MODULATION OF TIMP1 AND TIMP2 EXPRESSION

SEQUENCE LISTING

The instant application contains a Sequence Listing which is entitled 224-PCT1_ST25.txt, said ASCII copy, created on Aug. 24, 2011 and is 910 kb in size, is hereby incorporated by reference in its entirety.

FIELD OF THE INVENTION

Provided herein are compositions and methods for modulating expression of TIMP1 and TIMP2.

BACKGROUND OF THE INVENTION

Sato, Y., et al. disclose the administration of vitamin A-coupled liposomes to deliver small interfering RNA (siRNA) against gp46, the rat homolog of human heat shock protein 47, to liver cirrhosis rat animal models. Sato, Y., et al., Nature Biotechnology, vol. 26(4), p. 431-442 (2008).

Chen, J-J., et al. disclose transfecting human keloid samples with HSP-47-shRNA (small hairpin RNA) to examine proliferation of keloid fibroblast cells. Chen, J-J., et al., British Journal of Dermatology, vol. 156, p. 1188-1195 (2007).

PCT Patent Publication No. WO 2006/068232 discloses an astrocyte specific drug carrier which includes a retinoid derivative and/or a vitamin A analog.

PCT Patent Publication Nos. WO 2008/104978 and WO 2007/091269 disclose siRNA structures and compounds.

PCT Patent Publication No. WO 2011/072082 discloses double stranded RNA compounds targeting HSP47 (SERPINH1).

SUMMARY OF THE INVENTION

Compositions, methods and kits for modulating expression of target genes are provided herein. In various aspects and embodiments, compositions, methods and kits provided herein modulate expression of tissue inhibitor of metalloproteinases 1 and tissue inhibitor of metalloproteinases 2 also known as TIMP1 and TIMP2, respectively. The compositions, methods and kits may involve use of nucleic acid molecules (for example, short interfering nucleic acid (siNA), short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA) or short hairpin RNA (shRNA)) that bind a nucleotide sequence (such as an mRNA sequence) encoding TIMP1 and TIMP2, for example, the mRNA coding sequence for human TIMP1 exemplified by SEQ ID NO:1 and the mRNA coding sequence for human TIMP2 exemplified by SEQ ID NO:2. In certain preferred embodiments, the compositions, methods and kits disclosed herein inhibit expression of TIMP1 or TIMP2. For example, siNA molecules (e.g., RISC length dsNA molecules or Dicer length dsNA molecules) are provided that down regulate, reduce or inhibit TIMP1 or TIMP2 expression. Also provided are compositions, methods and kits for treating and/or preventing diseases, conditions or disorders associated with TIMP1 and TIMP2, including organ specific fibrosis associated with at least one of brain, skin fibrosis, lung fibrosis, liver fibrosis, kidney fibrosis, heart fibrosis, vascular fibrosis, bone marrow fibrosis, eye fibrosis, intestinal fibrosis, vocal cord fibrosis or other fibrosis. Specific indications include liver fibrosis, cirrhosis, pulmonary fibrosis including Interstitial lung fibrosis (ILF), kidney fibrosis resulting from any condition (e.g., CKD including ESRD), peritoneal fibrosis, chronic hepatic damage, fibrillogenesis, fibrotic diseases in other organs, abnormal scarring (keloids) associated with all possible types of skin injury accidental and jatrogenic (operations); scleroderma; cardiofibrosis, failure of glaucoma filtering operation; brain fibrosis associated with cerebral infarction; and intestinal adhesions and Crohn's disease. The compounds are useful in treating organ specific indications including those shown in Table I infra.

In one aspect, provided are nucleic acid molecules (e.g., siNA molecules) in which (a) the nucleic acid molecule includes a sense strand (passenger strand) and an antisense strand (guide strand); (b) each strand of the nucleic acid molecule is independently 15 to 49 nucleotides in length; (c) a 15 to 49 nucleotide sequence of the antisense strand is complementary to a sequence of an mRNA encoding a human TIMP (e.g., SEQ ID NO: 1 or SEQ ID NO:2); and (d) a 15 to 49 nucleotide sequence of the sense strand is complementary to the sequence of the antisense strand and includes a 15 to 49 nucleotide sequence of an mRNA encoding human TIMP1 or TIMP2 (e.g., SEQ ID NO: 1 or SEQ ID NO:2, respectively). In various embodiments the sense and antisense strands generate a 15 to 49 base pair duplex.

In certain embodiments, the sequence of the antisense strand that is complementary to a sequence of an mRNA encoding human TIMP1 includes a sequence complimentary to a sequence between nucleotides 193-813 or 1-192; or 813-893 of SEQ ID NO: 1; or between nucleotides 1-200; or 800-893 of SEQ ID NO: 1.

In certain embodiments the sequence of the antisense comprises an antisense sequence set forth in any one of Tables A1-A8 or C. In preferred embodiments the sequence of the antisense comprises an antisense sequence set forth in Tables A3, A4, A7, A8, or C. In some embodiments the antisense and sense strands are selected from the sequence pairs set forth in Table A3 or Table A4. In some embodiments the antisense and sense strands are selected from the sequence pairs set forth in Table A7 or Table A8. In some embodiments the antisense and sense strands are selected from the sequence pairs set forth in Table C.

In certain embodiments, the sequence of the antisense strand that is complementary to a sequence of an mRNA encoding human TIMP2 includes a sequence complimentary to a sequence between nucleotides 303-962 or 1-303; or 962-3369; of SEQ ID NO: 2; or between nucleotides 1-350; or 950-3369 of SEQ ID NO: 2.

In certain embodiments the sequence of the antisense comprises an antisense sequence set forth in any one of Tables B1-B8 or D. In preferred embodiments the sequence of the antisense comprises an antisense sequence set forth in Tables B3, B4, B7, B8, D. In some embodiments the antisense and sense strands are selected from the sequence pairs set forth in Table B3 or Table B4. In some embodiments the antisense and sense strands are selected from the sequence pairs set forth in Table B7 or Table B8. In some embodiments the antisense and sense strands are selected from the sequence pairs set forth in Table D.

In some embodiments, the antisense strand includes a sequence that is complementary to a sequence of an mRNA encoding human TIMP1 corresponding to nucleotides 355-373 of SEQ ID NO: 1 or a portion thereof; or nucleotides 620-638 of SEQ ID NO: 1 or a portion thereof; or nucleotides 640-658 of SEQ ID NO: 1 or a portion thereof.

In some embodiments, the antisense strand includes a sequence that is complementary to a sequence of an mRNA encoding human TIMP2 corresponding to nucleotides 421-439 of SEQ ID NO: 2 or a portion thereof; or nucleotides 502-520 of SEQ ID NO: 2 or a portion thereof; or nucleotides 523-541 of SEQ ID NO: 2 or a portion thereof; or nucleotides 625-643 of SEQ ID NO: 2 or a portion thereof; or nucleotides 629-647 of SEQ ID NO: 2 or a portion thereof

In some embodiments, the antisense strand of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes a sequence corresponding to any one of the antisense sequences shown in Table A1 or A5. In certain preferred embodiments the antisense strand and the strand are selected from the sequence pairs shown in Table A1. In certain preferred embodiments the antisense strand and the sense strand are selected from the sequence pairs shown in Table A5. In some preferred embodiments the antisense and sense strands are selected from the sequence pairs shown in Table A3 or Table A7.

In certain embodiments, the antisense strand of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes a sequence corresponding to any one of the antisense sequences shown in Table C.

In various embodiments of nucleic acid molecules (e.g., siNA molecules) as disclosed herein, the antisense strand may be 15 to 49 nucleotides in length (e.g., 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48 or 49 nucleotides in length); or 17-35 nucleotides in length; or 17-30 nucleotides in length; or 15-25 nucleotides in length; or 18-25 nucleotides in length; or 18-23 nucleotides in length; or 19-21 nucleotides in length; or 25-30 nucleotides in length; or 26-28 nucleotides in length. Similarly the sense strand of nucleic acid molecules (e.g., siNA molecules) as disclosed herein may be 15 to 49 nucleotides in length (e.g., 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48 or 49 nucleotides in length); or 17-35 nucleotides in length; or 17-30 nucleotides in length; or 15-25 nucleotides in length; or 18-25 nucleotides in length; or 18-23 nucleotides in length; or 19−21 nucleotides in length; or 25-30 nucleotides in length; or 26-28 nucleotides in length. The duplex region of the nucleic acid molecules (e.g., siNA molecules) as disclosed herein may be 15-49 nucleotides in length (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48 or 49 nucleotides in length); 18-40 nucleotides in length; or 15-35 nucleotides in length; or 15-30 nucleotides in length; or about 15-25 nucleotides in length; or 17-25 nucleotides in length; or 17-23 nucleotides in length; or 17-21 nucleotides in length; or 19−21 nucleotides in length, or 25-30 nucleotides in length; or 25-28 nucleotides in length. In some embodiments the duplex region of the nucleic acid molecules (e.g., siNA molecules) is 19 nucleotides in length.

