME: −1 ORF: 12 LEN: 630

1311
2465
Similar to gi|8570063|dbj|BAA96768.1|hypothetical

protein [Oryza sativa]

1325

Similar to GPDA_CUPLA P52425 CUPHEA

LANCEOLATA. GLYCEROL-3-PHOSPHATE

DEHYDROGENASE (NAD+) (EC 1.1.1.8).

1553
2633
Similar to gi|6453896|gb|AAF09079.1|AC011663_15

5778

unknown protein [Arabidopsis thaliana]

1185
2395
Similar to gi|445137|prf||1908437A topoisomerase I
3117, 3315,
4958

[Arabidopsis thaliana]
4532, 4531

1283
2452
Similar to gi|6665551|gb|AAF22920.1|AC013289_14
2845, 2843,

hypothetical protein [Arabidopsis thaliana]
2814, 2813,

3259

1422
2515
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF011984 ST(F) HTC074722-

A01.F.42 FRAME: −1 ORF: 79 LEN: 906

1117
2335
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF019746 ST(F) HTC133378-

A01.R.14 FRAME: −1 ORF: 15 LEN: 888

1302

Similar to gi|3152572|gb|AAC17053.1|Contains
4126, 4128,

homology to DNAJ heatshock protein gb|U32803 from
4127

Haemophilus influenzae. [Arabidopsis thaliana]

1438
2530
Similar to gi|2160143|gb|AAB60765.1|F19K23.12

gene product [Arabidopsis thaliana]

1494
2576
Similar to gi|2244963|emb|CAB10384.1|hypothetical

protein [Arabidopsis thaliana]

1415
2508
Similar to YT19_MYCTU P71555

MYCOBACTERIUM TUBERCULOSIS.

HYPOTHETICAL 46.1 KD PROTEIN CY10D7.19C.

1442

Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF017606 ST(F) HTC117204-

A01.18 FRAME: 2 ORF: 5 LEN: 1041

1532
2613
Similar to GAST_RAT P04563 RATTUS

NORVEGICUS
(RAT). GASTRIN PRECURSOR.

1167
2381
Similar to gi|4584527|emb|CAB40758.1|putative
2934, 3436

5698

protein [Arabidopsis thaliana]

1199
2402
Similar to Y08F_MYCTU Q11052

MYCOBACTERIUM TUBERCULOSIS. PROBABLE

REGULATORY PROTEIN CY50.15.

1178
2391
Similar to gi|5852089|emb|CAB55396.1|zwh12.1

5134

[Oryza sativa]

1349

Similar to gi|6498440|dbj|BAA87843.1|hypothetical

protein [Oryza sativa]

1200
2403
Open Reading Frame OS_ORF001461 HTC008302-

A01.23 FRAME: 1 ORF: 10 LEN: 2289

1430
2523
Open Reading Frame OS_ORF018292 HTC121996-

A01.44 FRAME: −2 ORF: 18 LEN: 1551

1418
2511
Open Reading Frame OS_ORF020505 ST(R)

HTC138244-A01.16 FRAME: −3 ORF: 4 LEN: 687

1246
2433
Similar to gi|3080410|emb|CAA18729.1|hypothetical
4568, 4094,
4854
5409

protein [Arabidopsis thaliana]
4095, 4092,

2807, 2799,

3068, 4307,

4699, 4093,

4087, 4498,

3998, 4567,

4499

1564
2643
Similar to gi|8809705|dbj|BAA97246.1|26S
3076, 3075

5705

proteasome/non-ATPase regulatory subunit

[Arabidopsis thaliana]

1428
2521
Open Reading Frame OS_ORF003246 HTC018855-

A01.26 FRAME: −3 ORF: 13 LEN: 993

1348
2480
Similar to gi|8099228|gb|AAF72076.1|AC025098_10

hypothetical protein [Oryza sativa]

1197
2401
Similar to AG84_MYCLE P46815

MYCOBACTERIUM LEPRAE. ANTIGEN 84.

1217
2413
Similar to CYP4_CYNCA P40781 CYNARA
4623, 2801,
4883
5234

CARDUNCULUS (CARDOON). CYPRO4
4624

PROTEIN.

1306

Open Reading Frame OS_ORF003828 HTC022181-

A01.11 FRAME: −2 ORF: 2 LEN: 660

1531
2612
Open Reading Frame OS_ORF016113 HTC105925-
2985

A01.R.13 FRAME: 1 ORF: 12 LEN: 687

1439
2531
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF007855 ST(F) HTC046991-

A01.F.4 FRAME: −2 ORF: 2 LEN: 510

1488
2571
Similar to HSTO_VIBCH Q07425 VIBRIO

CHOLERAE. HEAT-STABLE ENTEROTOXIN STO

PRECURSOR (O1-ST).

1569
2648
Open Reading Frame OS_ORF006104 ST(R)

HTC036523-A01.29 FRAME: 1 ORF: 7 LEN: 543

1202
2405
Open Reading Frame OS_ORF018301 HTC122064-

A01.R.12 FRAME: 1 ORF: 5 LEN: 744

1573
2650
Similar to gi|8778489|gb|AAF79497.1|AC002328_5

F20N2.12 [Arabidopsis thaliana]

1516
2597
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF012764 ST(F) HTC080285-

A01.26 FRAME: 2 ORF: 22 LEN: 669

1234

Similar to gi|6041840|gb|AAF02149.1|AC009853_9
2946

5341

hypothetical protein [Arabidopsis thaliana]

1250

Similar to gi|9294584|dbj|BAB02865.1|
2846, 4176,
4824

gb|AAF08583.1˜gene_id: MFJ20.18˜similar to
2847, 4175

unknown protein [Arabidopsis thaliana]

1566
2645
Similar to YOP3_CAEEL Q22695

CAENORHABDITIS ELEGANS
. HYPOTHETICAL

41.0 KD PROTEIN T23F11.3 IN CHROMOSOME III.

1091
2321
Open Reading Frame OS_ORF021003 HTC142458-

A01.F.9 FRAME: −3 ORF: 1 LEN: 657

1392
2499
Similar to YSV4_CAEEL Q10010

5176
5918

CAENORHABDITIS ELEGANS
. HYPOTHETICAL

26.6 KD PROTEIN T19C3.4 IN CHROMOSOME III.

1103

Similar to GDIT_MOUSE Q62160 MUS MUSCULUS

4974
5921

(MOUSE). RHO GDP-DISSOCIATION INHIBITOR 3

(RHO GDI 3) (RHO-GDI2).

1536
2617
Open Reading Frame OS_ORF004492 HTC026407-

A01.7 FRAME: −1 ORF: 5 LEN: 666

1371
2490
Similar to gi|7486436|pir||T02408 hypothetical protein

4924
5904

F4I1.34 - Arabidopsis thaliana

1440
2532
Similar to YPOL_IPNVJ P22931 INFECTIOUS

PANCREATIC NECROSIS VIRUS (SEROTYPE

JASPER) (IPNV). HYPOTHETICAL 17.3 KD

PROTEIN (SMALL ORF).

1196

Similar to gi|7484807|pir||T01259 AMP deaminase

4869

homolog F16M14.21 - Arabidopsis thaliana

1308
2463
Similar to YNX1_YEAST P53860

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). HYPOTHETICAL 40.7 KD PROTEIN IN

SIN4-URE2 INTERGENIC REGION.

1554
2634
Similar to gi|3355466|gb|AAC27828.1|unknown

5916

protein [Arabidopsis thaliana]

1320

Open Reading Frame OS_ORF006563 ST(R)
3427

5564

HTC039403-A01.F.12 FRAME: 2 ORF: 1 LEN: 600

1329

Similar to gi|2129707|pir||S71165 RNA-directed DNA

polymerase (EC 2.7.7.49) - Arabidopsis thaliana

retrotransposon 2 (fragment)

1254

Similar to CISY_COXBU P18789 COXIELLA
4387
5158
5657

BURNETII. CITRATE SYNTHASE (EC 4.1.3.7).

1483
2568
Open Reading Frame OS_ORF013069 HTC082606-

A01.F.5 FRAME: −1 ORF: 7 LEN: 612

1458
2548
Similar to HB2U_MOUSE P06344 MUS

MUSCULUS
(MOUSE). H-2 CLASS II

HISTOCOMPATIBILITY ANTIGEN, A-U BETA

CHAIN PRECURSOR.

1319
2471
Similar to gi|8778212|gb|AAF79221.1|AC006917_6
4691

F10B6.10 [Arabidopsis thaliana]

1409
2507
Similar to gi|6815065|dbj|BAA90352.1|hypothetical

protein [Oryza sativa]

1487

Similar to gi|7670039|dbj|BAA94993.1|invertase

5844

inhibitor-like protein [Arabidopsis thaliana]

1156
2371
Similar to gi|1707016|gb|AAC69127.1|putative AP2

5424

domain transcription factor [Arabidopsis thaliana]

1187

Similar to gi|7523418|emb|CAB86437.1|putative
3270

protein [Arabidopsis thaliana]

1502
2583
Similar to FLAW_DESDE P80312 DESULFOVIBRIO

DESULFURICANS. FLAVODOXIN (FRAGMENT).

1344
2478
Similar to gi|6728874|gb|AAF26947.1|AC008113_18
2679, 2678,

5383

F12A21.16 [Arabidopsis thaliana]
2680

1462

Similar to gi|3080386|emb|CAA18706.1|hypothetical

5339

protein [Arabidopsis thaliana]

1189

Similar to NXS1_ACAAN P01434 ACANTHOPHIS

ANTARCTICUS (COMMON DEATH ADDER).

SHORT NEUROTOXIN 1 (TOXIN AA C).

1420
2513
Similar to gi|3786014|gb|AAC67360.1|hypothetical

protein [Arabidopsis thaliana]

1400

Open Reading Frame OS_ORF021917 HTC150055-

A01.F.6 FRAME: −1 ORF: 1 LEN: 603

1588
2665
Similar to gi|7269937|emb|CAB81030.1|putative

5727

protein [Arabidopsis thaliana]

1543

Similar to gi|2827547|emb|CAA16555.1|predicted

5046
5623

protein [Arabidopsis thaliana]

1584
2661
Similar to gi|2245140|emb|CAB10561.1|SUPERMAN

like protein [Arabidopsis thaliana]

1298

Similar to SYY_HUMAN P54577 HOMO SAPIENS
3483
4814
5701

(HUMAN). TYROSYL-TRNA SYNTHETASE (EC

6.1.1.1) (TYROSYL—TRNA LIGASE) (TYRRS).

1395
2501
Similar to gi|5091500|dbj|BAA78735.1|Hypothetical

protein [Oryza sativa]

1555

Similar to SWH1_YEAST P39555 P80234

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). SWH1 PROTEIN.

1102

Similar to gi|4337193|gb|AAD18107.1|hypothetical

5574

protein [Arabidopsis thaliana]

1266
2443
Open Reading Frame OS_ORF002545 HTC014886-

5844

A01.21 FRAME: 1 ORF: 6 LEN: 1299

1587
2664
Similar to gi|7543889|emb|CAB87198.1|putative

protein [Arabidopsis thaliana]

1452
2542
Similar to gi|8346561|emb|CAB93725.1|putative

5502

protein [Arabidopsis thaliana]

1307

Similar to VV_PHODV P35941 PHOCINE
3429, 3428
4979
5706

DISTEMPER VIRUS (PDV). NONSTRUCTURAL

PROTEIN V.

1301
2462
Open Reading Frame OS_ORF022234 ST(R)

HTC153141-A01.F.17 FRAME: −3 ORF: 24 LEN: 525

1255
2437
Similar to gi|4508069|gb|AAD21413.1|12246
3098

1263

Similar to gi|7019659|emb|CAB75760.1|beta-N-
2960

5650

acetylhexosaminidase-like protein [Arabidopsis

thaliana
]

1245
2432
Similar to ORYB_ORYSA P25777 ORYZA SATIVA
3319, 3318,

5472

(RICE). ORYZAIN BETA CHAIN PRECURSOR (EC
3942, 3943,

3.4.22.—).
3939

1277
2448
Similar to gi|8778457|gb|AAF79465.1|AC022492_9
3026
5109
5330

F1L3.17 [Arabidopsis thaliana]

1172
2385
Open Reading Frame OS_ORF016335 HTC107779-
4005, 4371,
5142
5415

A01.F.23 FRAME: 3 ORF: 1 LEN: 783
4518, 4108,

3032, 4517,

4004, 4519,

3031, 2977

1581
2658
Similar to gi|9229298|dbj|BAA99601.1|
4328, 4327,

gene_id: MDC16.12˜similar to unknown protein
4325

(gb|AAC36161.1) [Arabidopsis thaliana]

1089
2320
Similar to gi|8810466|gb|AAF80127.1|AC024174_9
4223, 4222

Contains similarity to an unknown protein T1B3.16

gi|4432844 from Arabidopsis thaliana BAC T1B3

gb|AC006283. ESTs gb|AI992784, gb|T45131,

gb|AA586122 come from this gene.

1552
2632
Open Reading Frame OS_ORF011826 ST(R)

HTC073567-A01.24 FRAME: −2 ORF: 3 LEN: 540

1574
2651
Open Reading Frame OS_ORF003772 HTC021944-

A01.16 FRAME: −1 ORF: 5 LEN: 702

1271
2446
Similar to THIJ_ECOLI Q46948 ESCHERICHIA
4319, 4137,

5347

COLI
. 4-METHYL-5(B-HYDROXYETHYL)-
4321, 3479,

THIAZOLE MONOPHOSPHATE
4320, 4136,

BIOSYNTHESISENZYME.
2745

1524
2605
Similar to gi|2224929|gb|AAC49747.1|ethylene-

5662

insensitive3-like2 [Arabidopsis thaliana]

1098

Similar to gi|3319884|emb|CAA11891.1|PRT1

5040

[Arabidopsis thaliana]

1472
2560
Similar to ACH7_BOVIN P54131 BOS TAURUS

(BOVINE). NEURONAL ACETYLCHOLINE

RECEPTOR PROTEIN, ALPHA-7 CHAIN

PRECURSOR.

1216
2412
Similar to gi|9294631|dbj|BAB02970.1|Na/Ca, K-
4578, 4577

exchanger-like protein [Arabidopsis thaliana]

1237
2425
Open Reading Frame OS_ORF009851 ST(R)
2761
4789
5732

HTC059249-A01.20 FRAME: −1 ORF: 4 LEN: 588

1565
2644
Open Reading Frame OS_ORF018288 HTC121964-

A01.12 FRAME: −1 ORF: 9 LEN: 738

1269
2445
Similar to HIT1_YEAST P46973
3099

5878

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). HIT1 PROTEIN.

1426
2519
Similar to gi|6572079|emb|CAB63022.1|putative
3309

5865

protein [Arabidopsis thaliana]

1465
2554
Similar to DRNE_AERHY P39658 AEROMONAS

HYDROPHILA. EXTRACELLULAR

DEOXYRIBONUCLEASE PRECURSOR (EC

3.1.21.—) (DNASE).

1343

Open Reading Frame OS_ORF001231 HTC006970-

5734

A01.14 FRAME: −1 ORF: 1 LEN: 792

1313
2467
Open Reading Frame OS_ORF012800 HTC080550-

A01.R.28 FRAME: −1 ORF: 6 LEN: 936

1413

Similar to gi|3860275|gb|AAC73043.1|putative CEN
3078
4848

(centroradialis)-like phosphatidylethanolamine-binding

protein [Arabidopsis thaliana]

1434

Similar to gi|3080367|emb|CAA18624.1|hypothetical

protein [Arabidopsis thaliana]

1528
2609
Similar to YK67_YEAST P36163

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). HYPOTHETICAL 35.8 KD PROTEIN IN

PRP16-SRP40 INTERGENIC REGION.

1297
2459
Similar to PM1_HUMAN P17152 HOMO SAPIENS
3297
4774
5463

(HUMAN). PUTATIVE RECEPTOR PROTEIN.

1446
2537
Similar to YX28_MYCTU Q10818

MYCOBACTERIUM TUBERCULOSIS.

HYPOTHETICAL 52.9 KD PROTEIN CY274.28C.

1327
2474
Similar to gi|6899931|emb|CAB71881.1|putative

protein [Arabidopsis thaliana]

1383

Similar to gi|4538965|emb|CAB39789.1|hypothetical

protein [Arabidopsis thaliana]

1060
2301
Similar to gi|7339705|dbj|BAA92910.1|ESTs

5707

D23839(R0339),AU082696(E61918) correspond to a

region of the predicted gene.; Similar to Arabidopsis

thaliana
chromosome 4 BAC clone F28J12; putative

protein. (AL021710) [Oryza sativa]

1471
2559
Open Reading Frame OS_ORF019456 ST(R)

5747

HTC131006-A01.55 FRAME: −1 ORF: 11 LEN: 534

1423
2516
Similar to CDN7_HUMAN P55273 Q13102 HOMO

SAPIENS
(HUMAN). CYCLIN-DEPENDENT

KINASE 4 INHIBITOR D (P19-INK4D).

1035

Similar to gi|8468000|dbj|BAA96601.1|Similar to
3495, 3496,

Arabidopsis thaliana
chromosome 2 BAC clone
3001

F13A10; putative ubiquitin. (AC006418) [Oryza

sativa
]

1201
2404
Similar to gi|5803260|dbj|BAA83570.1|Similar to
2890
4913
5325

wak1 gene (AJ009696) [Oryza sativa]

1495
2577
Open Reading Frame OS_ORF013227 HTC083811-
2907

A01.R.24 FRAME: 2 ORF: 4 LEN: 699

1577
2654
Open Reading Frame OS_ORF001833 HTC010638-

A01.22 FRAME: 1 ORF: 12 LEN: 618

1267

Similar to gi|7649363|emb|CAB89044.1|putative
3724, 3373
4782

protein [Arabidopsis thaliana]

1274

Similar to MTAB_SYNP2 P34883
3430

SYNECHOCOCCUS SP. (STRAIN PCC 7002)

(AGMENELLUM QUADRUPLICATUM).

MODIFICATION METHYLASE AQUI BETA

SUBUNIT (EC 2.1.1.73) (CYTOSINE-SPECIFIC

METHYLTRANSFERASE AQUI BETA SUBUNIT)

(M.AQUI BETA SUBUNIT).

1158
2373
Open Reading Frame OS_ORF006648 ST(R)

5833

HTC039909-A01.F.23 FRAME: 2 ORF: 9 LEN: 579

1080
2316
Similar to gi|8096314|dbj|BAA95817.1|hypothetical

5761

protein [Oryza sativa]

1303

Similar to YSX3_CAEEL Q10022
4125, 2853

5392

CAENORHABDITIS ELEGANS
. HYPOTHETICAL

39.0 KD PROTEIN T28D9.3 IN CHROMOSOME II.

1405

Similar to gi|7406400|emb|CAB85510.1|putative

4936
5348

protein [Arabidopsis thaliana]

1270

Similar to CDS1_HUMAN Q92903 O00163 HOMO

4795
5317

SAPIENS
(HUMAN). PHOSPHATIDATE

CYTIDYLYLTRANSFERASE (EC 2.7.7.41) (CDP-

DIGLYCERIDESYNTHETASE) (CDP-

DIGLYCERIDE PYROPHOSPHORYLASE) (CDP-

DIACYLGLYCEROLSYNTHASE) (CDS)

(CTP: PHOSPHATIDATE

CYTIDYLYLTRANSFERASE) (CDP-DAG)

1568
2647
Similar to FER_SYNY3 P27320 SYNECHOCYSTIS
3710, 3707,
5130
5686

SP. (STRAIN PCC 6803). FERREDOXIN I.
3709, 4495

1397
2503
Similar to PR1_MEDTR Q40374 MEDICAGO

5636

TRUNCATULA
(BARREL MEDIC).

PATHOGENESIS-RELATED PROTEIN PR-1

PRECURSOR.

1209

Similar to gi|5852181|emb|CAB55419.1|zhb0011.1

[Oryza sativa]

1352
2481
Similar to AGI2_WHEAT P02876 TRITICUM
4566, 4221
4879
5466

AESTIVUM
(WHEAT). AGGLUTININ ISOLECTIN

2 PRECURSOR (WGA2) (ISOLECTIN D).

1310

Similar to TAL1_MOUSE Q93092 P70358 MUS
3015, 3014,

MUSCULUS
(MOUSE). TRANSALDOLASE (EC
3013

2.2.1.2).

1286

Similar to YRP3_THEAC Q03021
3289

5671

THERMOPLASMA ACIDOPHILUM.

HYPOTHETICAL 21.7 KD PROTEIN IN RPOA2 3

REGION (ORF186).

1541
2622
Similar to ENP2_TORCA P14401 TORPEDO

5566

CALIFORNICA
(PACIFIC ELECTRIC RAY).

ELECTROMOTOR NEURON-ASSOCIATED

PROTEIN 2 (FRAGMENT).

1149

Similar to gi|7021732|gb|AAF35413.1|unknown

5119
5497

protein [Arabidopsis thaliana]

1501
2582
Open Reading Frame containing a Sage tag sequence
4587, 4586

5919

near 3 end OS_ORF012155 ST(F) HTC075889-

A01.R.16 FRAME: 2 ORF: 1 LEN: 573

1290

Open Reading Frame OS_ORF007256 ST(R)

HTC043276-A01.F.9 FRAME: 3 ORF: 8 LEN: 555

1285

Similar to gi|7270231|emb|CAB80001.1|putative
3719, 2897

pyrophosphate-fructose-6-phosphate 1-

phosphotransferase [Arabidopsis thaliana]

1366
2485
Similar to VIV_ORYSA P37398 ORYZA SATIVA

5844

(RICE). VIVIPAROUS PROTEIN HOMOLOG.

1253
2436
Open Reading Frame OS_ORF002306 HTC013290-

A01.20 FRAME: −3 ORF: 3 LEN: 807

1499
2580
Open Reading Frame OS_ORF017188 HTC114338-

A01.F.19 FRAME: 2 ORF: 2 LEN: 978

1281

Similar to CLPX_HAEIN P44838 HAEMOPHILUS

INFLUENZAE. ATP-DEPENDENT CLP PROTEASE

ATP-BINDING SUBUNIT CLPX.

1402
2505
Similar to gi|2244937|emb|CAB10359.1|hypothetical

protein [Arabidopsis thaliana]

1535
2616
Similar to gi|2583128|gb|AAB82637.1|hypothetical
2722, 2721,

5285

protein [Arabidopsis thaliana]
2970, 2995

1575
2652
Open Reading Frame OS_ORF013232 HTC083848-

A01.22 FRAME: −1 ORF: 8 LEN: 780

1357
2482
Similar to YNQ8_YEAST P53889

4841
5495

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). HYPOTHETICAL 28.8 KD PROTEIN IN

PSD1-SKO1 INTERGENIC REGION.

1322
2473
Similar to gi|6056415|gb|AAF02879.1|AC009525_13

Unknown protein [Arabidopsis thaliana]

1453
2543
Similar to gi|7523667|gb|AAF63107.1|AC006423_8
3493

Hypothetical protein [Arabidopsis thaliana]

1097

Similar to gi|4768982|gb|AAD29704.1|AF140491_1

4838

hypothetical protein [Oryza sativa]

1337

Open Reading Frame OS_ORF017842 ST(R)

HTC119007-A01.R.12 FRAME: 2 ORF: 7 LEN: 513

1251

Similar to gi|1546055|gb|AAB72019.1|cyclin type B-

like [Zea mays]

1169
2382
Similar to gi|4249412|gb|AAD13709.1|hypothetical
2962

protein [Arabidopsis thaliana]

1262
2441
Similar to gi|169775|gb|AAA33897.1|alpha-amylase
3665, 4214,

5521

precursor (EC 3.2.1.1)
3663, 3673,

3702, 3695,

3704, 3701,

3667, 3705,

3700, 3703,

3698, 3672,

3680, 3697,

4215, 3699,

3664, 3674,

3682, 3666,

3681

1282
2451
Open Reading Frame OS_ORF019538 HTC131716-

5890

A01.11 FRAME: 2 ORF: 1 LEN: 1137

1224

Similar to LDS_DROME P34739 DROSOPHILA
3426
4900

MELANOGASTER
(FRUIT FLY). PROBABLE

HELICASE LODESTAR.

1562
2641
Similar to gi|8777301|dbj|BAA96891.1|tyrosine

aminotransferase-like protein [Arabidopsis thaliana]

1221

Similar to gi|7406459|emb|CAB85561.1|myotubularin-

like protein [Arabidopsis thaliana]

1410

Similar to gi|4586118|emb|CAB40954.1|putative

5358

protein [Arabidopsis thaliana]

1275
2447
Open Reading Frame OS_ORF011566 HTC071687-

A01.30 FRAME: −1 ORF: 21 LEN: 711

1257
2439
Similar to gi|5257266|dbj|BAA81765.1|EST

C99024(E4337) corresponds to a region of the

predicted gene.; Similar to Silk moth; silkworm final

instar larvae posterior. (D83241) [Oryza sativa]

1376

Similar to gi|5823323|gb|AAD53100.1|AF175995_1

5284

putative transcription factor [Arabidopsis thaliana]

1198

Open Reading Frame OS_ORF002724 HTC015879-

A01.32 FRAME: 2 ORF: 13 LEN: 1620

1075
2312
Open Reading Frame OS_ORF019153 ST(R)

5850

HTC128490-A01.20 FRAME: 1 ORF: 17 LEN: 555

1597
2672
Open Reading Frame OS_ORF020403 HTC137549-

5091
5794

A01.F.20 FRAME: −3 ORF: 27 LEN: 741

1491
2574
Similar to gi|7523392|emb|CAB86450.1|putative
4405, 4406
5070
5361

protein [Arabidopsis thaliana]

1226

Similar to gi|3193293|gb|AAC19277.1|contains a short
3790
5145
5379

region of similarity to another Arabidopsis hypothetical

protein F19K23.8 (GB: AC000375) [Arabidopsis

thaliana
]

1304

Similar to gi|6520233|dbj|BAA87958.1|CW14
4195, 4193,
5017
5590

[Arabidopsis thaliana]
4194

1505
2586
Similar to gi|4914444|emb|CAB43647.1|hypothetical
3213

protein [Arabidopsis thaliana]

1328

Open Reading Frame OS_ORF006440 HTC038643-

5271

A01.R.16 FRAME: 2 ORF: 11 LEN: 738

1122
2340
Open Reading Frame OS_ORF009333 ST(R)

HTC055987-A01.R.26 FRAME: 1 ORF: 21 LEN: 561

1556
2635
Similar to gi|3482932|gb|AAC33217.1|AAC33217
4676, 3221,
4810

Hypothetical protein [Arabidopsis thaliana]
4675, 4157,

4503

1586
2663
Similar to gi|3702336|gb|AAC62893.1|3-methyl-2-

5849

oxobutanoate hydroxy-methyl-transferase [Arabidopsis

thaliana
]

1412

Similar to gi|7268365|emb|CAB78658.1|pore protein
2958

homolog [Arabidopsis thaliana]

1182

Open Reading Frame OS_ORF020271 ST(R)
4696
4773
5403

HTC136732-A01.14 FRAME: 3 ORF: 2 LEN: 1212

1222
2417
Similar to gi|4512698|gb|AAD21751.1|unknown
4636, 3440,
4962

protein [Arabidopsis thaliana]
3033

1175
2388
Open Reading Frame OS_ORF014527 HTC093803-
3497, 2824,

A01.F.24 FRAME: 1 ORF: 21 LEN: 1272
2913

1273

Similar to BLA2_BACCE P04190 BACILLUS

CEREUS
. BETA-LACTAMASE PRECURSOR,

TYPE II (EC 3.5.2.6)

(PENICILLINASE)(CEPHALOSPORINASE).

1247
2434
Similar to PYR5_DROME Q01637 Q24221
4513, 4512,
5105
5585

DROSOPHILA MELANOGASTER (FRUIT FLY).
4511

URIDINE 5-MONOPHOSPHATE SYNTHASE

(UMP SYNTHASE)

(OROTATEPHOSPHORIBOSYLTRANSFERASE

(EC 2.4.2.10) AND OROTIDINE 5-

PHOSPHATEDECARBOXYLASE (EC 4.1.1.23))

(RUDIMENTARY-LIKE PROTEIN).

1170
2383
Open Reading Frame OS_ORF006653 HTC039934-
3304, 4631,
5080

A01.R.8 FRAME: −2 ORF: 1 LEN: 762
4630, 3279

1493

Open Reading Frame OS_ORF010496 HTC064014-
3334, 3333,
4929

A01.6 FRAME: 3 ORF: 3 LEN: 726
3474

1457
2547
Similar to gi|3860249|gb|AAC73017.1|unknown
4165, 4163,

5568

protein [Arabidopsis thaliana]

1378

Similar to gi|4581182|gb|AAD24665.1|AC006220_21

hypothetical protein [Arabidopsis thaliana]

1070
2307
Similar to gi|8778386|gb|AAF79394.1|AC068197_4
4673, 4672

5492

F16A14.6 [Arabidopsis thaliana]

1490
2573
Similar to gi|2245070|emb|CAB10493.1|hypothetical
2810, 2878,

protein [Arabidopsis thaliana]
3246, 3095

1360

Similar to gi|2342691|gb|AAB70418.1|F7G19.26

[Arabidopsis thaliana]

1572

Similar to TXLA_SYNP7 P35088

SYNECHOCOCCUS SP. (STRAIN PCC 7942)

(ANACYSTIS NIDULANS R2). THIOL: DISULFIDE

INTERCHANGE PROTEIN TXLA.

1590

Similar to gi|4512686|gb|AAD21740.1|hypothetical

5443

protein [Arabidopsis thaliana]

1503
2584
Open Reading Frame OS_ORF010771 ST(R)
4430, 2930
5036

HTC066124-A01.26 FRAME: 3 ORF: 24 LEN: 1098

1449
2540
Similar to gi|6996304|emb|CAB75465.1|putative

protein [Arabidopsis thaliana]

1489
2572
Open Reading Frame OS_ORF011581 ST(R)

HTC071843-A01.19 FRAME: −3 ORF: 1 LEN: 501

1336

Similar to gi|6648207|gb|AAF21205.1|AC013483_29

5589

unknown protein [Arabidopsis thaliana]

1215
2411
Open Reading Frame OS_ORF012733 ST(R)

5516

HTC080054-A01.8 FRAME: 2 ORF: 1 LEN: 657

1474
2561
Similar to gi|13219|emb|CAA34122.1|cytochrome

oxidase subunit I [Oryza sativa]

1421
2514
Similar to gi|3582319|gb|AAC35216.1|unknown

5419

protein [Arabidopsis thaliana]

1333

Similar to gi|7413597|emb|CAB86087.1|putative
4542

5591

protein [Arabidopsis thaliana]

1244
2431
Similar to gi|7258378|emb|CAB77594.1|putative
4301

5681

protein [Arabidopsis thaliana]

1194

Similar to gi|3805853|emb|CAA21473.1|putative
3097, 3110,
4805
5418

protein [Arabidopsis thaliana]
3096

1346

Similar to gi|3550661|emb|CAA04670.1|39 kDa EF-
4156

5552

Hand containing protein [Solanum tuberosum]

1318
2470
Similar to ILVE_METJA Q58414
2780, 2779

5836

METHANOCOCCUS JANNASCHII. PUTATIVE

BRANCHED-CHAIN AMINO ACID

AMINOTRANSFERASE (EC

2.6.1.42)(TRANSAMINASE B) (BCAT).

1116
2334
Similar to gi|4539467|emb|CAB39947.1|putative

protein [Arabidopsis thaliana]

1191

Open Reading Frame OS_ORF017317 HTC115428-

5232

A01.3 FRAME: −1 ORF: 3 LEN: 732

1043

Similar to gi|421918|pir||PQ0549 acid phosphatase-1

5316

(EC 3.1.3.—) —tomato (fragment)

1219
2415
Similar to gi|8885579|dbj|BAA97509.1|receptor-like
3303, 3232

protein kinase [Arabidopsis thaliana]

1341

Similar to gi|6587806|gb|AAF18497.1|AC010924_10

5254

Contains similarity to gb|M82916 MRS2 protein from

Saccharomyces cerivisae
. ESTs gb|N96043,

gb|AI998651, gb|AA585850, gb|T42027 come from

this gene. [Arabidopsis thaliana]

1387

Similar to gi|9229506|dbj|BAB00011.1|
4541
5216
5811

gene_id: MIL23.18˜similar to unknown protein

(gb|AAB61516.1) [Arabidopsis thaliana]

1210
2408
Open Reading Frame OS_ORF019147 HTC128421-

A01.R.36 FRAME: −2 ORF: 8 LEN: 849

1166

Similar to gi|1247314|emb|CAA01765.1|ACC34
3261, 3293

5286

ACCase [Zea mays]

1248
2435
Similar to gi|3176677|gb|AAC18800.1|Similar to S.
3865, 3866
4833

cerevisiae
SIK1P protein, A_TM021B04.13 from A.

thaliana
BAC gb|AF007271. [Arabidopsis thaliana]

1567
2646
Similar to gi|6091768|gb|AAF03478.1|AC009327_17

5518

hypothetical protein [Arabidopsis thaliana]

1064

Similar to SMN1_BOVIN O18870 BOS TAURUS

(BOVINE). SURVIVAL MOTOR NEURON

PROTEIN 1 (FRAGMENT).

1518
2599
Open Reading Frame OS_ORF012554 HTC078773-

A01.17 FRAME: −2 ORF: 7 LEN: 927

1212

Open Reading Frame OS_ORF017514 HTC116489-
3017, 3205,

A01.F.13 FRAME: −1 ORF: 13 LEN: 1107
3018, 3016

1118
2336
Similar to BP4C_BRANA P41506 BRASSICA

NAPUS (RAPE). BP4C PROTEIN.

1276

Similar to YDIB_HAEIN P44774 HAEMOPHILUS
3359
5082
5679

INFLUENZAE. HYPOTHETICAL PROTEIN HI0607.

1497

Similar to gi|4895168|gb|AAD32756.1|AC007662_1

putative replication protein A1 [Arabidopsis thaliana]

1482
2567
Open Reading Frame OS_ORF018605 HTC124146-

A01.F.10 FRAME: 1 ORF: 10 LEN: 933

1071
2308
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF018748 ST(F) HTC125352-

A01.F.9 FRAME: 2 ORF: 7 LEN: 708

1184
2394
Similar to gi|508545|gb|AAA76580.1|zein
3231

1354

Similar to gi|2739000|gb|AAB94588.1|CYP71D10p
4562, 3780,

[Glycine max]
3878, 4600,

4658, 3130,

3080, 3129,

4599, 3781,

4561, 3779,

3142

1128
2345
Open Reading Frame OS_ORF007317 HTC043588-

A01.30 FRAME: −3 ORF: 9 LEN: 1224

1388

Similar to gi|7271065|emb|CAB80673.1|putative
2805, 4543
4831

protein [Arabidopsis thaliana]

1379
2493
Similar to gi|4432835|gb|AAD20684.1|unknown
3706
4972
5604

protein [Arabidopsis thaliana]

1293

Similar to KC21_SCHPO P40231
3188
5063

SCHLZOSACCHAROMYCES POMBE (FISSION

YEAST). CASEIN KINASE II, ALPHA CHAIN (CK

II) (EC 2.7.1.37).

1192
2399
Similar to gi|2827630|emb|CAA16582.1|putative
3195, 3194,

protein [Arabidopsis thaliana]
2888

1223
2418
Similar to gi|5059025|gb|AAD38873.1|AF110382_1 3-
2720
4850
5793

hydroxy-3-methylglutaryl-coenzyme A reductase

[Oryza sativa]

[0683]

9

TABLE 3

SEQ ID NOs: and corresponding description for Oryza genes which are expressed

in an aleurone-specific manner and further the SEQ ID NOs for the corresponding

homologous sequences found in wheat, banana and maize

ORF
Promo

Bana
Maize

(SEQ
(SEQ

Wheat
(SEQ
(SEQ

ID)
ID)
Description
(SEQ ID)
ID)
ID)

Aleurone

1324

Similar to gi|5915837|sp|O81974|C7D8_SOYBN

5724

CYTOCHROME P450 71D8 (P450 CP7)

1150
2366
Similar to gi|1346724|sp|P48007|PIST_ARATH
3321

5530

FLORAL HOMEOTIC PROTEIN PISTILLATA

1045
2290
Similar to gi|3549657|emb|CAA20568.1|putative

protein [Arabidopsis thaliana]

1354

Similar to gi|2739000|gb|AAB94588.1|CYP71D10p
4562, 3780,

[Glycine max]
3878, 4600,

4658, 3130,

3080, 3129,

4599, 3781,

4561, 3779,

3142

1165
2380
Similar to gi|924624|gb|AAA80496.1|flower-specific

gamma-thionin-like protein/acidic protein precursor

1308
2463
Similar to YNX1_YEAST P53860

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). HYPOTHETICAL 40.7 KD PROTEIN IN

SIN4-URE2 INTERGENIC REGION.

1547
2627
Similar to gi|8778731|gb|AAF79739.1|AC005106_20

T25N20.6 [Arabidopsis thaliana]

1255
2437
Similar to gi|4508069|gb|AAD21413.1|12246
3098

1373

Similar to gi|4490708|emb|CAB38842.1|putative

5168
5776

protein [Arabidopsis thaliana]

1305

Similar to YNT1_ANASP Q05067 ANABAENA SP.

(STRAIN PCC 7120). HYPOTHETICAL ABC

TRANSPORTER ATP-BINDING PROTEIN IN

NTCA/BIFA 3 REGION (ORF1) (FRAGMENT).

1515
2596
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF013547 ST(F) HTC086635-

A01.R.5 FRAME: −3 ORF: 2 LEN: 738

1467
2556
Similar to gi|3790581|gb|AAC69853.1|RING-H2
4303, 4304
4857

finger protein RHB 1 a [Arabidopsis thaliana]

1390
2497
Similar to gi|1345528|emb|CAA54682.1|ES43
3896, 3898,

[Hordeum vulgare]
3897, 3895

1520
2601
Similar to gi|2828289|emb|CAA16703.1|hypothetical
4483, 2863

5901

protein [Arabidopsis thaliana]

1511
2592
Similar to gi|3152568|gb|AAC17049.1|Similar to
3235, 4493
5025

hypothetical protein product gb|Z97337 from A.

thaliana
. EST gb|H76597 comes from this gene.

[Arabidopsis thaliana]

1432
2525
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF004912 ST(F) HTC028900-

A01.F.8 FRAME: −1 ORF: 1 LEN: 1140

1211

Similar to gi|4406810|gb|AAD20118.1|unknown

5465

protein [Arabidopsis thaliana]

1213
2409
Similar to gi|6562257|emb|CAB62627.1|putative
4453, 4452
4914
5390

protein [Arabidopsis thaliana]

1461
2551
Similar to gi|2245101|emb|CAB10523.1|hypothetical

4896

protein [Arabidopsis thaliana]

1252

Similar to gi|7413593|emb|CAB86083.1|putative
3990, 3991
4832

protein [Arabidopsis thaliana]

1374

Similar to gi|1402891|emb|CAA66823.1|unknown

[Arabidopsis thaliana]

1338
2477
Similar to gi|3894216|dbj|BAA34599.1|elongation
4134, 4135,

5550

factor 1 beta 2 [Oryza sativa]
4133

1416
2509
Open Reading Frame OS_ORF001739 HTC010017-

A01.13 FRAME: 1 ORF: 1 LEN: 1221

1291
2456
Similar to YNU6_CAEEL P50444

4780

CAENORHABDITIS ELEGANS
. HYPOTHETICAL

42.9 KD PROTEIN R74.6 IN CHROMOSOME III.

1356

Similar to gi|4768996|gb|AAD29711.1|AF140498_1

hypothetical protein [Oryza sativa]

1358
2483
Similar to gi|7670024|dbj|BAA94978.1|contains

5473

similarity to similar to ubiquitin conjugating

enzyme˜gene_id: K14A17.7 [Arabidopsis thaliana]

1196

Similar to gi|7484807|pir||T01259 AMP deaminase

4869

homolog F16M14.21 - Arabidopsis thaliana

1340

Open Reading Frame OS_ORF006899 HTC041396-

5327

A01.41 FRAME: 2 ORF: 2 LEN: 849

1579
2656
Similar to GREA_MYCLE P46808

MYCOBACTERIUM LEPRAE
. TRANSCRIPTION

ELONGATION FACTOR GREA (TRANSCRIPT

CLEAVAGE FACTORGREA).

1470

Similar to gi|482709|pir||A61062 NADH

5058

dehydrogenase (ubiquinone) (EC 1.6.5.3) chain 4 -

soybean mitochondrion (fragment)

1480

Similar to YIA7_YEAST P40555
2693

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). HYPOTHETICAL 24.8 KD PROTEIN IN

FAA3-BET1 INTERGENIC REGION.

1560
2639
Similar to PHS_PSEAE P43335 PSEUDOMONAS
3504, 3505,
4822

AERUGINOSA
. PTERIN-4-ALPHA-
3503, 3500,

CARBINOLAMINE DEHYDRATASE (EC 4.2.1.96)
3508

(PHS) (4-ALPHA-HYDROXY-

TETRAHYDROPTERIN DEHYDRATASE)

(PHENYLALANINEHYDROXYLASE-

STIMULATING PROTEIN) (PCD).

1332

Similar to gi|6017106|gb|AAF01589.1|AC009895_10
4039, 4038
4797
5633

hypothetical protein [Arabidopsis thaliana]

1243
2430
Similar to gi|8778718|gb|AAF79726.1|AC005106_7
4318, 4317,
5135

T25N20.15 [Arabidopsis thaliana]
4689

1335

Similar to gi|8671775|gb|AAF78381.1|AC069551_14

T10O22.22 [Arabidopsis thaliana]

1185
2395
Similar to gi|445137|prf∥908437A topoisomerase I
3117, 3315,
4958

[Arabidopsis thaliana]
4532, 4531

1345

Similar to gi|7269851|emb|CAB79710.1|putative

protein [Arabidopsis thaliana]

1286

Similar to YRP3_THEAC Q03021
3289

5671

THERMOPLASMA ACIDOPHILUM
.

HYPOTHETICAL 21.7 KD PROTEIN IN RPOA2 3

REGION (ORF186).

1537
2618
Similar to PDI_CHICK P09102 Q90969 GALLUS
3507, 3506,
4911
5311

GALLUS
(CHICKEN). PROTEIN DISULFIDE
3499, 3498

ISOMERASE (PDI) (EC 5.3.4.1)/PROLYL 4-

HYDROXYLASEBETA SUBUNIT (EC 1.14.11.2)/

CELLULAR THYROID HORMONE

BINDINGPROTEIN.

1363
2484
Similar to gi|1695698|dbj|BAA13181.1|C-type cyclin

[Oryza sativa]

1226

Similar to gi|3193293|gb|AAC19277.1|contains a short
3790
5145
5379

region of similarity to another Arabidopsis hypothetical

protein F19K23.8 (GB: AC000375) [Arabidopsis

thaliana
]

1372

Similar to gi|7288033|emb|CAB81795.1|putative

5803

protein [Arabidopsis thaliana]

1388

Similar to gi|7271065|emb|CAB80673.1|putative
2805, 4543
4831

protein [Arabidopsis thaliana]

1053

Similar to gi|7573384|emb|CAB87688.1|putative
3444
4957

protein [Arabidopsis thaliana]

1216
2412
Similar to gi|9294631|dbj|BAB02970.1|Na/Ca, K-
4578, 4577

exchanger-like protein [Arabidopsis thaliana]

1333

Similar to gi|7413597|emb|CAB86087.1|putative
4542

5591

protein [Arabidopsis thaliana]

1336

Similar to gi|6648207|gb|AAF21205.1|AC013483_29

5589

unknown protein [Arabidopsis thaliana]

1218
2414
Similar to gi|2828295|emb|CAA16709.1|putative
4604, 3397,
5038

protein [Arabidopsis thaliana]
2920, 4605

1359

Similar to AEFA_ECOLI P77338 ESCHERICHIA

COLI
. AEFA PROTEIN.

1274

Similar to MTAB_SYNP2 P34883
3430

SYNECHOCOCCUS SP. (STRAIN PCC 7002)

(AGMENELLUM QUADRUPLICATUM).

MODIFICATION METHYLASE AQUI BETA

SUBUNIT (EC 2.1.1.73) (CYTOSINE-SPECIFIC

METHYLTRANSFERASE AQUI BETA SUBUNIT)

(M. AQUI BETA SUBUNIT).

1126

Similar to YP99_CAEEL Q09477

CAENORHABDITIS ELEGANS
. HYPOTHETICAL

22.7 KD PROTEIN C28H8.9 IN CHROMOSOME III.

1531
2612
Open Reading Frame OS_ORF016113 HTC105925-
2985

A01.R.13 FRAME: 1 ORF: 12 LEN: 687

1424
2517
Similar to gi|4337197|gb|AAD18111.1|AIG2-like
4669

protein [Arabidopsis thaliana]

1260

Similar to gi|5881963|gb|AAD55139.1|AF066079_1

5395

dihydrolipoamide S-acetyltransferase [Arabidopsis

thaliana
]

1329

Similar to gi|2129707|pir||S71165 RNA-directed DNA

polymerase (EC 2.7.7.49) - Arabidopsis thaliana

retrotransposon 2 (fragment)

1439
2531
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF007855 ST(F) HTC046991-

A01.F.4 FRAME: −2 ORF: 2 LEN: 510

1513
2594
Similar to gi|9294219|dbj|BAB02121.1|

4834

gb|AAF01563.1˜gene_id: K17E12.8˜similar to

unknown protein [Arabidopsis thaliana]

1176
2389
Similar to gi|3757521|gb|AAC64223.1|putative
3134, 3133,

ubiquitin-conjugating enzyme [Arabidopsis thaliana]
3284

1194

Similar to gi|3805853|emb|CAA21473.1|putative
3097, 3110,
4805
5418

protein [Arabidopsis thaliana]
3096

1490
2573
Similar to gi|2245070|emb|CAB10493.1|hypothetical
2810, 2878,

protein [Arabidopsis thaliana]
3246, 3095

1365

Similar to gi|3249086|gb|AAC24070.1|Contains
3963, 3960,
4907

similarity to 21 KD subunit of the Arp2/3 protein
3962, 3961

complex (ARC21) gb|AF006086 from Homo sapiens.

EST gb|Z37222 comes [Arabidopsis thaliana]

1183

Similar to gi|9294228|dbj|BAB02130.1|
2795, 3168,

5252

gb|AAD39565.1˜gene_id: MLD15.4˜similar to
3169, 2796

unknown protein [Arabidopsis thaliana]

1234

Similar to gi|6041840|gb|AAF02149.1|AC009853_9
2946

5341

hypothetical protein [Arabidopsis thaliana]

1169
2382
Similar to gi|4249412|gb|AAD13709.1|hypothetical
2962

protein [Arabidopsis thaliana]

1300
2461
Similar to gi|4582787|emb|CAB40376.1|adenosine
4033, 4034,
4806
5804

kinase [Zea mays]
4035

1323

Similar to DAPF_HAEIN P44859 HAEMOPHILUS
4147

INFLUENZAE
. DIAMINOPIMELATE EPIMERASE

(EC 5.1.1.7).

1474
2561
Similar to gi|13219|emb|CAA34122.1|cytochrome

oxidase subunit I [Oryza sativa]

1277
2448
Similar to gi|8778457|gb|AAF79465.1|AC022492_9
3026
5109
5330

F1L3.17 [Arabidopsis thaliana]

1435
2527
Similar to gi|4883606|gb|AAD31575.1|AC006922_7
4003
4965
5396

putative cis-Golgi SNARE protein [Arabidopsis

thaliana
]

1456
2546
Similar to gi|6041852|gb|AAF02161.1|AC009853_21
3360

5426

unknown protein, 3 partial [Arabidopsis thaliana]

1270

Similar to CDS1_HUMAN Q92903 O00163 HOMO

4795
5317

SAPIENS
(HUMAN). PHOSPHATIDATE

CYTIDYLYLTRANSFERASE (EC 2.7.7.41) (CDP-

DIGLYCERIDESYNTHETASE) (CDP-

DIGLYCERIDE PYROPHOSPHORYLASE) (CDP-

DIACYLGLYCEROLSYNTHASE) (CDS)

(CTP: PHOSPHATIDATE

CYTIDYLYLTRANSFERASE) (CDP-

DAGSYNTHASE).

1170
2383
Open Reading Frame OS_ORF006653 HTC039934-
3304, 4631,
5080

A01.R.8 FRAME: −2 ORF: 1 LEN: 762
4630, 3279

1281

Similar to CLPX_HAEIN P44838 HAEMOPHILUS

4802
5736

INFLUENZAE
. ATP-DEPENDENT CLP PROTEASE

ATP-BINDING SUBUNIT CLPX.

1167
2381
Similar to gi|4584527|emb|CAB40758.1|putative
2934, 3436

5698

protein [Arabidopsis thaliana]

1402
2505
Similar to gi|2244937|emb|CAB10359.1|hypothetical

protein [Arabidopsis thaliana]

1482
2567
Open Reading Frame OS_ORF018605 HTC124146-

A01.F.10 FRAME: 1 ORF: 10 LEN: 933

1327
2474
Similar to gi|6899931|emb|CAB71881.1|putative

protein [Arabidopsis thaliana]

1493

Open Reading Frame OS_ORF010496 HTC064014-
3334, 3333,
4929

A01.6 FRAME: 3 ORF: 3 LEN: 726
3474

1298

Similar to SYY_HUMAN P54577 HOMO SAPIENS
3483
4814
5701

(HUMAN). TYROSYL-TRNA SYNTHETASE (EC

6.1.1.1) (TYROSYL-TRNA LIGASE) (TYRRS).

1341

Similar to gi|6587806|gb|AAF18497.1|AC010924_10

5254

Contains similarity to gb|M82916 MRS2 protein from

Saccharomyces cerivisae
. ESTs gb|N96043,

gb|AI998651, gb|AA585850, gb|T42027 come from

this gene. [Arabidopsis thaliana]

1357
2482
Similar to YNQ8_YEAST P53889

4841
5495

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). HYPOTHETICAL 28.8 KD PROTEIN IN

PSD1-SKO1 INTERGENIC REGION.

1242
2429
Similar to gi|6466961|gb|AAF13096.1|AC009176_23
2850, 2849
4919
5486

hypothetical protein [Arabidopsis thaliana]

1172
2385
Open Reading Frame OS_ORF016335 HTC107779-
4005, 4371,
5142
5415

A01.F.23 FRAME: 3 ORF: 1 LEN: 783
4518, 4108,

3032, 4517,

4004, 4519,

3031, 2977

1553
2633
Similar to gi|6453896|gb|AAF09079.1|AC011663_15

5778

unknown protein [Arabidopsis thaliana]

1420
2513
Similar to gi|3786014|gb|AAC67360.1|hypothetical

protein [Arabidopsis thaliana]

1174
2387
Similar to gi|7267302|emb|CAB81084.1|UV-damaged
2881, 4402,

DNA binding factor-like protein [Arabidopsis thaliana]
4403, 4401,

2798, 4282

1347
2479
Similar to gi|9294416|dbj|BAB02497.1|
2750, 2749,
5074
5435

gene_id: MOE17.21˜ref|NP_002083.1˜similar to
2751

unknown protein [Arabidopsis thaliana]

1391
2498
Similar to gi|7248391|dbj|BAA92714.1|hypothetical

protein [Oryza sativa]

1265
2442
Similar to CCB2_RABIT P54288 ORYCTOLAGUS
4082, 4081,
5146
5660

CUNICULUS
(RABBIT). DIHYDROPYRIDINE-
2941, 4056

SENSITIVE L-TYPE, CALCIUM CHANNEL BETA-

2 SUBUNIT (CAB2).

1297
2459
Similar to PM1_HUMAN P17152 HOMO SAPIENS
3297
4774
5463

(HUMAN). PUTATIVE RECEPTOR PROTEIN.

1562
2641
Similar to gi|8777301|dbj|BAA96891.1|tyrosine

aminotransferase-like protein [Arabidopsis thaliana]

1574
2651
Open Reading Frame OS_ORF003772 HTC021944-

A01.16 FRAME: −1 ORF: 5 LEN: 702

1224

Similar to LDS_DROME P34739 DROSOPHILA
3426
4900

MELANOGASTER
(FRUIT FLY). PROBABLE

HELICASE LODESTAR.

1503
2584
Open Reading Frame OS_ORF010771 ST (R)
4430, 2930
5036

HTC066124-A01.26 FRAME: 3 ORF: 24 LEN: 1098

1295

Similar to gi|7488260|pir||T00673 protein kinase

homolog F6E13.6 - Arabidopsis thaliana

1481
2566
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF013162 ST(F) HTC083361-

A01.F.40 FRAME: −2 ORF: 1 LEN: 696

[0684]

10

TABLE 4

SEQ ID NOs and corresponding description for Oryza genes which are expressed

in an endosperm-specific manner and further the SEQ ID NOs for the corresponding

homologous sequences found in wheat, banana and maize

ORF
Promo

Bana
Maize

(SEQ
(SEQ

Wheat
(SEQ
(SEQ

ID)
ID)
Description
(SEQ ID)
ID)
ID)

Endosperm

1088

Similar to gi|4539346|emb|CAB37494.1|putative

protein [Arabidopsis thaliana]

1155

Similar to YHJD_ECOLI P37642 ESCHERICHIA

COLI
. HYPOTHETICAL 37.9 KD PROTEIN IN

TREF-KDGK INTERGENIC REGION (O337).

1082

Similar to gi|4586037|gb|AAD25655.1|AC007109_13
4048, 4549,

5796

putative heat shock protein [Arabidopsis thaliana]
4550, 3403,

4548, 3402,

4043

1141
2358
Open Reading Frame OS_ORF002232 HTC012937-

5770

A01.25 FRAME: −2 ORF: 24 LEN: 855

1125
2343
Similar to ABP1_YEAST P15891

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). ACTIN BINDING PROTEIN.

1161
2376
Similar to gi|9081787|dbj|BAA99526.1|hypothetical

protein [Oryza sativa]

1104

Similar to YC06_KLEPN Q48452 KLEBSIELLA

PNEUMONIAE
. HYPOTHETICAL 80.4 KD

PROTEIN IN CPS REGION (ORF6).

1072
2309
Similar to gi|6466941|gb|AAF13076.1|AC009176_3

unknown protein [Arabidopsis thaliana]

1469
2558
Similar to gi|4204311|gb|AAD10692.1|lcl|prt_seq No

5876

definition line found

1441
2533
Similar to ELI1_PHYCR P41802 PHYTOPHTHORA

CRYPTOGEA
. ACIDIC ELICITIN A1 PRECURSOR.

1261
2440
Open Reading Frame OS_ORF011947 ST (R)

5722

HTC074509-A01.R.21 FRAME: 3 ORF: 3 LEN: 528

1142
2359
Similar to VNFG_AZOCH PI 5333 AZOTOBACTER

CHROOCOCCUM
MCD 1. NITROGENASE

VANADIUM-IRON PROTEIN DELTA CHAIN (EC

1.18.6.1) (NITROGENASE COMPONENT I)

(DINITROGENASE).

1287
2453
Open Reading Frame OS_ORF003469 HTC020152-

5693

A01.25 FRAME: −2 ORF: 16 LEN: 1140

1111
2329
Open Reading Frame OS_ORF018782 HTC125558-

A01.F.12 FRAME: −3 ORF: 4 LEN: 729

1109
2327
Similar to gi|18583|emb|CAA48907.1|nodulin

[Glycine max]

1157
2372
Open Reading Frame OS_ORF001203 HTC006819-

5588

A01.28 FRAME: −3 ORF: 1 LEN: 777

1425
2518
Similar to VE1_HPV63 Q07847 HUMAN

PAPILLOMAVIRUS TYPE 63. REPLICATION

PROTEIN E1.

1094

Open Reading Frame OS_ORF019404 HTC130656-

4940

A01.F.12 FRAME: −2 ORF: 1 LEN: 678

1062

Open Reading Frame OS_ORF002475 HTC014377-
2786, 4649,

5241

A01.16 FRAME: −3 ORF: 18 LEN: 693
4629, 4648,

2882, 4589,

4628

1065
2303
Similar to gi|995619|emb|CAA62665.1|lectin like
3303, 3232,

protein [Arabidopsis thaliana]
4027

1504
2585
Similar to YPPG_BACSU P50835 BACILLUS

SUBTILIS
. HYPOTHETICAL 14.5 KD PROTEIN IN

PONA-COTD INTERGENIC REGION.

1241
2428
Similar to gi|5295948|dbj|BAA81849.1|hypothetical

protein [Oryza sativa]

1558
2637
Similar to YQJL_BACSU P54549 BACILLUS

SUBTILIS
. HYPOTHETICAL 28.2 KD PROTEIN IN

GLNQ-ANSR INTERGENIC REGION.

1549
2629
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF010160 ST(F) HTC061531-

A01.F.19 FRAME: −1 ORF: 1 LEN: 1017

1596
2671
Similar to 7B2_XENLA P18844 XENOPUS LAEVIS

(AFRICAN CLAWED FROG), NEUROENDOCRINE

PROTEIN 7B2 (SECRETOGRANIN V)

(FRAGMENT).

1510
2591
Open Reading Frame OS_ORF018745 HTC125312-

A01.R.20 FRAME: −3 ORF: 28 LEN: 795

1063
2302
“““ Similar to HPI2_ECTVA P38524

ECTOTHIORHODOSPIRA VACUOLATA
. HIGH

POTENTIAL IRON-SULFUR PROTEIN, ISOZYME

2 (HIPIP 2). ”””

1238
2426
Similar to gi|7716575|gb|AAF68437.1|putative DNA
3138, 2887,

5852

cytosine methyltransferase MET3 [Zea mays]
3137, 2886,

3238, 2950,

3128

1582
2659
Open Reading Frame OS_ORF008474 HTC051016-

A01.R.13 FRAME: 2 ORF: 12 LEN: 681

1436
2528
Open Reading Frame OS_ORF016926 HTC112251-

5191
5863

A01.14 FRAME: 1 ORF: 10 LEN: 654

1375
2491
Similar to gi|7340854|dbj|BAA92944.1|hypothetical

protein [Oryza sativa]

1208
2407
Open Reading Frame OS_ORF011285 HTC069506-
3303, 4027,

A01.R.4 FRAME: −2 ORF: 3 LEN: 786
2712, 4028,

3232

1589
2666
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF021256 ST(F) HTC144712-

A01.R.2 FRAME: 2 ORF: 7 LEN: 528

1545
2625
Open Reading Frame OS_ORF014969 HTC097200-

A01.R.41 FRAME: −1 ORF: 13 LEN: 876

1296
2458
Similar to gi|9294401|dbj|BAB02482.1|
4380

gene_id: MOE17.5˜unknown protein [Arabidopsis

thaliana
]

1138
2355
Similar to gi|82583|pir||E22364 alpha/beta-gliadin

precursor (clone A1235) - wheat

1496
2578
Similar to WAP_CAMDR P09837 CAMELUS
2815, 2968

DROMEDARIUS
(DROMEDARY) (ARABIAN

CAMEL). WHEY ACIDIC PROTEIN (WAP).

1529
2610
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF020346 ST(F) HTC137170-

A01.19 FRAME: −2 ORF: 3 LEN: 1437

1129
2346
Similar to CASK_ODOHE Q95225 Q95226

ODOCOILEUS HEMIONUS
(MULE DEER)

(BLACK-TAILED DEER). KAPPA CASEIN

(FRAGMENT).

1314

Open Reading Frame OS_ORF004164 ST(R)
3473

5906

HTC024228-A01.36 FRAME: 1 ORF: 7 LEN: 549

1476

Similar to YXEP_BACSU P54955 BACILLUS

SUBTILIS
. HYPOTHETICAL 41.6 KD PROTEIN IN

IDH-DEOR INTERGENIC REGION.

1101

Similar to gi|2961389|emb|CAA18136.1|purple acid
4062, 4063
5112
5835

phosphatase like protein [Arabidopsis thaliana]

1380

Similar to gi|6289052|gb|AAF06789.1|AF192975_1
4351, 3043,
4829

unknown [Oryza sativa]
4350, 3044,

3042

1386

Similar to gi|4185501|gb|AAD09105.1|fertilization-
2870, 2869

independent seed 2 protein [Arabidopsis thaliana]

1231
2422
Open Reading Frame OS_ORF014200 HTC091206-

A01.F.14 FRAME: −2 ORF: 5 LEN: 906

1517
2598
Similar to gi|8843783|dbj|BAA97331.1|

gb|AAC80581.1˜gene_id: MZN1.7˜similar to unknown

protein [Arabidopsis thaliana]

1539
2620
Open Reading Frame OS_ORF012379 ST(R)

HTC077361-A01.R.25 FRAME: −1 ORF: 6 LEN: 1119

1123
2341
Open Reading Frame OS_ORF010912 HTC067127-

A01.F.24 FRAME: 1 ORF: 17 LEN: 675

1121
2339
Open Reading Frame OS_ORF014277 HTC091891-

A01.F.5 FRAME: 1 ORF: 4 LEN: 669

1417
2510
Open Reading Frame OS_ORF000206 HTC001182-

A01.25 FRAME: −3 ORF: 23 LEN: 915

1477
2563
Open Reading Frame OS_ORF006071 HTC036306-

A01.27 FRAME: 1 ORF: 7 LEN: 1761

1073
2310
Similar to gi|5803244|dbj|BAA83554.1|Similar to
3323, 4292,
4789
5617

hexose carrier protein HEX6 &RCCHCP_1 (Q07423)
3324

[Oryza sativa]

1486
2570
Similar to E321_ADE1P P35770 HUMAN

ADENOVIRUS TYPE 11 (AD11P) (STRAIN

SLOBISKI). EARLY E3 20.6 KD GLYCOPROTEIN.

1571
2649
Similar to IM23_YEAST P32897

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). MITOCHONDRIAL IMPORT INNER

MEMBRANE TRANSLOCASE SUBUNIT

TIM23(MITOCHONDRIAL PROTEIN IMPORT

PROTEIN 3) (MITOCHONDRIAL PROTEIN

IMPORTPROTEIN MAS6) (MEMBRANE IMPORT

MACHINERY PROTEIN MIM2

1124
2342
Open Reading Frame OS_ORF010827 HTC066509-

A01.F.19 FRAME: 2 ORF: 28 LEN: 675

1521
2602
Similar to gi|9280680|gb|AAF86549.1|AC069252_8
3370, 3408,
5064
5802

F2E2.12 [Arabidopsis thaliana]
3372, 3371

1492
2575
Similar to YD57_SCHPO Q10311

SCHIZOSACCHAROMYCES POMBE
(FISSION

YEAST). HYPOTHETICAL 25.9 KD PROTEIN,

C6C3.07 IN CHROMOSOME I.

1450

Similar to YAJO_ECOLI P77735 ESCHERICHIA

COLI
. HYPOTHETICAL OXIDOREDUCTASE IN

PGPA-ISPA INTERGENIC REGION.

1154
2370
Similar to gi|6581058|gb|AAF18438.1|AF192467_1

5519

Sgt1 [Oryza sativa]

1447
2538
Similar to gi|7487883|pir||T00987 hypothetical protein

4803

T9J22.21 - Arabidopsis thaliana

1551
2631
Open Reading Frame OS_ORF013836 HTC088733-

A01.F.19 FRAME: 1 ORF: 19 LEN: 1476

1546
2626
Open Reading Frame OS_ORF013277 HTC084148-

A01.5 FRAME: 3 ORF: 1 LEN: 735

1160
2375
Similar to YJEQ_ECOLI P39286 ESCHERICHIA

COLI
. HYPOTHETICAL 37.7 KD PROTEIN IN PSD-

AMIB INTERGENIC REGION (F337).

1059
2300
Open Reading Frame OS_ORF001606 HTC009227-

A01.48 FRAME: 2 ORF: 25 LEN: 1299

1419
2512
Similar to YV23_MYCLE P54580

5408

MYCOBACTERIUM LEPRAE
. HYPOTHETICAL

27.9 KD PROTEIN B2168_C2_209.

1334

Open Reading Frame OS_ORF004663 HTC027383-

5757

A01.F.15 FRAME: 1 ORF: 3 LEN: 663

1177
2390
Open Reading Frame containing a Sage tag sequence
3365, 4159,
4989

near 3 end OS_ORF001044 ST(F) HTC005847-
2769, 3364,

A01.28 FRAME: −2 ORF: 3 LEN: 783
4496, 4497,

2768, 2809,

4158, 3271,

3109, 4530,

2932, 3269,

3295, 2707

1385
2495
Similar to gi|2911041|emb|CAA17551.1|kinetochore

5187
5238

(SKP1p)-like protein [Arabidopsis thaliana]

1433
2526
Similar to gi|6453867|gb|AAF09051.1|AC011717_18

hypothetical protein [Arabidopsis thaliana]

1527
2608
Open Reading Frame OS_ORF013101 HTC082889-

A01.R.9 FRAME: −1 ORF: 7 LEN: 690

1279
2450
Similar to gi|2245022|emb|CAB10442.1|hypothetical

5862

protein [Arabidopsis thaliana]

1284

Similar to HIS8_MYCSM P28735

MYCOBACTERIUM SMEGMATIS
. HISTIDINOL-

PHOSPHATE AMINOTRANSFERASE (EC 2.6.1.9)

(IMIDAZOLE ACETOL-PHOSPHATE

TRANSAMINASE) (FRAGMENT).

1137
2354
Similar to LECG_ARAHY P02872 ARACHIS

HYPOGAEA
(PEANUT). GALACTOSE-BINDING

LECTIN PRECURSOR (AGGLUTININ) (PNA).