In certain embodiments, the sense and antisense strands of a nucleic acid (e.g., an siNA nucleic acid molecule) as provided herein are separate polynucleotide strands. In some embodiments, the separate antisense and sense strands form a double stranded structure via hydrogen bonding, for example, Watson-Crick base pairing. In some embodiments the sense and antisense strands are two separate strands that are covalently linked to each other. In other embodiments, the sense and antisense strands are part of a single polynucleotide strand having both a sense and antisense region; in some preferred embodiments the polynucleotide strand has a hairpin structure.

In certain embodiments, the nucleic acid molecule (e.g., siNA molecule) is a double stranded nucleic acid (dsNA) molecule that is symmetrical with regard to overhangs, and has a blunt end on both ends. In other embodiments the nucleic acid molecule (e.g., siNA molecule) is a dsNA molecule that is symmetrical with regard to overhangs, and has an overhang on both ends of the dsNA molecule; preferably the molecule has overhangs of 1, 2, 3, 4, 5, 6, 7, or 8 nucleotides; preferably the molecule has 2 nucleotide overhangs. In some embodiments the overhangs are 5′ overhangs; in alternative embodiments the overhangs are 3′ overhangs. In certain embodiments, the overhang nucleotides are modified with modifications as disclosed herein. In some embodiments the overhang nucleotides are 2′-deoxyribonucleotides.

In some embodiments the molecules comprise non-nucleotide overhangs at one or more of the 5′ or 3′ terminus of the sense and/or antisense strands. Such non-nucleotide overhangs include abasic ribo- and deoxyribo-nucleotide moieties, alkyl moieties including C3-C3 moieties and amino carbon chains.

In certain preferred embodiments, the nucleic acid molecule (e.g., siNA molecule) is a dsNA molecule that is asymmetrical with regard to overhangs, and has a blunt end on one end of the molecule and an overhang on the other end of the molecule. In certain embodiments the overhang is 1, 2, 3, 4, 5, 6, 7, or 8 nucleotides; preferably the overhang is 2 nucleotides. In some preferred embodiments an asymmetrical dsNA molecule has a 3′-overhang (for example a two nucleotide 3′-overhang) on one side of a duplex occurring on the sense strand; and a blunt end on the other side of the molecule. In some preferred embodiments an asymmetrical dsNA molecule has a 5′-overhang (for example a two nucleotide 5′-overhang) on one side of a duplex occurring on the sense strand; and a blunt end on the other side of the molecule. In other preferred embodiments an asymmetrical dsNA molecule has a 3′-overhang (for example a two nucleotide 3′-overhang) on one side of a duplex occurring on the antisense strand; and a blunt end on the other side of the molecule. In some preferred embodiments an asymmetrical dsNA molecule has a 5′-overhang (for example a two nucleotide 5′-overhang) on one side of a duplex occurring on the antisense strand; and a blunt end on the other side of the molecule. In certain preferred embodiments, the overhangs are 2′-deoxyribonucleotides. Examples of siNA compounds having a terminal dTdT are found in Tables C and D, infra.

In some embodiments, the nucleic acid molecule (e.g., siNA molecule) has a hairpin structure (having the sense strand and antisense strand on one polynucleotide), with a loop structure on one end and a blunt end on the other end. In some embodiments, the nucleic acid molecule has a hairpin structure, with a loop structure on one end and an overhang end on the other end (for example a 1, 2, 3, 4, 5, 6, 7, or 8 nucleotide overhang); in certain embodiments, the overhang is a 3′-overhang; in certain embodiments the overhang is a 5′-overhang; in certain embodiments the overhang is on the sense strand; in certain embodiments the overhang is on the antisense strand.

The nucleic acid molecules (e.g., siNA molecule) disclosed herein may include one or more modifications or modified nucleotides such as described herein. For example, a nucleic acid molecule (e.g., siNA molecule) as provided herein may include a modified nucleotide having a modified sugar; a modified nucleotide having a modified nucleobase; or a modified nucleotide having a modified phosphate group. Similarly, a nucleic acid molecule (e.g., siNA molecule) as provided herein may include a modified phosphodiester backbone and/or may include a modified terminal phosphate group.

Nucleic acid molecules (e.g., siNA molecules) as provided may have one or more nucleotides that include a modified sugar moiety, for example as described herein. In some preferred embodiments the modified sugar moiety is selected from the group consisting of 2′-O-methyl, 2′-methoxyethoxy, 2′-deoxy, 2′-fluoro, 2′-allyl, 2′-O-[2-(methylamino)-2-oxoethyl], 4′-thio, 4′-(CH₂)₂—O-2′-bridge, 2′-locked nucleic acid, and 2′-O—(N-methylcarbamate).

Nucleic acid molecules (e.g., siNA molecules) as provided may have one or more modified nucleobase(s) for example as described herein, which preferably may be one selected from the group consisting of xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, amino, thiol, thioalkyl, hydroxyl and other 8-substituted adenines and guanines, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine, and acyclonucleotides.

Nucleic acid molecules (e.g., siNA molecules) as provided may have one or more modifications to the phosphodiester backbone, for example as described herein. In some preferred embodiments the phosphodiester bond is modified by substituting the phosphodiester bond with a phosphorothioate, 3′-(or -5′)deoxy-3′-(or -5′)thio-phosphorothioate, phosphorodithioate, phosphoroselenates, 3′-(or -5′)deoxy phosphinates, borano phosphates, 3′-(or -5′)deoxy-3′-(or 5′-) amino phosphoramidates, hydrogen phosphonates, borano phosphate esters, phosphoramidates, alkyl or aryl phosphonates and phosphotriester or phosphorus linkages.

In various embodiments, the provided nucleic acid molecules (e.g., siNA molecules) may include one or modifications in the sense strand but not the antisense strand; in other embodiments the provided nucleic acid molecules (e.g., siNA molecules) include one or more modifications in the antisense strand but not the sense strand; in yet other embodiments, the provided nucleic acid molecules (e.g., siNA molecules) include one or more modifications in the both the sense strand and the antisense strand.

In some embodiments in which the provided nucleic acid molecules (e.g., siNA molecules) have modifications, the sense strand includes a pattern of alternating modified and unmodified nucleotides, and/or the antisense strand includes a pattern of alternating modified and unmodified nucleotides; in some preferred versions of such embodiments the modification is a 2′-O-methyl (2′ methoxy or 2′OMe) sugar moiety. The pattern of alternating modified and unmodified nucleotides may start with a modified nucleotide at the 5′ end or 3′ end of one of the strands; for example the pattern of alternating modified and unmodified nucleotides may start with a modified nucleotide at the 5′ end or 3′ end of the sense strand and/or the pattern of alternating modified and unmodified nucleotides may start with a modified nucleotide at the 5′ end or 3′ end of the antisense strand. When both the antisense and sense strand include a pattern of alternating modified nucleotides, the pattern of modified nucleotides may be configured such that modified nucleotides in the sense strand are opposite modified nucleotides in the antisense strand; or there may be a phase shift in the pattern such that modified nucleotides of the sense strand are opposite unmodified nucleotides in the antisense strand and vice-versa.

The nucleic acid molecules (e.g., siNA molecules) as provided herein may include 1-3 (i.e., 1, 2 or 3) deoxyribonucleotides at the 3′ end of the sense and/or the antisense strand.

The nucleic acid molecules (e.g., siNA molecules) as provided herein may include a phosphate group at the 5′ end of the sense and/or the antisense strand.

In one aspect, provided are double stranded nucleic acid molecules having the structure (A1):

(A1) 5′ (N)x-Z 3′ (antisense strand)

3′ Z′-(N′)y-z″ 5′ (sense strand)

wherein each of N and N′ is a nucleotide which may be unmodified or modified, or an unconventional moiety;

wherein each of (N)x and (N′)y is an oligonucleotide in which each consecutive N or N′ is joined to the next N or N′ by a covalent bond; wherein each of Z and Z′ is independently present or absent, but if present independently includes 1-5 consecutive nucleotides or non-nucleotide moieties or a combination thereof covalently attached at the 3′ terminus of the strand in which it is present;

wherein z″ may be present or absent, but if present is a capping moiety covalently attached at the 5′ terminus of (N′)y;

each of x and y is independently an integer from 18 to 40;

wherein the sequence of (N′)y has complementarity to the sequence of (N)x; and wherein (N)x includes an antisense sequence to SEQ ID NO:1 or to SEQ ID NO:2.

In some embodiments (N)x includes an antisense sequence to SEQ ID NO: 1. In some embodiments (N)x includes an antisense oligonucleotide present in any one of Tables A1, A2, A3 or A4. In other embodiments (N)x is selected from an antisense oligonucleotide present in Tables A3 or A4.

In certain preferred embodiments, the antisense strand of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes a sequence corresponding to any one of the antisense sequences shown on Table A1. In certain preferred embodiments the antisense strand and the strand are selected from the sequence pairs shown in Table A2. In certain preferred embodiments the antisense strand and the strand are active in more than one species (human and at least one other species) and are selected from the sequence pairs shown in Table A2. In certain preferred embodiments the antisense strand and the strand are selected from the sequence pairs shown in Table A3, and preferably in Table A4. In some embodiments the antisense and sense strands are selected from the sequence pairs set forth in duplexes siTIMP1_p2; siTIMP1_p6; siTIMP1_p14; siTIMP1_p16; siTIMP1_p17; siTIMP1_p19; siTIMP1_p20; siTIMP1_p21; siTIMP1_p23; siTIMP1_p24; siTIMP1_p27; siTIMP1_p29; siTIMP1_p31; siTIMP1_p33; siTIMP1_p38; siTIMP1_p42; siTIMP1_p43; siTIMP1_p45; siTIMP1_p49; siTIMP1_p60; siTIMP1_p71; siTIMP1_p73; siTIMP1_p77; siTIMP1_p78; siTIMP1_p79; siTIMP1_p85; siTIMP1_p89; siTIMP1_p91; siTIMP1_p96; siTIMP1_p98; siTIMP1_p99 and siTIMP1_p108, shown in Table A3 infra.

In some embodiments the antisense and sense strands are selected from the sequence pairs set forth in siTIMP1_p2 (SEQ ID NOS:267 and 299); siTIMP1_p6 (SEQ ID NOS:268 and 300); siTIMP1_p14 (SEQ ID NOS:269 and 301); siTIMP1_p16 (SEQ ID NOS:270 and 302); siTIMP1_p17 (SEQ ID NOS:271 and 303); siTIMP1_p19 (SEQ ID NOS:272 and 304); siTIMP1_p20 (SEQ ID NOS:273 and 305); siTIMP1_p21 (SEQ ID NOS:274 and 306); siTIMP1_p23 (SEQ ID NOS:275 and 307; siTIMP1_p29 (278 and 310); siTIMP1_p33 (280 and 312); siTIMP1_p38 (SEQ ID NOS:281 and 313); siTIMP1_p42 (282 and 314); siTIMP1_p43 (SEQ ID NOS:283 and 315); siTIMP1_p45 (284 and 316); siTIMP1_p60 (SEQ ID NOS:286 and 318); siTIMP1_p71 (SEQ ID NOS:287 and 319); siTIMP1_p73 (SEQ ID NOS:288 and 320); siTIMP1_p78 (290 and 322); siTIMP1_p79 (SEQ ID NOS:291 and 323); siTIMP1_p85 (SEQ ID NOS:292 and 324); siTIMP1_p89 (SEQ ID NOS:293 and 325); siTIMP1_p91 (SEQ ID NOS:294 and 326); siTIMP1_p96 (SEQ ID NOS:295 and 327); siTIMP1_p98 (SEQ ID NOS:296 and 328); siTIMP1_p99 (SEQ ID NOS:297 and 329) and siTIMP1_p108 (SEQ ID NOS:298 and 330), shown in Table A4, infra.

In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p2 (SEQ ID NOS:267 and 299). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p6 (SEQ ID NOS:268 and 300). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p14 (SEQ ID NOS:269 and 301). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p16 (SEQ ID NOS:270 and 302). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p17 (SEQ ID NOS:271 and 303). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p19 (SEQ ID NOS:272 and 304). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p20 (SEQ ID NOS:273 and 305). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p21 (SEQ ID NOS:274 and 306). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p23 (SEQ ID NOS:275 and 307. In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p29 (278 and 310). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p33 (280 and 312). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p38 (SEQ ID NOS:281 and 313). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p42 (282 and 314). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p43 (SEQ ID NOS:283 and 315). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p45 (284 and 316). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p60 (SEQ ID NOS:286 and 318). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p71 (SEQ ID NOS:287 and 319). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p73 (SEQ ID NOS:288 and 320). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p78 (290 and 322). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p79 (SEQ ID NOS:291 and 323). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p85 (SEQ ID NOS:292 and 324). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p89 (SEQ ID NOS:293 and 325). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p91 (SEQ ID NOS:294 and 326). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p96 (SEQ ID NOS:295 and 327). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p98 (SEQ ID NOS:296 and 328). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p99 (SEQ ID NOS:297 and 329). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p108 (SEQ ID NOS:298 and 330), shown in Table A4.

In some embodiments (N)x includes an antisense sequence to SEQ ID NO:2. In some embodiments (N)x includes an antisense oligonucleotide present in any one of Tables B1, B2, B3 or B4. In other embodiments (N)x is selected from an antisense oligonucleotide present in Tables B3 or B4.

In some embodiments the antisense and sense strands are selected from the sequence pairs set forth in siTIMP2_p4; siTIMP2_p16; siTIMP2_p17; siTIMP2_p18; siTIMP2_p20; siTIMP2_p24; siTIMP2_p25; siTIMP2_p27; siTIMP2_p29; siTIMP2_p30; siTIMP2_p33; siTIMP2_p35; siTIMP2_p37; siTIMP2_p38; siTIMP2_p39; siTIMP2_p40; siTIMP2_p41; siTIMP2_p44; siTIMP2_p46; siTIMP2_p51; siTIMP2_p55; siTIMP2_p61; siTIMP2_p62; siTIMP2_p64; siTIMP2_p65; siTIMP2_p67; siTIMP2_p68; siTIMP2_p69; siTIMP2_p71; siTIMP2_p75; siTIMP2_p76; siTIMP2_p78; siTIMP2_p79; siTIMP2_p82; siTIMP2_p83; siTIMP2_p84; siTIMP2_p85; siTIMP2_p86; siTIMP2_p87; siTIMP2_p88; siTIMP2_p89; siTIMP2_p90; siTIMP2_p91; siTIMP2_p92; siTIMP2_p93; siTIMP2_p94; siTIMP2_p95; siTIMP2_p96; siTIMP2_p97; siTIMP2_p98; siTIMP2_p99; siTIMP2_p100; and siTIMP2_p101 and siTIMP2_p1102, shown in Table B3, infra.

In some embodiments the antisense and sense strands are selected from the sequence pairs set forth in siTIMP2_p27 (SEQ ID NOS:2478 and 2531); siTIMP2_p29 (SEQ ID NOS:2479 and 2532); siTIMP2_p30 (SEQ ID NOS:2480 and 2533); siTIMP2_p39 (SEQ ID NOS:2485 and 2538); siTIMP2_p40 (SEQ ID NOS:2486 and 2539); siTIMP2_p41 (SEQ ID NOS:2487 and 2540); siTIMP2_p46 (SEQ ID NOS:2489 and 2542); siTIMP2_p55 (SEQ ID NOS:2491 and 2544); siTIMP2_p62 (SEQ ID NOS:2493 and 2546); siTIMP2_p68 (SEQ ID NOS:2497 and 2550); siTIMP2_p69 (SEQ ID NOS:2498 and 2551); siTIMP2_p71 (SEQ ID NOS:2499 and 2552); siTIMP2_p76 (SEQ ID NOS:2501 and 2554); siTIMP2_p78 (SEQ ID NOS:2502 and 2555); siTIMP2_p89 (SEQ ID NOS:2511 and 2564); siTIMP2_p91 (SEQ ID NOS:2513 and 2566); siTIMP2_p93 (SEQ ID NOS:2515 and 2568); siTIMP2_p95 (SEQ ID NOS:2517 and 2570); siTIMP2_p97 (SEQ ID NOS:2519 and 2572); siTIMP2_p98 (SEQ ID NOS:2520 and 2573); and siTIMP2_p100 (SEQ ID NOS:2522 and 2575), shown in Table B4, infra.