1171
2384
“““ Similar to gi|9293951|dbj|BAB01854.1|DNA-
2884, 3900,

directed RNA polymerase, subunit B [Arabidopsis
3904

thaliana
] ”””

1509
2590
Similar to gi|6553925|gb|AAF16590.1|AC012329_14

hypothetical protein [Arabidopsis thaliana]

1353

Open Reading Frame OS_ORF008479 HTC051059-
3493

A01.11 FRAME: 3 ORF: 6 LEN: 933

1180
2392
Open Reading Frame OS_ORF007418 HTC044323-
2953, 3955,

5813

A01.R.10 FRAME: 1 ORF: 1 LEN: 705
3954, 3953

1437
2529
Open Reading Frame OS_ORF020518 HTC138308-

5896

A01.F.6 FRAME: −2 ORF: 4 LEN: 1080

1315
2468
Similar to gi|6899895|emb|CAB71904.1|RAV-like

5588

protein [Arabidopsis thaliana]

1057

Open Reading Frame OS_ORF008654 ST(R)
3141, 3121,

5872

HTC051926-A01.R.21 FRAME: 3 ORF: 16 LEN: 597
2918

1096
2323
Open Reading Frame OS_ORF013567 HTC086832-
3731

5548

A01.R.10 FRAME: −2 ORF: 6 LEN: 651

1130
2347
Open Reading Frame OS_ORF009250 ST(R)

5536

HTC055587-A01.R.20 FRAME: −2 ORF: 18 LEN: 609

1454
2544
“““ Similar to KR62_SHEEP P02448 OVIS ARIES

(SHEEP). KERATIN, HIGH-TYROSINE MATRIX

PROTEIN (COMPONENT 0.62). ”””

1538
2619
Open Reading Frame OS_ORF012452 HTC077995-

5815

A01.R.13 FRAME: 3 ORF: 12 LEN: 666

1289
2455
Similar to gi|556902|emb|CAA84288.1|54-kD signal
4083, 3716,

5251

recognition particle (SRP) specific protein
4085, 4086

[Lycopersicon esculentum]

1268
2444
Open Reading Frame containing a Sage tag sequence

5334

near 3 end OS_ORF010085 ST(F) HTC060921-A013

FRAME: −2 ORF: 7 LEN: 582

1464
2553
Similar to gi|8096408|dbj|BAA95878.1|EST

AU062706 (C30225) corresponds to a region of the

predicted gene. ˜hypothetical protein [Oryza sativa]

1512
2593
Similar to gi|6714422|gb|AAF26110.1|AC012328_13
2965, 3280

hypothetical protein [Arabidopsis thaliana]

1235
2423
Open Reading Frame containing a Sage tag sequence

5285

near 3 end OS_ORF003649 ST(F) HTC021208-

A01.22 FRAME: −3 ORF: 14 LEN: 1257

1468
2557
Open Reading Frame OS_ORF006107 HTC036528-

A01.30 FRAME: −2 ORF: 28 LEN: 795

1561
2640
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF001814 ST(F) HTC010532-

A01.14 FRAME: 3 ORF: 17 LEN: 948

1203

Open Reading Frame OS_ORF017107 HTC113682-

A01.F.39 FRAME: 1 ORF: 16 LEN: 741

1381

Open Reading Frame OS_ORF004338 HTC025425-

5583

A01.1 9 FRAME: 3 ORF: 4 LEN: 657

1236
2424
Open Reading Frame OS_ORF003108 HTC018151-
3255, 4619,
5065
5726

A01.14 FRAME: −3 ORF: 3 LEN: 909
4618, 3287

1429
2522
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF010917 ST(F) HTC067133-

A01.F.25 FRAME: −1 ORF: 36 LEN: 543

1443
2534
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF015365 ST(F) HTC100104-

A01.R.5 FRAME: −3 ORF: 2 LEN: 633

1113
2331
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF016057 ST(F) HTC105401-

A01.F.20 FRAME: 1 ORF: 20 LEN: 834

1407
2506
Similar to gi|7630235|dbj|BAA94768.1|hypothetical

protein [Oryza sativa]

1220
2416
Open Reading Frame OS_ORF017123 HTC113816-
3009, 2951

5741

A01.28 FRAME: −1 ORF: 4 LEN: 828

1431
2524
Similar to gi|6562304|emb|CAB62602.1|putative

5522

protein [Arabidopsis thaliana]

1522
2603
Similar to gi|5734723|gb|AAD49988.1|AC007259_1

receptor-like protein kinase [Arabidopsis thaliana]

1084
2318
Similar to gi|7573432|emb|CAB87748.1|putative
4534, 4535,

protein [Arabidopsis thaliana]
4533

1475
2562
Similar to NODB_AZOCA Q07740

AZORHIZOBIUM CAULINODANS
.

CHITOOLIGOSACCHARIDE DEACETYLASE (EC

3.5.1.-) (NODULATION PROTEIN B).

1288
2454
Open Reading Frame containing a Sage tag sequence
2814, 2813

5355

near 3 end OS_ORF008809 ST(F) HTC052791-

A01.R.20 FRAME: −2 ORF: 10 LEN: 759

1227
2419
Open Reading Frame OS_ORF014096 HTC090622-
3291, 3330,
4847
5509

A01.F.4 FRAME: 1 ORF: 2 LEN: 663
4055, 3292,

2964

1444
2535
Similar to CY2_RHOTE P00098 RHODOCYCLUS

TENUIS
(RHODOSPIRILLUM TENUE).

CYTOCHROME C2.

1292
2457
Similar to BZTA_RHOCA Q52663 RHODOBACTER

CAPSULATUS
(RHODOPSEUDOMONAS

CAPSULATA
).

GLUTAMATE/GLUTAMINE/ASPARTATE/ASPAR-

AGINE-BINDING PROTEIN PRECURSORBZTA.

1557
2636
Open Reading Frame OS_ORF021175 HTC144175-
4019

5355

A01.R.30 FRAME: 3 ORF: 14 LEN: 1191

1361

Similar to gi|6520227|dbj|BAA87955.1|ZCW7

[Arabidopsis thaliana]

1595
2670
Open Reading Frame containing a Sage tag sequence

5885

near 3 end OS_ORF007923 ST(F) HTC047502-

A01.R.12 FRAME: −2 ORF: 12 LEN: 567

1370
2489
Open Reading Frame OS_ORF018320 HTC122173-

A01.11 FRAME: 1 ORF: 9 LEN: 846

1058
2299
Similar to COMI_DICDI Q03380 DICTYOSTELIUM
3256, 2682

DISCOIDEUM
(SLIME MOLD). COMITIN (CABP1-

RELATED PROTEIN P24) (24 KD ACTIN-BINDING

PROTEIN).

1050
2295
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF002649 ST(F) HTC015461 -

A01.45 FRAME: 1 ORF: 4 LEN: 897

1455
2545
Open Reading Frame OS_ORF004035 HTC023345-

A01.22 FRAME: 3 ORF: 3 LEN: 852

1280

Open Reading Frame OS_ORF016729 ST(R)

5891

HTC110880-A01.F.12 FRAME: 3 ORF: 15 LEN: 510

1061

Similar to gi|6437533|gb|AAF08565.1|AC012193_14
2852
4793

hypothetical protein [Arabidopsis thaliana]

1398
2504
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF008116 ST(F) HTC048551-

A01.42 FRAME: 1 ORF: 4 LEN: 567

1086

Similar to YRBB_ECOLI P45389 ESCHERICHIA

COLI
. HYPOTHETICAL 14.4 KD PROTEIN IN

MURA-RPON INTERGENIC REGION (F129).

1576
2653
Similar to P30_TOXGO P13664 TOXOPLASMA

GONDII
. MAJOR SURFACE ANTIGEN P30

PRECURSOR.

1523
2604
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF004361 ST(F) HTC025646-A01.5

FRAME: −1 ORF: 3 LEN: 648

1448
2539
Open Reading Frame OS_ORF007167 HTC042869-

A01.R.21 FRAME: 3 ORF: 21 LEN: 651

1411

Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF012877 ST(F) HTC080961-

A01.F.19 FRAME: 2 ORF: 1 LEN: 537

1205

Open Reading Frame OS_ORF012677 HTC079731-

A01.5 FRAME: −2 ORF: 2 LEN: 855

1076

Similar to gi|4512702|gb|AAD21755.1|putative WD-
3377, 3376

40 repeat protein [Arabidopsis thaliana]

1056
2298
Open Reading Frame OS_ORF014992 ST(R)
3090, 3148,

5908

HTC097367-A01.F.13 FRAME: −3 ORF: 6 LEN: 642
3147, 3146

1530
2611
“““ Similar to gi|3335347|gb|AAC27149.1|Contains

5831

similarity to ARI, RING finger protein gb|X98309 from

Drosophila melanogaster
. ESTs gb|T44383,

gb|W43120, gb|N65868, gb|H36013, gb|AA042241,

gb|T76869 and gb|AA042359 come from this gene.

[Arabidopsis tha

1559
2638
Similar to gi|3738091|gb|AAC63588.1|putative bHLH

transcription factor [Arabidopsis thaliana]

1550
2630
Similar to gi|8843759|dbj|BAA97307.1|
3624, 3796,

emb|CAB62602.1˜gene_id: MXK3.18˜similar to
3623, 3621,

unknown protein [Arabidopsis thaliana]
4666, 3622

1115
2333
Open Reading Frame OS_ORF002824 HTC016383-

A01.16 FRAME: 3 ORF: 18 LEN: 744

1368
2487
Open Reading Frame OS_ORF013471 HTC085904-

5631

A01.R.22 FRAME: 2 ORF: 1 LEN: 657

1585
2662
Similar to UL34_HCMVA P16812 HUMAN

CYTOMEGALOVIRUS (STRAIN AD169).

HYPOTHETICAL PROTEIN UL34.

1331
2476
Open Reading Frame OS_ORF013279 HTC084207-

A01.F.22 FRAME: 3 ORF: 19 LEN: 930

1485

Similar to 5HT1_APLCA Q16950 APLYSIA

CALIFORNICA
(CALIFORNIA SEA HARE). 5-

HYDROXYTRYPTAMINE 1 RECEPTOR (5-HTB1)

(SEROTONIN RECEPTOR 1).

1214
2410
Open Reading Frame containing a Sage tag sequence
3708
4878
5231

near 3 end OS_ORF013972 ST(F) HTC089849-

A01.22 FRAME: 2 ORF: 16 LEN: 537

1389
2496
Similar to gi|3941526|gb|AAC83639.1|putative
3692, 3694,
4886

transcription factor [Arabidopsis thaliana]
2904, 4427,

3915, 4428,

3693

1240

Similar to gi|1086540|gb|AAC49219.1|Ra

1478
2564
Open Reading Frame OS_ORF018918 ST(R)

HTC126528-A01.F.14 FRAME: 3 ORF: 17 LEN: 513

1362

Similar to YIHI_ECOLI P32130 ESCHERICHIA

COLI
. HYPOTHETICAL 19.1 KD PROTEIN IN

POLA-HEMN INTERGENIC REGION (O169).

1195
2400
Similar to gi|4455283|emb|CAB36819.1|L1 specific
2972
4821
5359

homeobox gene ATML1/ovule-specific homeobox

protein A20 [Arabidopsis thaliana]

1526
2607
Open Reading Frame OS_ORF014719 HTC095181-

A01.R.17 FRAME: 1 ORF: 6 LEN: 930

1548
2628
Similar to gi|6996252|emb|CAB75478.1|putative

protein [Arabidopsis thaliana]

1239
2427
Similar to gi|7362762|emb|CAB83132.1|putative
3161, 3160,

53

protein [Arabidopsis thaliana]
3936, 3938,

3937, 2956

1404

Similar to gi|7268671|emb|CAB78879.1|myb-like

protein [Arabidopsis thaliana]

1570

Open Reading Frame OS_ORF021360 HTC145470-

A01.R.8 FRAME: 2 ORF: 9 LEN: 660

1514
2595
Open Reading Frame containing a Sage tag sequence
3877, 4379,
5208

near 3 end OS_ORF019284 ST(F) HTC129613-
3406, 3407,

A01.R.5 FRAME: −3 ORF: 2 LEN: 534
3405

1525
2606
Open Reading Frame OS_ORF014843 HTC096188-

5258

A01.R.23 FRAME: 3 ORF: 4 LEN: 942

1225

Similar to gi|3927830|gb|AAC79587.1|hypothetical
4474, 4473

protein [Arabidopsis thaliana]

1342

Similar to gi|6137251|sp|O22757|YML2_ARATH

HYPOTHETICAL MLO-LIKE PROTEIN F5J6.23

1188
2397
Open Reading Frame containing a Sage tag sequence
3790, 3331,

near 3 end OS_ORF013981 ST(F) HTC089945-
2943

A01.R.1 FRAME: 1 ORF: 1 LEN: 540

1473

“““ Similar to UL55_HSVEB P28963 EQUINE

HERPES VIRUS TYPE 1 (STRAIN AB4P) (EHV-1),

AND EQUINE HERPES VIRUS TYPE 1 (STRAIN

KENTUCKY A) (EHV-1). GENE 4 PROTEIN (ORF

L2). ”””

1173

Similar to gi|2982442|emb|CAA18250.1|hypothetical

protein [Arabidopsis thaliana]

1393
2500
Similar to MERC_THIFE P22905 THIOBACILLUS

FERROOXIDANS
. MERCURIC RESISTANCE

PROTEIN MERC.

1593
2669
Similar to gi|9294053|dbj|BAB02010.1|

gb|AAD03575.1˜gene_id: MOB24.16˜similar to

unknown protein [Arabidopsis thaliana]

1168

Similar to gi|4733891|gb|AAD17931.2|unconventional
3462, 3267,

myosin heavy chain [Zea mays]
3079

Similar to SG12_CAEEL P46564

CAENORHABDITIS ELEGANS
. SRG-12 PROTEIN.

1542
2623
Open Reading Frame OS_ORF009690 ST(R)
4113, 4114

HTC058211-A01.F.15 FRAME: −2 ORF: 2 LEN: 975

1479
2565
Open Reading Frame OS_ORF016333 HTC107775-

A01.R.12 FRAME: −1 ORF: 12 LEN: 630

1311
2465
Similar to gi|8570063|dbj|BAA96768.1|hypothetical

protein [Oryza sativa]

1283
2452
Similar to gi|6665551|gb|AAF22920.1|AC013289_14
2845, 2843,

hypothetical protein [Arabidopsis thaliana]
2814, 2813,

3259

1422
2515
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF011984 ST(F) HTC074722-

A01.F.42 FRAME: −1 ORF: 79 LEN: 906

1302

Similar to gi|3152572|gb|AAC17053.1|Contains
4126, 4128,

homology to DNAJ heatshock protein gb|U32803 from
4127

Haemophilus influenzae
. [Arabidopsis thaliana]

1438
2530
Similar to gi|2160143|gb|AAB60765.1|F19K23.12

gene product [Arabidopsis thaliana]

1494
2576
Similar to gi|2244963|emb|CAB10384.1|hypothetical

protein [Arabidopsis thaliana]

1415
2508
Similar to YT19_MYCTU P71555

MYCOBACTERIUM TUBERCULOSIS
.

HYPOTHETICAL 46.1 KD PROTEIN CY10D7.19C.

1442

Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF017606 ST(F) HTC117204-

A01.18 FRAME: 2 ORF: 5 LEN: 1041

1532
2613
Similar to GAST_RAT P04563 RATTUS

NORVEGICUS
(RAT). GASTRIN PRECURSOR.

1199
2402
Similar to Y08F_MYCTU Q11052

MYCOBACTERIUM TUBERCULOSIS
. PROBABLE

REGULATORY PROTEIN CY50.15.

1349

Similar to gi|6498440|dbj|BAA87843.1|hypothetical

protein [Oryza sativa]

1418
2511
Open Reading Frame OS_ORF020505 ST(R)

HTC138244-A01.16 FRAME: −3 ORF: 4 LEN: 687

1246
2433
Similar to gi|3080410|emb|CAA18729.1|hypothetical
4568, 4094,
4854
5409

protein [Arabidopsis thaliana]
4095, 4092,

2807, 2799,

3068, 4307,

4699, 4093,

4087, 4498,

3998, 4567,

4499

1564
2643
Similar to gi|8809705|dbj|BAA97246.1|26S
3076, 3075

proteasome/non-ATPase regulatory subunit

[Arabidopsis thaliana]

1348
2480
Similar to gi|8099228|gb|AAF72076.1|AC025098_10

hypothetical protein [Oryza sativa]

1217
2413
Similar to CYP4_CYNCA P40781 CYNARA
4623, 2801,

CARDUNCULUS
(CARDOON). CYPRO4
4624

PROTEIN.

1306

Open Reading Frame OS_ORF003828 HTC022181-

A01.11 FRAME: −2 ORF: 2 LEN: 660

1488
2571
Similar to HSTO_VIBCH Q07425 VIBRIO

CHOLERAE
. HEAT-STABLE ENTEROTOXIN STO

PRECURSOR (O1-ST).

1202
2405
Open Reading Frame OS_ORF018301 HTC122064-

A01.R.12 FRAME: 1 ORF: 5 LEN: 744

1566
2645
Similar to YOP3_CAEEL Q22695

CAENORHABDITIS ELEGANS
. HYPOTHETICAL

41.0 KD PROTEIN T23F11.3 IN CHROMOSOME III.

1536
2617
Open Reading Frame OS_ORF004492 HTC026407-

A01.7 FRAME: −1 ORF: 5 LEN: 666

1554
2634
Similar to gi|3355466|gb|AAC27828.1|unknown

5705

protein [Arabidopsis thaliana]

1320

Open Reading Frame OS_ORF006563 ST(R)
3427

5564

HTC039403-A01.F.12 FRAME: 2 ORF: 1 LEN: 600

1254

Similar to CISY_COXBU P18789 COXIELLA
4387
5158
5657

BURNETII
. CITRATE SYNTHASE (EC 4.1.3.7).

1483
2568
Open Reading Frame OS_ORF013069 HTC082606-

A01.F.5 FRAME: −1 ORF: 7 LEN: 612

1458
2548
“““ Similar to HB2U_MOUSE P06344 MUS

MUSCULUS
(MOUSE). H-2 CLASS II

HISTOCOMPATIBILITY ANTIGEN, A-U BETA

CHAIN PRECURSOR. ”””

1319
2471
Similar to gi|8778212|gb|AAF79221.1|AC006917_6
4691

F10B6.10 [Arabidopsis thaliana]

1409
2507
Similar to gi|6815065|dbj|BAA90352.1|hypothetical

protein [Oryza sativa]

1487

Similar to gi|7670039|dbj|BAA94993.1|invertase

5844

inhibitor-like protein [Arabidopsis thaliana]

1187

Similar to gi|7523418|emb|CAB86437.1|putative
3270

protein [Arabidopsis thaliana]

1502
2583
Similar to FLAW_DESDE P80312 DESULFOVIBRIO

DESULFURICANS
. FLAVODOXIN (FRAGMENT).

1344
2478
Similar to gi|6728874|gb|AAF26947.1|AC008113_18
2679, 2678,

5383

F12A21.16 [Arabidopsis thaliana]
2680

Similar to gi|549885|gb|AAA56900.1|homeobox

protein

1462

Similar to gi|3080386|emb|CAA18706.1|hypothetical

5339

protein [Arabidopsis thaliana]

1189

Similar to NXS1_ACAAN P01434 ACANTHOPHIS

ANTARCTICUS
(COMMON DEATH ADDER).

SHORT NEUROTOXIN 1 (TOXIN AA C).

1400

Open Reading Frame OS_ORF021917 HTC150055-

A01.F.6 FRAME: −1 ORF: 1 LEN: 603

1543

Similar to gi|2827547|emb|CAA16555.1|predicted

5046
5623

protein [Arabidopsis thaliana]

1395
2501
Similar to gi|5091500|dbj|BAA78735.1|Hypothetical

protein [Oryza sativa]

1555

Similar to SWH1_YEAST P39555 P80234

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). SWH1 PROTEIN.

1102

Similar to gi|4337193|gb|AAD18107.1|hypothetical

5574

protein [Arabidopsis thaliana]

1266
2443
Open Reading Frame OS_ORF002545 HTC014886-

5844

A01.21 FRAME: 1 ORF: 6 LEN: 1299

1587
2664
Similar to gi|7543889|emb|CAB87198.1|putative

protein [Arabidopsis thaliana]

1452
2542
Similar to gi|8346561|emb|CAB93725.1|putative

protein [Arabidopsis thaliana]

1301
2462
Open Reading Frame OS_ORF022234 ST(R)

HTC153141-A01.F.17 FRAME: −3 ORF: 24 LEN: 525

1581
2658
Similar to gi|9229298|dbj|BAA99601.1|
4328, 4327,

gene_id: MDC16.12˜similar to unknown protein
4325

(gb|AAC36161.1) [Arabidopsis thaliana]

1089
2320
“““ Similar to gi|8810466|gb|AAF80127.1|AC024174_9
4223, 4222

Contains similarity to an unknown protein T1B3.16

gi|4432844 from Arabidopsis thaliana BAC T1B3

gb|AC006283. ESTs gb|AI992784, gb|T45131,

gb|AA586122 come from this gene. ”””

1552
2632
Open Reading Frame OS_ORF011826 ST(R)

5502

HTC073567-A01.24 FRAME: −2 ORF: 3 LEN: 540

1524
2605
Similar to gi|2224929|gb|AAC49747.1|ethylene-

5662

insensitive3-like2 [Arabidopsis thaliana]

1098

Similar to gi|3319884|emb|CAA11891.1|PRT1

5040

[Arabidopsis thaliana]

1472
2560
“““ Similar to ACH7_BOVIN P54131 BOS TAURUS

(BOVINE). NEURONAL ACETYLCHOLINE

RECEPTOR PROTEIN, ALPHA-7 CHAIN

PRECURSOR. ”””

1237
2425
Open Reading Frame OS_ORF009851 ST(R)
2761
4789
5732

HTC059249-A01.20 FRAME: −1 ORF: 4 LEN: 588

Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF013696 ST(F) HTC087783-

A01.F.16 FRAME: 2 ORF: 9 LEN: 564

1565
2644
Open Reading Frame OS_ORF018288 HTC121964-

A01.12 FRAME: −1 ORF: 9 LEN: 738

1269
2445
Similar to HIT1_YEAST P46973
3099

5878

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). HIT1 PROTEIN.

1343

Open Reading Frame OS_ORF001231 HTC006970-

5734

A01.14 FRAME: −1 ORF: 1 LEN: 792

1313
2467
Open Reading Frame OS_ORF012800 HTC080550-

A01.R.28 FRAME: −1 ORF: 6 LEN: 936

1413

Similar to gi|3860275|gb|AAC73043.1|putative CEN
3078
4848

(centroradialis)-like phosphatidylethanolamine-binding

protein [Arabidopsis thaliana]

1446
2537
Similar to YX28_MYCTU Q10818

MYCOBACTERIUM TUBERCULOSIS
.

HYPOTHETICAL 52.9 KD PROTEIN CY274.28C.

1471
2559
Open Reading Frame OS_ORF019456 ST(R)

5747

HTC131006-A01.55 FRAME: −1 ORF: 11 LEN: 534

1423
2516
Similar to CDN7_HUMAN P55273 Q13102 HOMO

SAPIENS
(HUMAN). CYCLIN-DEPENDENT

KINASE 4 INHIBITOR D (P19-INK4D).

1201
2404
Similar to gi|5803260|dbj|BAA83570.1|Similar to
2890
4913
5325

wak1 gene (AJ009696) [Oryza sativa]

1495
2577
Open Reading Frame OS_ORF013227 HTC083811-
2907

A01.R.24 FRAME: 2 ORF: 4 LEN: 699

1267

Similar to gi|7649363|emb|CAB89044.1|putative
3724, 3373
4782

protein [Arabidopsis thaliana]

1080
2316
Similar to gi|8096314|dbj|BAA95817.1|hypothetical

5761

protein [Oryza sativa]

1405

Similar to gi|7406400|emb|CAB85510.1|putative

protein [Arabidopsis thaliana]

1397
2503
Similar to PR1_MEDTR Q40374 MEDICAGO

5636

TRUNCATULA
(BARREL MEDIC).

PATHOGENESIS-RELATED PROTEIN PR-1

PRECURSOR.

1209

Similar to gi|5852181|emb|CAB55419.1|zhb0011.1

[Oryza sativa]

1253
2436
Open Reading Frame OS_ORF002306 HTC013290-

5676

A01.20 FRAME: −3 ORF: 3 LEN: 807

1499
2580
Open Reading Frame OS_ORF017188 HTC114338-

A01.F.19 FRAME: 2 ORF: 2 LEN: 978

Similar to gi|4928753|gb|AAD33717.1|AF136540_1

YABBY3 [Arabidopsis thaliana]

1575
2652
Open Reading Frame OS_ORF013232 HTC083848-

A01.22 FRAME: −1 ORF: 8 LEN: 780

1322
2473
Similar to gi|6056415|gb|AAF02879.1|AC009525_13

Unknown protein [Arabidopsis thaliana]

1453
2543
Similar to gi|7523667|gb|AAF63107.1|AC006423_8
3493

Hypothetical protein [Arabidopsis thaliana]

1337

Open Reading Frame OS_ORF017842 ST(R)

HTC119007-A01.R.12 FRAME: 2 ORF: 7 LEN: 513

1251

Similar to gi|1546055|gb|AAB72019.1|cyclin type B-

like [Zea mays]

1221

Similar to gi|7406459|emb|CAB85561.1|myotubularin-

like protein [Arabidopsis thaliana]

1275
2447
Open Reading Frame OS_ORF011566 HTC071687-

A01. 30 FRAME: −1 ORF: 21 LEN: 711

1257
2439
Similar to gi|5257266|dbj|BAA81765.1|EST

C99024 (E4337) corresponds to a region of the

predicted gene.; Similar to Silk moth; silkworm final

instar larvae posterior. (D83241) [Oryza sativa]

1376

Similar to gi|5823323|gb|AAD53100.1|AF175995_1

5284

putative transcription factor [Arabidopsis thaliana]

1198

Open Reading Frame OS_ORF002724 HTC015879-

A01.32 FRAME: 2 ORF: 13 LEN: 1620

1075
2312
Open Reading Frame OS_ORF019153 ST(R)

5850

HTC128490-A01.20 FRAME: 1 ORF: 17 LEN: 555

1304

Similar to gi|6520233|dbj|BAA87958.1|CW14
4195, 4193,
5017
5590

[Arabidopsis thaliana]
4194

1505
2586
Similar to gi|4914444|emb|CAB43647.1|hypothetical
3213

protein [Arabidopsis thaliana]

1328

Open Reading Frame OS_ORF006440 HTC038643-

5271

A01.R.16 FRAME: 2 ORF: 11 LEN: 738

1556
2635
Similar to gi|3482932|gb|AAC33217.1|AAC33217
4676, 3221,
4810

Hypothetical protein [Arabidopsis thaliana]
4675, 4157,

4503

1182

Open Reading Frame OS_ORF020271 ST(R)
4696
4773
5403

HTC136732-A01.14 FRAME: 3 ORF: 2 LEN: 1212

1273

“““ Similar to BLA2_BACCE P04190 BACILLUS

CEREUS
. BETA-LACTAMASE PRECURSOR,

TYPE H (EC 3.5.2.6)

(PENICILLINASE) (CEPHALOSPORINASE). ”””

1457
2547
Similar to gi|3860249|gb|AAC73017.1|unknown
4165, 4163,

5568

protein [Arabidopsis thaliana]
4164

1070
2307
Similar to gi|8778386|gb|AAF79394.1|AC068197_4
4673, 4672

5492

F16A14.6 [Arabidopsis thaliana]

1360

Similar to gi|2342691|gb|AAB70418.1|F7G19.26

[Arabidopsis thaliana]

1572

Similar to TXLA_SYNP7 P35088

SYNECHOCOCCUS SP. (STRAIN PCC 7942)

(ANACYSTIS NIDULANS R2). THIOL: DISULFIDE

INTERCHANGE PROTEIN TXLA.

1590

Similar to gi|4512686|gb|AAD21740.1|hypothetical

5443

protein [Arabidopsis thaliana]

1489
2572
Open Reading Frame OS_ORF011581 ST(R)

HTC071843-A01.19 FRAME: −3 ORF: 1 LEN: 501

1215
2411
Open Reading Frame OS_ORF012733 ST(R)

5516

HTC080054-A01.8 FRAME: 2 ORF: 1 LEN: 657

1244
2431
Similar to gi|7258378|emb|CAB77594.1|putative
4301

5681

protein [Arabidopsis thaliana]

1043

Similar to gi|421918|pir||PQ0549 acid phosphatase-1

5316

(EC 3.1.3.-) - tomato (fragment)

1219
2415
Similar to gi|8885579|dbj|BAA97509.1|receptor-like
3303, 3232

(protein kinase [Arabidopsis thaliana]

1387

Similar to gi|9229506|dbj|BAB00011.1|
4541
5216
5811

gene id: MIL23.18˜similar to unknown protein

(gb|AAB61516.1) [Arabidopsis thaliana]

1210
2408
Open Reading Frame OS_ORF019147 HTC128421-

A01.R.36 FRAME: −2 ORF: 8 LEN: 849

1212

Open Reading Frame OS_ORF017514 HTC116489-
3017, 3205,

A01.F.13 FRAME: −1 ORF: 13 LEN: 1107
3018, 3016

1497

Similar to gi|4895168|gb|AAD32756.1|AC007662_1

putative replication protein A1 [Arabidopsis thaliana]

1184

Similar to gi|508545|gb|AAA76580.1|zein
3231

1128

Open Reading Frame OS_ORF007317 HTC043588-

A01.30 FRAME: −3 ORF: 9 LEN: 1224

1192
2399
Similar to gi|2827630|emb|CAA16582.1|putative
3195, 3194,

protein [Arabidopsis thaliana]
2888

[0685]

11

TABLE 5

SEQ ID NOs and corresponding description for Oryza genes which are expressed

in an embryo-specific manner and further the SEQ ID NOs for the corresponding

homologous sequences found in wheat, banana and maize.

ORF
Promo

Bana
Maize

(SEQ
(SEQ

Wheat
(SEQ
(SEQ

ID)
ID)
Description
(SEQ ID)
ID)
ID)

Embryo

1079
2315
Similar to NEPU_THEVU Q08751
3665, 4214,
4972
5604

THERMOACTINOMYCES VULGARIS
.
3702, 3704,

NEOPULLULANASE (EC 3.2.1.135) (ALPHA-
3663, 3695,

AMYLASE II).
3701, 3673,

3705, 3700,

3667, 3703,

3698, 3672,

3680, 3697,

3699, 4215,

3682, 3674,

3664, 3681,

3666, 2978,

3181

1412

Similar to gi|7268365|emb|CAB78658.1| pore protein
2958

homolog [Arabidopsis thaliana]

1294

Similar to gi|804946|emb|CAA85389.1| acyl-(acyl
3468, 3467
4966
5824

carrier protein) thioesterase [Arabidopsis thaliana]

1346

Similar to gi|3550661|emb|CAA04670.1| 39 kDa EF-
4156

5552

Hand containing protein [Solanum tuberosum]

1534
2615
Similar to gi|4140257|emb|CAA10352.1| LEA-like

5805

protein [Arabidopsis thaliana]

1325

Similar to GPDA_CUPLA P52425 CUPHEA

LANCEOLATA
. GLYCEROL-3-PHOSPHATE

DEHYDROGENASE (NAD+) (EC 1.1.1.8).

1276

Similar to YDIB_HAEIN P44774 HAEMOPHILUS
3359
5082
5679

INFLUENZAE
. HYPOTHETICAL PROTEIN HI0607.

1352
2481
Similar to AGI2_WHEAT P02876 TRITICUM
4566, 4221
4879
5466

AESTIVUM
(WHEAT). AGGLUTININ ISOLECTIN

2 PRECURSOR (WGA2) (ISOLECTIN D).

1285

Similar to gi|7270231|emb|CAB80001.1| putative
3719, 2897

pyrophosphate-fructose-6-phosphate 1-

phosphotransferase [Arabidopsis thaliana]

1233

Similar to YDB3_SCHPO Q10356
4321, 4320

SCHIZOSACCHAROMYCES POMBE
(FISSION

YEAST). HYPOTHETICAL 21.1 KD PROTEIN

C22E12.03C IN CHROMOSOME I.

1588
2665
Similar to gi|7269937|emb|CAB81030.1| putative

protein [Arabidopsis thaliana]

1223
2418
Similar to gi|5059025|gb|AAD38873.1|AF110382_1 3-
2720

5347

hydroxy-3-methylglutaryl-coenzyme A reductase

[Oryza sativa]

1207

Similar to gi|6692109|gb|AAF24574.1|AC007764_16

4844
5614

F22C12.18 [Arabidopsis thaliana]

1166

Similar to gi|1247314|emb|CAA01765.1| ACC34
3261, 3293

5286

ACCase [Zea mays]

1568
2647
Similar to PER_SYNY3 P27320 SYNECHOCYSTIS
3710, 3707,

SP. (STRAIN PCC 6803). FERREDOXIN I.
3709, 4495

1567
2646
Similar to gi|6091768|gb|AAF03478.1|AC009327_17

5518

hypothetical protein [Arabidopsis thaliana]

1307

Similar to VV_PHODV P35941 PHOCINE
3429, 3428
4979
5706

DISTEMPER VIRUS (PDV). NONSTRUCTURAL

PROTEIN V.

1293

“““ Similar to KC21_SCHPO P40231
3188
5063

SCHIZOSACCHAROMYCES POMBE
(FISSION

YEAST). CASEIN KINASE II, ALPHA CHAIN (CK

II) (EC 2.7.1.37). ”””

1310

Similar to TAL1_MOUSE Q93092 P70358 MUS
3015, 3014,

MUSCULUS
(MOUSE). TRANSALDOLASE (EC
3013

2.2.1.2).

1518
2599
Open Reading Frame OS_ORF012554 HTC078773-

A01.17 FRAME: −2 ORF: 7 LEN: 927

1222
2417
Similar to gi|4512698|gb|AAD21751.1| unknown
4636, 3440,
4962

protein [Arabidopsis thaliana]
3033

1586
2663
Similar to gi|3702336|gb|AAC62893.1| 3-methyl-2-

5849

oxobutanoate hydroxy-methyl-transferase [Arabidopsis

thaliana
]

1250

Similar to gi|9294584|dbj|BAB02865.1|
2846, 4176,
4824

gb|AAF08583.1˜gene_id: MFJ20.18˜similar to
2847, 4175

unknown protein [Arabidopsis thaliana]

1382

Similar to gi|8778307|gb|AAF79316.1|AC002304_9

F14J16.15 [Arabidopsis thaliana]

1197
2401
Similar to AG84_MYCLE P46815

MYCOBACTERIUM LEPRAE
. ANTIGEN 84.

1394

Similar to ADX_CHICK P13216 GALLUS GALLUS

4815
5357

(CHICKEN). ADRENODOXIN PRECURSOR

(ADRENAL FERREDOXIN) (FRAGMENT).

1584
2661
Similar to gi|2245140|emb|CAB10561.1| SUPERMAN

like protein [Arabidopsis thaliana]

1421
2514
Similar to gi|3582319|gb|AAC35216.1| unknown

5419

protein [Arabidopsis thaliana]

1271
2446
Similar to THIJ_ECOLI Q46948 ESCHERICHIA
4319, 4137,

5347

COLI
. 4-METHYL-5(B-HYDROXYETHYL)-
4321, 3479,

THIAZOLE MONOPHOSPHATE
4320, 4136,

BIOSYNTHESISENZYME.
2745

1434

Similar to gi|3080367|emb|CAA18624.1| hypothetical

protein [Arabidopsis thaliana]

1399

Similar to ABP4_MAIZE P33488 ZEA MAYS

5445

(MAIZE). AUXIN-BINDING PROTEIN 4

PRECURSOR (ABP).

1410

Similar to gi|4586118|emb|CAB40954.1| putative

5358

protein [Arabidopsis thaliana]

1191

Open Reading Frame OS_ORF017317 HTC115428-

5232

A01.3 FRAME: −1 ORF: 3 LEN: 732

1563
2642
Similar to gi|6539566|dbj|BAA88183.1| Similar to
4551, 4552

phosphoribosyl-ATP pyrophosphohydrolase

(AB006082) [Oryza sativa]

1181
2393
Similar to gi|7485913|pir||T00906 hypothetical protein
4560, 3029,
4995
5829

F21B7.20 - Arabidopsis thaliana
4559, 4607,

4606

1491
2574
Similar to gi|7523392|emb|CAB86450.1| putative
4405, 4406
5070
5361

protein [Arabidopsis thaliana]

1378

Similar to gi|4581182|gb|AAD24665.1|AC006220_21

hypothetical protein [Arabidopsis thaliana]

1535
2616
Similar to gi|2583128|gb|AAB82637.1| hypothetical
2722, 2721,

protein [Arabidopsis thaliana]
2970, 2995

1204
2406
Similar to CLPB_SYNY3 P74361 SYNECHOCYSTIS
2859, 2933,

5799

SP. (STRAIN PCC 6803). CLPB PROTEIN.
4641, 2858,

2857, 2971

1406

“““ Similar to gi|7076784|emb|CAB75899.1| 2-

oxoglutarate dehydrogenase, E1 subunit-like protein

[Arabidopsis thaliana] “““

1541
2622
Similar to ENP2_TORCA P14401 TORPEDO

5566

CALIFORNICA
(PACIFIC ELECTRIC RAY).

ELECTROMOTOR NEURON-ASSOCIATED

PROTEIN 2 (FRAGMENT).

1282
2451
Open Reading Frame OS_ORF019538 HTC131716-

5890

A01.11 FRAME: 2 ORF: 1 LEN: 1137

1228

Similar to gi|1839244|gb|AAB46988.1| EGF receptor
2855, 2854,
4910
5869

like protein [Arabidopsis thaliana]
3691, 2959

1290

Open Reading Frame OS_ORF007256 ST(R)

HTC043276-A01.F.9 FRAME: 3 ORF: 8 LEN: 555

1573
2650
Similar to gi|8778489|gb|AAF79497.1|AC002328_5

F20N2.12 [Arabidopsis thaliana]

1500
2581
Similar to gi|7488434|pir||T06699 zinc finger protein
3190, 3100,

T29H11.50 - Arabidopsis thaliana
3893

1193

Similar to gi|3600048|gb|AAC35535.1| similar to

hypothetical proteins in Schizosaccharomyces pombe

(GB: Z98533) and C. elegans (GB: Z48334 and Z78419)

[Arabidopsis thaliana]

1594

Similar to gi|4337176|gb|AAD18097.1| T31J12.4
4653, 2811,

[Arabidopsis thaliana]
4654

1392
2499
Similar to YSV4_CAEEL Q10010

5176
5918

CAENORHABDITIS ELEGANS
. HYPOTHETICAL

26.6 KD PROTEIN T19C3.4 IN CHROMOSOME III.

1445
2536
Open Reading Frame OS_ORF011257 HTC069347-

A01.F.8 FRAME: −1 ORF: 1 LEN: 786

1259

Open Reading Frame containing a Sage tag sequence
2895, 3493

near 3 end OS_ORF006433 ST(F) HTC038577-

A01.35 FRAME: −3 ORF: 29 LEN: 675

1501
2582
Open Reading Frame containing a Sage tag sequence
4587, 4586

5919

near 3 end OS_ORF012155 ST(F) HTC075889-

A01.R.16 FRAME: 2 ORF: 1 LEN: 573

1321
2472
Similar to gi|4895195|gb|AAD32782.1|AC007661_19
2781
4790
5843

putative mitochondrial carrier protein [Arabidopsis

thaliana
]

1440
2532
Similar to YPOL_IPNVJ P22931 INFECTIOUS

PANCREATIC NECROSIS VIRUS (SEROTYPE

JASPER) (IPNV). HYPOTHETICAL 17.3 KD

PROTEIN (SMALL ORF).

1179

Similar to gi|4467146|emb|CAB37515.1| galactosidase
4284
4784
5691

like protein [Arabidopsis thaliana]

1262
2441
Similar to gi|169775|gb|AAA33897.1|alpha-amylase
3665, 4214,

5521

precursor (EC 3.2.1.1)
3663, 3673,

3702, 3695,

3704, 3701,

3667, 3705,

3700, 3703,

3698, 3672,

3680, 3697,

4215, 3699,

3664, 3674,

3682, 3666,

3681

1175
2388
Open Reading Frame OS_ORF014527 HTC093803-
3497, 2824,

A01.F.24 FRAME: 1 ORF: 21 LEN: 1272
2913

1426
2519
Similar to gi|6572079|emb|CAB63022.1|putative
3309

5865

protein [Arabidopsis thaliana]

1190
2398
Similar to UBPT_CAEEL Q17361

CAENORHABDITIS ELEGANS
. QUEUINE TRNA-

RIBOSYLTRANSFERASE (EC 2.4.2.29) (TRNA-

GUANINETRANSGLYCOSYLASE) (GUANINE

INSERTION ENZYME).

1540
2621
Similar to gi|685234|emb|CAA56426.1|H1

[Arabidopsis thaliana]

1366
2485
Similar to VIV_ORYSA P37398 ORYZA SATIVA

5844

(RICE). VIVIPAROUS PROTEIN HOMOLOG.

1318
2470
Similar to ILVE_METJA Q58414
2780, 2779

5836

METHANOCOCCUS JANNASCHII
. PUTATIVE

BRANCHED-CHAIN AMINO ACID

AMINOTRANSFERASE (EC

2.6.1.42)(TRANSAMINASE B) (BCAT).

1248
2435
“““ Similar to gi|3176677|gb|AAC18800.1| Similar to S.
3865, 3866
4833

cerevisiae
SIK1P protein, A_TM021B04.13 from A.

thaliana
BAC gb|AF007271. [Arabidopsis thaliana] ”””

1371
2490
Similar to gi|7486436|pir||T02408 hypothetical protein

4924
5904

F4I1.34 - Arabidopsis thaliana

1247
2434
Similar to PYR5_DROME Q01637 Q24221
4513, 4512,
5105
5585

DROSOPHILA MELANOGASTER
(FRUIT FLY).
4511

URIDINE 5-MONOPHOSPHATE SYNTHASE

(UMP SYNTHASE)

(OROTATEPHOSPHORIBOSYLTRANSFERASE

(EC 2.4.2.10) AND OROTIDINE 5 -

PHOSPHATEDECARBOXYLASE (EC 4.1.1.23))

(RUDIMENTARY-LIKE PROTEIN).

1245
2432
Similar to ORYB_ORYSA P25777 ORYZA SATIVA
3319, 3318,

5472

(RICE). ORYZAIN BETA CHAIN PRECURSOR (EC
3942, 3943,

3.4.22.-).
3939

1312
2466
“““ Similar to gi|6063552|dbj|BAA85412.1| ESTs
4545

5540

AU065232(E60855), C23624(S1554),

AU078241(E60855) correspond to a region of the

predicted gene.; similar to putative adenylate kinase.

(AC005896) [Oryza sativa] ”””

1577
2654
Open Reading Frame OS_ORF001833 HTC010638-

A01.22 FRAME: 1 ORF: 12 LEN: 618

1430
2523
Open Reading Frame OS_ORF018292 HTC121996-

A01.44 FRAME: −2 ORF: 18 LEN: 1551

Similar to ADX_SHEEP P29330 OVIS ARIES

(SHEEP). ADRENODOXIN (ADRENAL

FERREDOXIN).

1451
2541
Similar to gi|8843778|dbj|BAA97326.1|

5380

emb|CAB85555.1˜gene_id: MZN1.2˜similar to

unknown protein [Arabidopsis thaliana]

1401

Similar to LAMC_DROME Q03427 DROSOPHILA

MELANOGASTER
(FRUIT FLY). LAMIN C (PG-IF).

1528
2609
Similar to YK67_YEAST P36163

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). HYPOTHETICAL 35.8 KD PROTEIN IN

PRP16-SRP40 INTERGENIC REGION.

[0686]

12

TABLE 6

SEQ ID NOs and corresponding description for Oryza genes which are expressed

in a leaf- and stem-specific manner and further the SEQ ID NOs for the corresponding

homologous sequences found in wheat, banana and maize.

ORF
Promo

Bana
Maize

(SEQ
(SEQ

Wheat
(SEQ
(SEQ

ID)
ID)
Description
(SEQ ID)
ID)
ID)

Leaf/stem (green-tissue)

402

Similar to gi|6633822|gb|AAF19681.1|AC009519_15

5446

F1N19.25 [Arabidopsis thaliana]

404
1887
Similar to gi|4567284|gb|AAD23697.1|AC006841_30
4382, 4381

unknown protein [Arabidopsis thaliana]

400

Similar to EFG_THEMA P38525 THERMOTOGA
3164, 3420,
4973

MARITIMA
. ELONGATION FACTOR G (EF-G).
3421

399

Similar to gi|4164416|emb|CAA10640.1| ferredoxin
3355, 3294,
4942

dependent-glutamate synthase Fd-Gogat [Oryza sativa]
3356, 3354

401

Similar to gi|2331139|gb|AAB66888.1| 2-
4237, 3069,
5027
5525

oxoglutarate/malate translocator [Oryza sativa]
4238, 4236

403
1886
Similar to gi|9247022|gb|AAF86253.1|AF272040_1

5222
5417

timing of CAB expression 1-like protein [Arabidopsis

thaliana
]

413

Similar to gi|2160148|gb|AAB60770.1| EST gb|H37044

5772

comes from this gene. [Arabidopsis thaliana]

411

Similar to gi|9293944|dbj|BAB01847.1| contains

similarity to 30s ribosomal protein

s1˜gene_id: MYM9.4 [Arabidopsis thaliana]

414

Similar to gi|1323698|gb|AAC49434.1| DCL
3310

5759

415
1889
Similar to gi|2317900|gb|AAB66369.1| Sali3-2

[Glycine max]

407

Similar to gi|5903052|gb|AAD55611.1|AC008016_21

5275

Contains PF|00561 alpha/beta hydrolase fold.

[Arabidopsis thaliana]

410

Similar to gi|6573763|gb|AAF17683.1|AC009243_10

F28K19.14 [Arabidopsis thaliana]

416
1890
Similar to gi|7572943|emb|CAA60774.1| ribosomal
3390
4931
5880

protein L35 [Arabidopsis thaliana]

409

Similar to gi|4454459|gb|AAD20906.1| unknown
4703, 4705,
4899

protein [Arabidopsis thaliana]
4704

408

Similar to RK1_PORPU P51338 PORPHYRA
3152
4849
5628

PURPUREA
. CHLOROPLAST 50S RIBOSOMAL

PROTEIN L1.

412
1888
Similar to YAAE_BACSU P37528 BACILLUS

5042
5292

SUBTILIS
. HYPOTHETICAL 21.4 KD PROTEIN IN

DACA-SERS INTERGENIC REGION.

405

Similar to gi|437020|gb|AAA34187.1| phytoene
4668, 4667,
5219
5669

synthase
4227

406

Similar to gi|6006360|dbj|BAA84790.1| Similar to 1-

5451

aminocyclopropane-1-carboxylate synthase (U35779)

[Oryza sativa]

439

Similar to gi|4512678|gb|AAD21732.1| unknown

4953

protein [Arabidopsis thaliana]

421

Open Reading Frame containing a Sage tag sequence
3313, 3000,
4861
5274

near 3 end OS_ORF009925 ST(F) HTC059815-
3312, 3980,

A01.R.6 FRAME: −1 ORF: 3 LEN: 513
3977, 4544,

3979, 3976,

2999, 3978

446
1902
Open Reading Frame OS_ORF005313 HTC031638-

A01.6 FRAME: 1 ORF: 3 LEN: 1050

448
1904
Similar to gi|7267268|emb|CAB81051.1| 3 (2 ), 5 -

BISPHOSPHATE NUCLEOTIDASE-like protein

[Arabidopsis thaliana]

419

Similar to gi|5734746|gb|AAD50011.1|AC007651_6
2896, 4426
4994

Similar to translation initiation factor IF2 [Arabidopsis

thaliana
]

431

Similar to gi|5903095|gb|AAD55653.1|AC008017_26

Unknown protein [Arabidopsis thaliana]

424

Similar to gi|7209640|dbj|BAA92288.1| SigF
4571, 4570

5777

[Arabidopsis thaliana]

451
1907
Similar to gi|6646755|gb|AAF21067.1|AC013258_5
3265

unknown protein [Arabidopsis thaliana]

428

Similar to YX11_MYCTU Q10806 Q10805

MYCOBACTERIUM TUBERCULOSIS
.

HYPOTHETICAL 29.6 KD PROTEIN

CY274.11C/10C.

430

Similar to gi|8954044|gb|AAF82218.1|AC067971_26

4794

Contains similarity to serine-threonine protein

phosphatase - fission yeast from Schizosaccharomyces

pombe
gb|AL031179. ESTs gb|T88261, gb|T04457,

gb|AA585938, gb|AA650911 and gb|AA598061 come

from this ge

450
1906
Similar to gi|8778304|gb|AAF79313.1|AC002304_6
3019, 3209,

5523

F14J16.9 [Arabidopsis thaliana]
3210

438

Similar to gi|7770346|gb|AAF69716.1|AC016041_21
4265

F27J15.15 [Arabidopsis thaliana]

436

Similar to PILB_NEIGO P14930 NEISSERIA
2771, 2772,
5079
5605

GONORRHOEAE
. PILB PROTEIN.
2770

422
1893
Open Reading Frame OS_ORF008685 HTC052101-
4017, 4018
5077
5268

A01.R.17 FRAME: −3 ORF: 9 LEN: 1035

417
1891
Similar to gi|4455367|emb|CAB36777.1| putative

protein [Arabidopsis thaliana]

433
1897
Similar to gi|7981380|emb|CAB91874.1| myb-related

4786

protein [Lycopersicon esculentum]

456
1912
Similar to RL34_MYCGE P47704 MYCOPLASMA
4688, 4687

GENITALIUM
. 50S RIBOSOMAL PROTEIN L34.

453
1909
Similar to gi|6642665|gb|AAF20245.1|AC015450_6
3932

5370

putative cinnamoyl-CoA reductase [Arabidopsis

thaliana
]

426
1895
Similar to gi|3386548|gb|AAC28391.1| H-protein
3509, 3510

5482

promoter binding factor-2b [Arabidopsis thaliana]

418
1892
Similar to gi|7141304|gb|AAF37281.1|RSH1

[Arabidopsis thaliana]

435
1899
Similar to gi|6358779|gb|AAF07360.1|AC010852_1
4525, 4526,
5175
5499

unknown protein [Arabidopsis thaliana]
4523

447
1903
Open Reading Frame OS_ORF019640 HTC132705-
4057, 2760,
5229

A01.R.14 FRAME: −3 ORF: 3 LEN: 888
2759

437

Similar to gi|2462839|gb|AAB72174.1|unknown
4172, 4171
5021
5615

protein [Arabidopsis thaliana]

429

Similar to gi|8777302|dbj|BAA96892.1|translation
4615, 4616
4817

releasing factor RF-2 [Arabidopsis thaliana]

449
1905
Similar to SYT_HELPY P56071 HELICOBACTER
2687, 2741
5059
5444

PYLORI
(CAMPYLOBACTER PYLORI).

THREONYL-TRNA SYNTHETASE (EC 6.1.1.3)

(THREONINE--TRNA LIGASE)(THRRS).

455
1911
Open Reading Frame OS_ORF002259 HTC013114-

A01.10 FRAME: 1 ORF: 7 LEN: 792

423

Similar to gi|3746964|gb|AAC64139.1| signal
2744
4950

recognition particle 54 kDa subunit precursor

[Arabidopsis thaliana]

427

Similar to gi|6016707|gb|AAF01533.1|AC009325_3
2732, 2730,

putative thylakoid lumen rotamase [Arabidopsis
2731

thaliana
]

432
1896
Open Reading Frame OS_ORF014047 HTC090350-
4316, 4314,
5180

A01.F.8 FRAME: −3 ORF: 3 LEN: 633
4315

441

Similar to gi|4531443|gb|AAD22128.1|AC006224_10
3126, 3127
5139
5551

50S ribosomal protein L3 [Arabidopsis thaliana]

425
1894
Similar to ENO1_MAIZE P26301 ZEA MAYS
3798, 3797
5137
5567

(MAIZE). ENOLASE 1 (EC 4.2.1.11) (2-

PHOSPHOGLYCERATE DEHYDRATASE 1) (2-

PHOSPHO-D-GLYCERATE HYDRO-LYASE 1).

452
1908
Similar to gi|6041833|gb|AAF02142.1|AC009853_2

unknown protein [Arabidopsis thaliana]

442

Similar to gi|133028|sp|P25864|RK9_ARATH 50S

RIBOSOMAL PROTEIN L9, CHLOROPLAST

PRECURSOR (CL9)

434
1898
Similar to gi|3157934|gb|AAC17617.1| Similar to

4776
5800

hypothetical protein F09E5.8 gb|U37429 from C.

elegans
. ESTs gb|T42019 and gb|N97000 come from

this gene. [Arabidopsis thaliana]

443
1900
Open Reading Frame OS_ORF003358 HTC019440-

A01.13 FRAME: −2 ORF: 3 LEN: 702

440

Similar to YC37_PORPU P51191 PORPHYRA
3036

5346

PURPUREA
. HYPOTHETICAL 20.0 KD PROTEIN

YCF37 (ORF173).

445
1901
Open Reading Frame OS_ORF018286 HTC121926-

A01.R.44 FRAME: 3 ORF: 5 LEN: 1557

444

Open Reading Frame OS_ORF000886 ST(R)

HTC005025-A01.4 FRAME: −1 ORF: 3 LEN: 648

454
1910
Similar to RK24_PEA P11893 PISUM SATIVUM
3159, 3158,
4945

(GARDEN PEA). 50S RIBOSOMAL PROTEIN L24,
3157

CHLOROPLAST PRECURSOR (CL24).

420

Similar to gi|3775987|emb|CAA09196.1| RNA helicase
2954

5326

[Arabidopsis thaliana]

458
1913
Similar to YCB1_PSEDE P29943 PSEUDOMONAS
2677

5404

DENITRIFICANS
. HYPOTHETICAL 10.3 KD

PROTEIN IN COBS 5 REGION (ORF1).

460
1914
Similar to gi|4732091|gb|AAD28599.1|AF126742_1

4918

bundle sheath defective protein 2 [Zea mays]

461
1915
Similar to RK25_PEA P11892 PISUM SATIVUM

5431

(GARDEN PEA). 50S RIBOSOMAL PROTEIN CL25,

CHLOROPLAST PRECURSOR.

464
1918
Similar to ESL2_MYCPN P75311 MYCOPLASMA

5494

PNEUMONIAE
. PUTATIVE ESTERASE/LIPASE 2

(EC 3.1.-.-).

463
1917
Similar to gi|22349|emb|CAA78772.1| putative iojap
4508, 4509,
4920

protein [Zea mays]
2894

457

Similar to gi|4263509|gb|AAD15335.1| hypothetical

5083

protein [Arabidopsis thaliana]

462
1916
Similar to gi|4468817|emb|CAB38218.1| putative
4079, 4077,
4934

protein [Arabidopsis thaliana]
4078, 4210,

4209

459

Similar to gi|2244889|emb|CAB10310.1| cytochrome

5131

P450 like protein [Arabidopsis thaliana]

[0687]

13

TABLE 7

SEQ ID NOs and corresponding description for Oryza genes which are expressed

in a panicle-specific manner and further the SEQ ID NOs for the corresponding

homologous sequences found in wheat, banana and maize.

ORF
Prom

Bana
Maize

SEQ
SEQ

Wheat
(SEQ
(SEQ

ID
ID
Description
(SEQ ID)
ID)
ID)

Panicle

503
1944
Similar to gi|6002797|gb|AAF00147.1|AF149814_1
3260

5783

unknown [Oryza sativa]

737
2098
Similar to gi|7339700|dbj|BAA92905.1| hypothetical

protein [Oryza sativa]

689
2054
Similar to gi|6002790|gb|AAF00143.1|AF149811_1
4480, 4680,

hypothetical protein [Oryza sativa]
4681, 4310,

4311, 2733,

2734, 4309,

4479, 3240,

4478

514
1948
Similar to H2B1_MAIZE P30755 ZEA MAYS
3772, 3771,
5189
5575

(MAIZE). HISTONE H2B.1.
4277, 4066,

3775, 4110,

4269, 4155,

3754, 4105,

3720, 4191,

4118, 3773,

4117, 3767,

4174, 4109,

3726, 3712,

4267, 3777,

4276, 4206,

3738, 3749,

4205, 4031,

3734, 4173,

3769, 4145,

3727, 4192,

4051, 4032,

4084, 4064,

3736, 4138,

4122, 4123,

4065, 4275,

3744, 4120,

4119, 4270,

3722, 4121

511

Similar to gi|736716|dbj|BAA04695.1| rice anther

5889

specific protein [Oryza sativa]

482

Similar to gi|5679840|emb|CAB51833.1|11332.4
3442, 3443,
5106
5613

[Oryza sativa]
3441

723

Similar to gi|1778444|gb|AAB40728.1| putative protein
3646, 3322,
4878
5263

kinase PK9 [Arabidopsis thaliana]
4433, 3645,

3643, 3660,

3641, 3642,

3659, 3387,

3539, 2692,

3816, 2793

635

Similar to gi|1771734|emb|CAA61106.1| GB1 protein

4948
5713

[Solanum tuberosum]

592

“““ Similar to gi|1836024|gb|AAB46825.1|
3470, 3276,

5682

Cel2 = cellulase 2 [Lycopersicon esculentum = tomatoes,
3899

Mill., cv. Castlemart, flower abscission zones, Peptide

Partial, 169 aa] ”””

673
2040
Similar to gi|5852174|emb|CAB55412.1| zhb0004.1

[Oryza sativa]

639

Similar to RECA_SPIME Q54428 SPIROPLASMA
4360

MELLIFERUM
. RECA PROTEIN (FRAGMENT).

683
2049
Similar to THGF_TOBAC P32026 NICOTIANA

TABACUM
(COMMON TOBACCO). FLOWER-

SPECIFIC GAMMA-THIONIN PRECURSOR.

526
1959
Similar to ZN85_HUMAN Q03923 HOMO SAPIENS
3102, 3100

(HUMAN). ZINC FINGER PROTEIN 85 (ZINC

FINGER PROTEIN HPF4) (HTF1).

Similar to gi|3643596|gb|AAC42243.1|hypothetical

protein [Arabidopsis thaliana]

524
1957
Similar to gi|5430759|gb|AAD43159.1|AC007504_14

Unknown Protein [Arabidopsis thaliana]

719
2084
Similar to gi|4007852|emb|CAA10349.1|pollen

allergen (group II) [Triticum aestivum]

770
2116
Similar to LA52_LYCES P13447 LYCOPERSICON

5441

ESCULENTUM
(TOMATO). ANTHER SPECIFIC

LAT52 PROTEIN PRECURSOR.

616

Similar to gi|2645170|dbj|BAA23618.1| YY2 protein

[Oryza sativa]

720
2085
Similar to gi|972513|emb|CAA90746.1| pollen

allergen-like protein [Triticum aestivum]

731
2094
Similar to gi|4105160|gb|AAD02278.1| cell wall
3120

5560

invertase Incw3 [Zea mays]

585

Similar to gi|2894378|emb|CAA74910.1| putative
4383, 4385,
4852

ribophorin I homologue [Hordeum vulgare]
4384

497
1939
Similar to gi|1694892|emb|CAA57556.1| cyclin [Oryza

sativa
]

509

Similar to gi|6646756|gb|AAF21068.1|AC013258_6

4859

putative DNA-3-methyladenine glycosylase I

[Arabidopsis thaliana]

688
2053
Similar to V07K_PMV P20954 PAPAYA MOSAIC
2725, 2866,

5860

POTEXVIRUS (PMV). 7 KD PROTEIN (ORF 4).
2865, 2724,

2973

670
2037
Similar to YEA3_YEAST P40005
4041, 4040,
4887

SACCHAROMYCES CEREVISIAE
(BAKER S
4042

YEAST). HYPOTHETICAL 14.3 KD PROTEIN IN

GCN4-WBP1 INTERGENIC REGION.

622

Similar to gi|3695392|gb|AAC62794.1| T2L5.6 gene

5700

product [Arabidopsis thaliana]

721
2086
Similar to gi|6728866|gb|AAF26939.1|AC008113_10
3495, 3496

5302

F12A21.21 [Arabidopsis thaliana]

615
2015
Similar to AROB_PSEAE P34002 PSEUDOMONAS
4434, 4436,
4939

AERUGINOSA
. 3-DEHYDROQUINATE
4435

SYNTHASE (EC 4.6.1.3) (FRAGMENT).

472
1924
Similar to gi|2129665|pir||S65571 pattern formation
4295, 4293,
4858

protein GNOM - Arabidopsis thaliana
4294

575
1995
Similar to gi|6002784|gb|AAF00140.1|AF149808_1
2735, 2736,
4988

hypothetical protein [Oryza sativa]
2737

567
1990
Similar to gi|4468193|emb|CAB38030.1| inosine
4521, 4522,
4872
5365

monophosphate dehydrogenase [Glycine max]
4520, 2980

577

“““ Similar to gi|6498438|dbj|BAA87841.1| EST

C93513(C53164) corresponds to a region of the

predicted gene.; Similar to Arabidopsis thaliana

chromosome II BAC F5H14 genomic

sequence, hypothetical protein. (AC006234) [Oryza

sativa
] ”””

718
2083
Similar to gi|7269452|emb|CAB79456.1| putative

peroxidase [Arabidopsis thaliana]

646
2028
Similar to HCD2_MOUSE O08756 MUS
3785, 3784,

MUSCULUS
(MOUSE). 3-HYDROXYACYL-COA
3786, 3783,

DEHYDROGENASE TYPE II (EC 1.1.1.35)
3258, 3788,

(ENDOPLASMICRETICULUM-ASSOCIATED
3782, 3787

AMYLOID BETA-PEPTIDE BINDING PROTEIN).

584

Similar to gi|4490341|emb|CAB38623.1| putative

4840
5694

protein [Arabidopsis thaliana]

518
1951
Similar to gi|4056436|gb|AAC98009.1| EST

5801

gb|AA650912 comes from this gene. [Arabidopsis

thaliana
]

583
2000
Similar to gi|7960739|emb|CAB92061.1| putative

4862

protein [Arabidopsis thaliana]

552
1981
“““ Similar to gi|7630236|dbj|BAA94769.1| Similar to
2891, 3264

Arabidopsis thaliana
chromosome 4, BAC clone

F4D11; putative myb-protein. (AL022537) [Oryza

sativa
] ”””

668
2036
Similar to gi|20310|emb|CAA78897.1| pollen specific
3178, 3177,

5441

gene [Oryza sativa]
3176

659
2032
Similar to gi|1167557|gb|AAA85863.1| glycine-rich

5468

protein

539
1972
Similar to DDX8_HUMAN Q14562 HOMO SAPIENS
2947, 2691,
5024

(HUMAN). PROBABLE ATP-DEPENDENT RNA
3306

HELICASE HRH1 (DEAH BOX PROTEIN 8).

487

Similar to DCP3_ORYSA P51849 ORYZA SATIVA
4009, 4008,
5184
5685

(RICE). PYRUVATE DECARBOXYLASE
4010, 4007,

ISOZYME 3 (EC 4.1.1.1) (PDC).
4006, 3751,

3711, 3715,

3586

663

Similar to CB20_HUMAN P52298 HOMO SAPIENS

5845

(HUMAN). 20 KD NUCLEAR CAP BINDING

PROTEIN (NCBP 20 KD SUBUNIT) (CBP20).

601

“““ Similar to TCPB_MOUSE P80314 MUS
3966
5156

MUSCULUS
(MOUSE). T-COMPLEX PROTEIN 1,

BETA SUBUNIT (TCP-1-BETA) (CCT-BETA). ”””

608

Similar to gi|940383|dbj|BAA08113.1| GTP
3030, 2752,
4813
5925

cyclohydrolase II [Arabidopsis thaliana]
3463, 4400

544

Similar to gi|7594515|emb|CAB88040.1| putative
3469, 4683,

protein [Arabidopsis thaliana]
4682

612
2014
Similar to gi|3860247|gb|AAC73015.1| putative dTDP-
3844, 3839,
5005
5370

glucose 4-6-dehydratase [Arabidopsis thaliana]
3595, 3837,

3843

641

Similar to gi|4874313|gb|AAD31375.1|AC006053_17
4468, 4469,
4798

putative protein phosphatase 2C [Arabidopsis thaliana]
4467

621

Similar to gi|3128234|gb|AAC26714.1| hypothetical
2783
5126

protein [Arabidopsis thaliana]

609
2013
Similar to AP47_MOUSE P35585 MUS MUSCULUS
3800, 3799
4813
5925

(MOUSE). CLATHRIN COAT ASSEMBLY

PROTEIN AP47 (CLATHRIN COAT ASSOCIATED

PROTEINAP47) (GOLGI ADAPTOR AP-1 47 KD

PROTEIN) (HA1 47 KD SUBUNIT)

(CLATHRINASSEMBLY PROTEIN ASSEMBLY

PROTEIN COMPLEX 1 MEDIUM CHAIN).

551
1980
“““ Similar to gi|5091526|dbj|BAA78761.1| ESTs
4481, 4664,

C27722(C52692), AU058088(S0509) correspond to a
4404, 4482

region of the predicted gene.; Similar to Arabidopsis

thaliana
ribonucleoside-diphosphate reductase large

subunit mRNA, complete cds. (AF092841) [Oryza

sativa
] ”””

712
2077
Similar to gi|4726112|gb|AAD28312.1|AC006436_3
4553, 4555,

5373

hypothetical protein [Arabidopsis thaliana]
4554

695
2060
Similar to gi|2245128|emb|CAB10549.1| peroxidase

5172
5596

like protein [Arabidopsis thaliana]

636

Similar to gi|6715737|gb|AAF26498.1|AC016447_21

5333

putative zinc linger protein [Arabidopsis thaliana]

629
2021
Similar to AAPC_PENCL Q40784 PENNISETUM
4283, 3458
4812
5320

CILIARE
(BUFFELGRASS). POSSIBLE

APOSPORY-ASSOCIATED PROTEIN C.

499
1940
Similar to gi|2961437|gb|AAC05723.1| MADS box

5225
5530

protein [Oryza sativa]

574
1994
Similar to PRVA_ESOLU P02628 ESOX LUCIUS
4565, 3981,
5048
5509

(NORTHERN PIKE). PARVALBUMIN ALPHA.
3517, 2914,

3170, 3518,

2864, 4055,

3292, 4620,

3369, 4621

505
1946
Similar to gi|3831445|gb|AAC69928.1| putative rac
3242, 3320

5720

GTPase activating protein [Arabidopsis thaliana]

658

Similar to gi|7488300|pir||T01457 rho protein GDP-

5504

dissociation inhibitor homolog F24O1.19 - Arabidopsis

thaliana

512

Similar to gi|4741186|emb|CAB41852.1| putative

protein [Arabidopsis thaliana]

529
1962
Similar to gi|4454006|emb|CAA23059.1| hypothetical
3388, 3389

5790

protein [Arabidopsis thaliana]

680
2047
Similar to gi|4678204|gb|AAD26950.1|AC007134_8
4617

5278

hypothetical protein [Arabidopsis thaliana]

642

Similar to gi|8072394|gb|AAF71982.1|AC013453_7
4447, 4446

Putative cyclin [Arabidopsis thaliana]

664

Similar to gi|6691219|gb|AAF24557.1|AC007508_20
3789

5553

F1K23.4 [Arabidopsis thaliana]

533
1966
Similar to gi|2832357|emb|CAA74400.1| HMG protein

5533

[Arabidopsis thaliana]

508

Similar to gi|6553913|gb|AAF16578.1|AC012329_2
4366

unknown protein [Arabidopsis thaliana]

569
1992
Similar to gi|6630542|gb|AAF19561.1|AC011708_4
3202, 2906,

hypothetical protein [Arabidopsis thaliana]
3203, 4367,

3204

520
1953
Similar to gi|6642648|gb|AAF20229.1|AC012395_16
4060

5587

unknown protein [Arabidopsis thaliana]

589
2002
Similar to gi|7363275|dbj|BAA93019.1| hypothetical
2827

5917

protein [Oryza sativa]

579
1997
Similar to gi|8247759|dbj|BAA96421.1| GAMyb
4428, 4698

5269

protein [Triticum aestivum]

623
2017
Similar to gi|3420299|gb|AAC33765.1| jab1 protein

4949
5705

[Oryza sativa subsp. indica]

602
2010
Similar to gi|3892045|gb|AAC78253.1|AAC78253

4785
5683

putative zinc finger protein [Arabidopsis thaliana]

656

Similar to RL15_BACST P04452 BACILLUS
2727, 2726
4819
5728

STEAROTHERMOPHILUS
. 50S RIBOSOMAL

PROTEIN L15.

573
1993
Similar to AMPE_RAT P50123 RATTUS
3299

NORVEGICUS
(RAT). GLUTAMYL

AMINOPEPTIDASE (EC 3.4.1 1.7) (EAP)

(AMINOPEPTIDASE A) (APA)(FRAGMENT).

679
2046
Similar to T2AG_DROME P52656 DROSOPHILA

5166
5496

MELANOGASTER
(FRUIT FLY).

TRANSCRIPTION INITIATION FACTOR IIA

GAMMA CHAIN (TFIIA P14 SUBUNIT)(TFIIA-14)

(DTFIIA-S) (TFIIA-GAMMA).

678
2045
Similar to gi|9293905|dbj|BAB01808.1|

5791

gene_id: MVE11.18˜unknown protein [Arabidopsis

thaliana
]

559
1984
Similar to gi|6573708|gb|AAF17628.1|AC009978_4
3340
4783
5264

T23E18.8 [Arabidopsis thaliana]

596
2007
Similar to gi|5734743|gb|AAD50008.1|AC007651_3
3085
4870

Hypothetical Protein [Arabidopsis thaliana]

690
2055
Similar to gi|6957509|gb|AAF32431.1| hypothetical

protein [Arabidopsis thaliana]

591
2004
Similar to gi|4581047|gb|AAD24584.1|AF134807_1
3332

putative dihydroflavonol reductase [Oryza sativa]

638

Similar to FABB_HORVU P23902 HORDEUM

5113
5748

VULGARE
(BARLEY). 3-OXOACYL-[ACYL-

CARRIER-PROTEIN] SYNTHASE I PRECURSOR

(EC 2.3.1.41)(BETA-KETOACYL-ACP SYNTHASE

I) (KAS I).

735

Similar to gi|1890352|emb|CAA62744.1| transcription

4830
5774

factor L2 [Arabidopsis thaliana]

536
1969
Similar to ARNO_HUMAN Q99418 HOMO
3492, 2702,
5221

SAPIENS
(HUMAN). ARF NUCLEOTIDE-BINDING
3491, 3281

SITE OPENER (ARNO PROTEIN) (ARF

EXCHANGEFACTOR).

Similar to RL4_MYCBO O06045

MYCOBACTERIUM BOVIS
. 50S RIBOSOMAL

PROTEIN L4.

488
1934
Similar to MIP_TRYCR Q09734 TRYPANOSOMA
4097, 4101,
5041
5453

CRUZI
. MACROPHAGE INFECTIVITY
2674, 2675,

POTENTIATOR PRECURSOR (PEPTIDYL-
2676, 4100,

PROLYLCIS-TRANS ISOMERASE) (EC 5.2.1.8)
2961

(PPIASE) (ROTAMASE).

521
1954
Similar to gi|6523046|emb|CAB62314.1| hypothetical

5602

protein [Arabidopsis thaliana]

631

Similar to gi|2864614|emb|CAA16961.1| putative
4339, 2828,

protein [Arabidopsis thaliana]
2829

640
2025
Similar to gi|7485445|pir||T05519 hypothetical protein

5378

F13M23.120 - Arabidopsis thaliana (fragment)

628

“““ Similar to gi|3176691|gb|AAC18814.1| Contains

5235

homology to serine/threonine protein kinase gb|X99618

from Mycobacterium tuberculosis. ESTs gb|F14403,

gb|F14404, and gb|N96730 come from this gene.

[Arabidopsis thaliana] ”””

610

Similar to gi|4490311|emb|CAB38802.1| putative

4796
5752

protein [Arabidopsis thaliana]

661
2034
Similar to gi|4966372|gb|AAD34703.1|AC006341_31

5280

ESTs gb|N38586 and gb|N38613 come from this gene.

[Arabidopsis thaliana]

713
2078
Similar to CAH4_MOUSE Q64444 MUS

5746

MUSCULUS
(MOUSE). CARBONIC ANHYDRASE

IV PRECURSOR (EC 4.2.1.1) (CARBONATE

DEHYDRATASEIV).

648

Similar to RL25_HELPY P56078 HELICOBACTER
3201, 3200,

5697

PYLORI
(CAMPYLOBACTER PYLORI).
3199

PROBABLE 50S RIBOSOMAL PROTEIN L25.

550

Similar to gi|9295705|gb|AAF87011.1|AC005292_20

F26F24.21 [Arabidopsis thaliana]

792
2135
Similar to gi|9293898|dbj|BAB01801.1| MAP (mitogen
2929, 2806

5350

activated protein) kinase-like protein [Arabidopsis

thaliana
]

681
2048
Similar to gi|5123936|emb|CAB45494.1| hypothetical

protein [Arabidopsis thaliana]

655
2031
Similar to gi|4263510|gb|AAD15336.1| hypothetical

protein [Arabidopsis thaliana]

701
2066
Similar to gi|6573734|gb|AAF17654.1|AC009398_3

5798

F20B24.4 [Arabidopsis thaliana]

549
1979
Similar to gi|5295966|dbj|BAA81867.1| Similar to

4894

Glycine max gmsti mRNA.(X79770) [Oryza sativa]

614

Similar to gi|4006898|emb|CAB16828.1| splicing
3189, 3815,
4853
5338

factor-like protein [Arabidopsis thaliana]
2816

649

Similar to gi|7573353|emb|CAB87659.1| putative
4594

protein [Arabidopsis thaliana]

736
2097
Similar to gi|6983874|dbj|BAA90809.1| hypothetical

5709

protein [Oryza sativa]

717
2082
Similar to gi|2660676|gb|AAC79147.1| Dreg-2 like
4370, 4369,
5030

protein [Arabidopsis thaliana]
4368

587

Similar to gi|9294227|dbj|BAB02129.1| P-glycoprotein;
3365, 4159,
4964
5312

multi-drug resistance related; ABC transporter-like
2769, 3364,

protein [Arabidopsis thaliana]
4496, 4497,

2809, 2768,

3269, 4580,

3271, 4530,

4158, 3295,

3109, 2932,

2707

652
2029
Similar to gi|5051937|gb|AAD38371.1| MADS-box

5226
5837

protein FDRMADS2 [Oryza sativa]

630

Similar to gi|9279658|dbj|BAB01174.1|
3131

emb|CAA18710.1˜gene_id: MIE15.3˜strong similarity

to unknown protein [Arabidopsis thaliana]

726
2090
Similar to PRO2_MAIZE P35082 ZEA MAYS
3941, 4030,
4792
5514

(MAIZE). PROFILIN 2.
3940, 4665

478
1927
Similar to gi|4038491|emb|CAA10482.1| poly(ADP-

ribose) polymerase [Arabidopsis thaliana]

576

Similar to 4CL1_SOYBN P31686 GLYCINE MAX
3996, 3993
5092
5594

(SOYBEAN). 4-COUMARATE--COA LIGASE 1 (EC

6.2.1.12) (4CL) (CLONE 4CL14)(FRAGMENT).

708
2073
Similar to gi|6630873|gb|AAF19609.1|AF182953_1

4926

Surfeit 1 [Arabidopsis thaliana]

657

Similar to gi|6715648|gb|AAF26475.1|AC007323_16

4921

T25K16.5 [Arabidopsis thaliana]

586
2001
Similar to gi|5931661|emb|CAB56584.1| squamosa
2988

5529

(promoter binding protein-like 4 [Arabidopsis thaliana]

588

Similar to gi|5903086|gb|AAD55644.1|AC008017_17
2797, 2705,
4777
5867

ACE [Arabidopsis thaliana]
2706, 3008

538
1971
Similar to gi|3785995|gb|AAC67341.1| unknown
2808, 2825,

protein [Arabidopsis thaliana]
2833

582
1999
Similar to gi|7486938|pir||T00395 hypothetical protein

T13E15.1 - Arabidopsis thaliana (fragment)

672
2039
“““ Similar to gi|7269834|emb|CAB79694.1| beta-1, 3-

glucanase-like protein [Arabidopsis thaliana] ”””

580

Similar to gi|4544386|gb|AAD22296.1|AC007047_5

5680

putative CDC21 protein [Arabidopsis thaliana]

691
2056
Similar to gi|4096103|gb|AAD10483.1| p34cdc2
3035, 3092,

5818

[Triticum aestivum]
2839, 3431,

3282, 4407,

2957, 3288,

4153, 4154,

4408

605
2012
Similar to gi|3834307|gb|AAC83023.1|Strong
3314, 3927,
4788

similarity to gene T10I14.120 gi|2832679 putative
3929, 3928

protein from Arabidopsis thaliana BAC gb|AL021712.

ESTs gb|N65887 and gb|N65627 come from this gene.

555
1983
Similar to gi|5725522|gb|AAD48088.1| replication
3132, 3283

5272

origin activator 4 [Zea mays]

634
2023
Similar to gi|7801686|emb|CAB91606.1| transporter-

4992

like protein [Arabidopsis thaliana]

632

Similar to gi|3080448|emb|CAA18765.1| putative
2831

protein [Arabidopsis thaliana]

Similar to gi|4218115|emb|CAA22969.1| putative

protein [Arabidopsis thaliana]

578
1996
Similar to gi|7270014|emb|CAB79830.1| kinase
4650

binding protein-like [Arabidopsis thaliana]

669

Similar to gi|5931645|emb|CAB56576.1|squamosa

promoter binding protein-like 2 [Arabidopsis thaliana]

598
2008
Similar to gi|6017111|gb|AAF01594.1|AC009895_15
3425

5244

unknown protein [Arabidopsis thaliana]

654
2030
Similar to CSR2_RAT Q62908 RATTUS

5774

NORVEGICUS
(RAT). SMOOTH MUSCLE CELL

LIM PROTEIN (CYSTEINE-RICH PROTEIN 2)

(CRP2).

698
2063
Similar to KDSA_CHLTR P77849 CHLAMYDIA
2826, 3039

TRACHOMATIS
. 2-DEHYDRO-3-

DEOXYPHOSPHOOCTONATE ALDOLASE (EC

4.1.2.16) (PHOSPHO-2-DEHYDRO-3-

DEOXYOCTONATE ALDOLASE) (3-DEOXY-D-

MANNO-OCTULOSONIC ACID8-PHOSPHATE

SYNTHETASE) (KDO 8-P SYNTHASE).

674
2041
Similar to IFEA_ASCSU P23730 ASCARIS SUUM
3327, 3326,

5233

(PIG ROUNDWORM) (ASCARIS
3325

LUMBRICOIDES
). INTERMEDIATE FILAMENT

PROTEIN A (IF-A) (FRAGMENT).

703
2068
Similar to SUBT_BACS9 P28842 BACILLUS SP.

(STRAIN TA39). SUBTILISIN PRECURSOR (EC

3.4.21.62).

554
1982
Similar to SYT3_MOUSE O35681 MUS MUSCULUS
3052, 4663,

5626

(MOUSE). SYNAPTOTAGMIN III (SYTIII).
3546, 4662,

4637, 3547,

4297, 4306,

3556, 3434,

4296, 3433,

4305, 3545

707
2072
Similar to VT3A_CAPVI P18387 CAPRIPOXVIRUS

(STRAIN INS-1). PROTEIN T3A.

682

Similar to YZ06_MYCTU Q10540

5154
5789

MYCOBACTERIUM TUBERCULOSIS
.

HYPOTHETICAL 43.6 KD PROTEIN CY31.06C.

603
2011
Similar to gi|7269674|emb|CAB79622.1| putative
3273

protein [Arabidopsis thaliana]

716
2081
Similar to gi|3912930|gb|AAC78714.1| hypothetical

5838

protein [Arabidopsis thaliana]

627
2020
Similar to gi|3080363|emb|CAA18620.1| puatative
3416, 3415
5071

protein [Arabidopsis thaliana]

597

Similar to gi|4263047|gb|AAD15316.1| hypothetical
2818

protein [Arabidopsis thaliana]

700
2065
Similar to gi|2935575|gb|AAC32818.1| KNOX class
3686, 3685,
5127
5412

homeodomain protein [Oryza sativa]
3683, 3687,

3684

645
2027
Similar to gi|3142292|gb|AAC16743.1| Contains
4595
5133
5620

similarity to tetratricopeptide repeat protein gb|U46571

from homo sapiens. EST gb|Z47802 and gb|Z48402

come from this gene. [Arabidopsis thaliana]

619
2016
Similar to gi|5852183|emb|CAB55421.1| zhb0013.1

5771

[Oryza sativa]

507
1947
Similar to gi|7485636|pir||T00886 hypothetical protein

F17K2.26 - Arabidopsis thaliana

710
2075
Similar to gi|3688170|emb|CAA21198.1| putative
4547, 4546,
5089
5641

protein [Arabidopsis thaliana]
4014, 4013

502
1943
Similar to gi|1172441|sp|Q04088|PF21_ARATH

POSSIBLE TRANSCRIPTION FACTOR POSF21

532
1965
Similar to gi|8927660|gb|AAF82151.1|AC034256_15
2767, 2766
4839

Contains similarity to an unknown protein T21F11.5

gi|6730725 from Arabidopsis thaliana BAC T21F11

gb|AC018849 and contains a Ribosomal Protein S15

PF|00312 domain.

543
1974
Similar to SCII_CHICK Q90988 GALLUS GALLUS
4112, 4111

(CHICKEN). CHROMOSOME SCAFFOLD

PROTEIN SCII.

540

Similar to gi|4885026|gb|AAD31926.1|AF147738_1
3082, 4288

5287

myosin VIII ZMM3 [Zea mays]

504
1945
Similar to RB46_HUMAN Q16576 HOMO SAPIENS

4963
5402

(HUMAN). HISTONE ACETYLTRANSFERASE

TYPE B SUBUNIT 2 (RETINOBLASTOMA

BINDINGPROTEIN P46).

665
2035
Similar to gi|3193331|gb|AAC19313.1| F6N15.22 gene

4971
5592

product [Arabidopsis thaliana]

692
2057
Similar to gi|4567265|gb|AAD23678.1|AC006841_7
2740, 2739,

5343

putative kinesin heavy chain [Arabidopsis thaliana]
3476, 3475,

3113, 3089

625
2019
Similar to gi|9294284|dbj|BAB02186.1| vacuolar ATP

synthase subunit AC39 [Arabidopsis thaliana]

671
2038
Similar to gi|8809704|dbj|BAA97245.1| contains

similarity to unknown

protein˜emb|CAA22897.1˜gene_id: MQM1.18

[Arabidopsis thaliana]

626

Similar to gi|6862912|gb|AAF30301.1|AC018907_1
4679
5201
5439

unknown protein [Arabidopsis thaliana]

571

Similar to gi|6692677|gb|AAF24811.1|AC007592_4
4686

F12K11.7 [Arabidopsis thaliana]

557

Similar to gi|5262166|emb|CAB45809.1| putative
3236, 4591,

serine proteinase [Arabidopsis thaliana]
4590

556

Similar to gi|1816588|gb|AAC50021.1| LON2 [Zea
2902, 3045

5881

mays
]

566
1989
Similar to gi|2244894|emb|CAB10316.1| lupeol

5132

synthase like protein [Arabidopsis thaliana]

466

Similar to P5CS_CAEEL P54889
3317, 3278
4888
5797

CAENORHABDITIS ELEGANS
: PROBABLE

DELTA 1-PYRROLINE-5-CARBOXYLATE

SYNTHETASE (P5CS) (CONTAINS: GLUTAMATE

5-KINASE (EC 2.7.2.11) (GAMMA-GLUTAMYL

KINASE) (GK)/GAMMA-GLUTAMYL

PHOSPHATE REDUCTASE (GPR) (EC 1.2.1.41)

(GLUTAMATE-5-S

660
2033
“““ Similar to KITH_RAT P27158 RATTUS
4023, 4022
4877

NORVEGICUS
(RAT). THYMIDINE KINASE,

CYTOSOLIC (EC 2.7.1.21) (FRAGMENT). ”””

527
1960
Similar to NODH_RHITR P52994 RHIZOBIUM
3266, 3448,
5007
5467

TROPICI
. NODULATION PROTEIN H (EC 2.8.2.-).
2823

542
1973
Similar to SKIW_HUMAN Q15477 Q12902 O15005
3386, 3385
5031
5888

Q15476 HOMO SAPIENS (HUMAN). HELICASE

SKI2W (HELICASE-LIKE PROTEIN HLP).

624
2018
Similar to UBPX_CAEEL P34547
3048, 3046,

5807

CAENORHABDITIS ELEGANS
. PROBABLE
3047, 3861,

UBIQUITIN CARBOXYL-TERMINAL
3863, 3862

HYDROLASE R10E11.3 (EC 3.1.2.15)(UBIQUITIN

THIOLESTERASE) (UBIQUITIN-SPECIFIC

PROCESSING PROTEASE)(DEUBIQUITINATING

ENZYME).

541

Similar to gi|3913525|sp|O48901|DPOD_SOYBN

5903

DNA POLYMERASE DELTA CATALYTIC CHAIN

546
1976
“““ Similar to gi|8493583|gb|AAF75806.1|AC011000_9
3375, 3374

Contains strong similarity to CLV1 receptor kinase

from Arabidopsis thaliana gb|U96879, and contains a

Eukaryotic Kinase PF|00069 domain and multiple

Leucine Rich Repeats PF|00560. ”””

562
1985
Similar to gi|6523034|emb|CAB62302.1| receptor
4627

5241

protein kinase-like protein [Arabidopsis thaliana]

600

Similar to gi|7263554|emb|CAB81591.1| putative

5742

protein [Arabidopsis thaliana]

607

Similar to gi|3738319|gb|AAC63660.1| hypothetical
2842
5125

protein [Arabidopsis thaliana]

515

Similar to gi|4406763|gb|AAD20074.1| unknown

4845
5538

protein [Arabidopsis thaliana]

667

Similar to gi|7573319|emb|CAB87637.1| cinnamoyl
4329, 3094

5475

CoA reductase-like protein [Arabidopsis thaliana]

637
2024
Similar to gi|2583126|gb|AAB82635.1| putative
3105

RAD51C-like DNA repair protein [Arabidopsis

thaliana
]

568
1991
Similar to gi|2583120|gb|AAB82629.1| putative
3118, 3471

5922

receptor-like protein kinase [Arabidopsis thaliana]

519
1952
Similar to gi|4584352|gb|AAD25146.1|AC006420_1

putative retroelement pol polyprotein [Arabidopsis

thaliana
]

666

Similar to gi|4337210|gb|AAD18124.1| unknown

protein [Arabidopsis thaliana]

644
2026
Similar to gi|4337206|gb|AAD18120.1| putative

replication protein A1 [Arabidopsis thaliana]

647

Similar to gi|3757522|gb|AAC64224.1| putative
3363
5008
5601

splicing factor [Arabidopsis thaliana]

528
1961
Similar to gi|6850858|emb|CAB71097.1| putative
3478, 4584,

5908

protein [Arabidopsis thaliana]
3148

558

Similar to gi|7485434|pir||T02536 hypothetical protein
4470, 2893
4768
5750

F13M22.20 - Arabidopsis thaliana

604

Similar to gi|7485872|pir||T00952 hypothetical protein

F20D22.2 - Arabidopsis thaliana

537
1970
Similar to gi|4006911|emb|CAB16841.1| trichohyalin
4472, 4471,
5032

like protein [Arabidopsis thaliana]
3186, 3185,

4485, 3187

572

Similar to gi|6681327|gb|AAF23244.1|AC015985_2
3957
4928

putative phosphatidylinositol-4-phosphate 5-kinase

[Arabidopsis thaliana]

570

Similar to gi|7021723|gb|AAF35404.1| hypothetical
3062, 4376,

protein [Arabidopsis thaliana]
3103, 4375

696
2061
Similar to gi|6562267|emb|CAB62637.1| putative
2739, 2740,

5512

protein [Arabidopsis thaliana]
4181, 4398,

4180

595
2006
Similar to gi|6862936|gb|AAF30324.1|AC019018_2
3901, 3902,

unknown protein [Arabidopsis thaliana]
3903

506

Similar to gi|6751691|gb|AAF27674.1|AC018908_13

unknown protein [Arabidopsis thaliana]

498

Similar to gi|2462753|gb|AAB71972.1| putative
2714

polygalacturonase [Arabidopsis thaliana]

484
1931
Similar to gi|5932543|gb|AAD56998.1|AC009465_12
2929, 3466

putative mitogen activated protein kinase kinase

[Arabidopsis thaliana]

475

Similar to gi|1149569|emb|CAA90703.1| HD-zip
4432
4997
5237

[Arabidopsis thaliana]

491
1935
Similar to gi|4107009|dbj|BAA36298.1| OSK1 [Oryza
3050
4930

sativa
]

560

Similar to gi|8570051|dbj|BAA96756.1| Similar to

Drosophila melanogaster
shuttle craft protein (U09306)

[Oryza sativa]

467
1920
Similar to gi|4249575|dbj|BAA74947.1| thymidylate

synthase [Oryza sativa]

715
2080
“““ Similar to gi|9049453|dbj|BAA99418.1| contains

ESTs AU090583(S3043), D40865(S3043)˜unknown

protein [Oryza sativa] ”””

643

Similar to CTPT_PLAFK P49587 PLASMODIUM

4770
5447

FALCIPARUM
(ISOLATE K1/THAILAND).

CHOLINEPHOSPHATE

CYTIDYLYLTRANSFERASE (EC 2.7.7.15)

(PHOSPHORYLCHOLINETRANSFERASE) (CT).

677
2044
Similar to MDM2_MOUSE P23804 Q64330 Q61040
3207, 3206

MUS MUSCULUS
(MOUSE). MDM2 PROTEIN

(P53-ASSOCIATED PROTEIN).

704
2069
“““ Similar to LIPG_CANFA P80035 O02857 CANIS
3234

FAMILIARIS
(DOG). TRIACYLGLYCEROL

LIPASE PRECURSOR (EC 3.1.1.3) (LIPASE,

GASTRIC). ”””

495
1937
Similar to PMS2_MOUSE P54279 MUS MUSCULUS

4863

(MOUSE). PMS1 PROTEIN HOMOLOG 2 (DNA

MISMATCH REPAIR PROTEIN PMS2).

611

Similar to PCP1_MOUSE P20943 MUS MUSCULUS
4693, 4692,
5134

(MOUSE). PURKINJE CELL PROTEIN 1 (PROTEIN
3225

PCD-6) (FRAGMENT).

725
2089
“““ Similar to T2FB_HUMAN P13984 HOMO
4488, 4487,
5213

SAPIENS
(HUMAN). TRANSCRIPTION
4486

INITIATION FACTOR IIF, BETA SUBUNIT (TFIIF-

BETA)(TRANSCRIPTION INITIATION FACTOR

RAP30). ”””

697
2062
Similar to TRF1_HUMAN P54274 HOMO SAPIENS

(HUMAN). TELOMERIC REPEAT BINDING

FACTOR 1.

477

Similar to YE0K_SCHPO O13816

5081
5712

SCHIZOSACCHAROMYCES POMBE
(FISSION

YEAST). HYPOTHETICAL PROTEIN C17H9.20 IN

CHROMOSOME I (FRAGMENT).

525
1958
Similar to YCB6_PSEDE P29939 PSEUDOMONAS

DENITRIFICANS
. HYPOTHETICAL 15.0 KD

PROTEIN IN COBO 3 REGION (ORF6).

479
1928
Similar to gi|4510342|gb|AAD21431.1| putative protein
3381, 3228,
5144

kinase [Arabidopsis thaliana]
3949, 3380,

3456, 3948,

2856, 3165

633
2022
Similar to gi|6714278|gb|AAF25974.1|AC017118_11

4874
5375

F6N18.17 [Arabidopsis thaliana]

617

Similar to gi|3738297|gb|AAC63639.1| unknown

5503

protein [Arabidopsis thaliana]

510

Similar to gi|7486478|pir||T00684 hypothetical protein
3740

5842

F6E13.17 - Arabidopsis thaliana

485
1932
Similar to gi|7435675|pir||T01351 subtilisin-like

5684

proteinase homolog F6N15.3 - Arabidopsis thaliana

476

Similar to gi|4220529|emb|CAA23002.1| putative

protein [Arabidopsis thaliana]

501
1942
Similar to gi|7269445|emb|CAB79449.1| predicted

5034

protein destination factor [Arabidopsis thaliana]

471
1923
Similar to gi|5732072|gb|AAD48971.1|AF162444_3
2921, 3112,
4855

contains similarity to glucan synthases [Arabidopsis
2908, 3243,

thaliana
]
2979

545
1975
Similar to gi|7267253|emb|CAB81036.1| putative WD-
3010

repeat membrane protein [Arabidopsis thaliana]

500
1941
Similar to gi|5902378|gb|AAD55480.1|AC009322_20

5586

Unknown protein [Arabidopsis thaliana]

469

Similar to gi|5103819|gb|AAD39649.1|AC007591_14
2998, 2997

5321

EST gb|H77143 comes from this gene. [Arabidopsis

thaliana
]

486
1933
Similar to gi|6006864|gb|AAF00640.1|AC009540_17

5648

hypothetical protein [Arabidopsis thaliana]

474
1926
Similar to gi|3093294|emb|CAA73320.1|putative villin
3992
4991

[Arabidopsis thaliana]

561

Similar to AC15_MOUSE P35601 MUS MUSCULUS
2938

(MOUSE). ACTIVATOR 1 140 KD SUBUNIT

(REPLICATION FACTOR C LARGE SUBUNIT)

(A1140 KD SUBUNIT) (RF-C 140 KD SUBUNIT)

(ACTIVATOR 1 LARGE SUBUNIT)(A1-P145)

(DIFFERENTIATION SPECIFIC ELEMENT

BINDING PROTEIN)(ISRE-BINDIN

613

Similar to CAP_SCHPO P36621

5394

SCHIZOSACCHAROMYCES POMBE
(FISSION

YEAST). ADENYLYL CYCLASE-ASSOCIATED

PROTEIN (CAP).

760

Similar to CAP_YEAST P17555

5328

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). ADENYLYL CYCLASE-ASSOCIATED

PROTEIN (CAP).

714
2079
Similar to DPA4_BPT4 P04526 BACTERIOPHAGE
4184, 4185,
5076

T4. DNA POLYMERASE ACCESSORY PROTEIN
4186

44 (PROTEIN GP44).

470
1922
Similar to GDS1_BOVIN Q04173 BOS TAURUS
3455, 3257,

(BOVINE). RAP1 GTPASE-GDP DISSOCIATION
3454

STIMULATOR 1 (SMG P21 STIMULATORY

GDP/GTPEXCHANGE PROTEIN) (SMG GDS

PROTEIN).

523
1956
“““ Similar to HA15_MOUSE P06339 MUS

MUSCULUS
(MOUSE). H-2 CLASS I

HISTOCOMPATIBILITY ANTIGEN, D-37 ALPHA

CHAIN PRECURSOR. ”””

489

Similar to GRK5_RAT Q62833 RATTUS
3228, 3381,
4876
5261

NORVEGICUS
(RAT). G PROTEIN-COUPLED
3949, 3165,

RECEPTOR KINASE GRK5 (EC 2.7.1.-).
2856, 3948,

3947, 3380

724
2088
Similar to MTBS_BPSPR P00476 BACTERIOPHAGE

SPR. MODIFICATION METHYLASE BSU SPRI (EC

2.1.1.73) (CYTOSINE-

SPECIFICMETHYLTRANSFERASE BSU SPRI)

(M. SPRI).

593
2005
Similar to OLED_STRAT Q53685 STREPTOMYCES

4891
5737

ANTIBIOTICUS
. OLEANDOMYCIN

GLYCOSYLTRANSFERASE (EC 2.4.1.-).

653

Similar to NFI_ECOLI P32679 ESCHERICHIA COLI.

ENDONUCLEASE V (EC 3.1.-.-) (DEOXYINOSINE

3 ENDONUCLEASE).

618

Similar to PAN1_RAT P21676 RATTUS
3398

NORVEGICUS
(RAT). TRANSCRIPTIONAL

REGULATORY PROTEIN PAN-1 (FRAGMENT).

564
1987
Similar to RBTR_KLEAE P07760 KLEBSIELLA

5696

AEROGENES
. RIBITOL (RBT) OPERON

REPRESSOR.

687

Similar to YCGN_ECOLI P76005 ESCHERICHIA

COLI
. HYPOTHETICAL 18.6 KD PROTEIN IN

MINC-SHEA INTERGENIC REGION.

662

Similar to YJO5_YEAST P47008

5382

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). HYPOTHETICAL 34.4 KD PROTEIN IN

IDS2-MPI2 INTERGENIC REGION.

684
2050
Similar to ATH1_ARATH P48731 ARABIDOPSIS

5469

THALIANA
(MOUSE-EAR CRESS). HOMEOBOX

PROTEIN ATH1.

483
1930
Similar to gi|9294575|dbj|BAB02856.1| contains
4536, 2910
4897

similarity to Ac-like

transposase˜gb|AAC61291.1˜gene_id: MFJ20.8

[Arabidopsis thaliana]

480

Similar to gi|8809655|dbj|BAA97206.1| beta-

4875
5554

galactosidase [Arabidopsis thaliana]

685
2051
Similar to gi|4914365|gb|AAD32902.1|AC007289_9

hypothetical protein [Arabidopsis thaliana]

676
2043
Similar to gi|4006876|emb|CAB16794.1| hypothetical
4420, 2952,

5743

protein [Arabidopsis thaliana]
4421

513

Similar to gi|6642679|gb|AAF20259.1|AC015450_20

5354

unknown protein [Arabidopsis thaliana]

768

Similar to gi|6522538|emb|CAB61981.1| putative

protein [Arabidopsis thaliana]

468
1921
Similar to gi|5263313|gb|AAD41415.1|AC007727_4

5782

Contains similarity to gb|U07707 epidermal growth

factor receptor substrate (eps15) from Homo sapiens

and contains 2 PF|00036 EF hand domains. ESTs

gb|T44428 and gb|AA395440 come from this gene.

[Arabidopsis

705
2070
Similar to gi|2443889|gb|AAB71482.1| similar to S-

linalool synthase gp|U58314|1491939 [Arabidopsis

thaliana
]

702
2067
Open Reading Frame OS_ORF000472 HTC002653-

5073
5471

A01.19 FRAME: 1 ORF: 11 LEN: 813

693
2058
Open Reading Frame containing a Sage tag sequence
3275, 4684,

near 3 end OS_ORF002835 ST(F) HTC016439-
4685

A01.22 FRAME: 2 ORF: 25 LEN: 591

651

Open Reading Frame OS_ORF003267 HTC018975-

A01.29 FRAME: −1 ORF: 3 LEN: 729

530
1963
Open Reading Frame OS_ORF003351 HTC019414-

5304

A01.6 FRAME: −1 ORF: 3 LEN: 1146

711
2076
Open Reading Frame containing a Sage tag sequence
4098, 4655,

5310

near 3 end OS_ORF003748 ST(F) HTC021811-
4099

A01.17 FRAME: 3 ORF: 5 LEN: 795

675
2042
Open Reading Frame OS_ORF003935 HTC022845-

A01.8 FRAME: −2 ORF: 3 LEN: 960

516
1949
Open Reading Frame OS_ORF005303 HTC031545-
3218, 3216,
5147
5711

A01.F.6 FRAME: 3 ORF: 2 LEN: 654
3418, 3419,

3417, 3217

492

Open Reading Frame containing a Sage tag sequence
2705, 2706,

5887

near 3 end OS_ORF005327 ST(F) HTC031694-
2797, 3008

A01.R.34 FRAME: 2 ORF: 40 LEN: 765

481
1929
Open Reading Frame OS_ORF005936 HTC035449-
2948
4915
5384

A01.R.36 FRAME: 1 ORF: 20 LEN: 795

548
1978
Open Reading Frame OS_ORF006462 HTC038737-
2835, 2836,

5898

A01.R.26 FRAME: −3 ORF: 4 LEN: 1695
2834

465
1919
Open Reading Frame OS_ORF007748 HTC046412-
4335, 4151,

5391

A01.R.17 FRAME: 3 ORF: 9 LEN: 663
3387, 4152

563
1986
Open Reading Frame OS_ORF008766 HTC052601-

A01.R.17 FRAME: −3 ORF: 5 LEN: 918

517
1950
Open Reading Frame OS_ORF009548 HTC057155-

5422

A01.F.7 FRAME: 3 ORF: 3 LEN: 735

494

Open Reading Frame OS_ORF010156 HTC061467-
3247, 2921,

5307

A01.19 FRAME: 1 ORF: 6 LEN: 690
2804, 2803,

3243, 2802

535
1968
Open Reading Frame OS_ORF010961 HTC067473-

5775

A01.F.46 FRAME: −1 ORF: 2 LEN: 603

473
1925
Open Reading Frame containing a Sage tag sequence
3423, 3308,

5717

near 3 end OS_ORF011018 ST(F) HTC067863-
3422

A01.F.16 FRAME: 3 ORF: 10 LEN: 930

493
1936
Open Reading Frame OS_ORF011099 HTC068383-
4014, 4013
5089
5641

A01.F.28 FRAME: 2 ORF: 3 LEN: 882

706
2071
Open Reading Frame OS_ORF011137 HTC068634-

5500

A01.F.2 FRAME: 1 ORF: 1 LEN: 651

650

Open Reading Frame OS_ORF011630 HTC072195-
3322, 3646,
5014
5306

A01.R.11 FRAME: 1 ORF: 3 LEN: 678
4433, 3642,

3660, 3641,

3539, 3816

599
2009
Open Reading Frame containing a Sage tag sequence
2784

5619

near 3 end OS_ORF012797 ST(F) HTC080541-

A01.F.1 FRAME: −1 ORF: 1 LEN: 732

522
1955
Open Reading Frame OS_ORF013410 ST(R)

HTC085428-A01.F.6 FRAME: 1 ORF: 8 LEN: 501

534
1967
Open Reading Frame OS_ORF013411 ST(R)

HTC085428-A01.F.6 FRAME: 2 ORF: 1 LEN: 534

722
2087
Open Reading Frame containing a Sage tag sequence
3214, 4389,
5096

near 3 end OS_ORF014631 ST(F) HTC094453-
2868, 4390,

A01.F.22 FRAME: 2 ORF: 19 LEN: 546
4388, 2940

496
1938
Open Reading Frame OS_ORF015055 HTC097923-

5102
5313

A01.R.15 FRAME: 2 ORF: 9 LEN: 1218

594

Open Reading Frame containing a Sage tag sequence
4574, 4363,
4827
5537

near 3 end OS_ORF016056 ST(F) HTC105399-A01.5
4362

FRAME: 2 ORF: 2 LEN: 531

490

Open Reading Frame OS_ORF016360 HTC108019-
3484, 4330,

5873

A01.28 FRAME: −2 ORF: 1 LEN: 861
4002, 4001

531
1964
Open Reading Frame OS_ORF017250 HTC114893-

A01.R.22 FRAME: −2 ORF: 4 LEN: 963

699
2064
Open Reading Frame OS_ORF017431 HTC116001-

A01.F.44 FRAME: −3 ORF: 11 LEN: 2058

590
2003
Open Reading Frame OS_ORF018615 HTC124258-
4413, 3465,

5483

A01.R.18 FRAME: 2 ORF: 14 LEN: 960
4414, 4412

694
2059
Open Reading Frame OS_ORF018734 ST(R)

HTC125171-A01.F.33 FRAME: 3 ORF: 21 LEN: 1134

606

Open Reading Frame OS_ORF018897 HTC126208-
3901, 3903,

A01.R.39 FRAME: 1 ORF: 3 LEN: 771
3902

547
1977
Open Reading Frame OS_ORF018926 HTC126702-
4558, 2981,
4895
5634

A01.F.22 FRAME: 2 ORF: 2 LEN: 885
3307, 4204,

2800

686
2052
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF018967 ST(F) HTC127058-

A01.F.21 FRAME: 3 ORF: 7 LEN: 573

565
1988
Open Reading Frame containing a Sage tag sequence
4000
5138
5337

near 3 end OS_ORF019436 ST(F) HTC130824-

A01.R.4 FRAME: −1 ORF: 4 LEN: 552

709
2074
Open Reading Frame OS_ORF019785 HTC133657-

A01.F.8 FRAME: 1 ORF: 3 LEN: 669

581
1998
Open Reading Frame OS_ORF020319 HTC137006-
3074, 3073,

5870

A01.F.12 FRAME: 1 ORF: 2 LEN: 789
2797

620

Open Reading Frame OS_ORF020341 HTC137133-

A01.R.7 FRAME: −1 ORF: 1 LEN: 657

788
2132
Open Reading Frame OS_ORF021355 HTC145457-

A01.R.6 FRAME: 1 ORF: 1 LEN: 663

553

Open Reading Frame OS_ORF021918 HTC150081-
3229, 3412,
4905

A01.F.16 FRAME: 2 ORF: 3 LEN: 654
3411, 2785,

4527, 4528,

4524

[0688]

14

TABLE 8

SEQ ID NOs and corresponding description for Oryza genes which are expressed

in a root-specific manner and further the SEQ ID NOs for the corresponding

homologous sequences found in wheat, banana and maize.

ORF
Promo

Wheat
Bana
Maize

(SEQ
(SEQ

(SEQ
(SEQ
(SEQ

ID)
ID)
Description
ID)
ID)
ID)

Root

838
2164
Similar to gi|6979322|gb|AAF34415.1|AF172282_4

unknown protein [Oryza sativa]

821
2156
Similar to gi|2696223|dbj|BAA23807.1| chitinase

5454

[Oryza sativa]

Similar to gi|1621493|dbj|BAA12902.1| reverse

transcriptase [Oryza sativa]

917
2210
Similar to gi|6539565|dbj|BAA88182.1| EST
4460, 4459,

5832

AU058092(S1536) corresponds to a region of the
4458, 4603

predicted gene.; Similar to presenilin (AC003981)

[Oryza sativa]

Similar to gi|7442171|pir||T04166 thaumatin-like

protein - rice

1013
2269
Similar to gi|312290|emb|CAA46022.1| ORF [Oryza
3997
5095
5879

sativa
]

Similar to gi|902266|emb|CAA60331.1| ORF46 [Zea

mays
]

835
2163
Similar to gi|18782|emb|CAA78030.1| wound-induced

5228
5376

protein [Glycine max]

890

Similar to gi|5139503|emb|CAB45558.1| sucrose-
4354, 3445,
5101
5914

phosphate synthase 1 [Hordeum vulgare]
4352, 4353

907
2205
Similar to C861_ARATH P48422 ARABIDOPSIS
4608, 2911

5599

THALIANA
(MOUSE-EAR CRESS).

CYTOCHROME P450 LXXXVI (EC 1.14.-.-).

946
2224
Similar to PP1_PHAVU P48490 PHASEOLUS
4308, 4504,
5198
5785

VULGARIS
(KIDNEY BEAN) (FRENCH BEAN).
3227, 3070,

SERINE/THREONINE PROTEIN PHOSPHATASE
2821, 3226

PP1 (EC 3.1.3.16).

874
2187
Similar to gi|349211|gb|AAA32894.1| ubiquitin
4634, 4635,
5151
5323

conjugating enzyme
3061, 3401,

3400, 3399,

4167, 4166,

4419, 4418,

4417, 4168,

3066, 3067,

3065, 3059,

3305, 3060,

3192, 3457,

3191, 2738,

4415, 4416

919

Similar to gi|893406|dbj|BAA04612.1| enolase [Oryza
3551, 3063,

5240

sativa
]
3797

Similar to LOX2_ORYSA P29250 ORYZA SATIVA

(RICE). LIPOXYGENASE L-2 (EC 1.13.11.12).

831

Similar to gi|7267519|emb|CAB78002.1| peroxidase C2

5678

precursor like protein [Arabidopsis thaliana]

850
2174
Similar to gi|8927669|gb|AAF82160.1|AC068143_2
4678, 4677

5652

Contains similarity to an acyl-CoA oxidase (ASX2)

mRNA from Arabidopsis thaliana gb|AF057043 and

contains an acyl-CoA oxidase PF|01756 domain.

980

Similar to gi|5042458|gb|AAD38295.1|AC007789_21
4226
5020
5762

putative geranylgeranyl pyrophosphate synthase [Oryza

sativa
]

931

Similar to gi|2129705|pir||S71183 RNA-directed DNA
2928

Polymerase (EC 2.7.7.49) (clone NING8) - Arabidopsis

thaliana
retrotransposon Ta16 (fragment)

820
2155
Similar to gi|1890323|emb|CAA72490.1| peroxidase

ATP29a [Arabidopsis thaliana]

972
2237
Similar to gi|8096589|dbj|BAA96162.1| Similar to

5905

Oryza sativa
bZIP transcriptional activator RF2a

(AF005492)

971
2236
Similar to gi|5360178|gb|AAD42895.1|AF159882_1
4131, 3078,
4848

Cen-like protein FDR2 [Oryza sativa]
4132

903
2202
Similar to gi|533707|gb|AAA67356.1|3-
3764, 4036

5374

methylcrotonyl-CoA carboxylase precursor

973
2238
Similar to gi|4337192|gb|AAD18106.1| unknown

5039
5689

protein [Arabidopsis thaliana]

997
2254
Similar to gi|4972062|emb|CAB43930.1| putative
4024, 2889,
4985
5260

protein [Arabidopsis thaliana]
3931, 3930

912

Similar to gi|6686410|gb|AAF23844.1|AC007234_16
4148, 4149
4846

F1E22.4 [Arabidopsis thaliana]

854
2178
Similar to gi|928925|emb|CAA60516.1| protein kinase
3196, 3251

5808

catalytic domain (fragment) [Arabidopsis thaliana]

807
2147
Similar to gi|2920839|gb|AAC04628.1| Os-FIERG2
3627, 3626

gene product [Oryza sativa]

969

Similar to gi|3264600|gb|AAC24571.1| hypoxically
2696, 2694,

5598

induced transcript 2 [Zea mays]
2695, 3298

893

Similar to COPP_HELPY Q48271 Q48257 O07682
2716, 3233,
4811
5740

HELICOBACTER PYLORI
(CAMPYLOBACTER
2717, 2715,

PYLORI
). COP ASSOCIATED PROTEIN (COPPER
2996, 4670

ION BINDING PROTEIN).

1003
2259
Similar to F4ST_FLACH P52837 FLAVERIA

5710

CHLORAEFOLIA
. FLAVONOL 4 -

SULFOTRANSFERASE (EC 2.8.2.-) (F4-ST).

Similar to gi|5733875|gb|AAD49763.1|AC007932_11

F11A17.11 [Arabidopsis thaliana]

Similar to gi|8920602|gb|AAF81324.1|AC007767_4

F5D14.4 [Arabidopsis thaliana]

950

Similar to gi|5734731|gb|AAD49996.1|AC007259_9

bifunctional nuclease bfh1 [Arabidopsis thaliana]

994
2252
Similar to gi|3549676|emb|CAA20587.1| putative

protein [Arabidopsis thaliana]

1010
2266
Similar to gi|4558683|gb|AAD22700.1|AC006586_9

putative retroelement pol polyprotein [Arabidopsis

thaliana
]

804

Similar to gi|6224924|gb|AAF06016.1|AF194171_1
4331, 2822,
5051

putative serine/threonine kinase [Hordeum vulgare]
3254, 3239

1012
2268
Similar to gi|1755176|gb|AAB51577.1| germin-like
4115, 4075,
5205
5760

protein [Arabidopsis thaliana]
4073, 4575,

4074, 4592,

4593, 4076,

4576

948
2225
Similar to gi|3925235|gb|AAC79955.1| peroxidase K

5120
5640

[Zea mays]

977
2239
Similar to gi|3941500|gb|AAC83626.1| putative

4886
5658

transcription factor [Arabidopsis thaliana]

959
2230
Similar to gi|5042456|gb|AAD38293.1|AC007789_19
3922, 4050
4956
5481

putative pathogenesis related protein [Oryza sativa]

808
2148
Similar to gi|7487384|pir||T13003 hypothetical protein

T24C20.20 - Arabidopsis thaliana

864

Similar to gi|7939506|dbj|BAA95709.1|
3208

gene_id: K1G2.5˜similar to unknown protein

(gb|AAB61497.1) [Arabidopsis thaliana]

1002
2258
Similar to gi|6729546|emb|CAB67631.1| putative
3453, 3452

5498

protein [Arabidopsis thaliana]

960
2231
Similar to gi|6581046|gb|AAF18432.1|AF192261_1

5069
5882

Rar1 [Hordeum vulgare]

928
2215
Similar to gi|6728960|gb|AAF26958.1|AC018363_3
3003, 3351,
4769

unknown protein [Arabidopsis thaliana]
3350, 2990

870
2185
Similar to gi|2245139|emb|CAB10560.1| hypothetical

5440

protein [Arabidopsis thaliana]

915
2209
Similar to KAPC_YEAST P05986
4392, 2905,
5179

SACCHAROMYCES CEREVISIAE
(BAKER S
4695, 3163,

YEAST). CAMP-DEPENDENT PROTEIN KINASE
4694, 2944,

TYPE 3 (EC 2.7.1.37) (PKA 3).
4394, 3263,

3449, 4393,

4080, 3088,

3237, 2754,

2753, 2987

968
2235
Similar to SUHA_RAT P22789 RATTUS

NORVEGICUS
(RAT). ALCOHOL

SULFOTRANSFERASE A (EC 2.8.2.2)

(HYDROXYSTEROIDSULFOTRANSFERASE A)

(STA) (ANDROSTERONE-SULFATING

SULFOTRANSFERASE)(AD-ST) (ST-40).

894
2199
Similar to TPS1_SCHPO P40387

5029

SCHIZOSACCHAROMYCES POMBE
(FISSION

YEAST). ALPHA, ALPHA-TREHALOSE-

PHOSPHATE SYNTHASE (UDP-FORMING) (EC

2.4.1.15)(TREHALOSE-6-PHOSPHATE

SYNTHASE) (UDP-GLUCOSE-

GLUCOSEPHOSPHATEGLUCOSYL-

TRANSFERASE).

987
2246
Similar to YYBP_BACSU P37488 BACILLUS

5688

SUBTILIS
. HYPOTHETICAL 16.0 KD PROTEIN IN

COTF-TETB INTERGENIC REGION.

829

Similar to gi|8885556|dbj|BAA97486.1| zinc
4103, 4102,
5174

transporter [Arabidopsis thaliana]
3286, 3002

983
2242
Similar to gi|8468030|dbj|BAA96630.1| hypothetical

protein [Oryza sativa]

843
2169
Similar to gi|9294101|dbj|BAB01953.1| contains
3813, 3817,
4933
5459

similarity to AAA-type ATPase˜gene_id: T20D4.2
3812

[Arabidopsis thaliana]

Similar to SUI1_SALBA O48650 SALIX BAKKO

(JAPANESE WILLOW). PROTEIN TRANSLATION

FACTOR SUI1 HOMOLOG.

937

Similar to gi|8920562|gb|AAF81284.1|AC027656_1

5227
5703

Contains similarity to LAG1 homolog 1 from

Arabidopsis thaliana
gb|AF198179.

863
2183
Similar to gi|2245131|emb|CAB10552.1| hypothetical
4443, 4442,
5100
5282

protein [Arabidopsis thaliana]
3338, 3337,

3339

914

Similar to gi|3550985|dbj|BAA32704.1| OsS5a [Oryza

4864
5895

sativa
]

891

Similar to gi|4768998|gb|AAD29712.1|AF140499_1
3241, 4326,
5162
5399

chloroplast envelope calcium ATPase precursor [Oryza
3250, 3007,

sativa
]
2885, 2986

828
2160
Similar to gi|4894182|emb|CAB43506.1| 12-
2876, 2742,
4908
5432

oxophytodienoate reductase [Lycopersicon esculentum]
4690, 3223,

3224, 2700,

2701, 4657,

4246, 4247,

4644, 4249,

4656, 4643

836

Similar to gi|230252|pdb|1PI2|Bowman-Birk

Proteinase Inhibitor PI-Ii

Similar to gi|8778336|gb|AAF79344.1|AC007887_3

F15O4.6 [Arabidopsis thaliana]

846
2172
Similar to gi|7487145|pir||T02706 hypothetical protein

5547

T18E12.13 - Arabidopsis thaliana

927
2214
Similar to gi|3152556|gb|AAC17037.1| Contains
4340, 4341,

5556

similarity to S. cerevisiae hypothetical protein
4342

YOR197w, gb|Z75105. [Arabidopsis thaliana]

898
2200
Similar to gi|3687656|gb|AAC62209.1| putative
4356, 4355

5236

ethylene receptor; ERS2 [Arabidopsis thaliana]

817

Similar to PUR2_SALTY P26977 SALMONELLA
3987, 3985,

TYPHIMURIUM
. PHOSPHORIBOSYLAMINE--
3986

GLYCINE LIGASE (EC 6.3.4.13) (GARS)

(GLYCINAMIDERIBONUCLEOTIDE

SYNTHETASE)

(PHOSPHORIBOSYLGLYCINAMIDE

SYNTHETASE).

Similar to RNP_CHESE P04061 CHELYDRA

SERPENTINA
(SNAPPING TURTLE).

RIBONUCLEASE (EC 3.1.27.5).

Similar to gi|9049462|dbj|BAA99427.1| hypothetical

protein [Oryza sativa]

814

Similar to gi|2792202|gb|AAB96976.1| NBS-LRR type

resistance protein [Hordeum vulgare]

995
2253
Similar to gi|2605625|dbj|BAA23341.1| OSMYB5
4463, 3481,
4998
5296

[Oryza sativa]
3482, 4428,

3692, 3694

837

Similar to gi|7340917|dbj|BAA92989.1| ESTs

AU083020(S13622), AU083021(S13622) correspond to

a region of the predicted gene.; hypothetical protein

[Oryza sativa]

909
2207
Similar to gi|6682234|gb|AAF23286.1|AC016661_11
3184, 3183,
4772
5577

putative ankyrin [Arabidopsis thaliana]
4259, 2969

862

Similar to HBPB_ARATH P43273 ARABIDOPSIS
3162, 3450,
4781

THALIANA
(MOUSE-EAR CRESS).
4516

TRANSCRIPTION FACTOR HBP-1B.

857

Similar to gi|4966357|gb|AAD34688.1|AC006341_16
2926, 2925,
4799
5490

> F3O9.16 [Arabidopsis thaliana]
2723, 2924

905

Similar to gi|2262105|gb|AAB63613.1| unknown
3140, 3316,
5128

protein
3139, 3296,

4059, 4058,

4569

934

Similar to gi|5903043|gb|AAD55602.1|AC008016_12

Similar to gb|X80301 auxin-independent growth

promoter (axi 1) from Nicotiana tabacum. EST

gb|AA605466 comes from this gene. [Arabidopsis

thaliana
]

872
2186
Similar to gi|6723432|emb|CAB66925.1| ADP-

4816
5377

RIBOSYLATION FACTOR-like protein [Arabidopsis

thaliana
]

923
2213
Similar to gi|6681341|gb|AAF23258.1|AC015985_16
4542

5591

putative RING zinc finger protein [Arabidopsis

thaliana
]

920
2211
Similar to gi|6911848|emb|CAB72148.1| n-

5298

acetylglucosaminyl-phosphatidylinositol-like protein

[Arabidopsis thaliana]

Similar to gi|1353266|gb|AAB01678.1| Fe(II) transport

protein

855
2179
Similar to MSK_MOUSE Q60670 MUS MUSCULUS
3163, 2905,

(MOUSE). PUTATIVE SERINE/THREONINE-
4694, 3263,

PROTEIN KINASE MSK (EC 2.7.1.-) (HRT-
2944, 4639,

20) (MYOCARDIAL SNF1-LIKE KINASE)
4213, 3088,

(FRAGMENT).
3237, 4392,

3449, 4638

979
2240
Similar to LDHH_RABIT P13490 ORYCTOLAGUS
3057, 3056,
4779
5745

CUNICULUS
(RABBIT). L-LACTATE
2728

DEHYDROGENASE H CHAIN (EC 1.1.1.27) (LDH-

B) (FRAGMENT).

1019

Similar to gi|8885533|dbj|BAA97463.1|
4107, 4106,

5810

gene_id: F17P19.10˜unknown protein [Arabidopsis
4104

thaliana
]

Similar to gi|3786001|gb|AAC67347.1|unknown

protein [Arabidopsis thaliana]

1011
2267
Similar to gi|3928079|gb|AAC79605.1| hypothetical

protein [Arabidopsis thaliana]

884
2196
Similar to gi|5262790|emb|CAB45895.1| carbonic

5773

anhydrase-like protein [Arabidopsis thaliana]

844
2170
Similar to gi|7485276|pir||T08859 hypothetical protein

5265

A_TM017A05.4 - Arabidopsis thaliana

810

Similar to gi|2072727|emb|CAA73170.1| Fd-GOGAT

5460

protein [Oryza sativa]

824
2157
Similar to gi|5672692|dbj|BAA82696.1| nuclease I
3762, 3696

5715

[Hordeum vulgare]

981
2241
Similar to gi|6143866|gb|AAF04413.1|AC010927_6
3803, 3802
5003

hypothetical protein [Arabidopsis thaliana]

830
2161
Similar to GTT1_HUMAN P30711 O00226 HOMO
4465, 4464,
4836

SAPIENS
(HUMAN). GLUTATHIONE S-
4466

TRANSFERASE THETA 1 (EC 2.5.1.18) (CLASS-

THETA).

1009
2265
Similar to gi|6566348|dbj|BAA88269.1| RNA binding
2763
5111
5259

protein [Arabidopsis thaliana]

Similar to RPB8_HUMAN P52434 P53802 HOMO

SAPIENS
(HUMAN). DNA-DIRECTED RNA

POLYMERASES I, II, AND III 17.1 KD

POLYPEPTIDE (EC 2.7.7.6) (RPB17) (RPB8).

989
2248
Similar to VPR2_MOUSE P13373 MUS MUSCULUS

(MOUSE). IMMUNOGLOBULIN OMEGA CHAIN

PRECURSOR (V(PREB)2 PROTEIN).

840
2166
Similar to TPMB_RABIT P02560 ORYCTOLAGUS

CUNICULUS
(RABBIT), MUS MUSCULUS

(MOUSE), AND RATTUS NORVEGICUS (RAT).

TROPOMYOSIN BETA CHAIN, SKELETAL

MUSCLE.

834
2162
Similar to YR81_CAEEL Q09566

5178
5893

CAENORHABDITIS ELEGANS
. HYPOTHETICAL

35.0 KD PROTEIN F48E8.1 IN CHROMOSOME III.

805
2146
Similar to VA5_POLAN Q05109 POLISTES

5178
5893

ANNULARIS
(PAPER WASP). VENOM

ALLERGEN 5 PRECURSOR (ANTIGEN 5) (AG5)

(ALLERGEN POL A 5) (POL AV) (FRAGMENT).

Similar to YGI0_YEAST P53157

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). HYPOTHETICAL 15.0 KD PROTEIN IN

SCY1-DBP3 INTERGENIC REGION.

Similar to gi|8778631|gb|AAF79639.1|AC025416_13

F5O11.20 [Arabidopsis thaliana]

1006
2262
Similar to gi|7487595|pir||T00816 hypothetical protein

T32G6.12 - Arabidopsis thaliana

873

Similar to gi|4314355|gb|AAD15566.1| unknown

4955

protein [Arabidopsis thaliana]

Similar to gi|3201616|gb|AAC20723.1| hypothetical

protein [Arabidopsis thaliana]

984
2243
Similar to gi|2558660|gb|AAB81674.1| unknown

5630

protein [Arabidopsis thaliana]

826
2158
Similar to gi|5823325|gb|AAD53101.1|AF175996_1

4886
5381

putative transcription factor [Arabidopsis thaliana]

986
2245
Similar to gi|6453890|gb|AAF09073.1|AC011663_9

4981
5646

hypothetical protein [Arabidopsis thaliana]

806

Similar to gi|20242|emb|CAA36189.1| GOS9 [Oryza

sativa
]

875
2188
Similar to gi|4056457|gb|AAC98030.1| ESTs

5013
5505

gb|234051 and gb|F13722 come from this gene.

[Arabidopsis thaliana]

868
2184
Similar to gi|5042453|gb|AAD38290.1|AC007789_16
3922, 4050

putative pathogenesis related protein [Oryza sativa]

Similar to gi|7228462|dbj|BAA92422.1| ESTs

AU081576(R0541), AU032412(R4029) correspond to a

region of the predicted gene.; Similar to A. thaliana

mRNA for peroxidase ATP18a. (X98804) [Oryza

sativa
]

954

Similar to gi|5852096|emb|CAB55403.1| zwh19.1

5122
5513

[Oryza sativa]

1016
2272
Similar to HAP5_YEAST Q02516 Q08827
3034, 3988,
5037
5625

SACCHAROMYCES CEREVISIAE
(BAKER S
3344, 3343

YEAST). HAP5 TRANSCRIPTIONAL ACTIVATOR.

Similar to gi|8778406|gb|AAF79414.1|AC068197_24

F16A14.11 [Arabidopsis thaliana]

860
2181
Similar to gi|6729039|gb|AAF27035.1|AC009177_25
4396, 4397,
4866
5353

unknown protein [Arabidopsis thaliana]
4395

996

Similar to gi|6006895|gb|AAF00670.1|AC008153_22
2892

5439

hypothetical protein [Arabidopsis thaliana]

962
2232
Similar to gi|5295986|dbj|BAA81884.1| MADS box-

5225
5545

like protein [Oryza sativa]

974

Similar to gi|9279651|dbj|BAB01151.1| flavonol 3-O-

glucosyltransferase-like protein [Arabidopsis thaliana]

Similar to gi|7670036|dbj|BAA94990.1|

gb|AAD22658.1˜gene_id: K14A17.19˜similar to

unknown protein [Arabidopsis thaliana]

976

Similar to gi|3786011|gb|AAC67357.1| putative RNA-
4645

5273

binding protein [Arabidopsis thaliana]

832

Similar to gi|6503288|gb|AAF14664.1|AC011713_12

Similar to gb|D17443 major intrinsic protein from

Oryza sativa
. EST gb|AI998369 comes from this gene.

[Arabidopsis thaliana]

963

Similar to gi|4204294|gb|AAD10675.1| lcl|prt_seq No
3125, 3123,
4823
5768

definition line found
3124, 3122

1005
2261
Similar to gi|6041850|gb|AAF02159.1|AC009853_19
4537, 4572

unknown protein [Arabidopsis thaliana]

913

Similar to INB1_CAEEL Q09626
3876, 4583,
5028
5924

CAENORHABDITIS ELEGANS
. PROBABLE
4582, 4611

INSULIN-LIKE PEPTIDE BETA-TYPE 1

PRECURSOR.

Similar to VMT2_INBAD P13882 INFLUENZA B

VIRUS (STRAIN B/ANN ARBOR/1/66 [WILD-

TYPE]). PROBABLE MATRIX (M2) PROTEIN.

1007
2263
Similar to gi|6227004|gb|AAF06040.1|AC009360_5

F16G16.5 [Arabidopsis thaliana]

910
2208
Similar to gi|6409176|gb|AAF07875.1| nitrate
3451, 4444,
5143

transporter [Oryza sativa]
2778

896

Similar to gi|2300156|emb|CAA02837.1| unnamed
3081, 4706,
5084
5814

protein product [Arabidopsis thaliana]
4707, 2982,

4708, 2900,

4492, 4491,

2792, 2791,

4490

943
2222
Similar to gi|7573456|emb|CAB87770.1| putative
3072, 3071
5055
5729

protein [Arabidopsis thaliana]

867

Similar to gi|3258570|gb|AAC24380.1| Unknown
3358, 3357

protein [Arabidopsis thaliana]

940
2220
Similar to gi|6562002|emb|CAB62491.1| hypothetical

5455

protein [Arabidopsis thaliana]

878
2191
Similar to gi|1871177|gb|AAB63537.1| unknown

4873
5342

protein [Arabidopsis thaliana]

1014
2270
Similar to gi|2065013|emb|CAA72363.1| cyclic
2755
5009
5886

phosphodiesterase [Arabidopsis thaliana]

947

Similar to gi|3687230|gb|AAC62128.1| unknown

4990

protein [Arabidopsis thaliana]

818
2153
Similar to gi|6689924|gb|AAF23902.1|AF194415_1
3107, 2787,

5501

MAP kinase homolog [Oryza sativa]
3272, 3116

881
2193
Similar to DHCA_RABIT P47844 ORYCTOLAGUS
4027, 3382,

5779

CUNICULUS
(RABBIT). CARBONYL
3383, 4026,

REDUCTASE (NADPH) (EC 1.1.1.184) (NADPH-
3384, 4025,

DEPENDENT CARBONYLREDUCTASE).
3303, 3285,

2955, 3232,

4671, 4585,

2712, 2673

882
2194
Similar to S111_PIG P31950 SUS SCROFA (PIG).
2713, 3419,
5169
5711

CALGIZZARIN (S100C PROTEIN).
3417, 3418,

2937, 3639,

3631, 3633,

4200, 3632,

2936, 3637,

3638, 3629,

3635, 3640,

3216, 3217,

3218, 3636,

3630, 3634,

3628, 4199

869

Similar to NODQ_RHIME P13442 RHIZOBIUM

4843
5283

MELILOTI
. PROBABLE SULFATE ADENYLATE

TRANSFERASE SUBUNIT 1 (EC 2.7.7.4) (ATP-

SULFURYLASE) (MODULATION PROTEIN Q).

801

Similar to PPCK_TRYCR P51058 TRYPANOSOMA
3300, 4461,

CRUZI
. PHOSPHOENOLPYRUVATE
4462

CARBOXYKINASE (ATP), GLYCOSOMAL (EC

4.1.1.49).

941

Similar to gi|9295687|gb|AAF86993.1|AC005292_2
3274
5054
5344

F26F24.2 [Arabidopsis thaliana]

942
2221
Similar to gi|8886993|gb|AAF80653.1|AC012190_9

5116

Similar to a dnaJ-like protein from Arabidopsis

thaliana
gb|Y11969. It contains a DnaJ domain

PF|00226. EST gb|H37613 comes from this gene.

957

Similar to gi|4539295|emb|CAB39598.1| putative

protein [Arabidopsis thaliana]

812

Similar to gi|4741195|emb|CAB41861.1| ABC
3024

transporter-like protein [Arabidopsis thaliana]

865

Similar to gi|4490316|emb|CAB38807.1| nucellin-like

5366

protein [Arabidopsis thaliana]

906
2204
Similar to gi|5732059|gb|AAD48958.1|AF149414_7
3330, 3037,
4865
5645

similar to Pfam families PF00069 (Eukaryotic protein
2681, 3291,

kinase domain; score = 180.8, E = 2.2e−50, N = 2) and
3329, 3292,

PF00036 (EF hand; score = 123.5, E = 4e−33, N = 1)
4431, 2964,

[Arabidopsis thaliana]
2686, 3328,

4621

1018
2274
Similar to gi|6017109|gb|AAF01592.1|AC009895_13
4358, 3198,

5913

hypothetical protein [Arabidopsis thaliana]
3197, 4357,

4359

856

Similar to ALAT_HUMAN P24298 P78398 Q93076

4801
5784

HOMO SAPIENS
(HUMAN). ALANINE

AMINOTRANSFERASE (EC 2.6.1.2) (GLUTAMIC--

PYRUVIC TRANSAMINASE) (GPT) (GLUTAMIC--

ALANINE TRANSAMINASE).

Similar to BST2_HUMAN Q10589 HOMO SAPIENS

(HUMAN). BONE MARROW STROMAL ANTIGEN

2 (BST-2).

Similar to FSHB_MOUSE Q60687 MUS MUSCULUS

(MOUSE). FOLLITROPIN BETA CHAIN

PRECURSOR (FOLLICLE-STIMULATING

HORMONE)(FSH-B).

966

Similar to CP24_MOUSE Q64441 MUS MUSCULUS
4562, 3780,
4856

(MOUSE). CYTOCHROME P450-CC24
4600, 3878,

MITOCHONDRIAL PRECURSOR (EC 1.14.-.-)
3130, 4599,

(P450-CC24) (VITAMIN D(3) 24-HYDROXYLASE)
3080, 3129,

(1,25-DIHYDROXYVITAMIN D(3) 24-
4561, 3781,

HYDROXYLASE) (24-OHASE).
3779, 3142

951
2227
Similar to GUN5_TRIRE P43317 TRICHODERMA
3093, 4139
5118
5288

REESEI
. ENDOGLUCANASE V PRECURSOR (EC

3.2.1.4) (ENDO-1,4-BETA-GLUCANASE

V)(CELLULASE V) (EG V).

904
2203
Similar to KR1_SVVD Q04543 SIMIAN
4212, 4211,

VARICELLA VIRUS (STRAIN DHV)
2832

(CERCOPITHECINE HERPESVIRUS 9).

SERINE/THREONINE-PROTEIN KINASE (EC

2.7.1.-).

Similar to MIH_CARMA Q27225 CARCINUS

MAENAS
(COMMON SHORE CRAB) (GREEN

CRAB). MOLT-INHIBITING HORMONE

PRECURSOR (MIH).

899

Similar to SRA5_CAEEL Q09207
3252, 3461,

CAENORHABDITIS ELEGANS
. SRA-5 PROTEIN.
3460

845
2171
Similar to XYN1_EMENI P55332 Q00173

5561

EMERICELLA NIDULANS
(ASPERGILLUS

NIDULANS
). ENDO-1,4-BETA-XYLANASE 1

PRECURSOR (EC 3.2.1.8) (XYLANASE 1)(1,4-

BETA-D-XYLAN XYLANOHYDROLASE 1).

902

Similar to gi|1313907|dbj|BAA12691.1| CDPK-related
4091, 3182

5758

protein kinase [Zea mays]

851
2175
Similar to gi|8468018|dbj|BAA96618.1| hypothetical

protein [Oryza sativa]

970

Similar to gi|6553889|gb|AAF16555.1|AC012563_8

5072
5635

putative RING zinc finger protein [Arabidopsis

thaliana
]

1004
2260
Similar to gi|7340671|emb|CAB82970.1| putative
2931

5721

protein [Arabidopsis thaliana]

Similar to gi|3063458|gb|AAC14046.1|AAC14046

F22O13.20 [Arabidopsis thaliana]

1001
2257
Similar to gi|4938502|emb|CAB43860.1| putative
4455, 4456,
5093

protein [Arabidopsis thaliana]
4457

918

Similar to gi|7573363|emb|CAB87669.1| putative
4625, 4626

protein [Arabidopsis thaliana]

958
2229
Similar to gi|7527730|gb|AAF63179.1|AC010657_15

T5E21.3 [Arabidopsis thaliana]

975

Similar to gi|6554473|gb|AAF16655.1|AC012394_4
2927, 4090

5528

putative RNA-binding protein [Arabidopsis thaliana]

Similar to ARGC_BACST Q07906 BACILLUS

STEAROTHERMOPHILUS
. N-ACETYL-GAMMA-

GLUTAMYL-PHOSPHATE REDUCTASE (EC

1.2.1.38) (AGPR) (N-ACETYL-GLUTAMATE

SEMIALDEHYDE DEHYDROGENASE) (NAGSA

DEHYDROGENASE)(FRAGMENT).

Similar to SUBT_BACMS P07518 BACILLUS

MESENTERICUS
. SUBTILISIN (EC 3.4.21.62)

(ALKALINE MESENTERICOPEPTIDASE).

Similar to IDH_METJA Q58991

METHANOCOCCUS JANNASCHII
. ISOCITRATE

DEHYDROGENASE (NADP) (EC 1.1.1.42)

(OXALOSUCCINATEDECARBOXYLASE) (IDH)

(NADP+-SPECIFIC ICDH) (IDP).

932

Similar to SYD_RAT P15178 RATTUS

NORVEGICUS
(RAT). ASPARTYL-TRNA

SYNTHETASE (EC 6.1.1.12) (ASPARTATE--TRNA

LIGASE)(ASPRS).

861
2182
Similar to YK56_YEAST P36156

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). HYPOTHETICAL 43.3 KD PROTEIN IN

SIS2-MTD1 INTERGENIC REGION.

853
2177
Similar to gi|2065531|gb|AAC49704.1| endo-1,4-beta-
2917, 3477,

5612

glucanase [Lycopersicon esculentum]
3028

Similar to gi|22347|emb|CAA41447.1| In2-1 [Zea

mays
]

Similar to gi|8778603|gb|AAF79611.1|AC027665_12

F5M15.17 [Arabidopsis thaliana]

949
2226
Similar to gi|2109293|gb|AAB69123.1| serine/threonine
2762, 2708
5087

protein kinase [Arabidopsis thaliana]

827
2159
Similar to gi|9294516|dbj|BAB02778.1| contains

5308

similarity to endo-1,3-1,4-beta-D-

glucanase˜gene_id: MDB19.8 [Arabidopsis thaliana]

998
2255
Similar to gi|8671834|gb|AAF78397.1|AC009273_3

5643

Contains similarity to a putative protein T2J13.100

gi|6522560 from Arabidopsis thaliana BAC T2J13

gb|AL132967.