In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p27 (SEQ ID NOS:2478 and 2531). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p29 (SEQ ID NOS:2479 and 2532). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p30 (SEQ ID NOS:2480 and 2533). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p39 (SEQ ID NOS:2485 and 2538). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p40 (SEQ ID NOS:2486 and 2539). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p41 (SEQ ID NOS:2487 and 2540). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p46 (SEQ ID NOS:2489 and 2542). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p55 (SEQ ID NOS:2491 and 2544). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p62 (SEQ ID NOS:2493 and 2546). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p68 (SEQ ID NOS:2497 and 2550). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p69 (SEQ ID NOS:2498 and 2551). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p71 (SEQ ID NOS:2499 and 2552). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p76 (SEQ ID NOS:2501 and 2554). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p78 (SEQ ID NOS:2502 and 2555). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p89 (SEQ ID NOS:2511 and 2564). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p91 (SEQ ID NOS:2513 and 2566). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p93 (SEQ ID NOS:2515 and 2568). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p95 (SEQ ID NOS:2517 and 2570). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p97 (SEQ ID NOS:2519 and 2572). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p98 (SEQ ID NOS:2520 and 2573). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p100 (SEQ ID NOS:2522 and 2575). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p102 (SEQ ID NOS:1007 and 1622).

In some embodiments the covalent bond joining each consecutive N or N′ is a phosphodiester bond.

In some embodiments x=y and each of x and y is 19, 20, 21, 22 or 23. In various embodiments x=y=19. In some embodiments the antisense and sense strands form a duplex by base pairing.

According to one embodiment provided are modified nucleic acid molecules having a structure (A2) set forth below:

(A2) 5′ N1-(N)x-Z 3′ (antisense strand)

3′ Z′-N2-(N′)y-z″ 5′ (sense strand)

wherein each of N2, N and N′ is independently an unmodified or modified nucleotide, or an unconventional moiety;

wherein each of (N)x and (N′)y is an oligonucleotide in which each consecutive N or N′ is joined to the adjacent N or N′ by a covalent bond;

wherein each of x and y is independently an integer of from 17 to 39;

wherein the sequence of (N′)y has complementarity to the sequence of (N)x and (N)x has complementarity to a consecutive sequence in a target mRNA selected from SEQ ID NO:1 and SEQ ID NO:2;

wherein N1 is covalently bound to (N)x and is mismatched to SEQ ID NO: 1 or to SEQ ID NO:2, wherein N1 is a moiety selected from the group consisting of uridine, modified uridine, ribothymidine, modified ribothymidine, deoxyribothymidine, modified deoxyribothymidine, riboadenine, modified riboadenine, deoxyriboadenine or modified deoxyriboadenine;

wherein N1 and N2 form a base pair;

wherein each of Z and Z′ is independently present or absent, but if present is independently 1-5 consecutive nucleotides or non-nucleotide moieties or a combination thereof covalently attached at the 3′ terminus of the strand in which it is present; and

wherein z″ may be present or absent, but if present is a capping moiety covalently attached at the 5′ terminus of (N′)y.

Molecules covered by the description of Structure A2 are also referred to herein as “18+1” or “18+1 mer”. In some embodiments the N2-(N′)y and N1-(N)x oligonucleotide strands useful in generating dsRNA compounds are presented in Tables A5, A6, A7, A8, B5, B6, B7 or B8. In some embodiments (N)x has complementarity to a consecutive sequence in SEQ ID NO:1 (human TIMP1 mRNA). In some embodiments (N)x includes an antisense oligonucleotide present in any one of Tables A5, A6, A7, and A8. In some embodiments x=y=18 and N1-(N)x includes an antisense oligonucleotide present in any one of Tables A3 or A4. In some embodiments x=y=19 or x=y=20. In certain preferred embodiments x=y=18.

In some embodiments the antisense and sense strands are selected from the sequence pairs set forth in siTIMP1_p1; siTIMP1_p3; siTIMP1_p4; siTIMP1_p5; siTIMP1_p7; siTIMP1_p8; siTIMP1_p9; siTIMP1_p10; siTIMP1_p11; siTIMP1_p12; siTIMP1_p13; siTIMP1_p15; siTIMP1_p118; siTIMP1_p22; siTIMP1_p25; siTIMP1_p26; siTIMP1_p28; siTIMP1_p30; siTIMP1_p32; siTIMP1_p34; siTIMP1_p35; siTIMP1_p36; siTIMP1_p37; siTIMP1_p39; siTIMP1_p40; siTIMP1_p41; siTIMP1_p44; siTIMP1_p46; siTIMP1_p47; siTIMP1_p48; siTIMP1_p50; siTIMP1_p51; siTIMP1_p52; siTIMP1_p53; siTIMP1_p54; siTIMP1_p55; siTIMP1_p56; siTIMP1_p57; siTIMP1_p58; siTIMP1_p59; siTIMP1_p61; siTIMP1_p62; siTIMP1_p63; siTIMP1_p64; siTIMP1_p65; siTIMP1_p66; siTIMP1_p67; siTIMP1_p68; siTIMP1_p69; siTIMP1_p70; siTIMP1_p72; siTIMP1_p74; siTIMP1_p75; siTIMP1_p76; siTIMP1_p80; siTIMP1_p81; siTIMP1_p82; siTIMP1_p83; siTIMP1_p84; siTIMP1_p86; siTIMP1_p87; siTIMP1_p88; siTIMP1_p90; siTIMP1_p92; siTIMP1_p93; siTIMP1_p94; siTIMP1_p95; siTIMP1_p97; siTIMP1_p100; siTIMP1_p101; siTIMP1_p102; siTIMP1_p103; siTIMP1_p104; siTIMP1_p105; siTIMP1_p106; siTIMP1_p109; siTIMP1_p110; siTIMP1_p111; siTIMP1_p112; siTIMP1_p113 and siTIMP1_p114, shown in Table A7, infra.

In some embodiments the antisense and sense strands are selected from the sequence pairs set forth in siTIMP1_p1 (SEQ ID NOS:845 and 926); siTIMP1_p4 (SEQ ID NOS:847 and 928; siTIMP1_p5 (SEQ ID NOS:848 and 929); siTIMP1_p7 (SEQ ID NOS:849 and 930); siTIMP1_p8 (SEQ ID NOS:850 and 931); siTIMP1_p9 (SEQ ID NOS:850 and 931); siTIMP1_p10 (SEQ ID NOS:852 and 933); siTIMP1_p11 (SEQ ID NOS:853 and 934); siTIMP1_p12 (SEQ ID NOS:854 and 935); siTIMP1_p13 (SEQ ID NOS:855 and 936); siTIMP1_p15 (SEQ ID NOS:856 and 937); siTIMP1_p18 (SEQ ID NOS:857 and 938); siTIMP1_p22 (SEQ ID NOS:858 and 939); siTIMP1_p26 (SEQ ID NOS:860 and 941); siTIMP1_p36 (SEQ ID NOS:866 and 947); siTIMP1_p37 (SEQ ID NOS:867 and 948); siTIMP1_p39 (SEQ ID NOS:868 and 949); siTIMP1_p40 (SEQ ID NOS:869 and 950); siTIMP1_p41 (SEQ ID NOS:870 and 951); siTIMP1_p44 (SEQ ID NOS:871 and 952); siTIMP1_p47 (SEQ ID NOS:873 and 954); siTIMP1_p48 (SEQ ID NOS:874 and 955); siTIMP1_p50 (SEQ ID NOS:875 and 956); siTIMP1_p51 (SEQ ID NOS:876 and 957); siTIMP1_p52 (SEQ ID NOS:877 and 958); siTIMP1_p55 (SEQ ID NOS:880 and 961); siTIMP1_p56 (SEQ ID NOS:881 and 962); siTIMP1_p58 (SEQ ID NOS:883 and 964); siTIMP1_p61 (SEQ ID NOS:885 and 966); siTIMP1_p64 (SEQ ID NOS:888 and 969); siTIMP1_p66 (SEQ ID NOS:890 and 971); siTIMP1_p68 (SEQ ID NOS:892 and 973); siTIMP1_p70 (SEQ ID NOS:894 and 975); siTIMP1_p75 (SEQ ID NOS:897 and 978); siTIMP1_p83 (SEQ ID NOS:902 and 983); siTIMP1_p86 (SEQ ID NOS:904 and 985); siTIMP1_p88 (SEQ ID NOS:906 and 987); siTIMP1_p92 (SEQ ID NOS:908 and 989); siTIMP1_p93 (SEQ ID NOS:909 and 990); siTIMP1_p95 (SEQ ID NOS:911 and 992); siTIMP1_p97 (SEQ ID NOS:912 and 993); siTIMP1_p102 (SEQ ID NOS:915 and 996); siTIMP1_p104 (SEQ ID NOS:917 and 998); siTIMP1_p105 (SEQ ID NOS:918 and 999); siTIMP1_p106 (SEQ ID NOS:919 and 1000); siTIMP1_p110 (SEQ ID NOS:921 and 1002) and siTIMP1_p112 (SEQ ID NOS:923 and 1004), shown in Table A8, infra.