944

Similar to gi|7658344|gb|AAF66134.1| unknown
4361, 4365,
5057
5335

protein [Arabidopsis thaliana]
4364

847

Similar to gi|4581139|gb|AAD24623.1|AC006919_2
2883, 3252,
4881

putative ABC transporter [Arabidopsis thaliana]
3290, 3230,

3077, 3461,

3460

842
2168
Similar to gi|6478930|gb|AAF14035.1|AC011436_19
3222

5527

unknown protein [Arabidopsis thaliana]

848
2173
Similar to gi|3522943|gb|AAC34225.1| putative ABC
3472, 2719,

transporter [Arabidopsis thaliana]
3365, 3295,

4159, 3109,

4581, 4580,

3364, 4158,

2809, 4496,

4497, 4160,

4530, 2932,

3271, 4529,

3269, 2707

925

Similar to gi|7452467|pir||T00932 hypothetical protein

T24P15.14 - Arabidopsis thaliana

964

Similar to gi|3080398|emb|CAA18718.1| putative

5243

protein [Arabidopsis thaliana]

952

Similar to gi|4467159|emb|CAB37528.1| hypothetical
4169
5171

protein [Arabidopsis thaliana]

967
2234
Similar to gi|6911879|emb|CAB72179.1| hypothetical
4489
4885

protein [Arabidopsis thaliana]

871

Similar to gi|6562261|emb|CAB62631.1| putative
3396, 3394,

5580

protein [Arabidopsis thaliana]
3395

833

Similar to gi|6403490|gb|AAF07830.1|AC010871_6

5331

putative SCO1 protein [Arabidopsis thaliana]

Similar to gi|6573782|gb|AAF17702.1|AC009243_29

F28K19.2 [Arabidopsis thaliana]

815

Similar to gi|5882745|gb|AAD55298.1|AC008263_29
4560

5299

F25A4.24 [Arabidopsis thaliana]

956

Similar to gi|2317901|gb|AAC24365.1| Similar to

4952

vesicle transport protein, PIR Accession Number

A55931 [Arabidopsis thaliana]

939
2219
Similar to gi|3850584|gb|AAC72124.1| ESTs

5159

gb|H37641 and gb|AA651422 come from this gene.

[Arabidopsis thaliana]

Similar to gi|2341032|gb|AAB70432.1| EST

gb|ATTS0956 comes from this gene. [Arabidopsis

thaliana
]

900

Similar to ANAG_HUMAN P54802 HOMO SAPIENS
4313, 4312
5010
5276

(HUMAN). ALPHA-N-

ACETYLGLUCOSAMINIDASE PRECURSOR (EC

3.2.1.50) (N-ACETYL-ALPHA-

GLUCOSAMINIDASE) (NAG).

876
2189
Similar to DP1_HUMAN Q00765 Q04198 HOMO

SAPIENS
(HUMAN). POLYPOSIS LOCUS

PROTEIN 1 (TB2 PROTEIN).

965
2233
Similar to LEPU_BACSU P42959 BACILLUS
4399

SUBTILIS
. SIGNAL PEPTIDASE I U (EC 3.4.21.89)

(SPASE I) (LEADER PEPTIDASE I).

Similar to YR73_ECOLI P21313 ESCHERICHIA

COLI
. HYPOTHETICAL 22.9 KD PROTEIN (ORF3)

(RETRON EC67).

Similar to gi|2062170|gb|AAB63644.1| unknown

protein

892

Similar to gi|7573426|emb|CAB87742.1| putative

4902

protein [Arabidopsis thaliana]

990

Similar to gi|4220531|emb|CAA23004.1| hypothetical

4993

protein [Arabidopsis thaliana]

879

Similar to gi|4538950|emb|CAB39774.1| putative

5002

protein [Arabidopsis thaliana]

889

Similar to gi|2335108|gb|AAC02769.1| putative zinc

protease [Arabidopsis thaliana]

Similar to gi|4006913|emb|CAB16843.1| hypothetical

protein [Arabidopsis thaliana]

825

Similar to gi|6633820|gb|AAF19679.1|AC009519_13
2909

F1N19.20 [Arabidopsis thaliana]

969

Similar to gi|6728988|gb|AAF26986.1|AC018363_31
2696, 2694,

5598

putative aspartyl protease [Arabidopsis thaliana]
2695, 3298

897

Similar to gi|6706418|emb|CAB66104.1| protease-like
3393, 3391,

protein [Arabidopsis thaliana]
3392

938

Similar to gi|433663|emb|CAA82234.1| myosin

[Arabidopsis thaliana]

982

Similar to ARGC_STRCO P54895 STREPTOMYCES

COELICOLOR
. N-ACETYL-GAMMA-GLUTAMYL-

PHOSPHATE REDUCTASE (EC 1.2.1.38) (AGPR)

(N-ACETYL-GLUTAMATE SEMIALDEHYDE

DEHYDROGENASE) (NAGSA

DEHYDROGENASE)(FRAGMENT).

Similar to DEZ_HUMAN Q99788 Q99789 HOMO

SAPIENS
(HUMAN). PROBABLE G PROTEIN-

COUPLED RECEPTOR DEZ.

908
2206
Similar to EPC_HUMAN P01854 HOMO SAPIENS
4640
4996
5526

(HUMAN). IG EPSILON CHAIN C REGION.

922

Similar to HEM1_EMENI P38092 EMERICELLA
2790

NIDULANS
(ASPERGILLUS NIDULANS). 5-

AMINOLEVULINIC ACID SYNTHASE,

MITOCHONDRIAL PRECURSOR (EC

2.3.1.37) (DELTA-AMINOLEVULINATE

SYNTHASE) (DELTA-ALA SYNTHETASE).

813
2151
Similar to LOXP_MOUSE P39655 MUS
3053, 4540,
4826
5578

MUSCULUS
(MOUSE). ARACHIDONATE 12-
3946, 4046,

LIPOXYGENASE, PLATELET-TYPE (EC
4372, 4538,

1.13.11.31) (12-LOX).
4539, 3424,

4373, 4047,

4374, 3945,

4045, 3944

819
2154
Similar to LIG_PHLRA P20010 PHLEBIA RADIATA
3413
5141

(WHITE-ROT FUNGUS). LIGNINASE III

PRECURSOR (EC 1.11.1.-) (LIGNIN

PEROXIDASE).

Similar to MDM2_MESAU Q60524

MESOCRICETUS AURATUS
(GOLDEN

HAMSTER). MDM2 PROTEIN (P53-ASSOCIATED

PROTEIN) (FRAGMENT).

803
2145
Similar to PEPG_LACDL P94869 LACTOBACILLUS

5875

DELBRUECKII
(SUBSP. LACTIS).

AMINOPEPTIDASE G (EC 3.4.22.-).

933

Similar to PPCT_BOVIN P02720 BOS TAURUS
3020, 3021
4999
5868

(BOVINE). PHOSPHATIDYLCHOLINE TRANSFER

PROTEIN (PC-TP).

916

Similar to RGS6_HUMAN P49758 HOMO SAPIENS

(HUMAN). REGULATOR OF G-PROTEIN

SIGNALING 6 (RGS6) (S914) (FRAGMENT).

Similar to SRE1_CRIGR Q60416 CRICETULUS

GRISEUS
(CHINESE HAMSTER). STEROL

REGULATORY ELEMENT BINDING PROTEIN-1

(SREBP-1) (STEROLREGULATORY ELEMENT-

BINDING TRANSCRIPTION FACTOR 1).

992
2250
Similar to UL31_HSVEB P28951 EQUINE

HERPESVIRUS TYPE 1 (STRAIN AB4P) (EHV-1).

GENE 29 PROTEIN.

866

Similar to UBPB_YEAST P36026
3863, 3048,

5806

SACCHAROMYCES CEREVISIAE
(BAKER S
3046, 3861,

YEAST). UBIQUITIN CARBOXYL-TERMINAL
3864

HYDROLASE 11 (EC 3.1.2.15)

(UBIQUITINTHIOLESTERASE 11) (UBIQUITIN-

SPECIFIC PROCESSING PROTEASE

11) (DEUBIQUITINATING ENZYME 11).

849

Similar to TAU_RAT P19332 RATTUS

NORVEGICUS
(RAT). MICROTUBULE-

ASSOCIATED PROTEIN TAU.

887
2198
Similar to UVRA_MYCPN P75176 MYCOPLASMA
3364, 4159,

PNEUMONIAE
. EXCINUCLEASE ABC SUBUNIT A.
3271, 2768,

4496, 4530,

4497, 2707,

3269, 4158,

3472, 4160,

3295

880
2192
Similar to Y05A_BPT4 P39256 BACTERIOPHAGE

T4. HYPOTHETICAL 39.7 KD PROTEIN IN NRDC-

TK INTERGENIC REGION.

911

Similar to XYNA_PSEFL P14768 PSEUDOMONAS

FLUORESCENS
. ENDO-1,4-BETA-XYLANASE A

PRECURSOR (EC 3.2.1.8) (XYLANASE A)(1,4-

BETA-D-XYLAN XYLANOHYDROLASE A)

(XYLA).

953

Similar to YKH1_CAEEL P34269
4176, 4175
5006
5571

CAENORHABDITIS ELEGANS
. HYPOTHETICAL

TYROSINASE-LIKE PROTEIN C02C2.1 IN

CHROMOSOME III.

Similar to YHHW_ECOLI P46852 ESCHERICHIA

COLI
. HYPOTHETICAL 26.3 KD PROTEIN IN

GNTR-GGT INTERGENIC REGION (F231).

Similar to YKQ5_YEAST P36051

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). HYPOTHETICAL 105.7 KD PROTEIN IN

TPK3-PIR1 INTERGENIC REGION.

935
2218
Similar to YIJ4_YEAST P40495
2704, 3150,
5078
5524

SACCHAROMYCES CEREVISIAE
(BAKER S
3151, 2703,

YEAST). HYPOTHETICAL 40.1 KD PROTEIN IN
3149

SGA1-KTR7 INTERGENIC REGION.

929
2216
Similar to YOO1_CAEEL P34633
3348, 3011,
5117

CAENORHABDITIS ELEGANS
. PUTATIVE
2698, 3012,

SERINE/THREONINE-PROTEIN KINASE ZK507.1
2699, 3349,

IN CHROMOSOME III(EC 2.7.1.-).
2697

895

Similar to YWJE_BACSU P45865 BACILLUS
2774, 2775,
4809

SUBTILIS
. HYPOTHETICAL 45.8 KD PROTEIN IN
2773

ACDA-NARI INTERGENIC REGION.

1008
2264
Similar to YZ05_MYCTU Q10539

MYCOBACTERIUM TUBERCULOSIS
.

HYPOTHETICAL 27.5 KD PROTEIN CY31.05.

Similar to gi|9294087|dbj|BAB01939.1|

gene_id: F1M23.14˜unknown protein [Arabidopsis

thaliana
]

978

Similar to gi|5262756|emb|CAB45904.1| putative
3956
5197

protein [Arabidopsis thaliana]

Similar to gi|6016690|gb|AAF01517.1|AC009991_13

unknown protein [Arabidopsis thaliana]

1000
2256
Similar to gi|4204282|gb|AAD10663.1| Hypothetical
3040, 3041

5921

protein [Arabidopsis thaliana]

822

Open Reading Frame OS ORF000020 HTC000072-

A01.16 FRAME: −1 ORF: 18 LEN: 669

883
2195
Open Reading Frame containing a Sage tag sequence

5787

near 3 end OS_ORF001346 ST(F) HTC007682-

A01.16 FRAME: 2 ORF: 9 LEN: 855

930
2217
Open Reading Frame OS_ORF001368 HTC007859-
4514, 4391,
4818
5839

A01.21 FRAME: 1 ORF: 12 LEN: 714
4515, 4377

802
2144
Open Reading Frame OS_ORF002810 ST(R)

4937
5576

HTC016316-A01.6 FRAME: 3 ORF: 3 LEN: 525

926

Open Reading Frame OS_ORF004258 ST(R)

5597

HTC024922-A01.3 FRAME: 3 ORF: 1 LEN: 861

Open Reading Frame OS_ORF004847 ST(R)

HTC028561-A01.R.13 FRAME: 1 ORF: 22 LEN: 501

955
2228
Open Reading Frame OS_ORF005022 ST(R)

HTC029643-A01.4 FRAME: 1 ORF: 1 LEN: 522

809
2149
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF005199 ST(F) HTC030875-

A01.18 FRAME: 2 ORF: 29 LEN: 567

852
2176
Open Reading Frame containing a Sage tag sequence

4878
5291

near 3 end OS_ORF006145 ST(F) HTC036786-

A01.F.12 FRAME: −2 ORF: 1 LEN: 507

Open Reading Frame OS_ORF007113 HTC042559-

A01.R.22 FRAME: −3 ORF: 34 LEN: 822

1015
2271
Open Reading Frame containing a Sage tag sequence

5294

near 3 end OS_ORF008466 ST(F) HTC050935-

A01.R.8 FRAME: −3 ORF: 2 LEN: 504

858
2180
Open Reading Frame OS_ORF008551 HTC051403-
4410, 4411,
5115
5912

A01.F.18 FRAME: 2 ORF: 18 LEN: 897
4021, 4409,

3538, 3514,

3542, 3519,

3541, 4020

921
2212
Open Reading Frame containing a Sage tag sequence
3242, 3320,

5877

near 3 end OS_ORF008787 ST(F) HTC052703-
2844

A01.R.16 FRAME: −1 ORF: 2 LEN: 591

811
2150
Open Reading Frame OS_ORF009745 HTC058532-

A01.R.12 FRAME: 2 ORF: 1 LEN: 732

988
2247
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF009938 ST(F) HTC059864-

A01.F.7 FRAME: −1 ORF: 1 LEN: 573

991
2249
Open Reading Frame OS_ORF010701 HTC065659-

A01.F.9 FRAME: 1 ORF: 24 LEN: 750

823

Open Reading Frame OS_ORF011291 HTC069604-

5250

A01.21 FRAME: −2 ORF: 1 LEN: 963

936

Open Reading Frame OS_ORF012525 HTC078561-

5018
5270

A01.R.14 FRAME: −2 ORF: 29 LEN: 687

1017
2273
Open Reading Frame containing a Sage tag sequence

5744

near 3 end OS_ORF014687 ST(F) HTC094931-

A01.R.16 FRAME: −2 ORF: 8 LEN: 876

886
2197
Open Reading Frame OS_ORF015057 HTC097936-
3493

A01.32 FRAME: 1 ORF: 20 LEN: 1020

816
2152
Open Reading Frame OS_ORF015958 HTC104357-
4673, 4672

A01.R.26 FRAME: −3 ORF: 29 LEN: 1713

885

Open Reading Frame OS_ORF015967 HTC104539-

A01.R.4 FRAME: −2 ORF: 1 LEN: 813

888

Open Reading Frame OS_ORF015975 HTC104583-
2883, 3252,

A01.R.8 FRAME: −1 ORF: 5 LEN: 702
3230, 4429,

3461, 3460

901
2201
Open Reading Frame OS_ORF016116 ST(R)
4334, 3083,

HTC105941-A01.R.24 FRAME: 3 ORF: 11 LEN: 570
3212, 4332,

4333, 2983

999

Open Reading Frame OS_ORF016142 HTC106153-

5242

A01.R.10 FRAME: 3 ORF: 4 LEN: 759

Open Reading Frame OS_ORF016435 ST(R)

HTC108657-A01.F.12 FRAME: 3 ORF: 19 LEN: 573

993
2251
Open Reading Frame OS_ORF016475 HTC108916-

A01.39 FRAME: 2 ORF: 5 LEN: 693

841
2167
Open Reading Frame OS_ORF016483 HTC108992-

A01.F.44 FRAME: 3 ORF: 18 LEN: 2754

924

Open Reading Frame OS_ORF016966 ST(R)

5421

HTC112541-A01.F.22 FRAME: −2 ORF: 4 LEN: 819

Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF017091 ST(F) HTC113530-

A01.R.5 FRAME: −2 ORF: 1 LEN: 531

985
2244
Open Reading Frame OS_ORF018374 HTC122609-

5192

A01.R.13 FRAME: 1 ORF: 5 LEN: 672

Open Reading Frame OS_ORF018673 ST(R)

HTC124756-A01.11 FRAME: 3 ORF: 16 LEN: 555

839
2165
Open Reading Frame OS_ORF020011 HTC135067-

5241

A01.F.24 FRAME: −1 ORF: 27 LEN: 606

961

Open Reading Frame containing a Sage tag sequence

5386

near 3 end OS_ORF021006 ST(F) HTC142475-

A01.F.34 FRAME: −3 ORF: 8 LEN: 969

945
2223
Open Reading Frame containing a Sage tag sequence

5767

near 3 end OS_ORF022122 ST(F) HTC151590-A01.7

FRAME: 1 ORF: 2 LEN: 501

877
2190
Open Reading Frame OS_ORF022130 HTC151702-

A01.R.7 FRAME: 2 ORF: 1 LEN: 765

[0689]

15

TABLE 9

SEQ ID NOs and corresponding description for Oryza genes which are express

in a pollen-specific manner and further the SEQ ID NOs for the corresponding

homologous sequences found in wheat, banana and maize

ORF
Promo

Bana
Maize

(SEQ
(SEQ

Wheat
(SEQ
(SEQ

ID)
ID)
Description
(SEQ ID)
ID)
ID)

Pollen

726
2090
Similar to PRO2_MAIZE P35082 ZEA MAYS
3941, 4030,
4792
5514

(MAIZE). PROFILIN 2.
3940, 4665

725
2089
Similar to T2FB_HUMAN P13984 HOMO SAPIENS
4488, 4487,
5213

(HUMAN). TRANSCRIPTION INITIATION
4486

FACTOR IIF, BETA SUBUNIT (TFIIF-

BETA)(TRANSCRIPTION INITIATION FACTOR

RAP30).

724
2088
Similar to MTBS_BPSPR P00476 BACTERIOPHAGE

SPR. MODIFICATION METHYLASE BSU SPRI (EC

2.1.1.73) (CYTOSINE-

SPECIFICMETHYLTRANSFERASE BSU SPRI)

(M. SPRI).

723

Similar to gi|1778444|gb|AAB40728.1| putative protein
3646, 3322,
4878
5263

kinase PK9 [Arabidopsis thaliana]
4433, 3645,

3643, 3660,

3641, 3642,

3659, 3387,

3539, 2692,

3816, 2793

728

Similar to GAG_GALV P21416 GIBBON APE

LEUKEMIA VIRUS. GAG POLYPROTEIN

(CONTAINS: CORE PROTEINS P15, P12, P30, P10).

Similar to gi|1785758|emb|CAA69842.1| orf153b

[Arabidopsis thaliana]

Similar to P200_MYCPN P75211 MYCOPLASMA

PNEUMONIAE
. PROTEIN P200.

727
2091
Similar to gi|870716|gb|AAA70313.1| Nad3 protein

Similar to YMI9_YEAST Q04502

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). VERY HYPOTHETICAL 14.2 KD

PROTEIN IN RPM2-TUB1 INTERGENIC REGION.

722
2087
Open Reading Frame containing a Sage tag sequence
3214, 4389,
5096

near 3 end OS_ORF014631 ST(F) HTC094453-
2868, 4390,

A01.F.22 FRAME: 2 ORF: 19 LEN: 546
4388, 2940

721
2086
Similar to gi|6728866|gb|AAF26939.1|AC008113_10
3495, 3496

5302

F12A21.21 [Arabidopsis thaliana]

729
2092
Similar to gi|3757513|gb|AAC64215.1| hypothetical

4951
5430

protein [Arabidopsis thaliana]

734

Similar to P24_CRIGR P49020 CRICETULUS
4291, 4290,
4884
5573

GRISEUS
(CHINESE HAMSTER). COP-COATED
4289

VESICLE MEMBRANE PROTEIN P24

PRECURSOR (FRAGMENT).

732
2095
Similar to gi|1841391|dbj|BAA10904.1| EL3 [Oryza

5097

sativa
]

Similar to gi|4775214|emb|CAB42596.1| unnamed

protein product [Arabidopsis thaliana]

Similar to gi|13209|emb|CAA36416.1| ATPase subunit

6 [Oryza sativa]

Similar to gi|870713|gb|AAA70309.1| unknown protein

Similar to gi|4584550|emb|CAB40780.1| hypothetical

protein [Arabidopsis thaliana]

731
2094
Similar to gi|4105160|gb|AAD02278.1| cell wall
3120

5560

invertase Incw3 [Zea mays]

730
2093
Similar to YEZ9_YEAST P39956
2935, 4484
4787

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). PUTATIVE 90.2 KD ZINC FINGER

PROTEIN IN CCA1-ADK2 INTERGENIC REGION.

Similar to gi|13203|emb|CAA37747.1| apocytochrome

b [Oryza sativa]

Similar to gi|13217|emb|CAA34898.1| cytochrome

oxidase subunit 3 (AA 1-265) [Oryza sativa]

736
2097
Similar to gi|6983874|dbj|BAA90809.1| hypothetical

5709

protein [Oryza sativa]

Similar to YM01_MARPO P38450 MARCHANTIA

POLYMORPHA
(LIVERWORT). HYPOTHETICAL

19.2 KD PROTEIN IN RPS2 3 REGION (ORF 168).

Similar to VG67_BPPZA P08386 BACTERIOPHAGE

PZA. EARLY PROTEIN GP16.7.

735

Similar to gi|1890352|emb|CAA62744.1| transcription

4830
5774

factor L2 [Arabidopsis thaliana]

743
2103
Similar to V07K_POPMV Q02122 POPLAR MOSAIC

VIRUS (ISOLATE ATCC PV275) (PMV). 7 KD

PROTEIN.

Similar to YNI1_YEAST P53937

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). PUTATIVE 40S MITOCHONDRIAL

RIBOSOMAL PROTEIN YNL081C.

740
2100
Similar to YKT5_YEAST P36046

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). HYPOTHETICAL 47.4 KD PROTEIN IN

PAS1-MST1 INTERGENIC REGION.

742
2102
Similar to gi|7267309|emb|CAB81091.1| N7-like

4983
5336

protein [Arabidopsis thaliana]

Similar to gi|897624|gb|AAA70274.1| S13 homologous

protein; putative

Similar to gi|3025870|gb|AAC26506.1| ribosomal

protein S4 [Oryza sativa]

Similar to gi|769715|dbj|BAA06819.1| ORF71 [Oryza

sativa
]

Similar to.gi|20382|emb|CAA29825.1| put. ORF 2

[Oryza sativa]

Similar to gi|769719|dbj|BAA06823.1| ORF91 [Oryza

sativa
]

Similar to gi|9294320|dbj|BAB02217.1|

gene_id: K24M9.8˜unknown protein [Arabidopsis

thaliana
]

737
2098
Similar to gi|7339700|dbj|BAA92905.1| hypothetical

protein [Oryza sativa]

Similar to gi|13985|emb|CAA47479.1| NADH-

dehydrogenase subunit 4L [Arabidopsis thaliana]

738

Similar to gi|2924780|gb|AAC04909.1| hypothetical

5555

protein [Arabidopsis thaliana]

739
2099
Similar to HEMA_IAXIA P28731 INFLUENZA A

VIRUS (STRAIN A/XIANFENG/3/89).

HEMAGGLUTININ PRECURSOR (FRAGMENT).

Similar to gi|7340645|emb|CAB82925.1| putative

protein [Arabidopsis thaliana]

Similar to CYB_LATCH O03176 LATIMERIA

CHALUMNAE
(LATIMERIA) (COELACANTH).

CYTOCHROME B (EC 1.10.2.2).

733
2096
Similar to gi|9280660|gb|AAF86529.1|AC002560_22

4923
5428

F21B7.23 [Arabidopsis thaliana]

741
2101
Similar to gi|600446|emb|CAA25566.1| cytochrome C

oxidase polypeptide II [Oryza sativa]

Similar to gi|82643|pir||JQ1447 NADH dehydrogenase

(ubiquinone) (EC 1.6.5.3) chain 5 - wheat

mitochondrion

796
2139
Similar to gi|929918|emb|CAA56786.1| actin-
3810, 3811,
4976
5854

depolymerizing factor [Zea mays]
3558, 3555,

3809, 3814,

3153, 3058,

3553, 3414

Similar to NXL4_BUNMU P15817 BUNGARUS

MULTICINCTUS
(MANY-BANDED KRAIT).

LONG NEUROTOXIN CR1 PRECURSOR (KAPPA

NEUROTOXIN).

750
2107
Similar to gi|8439465|emb|CAB94202.1| GDP
4142, 4501,
5053
5277

dissociation inhibitor [Lycopersicon esculentum]
4500, 3055,

3108, 3054

758

Similar to gi|6692688|gb|AAF24822.1|AC007592_15
2921

F12K11.17 [Arabidopsis thaliana]

795
2138
Similar to ATP0_ORYSA P15998 ORYZA SATIVA

5462

(RICE). ATP SYNTHASE ALPHA CHAIN,

MITOCHONDRIAL (EC 3.6.1.34).

787
2131
Similar to gi|4544420|gb|AAD22329.1|AC006955_15

En/Spm-like transposon protein [Arabidopsis thaliana]

791
2134
Open Reading Frame OS_ORF002847 HTC016575-
4345, 4344,

A01.12 FRAME: 2 ORF: 8 LEN: 1065
4343

788
2132
Open Reading Frame OS_ORF021355 HTC145457-

A01.R.6 FRAME: 1 ORF: 1 LEN: 663

794
2137
Similar to NECD_BOVIN P29554 BOS TAURUS
3983, 3518,

5509

(BOVINE). NEUROCALCIN DELTA.
2914, 3981,

3982, 3984,

2864, 4055,

3517, 3292

764
2114
Similar to gi|8096465|dbj|BAA94532.2| ESTs

5247

D40069(S1808), D40089(S1834), AU083572(S1834)

correspond to a region of the predicted gene. ˜Similar

to Citrus limon vacuolar V − H + ATPase subunit E

(AF165939) [Oryza sativa]

Similar to gi|2522193|gb|AAB80946.1| pyrroline-5-

carboxylate synthetase [Triticum aestivum]

Similar to gi|5688943|dbj|BAA82747.1| ribosomal

protein L5 [Oryza sativa]

789
2133
Similar to ABRA_ABRPR P11140 P28589 ABRUS

PRECATORIUS
(INDIAN LICORICE) (CRAB S

EYE). ABRIN-A PRECURSOR (RRNA N-

GLYCOSIDASE) (EC 3.2.2.22).

Similar to gi|226676|prf||1603356DD NADH

dehydrogenase ND1 [Oryza sativa]

Similar to COX2_MYCTU Q10375

MYCOBACTERIUM TUBERCULOSIS
. PUTATIVE

CYTOCHROME C OXIDASE POLYPEPTIDE II

PRECURSOR (EC 1.9.3.1) (CYTOCHROME AA3

SUBUNIT 2).

Similar to gi|769721|dbj|BAA06825.1| ORF483 [Oryza

sativa
]

770
2116
Similar to LA52_LYCES P13447 LYCOPERSICON

5441

ESCULENTUM
(TOMATO). ANTHER SPECIFIC

LAT52 PROTEIN PRECURSOR.

Similar to gi|5852177|emb|CAB55415.1| zhb0007.1

[Oryza sativa]

Similar to COX2_GEOSD P29657 GEOPHAGUS

STEINDACHNERI
. CYTOCHROME C OXIDASE

POLYPEPTIDE II (EC 1.9.3.1) (FRAGMENT).

769

Similar to RAN_BRARE P79735 BRACHYDANIO

5196
5723

RERIO
(ZEBRAFISH) (ZEBRA DANIO). GTP-

BINDING NUCLEAR PROTEIN RAN.

Similar to YNR1_YEAST P53887

SACCHAROMYCES CEREVISIA
E (BAKER S

YEAST). HYPOTHETICAL 14.6 KD PROTEIN IN

RPS3-PSD1 INTERGENIC REGION.

Similar to gi|7432558|pir||S71457 NADH

dehydrogenase (ubiquinone) (EC 1.6.5.3) chain 6 - rice

mitochondrion (fragment)

792
2135
Similar to gi|9293898|dbj|BAB01801.1| MAP (mitogen
2929, 2806

5350

activated protein) kinase-like protein [Arabidopsis

thaliana
]

Similar to YE66_METJA Q58861

METHANOCOCCUS JANNASCHII
.

HYPOTHETICAL PROTEIN MJ1466.

744
2104
Similar to VGLC_HSVE4 P22596 EQUINE

HERPESVIRUS TYPE 4 (STRAIN 1942) (EHV-4)

(EQUINE HERPESVIRUSTYPE 1 SUBTYPE 2).

GLYCOPROTEIN C PRECURSOR

(GLYCOPROTEIN 13).

Similar to gi|226686|prf||1603356L ORF 70 [Oryza

sativa
]

Similar to gi|7671432|emb|CAB89373.1| putative

protein [Arabidopsis thaliana]

Similar to YM03_MARPO P38452 MARCHANTIA

POLYMORPHA
(LIVERWORT). HYPOTHETICAL

19.3 KD PROTEIN IN RPS2 3 REGION (ORF 169).

760

Similar to CAP_YEAST P17555

5328

SACCHAROMYCES CEREVISIAE
(BAKER S

YEAST). ADENYLYL CYCLASE-ASSOCIATED

PROTEIN (CAP).

Similar to gi|1785731|emb|CAA69844.1| orf240a

[Arabidopsis thaliana]

Similar to gi|2832632|emb|CAA16761.1| hypothetical

protein [Arabidopsis thaliana]

Similar to VA19_VARY P33842 VARIOLA VIRUS.

PROTEIN A19.

756
2112
Similar to YO21_CAEEL P34671

CAENORHABDITIS ELEGANS
. HYPOTHETICAL

18.0 KD PROTEIN ZK688.1 IN CHROMOSOME III.

749
2106
Similar to gi|7446425|pir||T02306 hypothetical protein
2905, 4695,

5820

F13P17.2 - Arabidopsis thaliana
3163, 4694,

2944, 3263,

3449, 4392,

2987

Similar to NU2M_STRPU P15549

STRONGYLOCENTROTUS PURPURATUS

(PURPLE SEA URCHIN). NADH-UBIQUINONE

OXIDOREDUCTASE CHAIN 2 (EC 1.6.5.3).

Similar to gi|1334612|emb|CAA41034.1| nad1

[Triticum aestivum]

800
2143
Similar to gi|4741188|emb|CAB41854.1| hypothetical

4808
5452

protein [Arabidopsis thaliana]

Similar to gi|4106831|gb|AAD03035.1| apocytochrome

b [Solanum tuberosum]

Similar to gi|1173302|sp|P46773|RT03_ORYSA

MITOCHONDRIAL RIBOSOMAL PROTEIN S3

772
2118
Similar to gi|6997198|gb|AAF34860.1| putative

4944
5911

elicitor-responsive gene [Arabidopsis thaliana]

763

Open Reading Frame OS_ORF016189 ST(R)
4476, 4494,

HTC106572-A01.F.20 FRAME: 3 ORF: 2 LEN: 507
2867, 4477,

4475

Similar to gi|7267214|emb|CAB80821.1| putative

transposon protein [Arabidopsis thaliana]

Similar to PHZF_PSEAR Q51517 PSEUDOMONAS

AUREOFACIENS
. PROBABLE PHOSPHO-2-

DEHYDRO-3-DEOXYHEPTONATEALDOLASE

(EC 4.1.2.15)(PHOSPHO-2-KETO-3-

DEOXYHEPTONATE ALDOLASE) (DAHP

SYNTHETASE)(3-DEOXY-D-ARABINO-

HEPTULOSONATE 7-PHOSPHATE SYNTHASE).

482

Similar to gi|5679840|emb|CAB51833.1| 11332.4
3442, 3443,
5106
5613

[Oryza sativa]
3441

759

Similar to gi|6587831|gb|AAF18520.1|AC006551_6

Unknown protein [Arabidopsis thaliana]

Open Reading Frame OS_ORF018289 ST(R)

HTC121977-A01.R.21 FRAME: 1 ORF: 2 LEN: 609

774

Similar to 7B2_HUMAN P05408 P01164 HOMO

SAPIENS
(HUMAN). NEUROENDOCRINE

PROTEIN 7B2 PRECURSOR (SECRETORY

GRANULE ENDOCRINEPROTEIN I)

(SECRETOGRANIN V) (PITUITARY

POLYPEPTIDE).

Similar to gi|1785764|emb|CAA69794.1| orf262

[Arabidopsis thaliana]

Similar to gi|870717|gb|AAA70314.1| ribosomal

protein S12

751
2108
Similar to gi|4680495|gb|AAD27675.1|AF119222_7
3025

receptor kinase-like protein [Oryza sativa]

Similar to gi|1084436|pir||S46439 NADH

dehydrogenase (EC 1.6.99.3) - potato

746

Similar to gi|9229291|dbj|BAA99594.1|

dihydrolipoamide acetyltransferase [Arabidopsis

thaliana
]

784
2129
Similar to gi|4926831|gb|AAD32941.1|AC004135_16
3717, 3730,

T17H7.16 [Arabidopsis thaliana]
3729

Similar to NXSD_LATCO P10456 LATICAUDA

COLUBRINA
(YELLOW-LIPPED SEA KRAIT).

SHORT NEUROTOXTN D.

786
2130
Similar to UL04_HSVEB P28943 EQUINE

HERPES VIRUS TYPE 1 (STRAIN AB4P) (EHV-1).

GENE 58 PROTEIN.

Similar to MAPB_HUMAN P46821 HOMO SAPIENS

(HUMAN). MICROTUBULE-ASSOCIATED

PROTEIN IB.

755
2111
Similar to gi|7529257|emb|CAB86673.1| putative

protein [Arabidopsis thaliana]

Similar to GTH2_CORAU P48251 COREGONUS

AUTUMNALIS
(BAIKAL OMUL).

GONADOTROPIN BETA-H CHAIN PRECURSOR

(GTH-II).

785

Similar to gi|1173087|sp|P46801|RM16_ORYSA

MITOCHONDRIAL 60S RIBOSOMAL PROTEIN

L16

780
2125
Open Reading Frame containing a Sage tag sequence
2862, 2860,

5368

near 3 end OS_ORF001458 ST(F) HTC008279-
2861, 4052,

A01.14 FRAME: −1 ORF: 13 LEN: 537
4053, 4054

766
2115
Similar to gi|4406761|gb|AAD20072.1| putative
4652, 4651
4906
5289

ubiquinone biosynthesis protein [Arabidopsis thaliana]

757
2113
Similar to COPE_CRIGR Q60445 CRICETULUS
2777, 2776
5163
5293

GRISEUS (CHINESE HAMSTER). COATOMER

EPSILON SUBUNIT (EPSILON-COAT PROTEIN)

(EPSILON-COP) (LDLF).

799
2142
Similar to gi|7487633|pir||T02103 hypothetical protein

T3K9.7 - Arabidopsis thaliana

Similar to gi|769717|dbj|BAA06821.1| ORF76B [Oryza

sativa
]

761

Similar to gi|1098977|gb|AAB19030.1| myo-inositol
3027

monophosphatase 1

768

Similar to gi|6522538|emb|CAB61981.1| putative

protein [Arabidopsis thaliana]

747

Similar to gi|6063538|dbj|BAA85398.1| similar to sugar
2683, 2684,

transporter protein. (AL022604) [Oryza sativa]
2685, 3193

Similar to Y706_METJA Q58117

METHANOCOCCUS JANNASCHII
.

HYPOTHETICAL PROTEIN MJ0706.

748
2105
Similar to HMCS_DICDI P54872 DICTYOSTELIUM

5220
5449

DISCOIDEUM
(SLIME MOLD).

HYDROXYMETHYLGLUTARYL-COA

SYNTHASE (EC 4.1.3.5) (HMG-COA

SYNTHASE)(3-HYDROXY-3-

METHYLGLUTARYL COENZYME A SYNTHASE)

(FRAGMENT).

778
2123
Similar to YFEA_ECOLI P23842 ESCHERICHIA

COLI
. HYPOTHETICAL 19.0 KD PROTEIN IN

NUPC-ALAX INTERGENIC REGION.

779
2124
Similar to gi|4467116|emb|CAB37550.1| hypothetical
4162, 4161
5004
5401

protein [Arabidopsis thaliana]

Similar to gi|769718|dbj|BAA06822.1| ORF83 [Oryza

sativa
]

Similar to SCX5_CENNO P45663 CENTRUROIDES

NOXIUS
(MEXICAN SCORPION). TOXIN CNGTII

PRECURSOR.

Similar to E1BS_ADEM1 P12535 MOUSE

ADENO VIRUS TYPE 1 (MAV-1). E1B PROTEIN,

SMALL T-ANTIGEN (E1B 21 KD PROTEIN).

775
2120
Similar to gi|6851021|emb|CAA69741.3| orfX

[Arabidopsis thaliana]

797
2140
Similar to gi|7488710|pir||T08897 ribonuclease H -

soybean copia/Ty1-like retroelement SIRE-1

(fragment)

753
2109
Similar to gi|7487881|pir||T00982 hypothetical protein

T9J22. 16 - Arabidopsis thaliana

Similar to gi|6851012|emb|CAA69763.3| cytochrome c

biogenesis orf452 [Arabidopsis thaliana]

Similar to gi|266533|sp|Q00058|MI25_ORYSA

MITOCHONDRIAL 22 KD PROTEIN (ORF 25)

762

Similar to gi|6648208|gb|AAF21206.1|AC013483_30
4505, 4506,

putative phosphatidylinositol-4-phosphate 5-kinase
2945

[Arabidopsis thaliana]

767

Similar to gi|6437556|gb|AAF08583.1|AC011623_16

4909

unknown protein [Arabidopsis thaliana]

771
2117
Similar to gi|2288981|gb|AAB64310.1| putative Ca2+-

5223
5853

binding protein [Arabidopsis thaliana]

Similar to gi|4544414|gb|AAD22323.1|AC006955_9

hypothetical protein [Arabidopsis thaliana]

754
2110
Similar to YAFD_ECOLI P30865 P75671

ESCHERICHIA COLI
. HYPOTHETICAL 29.1 KD

PROTEIN IN ASPU-MLTD INTERGENIC REGION

(ORF259).

Similar to VL2_HPV51 P26539 HUMAN

PAPILLOMAVIRUS TYPE 51. MINOR CAPSID

PROTEIN L2.

782
2127
Similar to DPOL_VACCV P06856 VACCINIA

VIRUS (STRAIN WR). DNA POLYMERASE (EC

2.7.7.7).

Similar to gi|7486464|pir||T02471 hypothetical protein

F4I18.26 - Arabidopsis thaliana

Similar to gi|769707|dbj|BAA06811.1| ORF72B [Oryza

sativa
]

Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF001179 ST(F) HTC006678-A01.7

FRAME: −3 ORF: 6 LEN: 549

Similar to gi|928898|emb|CAA60524.1| protein kinase

catalytic domain (fragment) [Arabidopsis thaliana]

790

Similar to gi|4006886|emb|CAB16816.1| putative
4285, 4287,
4868

protein [Arabidopsis thaliana]
4286

752

Similar to gi|8096422|dbj|BAA95892.1| EST

D47996(S13901)SS3901_1A corresponds to a region

of the predicted gene. ˜Similar to Zea mays transposon

MuDR mudrA and mudrB genes; mudrA. (M76978)

[Oryza sativa]

773
2119
Similar to gi|7485912|pir||T00888 hypothetical protein

F21B7.2 - Arabidopsis thaliana

745

Similar to gi|4454484|gb|AAD20931.1| putative
3999
4983
5336

diacylglycerol kinase [Arabidopsis thaliana]

Similar to gi|5738367|emb|CAB52824.1| putative

protein [Arabidopsis thaliana]

Similar to gi|4680186|gb|AAD27554.1|AF111709_8

unknown [Oryza sativa subsp. indica]

777
2122
Open Reading Frame containing a Sage tag sequence

5212
5664

near 3 end OS_ORF005018 ST(F) HTC029605-

A01.R.14 FRAME: 2 ORF: 1 LEN: 510

783
2128
Open Reading Frame OS_ORF019510 HTC131468-

A01.F.21 FRAME: −3 ORF: 2 LEN: 741

Similar to gi|7486818|pir||T05789 hypothetical protein

M7J2.50 - Arabidopsis thaliana

781
2126
Open Reading Frame OS_ORF014283 HTC091925-

A01.22 FRAME: −1 ORF: 18 LEN: 930

765

Open Reading Frame OS_ORF008033 ST(R)

5699

HTC048091-A01.R.10 FRAME: −2 ORF: 15 LEN: 573

Similar to gi|133416|sp|P12091|RPOB_ORYSA DNA-

DIRECTED RNA POLYMERASE BETA CHAIN

Similar to gi|7770328|gb|AAF69698.1|AC016041_3

F27J15.7 [Arabidopsis thaliana]

776
2121
Open Reading Frame containing a Sage tag sequence

near 3 end OS_ORF007931 ST(F) HTC047564-

A01.R.36 FRAME: −3 ORF: 7 LEN: 615

Similar to MURC_STAAU O31211

STAPHYLOCOCCUS AUREUS
. UDP-N-

ACETYLMURAMATE--ALANINE LIGASE (EC

6.3.2.8) (UDP-N-ACETYLMURANOYL-L-

ALANINE SYNTHETASE).

793
2136
Open Reading Frame OS_ORF019825 ST(R)

HTC133880-A01.R.8 FRAME: 1 ORF: 6 LEN: 942

798
2141
Open Reading Frame OS_ORF008443 HTC050714-

A01.F.22 FRAME: −2 ORF: 32 LEN: 735

Similar to YCX1_CUSRE P32035 CUSCUTA

REFLEXA
(SOUTHERN ASIAN DODDER).

HYPOTHETICAL 6.8 KD PROTEIN IN TRNL 3

REGION (ORF 55).

[0690]

16

TABLE 10

This table identifies the start and end points

and the nucleotide sequence of trinucleotide repeat units

in the coding sequence of selected ORFs

SeqID
Start
End
Sequence

2
1342
1356
TGC

10
391
408
CGG

11
129
143
CGG

19
842
859
AGG

20
165
188
CGA

21
245
259
GGC

425
439
CGG

26
12
26
GGC

27
265
279
CGC

29
66
80
CGG

1369
1383
GGC

32
388
402
GGT

34
8
22
GCG

483
497
CCT

39
319
333
GAG

526
540
CCG

560
574
ACC

677
694
CCG

40
863
880
AG

41
115
135
GAG

44
151
165
TCC

399
413
CGC

597
611
CGC

958
972
CCG

49
727
744
CG

53
640
654
GCC

55
270
284
GCG

57
18
32
CTC

59
308
322
CCG

341
355
CGT

65
398
415
CCG

68
201
214
CT

83
262
276
CCG

311
328
ACC

359
376
AGC

95
958
972
CCG

96
70
90
GAG

99
639
656
CGG

102
582
596
CCT

103
41
61
ACC

184
198
GCG

104
144
161
CGG

106
360
377
CGG

109
150
170
GGT

112
243
257
ACG

126
485
499
CCG

732
746
CGG

128
651
665
CGG

130
83
98
AG

141
180
194
CGG

144
1436
1456
CCG

146
373
387
TCG

972
986
CCG

154
1227
1241
CCG

157
71
88
AGG

159
524
541
GAC

160
1075
1095
CCG

164
778
795
GTC

168
48
62
CGC

169
5
19
CGG

174
428
451
AGG

177
40
54
GGC

83
103
CGG

719
733
GCG

178
20
34
CGG

182
180
197
ACC

185
21
35
CCG

186
385
399
GCG

188
478
492
CCG

198
66
80
CGG

138
152
TCC

209
332
349
AG

221
253
266
CT

827
841
CGG

223
590
604
CCT

671
685
GCG

237
451
466
CCAT

246
208
231
GCG

249
114
131
CGC

130
144
GCA

253
280
315
AAG

255
40
60
GTC

259
1787
1801
GCG

260
193
207
GGC

422
436
GCG

690
707
AG

915
929
GCC

1777
1791
GAC

261
197
211
GCG

1464
1478
CGG

262
31
48
CAG

284
298
AGC

788
808
AGG

1061
1078
AGC

1485
1499
GCA

265
86
103
CGC

1160
1174
CGG

268
696
710
CGC

274
389
403
CCG

276
119
133
CCG

156
170
CGC

281
61
81
CCG

282
20
37
CCT

283
18
31
CT

286
293
313
CGG

287
201
218
CGG

290
279
293
CGG

291
272
289
GCC

295
80
94
CGG

1214
1231
ACG

311
801
815
AGC

1114
1128
CGG

312
718
732
GTC

316
609
623
CGG

318
567
581
TCG

322
183
197
AGG

323
569
583
GCG

324
487
501
CCG

326
639
653
CGG

329
5
25
CGG

332
418
437
TTAA

336
304
318
CCG

338
51
65
CGG

453
473
ACC

788
805
GCG

342
583
603
TCG

343
353
373
AGC

345
107
121
CCG

351
463
476
GA

561
575
CGG

353
30
44
CGG

192
206
CCT

357
132
158
CGG

359
318
332
CGG

363
146
160
ACG

364
939
959
CGC

365
605
619
CCG

1235
1249
CGG

366
714
729
TC

367
237
251
CGG

368
98
115
CGT

378
127
144
GAG

381
151
165
AGG

383
47
64
CCA

86
100
AGC

172
189
CAG

662
676
CGG

384
316
330
GGC

389
236
253
CGT

380
394
CGG

390
174
188
GCG

391
251
268
GCG

299
313
GCG

393
160
174
CGG

396
51
65
CGG

407
421
ACG

401
110
124
GAG

138
155
AGC

404
73
87
CCT

91
108
AGC

418
33
47
GTC

448
57
74
CCG

2606
2625
AAGC

475
42
56
CGG

479
38
52
GGT

481
166
180
CCG

493
342
356
ACC

494
511
CAC

496
292
306
AGC

502
80
94
CGG

505
148
174
GAG

511
173
187
GCG

517
1534
1551
GGC

518
436
450
AGG

529
1060
1077
GGT

1151
1165
AGG

1310
1324
CCG

1978
1992
AAG

539
11
25
CGG

540
83
100
AGG

546
21
35
GGC

547
18
32
GGC

564
112
126
CCG

145
162
CCG

477
500
CGC

574
146
160
GAG

576
1340
1354
CGA

580
63
80
CGG

584
12
29
CGC

589
276
293
CCG

591
874
888
AGC

594
65
79
CGG

602
500
514
CGG

608
622
CGG

612
3
17
GTC

636
170
184
CGC

643
44
58
AGG

648
98
112
ACC

654
623
637
AAG

658
74
88
AGG

676
256
270
GAG

678
417
431
AGC

680
158
172
AGG

681
613
627
GCT

689
135
150
CGTT

695
1275
1289
AGC

700
572
586
GAG

701
350
364
GCG

514
528
GGT

1107
1124
CGG

1529
1546
CGG

703
114
128
CGG

711
829
843
GAC

716
340
357
GCC

734
24
38
CCT

740
406
426
AAG

449
466
ATG

619
636
AAG

741
592
607
GGAG

742
19
36
CGC

940
957
GAT

777
279
302
CGA

438
461
CGG

791
2264
2281
AGC

797
50
67
CTT

803
88
102
CCG

824
29
43
TCG

826
363
377
ACG

838
59
73
AGC

237
251
ATC

842
233
246
AG

1103
1117
CCG

845
262
279
CGG

417
431
CGG

579
599
CGG

728
748
GCG

851
1206
1220
GCG

875
4
24
GCG

877
268
282
CCG

889
387
404
CGG

895
15
29
CGG

900
36
50
CCT

905
53
67
GCG

911
309
323
CCG

914
717
731
AGC

915
1286
1300
AGC

916
317
334
GCT

671
685
GCG

926
20
34
CCG

38
52
AAG

930
217
234
CCG

933
106
125
AG

940
33
50
CGG

951
768
781
CG

954
608
628
ACC

704
718
GCG

959
663
683
CTG

961
60
77
CGG

975
20
37
CGG

983
457
471
GAG

568
582
ACC

987
34
57
AAC

989
339
353
CGG

995
3298
3315
CCG

998
324
338
GAG

1000
230
247
AGG

371
385
AGG

1004
50
67
ACC

1010
450
463
CG

1013
59
73
CGG

159
179
CGG

1015
279
296
CGG

1017
157
171
GGA

353
370
AGA

1024
70
84
CGG

213
227
ACG

1023
1037
CGG

1026
1851
1866
CGTT

1046
49
66
CAG

1047
1401
1415
CGT

1049
147
161
CGG

3200
3217
CCG

1056
1300
1314
ATG

1062
113
127
AGG

1078
813
827
CGG

1246
1260
GGC

1112
468
482
CGG

1120
345
359
CGG

1130
157
177
GCG

206
220
AGA

1131
371
385
ACG

1133
624
638
CGG

1599
1613
CGG

2219
2236
GCG

1134
1421
1434
CT

1135
524
541
CGC

671
691
AGG

1376
1393
GCG

1137
809
823
ACG

1139
266
280
GTC

1148
563
583
CCA

1150
669
683
CCG

1153
536
550
CTG

1154
458
478
AGG

1159
310
330
GAG

1172
261
281
CGG

932
955
AGC

1178
1765
1779
CCG

2203
2220
CGT

1179
203
220
CCG

1180
38
52
CCT

1184
489
503
GCA

2658
2675
AGC

1220
1298
1315
GCC

1409
1426
ACC

1223
1727
1742
GAAA

1229
41
58
ACC

1233
396
410
CGC

1244
885
899
TGA

1245
213
227
CGG

1260
338
355
CGC

1264
81
95
CCG

1020
1037
CGG

1266
190
205
ATCG

493
513
GGT

1269
38
61
CCT

1271
54
68
CGC

1279
338
358
AGC

1282
248
262
CCG

829
843
GAC

1286
8
28
CCG

71
85
AGG

1287
23
37
ACC

1292
177
191
CCG

1297
4
21
GCG

1301
997
1012
AG

1312
47
67
CGG

1315
527
553
CCG

1334
585
604
AG

1351
559
576
ATT

1354
644
659
AG

1366
63
83
CGG

551
565
GCC

1367
283
300
CCG

1368
9
23
CGG

1369
213
233
CGC

439
453
GAG

1370
548
562
CCG

1376
56
70
GCG

1385
447
461
GGA

1387
5
19
CCG

1396
90
110
CGC

1424
1053
1067
GGC

1193
1207
CTT

1434
268
282
ATC

1435
12
29
GAG

330
344
GCG

1436
627
641
CGA

1452
16
33
GGC

1457
464
478
CCG

1458
130
144
ACC

1462
7
21
CGG

1466
97
112
ATCG

1479
168
182
CGG

248
262
GCA

1487
142
159
CGG

1493
2518
2532
AGC

2620
2640
AGC

1510
928
942
GAC

1517
687
701
CAA

973
987
CAA

1096
1113
AAG

1522
44
61
TCC

1528
334
348
CCG

1530
140
154
ACG

627
641
CGG

1534
1433
1447
CGG

1535
179
193
CCT

1537
153
173
CGA

338
352
CCG

1538
590
607
CCG

653
667
CGA

797
814
CGG

1540
160
174
GCG

529
543
GCG

1543
540
554
GGT

952
966
CAC

1544
227
241
CGG

676
690
GGC

1549
518
532
CCG

1550
28
45
CCG

1551
650
664
GCC

1563
123
137
GGC

1567
32
46
CGG

1580
34
51
CCG

1584
260
274
CCT

1590
4
21
AGG

124
138
CGT

1595
149
163
CGG

[0691]

17

TABLE 11

Swiss-Prot Data

Seq ID: 1
Seq ID: 801

Accession: P27322
Accession: Q9T074

Swissprot_id: HS72_LYCES
Swissprot_id: PPCK_ARATH

Gi_number: 123620
Gi_number: 12230482

Description: HEAT SHOCK COGNATE
Description: Phosphoenolpyruvate

70 KD PROTEIN 2
carboxykinase [ATP](PEP

Seq ID: 2
carboxykinase)

Accession: P28968
(Phosphoenolpyruvate carboxylase)

Swissprot_id: VGLX_HSVEB
(PEPCK)

Gi_number: 138350
Seq ID: 802

Description: GLYCOPROTEIN X
Accession: Q03663

PRECURSOR
Swissprot_id: GTX2_TOBAC

Seq ID: 3
Gi_number: 416650

Accession: Q9ZRR5
Description: Probable glutathione S-

Swissprot_id: TBA3_HORVU
transferase (Auxin-induced protein

Gi_number: 8928432
PGNT35/PCNT111)

Description: Tubulin alpha-3 chain
Seq ID: 803

Seq ID: 4
Accession: P80884

Accession: P03993
Swissprot_id: ANAN_ANACO

Swissprot_id: UBIQ_SOYBN
Gi_number: 13432122

Gi_number: 136673
Description: ANANAIN PRECURSOR

Description: UBIQUITIN
Seq ID: 804

Seq ID: 5
Accession: Q06548

Accession: O64937
Swissprot_id: APKA_ARATH

Swissprot_id: EF1A_ORYSA
Gi_number: 1168470

Gi_number: 6015059
Description: Protein kinase APK1A

Description: ELONGATION FACTOR 1-
Seq ID: 805

ALPHA (EF-1-ALPHA)
Accession: P35792

Seq ID: 6
Swissprot_id: PR12_HORVU

Accession: P13983
Gi_number: 548588

Swissprot_id: EXTN_TOBAC
Description: PATHOGENESIS-

Gi_number: 119714
RELATED PROTEIN PRB1-2

Description: Extensin precursor (Cell wall
PRECURSOR

hydroxyproline-rich
Seq ID: 806

glycoprotein)
Accession: P27349

Seq ID: 7
Swissprot_id: GOS9_ORYSA

Accession: O00555
Gi_number: 121528

Swissprot_id: CCAA_HUMAN
Description: G0S9 PROTEIN

Gi_number: 6166047
Seq ID: 807

Description: VOLTAGE-DEPENDENT
Accession: O43374

P/Q-TYPE CALCIUM CHANNEL
Swissprot_id: RSG5_HUMAN

ALPHA-1A
Gi_number: 13959542

SUBUNIT (CALCIUM
Description: RASGAP-ACTIVATING-

CHANNEL, L TYPE, ALPHA-1
LIKE PROTEIN 2

POLYPEPTIDE
Seq ID: 809

ISOFORM 4) (BRAIN
Accession: P29834

CALCIUM CHANNEL I) (BI)
Swissprot_id: GRP2_ORYSA

Seq ID: 8
Gi_number: 232183

Accession: Q99583
Description: GLYCINE-RICH CELL

Swissprot_id: MNT_HUMAN
WALL STRUCTURAL PROTEIN 2

Gi_number: 3914034
PRECURSOR

Description: MAX binding protein MNT
Seq ID: 810

(ROX protein) (MYC antagonist MNT)
Accession: Q03460

Seq ID: 9
Swissprot_id: GLSN_MEDSA

Accession: P35681
Gi_number: 417073

Swissprot_id: TCTP_ORYSA
Description: Glutamate synthase [NADH],

Gi_number: 549063
chloroplast precursor

Description: TRANSLATIONALLY
(NADH-GOGAT)

CONTROLLED TUMOR PROTEIN
Seq ID: 811

HOMOLOG (TCTP)
Accession: O23731

Seq ID: 10
Swissprot_id: CHS8_BROFI

Accession: P49311
Gi_number: 5921766

Swissprot_id: GRP2_SINAL
Description: CHALCONE SYNTHASE 8

Gi_number: 1346181
(NARINGENIN-CHALCONE

Description: Glycine-rich RNA-binding
SYNTHASE 8)

protein GRP2A
Seq ID: 812

Seq ID: 11
Accession: Q99758

Accession: P54258
Swissprot_id: ABC3_HUMAN

Swissprot_id: DRPL_RAT
Gi_number: 7387524

Gi_number: 1706520
Description: ATP-binding cassette, sub-

Description: ATROPHIN-1
family A, member 3 (ATP-binding

(DENTATORUBRAL-
cassette transporter 3) (ATP-

PALLIDOLUYSIAN ATROPHY
binding cassette 3) (ABC-C

PROTEIN)
transporter)

Seq ID: 13
Seq ID: 813

Accession: P02308
Accession: P29250

Swissprot_id: H4_WHEAT
Swissprot_id: LOX2_ORYSA

Gi_number: 122106
Gi_number: 126401

Description: HISTONE H4
Description: LIPOXYGENASE L-2

Seq ID: 14
Seq ID: 815

Accession: P57078
Accession: P13650

Swissprot_id: ANR3_HUMAN
Swissprot_id: DHGB_ACICA

Gi_number: 10719883
Gi_number: 118560

Description: Serine/threonine-protein
Description: Glucose dehydrogenase-B

kinase ANKRD3 (Ankyrin repeat
[pyrroloquinoline-quinone]

domain protein 3) (PKC-delta-
precursor

interacting protein kinase)
Seq ID: 816

Seq ID: 15
Accession: Q06915

Accession: P04050
Swissprot_id: EA6_ARATH

Swissprot_id: RPB1_YEAST
Gi_number: 1169451

Gi_number: 2507347
Description: Probable glucan endo-1,3-

Description: DNA-DIRECTED RNA
beta-glucosidase A6 precursor

POLYMERASE II LARGEST SUBUNIT
((1->3)-beta-glucan

(B220)
endohydrolase) ((1->3)-beta-glucanase)

Seq ID: 16
(Beta-1,3-endoglucanase)

Accession: Q06666
(Anther-specific protein A6)

Swissprot_id: T2_MOUSE
Seq ID: 817

Gi_number: 730888
Accession: P52420

Description: OCTAPEPTIDE-REPEAT
Swissprot_id: PUR2_ARATH

PROTEIN T2
Gi_number: 12644306

Seq ID: 17
Description: Phosphoribosylamine--glycine

Accession: Q9QX66
ligase, chloroplast precursor

Swissprot_id: REQN_MOUSE
(GARS) (Glycinamide

Gi_number: 13431818
ribonucleotide synthetase)

Description: ZINC-FINGER PROTEIN
(Phosphoribosylglycinamide

NEURO-D4
synthetase)

Seq ID: 18
Seq ID: 818

Accession: Q02817
Accession: Q07176

Swissprot_id: MUC2_HUMAN
Swissprot_id: MMK1_MEDSA

Gi_number: 2506877
Gi_number: 585519

Description: MUCIN 2 PRECURSOR
Description: MITOGEN-ACTIVATED

(INTESTINAL MUCIN 2)
PROTEIN KINASE HOMOLOG MMK1

Seq ID: 19
(MAP KINASE

Accession: P12978
MSK7) (MAP KINASE ERK1)

Swissprot_id: EBN2_EBV
Seq ID: 819

Gi_number: 119111
Accession: P11965

Description: EBNA-2 NUCLEAR
Swissprot_id: PERX_TOBAC

PROTEIN
Gi_number: 129837

Seq ID: 20
Description: Lignin forming anionic

Accession: P08640
peroxidase precursor

Swissprot_id: AMYH_YEAST
Seq ID: 820

Gi_number: 728850
Accession: P19135

Description: GLUCOAMYLASE S1/S2
Swissprot_id: PER2_CUCSA

PRECURSOR (GLUCAN
Gi_number: 129810

1,4-ALPHA-GLUCOSIDASE)
Description: Peroxidase 2

(1,4-ALPHA-D-GLUCAN
Seq ID: 821

GLUCOHYDROLASE)
Accession: P51614

Seq ID: 21
Swissprot_id: CHIA_VITVI

Accession: P21997
Gi_number: 1705812

Swissprot_id: SSGP_VOLCA
Description: ACIDIC ENDOCHITINASE

Gi_number: 134920
PRECURSOR

Description: SULFATED SURFACE
Seq ID: 822

GLYCOPROTEIN 185 (SSG 185)
Accession: Q9SYQ8

Seq ID: 22
Swissprot_id: CLV1_ARATH

Accession: Q9NZM4
Gi_number: 12643323

Swissprot_id: GSR1_HUMAN
Description: RECEPTOR PROTEIN

Gi_number: 18203330
KINASE CLAVATA1 PRECURSOR

Description: Glioma tumor suppressor
Seq ID: 823

candidate region gene 1 protein
Accession: P08640

Seq ID: 23
Swissprot_id: AMYH_YEAST

Accession: P48608
Gi_number: 728850

Swissprot_id: DIA_DROME
Description: GLUCOAMYLASE S1/S2

Gi_number: 13124711
PRECURSOR (GLUCAN

Description: DIAPHANOUS PROTEIN
1,4-ALPHA-GLUCOSIDASE)

Seq ID: 24
(1,4-ALPHA-D-GLUCAN

Accession: P27484
GLUCOHYDROLASE)

Swissprot_id: GRP2_NICSY
Seq ID: 824

Gi_number: 121631
Accession: P24021

Description: Glycine-rich protein 2
Swissprot_id: NUS1_ASPOR

Seq ID: 25
Gi_number: 128912

Accession: P31924
Description: NUCLEASE S1

Swissprot_id: SUS2_ORYSA
(ENDONUCLEASE S1) (SINGLE-

Gi_number: 401140
STRANDED-NUCLEATE

Description: Sucrose synthase 2 (Sucrose-
ENDONUCLEASE)

UDP glucosyltransferase 2)
(DEOXYRIBONUCLEASE S1)

Seq ID: 26
Seq ID: 825

Accession: P08640
Accession: Q01577

Swissprot_id: AMYH_YEAST
Swissprot_id: PKPA_PHYBL

Gi_number: 728850
Gi_number: 3122617

Description: GLUCOAMYLASE S1/S2
Description: Serine/threonine protein

PRECURSOR (GLUCAN
kinase PKPA

1,4-ALPHA-GLUCOSIDASE)
Seq ID: 826

(1,4-ALPHA-D-GLUCAN
Accession: P80073

GLUCOHYDROLASE)
Swissprot_id: MYB2_PHYPA

Seq ID: 27
Gi_number: 462669

Accession: P54774
Description: Myb-related protein Pp2

Swissprot_id: CC48_SOYBN
Seq ID: 827

Gi_number: 1705678
Accession: Q9ZT66

Description: CELL DIVISION CYCLE
Swissprot_id: E134_MAIZE

PROTEIN 48 HOMOLOG (VALOSIN
Gi_number: 8928122

CONTAINING
Description: Endo-1,3; 1,4-beta-D-

PROTEIN HOMOLOG) (VCP)
glucanase precursor

Seq ID: 28
Seq ID: 828

Accession: P33126
Accession: P77258

Swissprot_id: HS82_ORYSA
Swissprot_id: NEMA_ECOLI

Gi_number: 417154
Gi_number: 2499420

Description: HEAT SHOCK PROTEIN 82
Description: N-ethylmaleimide reductase

Seq ID: 29
(N-ethylmaleimide reducing

Accession: P08640
enzyme)

Swissprot_id: AMYH_YEAST
Seq ID: 829

Gi_number: 728850
Accession: P93329

Description: GLUCOAMYLASE S1/S2
Swissprot_id: NO20_MEDTR

PRECURSOR (GLUCAN
Gi_number: 3914142

1,4-ALPHA-GLUCOSIDASE)
Description: EARLY NODULIN 20

(1,4-ALPHA-D-GLUCAN
PRECURSOR (N-20)

GLUCOHYDROLASE)
Seq ID: 830

Seq ID: 30
Accession: P12653

Accession: P28968
Swissprot_id: GTH1_MAIZE

Swissprot_id: VGLX_HSVEB
Gi_number: 121695

Gi_number: 138350
Description: GLUTATHIONE S-

Description: GLYCOPROTEIN X
TRANSFERASE I (GST-I) (GST-29)

PRECURSOR
(GST

Seq ID: 31
CLASS-PHI)

Accession: P14641
Seq ID: 831

Swissprot_id: TBA2_MAIZE
Accession: P37835

Gi_number: 135411
Swissprot_id: PER2_ORYSA

Description: Tubulin alpha-2 chain (Alpha-
Gi_number: 585662

2 tubulin)
Description: Peroxidase precursor

Seq ID: 32
Seq ID: 832

Accession: P51968
Accession: P08995

Swissprot_id: RO31_XENLA
Swissprot_id: NO26_SOYBN

Gi_number: 1710625
Gi_number: 1352509

Description: Heterogeneous nuclear
Description: NODULIN-26 (N-26)

ribonucleoprotein A3 homolog 1
Seq ID: 833

(hnRNP A3(A))
Accession: O75880

Seq ID: 33
Swissprot_id: SCO1_HUMAN

Accession: P25439
Gi_number: 8134663

Swissprot_id: BRM_DROME
Description: SCO1 protein homolog,

Gi_number: 115132
mitochondrial precursor

Description: HOMEOTIC GENE
Seq ID: 834

REGULATOR (BRAHMA PROTEIN)
Accession: Q05968

Seq ID: 34
Swissprot_id: PR1_HORVU

Accession: P14328
Gi_number: 548592

Swissprot_id: SP96_DICDI
Description: PATHOGENESIS-

Gi_number: 134780
RELATED PROTEIN 1 PRECURSOR

Description: SPORE COAT PROTEIN
Seq ID: 835

SP96
Accession: P28814

Seq ID: 35
Swissprot_id: BARW_HORVU

Accession: Q02817
Gi_number: 114832

Swissprot_id: MUC2_HUMAN
Description: Barwin

Gi_number: 2506877
Seq ID: 836

Description: MUCIN 2 PRECURSOR
Accession: P07084

(INTESTINAL MUCIN 2)
Swissprot_id: IBBR_ORYSA

Seq ID: 36
Gi_number: 6166242

Accession: P03211
Description: BOWMAN-BIRK TYPE

Swissprot_id: EBN1_EBV
BRAN TRYPSIN INHIBITOR

Gi_number: 119110
PRECURSOR (RBTI)

Description: EBNA-1 NUCLEAR
(OSE727A)

PROTEIN
Seq ID: 839

Seq ID: 37
Accession: P29834

Accession: O23755
Swissprot_id: GRP2_ORYSA

Swissprot_id: EF2_BETVU
Gi_number: 232183

Gi_number: 6015065
Description: GLYCINE-RICH CELL

Description: ELONGATION FACTOR 2
WALL STRUCTURAL PROTEIN 2

(EF-2)
PRECURSOR

Seq ID: 38
Seq ID: 841

Accession: P25862
Accession: O14727

Swissprot_id: TBB1_AVESA
Swissprot_id: APAF_HUMAN

Gi_number: 135444
Gi_number: 3023307

Description: TUBULIN BETA-1 CHAIN
Description: Apoptotic protease activating

Seq ID: 39
factor 1 (Apaf-1)

Accession: P06876
Seq ID: 842

Swissprot_id: MYB_MOUSE
Accession: P35816

Gi_number: 127594
Swissprot_id: PDP1_BOVIN

Description: MYB PROTO-ONCOGENE
Gi_number: 548465

PROTEIN (C-MYB)
Description: [Pyruvate dehydrogenase

Seq ID: 40
[Lipoamide]]-phosphatase 1,

Accession: Q06666
mitochondrial precursor (PDP 1)

Swissprot_id: T2_MOUSE
(Pyruvate dehydrogenase

Gi_number: 730888
phosphatase, catalytic subunit 1)

Description: OCTAPEPTIDE-REPEAT
(PDPC 1)