In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p1 (SEQ ID NOS:845 and 926). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p4 (SEQ ID NOS:847 and 928. In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p5 (SEQ ID NOS:848 and 929). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p7 (SEQ ID NOS:849 and 930). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p8 (SEQ ID NOS:850 and 931). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p9 (SEQ ID NOS:850 and 931). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p10 (SEQ ID NOS:852 and 933). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p11 (SEQ ID NOS:853 and 934). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p12 (SEQ ID NOS:854 and 935). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p13 (SEQ ID NOS:855 and 936). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p15 (SEQ ID NOS:856 and 937). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p18 (SEQ ID NOS:857 and 938). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p22 (SEQ ID NOS:858 and 939). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p26 (SEQ ID NOS:860 and 941). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p36 (SEQ ID NOS:866 and 947). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p37 (SEQ ID NOS:867 and 948). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p39 (SEQ ID NOS:868 and 949). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p40 (SEQ ID NOS:869 and 950). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p41 (SEQ ID NOS:870 and 951). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p44 (SEQ ID NOS:871 and 952). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p47 (SEQ ID NOS:873 and 954). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p48 (SEQ ID NOS:874 and 955). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p50 (SEQ ID NOS:875 and 956). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p51 (SEQ ID NOS:876 and 957). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p52 (SEQ ID NOS:877 and 958). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p55 (SEQ ID NOS:880 and 961). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p56 (SEQ ID NOS:881 and 962). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p58 (SEQ ID NOS:883 and 964). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p61 (SEQ ID NOS:885 and 966). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p64 (SEQ ID NOS:888 and 969).

In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p66 (SEQ ID NOS:890 and 971). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p68 (SEQ ID NOS:892 and 973). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p70 (SEQ ID NOS:894 and 975). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p75 (SEQ ID NOS:897 and 978). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p83 (SEQ ID NOS:902 and 983). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p86 (SEQ ID NOS:904 and 985). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p88 (SEQ ID NOS:906 and 987). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p92 (SEQ ID NOS:908 and 989). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p93 (SEQ ID NOS:909 and 990). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p95 (SEQ ID NOS:911 and 992). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p97 (SEQ ID NOS:912 and 993). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p102 (SEQ ID NOS:915 and 996). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p104 (SEQ ID NOS:917 and 998). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p105 (SEQ ID NOS:918 and 999). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p106 (SEQ ID NOS:919 and 1000). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p110 (SEQ ID NOS:921 and 1002). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP1_p112 (SEQ ID NOS:923 and 1004).

In some preferred embodiments the nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the antisense strand and the sense strand of a sequence pair set forth in siTIMP1_p1 (SEQ ID NOS:845 and 926). In some preferred embodiments the nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the antisense strand and the sense strand of a sequence pair set forth in siTIMP1_p4 (SEQ ID NOS:847 and 928. In some preferred embodiments the nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the antisense strand and the sense strand of a sequence pair set forth in siTIMP1_p5 (SEQ ID NOS:848 and 929). In some preferred embodiments the nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the antisense strand and the sense strand of a sequence pair set forth in siTIMP1_p7 (SEQ ID NOS:849 and 930). In some preferred embodiments the nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the antisense strand and the sense strand of a sequence pair set forth in siTIMP1_p9 (SEQ ID NOS:850 and 931). In some preferred embodiments the nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the antisense strand and the sense strand of a sequence pair set forth in siTIMP_p10 (SEQ ID NOS:852 and 933). In some preferred embodiments the nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the antisense strand and the sense strand of a sequence pair set forth in siTIMP1_p11 (SEQ ID NOS:853 and 934). In some preferred embodiments the nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the antisense strand and the sense strand of a sequence pair set forth in siTIMP1_p12 (SEQ ID NOS:854 and 935). In some preferred embodiments the nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the antisense strand and the sense strand of a sequence pair set forth in siTIMP1_p13 (SEQ ID NOS:855 and 936). In some preferred embodiments the nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the antisense strand and the sense strand of a sequence pair set forth in siTIMP1_p15 (SEQ ID NOS:856 and 937). In some preferred embodiments the nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the antisense strand and the sense strand of a sequence pair set forth in siTIMP1_p18 (SEQ ID NOS:857 and 938). In some preferred embodiments the nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the antisense strand and the sense strand of a sequence pair set forth in siTIMP1_p44 (SEQ ID NOS:871 and 952). In some preferred embodiments the nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the antisense strand and the sense strand of a sequence pair set forth in siTIMP1_p48 (SEQ ID NOS:874 and 955). In some preferred embodiments the nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the antisense strand and the sense strand of a sequence pair set forth in siTIMP1_p51 (SEQ ID NOS:876 and 957). In some preferred embodiments the nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the antisense strand and the sense strand of a sequence pair set forth in siTIMP1_p52 (SEQ ID NOS:877 and 958).

In some embodiments (N)x has complementarity to a consecutive sequence in SEQ ID NO:2 (human TIMP2 mRNA). In some embodiments (N)x includes an antisense oligonucleotide present in any one of Tables B5, B6, B7, and B8. In some embodiments x=y=18 and N1-(N)x includes an antisense oligonucleotide present in any one of Tables B3 or B4. In some embodiments x=y=19 or x=y=20. In certain preferred embodiments x=y=18.

In some embodiments the antisense and sense strands are selected from the sequence pairs set forth in siTIMP2_p1; siTIMP2_p2; siTIMP2_p3; siTIMP2_p5; siTIMP2_p6; siTIMP2_p7; siTIMP2_p8; siTIMP2_p9; siTIMP2_p10; siTIMP2_p11; siTIMP2_p12; siTIMP2_p13; siTIMP2_p14; siTIMP2_p15; siTIMP2_p19; siTIMP2_p21; siTIMP2_p22; siTIMP2_p23; siTIMP2_p26; siTIMP2_p28; siTIMP2_p31; siTIMP2_p32; siTIMP2_p34; siTIMP2_p36; siTIMP2_p42; siTIMP2_p43; siTIMP2_p45; siTIMP2_p47; siTIMP2_p48; siTIMP2_p49; siTIMP2_p50; siTIMP2_p52; siTIMP2_p53; siTIMP2_p54; siTIMP2_p56; siTIMP2_p57; siTIMP2_p58; siTIMP2_p59; siTIMP2_p60; siTIMP2_p63; siTIMP2_p66; siTIMP2_p70; siTIMP2_p72; siTIMP2_p73; siTIMP2_p74; siTIMP2_p77; siTIMP2_p80 and siTIMP2_p81, shown in Table B7, infra.

In some embodiments the antisense and sense strands are selected from the sequence pairs set forth in siTIMP2_p6 (SEQ ID NOS:4771 and 4819); siTIMP2_p9 (SEQ ID NOS:4774 and 4822); siTIMP2_p15 (SEQ ID NOS:4780 and 4828); siTIMP2_p19 (SEQ ID NOS:4781 and 4829); siTIMP2_p21 (SEQ ID NOS:4782 and 4830); siTIMP2_p22 (SEQ ID NOS:4783 and 4831); siTIMP2_p23 (SEQ ID NOS:4784 and 4832); siTIMP2_p28 (SEQ ID NOS:4786 and 4834); siTIMP2_p31 (SEQ ID NOS:4787 and 4835); siTIMP2_p36 (SEQ ID NOS:4790 and 4838); siTIMP2_p42 (SEQ ID NOS:4791 and 4839); siTIMP2_p47 (SEQ ID NOS:4794 and 4842); siTIMP2_p50 (SEQ ID NOS:4797 and 4845); siTIMP2_p56 (SEQ ID NOS:4801 and 4849); siTIMP2_p57 (SEQ ID NOS:4802 and 4850); siTIMP2_p58 (SEQ ID NOS:4803 and 4851); siTIMP2_p60 (SEQ ID NOS:4805 and 4853); siTIMP2_p63 (SEQ ID NOS:4806 and 4854); siTIMP2_p70 (SEQ ID NOS:4808 and 4856); siTIMP2_p73 (SEQ ID NOS:4810 and 4858); siTIMP2_p74 (SEQ ID NOS:4811 and 4859); and siTIMP2_p81 (SEQ ID NOS:4814 and 4862), shown in Table B8, infra.

In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p6 (SEQ ID NOS:4771 and 4819). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p9 (SEQ ID NOS:4774 and 4822). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p15 (SEQ ID NOS:4780 and 4828). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p19 (SEQ ID NOS:4781 and 4829). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p21 (SEQ ID NOS:4782 and 4830). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p22 (SEQ ID NOS:4783 and 4831). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p23 (SEQ ID NOS:4784 and 4832). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p28 (SEQ ID NOS:4786 and 4834). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p31 (SEQ ID NOS:4787 and 4835). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p36 (SEQ ID NOS:4790 and 4838). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p42 (SEQ ID NOS:4791 and 4839). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p47 (SEQ ID NOS:4794 and 4842). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p50 (SEQ ID NOS:4797 and 4845). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p56 (SEQ ID NOS:4801 and 4849). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p57 (SEQ ID NOS:4802 and 4850). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p58 (SEQ ID NOS:4803 and 4851). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p60 (SEQ ID NOS:4805 and 4853). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p63 (SEQ ID NOS:4806 and 4854); siTIMP2_p70 (SEQ ID NOS:4808 and 4856). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p73 (SEQ ID NOS:4810 and 4858). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p74 (SEQ ID NOS:4811 and 4859). In some embodiments the antisense and sense strands of a nucleic acid molecule (e.g., a siNA molecule) as disclosed herein includes the sequence pairs set forth in siTIMP2_p81 (SEQ ID NOS:4814 and 4862).

In some embodiments N1 and N2 form a Watson-Crick base pair. In other embodiments N1 and N2 form a non-Watson-Crick base pair. In some embodiments N1 is a modified riboadenosine or a modified ribouridine.

In certain embodiments N1 is selected from the group consisting of riboadenosine, modified riboadenosine, deoxyriboadenosine, modified deoxyriboadenosine. In other embodiments N1 is selected from the group consisting of ribouridine, deoxyribouridine, modified ribouridine, and modified deoxyribouridine.

In certain embodiments N1 is selected from the group consisting of riboadenosine, modified riboadenosine, deoxyriboadenosine, modified deoxyriboadenosine and N2 is selected from the group consisting of ribouridine, deoxyribouridine, modified ribouridine, and modified deoxyribouridine. In certain embodiments N1 is selected from the group consisting of riboadenosine and modified riboadenosine and N2 is selected from the group consisting of ribouridine and modified ribouridine.

In certain embodiments N2 is selected from the group consisting of riboadenosine, modified riboadenosine, deoxyriboadenosine, modified deoxyriboadenosine and N1 is selected from the group consisting of ribouridine, deoxyribouridine, modified ribouridine, and modified deoxyribouridine. In certain embodiments N1 is selected from the group consisting of ribouridine and modified ribouridine and N2 is selected from the group consisting of riboadenine and modified riboadenine. In certain embodiments N1 is ribouridine and N2 is riboadenine.

In some embodiments of Structure (A2), N1 includes 2′OMe sugar-modified ribouracil or 2′OMe sugar-modified riboadenosine. In certain embodiments of structure (A), N2 includes a 2′OMe sugar modified ribonucleotide or deoxyribonucleotide.

In some embodiments Z and Z′ are absent. In other embodiments one of Z or Z′ is present.

In some embodiments each of N and N′ is an unmodified nucleotide. In some embodiments at least one of N or N′ includes a chemically modified nucleotide or an unconventional moiety. In some embodiments the unconventional moiety is selected from a mirror nucleotide, an abasic ribose moiety and an abasic deoxyribose moiety. In some embodiments the unconventional moiety is a mirror nucleotide, preferably an L-DNA moiety. In some embodiments at least one of N or N′ includes a 2′OMe sugar-modified ribonucleotide.

In some embodiments the sequence of (N′)y is fully complementary to the sequence of (N)x. In other embodiments the sequence of (N′)y is substantially complementary to the sequence of (N)x.

In some embodiments (N)x includes an antisense sequence that is fully complementary to about 17 to about 39 consecutive nucleotides in a target mRNA. In other embodiments (N)x includes an antisense that is substantially complementary to about 17 to about 39 consecutive nucleotides in a target mRNA. In some embodiments (N)x includes an antisense that is substantially complementary to about 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, to about 39 consecutive nucleotides in a target mRNA. In other embodiments (N)x includes an antisense that is substantially complementary to about 17 to about 23, 18 to about 23, 18 to about 21, or 18 to about 19 consecutive nucleotides in a target mRNA.

In some embodiments of Structure A1 and Structure A2 the compound is blunt ended, for example wherein both Z and Z′ are absent. In an alternative embodiment, at least one of Z or Z′ is present. Z and Z′ independently include one or more covalently linked modified and or unmodified nucleotides, including deoxyribonucleotides and ribonucleotides, or an unconventional moiety for example inverted abasic deoxyribose moiety or abasic ribose moiety; a non-nucleotide C3, C4 or C5 moiety, an amino-6 moiety, a mirror nucleotide and the like. In some embodiments each of Z and Z′ independently includes a C3 moiety or an amino-C6 moiety. In some embodiments Z′ is absent and Z is present and includes a non-nucleotide C3 moiety. In some embodiments Z is absent and Z′ is present and includes a non-nucleotide C3 moiety.

In some preferred embodiments of Structures A1 and Structure A2 an asymmetrical siNA compound molecule has a 3′ terminal non-nucleotide overhang (for example C3-C3 3′-overhang) on one side of a duplex occurring on the antisense strand; and a blunt end on the other side of the molecule. In some preferred embodiments z′ is present and the dsNA molecule has a 5′ terminal non-nucleotide overhang (for example an abasic moiety) on one side of a duplex occurring on the sense strand; and a blunt end on the other side of the molecule.

In some embodiments of Structure A1 and Structure A2 each N consists of an unmodified ribonucleotide. In some embodiments of Structure A1 and Structure A2 each N′ consists of an unmodified nucleotide. In preferred embodiments, at least one of N and N′ is a modified ribonucleotide or an unconventional moiety.

In other embodiments the compound of Structure A1 or Structure A2 includes at least one ribonucleotide modified in the sugar residue. In some embodiments the compound includes a modification at the 2′ position of the sugar residue. In some embodiments the modification in the 2′ position includes the presence of an amino, a fluoro, an alkoxy or an alkyl moiety. In certain embodiments the 2′ modification includes an alkoxy moiety. In preferred embodiments the alkoxy moiety is a methoxy moiety (also known as 2′-O-methyl; 2′OMe; 2′-OCH3). In some embodiments the nucleic acid compound includes 2′OMe sugar modified alternating ribonucleotides in one or both of the antisense and the sense strands. In other embodiments the compound includes 2′OMe sugar modified ribonucleotides in the antisense strand, (N)x or N1-(N)x, only. In certain embodiments the middle ribonucleotide of the antisense strand; e.g. ribonucleotide in position 10 in a 19-mer strand is unmodified. In various embodiments the nucleic acid compound includes at least 5 alternating 2′OMe sugar modified and unmodified ribonucleotides.

In additional embodiments the compound of Structure A1 or Structure A2 includes modified ribonucleotides in alternating positions wherein each ribonucleotide at the 5′ and 3′ termini of (N)x or N1-(N)x are modified in their sugar residues, and each ribonucleotide at the 5′ and 3′ termini of (N′)y or N2-(N)y are unmodified in their sugar residues.

In some embodiments, (N)x or N1-(N)x includes 2′OMe modified ribonucleotides at positions 2, 4, 6, 8, 11, 13, 15, 17 and 19. In other embodiments (N)x (N)x or N1-(N)x includes 2′OMe modified ribonucleotides at positions 1, 3, 5, 7, 9, 11, 13, 15, 17 and 19. In some embodiments (N)x or N1-(N)x includes 2′OMe modified pyrimidines. In some embodiments all the pyrimidine nucleotides in (N)x or N1-(N)x are 2′OMe modified. In some embodiments (N′)y or N2-(N′)y includes 2′OMe modified pyrimidines.

In some embodiments of Structure A1 and Structure A2, neither of the sense strand nor the antisense strand is phosphorylated at the 3′ and 5′ termini. In other embodiments one or both of the sense strand or the antisense strand are phosphorylated at the 3′ termini.