PROTEIN T2
Seq ID: 843

Seq ID: 41
Accession: P32839

Accession: P03211
Swissprot_id: BCS1_YEAST

Swissprot_id: EBN1_EBV
Gi_number: 2506091

Gi_number: 119110
Description: BCS1 PROTEIN

Description: EBNA-1 NUCLEAR
Seq ID: 844

PROTEIN
Accession: P46573

Seq ID: 42
Swissprot_id: APKB_ARATH

Accession: Q43247
Gi_number: 12644274

Swissprot_id: G3PE_MAIZE
Description: PROTEIN KINASE APK1B

Gi_number: 6166167
Seq ID: 845

Description: Glyceraldehyde 3-phosphate
Accession: P10496

dehydrogenase, cytosolic 3
Swissprot_id: GRP2_PHAVU

Seq ID: 43
Gi_number: 121632

Accession: Q40649
Description: GLYCINE-RICH CELL

Swissprot_id: R103_ORYSA
WALL STRUCTURAL PROTEIN 1.8

Gi_number: 2500353
PRECURSOR

Description: 60S RIBOSOMAL PROTEIN
(GRP 1.8)

L10-3 (QM/R22)
Seq ID: 846

Seq ID: 44
Accession: P39881

Accession: Q9LQZ7
Swissprot_id: CUT1_CANFA

Swissprot_id: COL6_ARATH
Gi_number: 729093

Gi_number: 17433066
Description: CCAAT displacement protein

Description: Zinc finger protein constans-
(Homeobox protein Clox)

like 6
(Clox-1)

Seq ID: 45
Seq ID: 847

Accession: P39858
Accession: O42690

Swissprot_id: CAPI_STAAU
Swissprot_id: CDR3_CANAL

Gi_number: 729026
Gi_number: 5921713

Description: CAPI PROTEIN
Description: OPAQUE-SPECIFIC ABC

Seq ID: 46
TRANSPORTER CDR3

Accession: P80299
Seq ID: 848

Swissprot_id: HYES_RAT
Accession: P08183

Gi_number: 462371
Swissprot_id: MDR1_HUMAN

Description: SOLUBLE EPOXIDE
Gi_number: 2506118

HYDROLASE (SEH) (EPOXIDE
Description: MULTIDRUG RESISTANCE

HYDRATASE)
PROTEIN 1 (P-GLYCOPROTEIN 1)

(CYTOSOLIC EPOXIDE
Seq ID: 849

HYDROLASE) (CEH)
Accession: P21997

Seq ID: 47
Swissprot_id: SSGP_VOLCA

Accession: O13759
Gi_number: 134920

Swissprot_id: CSX1_SCHPO
Description: SULFATED SURFACE

Gi_number: 3121946
GLYCOPROTEIN 185 (SSG 185)

Description: RNA-BINDING POST-
Seq ID: 850

TRANSCRIPTIONAL REGULATOR
Accession: O15254

CSX1
Swissprot_id: CAO3_HUMAN

Seq ID: 48
Gi_number: 17366151

Accession: O43516
Description: Acyl-coenzyme A oxidase 3,

Swissprot_id: WAIP_HUMAN
peroxisomal (Pristanoyl-CoA

Gi_number: 13124642
oxidase)

Description: WISKOTT-ALDRICH
Seq ID: 851

SYNDROME PROTEIN INTERACTING
Accession: P13983

PROTEIN (WASP
Swissprot_id: EXTN_TOBAC

INTERACTING PROTEIN)
Gi_number: 119714

(PRPL-2 PROTEIN)
Description: Extensin precursor (Cell wall

Seq ID: 49
hydroxyproline-rich

Accession: P25096
glycoprotein)

Swissprot_id: P21_SOYBN
Seq ID: 852

Gi_number: 129320
Accession: Q9SYQ8

Description: P21 PROTEIN
Swissprot_id: CLV1_ARATH

Seq ID: 50
Gi_number: 12643323

Accession: P49688
Description: RECEPTOR PROTEIN

Swissprot_id: RS2_ARATH
KINASE CLAVATA1 PRECURSOR

Gi_number: 3915847
Seq ID: 853

Description: 40S RIBOSOMAL PROTEIN
Accession: P05522

S2
Swissprot_id: GUN1_PERAE

Seq ID: 51
Gi_number: 121784

Accession: P33278
Description: ENDOGLUCANASE 1

Swissprot_id: SUI1_ORYSA
PRECURSOR (ENDO-1,4-BETA-

Gi_number: 462195
GLUCANASE)

Description: PROTEIN TRANSLATION
(ABSCISSION CELLULASE 1)

FACTOR SUI1 HOMOLOG (GOS2
Seq ID: 854

PROTEIN)
Accession: P43293

Seq ID: 52
Swissprot_id: NAK_ARATH

Accession: Q99583
Gi_number: 1171642

Swissprot_id: MNT_HUMAN
Description: Probable serine/threonine-

Gi_number: 3914034
protein kinase NAK

Description: MAX binding protein MNT
Seq ID: 855

(ROX protein) (MYC antagonist MNT)
Accession: P54646

Seq ID: 53
Swissprot_id: AAK2_HUMAN

Accession: P46602
Gi_number: 1703035

Swissprot_id: HAT3_ARATH
Description: 5′-AMP-activated protein

Gi_number: 12644275
kinase, catalytic alpha-2 chain

Description: Homeobox-leucine zipper
(AMPK alpha-2 chain)

protein HAT3 (HD-ZIP protein 3)
Seq ID: 856

Seq ID: 54
Accession: P34106

Accession: P21997
Swissprot_id: ALA2_PANMI

Swissprot_id: SSGP_VOLCA
Gi_number: 461498

Gi_number: 134920
Description: ALANINE

Description: SULFATED SURFACE
AMINOTRANSFERASE 2 (GPT)

GLYCOPROTEIN 185 (SSG 185)
(GLUTAMIC--PYRUVIC

Seq ID: 55
TRANSAMINASE 2)

Accession: P13983
(GLUTAMIC--ALANINE

Swissprot_id: EXTN_TOBAC
TRANSAMINASE 2)

Gi_number: 119714
(ALAAT-2)

Description: Extensin precursor (Cell wall
Seq ID: 858

hydroxyproline-rich
Accession: P10056

glycoprotein)
Swissprot_id: PAP3_CARPA

Seq ID: 56
Gi_number: 1709574

Accession: Q9SW70
Description: Caricain precursor (Papaya

Swissprot_id: SRP_VITRI
proteinase omega) (Papaya

Gi_number: 15214303
proteinase III) (PPIII) (Papaya

Description: Stress-related protein
peptidase A)

Seq ID: 57
Seq ID: 859

Accession: P53039
Accession: P28968

Swissprot_id: YIPA_YEAST
Swissprot_id: VGLX_HSVEB

Gi_number: 1724030
Gi_number: 138350

Description: YIP1 PROTEIN
Description: GLYCOPROTEIN X

Seq ID: 58
PRECURSOR

Accession: O22540
Seq ID: 860

Swissprot_id: RL11_ORYSA
Accession: O70579

Gi_number: 6093997
Swissprot_id: PM34_MOUSE

Description: 60S RIBOSOMAL PROTEIN
Gi_number: 12585304

L11
Description: Peroxisomal membrane

Seq ID: 59
protein PMP34 (34 kDa peroxisomal

Accession: Q03211
membrane protein) (Solute carrier

Swissprot_id: EXLP_TOBAC
family 25, member 17)

Gi_number: 544262
Seq ID: 861

Description: PISTIL-SPECIFIC
Accession: Q95107

EXTENSIN-LIKE PROTEIN
Swissprot_id: WASL_BOVIN

PRECURSOR (PELP)
Gi_number: 13431968

Seq ID: 60
Description: Neural Wiskott-Aldrich

Accession: P05203
syndrome protein (N-WASP)

Swissprot_id: H3_MAIZE
Seq ID: 862

Gi_number: 122085
Accession: P23923

Description: HISTONE H3
Swissprot_id: HBPB_WHEAT

Seq ID: 61
Gi_number: 122772

Accession: P29314
Description: TRANSCRIPTION FACTOR

Swissprot_id: RS9_RAT
HBP-1B

Gi_number: 1173286
Seq ID: 865

Description: 40S RIBOSOMAL PROTEIN
Accession: P81214

S9
Swissprot_id: CARP_SYNRA

Seq ID: 62
Gi_number: 5915874

Accession: P06599
Description: SYNCEPHAPEPSIN

Swissprot_id: EXTN_DAUCA
PRECURSOR

Gi_number: 119711
Seq ID: 866

Description: EXTENSIN PRECURSOR
Accession: O75317

Seq ID: 63
Swissprot_id: UBPC_HUMAN

Accession: P37705
Gi_number: 6707738

Swissprot_id: GRP3_DAUCA
Description: Ubiquitin carboxyl-terminal

Gi_number: 585217
hydrolase 12 (Ubiquitin

Description: GLYCINE RICH PROTEIN
thiolesterase 12) (Ubiquitin-

A3
specific processing protease

Seq ID: 64
12) (Deubiquitinating enzyme 12)

Accession: Q99091
(Ubiquitin hydrolyzing

Swissprot_id: CPR3_PETCR
enzyme 1)

Gi_number: 1169084
Seq ID: 868

Description: LIGHT-INDUCIBLE
Accession: P16273

PROTEIN CPRF-3
Swissprot_id: PRPX_HORVU

Seq ID: 65
Gi_number: 1346809

Accession: P13983
Description: PATHOGEN-RELATED

Swissprot_id: EXTN_TOBAC
PROTEIN

Gi_number: 119714
Seq ID: 869

Description: Extensin precursor (Cell wall
Accession: Q43295

hydroxyproline-rich
Swissprot_id: KAP1_ARATH

glycoprotein)
Gi_number: 7387811

Seq ID: 66
Description: Adenylylsulfate kinase 1,

Accession: P18566
chloroplast precursor (APS

Swissprot_id: RBS2_ORYSA
kinase) (Adenosine-

Gi_number: 132096
5′phosphosulfate kinase) (ATP

Description: Ribulose bisphosphate
adenosine-5′-phosphosulfate 3′-

carboxylase small chain A,
phosphotransferase)

chloroplast precursor (RuBisCO
Seq ID: 870

small subunit A)
Accession: P08393

Seq ID: 67
Swissprot_id: ICP0_HSV11

Accession: P03211
Gi_number: 124134

Swissprot_id: EBN1_EBV
Description: Trans-acting transcriptional

Gi_number: 119110
protein ICP0 (Immediate-early

Description: EBNA-1 NUCLEAR
protein IE110) (VMW110)

PROTEIN
(Alpha-0 protein)

Seq ID: 69
Seq ID: 872

Accession: P23246
Accession: P40616

Swissprot_id: SFPQ_HUMAN
Swissprot_id: ARL1_HUMAN

Gi_number: 1709851
Gi_number: 728888

Description: SPLICING FACTOR,
Description: ADP-RIBOSYLATION

PROLINE-AND GLUTAMINE-RICH
FACTOR-LIKE PROTEIN 1

(POLYPYRIMIDINE TRACT-
Seq ID: 874

BINDING PROTEIN-ASSOCIATED
Accession: P35135

SPLICING
Swissprot_id: UBC4_LYCES

FACTOR) (PTB-ASSOCIATED
Gi_number: 464981

SPLICING FACTOR) (PSF)
Description: UBIQUITIN-

(DNA-BINDING P52/P100
CONJUGATING ENZYME E2-17 KD

COMPLEX, 100 KDA SUBUNIT)
(UBIQUITIN-PROTEIN

Seq ID: 71
LIGASE) (UBIQUITIN

Accession: P22277
CARRIER PROTEIN)

Swissprot_id: R27A_HORVU
Seq ID: 876

Gi_number: 133898
Accession: Q00765

Description: 40S RIBOSOMAL PROTEIN
Swissprot_id: DP1_HUMAN

S27A
Gi_number: 232007

Seq ID: 72
Description: POLYPOSIS LOCUS

Accession: Q9SS17
PROTEIN 1 (TB2 PROTEIN)

Swissprot_id: RS24_ARATH
Seq ID: 877

Gi_number: 11134742
Accession: Q9NZW4

Description: 40S ribosomal protein S24
Swissprot_id: DSPP_HUMAN

Seq ID: 73
Gi_number: 17865470

Accession: P03993
Description: Dentin sialophosphoprotein

Swissprot_id: UBIQ_SOYBN
precursor [Contains: Dentin

Gi_number: 136673
phosphoprotein (Dentin

Description: UBIQUITIN
phosphophoryn) (DPP); Dentin

Seq ID: 74
sialoprotein (DSP)]

Accession: P24068
Seq ID: 878

Swissprot_id: OCS1_MAIZE
Accession: P21997

Gi_number: 1352613
Swissprot_id: SSGP_VOLCA

Description: OCS-ELEMENT BINDING
Gi_number 134920

FACTOR 1 (OCSBF-1)
Description: SULFATED SURFACE

Seq ID: 75
GLYCOPROTEIN 185 (SSG 185)

Accession: P05203
Seq ID: 881

Swissprot_id: H3_MAIZE
Accession: P43293

Gi_number: 122085
Swissprot_id: NAK_ARATH

Description: HISTONE H3
Gi_number: 1171642

Seq ID: 76
Description: Probable serine/threonine-

Accession: P49637
protein kinase NAK

Swissprot_id: RL2A_ARATH
Seq ID: 882

Gi_number: 1710530
Accession: P27164

Description: 60S ribosomal protein L27A
Swissprot_id: CAL3_PETHY

Seq ID: 77
Gi_number: 115492

Accession: P46297
Description: CALMODULIN-RELATED

Swissprot_id: RS23_FRAAN
PROTEIN

Gi_number: 1173187
Seq ID: 883

Description: 40S RIBOSOMAL PROTEIN
Accession: P11675

S23 (S12)
Swissprot_id: IE18_PRVIF

Seq ID: 78
Gi_number: 124178

Accession: P46297
Description: IMMEDIATE-EARLY

Swissprot_id: RS23_FRAAN
PROTEIN IE180

Gi_number: 1173187
Seq ID: 884

Description: 40S RIBOSOMAL PROTEIN
Accession: O52535

S23 (S12)
Swissprot_id: CAH_KLEPN

Seq ID: 79
Gi_number: 5915869

Accession: P93329
Description: Carbonic anhydrase precursor

Swissprot_id: NO20_MEDTR
(Carbonate dehydratase)

Gi_number: 3914142
Seq ID: 885

Description: EARLY NODULIN 20
Accession: O64637

PRECURSOR (N-20)
Swissprot_id: C7C2_ARATH

Seq ID: 80
Gi_number: 5915832

Accession: P49216
Description: Cytochrome P450 76C2

Swissprot_id: RS26_ORYSA
Seq ID: 886

Gi_number: 1350969
Accession: P10978

Description: 40S RIBOSOMAL PROTEIN
Swissprot_id: POLX_TOBAC

S26 (S31)
Gi_number: 130582

Seq ID: 81
Description: Retrovirus-related Pol

Accession: P03211
polyprotein from transposon TNT

Swissprot_id: EBN1_EBV
1-94 [Contains: Protease;

Gi_number: 119110
Reverse transcriptase;

Description: EBNA-1 NUCLEAR
Endonuclease]

PROTEIN
Seq ID: 887

Seq ID: 82
Accession: P06795

Accession: O48557
Swissprot_id: MDR1_MOUSE

Swissprot_id: RL17_MAIZE
Gi_number: 126927

Gi_number: 3914685
Description: Multidrug resistance protein 1

Description: 60S RIBOSOMAL PROTEIN
(P-glycoprotein 1)

L17
Seq ID: 888

Seq ID: 83
Accession: P51533

Accession: Q24523
Swissprot_id: PDRA_YEAST

Swissprot_id: BUN2_DROME
Gi_number: 1709621

Gi_number: 17366491
Description: ATP-dependent permease

Description: Bunched protein, class 2/class
PDR10

3 isoforms (Shortsighted
Seq ID: 889

protein)
Accession: P22817

Seq ID: 84
Swissprot_id: IDE_DROME

Accession: P00303
Gi_number: 124156

Swissprot_id: BABL_CUCSA
Description: INSULIN-DEGRADING

Gi_number: 114806
ENZYME (INSULYSIN) (INSULINASE)

Description: BASIC BLUE PROTEIN
(INSULIN

(CUSACYANIN) (PLANTACYANIN)
PROTEASE)

(CBP)
Seq ID: 890

Seq ID: 85
Accession: O22060

Accession: P17078
Swissprot_id: SPS1_CITUN

Swissprot_id: RL35_RAT
Gi_number: 3915023

Gi_number: 132917
Description: SUCROSE-PHOSPHATE

Description: 60S RIBOSOMAL PROTEIN
SYNTHASE 1

L35
(UDP-GLUCOSE-FRUCTOSE-

Seq ID: 86
PHOSPHATE

Accession: O08816
GLUCOSYLTRANSFERASE 1)

Swissprot_id: WASL_RAT
Seq ID: 891

Gi_number: 13431956
Accession: O81108

Description: Neural Wiskott-Aldrich
Swissprot_id: ACA2_ARATH

syndrome protein (N-WASP)
Gi_number: 12229639

Seq ID: 87
Description: Calcium-transporting ATPase

Accession: Q9M352
2, plasma membrane-type

Swissprot_id: R36B_ARATH
(Ca2+-ATPase, isoform 2)

Gi_number: 17865567
Seq ID: 893

Description: 60S ribosomal protein L36-2
Accession: Q9S7J8

Seq ID: 88
Swissprot_id: AHM5_ARATH

Accession: P35687
Gi_number: 12229667

Swissprot_id: RS21_ORYSA
Description: Copper-transporting ATPase

Gi_number: 548852
RAN1 (Responsive-to-antagonist

Description: 40S RIBOSOMAL PROTEIN
1)

S21
Seq ID: 894

Seq ID: 89
Accession: Q07158

Accession: P14328
Swissprot_id: TPS1_KLULA

Swissprot_id: SP96_DICDI
Gi_number: 586113

Gi_number: 134780
Description: ALPHA, ALPHA-

Description: SPORE COAT PROTEIN
TREHALOSE-PHOSPHATE SYNTHASE

SP96
[UDP-FORMING] 56

Seq ID: 90
KD SUBUNIT (TREHALOSE-6-

Accession: P13983
PHOSPHATE SYNTHASE)

Swissprot_id: EXTN_TOBAC
(UDP-GLUCOSE-

Gi_number: 119714
GLUCOSEPHOSPHATE

Description: Extensin precursor (Cell wall
GLUCOSYLTRANSFERASE)

hydroxyproline-rich
Seq ID: 895

glycoprotein)
Accession: P93400

Seq ID: 91
Swissprot_id: PLD_TOBAC

Accession: P08640
Gi_number: 3914361

Swissprot_id: AMYH_YEAST
Description: PHOSPHOLIPASE D

Gi_number: 728850
PRECURSOR (PLD) (CHOLINE

Description: GLUCOAMYLASE S1/S2
PHOSPHATASE)

PRECURSOR (GLUCAN
(PHOSPHATIDYLCHOLINE-

1,4-ALPHA-GLUCOSIDASE)
HYDROLYZING PHOSPHOLIPASE D)

(1,4-ALPHA-D-GLUCAN
Seq ID: 896

GLUCOHYDROLASE)
Accession: P49608

Seq ID: 92
Swissprot_id: ACOC_CUCMA

Accession: P27483
Gi_number: 1351856

Swissprot_id: GRP_ARATH
Description: ACONITATE HYDRATASE,

Gi_number: 121640
CYTOPLASMIC (CITRATE HYDROLYASE)

Description: GLYCINE-RICH CELL
(ACONITASE)

WALL STRUCTURAL PROTEIN
Seq ID: 897

PRECURSOR
Accession: P22817

Seq ID: 93
Swissprot_id: IDE_DROME

Accession: P08640
Gi_number: 124156

Swissprot_id: AMYH_YEAST
Description: INSULIN-DEGRADING

Gi_number: 728850
ENZYME (INSULYSIN) (INSULINASE)

Description: GLUCOAMYLASE S1/S2
(INSULIN

PRECURSOR (GLUCAN
PROTEASE)

1,4-ALPHA-GLUCOSIDASE)
Seq ID: 898

(1,4-ALPHA-D-GLUCAN
Accession: P49333

GLUCOHYDROLASE)
Swissport_id: ETR1_ARATH

Seq ID: 95
Gi_number: 1352397

Accession: P40602
Description: ETR1 protein

Swissprot_id: APG_ARATH
Seq ID: 899

Gi_number: 728867
Accession: P33302

Description: ANTER-SPECIFIC
Swissprot_id: PDR5_YEAST

PROLINE-RICH PROTEIN APG
Gi_number: 464819

PRECURSOR
Description: SUPPRESSOR OF

Seq ID: 96
TOXICITY OF SPORIDESMIN

Accession: P33485
Seq ID: 900

Swissprot_id: VNUA_PRVKA
Accession: P54802

Gi_number: 465445
Swissprot_id: ANAG_HUMAN

Description: PROBABLE NUCLEAR
Gi_number: 1703303

ANTIGEN
Description: Alpha-N-

Seq ID: 97
acetylglucosaminidase precursor

Accession: P70315
(N-acetyl-alpha-glucosaminidase)

Swissprot_id: WASP_MOUSE
(NAG)

Gi_number: 2499130
Seq ID: 901

Description: Wiskott-Aldrich syndrome
Accession: P29141

protein homolog (WASP)
Swissprot_id: SUBV_BACSU

Seq ID: 98
Gi_number: 135023

Accession: P10220
Description: Minor extracellular protease

Swissprot_id: TEGU_HSV11
VPR precursor

Gi_number: 135576
Seq ID: 902

Description: LARGE TEGUMENT
Accession: P53681

PROTEIN (VIRION PROTEIN UL36)
Swissprot_id: CRK_DAUCA

Seq ID: 99
Gi_number: 1706130

Accession: P11675
Description: CDPK-related protein kinase

Swissprot_id: IE18_PRVIF
(PK421)

Gi_number: 124178
Seq ID: 903

Description: IMMEDIATE-EARLY
Accession: P46401

PROTEIN IE180
Swissprot_id: BCCA_MYCTU

Seq ID: 100
Gi_number: 1168278

Accession: P13983
Description: Acetyl-/propionyl-coenzyme

Swissprot_id: EXTN_TOBAC
A carboxylase alpha chain

Gi_number: 119714
[Includes: Biotin carboxylase;

Description: Extensin precursor (Cell wall
Biotin carboxyl carrier

hydroxyproline-rich
protein (BCCP)]

glycoprotein)
Seq ID: 904

Seq ID: 101
Accession: Q02779

Accession: Q62376
Swissprot_id: M3KA_HUMAN

Swissprot_id: RU17_MOUSE
Gi_number: 6686295

Gi_number: 13633918
Description: MITOGEN-ACTIVATED

Description: U1 small nuclear
PROTEIN KINASE KINASE KINASE 10

ribonucleoprotein 70 kDa (U1 SNRNP 70
(MIXED

kDa) (snRNP70)
LINEAGE KINASE 2)

Seq ID: 102
(PROTEIN KINASE MST)

Accession: P03211
Seq ID: 906

Swissprot_id: EBN1_EBV
Accession: Q06850

Gi_number: 119110
Swissprot_id: CDP1_ARATH

Description: EBNA-1 NUCLEAR
Gi_number: 729092

PROTEIN
Description: Calcium-dependent protein

Seq ID: 103
kinase, isoform AK1 (CDPK)

Accession: P33485
Seq ID: 907

Swissprot_id: VNUA_PRVKA
Accession: P48422

Gi_number: 465445
Swissprot_id: C861_ARATH

Description: PROBABLE NUCLEAR
Gi_number: 13878905

ANTIGEN
Description: Cytochrome P450 86A1

Seq ID: 104
(CYPLXXXVI) (P450-dependent fatty

Accession: P21997
acid omega-hydroxylase)

Swissprot_id: SSGP_VOLCA
Seq ID: 908

Gi_number: 134920
Accession: P25297

Description: SULFATED SURFACE
Swissprot_id: PH84_YEAST

GLYCOPROTEIN 185 (SSG 185)
Gi_number: 1346710

Seq ID: 105
Description: INORGANIC PHOSPHATE

Accession: Q63003
TRANSPORTER PHO84

Swissprot_id: 5E5_RAT
Seq ID: 909

Gi_number: 2498095
Accession: P16157

Description: 5E5 ANTIGEN
Swissprot_id: ANK1_HUMAN

Seq ID: 106
Gi_number: 113884

Accession: Q02817
Description: Ankyrin 1 (Erythrocyte

Swissprot_id: MUC2_HUMAN
ankyrin) (Ankyrin R)

Gi_number: 2506877
Seq ID: 910

Description: MUCIN 2 PRECURSOR
Accession: P46032

(INTESTINAL MUCIN 2)
Swissprot_id: PT2B_ARATH

Seq ID: 107
Gi_number: 1172704

Accession: P13983
Description: Peptide transporter PTR2-B

Swissprot_id: EXTN_TOBAC
(Histidine transporting

Gi_number: 119714
protein)

Description: Extensin precursor (Cell wall
Seq ID: 911

hydroxyproline-rich
Accession: P26514

glycoprotein)
Swissprot_id: XYNA_STRLI

Seq ID: 109
Gi_number: 6226911

Accession: P18615
Description: ENDO-1,4-BETA-

Swissprot_id: RDP_HUMAN
XYLANASE A PRECURSOR

Gi_number: 1350554
(XYLANASE A)

Description: RD protein
(1,4-BETA-D-XYLAN

Seq ID: 110
XYLANOHYDROLASE A)

Accession: P21997
Seq ID: 912

Swissprot_id: SSGP_VOLCA
Accession: Q02775

Gi_number: 134920
Swissprot_id: SLU7_YEAST

Description: SULFATED SURFACE
Gi_number: 401091

GLYCOPROTEIN 185 (SSG 185)
Description: PRE-MRNA SPLICING

Seq ID: 111
FACTOR SLU7

Accession: Q00451
Seq ID: 913

Swissprot_id: PRF1_LYCES
Accession: Q04468

Gi_number: 1709767
Swissprot_id: TCMO_HELTU

Description: 36.4 KD PROLINE-RICH
Gi_number: 417863

PROTEIN
Description: TRANS-CINNAMATE 4-

Seq ID: 112
MONOOXYGENASE (CINNAMIC ACID

Accession: Q02817
4-HYDROXYLASE) (CA4H)

Swissprot_id: MUC2_HUMAN
(C4H) (P450C4H) (CYTOCHROME P450

Gi_number: 2506877
73)

Description: MUCIN 2 PRECURSOR
Seq ID: 914

(INTESTINAL MUCIN 2)
Accession: P55034

Seq ID: 113
Swissprot_id: PSD4_ARATH

Accession: P21997
Gi_number: 1709794

Swissprot_id: SSGP_VOLCA
Description: 26S proteasome regulatory

Gi_number: 134920
subunit S5A (Multiubiquitin

Description: SULFATED SURFACE
chain binding protein)

GLYCOPROTEIN 185 (SSG 185)
Seq ID: 915

Seq ID: 116
Accession: P06782

Accession: Q02817
Swissprot_id: SNF1_YEAST

Swissprot_id: MUC2_HUMAN
Gi_number: 134588

Gi_number: 2506877
Description: CARBON CATABOLITE

Description: MUCIN 2 PRECURSOR
DEREPRESSING PROTEIN KINASE

(INTESTINAL MUCIN 2)
Seq ID: 917

Seq ID: 117
Accession: O64668

Accession: P70315
Swissprot_id: PSNH_ARATH

Swissprot_id: WASP_MOUSE
Gi_number: 6093852

Gi_number: 2499130
Description: Presenilin homolog

Description: Wiskott-Aldrich syndrome
Seq ID: 919

protein homolog (WASP)
Accession: P26300

Seq ID: 121
Swissprot_id: ENO_LYCES

Accession: O22446
Gi_number: 119354

Swissprot_id: HDAC_ARATH
Description: ENOLASE (2-

Gi_number: 3023945
PHOSPHOGLYCERATE

Description: Histone deacetylase (HD)
DEHYDRATASE)

Seq ID: 122
(2-PHOSPHO-D-GLYCERATE

Accession: P03211
HYDRO-LYASE)

Swissprot_id: EBN1_EBV
Seq ID: 920

Gi_number: 119110
Accession: P37287

Description: EBNA-1 NUCLEAR
Swissprot_id: PIGA_HUMAN

PROTEIN
Gi_number: 585696

Seq ID: 124
Description: N-acetylglucosaminyl-

Accession: P08393
phosphatidylinositol biosynthetic

Swissprot_id: ICP0_HSV11
protein (GlcNac-PI synthesis

Gi_number: 124134
protein)

Description: Trans-acting transcriptional
(Phosphatidylinositol-glycan

protein ICP0 (Immediate-early
biosynthesis, class A

protein IE110) (VMW110)
protein) (PIG-A)

(Alpha-0 protein)
Seq ID: 921

Seq ID: 125
Accession: P21997

Accession: P49625
Swissprot_id: SSGP_VOLCA

Swissprot_id: RL5_ORYSA
Gi_number: 134920

Gi_number: 3915826
Description: SULFATED SURFACE

Description: 60S RIBOSOMAL PROTEIN
GLYCOPROTEIN 185 (SSG 185)

L5
Seq ID: 922

Seq ID: 126
Accession: O15269

Accession: P33485
Swissprot_id: LCB1_HUMAN

Swissprot_id: VNUA_PRVKA
Gi_number: 6685579

Gi_number: 465445
Description: Serine palmitoyltransferase 1

Description: PROBABLE NUCLEAR
(Long chain base

ANTIGEN
biosynthesis protein 1) (LCB 1)

Seq ID: 127
(Serine-palmitoyl-CoA

Accession: P14918
transferase 1) (SPT 1) (SPT1)

Swissprot_id: EXTN_MAIZE
Seq ID: 923

Gi_number: 119712
Accession: P13728

Description: EXTENSIN PRECURSOR
Swissprot_id: SGS3_DROYA

(PROLINE-RICH GLYCOPROTEIN)
Gi_number: 134469

Seq ID: 128
Description: Salivary glue protein SGS-3

Accession: P42736
precursor

Swissprot_id: CDI3_ARATH
Seq ID: 924

Gi_number: 1168862
Accession: P93846

Description: CADMIUM-INDUCED
Swissprot_id: CP51_SORBI

PROTEIN AS30
Gi_number: 5921924

Seq ID: 129
Description: Cytochrome P450 51

Accession: P33479
(CYPL1) (P450-L1A1) (Obtusifoliol

Swissprot_id: IE18_PRVKA
14-alpha demethylase)

Gi_number: 462387
Seq ID: 925

Description: IMMEDIATE-EARLY
Accession: P70315

PROTEIN IE180
Swissprot_id: WASP_MOUSE

Seq ID: 130
Gi_number: 2499130

Accession: Q95107
Description: Wiskott-Aldrich syndrome

Swissprot_id: WASL_BOVIN
protein homolog (WASP)

Gi_number: 13431968
Seq ID: 926

Description: Neural Wiskott-Aldrich
Accession: P13728

syndrome protein (N-WASP)
Swissprot_id: SGS3_DROYA

Seq ID: 132
Gi_number: 134469

Accession: P33485
Description: Salivary glue protein SGS-3

Swissprot_id: VNUA_PRVKA
precursor

Gi_number: 465445
Seq ID: 927

Description: PROBABLE NUCLEAR
Accession: P47179

ANTIGEN
Swissprot_id: DAN4_YEAST

Seq ID: 133
Gi_number: 1352944

Accession: Q02817
Description: Cell wall protein DAN4

Swissprot_id: MUC2_HUMAN
precursor

Gi_number: 2506877
Seq ID: 928

Description: MUCIN 2 PRECURSOR
Accession: Q9UJY5

(INTESTINAL MUCIN 2)
Swissprot_id: GGA1_HUMAN

Seq ID: 134
Gi_number: 14548066

Accession: Q9SYQ8
Description: ADP-RIBOSYLATION

Swissprot_id: CLV1_ARATH
FACTOR BINDING PROTEIN GGA1

Gi_number: 12643323
(GOLGI-LOCALIZED, GAMMA

Description: RECEPTOR PROTEIN
EAR-CONTAINING, ARF-BINDING

KINASE CLAVATA1 PRECURSOR
PROTEIN 1) (GAMMA-

Seq ID: 135
ADAPTIN RELATED PROTEIN 1)

Accession: O80340
Seq ID: 929

Swissprot_id: ERF4_ARATH
Accession: Q02779

Gi_number: 7531110
Swissprot_id: M3KA_HUMAN

Description: Ethylene responsive element
Gi_number: 6686295

binding factor 4 (AtERF4)
Description: MITOGEN-ACTIVATED

Seq ID: 136
PROTEIN KINASE KINASE KINASE 10

Accession: P08392
(MIXED

Swissprot_id: ICP4_HSV11
LINEAGE KINASE 2)

Gi_number: 124141
(PROTEIN KINASE MST)

Description: TRANS-ACTING
Seq ID: 930

TRANSCRIPTIONAL PROTEIN ICP4
Accession: P05143

(TRANSCRIPTIONAL
Swissprot_id: PRP3_MOUSE

ACTIVATOR IE175) (ALPHA-4
Gi_number: 131002

PROTEIN)
Description: PROLINE-RICH PROTEIN

Seq ID: 137
MP-3

Accession: Q03211
Seq ID: 931

Swissprot_id: EXLP_TOBAC
Accession: P08548

Gi_number: 544262
Swissprot_id: LIN1_NYCCO

Description: PISTIL-SPECIFIC
Gi_number: 126296

EXTENSIN-LIKE PROTEIN
Description: LINE-1 REVERSE

PRECURSOR (PELP)
TRANSCRIPTASE HOMOLOG

Seq ID: 138
Seq ID: 932

Accession: P18165
Accession: P04802

Swissprot_id: LORI_MOUSE
Swissprot_id: SYDC_YEAST

Gi_number: 126390
Gi_number: 135100

Description: LORICRIN
Description: ASPARTYL-TRNA

Seq ID: 139
SYNTHETASE, CYTOPLASMIC

Accession: O00268
(ASPARTATE--TRNA

Swissprot_id: T2D3_HUMAN
LIGASE) (ASPRS)

Gi_number: 3024681
Seq ID: 933

Description: TRANSCRIPTION
Accession: Q9UKL6

INITIATION FACTOR TFIID 135 KDA
Swissprot_id: PPCT_HUMAN

SUBUNIT
Gi_number: 15214192

(TAFII-135) (TAFII135) (TAFII-
Description: PHOSPHATIDYLCHOLINE

130) (TAFII130)
TRANSFER PROTEIN (PC-TP)

Seq ID: 140
Seq ID: 935

Accession: P42768
Accession: O13302

Swissprot_id: WASP_HUMAN
Swissprot_id: IDH1_AJECA

Gi_number: 1722836
Gi_number: 13124301

Description: WISKOTT-ALDRICH
Description: Isocitrate dehydrogenase

SYNDROME PROTEIN (WASP)
[NAD] subunit 1, mitochondrial

Seq ID: 141
precursor (Isocitric

Accession: P78621
dehydrogenase) (NAD+-specific ICDH)

Swissprot_id: SEPA_EMENI
Seq ID: 936

Gi_number: 15214279
Accession: Q27546

Description: CYTOKINESIS PROTEIN
Swissprot_id: IUNH_CRIFA

SEPA (FH1/2 PROTEIN) (FORCED
Gi_number: 2497465

EXPRESSION INHIBITION OF
Description: INOSINE-URIDINE

GROWTH A)
PREFERRING NUCLEOSIDE

Seq ID: 142
HYDROLASE

Accession: P46301
(IU-NUCLEOSIDE

Swissprot_id: RS25_LYCES
HYDROLASE) (PURINE

Gi_number: 1173234
NUCLEOSIDASE)

Description: 40S RIBOSOMAL PROTEIN
Seq ID: 937

S25
Accession: P27545

Seq ID: 143
Swissprot_id: LSS1_MOUSE

Accession: Q00519
Gi_number: 137047

Swissprot_id: XDH_MOUSE
Description: Longevity assurance homolog

Gi_number: 1722858
1 (UOG-1 protein)

Description: XANTHINE
Seq ID: 938

DEHYDROGENASE/OXIDASE
Accession: Q02440

[INCLUDES: XANTHINE
Swissprot_id: MY5A_CHICK

DEHYDROGENASE (XD);
Gi_number: 547967

XANTHINE OXIDASE (XO)
Description: Myosin Va (Myosin 5A)

(XANTHINE
(Dilute myosin heavy chain,

OXIDOREDUCTASE)]
non-muscle) (Myosin heavy chain

Seq ID: 144
P190) (Myosin-V)

Accession: Q43043
Seq ID: 939

Swissprot_id: PME_PETIN
Accession: Q9DCG6

Gi_number: 6093743
Swissprot_id: PHZ2_MOUSE

Description: PECTINESTERASE
Gi_number: 18202860

PRECURSOR (PECTIN
Description: Probable oxidoreductase

METHYLESTERASE) (PE)
0610038K03Rik

Seq ID: 145
Seq ID: 940

Accession: O76082
Accession: P06237

Swissprot_id: OCN2_HUMAN
Swissprot_id: NOH4_RHIME

Gi_number: 8928257
Gi_number: 128469

Description: Organic cation/carnitine
Description: NODULATION PROTEIN H

transporter 2 (Solute carrier
(HOST-SPECIFICITY OF

family 22, member 5) (High-
NODULATION

affinity sodium-dependent
PROTEIN D)

carnitine cotransporter)
Seq ID: 941

Seq ID: 146
Accession: Q43062

Accession: P07730
Swissprot_id: PME_PRUPE

Swissprot_id: GLU2_ORYSA
Gi_number: 6093744

Gi_number: 121475
Description: Pectinesterase PPE8B

Description: GLUTELIN TYPE II
precursor (Pectin methylesterase)

PRECURSOR
(PE)

Seq ID: 147
Seq ID: 942

Accession: Q43772
Accession: P39101

Swissprot_id: UDPG_HORVU
Swissprot_id: CAJ1_YEAST

Gi_number: 6136111
Gi_number: 729007

Description: UTP--GLUCOSE-1-
Description: CAJ1 protein

PHOSPHATE
Seq ID: 943

URIDYLYLTRANSFERASE (UDP-
Accession: P33479

GLUCOSE
Swissprot_id: IE18_PRVKA

PYROPHOSPHORYLASE)
Gi_number: 462387

(UDPGP) (UGPASE)
Description: IMMEDIATE-EARLY

Seq ID: 148
PROTEIN IE180

Accession: P24465
Seq ID: 944

Swissprot_id: CP71_PERAE
Accession: Q06136

Gi_number: 117188
Swissprot_id: FVT1_HUMAN

Description: CYTOCHROME P450 71A1
Gi_number: 544358

(CYPLXXIA1) (ARP-2)
Description: Follicular variant

Seq ID: 149
translocation protein 1 precursor

Accession: P32323
(FVT-1)

Swissprot_id: AGA1_YEAST
Seq ID: 945

Gi_number: 416592
Accession: P17180

Description: A-AGGLUTININ
Swissprot_id: PER3_ARMRU

ATTACHMENT SUBUNIT
Gi_number: 129812

PRECURSOR
Description: Peroxidase C3 precursor

Seq ID: 150
Seq ID: 946

Accession: P09195
Accession: P48490

Swissprot_id: F16P_WHEAT
Swissprot_id: PP1_PHAVU

Gi_number: 119745
Gi_number: 1346765

Description: FRUCTOSE-1,6-
Description: SERINE/THREONINE

BISPHOSPHATASE, CHLOROPLAST
PROTEIN PHOSPHATASE PP1

PRECURSOR
Seq ID: 948

(D-FRUCTOSE-1,6-
Accession: P22196

BISPHOSPHATE 1-
Swissprot_id: PER2_ARAHY

PHOSPHOHYDROLASE) (FBPASE)
Gi_number: 129808

Seq ID: 151
Description: Cationic peroxidase 2

Accession: Q9BYV1
precursor

Swissprot_id: AGT2_HUMAN
Seq ID: 949

Gi_number: 17432913
Accession: P57760

Description: Alanine--glyoxylate
Swissprot_id: ST16_RAT

aminotransferase 2, mitochondrial
Gi_number: 13124540

precursor (AGT 2) (Beta-alanine-
Description: Serine/threonine protein

pyruvate aminotransferase)
kinase 16 (Protein kinase PKL12)

(Beta-ALAAT II)
(Myristoylated and palmitoylated

Seq ID: 152
serine-threonine kinase)

Accession: P18583
(MPSK) (TGF-beta stimulated

Swissprot_id: SON_HUMAN
factor 1) (TSF-1)

Gi_number: 586013
Seq ID: 950

Description: SON PROTEIN (SON3)
Accession: P24289

Seq ID: 153
Swissprot_id: NUP1_PENCI

Accession: P76072
Gi_number: 128906

Swissprot_id: STFR_ECOLI
Description: NUCLEASE P1

Gi_number: 12643676
(ENDONUCLEASE P1)

Description: SIDE TAIL FIBER PROTEIN
(DEOXYRIBONUCLEASE P1)

HOMOLOG FROM LAMBDOID
Seq ID: 951

PROPHAGE RAC
Accession: P22420

Seq ID: 154
Swissprot_id: VE2_HPV47

Accession: P17814
Gi_number: 137682

Swissprot_id: 4CL1_ORYSA
Description: REGULATORY PROTEIN

Gi_number: 112802
E2

Description: 4-coumarate--CoA ligase 1
Seq ID: 953

(4CL 1) (4-coumaroyl-CoA
Accession: Q60715

synthase 1)
Swissprot_id: P4H1_MOUSE

Seq ID: 155
Gi_number: 2498740

Accession: P03211
Description: PROLYL 4-

Swissprot_id: EBN1_EBV
HYDROXYLASE ALPHA-1 SUBUNIT

Gi_number: 119110
PRECURSOR

Description: EBNA-1 NUCLEAR
Seq ID: 954

PROTEIN
Accession: P78621

Seq ID: 156
Swissprot_id: SEPA_EMENI

Accession: P39656
Gi_number: 15214279

Swissprot_id: OST4_HUMAN
Description: CYTOKINESIS PROTEIN

Gi_number: 730241
SEPA (FH1/2 PROTEIN) (FORCED

Description: DOLICHYL-
EXPRESSION INHIBITION OF

DIPHOSPHOOLIGOSACCHARIDE--
GROWTH A)

PROTEIN
Seq ID: 959

GLYCOSYLTRANSFERASE 48
Accession: P16273

KDA SUBUNIT PRECURSOR
Swissprot_id: PRPX_HORVU

(OLIGOSACCHARYL
Gi_number: 1346809

TRANSFERASE 48 KDA SUBUNIT)
Description: PATHOGEN-RELATED

(DDOST 48 KDA
PROTEIN

SUBUNIT)
Seq ID: 961

Seq ID: 157
Accession: P41151

Accession: O82256
Swissprot_id: HSF1_ARATH

Swissprot_id: COLA_ARATH
Gi_number: 12644262

Gi_number: 17432989
Description: HEAT SHOCK FACTOR

Description: Zinc finger protein constans-
PROTEIN 1 (HSF 1) (HEAT SHOCK

like 10
TRANSCRIPTION FACTOR 1)

Seq ID: 158
(HSTF 1)

Accession: P21997
Seq ID: 962

Swissprot_id: SSGP_VOLCA
Accession: Q38841

Gi_number: 134920
Swissprot_id: AG12_ARATH

Description: SULFATED SURFACE
Gi_number: 12643746

GLYCOPROTEIN 185 (SSG 185)
Description: Agamous-like MADS box

Seq ID: 159
protein AGL12

Accession: Q02910
Seq ID: 964

Swissprot_id: CPN_DROME
Accession: Q9NRA0

Gi_number: 416833
Swissprot_id: SPH2_HUMAN

Description: CALPHOTIN
Gi_number: 17369316

Seq ID: 160
Description: Sphingosine kinase 2 (SK 2)

Accession: P15792
(SPK 2)

Swissprot_id: KPK1_PHAVU
Seq ID: 965

Gi_number: 125568
Accession: P72660

Description: Protein kinase PVPK-1
Swissprot_id: LEP1_SYNY3

Seq ID: 161
Gi_number: 6225603

Accession: P40602
Description: Probable signal peptidase I-1

Swissprot_id: APG_ARATH
(SPase I-1) (Leader

Gi_number: 728867
peptidase I-1)

Description: ANTER-SPECIFIC
Seq ID: 966

PROLINE-RICH PROTEIN APG
Accession: P93531

PRECURSOR
Swissprot_id: C7D7_SOLCH

Seq ID: 162
Gi_number: 5915836

Accession: P41152
Description: CYTOCHROME P450 71D7

Swissprot_id: HSF3_LYCPE
Seq ID: 968

Gi_number: 729774
Accession: P52835

Description: HEAT SHOCK FACTOR
Swissprot_id: F3ST_FLABI

PROTEIN HSF30 (HEAT SHOCK
Gi_number: 1706738

TRANSCRIPTION
Description: FLAVONOL 3-

FACTOR 30) (HSTF 30) (HEAT
SULFOTRANSFERASE (F3-ST)

STRESS TRANSCRIPTION FACTOR)
Seq ID: 970

Seq ID: 163
Accession: Q06003

Accession: P05143
Swissprot_id: GOLI_DROME

Swissprot_id: PRP3_MOUSE
Gi_number: 462193

Gi_number: 131002
Description: Goliath protein (G1 protein)

Description: PROLINE-RICH PROTEIN
Seq ID: 971

MP-3
Accession: Q9ZNV5

Seq ID: 164
Swissprot_id: CEN_ARATH

Accession: O43516
Gi_number: 17366125

Swissprot_id: WAIP_HUMAN
Description: CENTRORADIALIS-like

Gi_number: 13124642
protein

Description: WISKOTT-ALDRICH
Seq ID: 972

SYNDROME PROTEIN INTERACTING
Accession: Q99090

PROTEIN (WASP
Swissprot_id: CPR2_PETCR

INTERACTING PROTEIN)
Gi_number: 2842757

(PRPL-2 PROTEIN)
Description: LIGHT-INDUCIBLE

Seq ID: 165
PROTEIN CPRF-2

Accession: P17784
Seq ID: 974

Swissprot_id: ALF_ORYSA
Accession: Q9MB73

Gi_number: 113622
Swissprot_id: LGT_CITUN

Description: FRUCTOSE-
Gi_number: 13431605

BISPHOSPHATE ALDOLASE,
Description: Limonoid UDP-

CYTOPLASMIC ISOZYME
glucosyltransferase (Limonoid

Seq ID: 166
glucosyltransferase) (Limonoid

Accession: P21997
GTase) (LGTase)

Swissprot_id: SSGP_VOLCA
Seq ID: 975

Gi_number: 134920
Accession: P48809

Description: SULFATED SURFACE
Swissprot_id: RB27_DROME

GLYCOPROTEIN 185 (SSG 185)
Gi_number: 1346955

Seq ID: 167
Description: Heterogeneous nuclear

Accession: P30364
ribonucleoprotein 27C (hnRNP 48)

Swissprot_id: ASPG_LUPAN
(HRP48.1)

Gi_number: 231573
Seq ID: 976

Description: L-ASPARAGINASE (L-
Accession: P13230

ASPARAGINE AMIDOHYDROLASE)
Swissprot_id: GRP3_ARTSA

Seq ID: 168
Gi_number: 121634

Accession: Q9UBQ6
Description: Glycine-rich protein GRP33

Swissprot_id: EXL2_HUMAN
Seq ID: 977

Gi_number: 9296986
Accession: P20024

Description: Exostosin-like 2 (EXT-related
Swissprot_id: MYB1_MAIZE

protein 2)
Gi_number: 127580

Seq ID: 169
Description: Myb-related protein Zm1

Accession: Q02817
Seq ID: 978

Swissprot_id: MUC2_HUMAN
Accession: Q9NVW2

Gi_number: 2506877
Swissprot_id: RNFB_HUMAN

Description: MUCIN 2 PRECURSOR
Gi_number: 13124522

(INTESTINAL MUCIN 2)
Description: RING FINGER PROTEIN 12

Seq ID: 170
(LIM DOMAIN INTERACTING RING

Accession: O54939
FINGER

Swissprot_id: DHB3_RAT
PROTEIN) (RING FINGER LIM

Gi_number: 3913460
DOMAIN-BINDING PROTEIN) (R-LIM)

Description: Estradiol 17 beta-
(NY-REN-43 ANTIGEN)

dehydrogenase 3 (17-beta-HSD 3)
Seq ID: 979

(Testicular 17-beta-
Accession: P22988

hydroxysteroid dehydrogenase)
Swissprot_id: LDHA_HORVU

Seq ID: 171
Gi_number: 126033

Accession: Q63003
Description: L-lactate dehydrogenase A

Swissprot_id: 5E5_RAT
(LDH-A)

Gi_number: 2498095
Seq ID: 980

Description: 5E5 ANTIGEN
Accession: P34802

Seq ID: 172
Swissprot_id: GGPP_ARATH

Accession: P14009
Gi_number: 13432144

Swissprot_id: 14KD_DAUCA
Description: GERANYLGERANYL

Gi_number: 112697
PYROPHOSPHATE SYNTHETASE,

Description: 14 KD PROLINE-RICH
CHLOROPLAST

PROTEIN DC2.15 PRECURSOR
PRECURSOR (GGPP

Seq ID: 173
SYNTHETASE) (GGPS) [INCLUDES:

Accession: P50172
DIMETHYLALLYLTRANSFERASE;

Swissprot_id: DHI1_MOUSE
GERANYLTRANSTRANSFERASE;

Gi_number: 1706408
FARNESYLTRANSTRANSFERASE]

Description: Corticosteroid 11-beta-
Seq ID: 981

dehydrogenase, isozyme 1 (11-DH)
Accession: P87146

(11-beta-hydroxysteroid
Swissprot_id: IM22_SCHPO

dehydrogenase 1) (11-beta-HSD1)
Gi_number: 3219815

(11beta-HSD1A)
Description: MITOCHONDRIAL

Seq ID: 174
IMPORT INNER MEMBRANE

Accession: P25866
TRANSLOCASE SUBUNIT

Swissprot_id: UBC2_WHEAT
TIM22 HOMOLOG

Gi_number: 136640
Seq ID: 982

Description: UBIQUITIN-
Accession: O26934

CONJUGATING ENZYME E2-17 KD
Swissprot_id: ARGC_METTH

(UBIQUITIN-PROTEIN
Gi_number: 8927968

LIGASE) (UBIQUITIN
Description: N-acetyl-gamma-glutamyl-

CARRIER PROTEIN)
phosphate reductase

Seq ID: 175
(N-acetyl-glutamate semialdehyde

Accession: P51614
dehydrogenase) (NAGSA

Swissprot_id: CHIA_VITVI
dehydrogenase)

Gi_number: 1705812
Seq ID: 983

Description: ACIDIC ENDOCHITINASE
Accession: P08640

PRECURSOR
Swissprot_id: AMYH_YEAST

Seq ID: 177
Gi_number: 728850

Accession: P48038
Description: GLUCOAMYLASE S1/S2

Swissprot_id: ACRO_RABIT
PRECURSOR (GLUCAN

Gi_number: 1351865
1,4-ALPHA-GLUCOSIDASE)

Description: Acrosin precursor
(1,4-ALPHA-D-GLUCAN

Seq ID: 179
GLUCOHYDROLASE)

Accession: P42736
Seq ID: 984

Swissprot_id: CDI3_ARATH
Accession: Q02817

Gi_number: 1168862
Swissprot_id: MUC2_HUMAN

Description: CADMIUM-INDUCED
Gi_number: 2506877

PROTEIN AS30
Description: MUCIN 2 PRECURSOR

Seq ID: 180
(INTESTINAL MUCIN 2)

Accession: Q42443
Seq ID: 985

Swissprot_id: THIH_ORYSA
Accession: O23066

Gi_number: 3915131
Swissprot_id: C862_ARATH

Description: THIOREDOXIN H-TYPE
Gi_number: 5915846

(TRX-H) (PHLOEM SAP 13 KDA
Description: Cytochrome P450 86A2

PROTEIN-1)
Seq ID: 986

Seq ID: 181
Accession: P18583

Accession: Q04629
Swissprot_id: SON_HUMAN

Swissprot_id: PSLA_YEAST
Gi_number: 586013

Gi_number: 18202481
Description: SON PROTEIN (SON3)

Description: PSL10 protein
Seq ID: 991

Seq ID: 182
Accession: P19275

Accession: P27884
Swissprot_id: VTP3_TTV1V

Swissprot_id: CCAA_RABIT
Gi_number: 139655

Gi_number: 399201
Description: VIRAL PROTEIN TPX

Description: VOLTAGE-DEPENDENT
Seq ID: 992

P/Q-TYPE CALCIUM CHANNEL
Accession: P47735

ALPHA-1A
Swissprot_id: RLK5_ARATH

SUBUNIT (CALCIUM
Gi_number: 1350783

CHANNEL, L TYPE, ALPHA-1
Description: Receptor-like protein kinase 5

POLYPEPTIDE
precursor

ISOFORM 4) (BRAIN
Seq ID: 994

CALCIUM CHANNEL I) (BI)
Accession: P13816

Seq ID: 183
Swissprot_id: GARP_PLAFF

Accession: P02350
Gi_number: 120943

Swissprot_id: RS3A_XENLA
Description: GLUTAMIC ACID-RICH

Gi_number: 133940
PROTEIN PRECURSOR

Description: 40S RIBOSOMAL PROTEIN
Seq ID: 995

S3A (S1A)
Accession: P80073

Seq ID: 184
Swissprot_id: MYB2_PHYPA

Accession: Q9S8P4
Gi_number: 462669

Swissprot_id: RHRE_PEA
Description: Myb-related protein Pp2

Gi_number: 18203442
Seq ID: 996

Description: Rhicadhesin receptor
Accession: Q41144

precursor (Germin-like protein)
Swissprot_id: STC_RICCO

Seq ID: 185
Gi_number: 3915039

Accession: Q07760
Description: SUGAR CARRIER

Swissprot_id: RL23_TOBAC
PROTEIN C

Gi_number: 730536
Seq ID: 997

Description: 60S RIBOSOMAL PROTEIN
Accession: P33215

L23
Swissprot_id: NED1_MOUSE

Seq ID: 186
Gi_number: 462692

Accession: P13983
Description: NEDD1 protein

Swissprot_id: EXTN_TOBAC
Seq ID: 998

Gi_number: 119714
Accession: P51617

Description: Extensin precursor (Cell wall
Swissprot_id: IRA1_HUMAN

hydroxyproline-rich
Gi_number: 8928535

glycoprotein)
Description: Interleukin-1 receptor-

Seq ID: 187
associated kinase 1 (IRAK-1)

Accession: Q9SP35
Seq ID: 999

Swissprot_id: IM17_ARATH
Accession: P29128

Gi_number: 12643851
Swissprot_id: ICP0_HSVBJ

Description: MITOCHONDRIAL
Gi_number: 124136

IMPORT INNER MEMBRANE
Description: Trans-acting transcriptional

TRANSLOCASE SUBUNIT
protein ICP0 (P135 protein)

TIM17
(IER 2.9/ER2.6)

Seq ID: 188
Seq ID: 1000

Accession: Q05466
Accession: P19338

Swissprot_id: HAT4_ARATH
Swissprot_id: NUCL_HUMAN

Gi_number: 462281
Gi_number: 128841

Description: Homeobox-leucine zipper
Description: Nucleolin (Protein C23)

protein HAT4 (HD-ZIP protein 4)
Seq ID: 1002

(HD-ZIP protein ATHB-2)
Accession: P13645

Seq ID: 189
Swissprot_id: K1CJ_HUMAN

Accession: P50160
Gi_number: 547749

Swissprot_id: TS2_MAIZE
Description: Keratin, type I cytoskeletal 10

Gi_number: 1717794
(Cytokeratin 10) (K10) (CK

Description: SEX DETERMINATION
10)

PROTEIN TASSELSEED 2
Seq ID: 1003

Seq ID: 190
Accession: P52839

Accession: O54939
Swissprot_id: FSTL_ARATH

Swissprot_id: DHB3_RAT
Gi_number: 1706917

Gi_number: 3913460
Description: Flavonol sulfotransferase-like

Description: Estradiol 17 beta-
(RaRO47)

dehydrogenase 3 (17-beta-HSD 3)
Seq ID: 1005

(Testicular 17-beta-
Accession: P24814

hydroxysteroid dehydrogenase)
Swissprot_id: GRR1_YEAST

Seq ID: 191
Gi_number: 121649

Accession: Q9WTV7
Description: GRR1 protein

Swissprot_id: RNFB_MOUSE
Seq ID: 1007

Gi_number: 13124535
Accession: O43791

Description: RING FINGER PROTEIN 12
Swissprot_id: SPOP_HUMAN

(LIM DOMAIN INTERACTING RING
Gi_number: 8134708

FINGER
Description: Speckle-type POZ protein

PROTEIN) (RING FINGER LIM
Seq ID: 1008

DOMAIN-BINDING PROTEIN) (R-LIM)
Accession: Q06003

Seq ID: 192
Swissprot_id: GOLI_DROME

Accession: Q06666
Gi_number: 462193

Swissprot_id: T2_MOUSE
Description: Goliath protein (G1 protein)

Gi_number: 730888
Seq ID: 1009

Description: OCTAPEPTIDE-REPEAT
Accession: P09651

PROTEIN T2
Swissprot_id: ROA1_HUMAN

Seq ID: 193
Gi_number: 133254

Accession: Q02817
Description: Heterogeneous nuclear

Swissprot_id: MUC2_HUMAN
ribonucleoprotein A1

Gi_number: 2506877
(Helix-destabilizing protein)

Description: MUCIN 2 PRECURSOR
(Single-strand binding

(INTESTINAL MUCIN 2)
protein) (hnRNP core protein A1)

Seq ID: 194
Seq ID: 1010

Accession: Q9Y252
Accession: P08640

Swissprot_id: RNF6_HUMAN
Swissprot_id: AMYH_YEAST

Gi_number: 13124536
Gi_number: 728850

Description: RING FINGER PROTEIN 6
Description: GLUCOAMYLASE S1/S2

Seq ID: 195
PRECURSOR (GLUCAN

Accession: Q06652
1,4-ALPHA-GLUCOSIDASE)

Swissprot_id: GSHZ_CITSI
(1,4-ALPHA-D-GLUCAN

Gi_number: 544437
GLUCOHYDROLASE)

Description: GLUTATHIONE
Seq ID: 1011

PEROXIDASE HOMOLOG (SALT-
Accession: P15533

ASSOCIATED PROTEIN)
Swissprot_id: RPT1_MOUSE

Seq ID: 197
Gi_number: 133482

Accession: O00268
Description: Down regulatory protein of

Swissprot_id: T2D3_HUMAN
interleukin 2 receptor

Gi_number: 3024681
Seq ID: 1012

Description: TRANSCRIPTION
Accession: Q9S8P4

INITIATION FACTOR TFIID 135 KDA
Swissprot_id: RHRE_PEA

SUBUNIT
Gi_number: 18203442

(TAFII-135) (TAFII135) (TAFII-
Description: Rhicadhesin receptor

130) (TAFII130)
precursor (Germin-like protein)

Seq ID: 198
Seq ID: 1013

Accession: P37705
Accession: P46897

Swissprot_id: GRP3_DAUCA
Swissprot_id: ATH7_ARATH

Gi_number: 585217
Gi_number: 1168548

Description: GLYCINE RICH PROTEIN
Description: HOMEOBOX-LEUCINE

A3
ZIPPER PROTEIN ATHB-7 (HD-ZIP

Seq ID: 199
PROTEIN

Accession: Q40635
ATHB-7)

Swissprot_id: VATL_ORYSA
Seq ID: 1014

Gi_number: 2493147
Accession: P13983

Description: VACUOLAR ATP
Swissprot_id: EXTN_TOBAC

SYNTHASE 16 KD PROTEOLIPID
Gi_number: 119714

SUBUNIT
Description: Extensin precursor (Cell wall

Seq ID: 201
hydroxyproline-rich

Accession: O04003
glycoprotein)

Swissprot_id: LG1_MAIZE
Seq ID: 1015

Gi_number: 6016502
Accession: P18583

Description: LIGULELESS1 PROTEIN
Swissprot_id: SON_HUMAN

Seq ID: 202
Gi_number: 586013

Accession: P80639
Description: SON PROTEIN (SON3)

Swissprot_id: IF5A_MAIZE
Seq ID: 1016

Gi_number: 12643437
Accession: Q02516

Description: INITIATION FACTOR 5A
Swissprot_id: HAP5_YEAST

(EIF-5A) (EIF-4D)
Gi_number: 2493550

Seq ID: 203
Description: TRANSCRIPTIONAL

Accession: P31673
ACTIVATOR HAP5

Swissprot_id: HS12_ORYSA
Seq ID: 1017

Gi_number: 399937
Accession: Q9Y252

Description: 17.4 KD CLASS I HEAT
Swissprot_id: RNF6_HUMAN

SHOCK PROTEIN
Gi_number: 13124536

Seq ID: 204
Description: RING FINGER PROTEIN 6

Accession: P27483
Seq ID: 1019

Swissprot_id: GRP_ARATH
Accession: P11845

Gi_number: 121640
Swissprot_id: IPP2_RABIT

Description: GLYCINE-RICH CELL
Gi_number: 1170582

WALL STRUCTURAL PROTEIN
Description: Protein phosphatase inhibitor

PRECURSOR
2 (IPP-2)

Seq ID: 205
Seq ID: 1020

Accession: P03211
Accession: Q09151

Swissprot_id: EBN1_EBV
Swissprot_id: GLU3_ORYSA

Gi_number: 119110
Gi_number: 1707986

Description: EBNA-1 NUCLEAR
Description: GLUTELIN TYPE-A III

PROTEIN
PRECURSOR

Seq ID: 206
Seq ID: 1021

Accession: Q43261
Accession: P20698

Swissprot_id: H2B3_MAIZE
Swissprot_id: PRO7_ORYSA

Gi_number: 3913804
Gi_number: 130959

Description: HISTONE H2B.3
Description: PROLAMIN PPROL 17

Seq ID: 207
PRECURSOR

Accession: Q07760
Seq ID: 1022

Swissprot_id: RL23_TOBAC
Accession: P14323

Gi_number: 730536
Swissprot_id: GLU4_ORYSA

Description: 60S RIBOSOMAL PROTEIN
Gi_number: 121476

L23
Description: GLUTELIN PRECURSOR

Seq ID: 208
Seq ID: 1023

Accession: Q41001
Accession: P29518

Swissprot_id: BCP_PEA
Swissprot_id: BT1_MAIZE

Gi_number: 2493318
Gi_number: 231654

Description: Blue copper protein precursor
Description: Brittle-1 protein, chloroplast

Seeq ID: 209
precursor

Accession: P21997
Seq ID: 1024

Swissprot_id: SSGP_VOLCA
Accession: P28968

Gi_number: 134920
Swissprot_id: VGLX_HSVEB

Description: SULFATED SURFACE
Gi_number: 138350

GLYCOPROTEIN 185 (SSG 185)
Description: GLYCOPROTEIN X

Seq ID: 210
PRECURSOR

Accession: P14009
Seq ID: 1025

Swissprot_id: 14 KD_DAUCA
Accession: Q01883

Gi_number: 112697
Swissprot_id: RA17_ORYSA

Description: 14 KD PROLINE-RICH
Gi_number: 548660

PROTEIN DC2.15 PRECURSOR
Description: SEED ALLERGENIC

Seq ID: 211
PROTEIN RA17 PRECURSOR

Accession: Q9P7J6
Seq ID: 1026

Swissprot_id: R17B_SCHPO
Accession: P53682

Gi_number: 15214229
Swissprot_id: CDP1_ORYSA

Description: 40S ribosomal protein S17-B
Gi_number: 1705733

Seq ID: 212
Description: Calcium-dependent protein

Accession: O74893
kinase, isoform 1 (CDPK 1)

Swissprot_id: RS20_SCHPO
Seq ID: 1027

Gi_number: 6094168
Accession: Q08047

Description: 40S RIBOSOMAL PROTEIN
Swissprot_id: GLGB_MAIZE

S20
Gi_number: 1169911

Seq ID: 213
Description: 1,4-alpha-glucan branching

Accession: P78621
enzyme IIB, chloroplast

Swissprot_id: SEPA_EMENI
precursor (Starch branching

Gi_number: 15214279
enzyme IIB) (Q-enzyme)

Description: CYTOKINESIS PROTEIN
Seq ID: 1028

SEPA (FH1/2 PROTEIN) (FORCED
Accession: P55241

EXPRESSION INHIBITION OF
Swissprot_id: GLG1_MAIZE

GROWTH A)
Gi_number: 1707924

Seq ID: 214
Description: Glucose-1-phosphate

Accession: Q96499
adenylyltransferase large subunit 1,

Swissprot_id: RL44_GOSHI
chloroplast precursor (ADP-

Gi_number: 2500380
glucose synthase) (ADP-glucose

Description: 60S RIBOSOMAL PROTEIN
pyrophosphorylase) (AGPASE S)

L44
(Alpha-D-glucose-1-phosphate

Seq ID: 215
adenyl transferase) (Shrunken-2)

Accession: P55852
Seq ID: 1029

Swissprot_id: SMT3_ARATH
Accession: Q42980

Gi_number: 2501448
Swissprot_id: OLE1_ORYSA

Description: UBIQUITIN-LIKE PROTEIN
Gi_number: 3334280

SMT3
Description: OLEOSIN 16 KD (OSE701)

Seq ID: 216
Seq ID: 1030

Accession: P53665
Accession: Q02921

Swissprot_id: ACPM_ARATH
Swissprot_id: NO93_SOYBN

Gi_number: 1703091
Gi_number: 730165

Description: Acyl carrier protein,
Description: EARLY NODULIN 93 (N-

mitochondrial precursor (ACP)
93)

(NADH-ubiquinone
Seq ID: 1032

oxidoreductase 9.6 kDa subunit)
Accession: P07206

(MtACP-1)
Swissprot_id: PULA_KLEPN

Seq ID: 217
Gi_number: 131589

Accession: O81277
Description: Pullulanase precursor (Alpha-

Swissprot_id: PSK5_ORYSA
dextrin

Gi_number: 18202216
endo-1,6-alpha-glucosidase)

Description: Phytosulfokines 5 precursor
(Pullulan 6-glucanohydrolase)

(Secretory protein SH27A)
Seq ID: 1033

[Contains: Phytosulfokine-alpha
Accession: P18165

(PSK-alpha)
Swissprot_id: LORI_MOUSE

(Phytosulfokine-a);
Gi_number: 126390

Phytosulfokine-beta (PSK-beta)
Description: LORICRIN

(Phytosulfokine-b)]
Seq ID: 1034

Seq ID: 219
Accession: Q43093

Accession: P11414
Swissprot_id: UGS3_PEA

Swissprot_id: RPB1_CRIGR
Gi_number: 2833384

Gi_number: 133323
Description: Glycogen [starch] synthase,

Description: DNA-DIRECTED RNA
chloroplast precursor (GBSSII)

POLYMERASE II LARGEST SUBUNIT
(Granule-bound starch synthase

(RPB1)
II)

Seq ID: 220
Seq ID: 1036

Accession: P27603
Accession: P23509

Swissprot_id: PHEA_PSEST
Swissprot_id: GLGS_SOLTU

Gi_number: 130055
Gi_number: 232164

Description: P-PROTEIN [INCLUDES:
Description: Glucose-1-phosphate

CHORISMATE MUTASE (CM);
adenylyltransferase small subunit,

PREPHENATE
chloroplast precursor (ADP-

DEHYDRATASE (PDT)]
glucose synthase) (ADP-glucose

Seq ID: 221
pyrophosphorylase) (AGPASE B)

Accession: P49455
(Alpha-D-glucose-1-phosphate

Swissprot_id: TPM4_DROME
adenyl transferase)