In some embodiments of Structure A1 and Structure A2 (N)y includes at least one unconventional moiety selected from a mirror nucleotide and a nucleotide joined to an adjacent nucleotide by a 2′-5′ internucleotide phosphate bond also known as 2′-5′ linked or 2′-5′ linkage. In some embodiments the unconventional moiety is a mirror nucleotide. In various embodiments the mirror nucleotide is selected from an L-ribonucleotide (L-RNA) and an L-deoxyribonucleotide (L-DNA). In preferred embodiments the mirror nucleotide is L-DNA.

In some embodiments of Structure A1 (N′)y includes at least one L-DNA moiety. In some embodiments x=y=19 and (N′)y, consists of unmodified ribonucleotides at positions 1-17 and 19 and one L-DNA at the 3′ penultimate position (position 18). In other embodiments x=y=19 and (N′)y consists of unmodified ribonucleotides at position 1-16 and 19 and two consecutive L-DNA at the 3′ penultimate position (positions 17 and 18). In various embodiments the unconventional moiety is a nucleotide joined to an adjacent nucleotide by a 2′-5′ internucleotide phosphate linkage. According to various embodiments (N′)y includes 2, 3, 4, 5, or 6 consecutive ribonucleotides at the 3′ terminus linked by 2′-5′ internucleotide linkages. In one embodiment, four consecutive nucleotides at the 3′ terminus of (N′)y are joined by three 2′-5′ phosphodiester bonds, wherein one or more of the 2′-5′ nucleotides which form the 2′-5′ phosphodiester bonds further includes a 3′-O-methyl (3′OMe) sugar modification. Preferably the 3′ terminal nucleotide of (N′)y includes a 2′OMe sugar modification. In certain embodiments x=y=19 and (N′)y includes two or more consecutive nucleotides at positions 15, 16, 17, 18 and 19 include a nucleotide joined to an adjacent nucleotide by a 2′-5′ internucleotide bond. In various embodiments the nucleotide forming the 2′-5′ internucleotide bond includes a 3′ deoxyribose nucleotide or a 3′ methoxy nucleotide. In some embodiments x=y=19 and (N′)y includes nucleotides joined to the adjacent nucleotide by a 2′-5′ internucleotide bond between positions 15-16, 16-17 and 17-18 or between positions 16-17, 17-18 and 18-19. In some embodiments x=y=19 and (N′)y includes nucleotides joined to the adjacent nucleotide by a 2′-5′ internucleotide bond between positions 16-17 and 17-18 or between positions 17-18 and 18-19 or between positions 15-16 and 17-18. In other embodiments the pyrimidine ribonucleotides (rU, rC) in (N′)y are substituted with nucleotides joined to the adjacent nucleotide by a 2′-5′ internucleotide bond.

In some embodiments of Structure A2, (N)y includes at least one L-DNA moiety. In some embodiments x=y=18 and (N′)y consists of unmodified ribonucleotides at positions 1-16 and 18 and one L-DNA at the 3′ penultimate position (position 17). In other embodiments x=y=18 and (N′)y consists of unmodified ribonucleotides at position 1-15 and 18 and two consecutive L-DNA at the 3′ penultimate position (positions 16 and 17). In various embodiments the unconventional moiety is a nucleotide joined to an adjacent nucleotide by a 2′-5′ internucleotide phosphate linkage. According to various embodiments (N′)y includes 2, 3, 4, 5, or 6 consecutive ribonucleotides at the 3′ terminus linked by 2′-5′ internucleotide linkages. In one embodiment, four consecutive nucleotides at the 3′ terminus of (N′)y are joined by three 2′-5′ phosphodiester bonds, wherein one or more of the 2′-5′ nucleotides which form the 2′-5′ phosphodiester bonds further includes a 3′-O-methyl (3′OMe) sugar modification. Preferably the 3′ terminal nucleotide of (N′)y includes a 2′OMe sugar modification. In certain embodiments x=y=18 and in (N′)y two or more consecutive nucleotides at positions 14, 15, 16, 17, and 18 include a nucleotide joined to an adjacent nucleotide by a 2′-5′ internucleotide bond. In various embodiments the nucleotide forming the 2′-5′ internucleotide bond includes a 3′ deoxyribose nucleotide or a 3′ methoxy nucleotide. In some embodiments x=y=18 and (N′)y includes nucleotides joined to the adjacent nucleotide by a 2′-5′ internucleotide bond between positions 15-16, 16-17 and 17-18 or between positions 16-17 and 17-18. In some embodiments x=y=18 and (N′)y includes nucleotides joined to the adjacent nucleotide by a 2′-5′ internucleotide bond between positions 14-15, 15-16, 16-17, and 17-18 or between positions 15-16, 16-17, and 17-18 or between positions 16-17 and 17-18 or between positions 17-18 or between positions 15-16 and 17-18. In other embodiments the pyrimidine ribonucleotides (rU, rC) in (N′)y are substituted with nucleotides joined to the adjacent nucleotide by a 2′-5′ internucleotide bond.

In some embodiments, x=y=19 and (N′)y comprises five consecutive nucleotides at the 3′ terminus joined by four 2′-5′ linkages, specifically the linkages between the nucleotides position 15-16, 16-17, 17-18 and 18-19.

In some embodiments the internucleotide linkages include phosphodiester bonds. In some embodiments x=y=19 and (N′)y comprises five consecutive nucleotides at the 3′ terminus joined by four 2′-5′ linkages and optionally further includes Z′ and z′ independently selected from an inverted abasic moiety and a C3 alkyl [C3; 1,3-propanediol mono(dihydrogen phosphate)] cap.

In some embodiments x=y=19 and (N′)y comprises an L-DNA position 18; and (N′)y optionally further includes Z′ and z′ independently selected from an inverted abasic moiety and a C3 alkyl [C3; 1,3-propanediol mono(dihydrogen phosphate)] cap.

In some embodiments (N′)y comprises a 3′ terminal phosphate. In some embodiments (N′)y comprises a 3′ terminal hydroxyl.

In some embodiments x=y=19 and (N)x includes 2′OMe sugar modified ribonucleotides at positions 1, 3, 5, 7, 9, 11, 13, 15, 17, 19 or at positions 2, 4, 6, 8, 11, 13, 15, 17, 19. In some embodiments x=y=19 and (N)x includes 2′OMe sugar modified pyrimidines. In some embodiments all pyrimidines in (N)x include the 2′OMe sugar modification.

In some embodiments x=y=18 and N2 is a riboadenine moiety.

In some embodiments in x=y=18, and N2-(N′)y comprises five consecutive nucleotides at the 3′ terminus joined by four 2′-5′ linkages, specifically the linkages between the nucleotides position 15-16, 16-17, 17-18 and 18-19. In some embodiments the linkages include phosphodiester bonds.

In some embodiments x=y=18 and N2-(N′)y comprises five consecutive nucleotides at the 3′ terminus joined by four 2′-5′ linkages and optionally further includes Z′ and z′ independently selected from an inverted abasic moiety and a C3 alkyl [C3; 1,3-propanediol mono(dihydrogen phosphate)] cap.

In some embodiments x=y=18 and N2-(N′)y comprises an L-DNA position 18; and (N′)y optionally further includes Z′ and z′ independently selected from an inverted abasic moiety and a C3 alkyl [C3; 1,3-propanediol mono(dihydrogen phosphate)] cap.

In some embodiments N2-(N′)y comprises a 3′ terminal phosphate. In some embodiments N2-(N′)y comprises a 3′ terminal hydroxyl.

In some embodiments x=y=18 and N1-(N)x includes 2′OMe sugar modified ribonucleotides at positions 1, 3, 5, 7, 9, 11, 13, 15, 17, 19 or at positions 2, 4, 6, 8, 11, 13, 15, 17, 19.

In some embodiments x=y=18 and N1-(N)x includes 2′OMe sugar modified pyrimidines. In some embodiments all pyrimidines in (N)x include the 2′OMe sugar modification. In some embodiments N1-(N)x further comprises an L-DNA at position 6 or 7 (5′>3′). In other embodiments N1-(N)x further comprises a ribonucleotide which generates a 2′5′ internucleotide linkage in between the ribonucleotides at positions 5-6 or 6-7 (5′>3′)

In additional embodiments N1-(N)x further includes Z wherein Z comprises a non-nucleotide overhang. In some embodiments the non-nucleotide overhang is C3-C3 [1,3-propanediol mono(dihydrogen phosphate)]2.