Gi_number: 1351285
Seq ID: 1037

Description: TROPOMYOSIN 1, FUSION
Accession: P38560

PROTEIN 33
Swissprot_id: GLN2_MAIZE

Seq ID: 223
Gi_number: 585202

Accession: P42145
Description: GLUTAMINE

Swissprot_id: HSP1_PSECU
SYNTHETASE ROOT ISOZYME 2

Gi_number: 1170404
(GLUTAMATE —AMMONIA

Description: Sperm protamine P1
LIGASE)

Seq ID: 224
Seq ID: 1038

Accession: P15941
Accession: P40602

Swissprot_id: MUC1_HUMAN
Swissprot_id: APG_ARATH

Gi_number: 547937
Gi_number: 728867

Description: MUCIN 1 PRECURSOR
Description: ANTER-SPECIFIC

(POLYMORPHIC EPITHELIAL MUCIN)
PROLINE-RICH PROTEIN APG

(PEM)
PRECURSOR

(PEMT) (EPISIALIN) (TUMOR-
Seq ID: 1039

ASSOCIATED MUCIN)
Accession: Q07322

(CARCINOMA-ASSOCIATED
Swissprot_id: EC40_DAUCA

MUCIN) (TUMOR-ASSOCIATED
Gi_number: 1706562

EPITHELIAL
Description: EMBRYOGENIC-CELL

MEMBRANE ANTIGEN)
PROTEIN 40 (ECP40)

(EMA) (H23AG) (PEANUT-REACTIVE
Seq ID: 1040

URINARY
Accession: P09789

MUCIN) (PUM) (BREAST
Swissprot_id: GRP1_PETHY

CARCINOMA-ASSOCIA>
Gi_number: 121627

Seq ID: 225
Description: GLYCINE-RICH CELL

Accession: P70315
WALL STRUCTURAL PROTEIN 1

Swissprot_id: WASP_MOUSE
PRECURSOR

Gi_number: 2499130
Seq ID: 1041

Description: Wiskott-Aldrich syndrome
Accession: P80873

protein homolog (WASP)
Swissprot_id: GS39_BACSU

Seq ID: 226
Gi_number: 3123232

Accession: P36782
Description: GENERAL STRESS

Swissprot_id: VE2_HPV12
PROTEIN 39 (GSP39)

Gi_number: 549237
Seq ID: 1042

Description: REGULATORY PROTEIN
Accession: P15590

E2
Swissprot_id: GLB1_MAIZE

Seq ID: 227
Gi_number: 121205

Accession: P04052
Description: Globulin-1 S allele precursor

Swissprot_id: RPB1_DROME
(GLB1-S) (7S-like)

Gi_number: 14286163
Seq ID: 1043

Description: DNA-DIRECTED RNA
Accession: P27061

POLYMERASE II LARGEST SUBUNIT
Swissprot_id: PPA1_LYCES

Seq ID: 228
Gi_number: 130718

Accession: P10162
Description: Acid phosphatase precursor 1

Swissprot_id: PRPL_HUMAN
Seq ID: 1044

Gi_number: 131011
Accession: P93329

Description: SALIVARY PROLINE-RICH
Swissprot_id: NO20_MEDTR

PROTEIN PO (ALLELE K) [CONTAINS:
Gi_number: 3914142

PEPTIDE P-D]
Description: EARLY NODULIN 20

Seq ID: 229
PRECURSOR (N-20)

Accession: P13983
Seq ID: 1046

Swissprot_id: EXTN_TOBAC
Accession: P21997

Gi_number: 119714
Swissprot_id: SSGP_VOLCA

Description: Extensin precursor (Cell wall
Gi_number: 134920

hydroxyproline-rich
Description: SULFATED SURFACE

glycoprotein)
GLYCOPROTEIN 185 (SSG 185)

Seq ID: 230
Seq ID: 1047

Accession: P13983
Accession: P12624

Swissprot_id: EXTN_TOBAC
Swissprot_id: MACS_BOVIN

Gi_number: 119714
Gi_number: 585447

Description: Extensin precursor (Cell wall
Description: MYRISTOYLATED

hydroxyproline-rich
ALANINE-RICH C-KINASE

glycoprotein)
SUBSTRATE (MARCKS)

Seq ID: 231
(ACAMP-81)

Accession: P05142
Seq ID: 1048

Swissprot_id: PRP2_MOUSE
Accession: Q02516

Gi_number: 130999
Swissprot_id: HAP5_YEAST

Description: Proline-rich protein MP-2
Gi_number: 2493550

precursor
Description: TRANSCRIPTIONAL

Seq ID: 232
ACTIVATOR HAP5

Accession: P13983
Seq ID: 1049

Swissprot_id: EXTN_TOBAC
Accession: Q9SYQ8

Gi_number: 119714
Swissprot_id: CLV1_ARATH

Description: Extensin precursor (Cell wall
Gi_number: 12643323

hydroxyproline-rich
Description: RECEPTOR PROTEIN

glycoprotein)
KINASE CLAVATA1 PRECURSOR

Seq ID: 233
Seq ID: 1050

Accession: P19706
Accession: P13983

Swissprot_id: MYSB_ACACA
Swissprot_id: EXTN_TOBAC

Gi_number: 1171093
Gi_number: 119714

Description: Myosin heavy chain IB
Description: Extensin precursor (Cell wall

(Myosin heavy chain IL)
hydroxyproline-rich

Seq ID: 234
glycoprotein)

Accession: P14918
Seq ID: 1051

Swissprot_id: EXTN_MAIZE
Accession: P21997

Gi_number: 119712
Swissprot_id: SSGP_VOLCA

Description: EXTENSIN PRECURSOR
Gi_number: 134920

(PROLINE-RICH GLYCOPROTEIN)
Description: SULFATED SURFACE

Seq ID: 239
GLYCOPROTEIN 185 (SSG 185)

Accession: P40603
Seq ID: 1052

Swissprot_id: APG_BRANA
Accession: P13983

Gi_number: 728868
Swissprot_id: EXTN_TOBAC

Description: ANTER-SPECIFIC
Gi_number: 119714

PROLINE-RICH PROTEIN APG
Description: Extensin precursor (Cell wall

(PROTEIN CEX)
hydroxyproline-rich

Seq ID: 240
glycoprotein)

Accession O60610
Seq ID: 1054

Swissprot_id: DIA1_HUMAN
Accession: Q02280

Gi_number: 6225268
Swissprot_id: CIKE_DROME

Description: DIAPHANOUS PROTEIN
Gi_number: 399253

HOMOLOG 1 (DIAPHANOUS-
Description: Potassium channel protein eag

RELATED FORMIN 1)
Seq ID: 1055

(DRF1)
Accession: P46573

Seq ID: 243
Swissprot_id: APKB_ARATH

Accession: P21997
Gi_number: 12644274

Swissprot_id: SSGP_VOLCA
Description: PROTEIN KINASE APK1B

Gi_number: 134920
Seq ID: 1056

Description: SULFATED SURFACE
Accession: P32583

GLYCOPROTEIN 185 (SSG 185)
Swissprot_id: SR40_YEAST

Seq ID: 244
Gi_number: 548976

Accession: P18431
Description: SUPPRESSOR PROTEIN

Swissprot_id: SGG_DROME
SRP40

Gi_number: 13124808
Seq ID: 1057

Description: PROTEIN KINASE
Accession: Q9UNQ0

SHAGGY (PROTEIN ZESTE-WHITE 3)
Swissprot_id: ABG2_HUMAN

Seq ID: 246
Gi_number: 17433731

Accession: P24856
Description: ATP-binding cassette, sub-

Swissprot_id: ANP_NOTCO
family G, member 2

Gi_number: 8488962
(Placenta-specific ATP-binding

Description: Antifreeze glycopeptide
cassette transporter)

polyprotein precursor (AFGP
(Breast cancer resistance protein)

polyprotein) [Contains: AFGP7
Seq ID: 1058

(AFGP 7); AFGP8 (AFGP 8)]
Accession: P46573

Seq ID: 248
Swissprot_id: APKB_ARATH

Accession: P16356
Gi_number: 12644274

Swissprot_id: RPB1_CAEEL
Description: PROTEIN KINASE APK1B

Gi_number: 133322
Seq ID: 1060

Description: DNA-DIRECTED RNA
Accession: P57721

POLYMERASE II LARGEST SUBUNIT
Swissprot_id: PCB3_HUMAN

Seq ID: 250
Gi_number: 12230427

Accession: P18165
Description: Poly(rC)-binding protein 3

Swissprot_id: LORI_MOUSE
(Alpha-CP3)

Gi_number: 126390
Seq ID: 1061

Description: LORICRIN
Accession: P22059

Seq ID: 252
Swissprot_id: OXYB_HUMAN

Accession: P21997
Gi_number: 129308

Swissprot_id: SSGP_VOLCA
Description: Oxysterol-binding protein

Gi_number: 134920
Seq ID: 1062

Description: SULFATED SURFACE
Accession: P14328

GLYCOPROTEIN 185 (SSG 185)
Swissprot_id: SP96_DICDI

Seq ID: 253
Gi_number: 134780

Accession: Q01538
Description: SPORE COAT PROTEIN

Swissprot_id: MYT1_HUMAN
SP96

Gi_number: 13638422
Seq ID: 1063

Description: MYELIN TRANSCRIPTION
Accession: P40603

FACTOR 1 (MYT1) (MYTI)
Swissprot_id: APG_BRANA

(PROTEOLIPID
Gi_number: 728868

PROTEIN BINDING PROTEIN)
Description: ANTER-SPECIFIC

(PLPB1)
PROLINE-RICH PROTEIN APG

Seq ID: 254
(PROTEIN CEX)

Accession: Q02817
Seq ID: 1064

Swissprot_id: MUC2_HUMAN
Accession: Q11207

Gi_number: 2506877
Swissprot_id: PPOL_ARATH

Description: MUCIN 2 PRECURSOR
Gi_number: 1709740

(INTESTINAL MUCIN 2)
Description: Poly [ADP-ribose]

Seq ID: 255
polymerase (PARP) (ADPRT) (NAD(+)

Accession: P17133
ADP-ribosyltransferase)

Swissprot_id: RU17_DROME
(Poly[ADP-ribose] synthetase)

Gi_number: 13638469
Seq ID: 1065

Description: U1 SMALL NUCLEAR
Accession: Q06548

RIBONUCLEOPROTEIN 70 KDA (U1
Swissprot_id: APKA_ARATH

SNRNP 70 KDA)
Gi_number: 1168470

(SNRNP70)
Description: Protein kinase APK1A

Seq ID: 256
Seq ID: 1066

Accession: P05527
Accession: P53392

Swissprot_id: HMIN_DROME
Swissprot_id: SUT2_STYHA

Gi_number: 123388
Gi_number: 1711617

Description: HOMEOBOX PROTEIN
Description: HIGH AFFINITY

INVECTED
SULPHATE TRANSPORTER 2

Seq ID: 257
Seq ID: 1067

Accession: O80340
Accession: P18583

Swissprot_id: ERF4_ARATH
Swissprot_id: SON_HUMAN

Gi_number: 7531110
Gi_number: 586013

Description: Ethylene responsive element
Description: SON PROTEIN (SON3)

binding factor 4 (AtERF4)
Seq ID: 1068

Seq ID: 258
Accession: P41230

Accession: P40954
Swissprot_id: SMCX_MOUSE

Swissprot_id: CHI3_CANAL
Gi_number: 17380305

Gi_number: 1168933
Description: SmcX protein (Xe169 protein)

Description: CHITINASE 3 PRECURSOR
Seq ID: 1069

Seq ID: 259
Accession: Q9Y705

Accession: Q02817
Swissprot_id: ALP4_SCHPO

Swissprot_id: MUC2_HUMAN
Gi_number: 18203637

Gi_number: 2506877
Description: Spindle pole body component

Description: MUCIN 2 PRECURSOR
Alp4

(INTESTINAL MUCIN 2)
Seq ID: 1070

Seq ID: 260
Accession: P52409

Accession: P11675
Swissprot_id: E13B_WHEAT

Swissprot_id: IE18_PRVIF
Gi_number: 1706551

Gi_number: 124178
Description: GLUCAN ENDO-1,3-BETA-

Description: IMMEDIATE-EARLY
GLUCOSIDASE PRECURSOR

PROTEIN IE180
((1->3)-BETA-GLUCAN

Seq ID: 261
ENDOHYDROLASE) ((1->3)-BETA-

Accession: P08640
GLUCANASE)

Swissprot_id: AMYH_YEAST
(BETA-1,3-

Gi_number: 728850
ENDOGLUCANASE)

Description: GLUCOAMYLASE S1/S2
Seq ID: 1071

PRECURSOR (GLUCAN
Accession: P10978

1,4-ALPHA-GLUCOSIDASE)
Swissprot_id: POLX_TOBAC

(1,4-ALPHA-D-GLUCAN
Gi_number: 130582

GLUCOHYDROLASE)
Description: Retrovirus-related Pol

Seq ID: 262
polyprotein from transposon TNT

Accession: P05790
1-94 [Contains: Protease;

Swissprot_id: FBOH_BOMMO
Reverse transcriptase;

Gi_number: 9087216
Endonuclease]

Description: FIBROIN HEAVY CHAIN
Seq ID: 1072

PRECURSOR (FIB-H) (H-FIBROIN)
Accession: P33485

Seq ID: 263
Swissprot_id: VNUA_PRVKA

Accession: Q02817
Gi_number: 465445

Swissprot_id: MUC2_HUMAN
Description: PROBABLE NUCLEAR

Gi_number: 2506877
ANTIGEN

Description: MUCIN 2 PRECURSOR
Seq ID: 1073

(INTESTINAL MUCIN 2)
Accession: Q07423

Seq ID: 264
Swissprot_id: HEX6_RICCO

Accession: Q9NYV4
Gi_number: 1708191

Swissprot_id: CRK7_HUMAN
Description: HEXOSE CARRIER

Gi_number: 12643825
PROTEIN HEX6

Description: CELL DIVISION CYCLE 2-
Seq ID: 1074

RELATED PROTEIN KINASE 7
Accession: P13816

(CDC2-RELATED PROTEIN
Swissprot_id: GARP_PLAFF

KINASE 7) (CRKRS)
Gi_number: 120943

Seq ID: 265
Description: GLUTAMIC ACID-RICH

Accession: Q42569
PROTEIN PRECURSOR

Swissprot_id: C901_ARATH
Seq ID: 1075

Gi_number: 5915851
Accession: P93531

Description: Cytochrome P450 90A1
Swissprot_id: C7D7_SOLCH

Seq ID: 266
Gi_number: 5915836

Accession: Q19200
Description: CYTOCHROME P450 71D7

Swissprot_id: STO1_CAEEL
Seq ID: 1076

Gi_number: 2493264
Accession: Q00808

Description: STO-1 PROTEIN
Swissprot_id: HET1_PODAN

Seq ID: 267
Gi_number: 3023956

Accession: P34579
Description: Vegetatible incompatibility

Swissprot_id: UN47_CAEEL
protein HET-E-1

Gi_number: 14917051
Seq ID: 1077

Description: Unc-47 protein
Accession: Q41819

Seq ID: 268
Swissprot_id: IAAG_MAIZE

Accession: O04681
Gi_number: 2501499

Swissprot_id: PT15_LYCES
Description: INDOLE-3-ACETATE

Gi_number: 7531180
BETA-GLUCOSYLTRANSFERASE

Description: PATHOGENESIS-
(IAA-GLU

RELATED GENES TRANSCRIPTIONAL
SYNTHETASE) ((URIDINE

ACTIVATOR PT15
5′-DIPHOSPHATE-

Seq ID: 269
GLUCOSE: INDOL-3-YLACETYL)-

Accession: P03211
BETA-D-GLUCOSYL

Swissprot_id: EBN1_EBV
TRANSFERASE)

Gi_number: 119110
Seq ID: 1078

Description: EBNA-1 NUCLEAR
Accession: Q9UMN6

PROTEIN
Swissprot_id: TRX2_HUMAN

Seq ID: 270
Gi_number: 12643900

Accession: P27884
Description: TRITHORAX HOMOLOG 2

Swissprot_id: CCAA_RABIT
(MIXED LINEAGE LEUKEMIA GENE

Gi_number: 399201
HOMOLOG 2

Description: VOLTAGE-DEPENDENT
PROTEIN)

P/Q-TYPE CALCIUM CHANNEL
Seq ID: 1079

ALPHA-1A
Accession: P27934

SUBUNIT (CALCIUM
Swissprot_id: AM3E_ORYSA

CHANNEL, L TYPE, ALPHA-1
Gi_number: 113683

POLYPEPTIDE
Description: ALPHA-AMYLASE

ISOFORM 4) (BRAIN
ISOZYME 3E PRECURSOR (1,4-

CALCIUM CHANNEL I) (BI)
ALPHA-D-GLUCAN

Seq ID: 271
GLUCANOHYDROLASE)

Accession: Q02817
Seq ID: 1080

Swissprot_id: MUC2_HUMAN
Accession: P03211

Gi_number: 2506877
Swissprot_id: EBN1_EBV

Description: MUCIN 2 PRECURSOR
Gi_number: 119110

(INTESTINAL MUCIN 2)
Description: EBNA-1 NUCLEAR

Seq ID: 272
PROTEIN

Accession: P28968
Seq ID: 1081

Swissprot_id: VGLX_HSVEB
Accession: P42777

Gi_number: 138350
Swissprot_id: GBF4_ARATH

Description: GLYCOPROTEIN X
Gi_number: 1169863

PRECURSOR
Description: G-box binding factor 4

Seq ID: 273
Seq ID: 1082

Accession: P13983
Accession: O89114

Swissprot_id: EXTN_TOBAC
Swissprot_id: DJB5_MOUSE

Gi_number: 119714
Gi_number: 18202246

Description: Extensin precursor (Cell wall
Description: DnaJ homolog subfamily B

hydroxyproline-rich
member 5 (Heat shock protein

glycoprotein)
Hsp40-3) (Heat shock protein

Seq ID: 275
cognate 40) (Hsc40)

Accession: P36024
Seq ID: 1083

Swissprot_id: SIS2_YEAST
Accession: P28656

Gi_number: 548925
Swissprot_id: NPL1_MOUSE

Description: SIS2 PROTEIN
Gi_number: 1709338

(HALOTOLERANCE PROTEIN HAL3)
Description: Nucleosome assembly protein

Seq ID: 276
1-like 1 (NAP-1 related

Accession: O80337
protein) (Brain protein DN38)

Swissprot_id: ERFI_ARATH
Seq ID: 1085

Gi_number: 7531107
Accession: Q9NR09

Description: ETHYLENE RESPONSIVE
Swissprot_id: BIR6_HUMAN

ELEMENT BINDING FACTOR 1
Gi_number: 12585192

(ATERF1)
Description: BACULOVIRAL IAP

Seq ID: 277
REPEAT-CONTAINING PROTEIN 6

Accession: P33485
(UBIQUITIN-CONJUGATING

Swissprot_id: VNUA_PRVKA
BIR-DOMAIN ENZYME APOLLON)

Gi_number: 465445
Seq ID: 1086

Description: PROBABLE NUCLEAR
Accession: P37702

ANTIGEN
Swissprot_id: MYRO_ARATH

Seq ID: 278
Gi_number: 585536

Accession: Q9WTV7
Description: Myrosinase precursor

Swissprot_id: RNFB_MOUSE
(Sinigrinase) (Thioglucosidase)

Gi_number: 13124535
Seq ID: 1090

Description: RING FINGER PROTEIN 12
Accession: O35973

(LIM DOMAIN INTERACTING RING
Swissprot_id: PER1_MOUSE

FINGER
Gi_number: 6093673

PROTEIN) (RING FINGER LIM
Description: Period circadian protein 1

DOMAIN-BINDING PROTEIN) (R-LIM)
(Circadian pacemaker protein

Seq ID: 279
Rigui) (mPER) (M-Rigui)

Accession: P18583
Seq ID: 1091

Swissprot_id: SON_HUMAN
Accession: P05143

Gi_number: 586013
Swissprot_id: PRP3_MOUSE

Description: SON PROTEIN (SON3)
Gi_number: 131002

Seq ID: 280
Description: PROLINE-RICH PROTEIN

Accession: O43516
MP-3

Swissprot_id: WAIP_HUMAN
Seq ID: 1092

Gi_number: 13124642
Accession: Q9NYV4

Description: WISKOTT-ALDRICH
Swissprot_id: CRK7_HUMAN

SYNDROME PROTEIN INTERACTING
Gi_number: 12643825

PROTEIN (WASP
Description: CELL DIVISION CYCLE 2-

INTERACTING PROTEIN)
RELATED PROTEIN KINASE 7

(PRPL-2 PROTEIN)
(CDC2-RELATED PROTEIN

Seq ID: 281
KINASE 7) (CRKRS)

Accession: Q9W611
Seq ID: 1093

Swissprot_id: RBMS_CHICK
Accession: P50156

Gi_number: 13124483
Swissprot_id: TIPG_ORYSA

Description: RNA-binding protein with
Gi_number: 1729971

multiple splicing homolog
Description: TONOPLAST INTRINSIC

(RBP-MS) (HEart, RRM
PROTEIN, GAMMA (GAMMA TIP)

Expressed Sequence) (Hermes)
(AQUAPORIN-TIP)

Seq ID: 282
Seq ID: 1095

Accession: Q03173
Accession: Q9SFF9

Swissprot_id: NDPP_MOUSE
Swissprot_id: GL17_ARATH

Gi_number: 1709249
Gi_number: 18203443

Description: NPC DERIVED PROLINE
Description: Germin-like protein subfamily

RICH PROTEIN 1 (NDPP-1)
1 member 7 precursor

Seq ID: 284
Seq ID: 1096

Accession: P06544
Accession: P32110

Swissprot_id: THI1_ANASO
Swissprot_id: GTX6_SOYBN

Gi_number: 135761
Gi_number: 417148

Description: Thioredoxin 1 (TRX-1)
Description: PROBABLE

(Thioredoxin M)
GLUTATHIONE S-TRANSFERASE

Seq ID: 285
(HEAT SHOCK PROTEIN

Accession: Q9WTV7
26A) (G2-4)

Swissprot_id: RNFB_MOUSE
Seq ID: 1097

Gi_number: 13124535
Accession: Q06003

Description: RING FINGER PROTEIN 12
Swissprot_id: GOLI_DROME

(LIM DOMAIN INTERACTING RING
Gi_number: 462193

FINGER
Description: Goliath protein (G1 protein)

PROTEIN) (RING FINGER LIM
Seq ID: 1099

DOMAIN-BINDING PROTEIN) (R-LIM)
Accession: P39163

Seq ID: 286
Swissprot_id: CHAC_ECOLI

Accession: Q40089
Gi_number: 12644253

Swissprot_id: ATP4_IPOBA
Description: CATION TRANSPORT

Gi_number: 2493046
PROTEIN CHAC

Description: ATP synthase delta' chain,
Seq ID: 1101

mitochondrial precursor
Accession: Q38924

Seq ID: 287
Swissprot_id: PPAF_ARATH

Accession: P36787
Gi_number: 2499542

Swissprot_id: VE2_HPV25
Description: IRON(III)-ZINC(II) PURPLE

Gi_number: 549242
ACID PHOSPHATASE PRECURSOR

Description: REGULATORY PROTEIN
(PAP)

E2
Seq ID: 1102

Seq ID: 288
Accession: Q99090

Accession: P70315
Swissprot_id: CPR2_PETCR

Swissprot_id: WASP_MOUSE
Gi_number: 2842757

Gi_number: 2499130
Description: LIGHT-INDUCIBLE

Description: Wiskott-Aldrich syndrome
PROTEIN CPRF-2

protein homolog (WASP)
Seq ID: 1103

Seq ID: 289
Accession: P52565

Accession: P11675
Swissprot_id: GDIR_HUMAN

Swissprot_id: IE18_PRVIF
Gi_number: 1707892

Gi_number: 124178
Description: Rho GDP-dissociation

Description: IMMEDIATE-EARLY
inhibitor 1 (Rho GDI 1) (Rho-GDI

PROTEIN IE180
alpha)

Seq ID: 290
Seq ID: 1105

Accession: O08816
Accession: O54956

Swissprot_id: WASL_RAT
Swissprot_id: DPE2_MOUSE

Gi_number: 13431956
Gi_number: 3913512

Description: Neural Wiskott-Aldrich
Description: DNA POLYMERASE

syndrome protein (N-WASP)
EPSILON SUBUNIT B (DNA

Seq ID: 291
POLYMERASE II

Accession: P17483
SUBUNIT B)

Swissprot_id: HXB4_HUMAN
Seq ID: 1107

Gi_number: 547692
Accession: Q50634

Description: HOMEOBOX PROTEIN
Swissprot_id: SECD_MYCTU

HOX-B4 (HOX-2F) (HOX-2.6)
Gi_number: 2498898

Seq ID: 292
Description: Protein-export membrane

Accession: Q53547
protein secD

Swissprot_id: EST2_PSEFL
Seq ID: 1108

Gi_number: 3023719
Accession: P08548

Description: CARBOXYLESTERASE 2
Swissprot_id: LIN1_NYCCO

(ESTERASE II)
Gi_number: 126296

Seq ID: 294
Description: LINE-1 REVERSE

Accession: P13983
TRANSCRIPTASE HOMOLOG

Swissprot_id: EXTN_TOBAC
Seq ID: 1110

Gi_number: 119714
Accession: Q9ZSK5

Description: Extensin precursor (Cell wall
Swissprot_id: ZOG_PHALU

hydroxyproline-rich
Gi_number: 6226510

glycoprotein)
Description: Zeatin O-glucosyltransferase

Seq ID: 295
(Zeatin

Accession: P47735
O-beta-D-glucosyltransferase)

Swissprot_id: RLK5_ARATH
Seq ID: 1112

Gi_number: 1350783
Accession: P28968

Description: Receptor-like protein kinase 5
Swissprot_id: VGLX_HSVEB

precursor
Gi_number: 138350

Seq ID: 296
Description: GLYCOPROTEIN X

Accession: P03211
PRECURSOR

Swissprot_id: EBN1_EBV
Seq ID: 1119

Gi_number: 119110
Accession: P42768

Description: EBNA-1 NUCLEAR
Swissprot_id: WASP_HUMAN

PROTEIN
Gi_number: 1722836

Seq ID: 297
Description: WISKOTT-ALDRICH

Accession: P23074
SYNDROME PROTEIN (WASP)

Swissprot_id: POL_SFV1
Seq ID: 1122

Gi_number: 400825
Accession: O08816

Description: POL polyprotein [Contains:
Swissprot_id: WASL_RAT

Protease; Reverse
Gi_number: 13431956

transcriptase; Endonuclease]
Description: Neural Wiskott-Aldrich

Seq ID: 298
syndrome protein (N-WASP)

Accession: P09189
Seq ID: 1125

Swissprot_id: HS7C_PETHY
Accession: P21997

Gi_number: 123650
Swissprot_id: SSGP_VOLCA

Description: HEAT SHOCK COGNATE
Gi_number: 134920

70 KD PROTEIN
Description: SULFATED SURFACE

Seq ID: 299
GLYCOPROTEIN 185 (SSG 185)

Accession: P43293
Seq ID: 1126

Swissprot_id: NAK_ARATH
Accession: P10220

Gi_number: 1171642
Swissprot_id: TEGU_HSV11

Description: Probable serine/threonine-
Gi_number: 135576

protein kinase NAK
Description: LARGE TEGUMENT

Seq ID: 300
PROTEIN (VIRION PROTEIN UL36)

Accession: P08775
Seq ID: 1127

Swissprot_id: RPB1_MOUSE
Accession: P42158

Gi_number: 133327
Swissprot_id: KC1D_ARATH

Description: DNA-directed RNA
Gi_number: 1170622

polymerase II largest subunit (RPB1)
Description: CASEIN KINASE I, DELTA

Seq ID: 301
ISOFORM LIKE (CKI-DELTA)

Accession: P36787
Seq ID: 1128

Swissprot_id: VE2_HPV25
Accession: Q9NZW4

Gi_number: 549242
Swissprot_id: DSPP_HUMAN

Description: REGULATORY PROTEIN
Gi_number: 17865470

E2
Description: Dentin sialophosphoprotein

Seq ID: 302
precursor [Contains: Dentin

Accession: O60508
phosphoprotein (Dentin

Swissprot_id: PR17_HUMAN
phosphophoryn) (DPP); Dentin

Gi_number: 17380181
sialoprotein (DSP)]

Description: Pre-mRNA splicing factor
Seq ID: 1130

PRP17 (hPRP17) (EH-binding
Accession: Q9Y5T5

protein 3) (Ehb3)
Swissprot_id: UBPG_HUMAN

Seq ID: 303
Gi_number: 6686071

Accession: Q02817
Description: Ubiquitin carboxyl-terminal

Swissprot_id: MUC2_HUMAN
hydrolase 16 (Ubiquitin

Gi_number: 2506877
thiolesterase 16) (Ubiquitin-

Description: MUCIN 2 PRECURSOR
specific processing protease

(INTESTINAL MUCIN 2)
16) (Deubiquitinating enzyme 16)

Seq ID: 304
(Ubiquitin processing

Accession: Q39017
protease UBP-M)

Swissprot_id: KDG1_ARATH
Seq ID: 1131

Gi_number: 2494034
Accession: Q02817

Description: Diacylglycerol kinase 1
Swissprot_id: MUC2_HUMAN

(Diglyceride kinase 1) (DGK 1)
Gi_number: 2506877

(DAG kinase 1)
Description: MUCIN 2 PRECURSOR

Seq ID: 305
(INTESTINAL MUCIN 2)

Accession: P51027
Seq ID: 1133

Swissprot_id: NRM1_CHICK
Accession: P08640

Gi_number: 1709350
Swissprot_id: AMYH_YEAST

Description: Natural resistance-associated
Gi_number: 728850

macrophage protein 1 (NRAMP
Description: GLUCOAMYLASE S1/S2

1)
PRECURSOR (GLUCAN

Seq ID: 306
1,4-ALPHA-GLUCOSIDASE)

Accession: Q96423
(1,4-ALPHA-D-GLUCAN

Swissprot_id: TCMO_GLYEC
GLUCOHYDROLASE)

Gi_number: 3915095
Seq ID: 1134

Description: TRANS-CINNAMATE 4-
Accession: P21997

MONOOXYGENASE (CINNAMIC ACID
Swissprot_id: SSGP_VOLCA

4-HYDROXYLASE) (CA4H)
Gi_number: 134920

(C4H) (P450C4H) (CYTOCHROME P450
Description: SULFATED SURFACE

73)
GLYCOPROTEIN 185 (SSG 185)

Seq ID: 307
Seq ID: 1135

Accession: P02812
Accession: P13983

Swissprot_id: PRP2_HUMAN
Swissprot_id: EXTN_TOBAC

Gi_number: 130998
Gi_number: 119714

Description: Salivary proline-rich protein
Description: Extensin precursor (Cell wall

precursor (Clone CP7)
hydroxyproline-rich

[Contains: Basic peptide P-F]
glycoprotein)

Seq ID: 308
Seq ID: 1137

Accession: P12783
Accession: P43293

Swissprot_id: PGKY_WHEAT
Swissprot_id: NAK_ARATH

Gi_number: 129916
Gi_number: 1171642

Description: PHOSPHOGLYCERATE
Description: Probable serine/threonine-

KINASE, CYTOSOLIC
protein kinase NAK

Seq ID: 309
Seq ID: 1141

Accession: P17840
Accession: P20026

Swissprot_id: SLS3_BRAOL
Swissprot_id: MYB1_HORVU

Gi_number: 134532
Gi_number: 127579

Description: S-locus-specific glycoprotein
Description: Myb-related protein Hv1

S13 precursor (SLSG-13)
Seq ID: 1143

Seq ID: 310
Accession: P13983

Accession: Q9Z2A7
Swissprot_id: EXTN_TOBAC

Swissprot_id: DGAT_MOUSE
Gi_number: 119714

Gi_number: 17374647
Description: Extensin precursor (Cell wall

Description: Diacylglycerol O-
hydroxyproline-rich

acyltransferase (Diglyceride
glycoprotein)

acyltransferase)
Seq ID: 1144

Seq ID: 311
Accession: P70315

Accession: P38564
Swissprot_id: WASP_MOUSE

Swissprot_id: MNBA_MAIZE
Gi_number: 2499130

Gi_number: 1346559
Description: Wiskott-Aldrich syndrome

Description: DNA-BINDING PROTEIN
protein homolog (WASP)

MNB1A
Seq ID: 1145

Seq ID: 312
Accession: P33313

Accession: P10496
Swissprot_id: CNS1_YEAST

Swissprot_id: GRP2_PHAVU
Gi_number: 465507

Gi_number: 121632
Description: CYCLOPHILIN SEVEN

Description: GLYCINE-RICH CELL
SUPPRESSOR 1 (STI1 STRESS-

WALL STRUCTURAL PROTEIN 1.8
INDUCIBLE

PRECURSOR
PROTEIN HOMOLOG)

(GRP 1.8)
Seq ID: 1146

Seq ID: 313
Accession: P50172

Accession: P40631
Swissprot_id: DHI1_MOUSE

Swissprot_id: MLH_TETTH
Gi_number: 1706408

Gi_number: 730030
Description: Corticosteroid 11-beta-

Description: Micronuclear linker histone
dehydrogenase, isozyme 1 (11-DH)

polyprotein (MIC LH)
(11-beta-hydroxysteroid

[Contains: Micronuclear linker
dehydrogenase 1) (11-beta-HSD1)

histone-alpha; Micronuclear
(11beta-HSD1A)

linker histone-beta; Micronuclear
Seq ID: 1147

linker histone-delta;
Accession: P08079

Micronuclear linker histone-
Swissprot_id: GDB0_WHEAT

gamma]
Gi_number: 121099

Seq ID: 315
Description: GAMMA-GLIADIN

Accession: O24215
PRECURSOR

Swissprot_id: DCAM_ORYSA
Seq ID: 1148

Gi_number: 6166113
Accession: P20026

Description: S-
Swissprot_id: MYB1_HORVU

ADENOSYLMETHIONINE
Gi_number: 127579

DECARBOXYLASE PROENZYME
Description: Myb-related protein Hv1

(ADOMETDC)
Seq ID: 1149

(SAMDC)
Accession: Q9UGP9

Seq ID: 316
Swissprot_id: WDR5_HUMAN

Accession: Q9LX45
Gi_number: 12230771

Swissprot_id: PIR4_ARATH
Description: WD-repeat protein 5

Gi_number: 14195010
Seq ID: 1150

Description: Pirin-like protein At3g59260
Accession: Q41276

Seq ID: 317
Swissprot_id: AP1_SINAL

Accession: P34913
Gi_number: 3913047

Swissprot_id: HYES_HUMAN
Description: Floral homeotic protein

Gi_number: 462369
APETALA1 (MADS C)

Description: Soluble epoxide hydrolase
Seq ID: 1151

(SEH) (Epoxide hydratase)
Accession: P49634

(Cytosolic epoxide hydrolase)
Swissprot_id: UBIQ_ACACA

(CEH)
Gi_number: 1351348

Seq ID: 318
Description: UBIQUITIN

Accession: P13983
Seq ID: 1153

Swissprot_id: EXTN_TOBAC
Accession: P01103

Gi_number: 119714
Swissprot_id: MYB_CHICK

Description: Extensin precursor (Cell wall
Gi_number: 127591

hydroxyproline-rich
Description: Myb proto-oncogene protein

glycoprotein)
(C-myb)

Seq ID: 320
Seq ID: 1154

Accession: Q9HTR0
Accession: Q08446

Swissprot_id: NOM2_PSEAE
Swissprot_id: SGT1_YEAST

Gi_number: 14285606
Gi_number: 2498910

Description: Probable multidrug resistance
Description: SGT1 PROTEIN

protein norM 2 (Na(+)/drug
Seq ID: 1156

antiporter) (Multidrug-efflux
Accession: P42736

transporter)
Swissprot_id: CDI3_ARATH

Seq ID: 321
Gi_number: 1168862

Accession: O43516
Description: CADMIUM-INDUCED

Swissprot_id: WAIP_HUMAN
PROTEIN AS30

Gi_number: 13124642
Seq ID: 1158

Description: WISKOTT-ALDRICH
Accession: P20025

SYNDROME PROTEIN INTERACTING
Swissprot_id: MYB3_MAIZE

PROTEIN (WASP
Gi_number: 127582

INTERACTING PROTEIN)
Description: Myb-related protein Zm38

(PRPL-2 PROTEIN)
Seq ID: 1159

Seq ID: 322
Accession: P17483

Accession: O43516
Swissprot_id: HXB4_HUMAN

Swissprot_id: WAIP_HUMAN
Gi_number: 547692

Gi_number: 13124642
Description: HOMEOBOX PROTEIN

Description: WISKOTT-ALDRICH
HOX-B4 (HOX-2F) (HOX-2.6)

SYNDROME PROTEIN INTERACTING
Seq ID: 1163

PROTEIN (WASP
Accession: Q09790

INTERACTING PROTEIN)
Swissprot_id: APS1_SCHPO

(PRPL-2 PROTEIN)
Gi_number: 1175461

Seq ID: 323
Description: Diadenosine 5′,5′′′-P1,P6-

Accession: Q12446
hexaphosphate hydrolase (Ap6A

Swissprot_id: LA17_YEAST
hydrolase)

Gi_number: 2498506
Seq ID: 1164

Description: PROLINE-RICH PROTEIN
Accession: O08808

LAS17
Swissprot_id: DIA1_MOUSE

Seq ID: 324
Gi_number: 6014968

Accession: Q00451
Description: Diaphanous protein homolog

Swissprot_id: PRF1_LYCES
1 (Diaphanous-related formin 1)

Gi_number: 1709767
(DRF1) (mDIA1) (p140mDIA)

Description: 36.4 KD PROLINE-RICH
Seq ID: 1165

PROTEIN
Accession: O65740

Seq ID: 326
Swissprot_id: DEF2_CAPAN

Accession: P39881
Gi_number: 17373811

Swissprot_id: CUT1_CANFA
Description: Defensin J1-2 precursor

Gi_number: 729093
Seq ID: 1166

Description: CCAAT displacement protein
Accession: O00763

(Homeobox protein Clox)
Swissprot_id: COA2_HUMAN

(Clox-1)
Gi_number: 2493312

Seq ID: 327
Description: ACETYL-COA

Accession: P10162
CARBOXYLASE 2 (ACC-BETA)

Swissprot_id: PRPL_HUMAN
[INCLUDES: BIOTIN

Gi_number: 131011
CARBOXYLASE]

Description: SALIVARY PROLINE-RICH
Seq ID: 1167

PROTEIN PO (ALLELE K) [CONTAINS:
Accession: O04716

PEPTIDE P-D]
Swissprot_id: MSH6_ARATH

Seq ID: 329
Gi_number: 6226648

Accession: P70315
Description: DNA mismatch repair protein

Swissprot_id: WASP_MOUSE
MSH6-1 (AtMsh6-1)

Gi_number: 2499130
Seq ID: 1168

Description: Wiskott-Aldrich syndrome
Accession: O08638

protein homolog (WASP)
Swissprot_id: MYHB_MOUSE

Seq ID: 330
Gi_number: 13431676

Accession: P52154
Description: MYOSIN HEAVY CHAIN,

Swissprot_id: RHO_MICLU
SMOOTH MUSCLE ISOFORM

Gi_number: 2507337
(SMMHC)

Description: Transcription termination
Seq ID: 1170

factor rho
Accession: P47990

Seq ID: 332
Swissprot_id: XDH_CHICK

Accession: P14897
Gi_number: 1351438

Swissprot_id: ELI9_HORVU
Description: XANTHINE

Gi_number: 119286
DEHYDROGENASE/OXIDASE

Description: Low molecular mass early
[INCLUDES: XANTHINE

light-inducible protein HV90,
DEHYDROGENASE (XD);

chloroplast precursor (ELIP)
XANTHINE OXIDASE (XO)

Seq ID: 333
(XANTHINE

Accession: Q39411
OXIDOREDUCTASE)]

Swissprot_id: RL26_BRARA
Seq ID: 1171

Gi_number: 3914740
Accession: Q42877

Description: 60S RIBOSOMAL PROTEIN
Swissprot_id: RPB2_LYCES

L26
Gi_number: 11134656

Seq ID: 335
Description: DNA-directed RNA

Accession: P19837
polymerase II 135 kDa polypeptide (RNA

Swissprot_id: SPD1_NEPCL
polymerase II subunit 2)

Gi_number: 1174414
Seq ID: 1172

Description: SPIDROIN 1 (DRAGLINE
Accession: Q05609

SILK FIBROIN 1)
Swissprot_id: CTR1_ARATH

Seq ID: 336
Gi_number: 1169128

Accession: P46665
Description: Serine/threonine-protein

Swissprot_id: HT14_ARATH
kinase CTR1

Gi_number: 12230908
Seq ID: 1173

Description: Homeobox-leucine zipper
Accession: P04323

protein HAT14 (HD-ZIP protein 14)
Swissprot_id: POL3_DROME

Seq ID: 337
Gi_number: 130405

Accession: P47815
Description: Retrovirus-related Pol

Swissprot_id: IF1A_WHEAT
polyprotein from transposon 17.6

Gi_number: 1352427
[Contains: Protease; Reverse

Description: Eukaryotic translation
transcriptase;

initiation factor 1A (EIF-1A)
Endonuclease]

(EIF-4C)
Seq ID: 1174

Seq ID: 338
Accession: Q16531

Accession: Q02817
Swissprot_id: DDB1_HUMAN

Swissprot_id: MUC2_HUMAN
Gi_number: 12643730

Gi_number: 2506877
Description: DNA DAMAGE BINDING

Description: MUCIN 2 PRECURSOR
PROTEIN 1 (DAMAGE-SPECIFIC DNA

(INTESTINAL MUCIN 2)
BINDING

Seq ID: 340
PROTEIN 1) (DDB P127

Accession: P08399
SUBUNIT) (DDBA) (UV-DAMAGED

Swissprot_id: PHX5_MOUSE
DNA-BINDING PROTEIN 1)

Gi_number: 2507093
(UV-DDB 1) (XERODERMA

Description: PER-HEXAMER REPEAT
PIGMENTOSUM

PROTEIN 5
GROUP E COMPLEMENTING

Seq ID: 341
PROTEIN) (XPCE) (X-ASSOCIATED

Accession: Q61189
PROTEIN 1) (XAP-1)

Swissprot_id: ICLN_MOUSE
Seq ID: 1175

Gi_number: 13431571
Accession: P10978

Description: Chloride conductance
Swissprot_id: POLX_TOBAC

regulatory protein ICln I(Cln)
Gi_number: 130582

(Chloride channel, nucleotide
Description: Retrovirus-related Pol

sensitive 1A) (Chloride ion
polyprotein from transposon TNT

current inducer protein) (ClCI)
1-94 [Contains: Protease;

Seq ID: 342
Reverse transcriptase;

Accession: Q02817
Endonuclease]

Swissprot_id: MUC2_HUMAN
Seq ID: 1176

Gi_number: 2506877
Accession: Q9NR09

Description: MUCIN 2 PRECURSOR
Swissprot_id: BIR6_HUMAN

(INTESTINAL MUCIN 2)
Gi_number: 12585192

Seq ID: 343
Description: BACULOVIRAL IAP

Accession: Q05193
REPEAT-CONTAINING PROTEIN 6

Swissprot_id: DYN1_HUMAN
(UBIQUITIN-CONJUGATING

Gi_number: 461976
BIR-DOMAIN ENZYME APOLLON)

Description: Dynamin-1
Seq ID: 1177

Seq ID: 345
Accession: P21448

Accession: O60610
Swissprot_id: MDR1_CRIGR

Swissprot_id: DIA1_HUMAN
Gi_number: 126924

Gi_number: 6225268
Description: Multidrug resistance protein 1

Description: DIAPHANOUS PROTEIN
(P-glycoprotein 1)

HOMOLOG 1 (DIAPHANOUS-
Seq ID: 1178

RELATED FORMIN 1)
Accession: P55180

(DRF1)
Swissprot_id: GALE_BACSU

Seq ID: 346
Gi_number: 1730193

Accession: P03211
Description: UDP-glucose 4-epimerase

Swissprot_id: EBN1_EBV
(Galactowaldenase) (UDP-galactose

Gi_number: 119110
4-epimerase)

Description: EBNA-1 NUCLEAR
Seq ID: 1179

PROTEIN
Accession: Q12381

Seq ID: 347
Swissprot_id: PR01_SCHPO

Accession: P05142
Gi_number: 12230438

Swissprot_id: PRP2_MOUSE
Description: Pre-mRNA splicing factor

Gi_number: 130999
prp1

Description: Proline-rich protein MP-2
Seq ID: 1180

precursor
Accession: P08640

Seq ID: 348
Swissprot_id: AMYH_YEAST

Accession: P13983
Gi_number: 728850

Swissprot_id: EXTN_TOBAC
Description: GLUCOAMYLASE S1/S2

Gi_number: 119714
PRECURSOR (GLUCAN

Description: Extensin precursor (Cell wall
1,4-ALPHA-GLUCOSIDASE)

hydroxyproline-rich
(1,4-ALPHA-D-GLUCAN

glycoprotein)
GLUCOHYDROLASE)

Seq ID: 350
Seq ID: 1181

Accession: P10323
Accession: P47179

Swissprot_id: ACRO_HUMAN
Swissprot_id: DAN4_YEAST

Gi_number: 113208
Gi_number: 1352944

Description: ACROSIN PRECURSOR
Description: Cell wall protein DAN4

Seq ID: 351
precursor

Accession: Q06666
Seq ID: 1182

Swissprot_id: T2_MOUSE
Accession: Q05609

Gi_number: 730888
Swissprot_id: CTR1_ARATH

Description: OCTAPEPTIDE-REPEAT
Gi_number: 1169128

PROTEIN T2
Description: Serine/threonine-protein

Seq ID: 352
kinase CTR1

Accession: P48634
Seq ID: 1183

Swissprot_id: BAT2_HUMAN
Accession: P22579

Gi_number: 1352066
Swissprot_id: SIN3_YEAST

Description: LARGE PROLINE-RICH
Gi_number: 2507475

PROTEIN BAT2 (HLA-B-ASSOCIATED
Description: PAIRED AMPHIPATHIC

TRANSCRIPT 2)
HELIX PROTEIN

Seq ID: 354
Seq ID: 1184

Accession: P10569
Accession: P58463

Swissprot_id: MYSC_ACACA
Swissprot_id: FXP2_MOUSE

Gi_number: 127749
Gi_number: 17433012

Description: Myosin IC heavy chain
Description: Forkhead box protein P2

Seq ID: 355
Seq ID: 1185

Accession: P14918
Accession: P30181

Swissprot_id: EXTN_MAIZE
Swissprot_id: TOP1_ARATH

Gi_number: 119712
Gi_number: 267146

Description: EXTENSIN PRECURSOR
Description: DNA topoisomerase I

(PROLINE-RICH GLYCOPROTEIN)
Seq ID: 1186

Seq ID: 356
Accession: P11087

Accession: Q63262
Swissprot_id: CA11_MOUSE

Swissprot_id: BRN1_RAT
Gi_number: 2506305

Gi_number: 5915802
Description: Collagen alpha 1(I) chain

Description: BRAIN-SPECIFIC
precursor

HOMEOBOX/POU DOMAIN PROTEIN
Seq ID: 1187

1 (BRN-1
Accession: P45181

PROTEIN)
Swissprot_id: PQQL_HAEIN

Seq ID: 357
Gi_number: 1175759

Accession: P37370
Description: Probable zinc protease pqqL

Swissprot_id: VRP1_YEAST
Seq ID: 1188

Gi_number: 2507155
Accession: Q9QYY8

Description: VERPROLIN
Swissprot_id: SPAS_MOUSE

Seq ID: 359
Gi_number: 12230605

Accession: P40603
Description: Spastin

Swissprot_id: APG_BRANA
Seq ID: 1190

Gi_number: 728868
Accession: O75317

Description: ANTER-SPECIFIC
Swissprot_id: UBPC_HUMAN

PROLINE-RICH PROTEIN APG
Gi_number: 6707738

(PROTEIN CEX)
Description: Ubiquitin carboxyl-terminal

Seq ID: 361
hydrolase 12 (Ubiquitin

Accession: Q95107
thiolesterase 12) (Ubiquitin-

Swissprot_id: WASL_BOVIN
specific processing protease

Gi_number: 13431968
12) (Deubiquitinating enzyme 12)

Description: Neural Wiskott-Aldrich
(Ubiquitin hydrolyzing

syndrome protein (N-WASP)
enzyme 1)

Seq ID: 362
Seq ID: 1191

Accession: P08001
Accession: Q55738

Swissprot_id: ACRO_PIG
Swissprot_id: GYRA_SYNY3

Gi_number: 113210
Gi_number: 8469101

Description: ACROSIN PRECURSOR (53
Description: DNA gyrase subunit A

KD FUCOSE-BINDING PROTEIN)
Seq ID: 1192

Seq ID: 363
Accession: Q99614

Accession: Q01484
Swissprot_id: TTC1_HUMAN

Swissprot_id: ANK2_HUMAN
Gi_number: 12585378

Gi_number: 1703310
Description: TETRATRICOPEPTIDE

Description: ANKYRIN 2 (BRAIN
REPEAT PROTEIN 1 (TPR REPEAT

ANKYRIN) (ANKYRIN B) (ANKYRIN,
PROTEIN 1)

NONERYTHROID)
Seq ID: 1193

Seq ID: 364
Accession: P14328

Accession: P28968
Swissprot_id: SP96_DICDI

Swissprot_id: VGLX_HSVEB
Gi_number: 134780

Gi_number: 138350
Description: SPORE COAT PROTEIN

Description: GLYCOPROTEIN X
SP96

PRECURSOR
Seq ID: 1194

Seq ID: 365
Accession: Q02817

Accession: Q9WTV7
Swissprot_id: MUC2_HUMAN

Swissprot_id: RNFB_MOUSE
Gi_number: 2506877

Gi_number: 13124535
Description: MUCIN 2 PRECURSOR

Description: RING FINGER PROTEIN 12
(INTESTINAL MUCIN 2)

(LIM DOMAIN INTERACTING RING
Seq ID: 1195

FINGER
Accession: P46607

PROTEIN) (RING FINGER LIM
Swissprot_id: HGL2_ARATH

DOMAIN-BINDING PROTEIN) (R-LIM)
Gi_number: 2506525

Seq ID: 366
Description: Homeobox protein

Accession: Q9UMN6
GLABRA2 (Homeobox-leucine zipper

Swissprot_id: TRX2_HUMAN
protein

Gi_number: 12643900
ATHB-10) (HD-ZIP protein

Description: TRITHORAX HOMOLOG 2
ATHB-10)

(MIXED LINEAGE LEUKEMIA GENE
Seq ID: 1196

HOMOLOG 2
Accession: Q01432

PROTEIN)
Swissprot_id: AMD3_HUMAN

Seq ID: 367
Gi_number: 399033

Accession: P33479
Description: AMP deaminase 3 (AMP

Swissprot_id: IE18_PRVKA
deaminase isoform E) (Erythrocyte AMP

Gi_number: 462387
deaminase)

Description: IMMEDIATE-EARLY
Seq ID: 1197

PROTEIN IE180
Accession: Q63003

Seq ID: 368
Swissprot_id: 5E5_RAT

Accession: P08640
Gi_number: 2498095

Swissprot_id: AMYH_YEAST
Description: 5E5 ANTIGEN

Gi_number: 728850
Seq ID: 1198

Description: GLUCOAMYLASE S1/S2
Accession: P10978

PRECURSOR (GLUCAN
Swissprot_id: POLX_TOBAC

1,4-ALPHA-GLUCOSIDASE)
Gi_number: 130582

(1,4-ALPHA-D-GLUCAN
Description: Retrovirus-related Pol

GLUCOHYDROLASE)
polyprotein from transposon TNT

Seq ID: 369
1-94 [Contains: Protease;

Accession: P13917
Reverse transcriptase;

Swissprot_id: 7SBG_SOYBN
Endonuclease]

Gi_number: 14549156
Seq ID: 1199

Description: BASIC 7S GLOBULIN
Accession: P34703

PRECURSOR (BG) (SBG7S)
Swissprot_id: EMB5_CAEEL

Seq ID: 370
Gi_number: 462008

Accession: P25012
Description: EMB-5 protein

Swissprot_id: CG22_SOYBN
Seq ID: 1201

Gi_number: 116162
Accession: Q9SYQ8

Description: G2/mitotic-specific cyclin
Swissprot_id: CLV1_ARATH

S13-7 (B-like cyclin)
Gi_number: 12643323

Seq ID: 371
Description: RECEPTOR PROTEIN

Accession: P08640
KINASE CLAVATA1 PRECURSOR

Swissprot_id: AMYH_YEAST
Seq ID: 1203

Gi_number: 728850
Accession: P08547

Description: GLUCOAMYLASE S1/S2
Swissprot_id: LIN1_HUMAN

PRECURSOR (GLUCAN
Gi_number: 126295

1,4-ALPHA-GLUCOSIDASE)
Description: LINE-1 REVERSE

(1,4-ALPHA-D-GLUCAN
TRANSCRIPTASE HOMOLOG

GLUCOHYDROLASE)
Seq ID: 1204

Seq ID: 373
Accession: P74361

Accession: P14328
Swissprot_id: CLPB_SYNY3

Swissprot_id: SP96_DICDI
Gi_number: 2493734

Gi_number: 134780
Description: ClpB protein

Description: SPORE COAT PROTEIN
Seq ID: 1205

SP96
Accession: P11369

Seq ID: 374
Swissprot_id: POL2_MOUSE

Accession: P33479
Gi_number: 130402

Swissprot_id: IE18_PRVKA
Description: Retrovirus-related POL

Gi_number: 462387
polyprotein [Contains: Reverse

Description: IMMEDIATE-EARLY
transcriptase; Endonuclease]

PROTEIN IE180
Seq ID: 1206

Seq ID: 375
Accession: P29141

Accession: P13983
Swissprot_id: SUBV_BACSU

Swissprot_id: EXTN_TOBAC
Gi_number: 135023

Gi_number: 119714
Description: Minor extracellular protease

Description: Extensin precursor (Cell wall
VPR precursor

hydroxyproline-rich
Seq ID: 1207

glycoprotein)
Accession: P04839

Seq ID: 376
Swissprot_id: C24B_HUMAN

Accession: Q03211
Gi_number: 115211

Swissprot_id: EXLP_TOBAC
Description: Cytochrome B-245 heavy

Gi_number: 544262
chain (P22 phagocyte B-cytochrome)

Description: PISTIL-SPECIFIC
(Neutrophil cytochrome B, 91 kDa

EXTENSIN-LIKE PROTEIN
polypeptide) (CGD91-PHOX)

PRECURSOR (PELP)
(GP91-PHOX) (Heme binding

Seq ID: 377
membrane glycoprotein GP91PHOX)

Accession: Q02817
(Cytochrome B(558) beta chain)

Swissprot_id: MUC2_HUMAN
(Superoxide-generating

Gi_number: 2506877
NADPH oxidase heavy cha>

Description: MUCIN 2 PRECURSOR
Seq ID: 1208

(INTESTINAL MUCIN 2)
Accession: Q06548

Seq ID: 379
Swissprot_id: APKA_ARATH

Accession: P08640
Gi_number: 1168470

Swissprot_id: AMYH_YEAST
Description: Protein kinase APK1A

Gi_number: 728850
Seq ID: 1209

Description: GLUCOAMYLASE S1/S2
Accession: Q13316

PRECURSOR (GLUCAN
Swissprot_id: DMP1_HUMAN

1,4-ALPHA-GLUCOSIDASE)
Gi_number: 7673998

(1,4-ALPHA-D-GLUCAN
Description: DENTIN MATRIX ACIDIC

GLUCOHYDROLASE)
PHOSPHOPROTEIN 1 PRECURSOR

Seq ID: 380
(DENTIN

Accession: P30962
MATRIX PROTEIN-1) (DMP-1)

Swissprot_id: CCMC_BRAJA
Seq ID: 1211

Gi_number: 399869
Accession: Q9NQE7

Description: HEME EXPORTER
Swissprot_id: TSSP_HUMAN

PROTEIN C (CYTOCHROME C-TYPE
Gi_number: 13633990

BIOGENESIS
Description: THYMUS-SPECIFIC

PROTEIN CYCZ)
SERINE PROTEASE PRECURSOR

Seq ID: 381
Seq ID: 1212

Accession: P52551
Accession: Q9NRA0

Swissprot_id: MYBB_XENLA
Swissprot_id: SPH2_HUMAN

Gi_number: 6226654
Gi_number: 17369316

Description: Myb-related protein B (B-
Description: Sphingosine kinase 2 (SK 2)

Myb) (Myb-related protein 1)
(SPK 2)

(XMYB1)
Seq ID: 1213

Seq ID: 382
Accession: Q02817

Accession: P10394
Swissprot_id: MUC2_HUMAN

Swissprot_id: POL4_DROME
Gi_number: 2506877

Gi_number: 130407
Description: MUCIN 2 PRECURSOR

Description: Retrovirus-related Pol
(INTESTINAL MUCIN 2)

polyprotein from transposon 412
Seq ID: 1214

[Contains: Protease; Reverse
Accession: Q9SYQ8

transcriptase;
Swissprot_id: CLV1_ARATH

Endonuclease]
Gi_number: 12643323

Seq ID: 383
Description: RECEPTOR PROTEIN

Accession: P17656
KINASE CLAVATA1 PRECURSOR

Swissprot_id: CC02_CAEEL
Seq ID: 1215

Gi_number: 115398
Accession: Q14258

Description: CUTICLE COLLAGEN 2
Swissprot_id: Z147_HUMAN

Seq ID: 384
Gi_number: 12585547

Accession: P37370
Description: Zinc finger protein 147

Swissprot_id: VRP1_YEAST
(Estrogen responsive finger

Gi_number: 2507155
protein) (Efp)

Description: VERPROLIN
Seq ID: 1216

Seq ID: 385
Accession: Q9EPQ0

Accession: P03211
Swissprot_id: NKX3_RAT

Swissprot_id: EBN1_EBV
Gi_number: 17865499

Gi_number: 119110
Description: Sodium/potassium/calcium

Description: EBNA-1 NUCLEAR
exchanger 3 precursor

PROTEIN
(Na(+)/K(+)/Ca(2+)-exchange

Seq ID: 386
protein 3) (Fragment)

Accession: P24007
Seq ID: 1217

Swissprot_id: RBS_PYRPY
Accession: P40781

Gi_number: 132153
Swissprot_id: CYP4_CYNCA

Description: Ribulose bisphosphate
Gi_number: 729273

carboxylase small chain, chloroplast
Description: CYPRO4 PROTEIN

precursor (RuBisCO small
Seq ID: 1218

subunit)
Accession: P56344

Seq ID: 388
Swissprot_id: CYSA_CHLVU

Accession: Q01540
Gi_number: 3023607

Swissprot_id: AG_BRANA
Description: Probable sulfate transport

Gi_number: 399096
ATP-binding protein cysA

Description: Agamous protein
Seq ID: 1219

Seq ID: 389
Accession: P46573

Accession: Q9WTV7
Swissprot_id: APKB_ARATH

Swissprot_id: RNFB_MOUSE
Gi_number: 12644274

Gi_number: 13124535
Description: PROTEIN KINASE APK1B

Description: RING FINGER PROTEIN 12
Seq ID: 1220

(LIM DOMAIN INTERACTING RING
Accession: P78621

FINGER
Swissprot_id: SEPA_EMENI

PROTEIN) (RING FINGER LIM
Gi_number: 15214279

DOMAIN-BINDING PROTEIN) (R-LIM)
Description: CYTOKINESIS PROTEIN

Seq ID: 390
SEPA (FH1/2 PROTEIN) (FORCED

Accession: Q96502
EXPRESSION INHIBITION OF

Swissprot_id: COL2_ARATH
GROWTH A)

Gi_number: 17433030
Seq ID: 1221

Description: Zinc finger protein
Accession: Q13614

CONSTANS-LIKE 2
Swissprot_id: MTR2_HUMAN

Seq ID: 391
Gi_number: 12644410

Accession: O60610
Description: MYOTUBULARIN-

Swissprot_id: DIA1_HUMAN
RELATED PROTEIN 2

Gi_number: 6225268
Seq ID: 1222

Description: DIAPHANOUS PROTEIN
Accession: P93329

HOMOLOG 1 (DIAPHANOUS-
Swissprot_id: NO20_MEDTR

RELATED FORMIN 1)
Gi_number: 3914142

(DRF1)
Description: EARLY NODULIN 20

Seq ID: 392
PRECURSOR (N-20)

Accession: P08723
Seq ID: 1223

Swissprot_id: SPBP_RAT
Accession: Q9XHL5

Gi_number: 134789
Swissprot_id: HMD3_ORYSA

Description: Prostatic spermine-binding
Gi_number: 11133198

protein precursor (SBP)
Description: 3-hydroxy-3-methylglutaryl-

Seq ID: 393
coenzyme A reductase 3 (HMG-CoA

Accession: Q9LRI7
reductase 3)

Swissprot_id: OSR8_ORYSA
Seq ID: 1224

Gi_number: 15214171
Accession: P79051

Description: Hydrophobic protein OSR8
Swissprot_id: RH16_SCHPO

Seq ID: 394
Gi_number: 14195095

Accession: Q27294
Description: DNA REPAIR PROTEIN

Swissprot_id: CAZ_DROME
RHP16 (RAD16 HOMOLOG)

Gi_number: 8928004
Seq ID: 1225

Description: RNA-binding protein cabeza
Accession: P39968

(Sarcoma-associated RNA-binding
Swissprot_id: VAC8_YEAST

fly homolog) (P19)
Gi_number: 731400

Seq ID: 395
Description: Vacuolar protein 8

Accession: P08640
Seq ID: 1226

Swissprot_id: AMYH_YEAST
Accession: Q9QYY8

Gi_number: 728850
Swissprot_id: SPAS_MOUSE

Description: GLUCOAMYLASE S1/S2
Gi_number: 12230605

PRECURSOR (GLUCAN
Description: Spastin

1,4-ALPHA-GLUCOSIDASE)
Seq ID: 1227

(1,4-ALPHA-D-GLUCAN
Accession: Q06850

GLUCOHYDROLASE
Swissprot_id: CDP1_ARATH

Seq ID: 396
Gi_number: 729092

Accession: P21997
Description: Calcium-dependent protein

Swissprot_id: SSGP_VOLCA
kinase, isoform AK1 (CDPK)

Gi_number: 134920
Seq ID: 1228

Description: SULFATED SURFACE
Accession: Q9TV36

GLYCOPROTEIN 185 (SSG 185)
Swissprot_id: FBN1_PIG

Seq ID: 397
Gi_number: 13626617

Accession: P03211
Description: Fibrillin 1 precursor

Swissprot_id: EBN1_EBV
Seq ID: 1229

Gi_number: 119110
Accession: P05659

Description: EBNA-1 NUCLEAR
Swissprot_id: MYSN_ACACA

PROTEIN
Gi_number: 127758

Seq ID: 398
Description: Myosin II heavy chain, non

Accession: O00268
muscle

Swissprot_id: T2D3_HUMAN
Seq ID: 1231

Gi_number: 3024681
Accession: P08548

Description: TRANSCRIPTION
Swissprot_id: LIN1_NYCCO

INITIATION FACTOR TFIID 135 KDA
Gi_number: 126296

SUBUNIT
Description: LINE-1 REVERSE

(TAFII-135) (TAFII135) (TAFII-
TRANSCRIPTASE HOMOLOG

130) (TAFII130)
Seq ID: 1233

Seq ID: 399
Accession: Q46948

Accession: P23225
Swissprot_id: THIJ_ECOLI

Swissprot_id: GLSF_MAIZE
Gi_number: 6686342

Gi_number: 121446
Description: 4-methyl-5(B-hydroxyethyl)-

Description: Ferredoxin-dependent
thiazole monophosphate

glutamate synthase, chloroplast
biosynthesis enzyme

precursor (Fd-GOGAT)
Seq ID: 1235

Seq ID: 400
Accession: P52706

Accession: P34811
Swissprot_id: MDL1_PRUSE

Swissprot_id: EFGC_SOYBN
Gi_number: 1708971

Gi_number: 461999
Description: (R)-MANDELONITRILE

Description: ELONGATION FACTOR G,
LYASE ISOFORM 1 PRECURSOR

CHLOROPLAST PRECURSOR (EF-G)
(HYDROXYNITRILE LYASE 1)

Seq ID: 401
((R)-OXYNITRILASE 1)

Accession: Q02978
Seq ID: 1236

Swissprot_id: M2OM_HUMAN
Accession: O23066

Gi_number: 400210
Swissprot_id: C862_ARATH

Description: MITOCHONDRIAL 2-
Gi_number: 5915846

OXOGLUTARATE/MALATE CARRIER
Description: Cytochrome P450 86A2

PROTEIN (OGCP)
Seq ID: 1237

Seq ID: 402
Accession: Q41144

Accession: P28284
Swissprot_id: STC_RICCO

Swissprot_id: ICP0_HSV2H
Gi_number: 3915039

Gi_number: 124135
Description: SUGAR CARRIER

Description: Trans-acting transcriptional
PROTEIN C

protein ICP0 (VMW118 protein)
Seq ID: 1238

Seq ID: 403
Accession: O88508

Accession: Q9SK53
Swissprot_id: DM3A_MOUSE

Swissprot_id: COL8_ARATH
Gi_number: 17374900

Gi_number: 17433082
Description: DNA (cytosine-5)-

Description: Zinc finger protein constans-
methyltransferase 3A (DNA

like 8
methyltransferase MmuIIIA)

Seq ID: 404
(DNA MTase MmuIIIA) (M.MmuIIIA)

Accession: P93236
Seq ID: 1239

Swissprot_id: ABA2_LYCES
Accession: Q42534

Gi_number: 5902706
Swissprot_id: PME2_ARATH

Description: Zeaxanthin epoxidase,
Gi_number: 17865767

chloroplast precursor
Description: Pectinesterase 2 precursor

Seq ID: 405
(Pectin methylesterase 2) (PE

Accession: Q9SSU8
2)

Swissprot_id: PSY_DAUCA
Seq ID: 1240

Gi_number: 8928282
Accession: P13526

Description: Phytoene synthase,
Swissprot_id: ARLC_MAIZE

chloroplast precursor
Gi_number: 114156

Seq ID: 406
Description: ANTHOCYANIN

Accession: P37821
REGULATORY LC PROTEIN

Swissprot_id: 1A1C_MALDO
Seq ID: 1241

Gi_number: 3041658
Accession: O00401

Description: 1-
Swissprot_id: WASL_HUMAN

AMINOCYCLOPROPANE-1-
Gi_number: 13431960

CARBOXYLATE SYNTHASE (ACC
Description: Neural Wiskott-Aldrich

SYNTHASE)
syndrome protein (N-WASP)

(S-ADENOSYL-L-
Seq ID: 1242

METHIONINE
Accession: Q02817

METHYLTHIOADENOSINE-LYASE)
Swissprot_id: MUC2_HUMAN

Seq ID: 408
Gi_number: 2506877

Accession: P48125
Description: MUCIN 2 PRECURSOR

Swissprot_id: RK1_CYAPA
(INTESTINAL MUCIN 2)

Gi_number: 1350623
Seq ID: 1243

Description: Cyanelle 50S ribosomal
Accession: P34693

protein L1
Swissprot_id: SYT1_CAEEL

Seq ID: 410
Gi_number: 464829

Accession: Q9WZV3
Description: SYNAPTOTAGMIN I

Swissprot_id: DNAJ_THEMA
Seq ID: 1244

Gi_number: 11132549
Accession: P21997

Description: Chaperone protein dnaJ
Swissprot_id: SSGP_VOLCA

Seq ID: 411
Gi_number: 134920

Accession: P29344
Description: SULFATED SURFACE

Swissprot_id: RR1_SPIOL
GLYCOPROTEIN 185 (SSG 185)

Gi_number: 133872
Seq ID: 1245

Description: 30S ribosomal protein S1,
Accession: P25777

chloroplast precursor (CS1)
Swissprot_id: ORYB_ORYSA

Seq ID: 414
Gi_number: 129232

Accession: Q42463
Description: ORYZAIN BETA CHAIN

Swissprot_id: DCL_LYCES
PRECURSOR

Gi_number: 6014934
Seq ID: 1246

Description: DCL PROTEIN,
Accession: P16166

CHLOROPLAST PRECURSOR
Swissprot_id: UFO1_MAIZE

(DEFECTIVE CHLOROPLASTS
Gi_number: 136743

AND LEAVES PROTEIN)
Description: Flavonol 3-O-

Seq ID: 415
glucosyltransferase (UDP-glucose

Accession: Q08298
flavonoid

Swissprot_id: RD22_ARATH
3-O-glucosyltransferase) (Bronze-

Gi_number: 1172874
1) (BZ-MCC allele)

Description: DEHYDRATION-
Seq ID: 1247

RESPONSIVE PROTEIN RD22
Accession: Q42586

PRECURSOR
Swissprot_id: PYR5_ARATH

Seq ID: 416
Gi_number: 2499945

Accession: P23326
Description: Uridine 5′-monophosphate

Swissprot_id: RK35_SPIOL
synthase (UMP synthase)

Gi_number: 132918
[Includes: Orotate

Description: 50S RIBOSOMAL PROTEIN
phosphoribosyltransferase (OPRtase);

L35, CHLOROPLAST PRECURSOR
Orotidine 5′-phosphate

(CL35)
decarboxylase (OMPdecase)]

Seq ID: 417
Seq ID: 1248

Accession: O59742
Accession: O42904

Swissprot_id: IF3X_SCHPO
Swissprot_id: PR31_SCHPO

Gi_number: 14916997
Gi_number: 12230414

Description: Probable eukaryotic
Description: Pre-mRNA splicing factor

translation initiation factor 3 135
prp31

kDa subunit (eIF3 p135)
Seq ID: 1250

(Translation initiation factor
Accession: P54001

eIF3, p135 subunit)
Swissprot_id: P4HA_RAT

Seq ID: 418
Gi_number: 1709530

Accession: O54408
Description: PROLYL 4-

Swissprot_id: RELA_BACSU
HYDROXYLASE ALPHA SUBUNIT

Gi_number: 6647736
PRECURSOR

Description: GTP
Seq ID: 1251

PYROPHOSPHOKINASE (ATP: GTP 3′-
Accession: P25011

PYROPHOSPHOTRANSFERASE)
Swissprot_id: CG21_SOYBN

(PPGPP SYNTHETASE I)
Gi_number: 116157

((P)PPGPP SYNTHETASE)
Description: G2/mitotic-specific cyclin

Seq ID: 419
S13-6 (B-like cyclin)

Accession: Q9SHI1
Seq ID: 1252

Swissprot_id: IF2C_ARATH
Accession: Q99615

Gi_number: 13627881
Swissprot_id: TTC2_HUMAN

Description: Translation initiation factor
Gi_number: 6831707

IF-2, chloroplast precursor
Description: TETRATRICOPEPTIDE

Seq ID: 420
REPEAT PROTEIN 2 (TPR REPEAT

Accession: Q9JIK5
PROTEIN 2)

Swissprot_id: DD21_MOUSE
Seq ID: 1253

Gi_number: 13959325
Accession: P16081

Description: NUCLEOLAR RNA
Swissprot_id: NIA1_ORYSA

HELICASE II (NUCLEOLAR RNA
Gi_number: 128186

HELICASE GU) (RH
Description: NITRATE REDUCTASE 1

II/GU) (DEAD BOX PROTEIN
(NR1)

21)
Seq ID: 1254

Seq ID: 421
Accession: P49299

Accession: P14328
Swissprot_id: CYSZ_CUCMA

Swissprot_id: SP96_DICDI
Gi_number: 1345933

Gi_number: 134780
Description: CITRATE SYNTHASE,

Description: SPORE COAT PROTEIN
GLYOXYSOMAL PRECURSOR (GCS)

SP96
Seq ID: 1255

Seq ID: 422
Accession: P32857

Accession: O81117
Swissprot_id: PTM1_YEAST

Swissprot_id: C941_VICSA
Gi_number: 417551

Gi_number: 17366212
Description: Protein PTM1 precursor

Description: Cytochrome P450 94A1
Seq ID: 1256

(P450-dependent fatty acid
Accession: P41214

omega-hydroxylase)
Swissprot_id: LIGA_HUMAN

Seq ID: 423
Gi_number: 13638201

Accession: P37107
Description: LIGATIN

Swissprot_id: SR5C_ARATH
(HEPATOCELLULAR CARCINOMA-

Gi_number: 586038
ASSOCIATED ANTIGEN 56)

Description: Signal recognition particle 54
Seq ID: 1257

kDa protein, chloroplast
Accession: P27483

precursor (SRP54) (54 chloroplast
Swissprot_id: GRP_ARATH

protein) (54CP) (FFC)
Gi_number: 121640

Seq ID: 424
Description: GLYCINE-RICH CELL

Accession: Q59914
WALL STRUCTURAL PROTEIN

Swissprot_id: HRDD_STRGR
PRECURSOR

Gi_number: 17366575
Seq ID: 1259

Description: RNA polymerase principal
Accession: P10978

sigma factor hrdD
Swissprot_id: POLX_TOBAC

Seq ID: 425
Gi_number: 130582

Accession: P42895
Description: Retrovirus-related Pol

Swissprot_id: ENO2_MAIZE
polyprotein from transposon TNT

Gi_number: 1169528
1-94 [Contains: Protease;

Description: ENOLASE 2 (2-
Reverse transcriptase;

PHOSPHOGLYCERATE
Endonuclease]

DEHYDRATASE 2)
Seq ID: 1260

(2-PHOSPHO-D-GLYCERATE
Accession: Q9R9N3

HYDRO-LYASE 2)
Swissprot_id: ODP2_RHIME

Seq ID: 426
Gi_number: 8474223

Accession: P38564
Description: Dihydrolipoamide

Swissprot_id: MNBA_MAIZE
acetyltransferase component of pyruvate

Gi_number: 1346559
dehydrogenase complex (E2)

Description: DNA-BINDING PROTEIN
Seq ID: 1261

MNB1A
Accession: P09406

Seq ID: 427
Swissprot_id: RU17_XENLA

Accession: O49939
Gi_number: 134091

Swissprot_id: TL40_SPIOL
Description: U1 small nuclear

Gi_number: 10720315
ribonucleoprotein 70 kDa (U1 snRNP 70 kDa)

Description: Peptidyl-prolyl cis-trans
(snRNP70) (U1-70K)

isomerase, chloroplast precursor
Seq ID: 1262

(40 kDa thylakoid lumen PPIase)
Accession: P27937

(40 kDa thylakoid lumen
Swissprot_id: AM3B_ORYSA

rotamase)
Gi_number: 113680

Seq ID: 429
Description: ALPHA-AMYLASE

Accession: O67695
ISOZYME 3B PRECURSOR (1,4-

Swissprot_id: RF2_AQUAE
ALPHA-D-GLUCAN

Gi_number: 6225943
GLUCANOHYDROLASE)

Description: Peptide chain release factor 2
Seq ID: 1263

(RF-2)
Accession: P06865

Seq ID: 430
Swissprot_id: HEXA_HUMAN

Accession: P32945
Gi_number: 123079

Swissprot_id: PPQ1_YEAST
Description: Beta-hexosaminidase alpha

Gi_number: 417746
chain precursor

Description: SERINE/THREONINE
(N-acetyl-beta-glucosaminidase)

PROTEIN PHOSPHATASE PPQ
(Beta-N-acetylhexosaminidase)

Seq ID: 432
(Hexosaminidase A)

Accession: Q9MUU5
Seq ID: 1264

Swissprot_id: RK5_MESVI
Accession: Q42798

Gi_number: 14548222
Swissprot_id: C931_SOYBN

Description: Chloroplast 50S ribosomal
Gi_number: 3913192

protein L5
Description: CYTOCHROME P450 93A1

Seq ID: 433
Seq ID: 1265

Accession: Q02817
Accession: P09406

Swissprot_id: MUC2_HUMAN
Swissprot_id: RU17_XENLA

Gi_number: 2506877
Gi_number: 134091

Description: MUCIN 2 PRECURSOR
Description: U1 small nuclear

(INTESTINAL MUCIN 2)
ribonucleoprotein 70 kDa (U1 snRNP 70 kDa)

Seq ID: 434
(snRNP70) (U1-70K)

Accession: O94903
Seq ID: 1266

Swissprot_id: POSC_HUMAN
Accession: P08640

Gi_number: 12230426
Swissprot_id: AMYH_YEAST

Description: Proline synthetase co-
Gi_number: 728850

transcribed bacterial homolog
Description: GLUCOAMYLASE S1/S2

protein
PRECURSOR (GLUCAN

Seq ID: 435
1,4-ALPHA-GLUCOSIDASE)

Accession: P57708
(1,4-ALPHA-D-GLUCAN

Swissprot_id: ISPF_PSEAE
GLUCOHYDROLASE)

Gi_number: 12643672
Seq ID: 1267

Description: 2C-METHYL-D-
Accession: O95405

ERYTHRITOL 2,4-
Swissprot_id: MADI_HUMAN

CYCLODIPHOSPHATE SYNTHASE
Gi_number: 15214067

(MECPS)
Description: MOTHERS AGAINST

Seq ID: 436
DECAPENTAPLEGIC HOMOLOG

Accession: Q9SEC2
INTERACTING

Swissprot_id: MSRA_LACSA
PROTEIN (MADH-

Gi_number: 12230349
INTERACTING PROTEIN) (SMAD

Description: Peptide methionine sulfoxide
ANCHOR FOR

reductase
RECEPTOR ACTIVATION)

(Protein-methionine-S-oxide
(RECEPTOR ACTIVATION ANCHOR)

reductase) (Peptide Met(O)
(HSARA)

reductase)
(NOVEL SERINE PROTEASE)

Seq ID: 439
(NSP)

Accession: Q9WZV3
Seq ID: 1268

Swissprot_id: DNAJ_THEMA
Accession: P21997

Gi_number: 11132549
Swissprot_id: SSGP_VOLCA

Description: Chaperone protein dnaJ
Gi_number: 134920

Seq ID: 440
Description: SULFATED SURFACE

Accession: P30260
GLYCOPROTEIN 185 (SSG 185)

Swissprot_id: CC27_HUMAN
Seq ID: 1269

Gi_number: 12644198
Accession: Q05859

Description: PROTEIN CDC27HS (CELL
Swissprot_id: FOR4_MOUSE

DIVISION CYCLE PROTEIN 27
Gi_number: 544344

HOMOLOG)
Description: FORMIN 4 (LIMB

(H-NUC)
DEFORMITY PROTEIN)

Seq ID: 441
Seq ID: 1270

Accession: O46894
Accession: O04940

Swissprot_id: RK3_GUITH
Swissprot_id: CDS1_SOLTU

Gi_number: 3914660
Gi_number: 3121837

Description: CHLOROPLAST 50S
Description: PHOSPHATIDATE

RIBOSOMAL PROTEIN L3
CYTIDYLYLTRANSFERASE (CDP-

Seq ID: 442
DIGLYCERIDE

Accession: P25864
SYNTHETASE) (CDP-

Swissprot_id: RK9_ARATH
DIGLYCERIDE

Gi_number: 133028
PYROPHOSPHORYLASE)

Description: 50S ribosomal protein L9,
(CDP-DIACYLGLYCEROL

chloroplast precursor (CL9)
SYNTHASE) (CDS)

Seq ID: 443
(CTP: PHOSPHATIDATE

Accession: Q03211
CYTIDYLYLTRANSFERASE)

Swissprot_id: EXLP_TOBAC
(CDP-DAG SYNTHASE) (CDP-DG

Gi_number: 544262
SYNTHETASE)

Description: PISTIL-SPECIFIC
Seq ID: 1271

EXTENSIN-LIKE PROTEIN
Accession: Q46948

PRECURSOR (PELP)
Swissprot_id: THIJ_ECOLI

Seq ID: 446
Gi_number: 6686342

Accession: O59742
Description: 4-methyl-5(B-hydroxyethyl)-

Swissprot_id: IF3X_SCHPO
thiazole monophosphate

Gi_number: 14916997
biosynthesis enzyme

Description: Probable eukaryotic
Seq ID: 1272

translation initiation factor 3 135
Accession: P15268

kDa subunit (eIF3 p135)
Swissprot_id: MOSA_MAIZE

(Translation initiation factor
Gi_number: 127243

eIF3, p135 subunit)
Description: AUTONOMOUS

Seq ID: 447
TRANSPOSABLE ELEMENT EN-1

Accession: P74070
MOSAIC PROTEIN

Swissprot_id: EFTS_SYNY3
(SUPPRESSOR-MUTATOR

Gi_number: 2494280
SYSTEM PROTEIN) (SPM)

Description: Elongation factor Ts (EF-Ts)
Seq ID: 1274

Seq ID: 448
Accession: P34881

Accession: Q42546
Swissprot_id: DNM1_ARATH

Swissprot_id: DPNP_ARATH
Gi_number: 462650

Gi_number: 3913518
Description: DNA (cytosine-5)-

Description: 3′(2′),5′-bisphosphate
methyltransferase AthI (DNA

nucleotidase
methyltransferase AthI) (DNA

(3′(2′),5-bisphosphonucleoside
Metase AthI) (M. AthI)

3′(2′)-phosphohydrolase)
Seq ID: 1276

(DPNPase)
Accession: Q58849

Seq ID: 449
Swissprot_id: AROD_METJA

Accession: Q55806
Gi_number: 11386641

Swissprot_id: SYT_SYNY3
Description: 3-dehydroquinate dehydratase

Gi_number: 2501062
(3-dehydroquinase) (Type I

Description: Threonyl-tRNA synthetase
DHQase)

(Threonine--tRNA ligase) (ThrRS)
Seq ID: 1277

Seq ID: 450
Accession: P55039

Accession: P21997
Swissprot_id: DRG2_HUMAN

Swissprot_id: SSGP_VOLCA
Gi_number: 1706518

Gi_number: 134920
Description: Developmentally regulated

Description: SULFATED SURFACE
GTP-binding protein 2 (DRG 2)

GLYCOPROTEIN 185 (SSG 185)
Seq ID: 1278

Seq ID: 451
Accession: P18161

Accession: P40477
Swissprot_id: KYK2_DICDI

Swissprot_id: N159_YEAST
Gi_number: 125874

Gi_number: 731862
Description: TYROSINE-PROTEIN

Description: Nucleoporin NUP159
KINASE 2

(Nuclear pore protein NUP159)
Seq ID: 1279

Seq ID: 453
Accession: Q02817

Accession: P51106
Swissprot_id: MUC2_HUMAN

Swissprot_id: DFRA_HORVU
Gi_number: 2506877

Gi_number: 1706372
Description: MUCIN 2 PRECURSOR

Description: DIHYDROFLAVONOL-4-
(INTESTINAL MUCIN 2)

REDUCTASE (DFR)
Seq ID: 1280

(DIHYDROKAEMPFEROL
Accession: Q01594

4-REDUCTASE)
Swissprot_id: ALLN_ALLSA

Seq ID: 454
Gi_number: 399028

Accession: P11893
Description: ALLIIN LYASE

Swissprot_id: RK24_PEA
PRECURSOR (ALLIINASE) (CYSTEINE

Gi_number: 132819
SULPHOXIDE

Description: 50S RIBOSOMAL PROTEIN
LYASE)

L24, CHLOROPLAST PRECURSOR
Seq ID: 1281

(CL24)
Accession: O87708

Seq ID: 455
Swissprot_id: CLPX_CAUCR

Accession: P37370
Gi_number: 6225165

Swissprot_id: VRP1_YEAST
Description: ATP-dependent Clp protease

Gi_number: 2507155
ATP-binding subunit clpX

Description: VERPROLIN
Seq ID: 1282

Seq ID: 456
Accession: O43791

Accession: P82244
Swissprot_id: SPOP_HUMAN

Swissprot_id: RK34_SPIOL
Gi_number: 8134708

Gi_number: 14285713
Description: Speckle-type POZ protein

Description: 50S ribosomal protein L34,
Seq ID: 1283

chloroplast precursor
Accession: O43791

Seq ID: 457
Swissprot_id: SPOP_HUMAN

Accession: Q13823
Gi_number: 8134708

Swissprot_id: NGP1_HUMAN
Description: Speckle-type POZ protein

Gi_number: 3334276
Seq ID: 1284

Description: Autoantigen NGP-1
Accession: P17731

Seq ID: 458
Swissprot_id: HIS8_BACSU

Accession: Q12238
Gi_number: 3123224

Swissprot_id: UV31_SCHPO
Description: HISTIDINOL-PHOSPHATE

Gi_number: 3024789
AMINOTRANSFERASE (IMIDAZOLE

Description: UV-INDUCED PROTEIN
ACETOL-PHOSPHATE

UVI31
TRANSAMINASE)

Seq ID: 459
Seq ID: 1285

Accession: Q42569
Accession: O08333

Swissprot_id: C901_ARATH
Swissprot_id: K6P1_STRCO

Gi_number: 5915851
Gi_number: 3122290

Description: Cytochrome P450 90A1
Description: 6-phosphofructokinase 1

Seq ID: 461
(Phosphofructokinase 1)

Accession: P11892
(Phosphohexokinase 1) (ATP-

Swissprot_id: RK25_PEA
PFK)

Gi_number: 132825
Seq ID: 1286

Description: 50S RIBOSOMAL PROTEIN
Accession: Q12196

CL25, CHLOROPLAST PRECURSOR
Swissprot_id: RIO1_YEAST

Seq ID: 462
Gi_number: 2500508

Accession: P78426
Description: RIO1 PROTEIN

Swissprot_id: HK61_HUMAN
Seq ID: 1287

Gi_number: 6016211
Accession: Q02817

Description: HOMEOBOX PROTEIN
Swissprot_id: MUC2_HUMAN

NKX-6.1
Gi_number: 2506877

Seq ID: 463
Description: MUCIN 2 PRECURSOR

Accession: P08640
(INTESTINAL MUCIN 2)

Swissprot_id: AMYH_YEAST
Seq ID: 1288

Gi_number: 728850
Accession: O43791

Description: GLUCOAMYLASE S1/S2
Swissprot_id: SPOP_HUMAN

PRECURSOR (GLUCAN
Gi_number: 8134708

1,4-ALPHA-GLUCOSIDASE)
Description: Speckle-type POZ protein

(1,4-ALPHA-D-GLUCAN
Seq ID: 1289

GLUCOHYDROLASE)
Accession: P49972

Seq ID: 464
Swissprot_id: SR52_LYCES

Accession: P16301
Gi_number: 1711512

Swissprot_id: LCAT_MOUSE
Description: SIGNAL RECOGNITION

Gi_number: 125994
PARTICLE 54 KD PROTEIN 2 (SRP54)

Description: PHOSPHATIDYLCHOLINE-
Seq ID: 1290

STEROL ACYLTRANSFERASE
Accession: P43293

PRECURSOR
Swissprot_id: NAK_ARATH

(LECITHIN-CHOLESTEROL
Gi_number: 1171642

ACYLTRANSFERASE)
Description: Probable serine/threonine-

(PHOSPHOLIPID-
protein kinase NAK

CHOLESTEROL ACYLTRANSFERASE)
Seq ID: 1291

Seq ID: 465
Accession: P48612

Accession: P43293
Swissprot_id: PELO_DROME

Swissprot_id: NAK_ARATH
Gi_number: 1352736

Gi_number: 1171642
Description: PELOTA PROTEIN

Description: Probable serine/threonine-
Seq ID: 1292

protein kinase NAK
Accession: P55081

Seq ID: 466
Swissprot_id: MFA1_HUMAN

Accession: O04226
Gi_number: 1709012

Swissprot_id: P5CS_ORYSA
Description: Microfibrillar-associated

Gi_number: 6225820
protein 1

Description: Delta 1-pyrroline-5-
Seq ID: 1293

carboxylate synthetase (P5CS)
Accession: Q08466

[Includes: Glutamate 5-kinase
Swissprot_id: KC22_ARATH

(Gamma-glutamyl kinase)
Gi_number: 13638265

(GK); Gamma-glutamyl
Description: CASEIN KINASE II, ALPHA

phosphate reductase (GPR)
CHAIN 2 (CK II)

(Glutamate-5-semialdehyde
Seq ID: 1294

dehydrogenase)
Accession: Q42712

(Glutamyl-gamma-semialdehyde
Swissprot_id: FATA_CORSA

dehydrogenase)]
Gi_number: 8469219

Seq ID: 467
Description: Oleoyl-acyl carrier protein

Accession: O81395
thioesterase, chloroplast

Swissprot_id: DRTS_MAIZE
precursor (18:0-acyl-carrier

Gi_number: 6685381
protein thioesterase)

Description: BIFUNCTIONAL
(18:0-ACP thioesterase) (Acyl-

DIHYDROFOLATE REDUCTASE-
[acyl-carrier protein]

THYMIDYLATE SYNTHASE
hydrolase) (Fragment)

(DHFR-TS) [INCLUDES:
Seq ID: 1295

DIHYDROFOLATE REDUCTASE;
Accession: P41892

THYMIDYLATE
Swissprot_id: CC7_SCHPO

SYNTHASE]
Gi_number: 1168817

Seq ID: 468
Description: Cell division control protein 7

Accession: P42566
Seq ID: 1296

Swissprot_id: EP15_HUMAN
Accession: P43035

Gi_number: 1169540
Swissprot_id: LIS1_MOUSE

Description: Epidermal growth factor
Gi_number: 1170795

receptor substrate 15 (Protein
Description: PLATELET-ACTIVATING

EPS15) (AF-1P protein)
FACTOR ACETYLHYDROLASE IB

Seq ID: 470
ALPHA

Accession: P52306
SUBUNIT (PAF

Swissprot_id: GDS1_HUMAN
ACETYLHYDROLASE 45 KDA

Gi_number: 1707895
SUBUNIT) (PAF-AH 45 KDA

Description: RAP1 GTPASE-GDP
SUBUNIT) (PAF-AH

DISSOCIATION STIMULATOR 1 (SMG
ALPHA) (PAFAH ALPHA)

P21
(LISSENCEPHALY-1

STIMULATORY GDP/GTP
PROTEIN) (LIS-1)

EXCHANGE PROTEIN) (SMG GDS
Seq ID: 1297

PROTEIN)
Accession: P22503

Seq ID: 471
Swissprot_id: GUN_PHAVU

Accession: P38631
Gi_number: 1346225

Swissprot_id: GLS1_YEAST
Description: ENDOGLUCANASE

Gi_number: 1346146
PRECURSOR (ENDO-1,4-BETA-

Description: 1,3-BETA-GLUCAN
GLUCANASE)

SYNTHASE COMPONENT GLS1
(ABSCISSION CELLULASE)

(1,3-BETA-D-GLUCAN-UDP
Seq ID: 1298

GLUCOSYLTRANSFERASE) (CND1
Accession: P95982

PROTEIN)
Swissprot_id: SYY_SULSO

(CWN53 PROTEIN) (FKS1
Gi_number: 2501078

PROTEIN) (PAPULACANDIN B
Description: Tyrosyl-tRNA synthetase

SENSITIVITY
(Tyrosine--tRNA ligase) (TyrRS)

PROTEIN 1)
Seq ID: 1300

Seq ID: 472
Accession: O49923

Accession: Q42510
Swissprot_id: ADK_PHYPA

Swissprot_id: EM30_ARATH
Gi_number: 17366025

Gi_number: 2498329
Description: Adenosine kinase (AK)

Description: PATTERN FORMATION
(Adenosine 5′-phosphotransferase)

PROTEIN EMB30
Seq ID: 1301

Seq ID: 473
Accession: O08816

Accession: P47735
Swissprot_id: WASL_RAT

Swissprot_id: RLK5_ARATH
Gi_number: 13431956

Gi_number: 1350783
Description: Neural Wiskott-Aldrich

Description: Receptor-like protein kinase 5
syndrome protein (N-WASP)

precursor
Seq ID: 1302

Seq ID: 474
Accession: Q99KV1

Accession: P20305
Swissprot_id: DJBB_MOUSE

Swissprot_id: GELS_PIG
Gi_number: 17375610

Gi_number: 121118
Description: DnaJ homolog subfamily B

Description: Gelsolin precursor, plasma
member 11 precursor

(Actin-depolymerizing factor)
Seq ID: 1305

(ADF) (Brevin)
Accession: Q99758

Seq ID: 475
Swissprot_id: ABC3_HUMAN

Accession: P46607
Gi_number: 7387524

Swissprot_id: HGL2_ARATH
Description: ATP-binding cassette, sub-

Gi_number: 2506525
family A, member 3 (ATP-binding

Description: Homeobox protein
cassette transporter 3) (ATP-

GLABRA2 (Homeobox-leucine zipper
binding cassette 3) (ABC-C

protein
transporter)

ATHB-10) (HD-ZIP protein
Seq ID: 1307

ATHB-10)
Accession: P43291

Seq ID: 477
Swissprot_id: ASK1_ARATH

Accession: P40541
Gi_number: 1168529

Swissprot_id: IRR1_YEAST
Description: Serine/threonine-protein

Gi_number: 731791
kinase ASK1

Description: IRR1 PROTEIN
Seq ID: 1309

Seq ID: 478
Accession: P42730

Accession: P18493
Swissprot_id: H101_ARATH

Swissprot_id: PPOL_BOVIN
Gi_number: 1170149

Gi_number: 130779
Description: HEAT SHOCK PROTEIN

Description: POLY [ADP-RIBOSE]
101

POLYMERASE (PARP) (ADPRT)
Seq ID: 1310

(NAD(+)
Accession: P30148

ADP-
Swissprot_id: TALB_ECOLI

RIBOSYLTRANSFERASE) (POLY[ADP-
Gi_number: 401158

RIBOSE] SYNTHETASE)
Description: Transaldolase B

Seq ID: 479
Seq ID: 1311

Accession: P15792
Accession: P37370

Swissprot_id: KPK1_PHAVU
Swissprot_id: VRP1_YEAST

Gi_number: 125568
Gi_number: 2507155

Description: Protein kinase PVPK-1
Description: VERPROLIN

Seq ID: 480
Seq ID: 1312

Accession: P48980
Accession: Q9X1I8

Swissprot_id: BGAL_LYCES
Swissprot_id: KAD_THEMA

Gi_number: 1352077
Gi_number: 9910756

Description: Beta-galactosidase precursor
Description: Adenylate kinase (ATP-AMP

(Lactase)
transphosphorylase)

(EXO-(1-->4)-beta-D-
Seq ID: 1313

galactanase)
Accession: P03211

Seq ID: 481
Swissprot_id: EBN1_EBV

Accession: O60610
Gi_number: 119110

Swissprot_id: DIA1_HUMAN
Description: EBNA-1 NUCLEAR

Gi_number: 6225268
PROTEIN

Description: DIAPHANOUS PROTEIN
Seq ID: 1314

HOMOLOG 1 (DIAPHANOUS-
Accession: Q04629

RELATED FORMIN 1)
Swissprot_id: PSLA_YEAST

(DRF1)
Gi_number: 18202481

Seq ID: 482
Description: PSL10 protein

Accession: P39014
Seq ID: 1315

Swissprot_id: MT30_YEAST
Accession: P70315

Gi_number: 730077
Swissprot_id: WASP_MOUSE

Description: MET30 protein
Gi_number: 2499130

Seq ID: 484
Description: Wiskott-Aldrich syndrome

Accession: Q01577
protein homolog (WASP)

Swissprot_id: PKPA_PHYBL
Seq ID: 1316

Gi_number: 3122617
Accession: Q9D832

Description: Serine/threonine protein
Swissprot_id: DJB4_MOUSE

kinase PKPA
Gi_number: 18202849

Seq ID: 485
Description: DnaJ homolog subfamily B

Accession: P29141
member 4

Swissprot_id: SUBV_BACSU
Seq ID: 1318

Gi_number: 135023
Accession: O07597

Description: Minor extracellular protease
Swissprot_id: DAAA_BACSU

VPR precursor
Gi_number: 3121979

Seq ID: 486
Description: D-alanine aminotransferase

Accession: P47735
(D-aspartate aminotransferase)

Swissprot_id: RLK5_ARATH
(D-amino acid aminotransferase)

Gi_number: 1350783
(D-amino acid

Description: Receptor-like protein kinase 5
transaminase) (DAAT)

precursor
Seq ID: 1319

Seq ID: 487
Accession: P13686

Accession: P51849
Swissprot_id: PPA5_HUMAN

Swissprot_id: DCP3_ORYSA
Gi_number: 130722

Gi_number: 1706331
Description: Tartrate-resistant acid

Description: PYRUVATE
phosphatase type 5 precursor

DECARBOXYLASE ISOZYME 3 (PDC)
(TR-AP) (Tartrate-resistant acid

Seq ID: 488
ATPase) (TrATPase)

Accession: Q43207
Seq ID: 1320

Swissprot_id: FKB7_WHEAT
Accession: P06921

Gi_number: 3023751
Swissprot_id: VE2_HPV05

Description: 70 kDa peptidylprolyl
Gi_number: 1352839

isomerase (Peptidylprolyl cis-trans
Description: REGULATORY PROTEIN

isomerase) (Cyclophilin) (PPiase)
E2

Seq ID: 489
Seq ID: 1321

Accession: P47997
Accession: P29518

Swissprot_id: G11A_ORYSA
Swissprot_id: BT1_MAIZE

Gi_number: 1346057
Gi_number: 231654

Description: Protein kinase G11A
Description: Brittle-1 protein, chloroplast

Seq ID: 490
precursor

Accession: O15523
Seq ID: 1322

Swissprot_id: DDXY_HUMAN
Accession: Q12899

Gi_number: 6014945
Swissprot_id: Z173_HUMAN

Description: DEAD-box protein 3, Y-
Gi_number: 17380344

chromosomal
Description: Zinc finger protein 173 (Acid

Seq ID: 491
finger protein) (AFP)

Accession: Q38997
Seq ID: 1323

Swissprot_id: KI10_ARATH
Accession: P74667

Gi_number: 6166239
Swissprot_id: DAPF_SYNY3

Description: SNF1-related protein kinase
Gi_number: 2494041

KIN10 (AKIN10)
Description: Diaminopimelate epimerase

Seq ID: 492
(DAP epimerase)

Accession: P52707
Seq ID: 1324

Swissprot_id: MDL3_PRUSE
Accession: P93531

Gi_number: 1708972
Swissprot_id: C7D7_SOLCH

Description: (R)-MANDELONITRILE
Gi_number: 5915836

LYASE ISOFORM 3 PRECURSOR
Description: CYTOCHROME P450 71D7

(HYDROXYNITRILE LYASE 3)
Seq ID: 1325

((R)-OXYNITRILASE 3)
Accession: P52425

Seq ID: 493
Swissprot_id: GPDA_CUPLA

Accession: Q02817
Gi_number: 1708025

Swissprot_id: MUC2_HUMAN
Description: GLYCEROL-3-PHOSPHATE

Gi_number: 2506877
DEHYDROGENASE [NAD+]

Description: MUCIN 2 PRECURSOR
Seq ID: 1326

(INTESTINAL MUCIN 2)
Accession: Q01042

Seq ID: 494
Swissprot_id: IE68_HSVSA

Accession: P38631
Gi_number: 266334

Swissprot_id: GLS1_YEAST
Description: IMMEDIATE-EARLY

Gi_number: 1346146
PROTEIN

Description: 1,3-BETA-GLUCAN
Seq ID: 1327

SYNTHASE COMPONENT GLS1
Accession: P21997

(1,3-BETA-D-GLUCAN-UDP
Swissprot_id: SSGP_VOLCA

GLUCOSYLTRANSFERASE) (CND1
Gi_number: 134920

PROTEIN)
Description: SULFATED SURFACE

(CWN53 PROTEIN) (FKS1
GLYCOPROTEIN 185 (SSG 185)

PROTEIN) (PAPULACANDIN B
Seq ID: 1329

SENSITIVITY
Accession: P10978

PROTEIN 1)
Swissprot_id: POLX_TOBAC

Seq ID: 495
Gi_number: 130582

Accession: P54278
Description: Retrovirus-related Pol

Swissprot_id: PMS2_HUMAN
polyprotein from transposon TNT

Gi_number: 1709685
1-94 [Contains: Protease;

Description: PMS1 protein homolog 2
Reverse transcriptase;

(DNA mismatch repair protein PMS2)
Endonuclease]

Seq ID: 496
Seq ID: 1332

Accession: Q02637
Accession: O60315

Swissprot_id: CEB_DROME
Swissprot_id: SIP1_HUMAN

Gi_number: 1345723
Gi_number: 13124503

Description: CCAAT/ENHANCER
Description: ZINC FINGER HOMEOBOX

BINDING PROTEIN (C/EBP) (SLOW
PROTEIN 1B (SMAD INTERACTING

BORDER CELL
PROTEIN

PROTEIN)
1)

Seq ID: 497
Seq ID: 1333

Accession: Q40671
Accession: O10296

Swissprot_id: CG2B_ORYSA
Swissprot_id: IAP1_NPVOP

Gi_number: 3913236
Gi_number: 2497245

Description: G2/mitotic-specific cyclin 2
Description: Apoptosis inhibitor 1 (IAP-1)

(B-like cyclin) (CYCOS2)
Seq ID: 1334

Seq ID: 498
Accession: P37370

Accession: Q02096
Swissprot_id: VRP1_YEAST

Swissprot_id: PGLR_PERAE
Gi_number: 2507155

Gi_number: 400758
Description: VERPROLIN

Description: Polygalacturonase precursor
Seq ID: 1335

(PG) (Pectinase)
Accession: Q9UBV2

Seq ID: 499
Swissprot_id: SE1L_HUMAN

Accession: Q07474
Gi_number: 13878770

Swissprot_id: MAD2_PETHY
Description: SEL-1 HOMOLOG

Gi_number: 729976
PRECURSOR (SUPPRESSOR OF LIN-

Description: Floral homeotic protein
12-LIKE

PMADS 2
PROTEIN) (SEL-1L)

Seq ID: 500
Seq ID: 1338

Accession: P18583
Accession: Q40680

Swissprot _id: SON_HUMAN
Swissprot_id: EF1B_ORYSA

Gi_number: 586013
Gi_number: 6166140

Description: SON PROTEIN (SON3)
Description: ELONGATION FACTOR 1-

Seq ID: 501
BETA (EF-1-BETA)

Accession: Q61548
Seq ID: 1339

Swissprot_id: A180_MOUSE
Accession: P14328

Gi_number: 2492687
Swissprot_id: SP96_DICDI

Description: CLATHRIN COAT
Gi_number: 134780

ASSEMBLY PROTEIN AP180
Description: SPORE COAT PROTEIN

(CLATHRIN COAT
SP96

ASSOCIATED PROTEIN
Seq ID: 1341

AP180) (PHOSPHOPROTEIN F1-20) (91 KDA
Accession: P14328

SYNAPTOSOMAL-
Swissprot_id: SP96_DICDI

ASSOCIATED PROTEIN)
Gi_number: 134780

Seq ID: 502
Description: SPORE COAT PROTEIN

Accession: P50809
SP96

Swissprot_id: VE2_HPV36
Seq ID: 1342

Gi_number: 1718125
Accession: O22815

Description: REGULATORY PROTEIN
Swissprot_id: MLO5_ARATH

E2
Gi_number: 6137253

Seq ID: 503
Description: MLO-like protein 5 (AtMlo5)

Accession: Q00624
Seq ID: 1343

Swissprot_id: ASO_BRANA
Accession: Q02817

Gi_number: 114268
Swissprot_id: MUC2_HUMAN

Description: L-ascorbate oxidase homolog
Gi_number: 2506877

precursor (Ascorbase)
Description: MUCIN 2 PRECURSOR

Seq ID: 504
(INTESTINAL MUCIN 2)

Accession: O22467
Seq ID: 1345

Swissprot_id: MSI1_ARATH
Accession: P78621

Gi_number: 3122387
Swissprot_id: SEPA_EMENI

Description: WD-40 repeat protein MSI1
Gi_number: 15214279

Seq ID: 505
Description: CYTOKINESIS PROTEIN

Accession: Q13459
SEPA (FH1/2 PROTEIN) (FORCED

Swissprot_id: MY9B_HUMAN
EXPRESSION INHIBITION OF

Gi_number: 14548118
GROWTH A)

Description: MYOSIN IXB
Seq ID: 1347

(UNCONVENTIONAL MYOSIN-9B)
Accession: Q12849

Seq ID: 508
Swissprot_id: GRF1_HUMAN

Accession: Q9HB07
Gi_number: 2500579

Swissprot_id: MYG1_HUMAN
Description: G-rich sequence factor-1

Gi_number: 14194963
(GRSF-1)

Description: MYG1 protein
Seq ID: 1349

Seq ID: 509
Accession: P08393

Accession: P05100
Swissprot_id: ICP0_HSV11

Swissprot_id: 3MG1_ECOLI
Gi_number: 124134

Gi_number: 112785
Description: Trans-acting transcriptional

Description: DNA-3-methyladenine
protein ICP0 (Immediate-early

glycosylase I (3-methyladenine-DNA
protein IE110) (VMW110)

glycosylase I, constitutive) (TAG
(Alpha-0 protein)

I) (DNA-3-methyladenine
Seq ID: 1350

glycosidase I)
Accession: Q9UMN6

Seq ID: 511
Swissprot_id: TRX2_HUMAN

Accession: O24356
Gi_number: 12643900

Swissprot_id: MEN8_SILLA
Description: TRITHORAX HOMOLOG 2

Gi_number: 6016542
(MIXED LINEAGE LEUKEMIA GENE

Description: MEN-8 protein precursor
HOMOLOG 2

Seq ID: 512
PROTEIN)

Accession: P40013
Seq ID: 1352

Swissprot_id: BIM1_YEAST
Accession: P11219

Gi_number: 731441
Swissprot_id: AGI_ORYSA

Description: BIM1 PROTEIN
Gi_number: 113509

Seq ID: 514
Description: LECTIN PRECURSOR

Accession: P30755
(AGGLUTININ)

Swissprot_id: H2B1_MAIZE
Seq ID: 1353

Gi_number: 399853
Accession: P04146

Description: HISTONE H2B.1
Swissprot_id: COPI_DROME

Seq ID: 516
Gi_number: 13124684

Accession: P08985
Description: Copia protein [Contains:

Swissprot_id: H2AV_DROME
Copia VLP protein; Copia protease]

Gi_number: 121989
Seq ID: 1354

Description: HISTONE H2A VARIANT
Accession: P93531

Seq ID: 517
Swissprot_id: C7D7_SOLCH

Accession: P28968
Gi_number: 5915836

Swissprot_id: VGLX_HSVEB
Description: CYTOCHROME P450 71D7

Gi_number: 138350
Seq ID: 1355

Description: GLYCOPROTEIN X
Accession: P28968

PRECURSOR
Swissprot_id: VGLX_HSVEB

Seq ID: 519
Gi_number: 138350

Accession: Q05654
Description: GLYCOPROTEIN X

Swissprot_id: RDPO_SCHPO
PRECURSOR

Gi_number: 1710054
Seq ID: 1357

Description: RETROTRANSPOSABLE
Accession: P76004

ELEMENT TF2 155 KDA PROTEIN
Swissprot_id: YCGM_ECOLI

Seq ID: 525
Gi_number: 9789812

Accession: P04323
Description: Protein ycgM

Swissprot_id: POL3_DROME
Seq ID: 1358

Gi_number: 130405
Accession: P33296

Description: Retrovirus-related Pol
Swissprot_id: UBC6_YEAST

polyprotein from transposon 17.6
Gi_number: 464983

[Contains: Protease; Reverse
Description: UBIQUITIN-

transcriptase;
CONJUGATING ENZYME E2-28.4 KD

Endonuclease]
(UBIQUITIN-PROTEIN

Seq ID: 526
LIGASE) (UBIQUITIN

Accession: P29375
CARRIER PROTEIN)

Swissprot_id: RBB2_HUMAN
Seq ID: 1360

Gi_number: 1710032
Accession: P51530

Description: Retinoblastoma-binding
Swissprot_id: DN2L_HUMAN

protein 2 (RBBP-2)
Gi_number: 2506893

Seq ID: 527
Description: DNA2-like homolog (DNA

Accession: P14233
replication helicase-like homolog)

Swissprot_id: TGAB_TOBAC
Seq ID: 1362

Gi_number: 135670
Accession: P05143

Description: TGACG-SEQUENCE
Swissprot_id: PRP3_MOUSE

SPECIFIC DNA-BINDING PROTEIN
Gi_number: 131002

TGA-1B (HSBF)
Description: PROLINE-RICH PROTEIN

Seq ID: 529
MP-3

Accession: P05423
Seq ID: 1363

Swissprot_id: BN51_HUMAN
Accession: P93411

Gi_number: 115081
Swissprot_id: CG1C_ORYSA

Description: BN51 protein
Gi_number: 3334144

Seq ID: 530
Description: G1/S-SPECIFIC CYCLIN C-

Accession: P08640
TYPE

Swissprot_id: AMYH_YEAST
Seq ID: 1365

Gi_number: 728850
Accession: O15145

Description: GLUCOAMYLASE S1/S2
Swissprot_id: AR21_HUMAN

PRECURSOR (GLUCAN
Gi_number: 3121765

1,4-ALPHA-GLUCOSIDASE)
Description: ARP2/3 COMPLEX 21 KDA

(1,4-ALPHA-D-GLUCAN
SUBUNIT (P21-ARC) (ACTIN-

GLUCOHYDROLASE)
RELATED

Seq ID: 532
PROTEIN 2/3 COMPLEX

Accession: P44389
SUBUNIT 3)

Swissprot_id: RS15_HAEIN
Seq ID: 1366

Gi_number: 1173205
Accession: P37398

Description: 30S ribosomal protein S15
Swissprot_id: VIV_ORYSA

Seq ID: 533
Gi_number: 586238

Accession: P40619
Description: VIVIPAROUS PROTEIN

Swissprot_id: HMGL_PHANI
HOMOLOG

Gi_number: 729736
Seq ID: 1367

Description: HMG1/2-LIKE PROTEIN
Accession: P25032

Seq ID: 535
Swissprot_id: EMP1_WHEAT

Accession: P43214
Gi_number: 119319

Swissprot_id: MPP2_PHLPR
Description: DNA-BINDING EMBP-1

Gi_number: 1171009
PROTEIN

Description: POLLEN ALLERGEN PHL P
Seq ID: 1368

2 PRECURSOR (PHL P II)
Accession: Q43716

Seq ID: 536
Swissprot_id: UFOG_PETHY

Accession: Q9Y6D5
Gi_number: 2501497

Swissprot_id: BIG2_HUMAN
Description: Flavonol 3-O-

Gi_number: 13123996
glucosyltransferase (UDP-glucose

Description: BREFELDIN A-INHIBITED
flavonoid

GUANINE NUCLEOTIDE-EXCHANGE
3-O-glucosyltransferase)

PROTEIN
(Anthocyanin rhamnosyl

2 (BREFELDIN A-INHIBITED
transferase)

GEP 2)
Seq ID: 1369

Seq ID: 537
Accession: P52285

Accession: P12957
Swissprot_id: FP21_DICDI

Swissprot_id: CALD_CHICK
Gi_number: 1706890

Gi_number: 2506984
Description: GLYCOPROTEIN FP21

Description: CALDESMON (CDM)
PRECURSOR

Seq ID: 538
Seq ID: 1370

Accession: Q9FJR0
Accession: P21997

Swissprot_id: RNT1_ARATH
Swissprot_id: SSGP_VOLCA

Gi_number: 18202906
Gi_number: 134920

Description: Regulator of nonsense
Description: SULFATED SURFACE

transcripts 1 homolog
GLYCOPROTEIN 185 (SSG 185)

Seq ID: 539
Seq ID: 1372

Accession: Q14562
Accession: P40602

Swissprot_id: DDX8_HUMAN
Swissprot_id: APG_ARATH

Gi_number: 3023637
Gi_number: 728867

Description: ATP-dependent helicase
Description: ANTER-SPECIFIC

DDX8 (RNA helicase HRH1) (DEAH-box
PROLINE-RICH PROTEIN APG

protein 8)
PRECURSOR

Seq ID: 540
Seq ID: 1373

Accession: Q9Y4I1
Accession: P36044

Swissprot_id: MY5A_HUMAN
Swissprot_id: MNN4_YEAST

Gi_number: 13431722
Gi_number: 3915759

Description: MYOSIN VA (MYOSIN 5A)
Description: MNN4 PROTEIN

(DILUTE MYOSIN HEAVY CHAIN,
Seq ID: 1376

NON-MUSCLE) (MYOSIN
Accession: P34127

HEAVY CHAIN 12) (MYOXIN)
Swissprot_id: MYBH_DICDI

Seq ID: 541
Gi_number: 462671

Accession: Q9LRE6
Description: Myb-like protein

Swissprot_id: DPOD_ORYSA
Seq ID: 1377

Gi_number: 13124219
Accession: P20025

Description: DNA polymerase delta
Swissprot_id: MYB3_MAIZE

catalytic subunit
Gi_number: 127582

Seq ID: 542
Description: Myb-related protein Zm38

Accession: Q15477
Seq ID: 1379

Swissprot_id: SKIW_HUMAN
Accession: P28968

Gi_number: 3123284
Swissprot_id: VGLX_HSVEB

Description: HELICASE SKI2W
Gi_number: 138350

(HELICASE-LIKE PROTEIN) (HLP)
Description: GLYCOPROTEIN X

Seq ID: 543
PRECURSOR

Accession: P50533
Seq ID: 1382

Swissprot_id: XCPE_XENLA
Accession: O15194

Gi_number: 1722856
Swissprot_id: NIF1_HUMAN

Description: CHROMOSOME
Gi_number: 17865502

ASSEMBLY PROTEIN XCAP-E
Description: Nuclear LIM interactor-

Seq ID: 544
interacting factor 1

Accession: P47735
(NLI-interacting factor 1) (NIF-

Swissprot_id: RLK5_ARATH
like protein) (YA22

Gi_number: 1350783
protein) (HYA22)

Description: Receptor-like protein kinase 5
Seq ID: 1384

precursor
Accession: P13027

Seq ID: 545
Swissprot_id: ARRS_MAIZE

Accession: P78706
Gi_number: 114217

Swissprot_id: RCO1_NEUCR
Description: ANTHOCYANIN

Gi_number: 2494901
REGULATORY R-S PROTEIN

Description: TRANSCRIPTIONAL
Seq ID: 1385

REPRESSOR RCO-1
Accession: P52285

Seq ID: 546
Swissprot_id: FP21_DICDI

Accession: P47735
Gi_number: 1706890

Swissprot_id: RLK5_ARATH
Description: GLYCOPROTEIN FP21

Gi_number: 1350783
PRECURSOR

Description: Receptor-like protein kinase 5
Seq ID: 1389

precursor
Accession: P80073

Seq ID: 547
Swissprot_id: MYB2_PHYPA

Accession: P25822
Gi_number: 462669

Swissprot_id: PUM_DROME
Description: Myb-related protein Pp2

Gi_number: 131605
Seq ID: 1391

Description: MATERNAL PUMILIO
Accession: P14328

PROTEIN
Swissprot_id: SP96_DICDI

Seq ID: 548
Gi_number: 134780

Accession: P23394
Description: SPORE COAT PROTEIN

Swissprot_id: PR28_YEAST
SP96

Gi_number: 1172596
Seq ID: 1392

Description: PRE-MRNA SPLICING
Accession: Q00765

FACTOR RNA HELICASE PRP28
Swissprot_id: DP1_HUMAN

(HELICASE CA8)
Gi_number: 232007

Seq ID: 549
Description: POLYPOSIS LOCUS

Accession: P31948
PROTEIN 1 (TB2 PROTEIN)

Swissprot_id: IEFS_HUMAN
Seq ID: 1394

Gi_number: 400042
Accession: Q9ZDW6

Description: Stress-induced-
Swissprot_id: FER2_RICPR

phosphoprotein 1 (STI1)
Gi_number: 7227897

(Hsp70/Hsp90-organizing
Description: Ferredoxin, 2Fe-2S

protein) (Transformation-sensitive
Seq ID: 1397

protein IEF SSP 3521)
Accession: Q40374

Seq ID: 551
Swissprot_id: PR1_MEDTR

Accession: P07742
Gi_number: 2500715

Swissprot_id: RIR1_MOUSE
Description: PATHOGENESIS-

Gi_number: 132609
RELATED PROTEIN PR-1 PRECURSOR

Description: Ribonucleoside-diphosphate
Seq ID: 1399

reductase M1 chain
Accession: P33488

(Ribonucleotide reductase large
Swissprot_id: ABP4_MAIZE

chain)
Gi_number: 461451

Seq ID: 552
Description: AUXIN-BINDING PROTEIN

Accession: Q08759
4 PRECURSOR (ABP)

Swissprot_id: MYB_XENLA
Seq ID: 1400

Gi_number: 730090
Accession: P10220

Description: Myb protein
Swissprot_id: TEGU_HSV11

Seq ID: 553
Gi_number: 135576

Accession: P51798
Description: LARGE TEGUMENT

Swissprot_id: CLC7_HUMAN
PROTEIN (VIRION PROTEIN UL36)

Gi_number: 12644301
Seq ID: 1403

Description: CHLORIDE CHANNEL
Accession: P52499

PROTEIN 7 (CLC-7)
Swissprot_id: RCC1_CANAL

Seq ID: 554
Gi_number: 1710046

Accession: Q9R0N7
Description: RCC1 protein

Swissprot_id: SYT7_MOUSE
Seq ID: 1404

Gi_number: 18203408
Accession: P10243

Description: Synaptotagmin VII (SytVII)
Swissprot_id: MYBA_HUMAN

Seq ID: 555
Gi_number: 1171089

Accession: Q43704
Description: Myb-related protein A (A-

Swissprot_id: MCM3_MAIZE
Myb)

Gi_number: 2497820
Seq ID: 1405

Description: DNA replication licensing
Accession: P45344

factor MCM3 homolog (Replication
Swissprot_id: YADR_HAEIN

origin activator) (ROA protein)
Gi_number: 1175501

Seq ID: 556
Description: Protein HI1723

Accession: P93648
Seq ID: 1406

Swissprot_id: LON2_MAIZE
Accession: P20967

Gi_number: 3914006
Swissprot_id: ODO1_YEAST

Description: Lon protease homolog 2,
Gi_number: 730221

mitochondrial precursor
Description: 2-OXOGLUTARATE

Seq ID: 557
DEHYDROGENASE E1 COMPONENT,

Accession: P20724
MITOCHONDRIAL

Swissprot_id: ELYA_BACSP
PRECURSOR (ALPHA-

Gi_number: 119309
KETOGLUTARATE

Description: Alkaline elastase YaB
DEHYDROGENASE)

precursor
Seq ID: 1408

Seq ID: 558
Accession: P42798

Accession: O59933
Swissprot_id: RS1A_ARATH

Swissprot_id: ER25_CANAL
Gi_number: 1173218

Gi_number: 6015108
Description: 40S ribosomal protein S15A

Description: C-4 methyl sterol oxidase
Seq ID: 1413

Seq ID: 559
Accession: Q9ZNV5

Accession: Q9QUR6
Swissprot_id: CEN_ARATH

Swissprot_id: PPCE_MOUSE
Gi_number: 17366125

Gi_number: 13633250
Description: CENTRORADIALIS-like

Description: Prolyl endopeptidase (Post-
protein

proline cleaving enzyme) (PE)
Seq ID: 1415

Seq ID: 560
Accession: P81489

Accession: P40798
Swissprot_id: PRPP_HUMAN

Swissprot_id: STC_DROME
Gi_number: 3914451

Gi_number: 730843
Description: SALIVARY PROLINE-RICH

Description: Shuttle craft protein
PROTEIN II-1

Seq ID: 561
Seq ID: 1416

Accession: P38630
Accession: P15941

Swissprot_id: RFC1_YEAST
Swissprot_id: MUC1_HUMAN

Gi_number: 584899
Gi_number: 547937

Description: Activator 1.95 kDa subunit
Description: MUCIN 1 PRECURSOR

(Replication factor C 95 kDa
(POLYMORPHIC EPITHELIAL MUCIN)

subunit) (Cell division control
(PEM)

protein 44)
(PEMT) (EPISIALIN) (TUMOR-

Seq ID: 562
ASSOCIATED MUCIN)

Accession: Q9SYQ8
(CARCINOMA-ASSOCIATED

Swissprot_id: CLV1_ARATH
MUCIN) (TUMOR-ASSOCIATED

Gi_number: 12643323
EPITHELIAL

Description: RECEPTOR PROTEIN
MEMBRANE ANTIGEN)

KINASE CLAVATA1 PRECURSOR
(EMA) (H23AG) (PEANUT-REACTIVE

Seq ID: 564
URINARY

Accession: P13983
MUCIN) (PUM) (BREAST

Swissprot_id: EXTN_TOBAC
CARCINOMA-ASSOCIA>

Gi_number: 119714
Seq ID: 1417

Description: Extensin precursor (Cell wall
Accession: P03360

hydroxyproline-rich
Swissprot_id: POL_AVIRE

glycoprotein)
Gi_number: 130584

Seq ID: 565
Description: POL polyprotein [Contains:

Accession: P08640
Reverse transcriptase;

Swissprot_id: AMYH_YEAST
Endonuclease]

Gi_number: 728850
Seq ID: 1419

Description: GLUCOAMYLASE S1/S2
Accession: P23246

PRECURSOR (GLUCAN
Swissprot_id: SFPQ_HUMAN

1,4-ALPHA-GLUCOSIDASE)
Gi_number: 1709851

(1,4-ALPHA-D-GLUCAN
Description: SPLICING FACTOR,

GLUCOHYDROLASE)
PROLINE-AND GLUTAMINE-RICH

Seq ID: 566
(POLYPYRIMIDINE TRACT-

Accession: P38605
BINDING PROTEIN-ASSOCIATED

Swissprot_id: CAS1_ARATH
SPLICING

Gi_number: 584882
FACTOR) (PTB-ASSOCIATED

Description: CYCLOARTENOL
SPLICING FACTOR) (PSF)

SYNTHASE (2,3-EPOXYSQUALENE--
(DNA-BINDING P52/P100

CYCLOARTENOL
COMPLEX, 100 KDA SUBUNIT)

CYCLASE)
Seq ID: 1420

Seq ID: 567
Accession: Q61768

Accession: Q9SA34
Swissprot_id: KINH_MOUSE

Swissprot_id: IMH2_ARATH
Gi_number: 2497519

Gi_number: 14194878
Description: KINESIN HEAVY CHAIN

Description: Probable inosine-5′-
(UBIQUITOUS KINESIN HEAVY

monophosphate dehydrogenase (IMP
CHAIN)

dehydrogenase) (IMPDH) (IMPD)
(UKHC)

Seq ID: 568
Seq ID: 1421

Accession: P43293
Accession: P08640

Swissprot_id: NAK_ARATH
Swissprot_id: AMYH_YEAST

Gi_number: 1171642
Gi_number: 728850

Description: Probable serine/threonine-
Description: GLUCOAMYLASE S1/S2

protein kinase NAK
PRECURSOR (GLUCAN

Seq ID: 569
1,4-ALPHA-GLUCOSIDASE)

Accession: P25386
(1,4-ALPHA-D-GLUCAN

Swissprot_id: USO1_YEAST
GLUCOHYDROLASE)

Gi_number: 137175
Seq ID: 1422

Description: Intracellular protein transport
Accession: P08640

protein USO1
Swissprot_id: AMYH_YEAST

Seq ID: 571
Gi_number: 728850

Accession: P10163
Description: GLUCOAMYLASE S1/S2

Swissprot_id: PRP4_HUMAN
PRECURSOR (GLUCAN

Gi_number: 131005
1,4-ALPHA-GLUCOSIDASE)

Description: SALIVARY PROLINE-RICH
(1,4-ALPHA-D-GLUCAN

PROTEIN PO PRECURSOR (ALLELE S)
GLUCOHYDROLASE)

Seq ID: 572
Seq ID: 1423

Accession: P38994
Accession: P16157

Swissprot_id: MSS4_YEAST
Swissprot_id: ANK1_HUMAN

Gi_number: 1709144
Gi_number: 113884

Description: Probable
Description: Ankyrin 1 (Erythrocyte

phosphatidylinositol-4-phosphate 5-kinase
ankyrin) (Ankyrin R)

MSS4
Seq ID: 1424

(1-phosphatidylinositol-4-
Accession: P54121

phosphate kinase) (PIP5K)
Swissprot_id: AIG2_ARATH

(PtdIns(4)P-5-kinase)
Gi_number: 1703220

(Diphosphoinositide kinase)
Description: AIG2 protein

Seq ID: 573
Seq ID: 1425

Accession: P37898
Accession: P26810

Swissprot_id: AAP1_YEAST
Swissprot_id: POL_MLVF5

Gi_number: 728771
Gi_number: 130641

Description: ALANINE/ARGININE
Description: POL POLYPROTEIN

AMINOPEPTIDASE
[CONTAINS: PROTEASE; REVERSE

Seq ID: 574
TRANSCRIPTASE;

Accession: P53683
RIBONUCLEASE H]

Swissprot_id: CDP2_ORYSA
Seq ID: 1426

Gi_number: 1705734
Accession: P23246

Description: Calcium-dependent protein
Swissprot_id: SFPQ_HUMAN

kinase, isoform 2 (CDPK 2)
Gi_number: 1709851

Seq ID: 576
Description: SPLICING FACTOR,

Accession: P17814
PROLINE-AND GLUTAMINE-RICH

Swissprot_id: 4CL1_ORYSA
(POLYPYRIMIDINE TRACT-

Gi_number: 112802
BINDING PROTEIN-ASSOCIATED

Description: 4-coumarate--CoA ligase 1
SPLICING

(4CL 1) (4-coumaroyl-CoA
FACTOR) (PTB-ASSOCIATED

synthase 1)
SPLICING FACTOR) (PSF)

Seq ID: 577
(DNA-BINDING P52/P100

Accession: P42704
COMPLEX, 100 KDA SUBUNIT)

Swissprot_id: L130_HUMAN
Seq ID: 1427

Gi_number: 1730078
Accession: Q06548

Description: 130 kDa leucine-rich protein
Swissprot_id: APKA_ARATH

(LRP 130) (GP130)
Gi_number: 1168470

Seq ID: 578
Description: Protein kinase APK1A

Accession: P78963
Seq ID: 1428

Swissprot_id: SKB1_SCHPO
Accession: Q02496

Gi_number: 12644354
Swissprot_id: MUC1_MOUSE

Description: SHK1 KINASE-BINDING
Gi_number: 547938

PROTEIN 1
Description: Mucin 1 precursor

Seq ID: 579
(Polymorphic epithelial mucin) (PEMT)

Accession: P80073
(Episialin)

Swissprot_id: MYB2_PHYPA
Seq ID: 1429

Gi_number: 462669
Accession: P08640

Description: Myb-related protein Pp2
Swissprot_id: AMYH_YEAST

Seq ID: 580
Gi_number: 728850

Accession: P29458
Description: GLUCOAMYLASE S1/S2

Swissprot_id: CC21_SCHPO
PRECURSOR (GLUCAN

Gi_number: 6226565
1,4-ALPHA-GLUCOSIDASE)

Description: CDC21 PROTEIN
(1,4-ALPHA-D-GLUCAN

Seq ID: 581
GLUCOHYDROLASE)

Accession: P52707
Seq ID: 1430

Swissprot_id: MDL3_PRUSE
Accession: O00268

Gi_number: 1708972
Swissprot_id: T2D3_HUMAN

Description: (R)-MANDELONITRILE
Gi_number: 3024681

LYASE ISOFORM 3 PRECURSOR
Description: TRANSCRIPTION

(HYDROXYNITRILE LYASE 3)
INITIATION FACTOR TFIID 135 KDA

((R)-OXYNITRILASE 3)
SUBUNIT

Seq ID: 582
(TAFII-135) (TAFII135) (TAFII-

Accession: P25439
130) (TAFII130)

Swissprot_id: BRM_DROME
Seq ID: 1431

Gi_number: 115132
Accession: Q02817

Description: HOMEOTIC GENE
Swissprot_id: MUC2_HUMAN

REGULATOR (BRAHMA PROTEIN)
Gi_number: 2506877

Seq ID: 583
Description: MUCIN 2 PRECURSOR

Accession: Q99614
(INTESTINAL MUCIN 2)

Swissprot_id: TTC1_HUMAN
Seq ID: 1432

Gi_number: 12585378
Accession: O18746

Description: TETRATRICOPEPTIDE
Swissprot_id: HSP1_PLAMS

REPEAT PROTEIN 1 (TPR REPEAT
Gi_number: 3023963

PROTEIN 1)
Description: Sperm protamine P1

Seq ID: 584
Seq ID: 1433

Accession: P45672
Accession: P08640

Swissprot_id: NIR3_AZOBR
Swissprot_id: AMYH_YEAST

Gi_number: 1171716
Gi_number: 728850

Description: NIFR3-LIKE PROTEIN
Description: GLUCOAMYLASE S1/S2

Seq ID: 585
PRECURSOR (GLUCAN

Accession: P07153
1,4-ALPHA-GLUCOSIDASE)

Swissprot_id: RIB1_RAT
(1,4-ALPHA-D-GLUCAN

Gi_number: 132560
GLUCOHYDROLASE)

Description: Dolichyl-
Seq ID: 1434

diphosphooligosaccharide--protein
Accession: Q02817

glycosyltransferase 67 kDa
Swissprot_id: MUC2_HUMAN

subunit precursor (Ribophorin
Gi_number: 2506877

I) (RPN-I)
Description: MUCIN 2 PRECURSOR

Seq ID: 586
(INTESTINAL MUCIN 2)

Accession: Q38741
Seq ID: 1435

Swissprot_id: SBP1_ANTMA
Accession: Q9SJL6

Gi_number: 6094239
Swissprot_id: GS27_ARATH

Description: SQUAMOSA-PROMOTER
Gi_number: 11132470

BINDING PROTEIN 1
Description: Probable 27 kDa Golgi

Seq ID: 587
SNARE protein (Golgi SNAP receptor

Accession: P21447
complex member 2)

Swissprot_id: MDR3_MOUSE
Seq ID: 1436

Gi_number: 266517
Accession: P21997

Description: Multidrug resistance protein 3
Swissprot_id: SSGP_VOLCA

(P-glycoprotein 3) (MDR1A)
Gi_number: 134920

Seq ID: 588
Description: SULFATED SURFACE

Accession: P52706
GLYCOPROTEIN 185 (SSG 185)

Swissprot_id: MDL1_PRUSE
Seq ID: 1439

Gi_number: 1708971
Accession: P10587

Description: (R)-MANDELONITRILE
Swissprot_id: MYHB_CHICK

LYASE ISOFORM 1 PRECURSOR
Gi_number: 3915778

(HYDROXYNITRILE LYASE 1)
Description: Myosin heavy chain, gizzard

((R)-OXYNITRILASE 1)
smooth muscle

Seq ID: 589
Seq ID: 1441

Accession: P21997
Accession: O96614

Swissprot_id: SSGP_VOLCA
Swissprot_id: SER1_GALME

Gi_number: 134920
Gi_number: 9087201

Description: SULFATED SURFACE
Description: Sericin-1 (Silk gum protein 1)

GLYCOPROTEIN 185 (SSG 185)
Seq ID: 1445

Seq ID: 591
Accession: P28968

Accession: P70362
Swissprot_id: VGLX_HSVEB

Swissprot_id: UFD1_MOUSE
Gi_number: 138350

Gi_number: 2501439
Description: GLYCOPROTEIN X

Description: Ubiquitin fusion degradation
PRECURSOR

protein 1 homolog (UB fusion
Seq ID: 1448

protein 1)
Accession: Q9UKN7

Seq ID: 592
Swissprot_id: MY15_HUMAN

Accession: P05522
Gi_number: 13124361

Swissprot_id: GUN1_PERAE
Description: Myosin XV (Unconventional

Gi_number: 121784
myosin-15)

Description: ENDOGLUCANASE 1
Seq ID: 1449

PRECURSOR (ENDO-1,4-BETA-
Accession: Q02817

GLUCANASE)
Swissprot_id: MUC2_HUMAN

(ABSCISSION CELLULASE 1)
Gi_number: 2506877

Seq ID: 593
Description: MUCIN 2 PRECURSOR

Accession: Q40286
(INTESTINAL MUCIN 2)

Swissprot_id: UFO4_MANES
Seq ID: 1450

Gi_number: 2501493
Accession: Q13303

Description: Flavonol 3-O-
Swissprot_id: KVB2_HUMAN

glucosyltransferase 4 (UDP-glucose
Gi_number: 18202496

flavonoid
Description: Voltage-gated potassium

3-O-glucosyltransferase 4)
channel beta-2 subunit (K+ channel

(Fragment)
beta-2 subunit) (Kv-beta-2)

Seq ID: 594
(HKvbeta2)

Accession: P52409
Seq ID: 1451

Swissprot_id: E13B_WHEAT
Accession: P27884

Gi_number: 1706551
Swissprot_id: CCAA_RABIT

Description: GLUCAN ENDO-1,3-BETA-
Gi_number: 399201

GLUCOSIDASE PRECURSOR
Description: VOLTAGE-DEPENDENT

((1->3)-BETA-GLUCAN
P/Q-TYPE CALCIUM CHANNEL

ENDOHYDROLASE) ((1->3)-BETA-
ALPHA-1A

GLUCANASE)
SUBUNIT (CALCIUM

(BETA-1,3-
CHANNEL, L TYPE, ALPHA-1

ENDOGLUCANASE)
POLYPEPTIDE

Seq ID: 595
ISOFORM 4) (BRAIN

Accession: P19706
CALCIUM CHANNEL I) (BI)

Swissprot_id: MYSB_ACACA
Seq ID: 1452

Gi_number: 1171093
Accession: P18583

Description: Myosin heavy chain IB
Swissprot_id: SON_HUMAN

(Myosin heavy chain IL)
Gi_number: 586013

Seq ID: 596
Description: SON PROTEIN (SON3)

Accession: P13728
Seq ID: 1453

Swissprot_id: SGS3_DROYA
Accession: P04146

Gi_number: 134469
Swissprot_id: COPI_DROME

Description: Salivary glue protein SGS-3
Gi_number: 13124684

precursor
Description: Copia protein [Contains:

Seq ID: 597
Copia VLP protein; Copia protease]

Accession: P16258
Seq ID: 1454

Swissprot_id: OXYB_RABIT
Accession: P13983

Gi_number: 129309
Swissprot_id: EXTN_TOBAC

Description: OXYSTEROL-BINDING
Gi_number: 119714

PROTEIN
Description: Extensin precursor (Cell wall

Seq ID: 599
hydroxyproline-rich

Accession: P52409
glycoprotein)

Swissprot_id: E13B_WHEAT
Seq ID: 1456

Gi_number: 1706551
Accession: O08808

Description: GLUCAN ENDO-1,3-BETA-
Swissprot_id: DIA1_MOUSE

GLUCOSIDASE PRECURSOR
Gi_number: 6014968

((1->3)-BETA-GLUCAN
Description: Diaphanous protein homolog

ENDOHYDROLASE) ((1->3)-BETA-
1 (Diaphanous-related formin 1)

GLUCANASE)
(DRF1) (mDIA1) (p140mDIA)

(BETA-1,3-
Seq ID: 1457

ENDOGLUCANASE)
Accession: P29836

Seq ID: 600
Swissprot_id: ICP0_HSVBK

Accession: P28968
GI_number: 266331

Swissprot_id: VGLX_HSVEB
Description: Trans-acting transcriptional

Gi_number: 138350
protein ICP0 (P135 protein)

Description: GLYCOPROTEIN X
(IER 2.9/ER2.6)

PRECURSOR
Seq ID: 1462

Seq ID: 601
Accession: Q9UKN7

Accession: P78371
Swissprot_id: MY15_HUMAN

Swissprot_id: TCPB_HUMAN
Gi_number: 13124361

Gi_number: 6094436
Description: Myosin XV (Unconventional

Description: T-complex protein 1, beta
myosin-15)

subunit (TCP-1-beta) (CCT-beta)
Seq ID: 1463

Seq ID: 602
Accession: Q05860

Accession: Q62520
Swissprot_id: FMN1_MOUSE

Swissprot_id: ZIC2_MOUSE
Gi_number: 544346

Gi_number: 3183503
Description: Formin 1 isoforms I/II/III

Description: Zinc finger protein ZIC2
(Limb deformity protein)

(Zinc finger protein of the
Seq ID: 1465

cerebellum 2)
Accession: Q05085

Seq ID: 603
Swissprot_id: CHL1_ARATH

Accession: Q9NYH9
Gi_number: 544018

Swissprot_id: HC66_HUMAN
Description: Nitrate/chlorate transporter

Gi_number: 18203325
Seq ID: 1467

Description: Hepatocellular carcinoma-
Accession: Q9NVW2

associated antigen 66
Swissprot_id: RNFB_HUMAN

Seq ID: 604
Gi_number: 13124522

Accession: Q61084
Description: RING FINGER PROTEIN 12

Swissprot_id: M3K3_MOUSE
(LIM DOMAIN INTERACTING RING

Gi_number: 2499641
FINGER

Description: MITOGEN-ACTIVATED
PROTEIN) (RING FINGER LIM

PROTEIN KINASE KINASE KINASE 3
DOMAIN-BINDING PROTEIN) (R-LIM)

(MAPK/ERK
(NY-REN-43 ANTIGEN)

KINASE KINASE 3) (MEK
Seq ID: 1469

KINASE 3) (MEKK 3)
Accession: O58263

Seq ID: 606
Swissprot_id: PFDA_PYRHO

Accession: Q59695
Gi_number: 12230417

Swissprot_id: ACOC_PSEPU
Description: Prefoldin alpha subunit

Gi_number: 7531037
(GimC alpha subunit)

Description: DIHYDROLIPOAMIDE
Seq ID: 1470

ACETYLTRANSFERASE COMPONENT
Accession: P27572

OF ACETOIN
Swissprot_id: NU4M_WHEAT

CLEAVING SYSTEM
Gi_number: 128766

(ACETOIN DEHYDROGENASE E2
Description: NADH-UBIQUINONE

COMPONENT)
OXIDOREDUCTASE CHAIN 4

Seq ID: 607
Seq ID: 1471

Accession: P49902
Accession: O08808

Swissprot_id: 5NTC_HUMAN
Swissprot_id: DIA1_MOUSE

Gi_number: 1703012
Gi_number: 6014968

Description: Cytosolic purine 5′-
Description: Diaphanous protein homolog

nucleotidase
1 (Diaphanous-related formin 1)

Seq ID: 608
(DRF1) (mDIA1) (p140mDIA)

Accession: P71684
Seq ID: 1474

Swissprot_id: GCH2_MYCTU
Accession: P08742

Gi_number: 3915713
Swissprot_id: COX1_MAIZE

Description: RIBOFLAVIN
Gi_number: 1169027

BIOSYNTHESIS PROTEIN RIBA
Description: CYTOCHROME C

[INCLUDES: GTP
OXIDASE POLYPEPTIDE I

CYCLOHYDROLASE II; 3,4-
Seq ID: 1476

DIHYDROXY-2-BUTANONE 4-
Accession: P54970

PHOSPHATE
Swissprot_id: ILL2_ARATH

SYNTHASE (DHBP
Gi_number: 1708462

SYNTHASE)]
Description: IAA-AMINO ACID

Seq ID: 609
HYDROLASE HOMOLOG 2

Accession: P35585
PRECURSOR

Swissprot_id: A1M1_MOUSE
Seq ID: 1480

Gi_number: 543817
Accession: O00233

Description: Adaptor-related protein
Swissprot_id: PSD9_HUMAN

complex 1, mu 1 subunit (Clathrin
Gi_number: 12230943

coat assembly protein AP47)
Description: 26S proteasome regulatory

(Clathrin coat associated
subunit p27 (26S proteasome

protein AP47) (Golgi adaptor AP-
non-ATPase subunit 9)

1 47 kDa protein) (HA1 47 kDa
Seq ID: 1481

subunit) (Clathrin assembly
Accession: P21519

protein assembly protein
Swissprot_id: MAM_DROME

complex 1 medium chain)
Gi_number: 126721

Seq ID: 610
Description: NEUROGENIC PROTEIN

Accession: P27644
MASTERMIND

Swissprot_id: PGLR_AGRTU
Seq ID: 1487

Gi_number: 129937
Accession: P12978

Description: POLYGALACTURONASE
Swissprot_id: EBN2_EBV

(PECTINASE) (PGL)
Gi_number: 119111

Seq ID: 611
Description: EBNA-2 NUCLEAR

Accession: P55180
PROTEIN

Swissprot_id: GALE_BACSU
Seq ID: 1489

Gi_number: 1730193
Accession: P93329

Description: UDP-glucose 4-epimerase
Swissprot_id: NO20_MEDTR

(Galactowaldenase) (UDP-galactose
Gi_number: 3914142

4-epimerase)
Description: EARLY NODULIN 20

Seq ID: 612
PRECURSOR (N-20)

Accession: P47179
Seq ID: 1490

Swissprot_id: DAN4_YEAST
Accession: Q07878

Gi_number: 1352944
Swissprot_id: VP13_YEAST

Description: Cell wall protein DAN4
Gi_number: 2499125

precursor
Description: VACUOLAR PROTEIN

Seq ID: 613
SORTING-ASSOCIATED PROTEIN

Accession: P40124
VPS13

Swissprot_id: CAP1_MOUSE
Seq ID: 1491

Gi_number: 729032
Accession: P41410

Description: ADENYLYL CYCLASE-
Swissprot_id: RA54_SCHPO

ASSOCIATED PROTEIN 1 (CAP 1)
Gi_number: 3123262

Seq ID: 614
Description: DNA REPAIR PROTEIN

Accession: P26368
RHP54 (RAD54 HOMOLOG)

Swissprot_id: U2AF_HUMAN
Seq ID: 1492

Gi_number: 267188
Accession: P10978

Description: Splicing factor U2AF 65 kDa
Swissprot_id: POLX_TOBAC

subunit (U2 auxiliary factor
Gi_number: 130582

65 kDa subunit) (U2 SNRNP
Description: Retrovirus-related Pol

auxiliary factor large subunit)
polyprotein from transposon TNT

Seq ID: 615
1-94 [Contains: Protease;

Accession: P57604
Reverse transcriptase;

Swissprot_id: AROB_BUCAI
Endonuclease]

Gi_number: 11131261
Seq ID: 1493

Description: 3-dehydroquinate synthase
Accession: P14922

Seq ID: 616
Swissprot_id: SSN6_YEAST

Accession: O04111
Gi_number: 117936

Swissprot_id: CHSY_PERFR
Description: GLUCOSE REPRESSION

Gi_number: 5921781
MEDIATOR PROTEIN

Description: CHALCONE SYNTHASE
Seq ID: 1494

(NARINGENIN-CHALCONE
Accession: P08640

SYNTHASE)
Swissprot_id: AMYH_YEAST

Seq ID: 618
Gi_number: 728850

Accession: P35336
Description: GLUCOAMYLASE S1/S2

Swissprot_id: PGLR_ACTCH
PRECURSOR (GLUCAN

Gi_number: 548488
1,4-ALPHA-GLUCOSIDASE)

Description: Polygalacturonase precursor
(1,4-ALPHA-D-GLUCAN

(PG) (Pectinase)
GLUCOHYDROLASE)

Seq ID: 620
Seq ID: 1495

Accession: P29599
Accession: Q05654

Swissprot_id: SUBB_BACLE
Swissprot_id: RDPO_SCHPO

Gi_number: 267046
Gi_number: 1710054

Description: SUBTILISIN BL
Description: RETROTRANSPOSABLE

(ALKALINE PROTEASE)
ELEMENT TF2 155 KDA PROTEIN

Seq ID: 623
Seq ID: 1496

Accession: P43588
Accession: Q9SYQ8

Swissprot_id: MPR1_YEAST
Swissprot_id: CLV1_ARATH

Gi_number: 1171012
Gi_number: 12643323

Description: Proteasome regulatory subunit
Description: RECEPTOR PROTEIN

RPN11 (MPR1 protein)
KINASE CLAVATA1 PRECURSOR

Seq ID: 624
Seq ID: 1497

Accession: P34547
Accession: Q24492

Swissprot_id: UBPX_CAEEL
Swissprot_id: RFA1_DROME

Gi_number: 14917050
Gi_number: 2498844

Description: Probable ubiquitin carboxyl-
Description: REPLICATION PROTEIN A

terminal hydrolase R10E11.3
70 KDA DNA-BINDING SUBUNIT (RP-

(Ubiquitin thiolesterase)
A)

(Ubiquitin-specific processing
(RF-A) (REPLICATION

protease) (Deubiquitinating
FACTOR-A PROTEIN 1) (SINGLE-

enzyme)
STRANDED

Seq ID: 625
DNA-BINDING PROTEIN)

Accession: Q9LHA4
(DMRPA1)

Swissprot_id: V0D2_ARATH
Seq ID: 1498

Gi_number: 12585471
Accession: Q05654

Description: Probable vacuolar ATP
Swissprot_id: RDPO_SCHPO

synthase subunit d 2 (V-ATPase d
Gi_number: 1710054

subunit 2) (Vacuolar proton pump
Description: RETROTRANSPOSABLE

d subunit 2)
ELEMENT TF2 155 KDA PROTEIN

Seq ID: 627
Seq ID: 1499

Accession: Q9H2C0
Accession: P10394

Swissprot_id: GAN_HUMAN
Swissprot_id: POL4_DROME

Gi_number: 13626745
Gi_number: 130407

Description: Gigaxonin
Description: Retrovirus-related Pol

Seq ID: 631
polyprotein from transposon 412

Accession: P32323
[Contains: Protease; Reverse

Swissprot_id: AGA1_YEAST
transcriptase;

Gi_number: 416592
Endonuclease]

Description: A-AGGLUTININ
Seq ID: 1500

ATTACHMENT SUBUNIT
Accession: P29375

PRECURSOR
Swissprot_id: RBB2_HUMAN

Seq ID: 633
Gi_number: 1710032

Accession: P23246
Description: Retinoblastoma-binding

Swissprot_id: SFPQ_HUMAN
protein 2 (RBBP-2)

Gi_number: 1709851
Seq ID: 1501

Description: SPLICING FACTOR,
Accession: P40477

PROLINE-AND GLUTAMINE-RICH
Swissprot_id: N159_YEAST

(POLYPYRIMIDINE TRACT-
Gi_number: 731862

BINDING PROTEIN-ASSOCIATED
Description: Nucleoporin NUP159

SPLICING
(Nuclear pore protein NUP159)

FACTOR) (PTB-ASSOCIATED
Seq ID: 1502

SPLICING FACTOR) (PSF)
Accession: P10394

(DNA-BINDING P52/P100
Swissprot_id: POL4_DROME

COMPLEX, 100 KDA SUBUNIT)
Gi_number: 130407

Seq ID: 635
Description: Retrovirus-related Pol

Accession: Q40687
polyprotein from transposon 412

Swissprot_id: GBB_ORYSA
[Contains: Protease; Reverse

Gi_number: 3023843
transcriptase;

Description: GUANINE NUCLEOTIDE-
Endonuclease]

BINDING PROTEIN BETA SUBUNIT
Seq ID: 1503

Seq ID: 636
Accession: Q9NZW4

Accession: P23950
Swissprot_id: DSPP_HUMAN

Swissprot_id: TISB_MOUSE
Gi_number: 17865470

Gi_number: 135863
Description: Dentin sialophosphoprotein

Description: Butyrate response factor 1
precursor [Contains: Dentin

(TIS11B protein)
phosphoprotein (Dentin

Seq ID: 637
phosphophoryn) (DPP); Dentin

Accession: O43502
sialoprotein (DSP)]

Swissprot_id: R51C_HUMAN
Seq ID: 1504

Gi_number: 3914534
Accession: P28968

Description: DNA repair protein RAD51
Swissprot_id: VGLX_HSVEB

homolog 3
Gi_number: 138350

Seq ID: 638
Description: GLYCOPROTEIN X

Accession: P23902
PRECURSOR

Swissprot_id: FABB_HORVU
Seq ID: 1505

Gi_number: 119784
Accession: P08640

Description: 3-oxoacyl-[acyl-carrier-
Swissprot_id: AMYH_YEAST

protein] synthase I, chloroplast
Gi_number: 728850

precursor (Beta-ketoacyl-ACP
Description: GLUCOAMYLASE S1/S2

synthase I) (KAS I)
PRECURSOR (GLUCAN

Seq ID: 639
1,4-ALPHA-GLUCOSIDASE)

Accession: P24074
(1,4-ALPHA-D-GLUCAN

Swissprot_id: RECA_RHILV
GLUCOHYDROLASE)

Gi_number: 132236
Seq ID: 1506

Description: RecA protein (Recombinase
Accession: P18583

A)
Swissprot_id: SON_HUMAN

Seq ID: 640
Gi_number: 586013

Accession: P08640
Description: SON PROTEIN (SON3)

Swissprot_id: AMYH_YEAST
Seq ID: 1508

Gi_number: 728850
Accession: P08640

Description: GLUCOAMYLASE S1/S2
Swissprot_id: AMYH_YEAST

PRECURSOR (GLUCAN
Gi_number: 728850

1,4-ALPHA-GLUCOSIDASE)
Description: GLUCOAMYLASE S1/S2

(1,4-ALPHA-D-GLUCAN
PRECURSOR (GLUCAN

GLUCOHYDROLASE)
1,4-ALPHA-GLUCOSIDASE)

Seq ID: 641
(1,4-ALPHA-D-GLUCAN

Accession: Q09172
GLUCOHYDROLASE)

Swissprot_id: P2C2_SCHPO
Seq ID: 1510

Gi_number: 1171963
Accession: P49118

Description: PROTEIN PHOSPHATASE
Swissprot_id: BIP_LYCES

2C HOMOLOG 2 (PP2C-2)
Gi_number: 1346172

Seq ID: 642
Description: Luminal binding protein

Accession: P25010
precursor (BiP) (78 kDa

Swissprot_id: CG2A_DAUCA
glucose-regulated protein

Gi_number: 116167
homolog) (GRP 78)

Description: G2/MITOTIC-SPECIFIC
Seq ID: 1513

CYCLIN C13-1 (A-LIKE CYCLIN)
Accession: P35817

Seq ID: 643
Swissprot_id: BDF1_YEAST

Accession: Q9Y5K3
Gi_number: 5921175

Swissprot_id: CTPU_HUMAN
Description: BDF1 PROTEIN

Gi_number: 12643330
Seq ID: 1514

Description: CHOLINEPHOSPHATE
Accession: P19683

CYTIDYLYLTRANSFERASE B
Swissprot_id: ROC4_NICSY

(PHOSPHORYLCHOLINE
Gi_number: 133248

TRANSFERASE B)
Description: 31 kDa ribonucleoprotein,

(CTP: PHOSPHOCHOLINE
chloroplast precursor

CYTIDYLYLTRANSFERASE B)
Seq ID: 1515

(CT B) (CCT B) (CCT-BETA)
Accession: P25822

Seq ID: 644
Swissprot_id: PUM_DROME

Accession: Q92373
Gi_number: 131605

Swissprot_id: RFA2_SCHPO
Description: MATERNAL PUMILIO

Gi_number: 2498849
PROTEIN

Description: Replication factor-A protein 2
Seq ID: 1516

(Single-stranded
Accession: Q9SYQ8

DNA-binding protein P30
Swissprot_id: CLV1_ARATH

subunit)
Gi_number: 12643323

Seq ID: 645
Description: RECEPTOR PROTEIN

Accession: P15705
KINASE CLAVATA1 PRECURSOR

Swissprot_id: STI1_YEAST
Seq ID: 1517

Gi_number: 134975
Accession: O97159

Description: HEAT SHOCK PROTEIN
Swissprot_id: CHDM_DROME

STI1
Gi_number: 13124018

Seq ID: 646
Description: CHROMODOMAIN

Accession: P50160
HELICASE-DNA-BINDING PROTEIN

Swissprot_id: TS2_MAIZE
MI-2 HOMOLOG

Gi_number: 1717794
(DMI-2)

Description: SEX DETERMINATION
Seq ID: 1518

PROTEIN TASSELSEED 2
Accession: P04929

Seq ID: 647
Swissprot_id: HRPX_PLALO

Accession: Q9Y2U8
Gi_number: 123530

Swissprot_id: MAN1_HUMAN
Description: HISTIDINE-RICH

Gi_number: 13629600
GLYCOPROTEIN PRECURSOR

Description: INNER NUCLEAR
Seq ID: 1520

MEMBRANE PROTEIN MAN1
Accession: P08393

Seq ID: 648
Swissprot_id: ICP0_HSV11

Accession: Q9ZCV3
Gi_number: 124134

Swissprot_id: RL25_RICPR
Description: Trans-acting transcriptional

Gi_number: 6225985
protein ICP0 (Immediate-early

Description: Probable 50S ribosomal
protein IE110) (VMW110)

protein L25
(Alpha-0 protein)

Seq ID: 649
Seq ID: 1522

Accession: Q9GZU7
Accession: P43293

Swissprot_id: NIF3_HUMAN
Swissprot_id: NAK_ARATH

Gi_number: 17865510
Gi_number: 1171642

Description: Nuclear LIM interactor-
Description: Probable serine/threonine-

interacting factor 3
protein kinase NAK

(NLI-interacting factor 3) (NLI-
Seq ID: 1525

IF)
Accession: P26599

Seq ID: 650
Swissprot_id: PTB_HUMAN

Accession: P46573
Gi_number: 131528

Swissprot_id: APKB_ARATH
Description: Polypyrimidine tract-binding

Gi_number: 12644274
protein (PTB) (Heterogeneous

Description: PROTEIN KINASE APK1B
nuclear ribonucleoprotein I)

Seq ID: 652
(hnRNP I) (57 kDa RNA-binding

Accession: P29383
protein PPTB-1)

Swissprot_id: AGL3_ARATH
Seq ID: 1526

Gi_number: 3915599
Accession: P04323

Description: AGAMOUS-LIKE MADS
Swissprot_id: POL3_DROME

BOX PROTEIN AGL3
Gi_number: 130405

Seq ID: 653
Description: Retrovirus-related Pol

Accession: P32679
polyprotein from transposon 17.6

Swissprot_id: NFI_ECOLI
[Contains: Protease; Reverse

Gi_number: 2506912
transcriptase;

Description: Endonuclease V
Endonuclease]

(Deoxyinosine 3′endonuclease)
Seq ID: 1528

Seq ID: 654
Accession: P47179

Accession: P29675
Swissprot_id: DAN4_YEAST

Swissprot_id: TSF3_HELAN
Gi_number: 1352944

Gi_number: 267177
Description: Cell wall protein DAN4

Description: POLLEN SPECIFIC
precursor

PROTEIN SF3
Seq ID: 1529

Seq ID: 656
Accession: Q63003

Accession: P36520
Swissprot_id: 5E5_RAT

Swissprot_id: RM10_YEAST
Gi_number: 2498095

Gi_number: 1710599
Description: 5E5 ANTIGEN

Description: 60S RIBOSOMAL PROTEIN
Seq ID: 1530

L10, MITOCHONDRIAL PRECURSOR
Accession: Q94981

(YML10)
Swissprot_id: ARI1_DROME

Seq ID: 657
Gi_number: 18202622

Accession: O48556
Description: Ariadne-1 protein (Ari-1)

Swissprot_id: IPYR_MAIZE
Seq ID: 1533

Gi_number: 4033424
Accession: P08640

Description: Soluble inorganic
Swissprot_id: AMYH_YEAST

pyrophosphatase (Pyrophosphate
Gi_number: 728850

phospho-hydrolase) (PPase)
Description: GLUCOAMYLASE S1/S2

Seq ID: 658
PRECURSOR (GLUCAN

Accession: P52565
1,4-ALPHA-GLUCOSIDASE)

Swissprot_id: GDIR_HUMAN
(1,4-ALPHA-D-GLUCAN

Gi_number: 1707892
GLUCOHYDROLASE)

Description: Rho GDP-dissociation
Seq ID: 1534

inhibitor 1 (Rho GDI 1) (Rho-GDI
Accession: P19837

alpha)
Swissprot_id: SPD1_NEPCL

Seq ID: 659
Gi_number: 1174414

Accession: P29834
Description: SPIDROIN 1 (DRAGLINE

Swissprot_id: GRP2_ORYSA
SILK FIBROIN 1)

Gi_number: 232183
Seq ID: 1535

Description: GLYCINE-RICH CELL
Accession: P21997

WALL STRUCTURAL PROTEIN 2
Swissprot_id: SSGP_VOLCA

PRECURSOR
Gi_number: 134920

Seq ID: 660
Description: SULFATED SURFACE

Accession: O81263
GLYCOPROTEIN 185 (SSG 185)

Swissprot_id: KITH_ORYSA
Seq ID: 1537

Gi_number: 7674094
Accession: P07237

Description: Thymidine kinase
Swissprot_id: PDI_HUMAN

Seq ID: 661
Gi_number: 2507460

Accession: P03211
Description: PROTEIN DISULFIDE

Swissprot_id: EBN1_EBV
ISOMERASE PRECURSOR (PDI)

Gi_number: 119110
(PROLYL

Description: EBNA-1 NUCLEAR
4-HYDROXYLASE BETA

PROTEIN
SUBUNIT) (CELLULAR THYROID

Seq ID: 662
HORMONE

Accession: P28968
BINDING PROTEIN) (P55)

Swissprot_id: VGLX_HSVEB
Seq ID: 1538

Gi_number: 138350
Accession: P08640

Description: GLYCOPROTEIN X
Swissprot_id: AMYH_YEAST

PRECURSOR
Gi_number: 728850

Seq ID: 663
Description: GLUCOAMYLASE S1/S2

Accession: P52298
PRECURSOR (GLUCAN

Swissprot_id: CB20_HUMAN
1,4-ALPHA-GLUCOSIDASE)

Gi_number: 1705651
(1,4-ALPHA-D-GLUCAN

Description: 20 KDA NUCLEAR CAP
GLUCOHYDROLASE)

BINDING PROTEIN (NCBP 20 KDA
Seq ID: 1539

SUBUNIT)
Accession: P40602

(CBP20)
Swissprot_id: APG_ARATH

Seq ID: 665
Gi_number: 728867

Accession: P33485
Description: ANTER-SPECIFIC

Swissprot_id: VNUA_PRVKA
PROLINE-RICH PROTEIN APG

Gi_number: 465445
PRECURSOR

Description: PROBABLE NUCLEAR
Seq ID: 1540

ANTIGEN
Accession: P48731

Seq ID: 667
Swissprot_id: ATH1_ARATH

Accession: P51109
Gi_number: 1351999

Swissprot_id: DFRA_MEDSA
Description: Homeobox protein ATH1

Gi_number: 1706375
Seq ID: 1542

Description: DIHYDROFLAVONOL-4-
Accession: P02845

REDUCTASE (DFR)
Swissprot_id: VIT2_CHICK

(DIHYDROKAEMPFEROL
Gi_number: 138595

4-REDUCTASE)
Description: VITELLOGENIN II

Seq ID: 668
PRECURSOR (MAJOR

Accession: P33050
VITELLOGENIN) [CONTAINS:

Swissprot_id: C13_MAIZE
LIPOVITELLIN I (LVI);

Gi_number: 416731
PHOSVITIN (PV); LIPOVITELLIN II

Description: Pollen specific protein C13
(LVII); YGP40]

precursor
Seq ID: 1543

Seq ID: 669
Accession: Q02817

Accession: O04003
Swissprot_id: MUC2_HUMAN

Swissprot_id: LG1_MAIZE
Gi_number: 2506877

Gi_number: 6016502
Description: MUCIN 2 PRECURSOR

Description: LIGULELESS1 PROTEIN
(INTESTINAL MUCIN 2)

Seq ID: 670
Seq ID: 1544

Accession: Q9LJ98
Accession: O08816

Swissprot_id: PFD2_ARATH
Swissprot_id: WASL_RAT

Gi_number: 12230458
Gi_number: 13431956

Description: Probable prefoldin subunit 2
Description: Neural Wiskott-Aldrich

Seq ID: 672
syndrome protein (N-WASP)

Accession: P23535
Seq ID: 1545

Swissprot_id: E13B_PHAVU
Accession: P23116

Gi_number: 119006
Swissprot_id: IF3A_MOUSE

Description: GLUCAN ENDO-1,3-BETA-
Gi_number: 6686292

GLUCOSIDASE, BASIC ISOFORM
Description: EUKARYOTIC

((1->3)-BETA-GLUCAN
TRANSLATION INITIATION FACTOR

ENDOHYDROLASE) ((1->3)-BETA-
3 SUBUNIT 10

GLUCANASE)
(EIF-3 THETA) (EIF3 P167)

(BETA-1,3-
(EIF3 P180) (EIF3 P185) (P162

ENDOGLUCANASE)
PROTEIN) (CENTROSOMIN)

Seq ID: 674
Seq ID: 1546

Accession: P08799
Accession: P23246

Swissprot_id: MYS2_DICDI
Swissprot_id: SFPQ_HUMAN

Gi_number: 127774
Gi_number: 1709851

Description: Myosin II heavy chain, non
Description: SPLICING FACTOR,

muscle
PROLINE-AND GLUTAMINE-RICH

Seq_ID: 675
(POLYPYRIMIDINE TRACT-

Accession: Q9Y5K1
BINDING PROTEIN-ASSOCIATED

Swissprot_id: SP11_HUMAN
SPLICING

Gi_number: 7674367
FACTOR) (PTB-ASSOCIATED

Description: SPO11 protein homolog
SPLICING FACTOR) (PSF)

Seq ID: 676
(DNA-BINDING P52/P100

Accession: Q63003
COMPLEX, 100 KDA SUBUNIT)

Swissprot_id: 5E5_RAT
Seq ID: 1548

Gi_number: 2498095
Accession: P28284

Description: 5E5 ANTIGEN
Swissprot_id: ICP0_HSV2H

Seq ID: 677
Gi_number: 124135

Accession: O42354
Description: Trans-acting transcriptional

Swissprot_id: MDM2_BRARE
protein ICP0 (VMW118 protein)

Gi_number: 8472496
Seq ID: 1549

Description: Ubiquitin-protein ligase E3
Accession: P08640

Mdm2 (P53-binding protein
Swissprot_id: AMYH_YEAST

Mdm2) (Double minute 2 protein)
Gi_number: 728850

Seq ID: 678
Description: GLUCOAMYLASE S1/S2

Accession: O43516
PRECURSOR (GLUCAN

Swissprot_id: WAIP_HUMAN
1,4-ALPHA-GLUCOSIDASE)

Gi_number: 13124642
(1,4-ALPHA-D-GLUCAN

Description: WISKOTT-ALDRICH
GLUCOHYDROLASE)

SYNDROME PROTEIN INTERACTING
Seq ID: 1550

PROTEIN (WASP
Accession: Q02817

INTERACTING PROTEIN)
Swissprot_id: MUC2_HUMAN

(PRPL-2 PROTEIN)
Gi_number: 2506877

Seq ID: 680
Description: MUCIN 2 PRECURSOR

Accession: P12978
(INTESTINAL MUCIN 2)

Swissprot_id: EBN2_EBV
Seq ID: 1551

Gi_number: 119111
Accession: P28968

Description: EBNA-2 NUCLEAR
Swissprot_id: VGLX_HSVEB

PROTEIN
Gi_number: 138350

Seq ID: 682
Description: GLYCOPROTEIN X

Accession: P09789
PRECURSOR

Swissprot_id: GRP1_PETHY
Seq ID: 1553

Gi_number: 121627
Accession: P21997

Description: GLYCINE-RICH CELL
Swissprot_id: SSGP_VOLCA

WALL STRUCTURAL PROTEIN 1
Gi_number: 134920

PRECURSOR
Description: SULFATED SURFACE

Seq ID: 683
GLYCOPROTEIN 185 (SSG 185)

Accession: P82659
Seq ID: 1554

Swissprot_id: THGF_HELAN
Accession: P18583

Gi_number: 11387188
Swissprot_id: SON_HUMAN

Description: Flower-specific gamma-
Gi_number: 586013

thionin precursor (Defensin SD2)
Description: SON PROTEIN (SON3)

Seq ID: 684
Seq ID: 1555

Accession: P48731
Accession: P08640

Swissprot_id: ATH1_ARATH
Swissprot_id: AMYH_YEAST

Gi_number: 1351999
Gi_number: 728850

Description: Homeobox protein ATH1
Description: GLUCOAMYLASE S1/S2

Seq ID: 686
PRECURSOR (GLUCAN

Accession: P52409
1,4-ALPHA-GLUCOSIDASE)

Swissprot_id: E13B_WHEAT
(1,4-ALPHA-D-GLUCAN

Gi_number: 1706551
GLUCOHYDROLASE)

Description: GLUCAN ENDO-1,3-BETA-
Seq ID: 1556

GLUCOSIDASE PRECURSOR
Accession: P13290

((1->3)-BETA-GLUCAN
Swissprot_id: VGLG_HSV2H

ENDOHYDROLASE) ((1->3)-BETA-
Gi_number: 138297

GLUCANASE)
Description: GLYCOPROTEIN G

(BETA-1,3-
Seq ID: 1557

ENDOGLUCANASE)
Accession: O43791

Seq ID: 688
Swissprot_id: SPOP_HUMAN

Accession: Q02224
Gi_number: 8134708

Swissprot_id: CENE_HUMAN
Description: Speckle-type POZ protein

Gi_number: 399227
Seq ID: 1559

Description: CENTROMERIC PROTEIN
Accession: O43516

E (CENP-E PROTEIN)
Swissprot_id: WAIP_HUMAN

Seq ID: 690
Gi_number: 13124642

Accession: P41892
Description: WISKOTT-ALDRICH

Swissprot_id: CC7_SCHPO
SYNDROME PROTEIN INTERACTING

Gi_number: 1168817
PROTEIN (WASP

Description: Cell division control protein 7
INTERACTING PROTEIN)

Seq ID: 691
(PRPL-2 PROTEIN)

Accession: Q9NYV4
Seq ID: 1560

Swissprot_id: CRK7_HUMAN
Accession: P43335

Gi_number: 12643825
Swissprot_id: PHS_PSEAE

Description: CELL DIVISION CYCLE 2-
Gi_number: 1172494

RELATED PROTEIN KINASE 7
Description: Pterin-4-alpha-carbinolamine

(CDC2-RELATED PROTEIN
dehydratase (PHS)

KINASE 7) (CRKRS)
(4-alpha-hydroxy-tetrahydropterin

Seq ID: 692
dehydratase) (Pterin

Accession: Q02224
carbinolamine dehydratase)

Swissprot_id: CENE_HUMAN
(PCD)

Gi_number: 399227
Seq ID: 1562

Description: CENTROMERIC PROTEIN
Accession: P04694

E (CENP-E PROTEIN)
Swissprot_id: ATTY_RAT

Seq ID: 693
Gi_number: 114714

Accession: Q27991
Description: Tyrosine aminotransferase (L-

Swissprot_id: MYHA_BOVIN
tyrosine:2-oxoglutarate

Gi_number: 13431706
aminotransferase) (TAT)

Description: Myosin heavy chain,
Seq ID: 1563

nonmuscle type B (Cellular myosin
Accession: O82768

heavy chain, type B) (Nonmuscle
Swissprot_id: HIS2_ARATH

myosin heavy chain-B)
Gi_number: 11132859

(NMMHC-B)
Description: Histidine biosynthesis

Seq ID: 694
bifunctional protein hisIE,

Accession: P04265
chloroplast precursor [Includes:

Swissprot_id: K2C2_XENLA
Phosphoribosyl-AMP

Gi_number: 125099
cyclohydrolase (PRA-CH);

Description: Keratin, type II cytoskeletal I
Phosphoribosyl-ATP

(Clone PUF164)
pyrophosphatase (PRA-PH)]

Seq ID: 695
Seq ID: 1564

Accession: P17180
Accession: P41878

Swissprot_id: PER3_ARMRU
Swissprot_id: PAD1_SCHPO

Gi_number: 129812
Gi_number: 3334476

Description: Peroxidase C3 precursor
Description: PROTEIN PAD1/SKS1

Seq ID: 696
Seq ID: 1566

Accession: Q02224
Accession: P22793

Swissprot_id: CENE_HUMAN
Swissprot_id: TRHY_SHEEP

Gi_number: 399227
Gi_number: 586122

Description: CENTROMERIC PROTEIN
Description: Trichohyalin

E (CENP-E PROTEIN)
Seq ID: 1567

Seq ID: 697
Accession: P22420

Accession: P54274
Swissprot_id: VE2_HPV47

Swissprot_id: TRF1_HUMAN
Gi_number: 137682

Gi_number: 2507149
Description: REGULATORY PROTEIN

Description: Telomeric repeat binding
E2

factor 1
Seq ID: 1568

Seq ID: 698
Accession: P27320

Accession: O50044
Swissprot_id: FER_SYNY3

Swissprot_id: KDSA_PEA
Gi_number: 2507573

Gi_number: 6647535
Description: Ferredoxin I

Description: 2-DEHYDRO-3-
Seq ID: 1569

DEOXYPHOSPHOOCTONATE
Accession: P08393

ALDOLASE
Swissprot_id: ICP0_HSV11

(PHOSPHO-2-DEHYDRO-3-
Gi_number: 124134

DEOXYOCTONATE ALDOLASE)
Description: Trans-acting transcriptional

(3-DEOXY-D-MANNO-
protein ICP0 (Immediate-early

OCTULOSONIC ACID 8-PHOSPHATE
protein IE110) (VMW110)

SYNTHETASE)
(Alpha-0 protein)

(KDO-8-PHOSPHATE
Seq ID: 1570

SYNTHETASE) (KDO 8-P SYNTHASE)
Accession: P10569

Seq ID: 699
Swissprot_id: MYSC_ACACA

Accession: P04323
Gi_number: 127749

Swissprot_id: POL3_DROME
Description: Myosin IC heavy chain

Gi_number: 130405
Seq ID: 1571

Description: Retrovirus-related Pol
Accession: P31271

polyprotein from transposon 17.6
Swissprot_id: HXAD_HUMAN

[Contains: Protease; Reverse
Gi_number: 2828197

transcriptase;
Description: Homeobox protein Hox-A13

Endonuclease]
(Hox-1J)

Seq ID: 700
Seq ID: 1572

Accession: Q41853
Accession: P48384

Swissprot_id: RSH1_MAIZE
Swissprot_id: THIM_PEA

Gi_number: 3024577
Gi_number: 1351239

Description: HOMEOBOX PROTEIN
Description: THIOREDOXIN M-TYPE,

ROUGH SHEATH 1
CHLOROPLAST PRECURSOR (TRX-M)

Seq ID: 701
Seq ID: 1573

Accession: P28968
Accession: P28968

Swissprot_id: VGLX_HSVEB
Swissprot_id: VGLX_HSVEB

Gi_number: 138350
Gi_number: 138350

Description: GLYCOPROTEIN X
Description: GLYCOPROTEIN X

PRECURSOR
PRECURSOR

Seq ID: 703
Seq ID: 1576

Accession: P28968
Accession: Q02817

Swissprot_id: VGLX_HSVEB
Swissprot_id: MUC2_HUMAN

Gi_number: 138350
Gi_number: 2506877

Description: GLYCOPROTEIN X
Description: MUCIN 2 PRECURSOR

PRECURSOR
(INTESTINAL MUCIN 2)

Seq ID: 704
Seq ID: 1578

Accession: P04634
Accession: Q02283

Swissprot_id: LIPG_RAT
Swissprot_id: HAT5_ARATH

Gi_number: 126307
Gi_number: 399900

Description: TRIACYLGLYCEROL
Description: Homeobox-leucine zipper

LIPASE, LINGUAL PRECURSOR
protein HAT5 (HD-ZIP protein 5)

(LINGUAL LIPASE)
(HD-ZIP protein ATHB-1)

Seq ID: 705
Seq ID: 1580

Accession: O24475
Accession: P08393

Swissprot_id: TSD1_ABIGR
Swissprot_id: ICP0_HSV11

Gi_number: 17367924
Gi_number: 124134

Description: Pinene synthase, chloroplast
Description: Trans-acting transcriptional

precursor (Beta-geraniolene
protein ICP0 (Immediate-early

synthase) ((−)-(1S,5S)-pinene
protein IE110) (VMW110)

synthase)
(Alpha-0 protein)

Seq ID: 706
Seq ID: 1585

Accession: P15233
Accession: P03186

Swissprot_id: PERC_ARMRU
Swissprot_id: TEGU_EBV

Gi_number: 129816
Gi_number: 135574

Description: Peroxidase C1C precursor
Description: LARGE TEGUMENT

Seq ID: 707
PROTEIN

Accession: Q02817
Seq ID: 1586

Swissprot_id: MUC2_HUMAN
Accession: Q9Y7B6

Gi_number: 2506877
Swissprot_id: PANB_EMENI

Description: MUCIN 2 PRECURSOR
Gi_number: 8134629

(INTESTINAL MUCIN 2)
Description: 3-methyl-2-oxobutanoate

Seq ID: 708
hydroxymethyltransferase

Accession: O57593
(Ketopantoate

Swissprot_id: SUR1_FUGRU
hydroxymethyltransferase)

Gi_number: 6094369
Seq ID: 1588

Description: SURFEIT LOCUS PROTEIN 1
Accession: Q06003

Seq ID: 710
Swissprot_id: GOLI_DROME

Accession: Q9JK11
Gi_number: 462193

Swissprot_id: RTN4_RAT
Description: Goliath protein (G1 protein)

Gi_number: 17367410
Seq ID: 1591

Description: Reticulon 4 (Neurite
Accession: P26861

outgrowth inhibitor) (Nogo protein)
Swissprot_id: RM06_MARPO

(Foocen) (Glut4 vesicle 20 kDa
Gi_number: 417682

protein)
Description: MITOCHONDRIAL 60S

Seq ID: 711
RIBOSOMAL PROTEIN L6

Accession: P14328
Seq ID: 1592

Swissprot_id: SP96_DICDI
Accession: O00401

Gi_number: 134780
Swissprot_id: WASL_HUMAN

Description: SPORE COAT PROTEIN
Gi_number: 13431960

SP96
Description: Neural Wiskott-Aldrich

Seq ID: 713
syndrome protein (N-WASP)

Accession: O52535
Seq ID: 1593

Swissprot_id: CAH_KLEPN
Accession: P09065

Gi_number: 5915869
Swissprot_id: HME1_MOUSE

Description: Carbonic anhydrase precursor
Gi_number: 462292

(Carbonate dehydratase)
Description: Homeobox protein engrailed-

Seq ID: 714
1 (Mo-En-1)

Accession: P35250
Seq ID: 1595

Swissprot_id: AC14_HUMAN
Accession: P33485

Gi_number: 2507300
Swissprot_id: VNUA_PRVKA

Description: ACTIVATOR 1 40 KDA
Gi_number: 465445

SUBUNIT (REPLICATION FACTOR C
Description: PROBABLE NUCLEAR

4O KDA
ANTIGEN

SUBUNIT) (A1 40 KDA
Seq ID: 1597

SUBUNIT) (RF-C 40 KDA SUBUNIT)
Accession: Q05063

(RFC40)
Swissprot_id: LYOX_CHICK

Seq ID: 715
Gi_number: 462560

Accession: P57078
Description: Protein-lysine 6-oxidase

Swissprot_id: ANR3_HUMAN
precursor (Lysyl oxidase)

Gi_number: 10719883

Description: Serine/threonine-protein

kinase ANKRD3 (Ankyrin repeat

domain protein 3) (PKC-delta-

interacting protein kinase)

Seq ID: 716

Accession: P42768

Swissprot_id: WASP_HUMAN

Gi_number: 1722836

Description: WISKOTT-ALDRICH

SYNDROME PROTEIN (WASP)

Seq ID: 717

Accession: Q94915

Swissprot_id: REG2_DROME

Gi_number: 6093951

Description: RHYTHMICALLY

EXPRESSED GENE 2 PROTEIN (DREG-

2)

Seq ID: 718

Accession: P03211

Swissprot_id: EBN1_EBV

Gi_number: 119110

Description: EBNA-1 NUCLEAR

PROTEIN

Seq ID: 719

Accession: P43214

Swissprot_id: MPP2_PHLPR

Gi_number: 1171009

Description: POLLEN ALLERGEN PHL P

2 PRECURSOR (PHL P II)

Seq ID: 720

Accession: P14947

Swissprot_id: MPL2_LOLPR

Gi_number: 126386

Description: Pollen allergen Lol p 2-A (Lol

p II-A)

Seq ID: 721

Accession: P08640

Swissprot_id: AMYH_YEAST

Gi_number: 728850

Description: GLUCOAMYLASE S1/S2

PRECURSOR (GLUCAN

1,4-ALPHA-D-GLUCOSIDASE)

(1,4-ALPHA-D-GLUCAN

GLUCOHYDROLASE)

Seq ID: 722

Accession: Q9WVK4

Swissprot_id: EHD1_MOUSE

Gi_number: 18203578

Description: EH-domain containing protein

1 (mPAST1)

Seq ID: 723

Accession: P46573

Swissprot_id: APKB_ARATH

Gi_number: 12644274

Description: PROTEIN KINASE APK1B

Seq ID: 724

Accession: P05790

Swissprot_id: FBOH_BOMMO

Gi_number: 9087216

Description: FIBROIN HEAVY CHAIN

PRECURSOR (FIB-H) (H-FIBROIN)

Seq ID: 725

Accession: P41900

Swissprot_id: T2FB_DROME

Gi_number: 1729817

Description: TRANSCRIPTION

INITIATION FACTOR IIF, BETA

SUBUNIT

(TFIIF-BETA)

Seq ID: 726

Accession: Q9FUD1

Swissprot_id: PROA_ORYSA

Gi_number: 14423855

Description: Profilin A

Seq ID: 727

Accession: P16265

Swissprot_id: NU3M_MAIZE

Gi_number: 1352562

Description: NADH-UBIQUINONE

OXIDOREDUCTASE CHAIN 3

Seq ID: 728

Accession: P10978

Swissprot_id: POLX_TOBAC

Gi_number: 130582

Description: Retrovirus-related Pol

polyprotein from transposon TNT

1-94 [Contains: Protease;

Reverse transcriptase;

Endonuclease]

Seq ID: 729

Accession: P17840

Swissprot_id: SLS3_BRAOL

Gi_number: 134532

Description: S-locus-specific glycoprotein

S13 precursor (SLSG-13)

Seq ID: 730

Accession: P29375

Swissprot_id: RBB2_HUMAN

Gi_number: 1710032

Description: Retinoblastoma-binding

protein 2 (RBBP-2)

Seq ID: 731

Accession: P26792

Swissprot_id: INV1_DAUCA

Gi_number: 124712

Description: BETA-

FRUCTOFURANOSIDASE,

INSOLUBLE ISOENZYME 1

PRECURSOR

(SUCROSE-6-PHOSPHATE

HYDROLASE 1) (INVERTASE 1) (CELL

WALL

BETA-FRUCTOSIDASE 1)

Seq ID: 732

Accession: Q60809

Swissprot_id: CNO7_MOUSE

Gi_number: 3219782

Description: CCR4-NOT transcription

complex, subunit 7 (CCR4-associated

factor 1) (CAF1)

Seq ID: 734

Accession: O35587

Swissprot_id: TM21_MESAU

Gi_number: 3915123

Description: Transmembrane protein

Tmp21 precursor (21 kDa

Transmembrane trafficking

protein) (Integral membrane

protein p23)

Seq ID: 735

Accession: P29675

Swissprot_id: TSF3_HELAN

Gi_number: 267177

Description: POLLEN SPECIFIC

PROTEIN SF3

Seq ID: 738

Accession: P21997

Swissprot_id: SSGP_VOLCA

Gi_number: 134920

Description: SULFATED SURFACE

GLYCOPROTEIN 185 (SSG 185)

Seq ID: 739

Accession: P03211

Swissprot_id: EBN1_EBV

Gi_number: 119110

Description: EBNA-1 NUCLEAR

PROTEIN

Seq ID: 740

Accession: Q9U7E0

Swissprot_id: ATRX_CAEEL

Gi_number: 17367114

Description: Transcriptional regulator

ATRX homolog (X-linked nuclear

protein-1)

Seq ID: 741

Accession: P00412

Swissprot_id: COX2_MAIZE

Gi_number: 1706052

Description: CYTOCHROME C

OXIDASE POLYPEPTIDE II

Seq ID: 742

Accession: P28284

Swissprot_id: ICP0_HSV2H

Gi_number: 124135

Description: Trans-acting transcriptional

protein ICP0 (VMW118 protein)

Seq ID: 745

Accession: P52824

Swissprot_id: KDGT_HUMAN

Gi_number: 1708624

Description: Diacylglycerol kinase, theta

(Diglyceride kinase)

(DGK-theta) (DAG kinase theta)

Seq ID: 746

Accession: O59816

Swissprot_id: ODP2_SCHPO

Gi_number: 3914192

Description: DIHYDROLIPOAMIDE

ACETYLTRANSFERASE COMPONENT

OF PYRUVATE

DEHYDROGENASE

COMPLEX, MITOCHONDRIAL

PRECURSOR (E2)

(PDC-E2)

Seq ID: 747

Accession: Q9NY64

Swissprot_id: GTR8_HUMAN

Gi_number: 17367002

Description: Solute carrier family 2,

facilitated glucose transporter,

member 8 (Glucose transporter

type 8) (Glucose transporter

type X1)

Seq ID: 748

Accession: P54873

Swissprot_id: HMCS_ARATH

Gi_number: 1708236

Description:

HYDROXYMETHYLGLUTARYL-COA

SYNTHASE (HMG-COA SYNTHASE)

(3-HYDROXY-3-

METHYLGLUTARYL COENZYME A

SYNTHASE)

Seq ID: 749

Accession: Q38997

Swissprot_id: KI10_ARATH

Gi_number: 6166239

Description: SNF1-related protein kinase

KIN10 (AKIN10)

Seq ID: 750

Accession: P39958

Swissprot_id: GDI1_YEAST

Gi_number: 729566

Description: SECRETORY PATHWAY

GDP DISSOCIATION INHIBITOR

Seq ID: 751

Accession: P08640

Swissprot_id: AMYH_YEAST

Gi_number: 728850

Description: GLUCOAMYLASE S1/S2

PRECURSOR (GLUCAN

1,4-ALPHA-GLUCOSIDASE)

(1,4-ALPHA-D-GLUCAN

GLUCOHYDROLASE)

Seq ID: 753

Accession: Q00808

Swissprot_id: HET1_PODAN

Gi_number: 3023956

Description: Vegetatible incompatibility

protein HET-E-1

Seq ID: 754

Accession: P21997

Swissprot_id: SSGP_VOLCA

Gi_number: 134920

Description: SULFATED SURFACE

GLYCOPROTEIN 185 (SSG 185)

Seq ID: 755

Accession: P27484

Swissprot_id: GRP2_NICSY

Gi_number: 121631

Description: Glycine-rich protein 2

Seq ID: 757

Accession: O64748

Swissprot_id: COPE_ARATH

Gi_number: 6647445

Description: Probable coatomer epsilon

subunit (Epsilon-coat protein)

(Epsilon-COP)

Seq ID: 758

Accession: P40989

Swissprot_id: GLS2_YEAST

Gi_number: 1707982

Description: 1,3-BETA-GLUCAN

SYNTHASE COMPONENT GLS2

(1,3-BETA-D-GLUCAN-UDP

GLUCOSYLTRANSFERASE)

Seq ID: 760

Accession: P54654

Swissprot_id: CAP_DICDI

Gi_number: 1705592

Description: ADENYLYL CYCLASE-

ASSOCIATED PROTEIN (CAP)

Seq ID: 761

Accession: P54927

Swissprot_id: MYO2_LYCES

Gi_number: 1709204

Description: Myo-inositol-1(or 4)-

monophosphatase 2 (IMPase 2) (IMP 2)

(Inositol monophosphatase 2)

Seq ID: 762

Accession: P38994

Swissprot_id: MSS4_YEAST

Gi_number: 1709144

Description: Probable

phosphatidylinositol-4-phosphate 5-kinase

MSS4

(1-phosphatidylinositol-4-

phosphate kinase) (PIP5K)

(PtdIns(4)P-5-kinase)

(Diphosphoinositide kinase)

Seq ID: 764

Accession: Q9SWE7

Swissprot_id: VATE_CITLI

Gi_number: 12585492

Description: Vacuolar ATP synthase

subunit E (V-ATPase E subunit)

(Vacuolar proton pump E subunit)

(CLVE-1)

Seq ID: 765

Accession: P22227

Swissprot_id: ZF42_MOUSE

Gi_number: 132461

Description: Zinc finger protein 42 (Zfp-

42) (REX-1 protein) (Reduced

expression-1 protein)

Seq ID: 766

Accession: P91428

Swissprot_id: COQ4_CAEEL

Gi_number: 3121872

Description: UBIQUINONE

BIOSYNTHESIS PROTEIN COQ4

HOMOLOG

Seq ID: 767

Accession: P16924

Swissprot_id: P4HA_CHICK

Gi_number: 129365

Description: PROLYL 4-

HYDROXYLASE ALPHA SUBUNIT

Seq ID: 768

Accession: P40318

Swissprot_id: SSM4_YEAST

Gi_number: 730835

Description: SSM4 PROTEIN

Seq ID: 769

Accession: P38546

Swissprot_id: RAN1_LYCES

Gi_number: 585777

Description: GTP-BINDING NUCLEAR

PROTEIN RAN1

Seq ID: 770

Accession: P33050

Swissprot_id: C13_MAIZE

Gi_number: 416731

Description: Pollen specific protein C13

precursor

Seq ID: 771

Accession: P25071

Swissprot_id: TCH3_ARATH

Gi_number: 17380537

Description: Calmodulin-related protein 3,

touch-induced

Seq ID: 777

Accession: P28968

Swissprot_id: VGLX_HSVEB

Gi_number: 138350

Description: GLYCOPROTEIN X

PRECURSOR

Seq ID: 778

Accession: P10401

Swissprot_id: POLY_DROME

Gi_number: 130583

Description: RETROVIRUS-RELATED

POL POLYPROTEIN FROM

TRANSPOSON GYPSY

[CONTAINS: REVERSE

TRANSCRIPTASE; ENDONUCLEASE]

Seq ID: 779

Accession: P08640

Swissprot_id: AMYH_YEAST

Gi_number: 728850

Description: GLUCOAMYLASE S1/S2

PRECURSOR (GLUCAN

1,4-ALPHA-GLUCOSIDASE)

(1,4-ALPHA-D-GLUCAN

GLUCOHYDROLASE)

Seq ID: 781

Accession: P10978

Swissprot_id: POLX_TOBAC

Gi_number: 130582

Description: Retrovirus-related Pol

polyprotein from transposon TNT

1-94 [Contains: Protease;

Reverse transcriptase;

Endonuclease]

Seq ID: 790

Accession: P53776

Swissprot_id: LHX4_MOUSE

Gi_number: 8247937

Description: LIM/HOMEOBOX

PROTEIN LHX4

Seq ID: 791

Accession: O35344

Swissprot_id: IMA3_MOUSE

Gi_number: 3122277

Description: Importin alpha-3 subunit

(Karyopherin alpha-3 subunit)

(Importin alpha Q2)

Seq ID: 792

Accession: Q01577

Swissprot_id: PKPA_PHYBL

Gi_number: 3122617

Description: Serine/threonine protein

kinase PKPA

Seq ID: 793

Accession: P14328

Swissprot_id: SP96_DICDI

Gi_number: 134780

Description: SPORE COAT PROTEIN

SP96

Seq ID: 794

Accession: P53683

Swissprot_id: CDP2_ORYSA

Gi_number: 1705734

Description: Calcium-dependent protein

kinase, isoform 2 (CDPK 2)

Seq ID: 795

Accession: P05492

Swissprot_id: ATP0_OENBI

Gi_number: 114408

Description: ATP synthase alpha chain,

mitochondrial

Seq ID: 796

Accession: P30175

Swissprot_id: ADF_LILLO

Gi_number: 231509

Description: Actin-depolymerizing factor

(ADF)

Seq ID: 797

Accession: P04146

Swissprot_id: COPI_DROME

Gi_number: 13124684

Description: Copia protein [Contains:

Copia VLP protein; Copia protease]

Seq ID: 798

Accession: P08547

Swissprot_id: LIN1_HUMAN

Gi_number: 126295

Description: LINE-1 REVERSE

TRANSCRIPTASE HOMOLOG

[0692]

18

TABLE 12

PCR

product

Promoter

size

Name
Unigene Number
forward primer
reverse primer
(bp)
Description

RC1
AC00713825/
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTC
1970

12797_s_at
CAAATTTTGGGTCATG
TTCTCCTATCTGCATAAA

GATTAGTTTCACGC
ATGGTATTTCACA

SEQ ID NO 6002
SEQ ID NO 6003

RC2
AC000132.6/
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTG
1003

16420_at
CAAGCCGCTTTCACTT
GCTTATTTGCACCGGTAT

GACGGAACTTGC
AAAGTTAGGGATC

SEQ ID NO 6004
SEQ ID NO 6005

RC3
WT755/
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTC
1260

14701_s_at
AGGCAACCCACCCTTC
CACGATGCAGAATAAAG

GGTGGTTG
GCATAAATTCAGAAGCA

SEQ ID NO 6006
SEQ ID NO 6007

RC4
AF08012011/
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTA
1970

16935_s_at
GGCACCTTCAAGTACC
TCCAAACTACTCTCCGC

AGTTTCCTTGAAATG
GAAGTGTGTG

SEQ ID NO 6008
SEQ ID NO 6009

RC5
Z151571/
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTC
1897

16982_at
GCAACGAATTTAATGG
GCAGAGGCTTATATAGA

TGCAATCGGATCATG
GGGGAG

SEQ ID NO 6010
SEQ ID NO 6011

RC6
AL023094323/
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTC
952

16515_s_at
GCTCTAGCTTTAGTCC
TTGCTTCCTCTTCTCTCT

CGGTTTGGTAACACC
CCTCTCCGATG

SEQ ID NO 6012
SEQ ID NO 6013

RC7
ATU5629/
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTC
1940

15180_s_at
GTCGACGTTACATGAG
CTCGGGTGTTTTGGTTT

GAACTTTCTTGTGC
GGAGAG

SEQ ID NO 6014
SEQ ID NO 6015

RC8
AF063901/
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTC
1276

14737_s_at
CAGGCCATACAGCTCT
ACACACACACACACAAAG

ATCGCCTCAGCCAG
GCCCATCAGGCCC

SEQ ID NO 6016
SEQ ID NO 6017

RC9
OS001432
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTG
2050
Similar to gi|3461812|gb|AAC32906.1|

GCATCCTCAACATACT
TGGAGGAGCACGCAGAG

putative basic blue protein

GAAACAATGTACTAAC
GA

(plantacyanin) [Arabidopsis thaliana]

SEQ ID NO 6018
SEQ ID NO 6019

RC10
OS004268
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTT
1947
Similar to YPU3_RHOCA P26159

ATGCCAGCCAAATTGC
GCCGGCCGGTGGGCTG

RHODOBACTER CAPSULATUS

CGGCCAAAGTGCCAAC
GTGCCT

(RHODOPSEUDOMONAS

SEQ ID NO 6020
SEQ ID NO 6021

CAPSULATA). HYPOTHETICAL 5.8

KD PROTEIN IN PUHA 5 REGION

(0RF55).

RC11
OS004356
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTC
1929
Similar to SAHH_PYRFU P50251

CCAATATGGATACAAT
GTCCATCTTTCCTTGCTC

PYROCOCCUS FURIOSUS.

CCGAGTAGTCCTTGTC
CTCTCACT

ADENOSYLHOMOCYSTEINASE (EC

G
SEQ ID NO 6023

3.3.1.1) (S-ADENOSYL-L-

SEQ ID NO 6022

HOMOCYSTEINEHYDROLASE)

(ADOHCYASE) (FRAGMENT).

RC12
OS005221_r_at
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTT
2053

CGAGCAGGTATCGAGC
GTCACCCACCCCAATCA

ATTGCCGTC
AGCTAAGCTATCT

SEQ ID NO 6024
SEQ ID NO 6025

RC13
OS024307_r_at
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTG
2000
Similar to gi|8777294|dbj|BAA96884.1|

ATGTGTAACACGCATG
TTGGATGAGGAGAAGGA

gb|AAD26867.1˜gene_id:MAB16.4˜

GTGTGATGG
TGGATGG

similar to unknown protein

SEQ ID NO 6026
SEQ ID NO 6027

[Arabidopsis thaliana]

RC14
OS014617.1_f_at
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTG
1989
Similar to gi|4191792|gb|AAD10161.1|

GTGCTGTAATAGCTTG
CTTAGTAGTAGTAATTGT

hypothetical protein [Arabidopsis

CCTTTGCTAAATC
TATTGTCTCCGG

thaliana
]

SEQ ID NO 6028
SEQ ID NO 6029

RC15
OS025078.1_r_at
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTT
1934
Similar to

AGCATCAAGAACCAGT
AAGGGGGTGTTTGGATA

gi|5932544|gb|AAD56999.1|AC00946

GAACGATGG
TAGGGTG

5_13 hypothetical protein

SEQ ID NO 6030
SEQ ID NO 6031

[Arabidopsis thaliana]

RC16
OS003603.1_r_at
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTTT
1951
Similar to YCE2_YEAST P25572

GAACTCTGGTCGTCAT
GGAGAGCTCGAGAGAGA

SACCHAROMYCES CEREVISIAE

CACCACACC
GGGTTG

(BAKER S YEAST). HYPOTHETICAL

SEQ ID NO 6032
SEQ ID NO 6033

13.3 KD PROTEIN IN PD|1-GLK1

INTERGENIC REGION.

RC17
OS_OF010093_
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTA
1923
Open Reading Frame

r_at
GCGCAAAACGGTATAG
GAGACTGGTAGTAGCAG

OS_ORF010093 ST(R) HTC060970-

GTCTGAACG
GGGGTGG

A01.F.4 FRAME: 1 ORF: 2 LEN: 891

SEQ ID NO 6034
SEQ ID NO 6035

RC18
OS019298_r_at
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTC
1927
Similar to YR01_CAEEL Q10014

CGCATATCTTATTGCTC
TGCTCGGCGAGGCAGG

CAENORHABDITIS ELEGANS.

CGTAGTTCGTATGAG
G

HYPOTHETICAL 26.0 KD PROTEIN

SEQ ID NO 6036
SEQ ID NO 6037

T25E4.1 IN CHROMOSOME II

PRECURSOR.

RC19
OS004151_r_at
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTC
1965
Similar to gi|3406035|gb|AAC29139.1|

ACGATCAGACTCCTAA
ATTGCGGCCAAAGCAAA

TINY [Arabidopsis thaliana]

TTGCCGCTC
GC

SEQ ID NO 6038
SEQ ID NO 6039

RC20
OS012854_r_at
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTTT
1991
Similar to YY19_HUMAN P09002

CTCGGAACACGAAAAC
CCGATCTCTTCCCATTTC

HOMO SAPIENS
(HUMAN).

CAACTCAAC
CATTC

HYPOTHETICAL Y-

SEQ ID NO 6040
SEQ ID NO 6041

CHROMOSOMAL 19 KD PROTEIN.

RC21
OS023348_r_at
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTC
1985
Similar to Y168_HUMAN P50749

GGCATAGGATTATGAA
ATCCTTAGATGCGCGGC

HOMO SAPIENS
(HUMAN).

TGGATGGTGC
CAG

HYPOTHETICAL PROTEIN

SEQ ID NO 6042
SEQ ID NO 6043

KIAA0168.

RC22
OS003824_r_at
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTG
1992
Similar to gi|8096630|

GGAGCATGTACTCTTT
CGGCCCGATGCGATCGG

dbj|BAA96201.1|hypothetical protein

ATAACTAACTTTACATG
SEQ ID NO 6045

[Oryza sativa]

SEQ ID NO 6044

RC23
OS007113_r_at
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTG
1970
Similar to

GTGATATACGCATAAG
AGCACGTGGTGCGAGGG

gi|6553904|gb|AAF16570.1|AC012563

GAATTATTTCCTCCG
AAG

_23 hypothetical protein

SEQ ID NO 6046
SEQ ID NO 6047

[Arabidopsis thaliana]

RC24
OS008815_r_at
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTG
1940
Similar to

TTCGAAATCGTGCATT
CTAGCAAGGGAGAGGTA

gi|1785674|emb|CAA69779.1| orf153a

CAACAAAGC
GCGGAAG

[Arabidopsis thaliana]

SEQ ID NO 6048
SEQ ID NO 6049

RC25
OS004598_r_at
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTG
1976
Similar to LSHB_MOUSE 009108

CTGTCACCGTCTTGAC
CGAACTAGATGGCGAGA

MUS MUSCULUS
(MOUSE).

CCGACTTC
TTTGGTC

LUTROPIN BETA CHAIN

SEQ ID NO 6050
SEQ ID NO 6051

PRECURSOR (LUTEINIZING

HORMONE) (LSH-B) (LH-

B)(FRAGMENT).

RC26
OS021684_r_at
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTA
1913
Similar to IHA_SHEEP P38440

GTACCCATGCCTTGCA
AGTCGCGCCACATTGCT

OVIS ARIES
(SHEEP). INHIBIN

ACAATGTCC
GTCATC

ALPHA CHAIN (FRAGMENT).

SEQ ID NO 6052
SEQ ID NO 6053

RC27
OS_ORF001938_
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTC
1949
Open Reading Frame

r_at
GCAAGGTGGACAATGT
AGAAGAGGAGTGATGGA

OS_ORF001938 HTC011169-A01.13

GTGGAGTTC
GAAGAAGGC

FRAME: 1 ORF: 2 LEN: 1011

SEQ ID NO 6054
SEQ ID NO 6055

RC28
OS_ORF013133_
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTG
1976
Open Reading Frame

r_at
GGGACCCATAGTCACT
CAGTCCCCTCCTCTTGC

OS_ORF013133 HTC083102-

GGGTGTTTG
AGC

A01.R.9 FRAME: −3 ORF: 2 LEN: 684

SEQ ID NO 6056
SEQ ID NO 6057

RC29
OS005221_r_at
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTT
1957
Similar to

TGGAGGAACGAAGCAG
GTCACCCACCCCAATCA

gi|8099126|dbj|BAA90498.1| rice

TAGCACAAG
AGCTAAG

ESTs AA754121, AW155454, D48581

SEQ ID NO 6058
SEQ ID NO 6059

correspond to a region of the

predicated gene; unknown protein

[Oryza sativa]

RC30
OS_ORF001266_
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTC
1920
Open Reading Frame

r_at
CAAGCTCACCGGCGTC
CACCGCCATCGACTCCT

OS_ORF001266 HTC007198-A01.6

GTACTC
ACTG

FRAME: −2 ORF: 1 LEN: 669

SEQ ID NO 6060
SEQ ID NO 6061

RC31
OS_ORF013948_
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTG
1946
Open Reading Frame

r_at
CCCGTCAGTTTAAATAT
CCAGGGGCAAGGGTAG

OS_ORF013948 HTC089691-

AGGCACCCG
GAGAG

A01.R.17 FRAME: 2 ORF: 4 LEN: 738

SEQ ID NO 6062
SEQ ID NO 6063

RC32
OS_ORF014602_
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTG
1997
Open Reading Frame containing a

r_at
CTCCAATCCTCGTCAA
TTGGACTGACATGTGGG

Sage tag sequence near 3 end

TCCCATC
GC

OS_ORF014602 ST(F) HTC094277-

SEQ ID NO 6064
SEQ ID NO 6065

A01.F.15 FRAME: 3 ORF: 1 LEN: 546

RC33
OS009022_r_at
TACAAAAAAGCAGGCT
TACAAGAAAGCTGGGTG
1999
Similar to

GTACATGTACCTGCAT
CCACGTACGTTACGATC

gi|5006851|gb|AAD37696.1|AF145727

CAGAATCTAGTTC
AGTAAC

_1 homeodomain leucine zipper

SEQ ID NO 6066
SEQ ID NO 6067

protein [Oryza sativa]

RC34
OS_ORF001266_
CACCCGGAGAAGCTCA
GTATGTTCGCCGTGGCC
1843
Similar to gi|3461812|gb|AAC32906.1|

r_at
CGCCCTTG
ATTTG

putative basic blue protein

SEQ ID NO 6068
SEQ ID NO 6069

(plantacyanin)

[Arabidopsis thaliana]

RC35
OS002956.1_s_
CACCCTTGCGTGCAAT
GAAATCGAACCGGACCC
1212
Similar to YPU3_RHOCA P26159

at
GATAGATGGTG
GAAC

RHODOBACTER CAPSULATUS

SEQ ID NO 6070
SEQ ID NO 6071

(RHODOPSEUDOMONAS

CAPSULATA). HYPOTHETICAL 5.8

KD PROTEIN IN PUHA 5 REGION

(ORF55).

RC36
OS008536.1_r_
CACCAGACACTGCAGA
CCATGAGATAGATGTGG
1926
Similar to SAHH_PYRFU P50251

at
GATCCTCTTG
ATGAGGTCC

PYROCOCCUS FURIOSUS.

SEQ ID NO 6072
SEQ ID NO 6073

ADENOSYLHOMOCYSTEINASE (EC

3.3.1.1) (S-ADENOSYL-L-

HOMOCYSTEINEHYDROLASE)

(ADOHOYASE) (FRAGMENT).

RC37
OS009022_r_
CACCAGACGAGTCTAG
CACCCATCACAAGCCAAT
Doublecheck

at
TGTCCATATAG
GCAGAAGC
3′ primer

SEQ ID NO 6074
SEQ ID NO 6075

RC38
OS022635_r_
CACCTCCGGTGTACTT
GACAAAGGAGTAGGATC
1890
Similar to gi|8777294|dbj|BAA96884.1|

at
CGAGATAGTC
AATGCATGC

gb|AAD26867.1-gene_id:MAB16.4-

SEQ ID NO 6076
SEQ ID NO 6077

similar to unknown protein

[Arabidopsis thaliana]

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[0995] All publications, patents and patent applications are incorporated herein by reference. While in the foregoing specification this invention has been described in relation to certain preferred embodiments thereof, and many details have been set forth for purposes of illustration, it will be apparent to those skilled in the art that the invention is susceptible to additional embodiments and that certain of the details described herein may be varied considerably without departing from the basic principles of the invention.

Number	Date	Country
60325448	Sep 2001	US
60325277	Sep 2001	US
60370620	Apr 2002	US

Rice promoters for regulation of plant expression

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