In some embodiments the double stranded molecules disclosed herein, in particular molecules set forth in Tables A3, A4, A7, A8 and B3, B4, B7 and B8, include one or more of the following modifications:

- a) N in at least one of positions 5, 6, 7, 8, or 9 from the 5′ terminus of the antisense strand is selected from a DNA, TNA, a 2′5′ nucleotide or a mirror nucleotide;
- b) N′ in at least one of positions 9 or 10 from the 5′ terminus of the sense strand is selected from a TNA, 2′5′ nucleotide and a pseudoUridine;
- c) N′ in 4, 5, or 6 consecutive positions at the 3′ terminus positions of (N′)y comprises a 2′5′ nucleotide;
- d) one or more pyrimidine ribonucleotides are 2′ modified in the sense strand, the antisense strand or both the sense strand and the antisense strand.

In some embodiments the double stranded molecules in particular molecules set forth in Tables A3, A4, A7, A8 and B3, B4, B7 and B8 include a combination of the following modifications

- a) the antisense strand includes a DNA, TNA, a 2′5′ nucleotide or a mirror nucleotide in at least one of positions 5, 6, 7, 8, or 9 from the 5′ terminus;
- b) the sense strand includes at least one of a TNA, a 2′5′ nucleotide and a pseudoUridine in positions 9 or 10 from the 5′ terminus; and
- c) one or more pyrimidine ribonucleotides are 2′ modified in the sense strand, the antisense strand or both the sense strand and the antisense strand.

In some embodiments the double stranded molecules in particular molecules set forth in Tables A3, A4, A7, A8 and B3, B4, B7 and B8 include a combination of the following modifications

- a) the antisense strand includes a DNA, 2′5′ nucleotide or a mirror nucleotide in at least one of positions 5, 6, 7, 8, or 9 from the 5′ terminus;
- b) the sense strand includes 4, 5, or 6 consecutive 2′5′ nucleotides at the 3′ penultimate or 3′ terminal positions; and
- c) one or more pyrimidine ribonucleotides are 2′ modified in the sense strand, the antisense strand or both the sense strand and the antisense strand.

In some embodiments of Structure A1 and/or Structure A2 (N)y includes at least one unconventional moiety selected from a mirror nucleotide, a 2′5′ nucleotide and a TNA. In some embodiments the unconventional moiety is a mirror nucleotide. In various embodiments the mirror nucleotide is selected from an L-ribonucleotide (L-RNA) and an L-deoxyribonucleotide (L-DNA). In preferred embodiments the mirror nucleotide is L-DNA. In certain embodiments the sense strand comprises an unconventional moiety in position 9 or 10 (from the 5′ terminus). In preferred embodiments the sense strand includes an unconventional moiety in position 9 (from the 5′ terminus). In some embodiments the sense strand is 19 nucleotides in length and comprises 4, 5, or 6 consecutive unconventional moieties in positions 15, (from the 5′ terminus). In some embodiments the sense strand includes 4 consecutive 2′5′ ribonucleotides in positions 15, 16, 17, and 18. In some embodiments the sense strand includes 5 consecutive 2′5′ ribonucleotides in positions 15, 16, 17, 18 and 19. In various embodiments the sense strand further comprises Z′. In some embodiments Z′ includes a C30H moiety or a C3Pi moiety.

In some embodiments of Structure A1 and/or Structure A2 (N)y comprises at least one unconventional moiety selected from a mirror nucleotide and a nucleotide joined to an adjacent nucleotide by a 2′-5′ internucleotide phosphate bond. In some embodiments the unconventional moiety is a mirror nucleotide. In various embodiments the mirror nucleotide is selected from an L-ribonucleotide (L-RNA) and an L-deoxyribonucleotide (L-DNA). In preferred embodiments the mirror nucleotide is L-DNA.

In some embodiments of Structure A1 (N′)y comprises at least one L-DNA moiety. In some embodiments x=y=19 and (N′)y consists of unmodified ribonucleotides at positions 1-17 and 19 and one L-DNA at the 3′ penultimate position (position 18). In other embodiments x=y=19 and (N′)y consists of unmodified ribonucleotides at position 1-16 and 19 and two consecutive L-DNA at the 3′ penultimate position (positions 17 and 18). In various embodiments the unconventional moiety is a nucleotide joined to an adjacent nucleotide by a 2′-5′ internucleotide phosphate linkage. According to various embodiments (N′)y comprises 2, 3, 4, 5, or 6 consecutive ribonucleotides at the 3′ terminus linked by 2′-5′ internucleotide linkages. In one embodiment, four consecutive nucleotides at the 3′ terminus of (N′)y are joined by three 2′-5′ phosphodiester bonds. In one embodiment, five consecutive nucleotides at the 3′ terminus of (N′)y are joined by four 2′-5′ phosphodiester bonds. In some embodiments, wherein one or more of the 2′-5′ nucleotides form a 2′-5′ phosphodiester bonds the nucleotide further comprises a 3′-O-methyl (3′OMe) sugar modification. In some embodiments the 3′ terminal nucleotide of (N′)y comprises a 3′OMe sugar modification. In certain embodiments x=y=19 and (N′)y comprises two or more consecutive nucleotides at positions 15, 16, 17, 18 and 19 comprise a nucleotide joined to an adjacent nucleotide by a 2′-5′ internucleotide bond. In various embodiments the nucleotide forming the 2′-5′ internucleotide bond comprises a 3′ deoxyribose nucleotide or a 3′ methoxy nucleotide. In some embodiments x=y=19 and (N′)y comprises nucleotides joined to the adjacent nucleotide by a 2′-5′ internucleotide bond between positions 15-16, 16-17 and 17-18 or between positions 16-17, 17-18 and 18-19. In some embodiments x=y=19 and (N′)y comprises nucleotides joined to the adjacent nucleotide by a 2′-5′ internucleotide bond between positions 16-17 and 17-18 or between positions 17-18 and 18-19 or between positions 15-16 and 17-18. In other embodiments the pyrimidine ribonucleotides (rU, rC) in (N′)y are substituted with nucleotides joined to the adjacent nucleotide by a 2′-5′ internucleotide bond.

In some embodiments of Structure A2 (N)y comprises at least one L-DNA moiety. In some embodiments x=y=18 and N2-(N′)y, consists of unmodified ribonucleotides at positions 1-17 and 19 and one L-DNA at the 3′ penultimate position (position 18). In other embodiments x=y=18 and N2-(N′)y consists of unmodified ribonucleotides at position 1-16 and 19 and two consecutive L-DNA at the 3′ penultimate position (positions 17 and 18). In various embodiments the unconventional moiety is a nucleotide joined to an adjacent nucleotide by a 2′-5′ internucleotide phosphate linkage. According to various embodiments N2-(N′)y comprises 2, 3, 4, 5, or 6 consecutive ribonucleotides at the 3′ terminus linked by 2′-5′ internucleotide linkages. In one embodiment, four consecutive nucleotides at the 3′ terminus of N2-(N′)y are joined by three 2′-5′ phosphodiester bonds, wherein one or more of the 2′-5′ nucleotides which form the 2′-5′ phosphodiester bonds further comprises a 3′-O-methyl (3′OMe) sugar modification. In some embodiments the 3′ terminal nucleotide of N2-(N′)y comprises a 2′OMe sugar modification. In certain embodiments x=y=18 and N2-(N′)y comprises two or more consecutive nucleotides at positions 15, 16, 17, 18 and 19 comprise a nucleotide joined to an adjacent nucleotide by a 2′-5′ internucleotide bond. In various embodiments the nucleotide forming the 2′-5′ internucleotide bond comprises a 3′ deoxyribose nucleotide or a 3′ methoxy nucleotide. In some embodiments x=y=18 and N2-(N′)y comprises nucleotides joined to the adjacent nucleotide by a 2′-5′ internucleotide bond between positions 16-17 and 17-18 or between positions 17-18 and 18-19 or between positions 15-16 and 17-18. In other embodiments the pyrimidine ribonucleotides (rU, rC) in (N′)y comprise nucleotides joined to the adjacent nucleotide by a 2′-5′ internucleotide bond.

In further embodiments of Structures A1 and A2 (N′)y comprises 1-8 modified ribonucleotides wherein the modified ribonucleotide is a deoxyribose (DNA) nucleotide. In certain embodiments (N′)y comprises 1, 2, 3, 4, 5, 6, 7, or up to 8 DNA moieties. In further embodiments of Structures A1 and A2 (N′)y includes 1-8 modified ribonucleotides wherein the modified ribonucleotide is a DNA nucleotide. In certain embodiments (N′)y includes 1, 2, 3, 4, 5, 6, 7, or up to 8 DNA moieties.

In some embodiments either Z or Z′ is present and independently includes two non-nucleotide moieties.

In additional embodiments Z and Z′ are present and each independently includes two non-nucleotide moieties.

In some embodiments each of Z and Z′ includes an abasic moiety, for example a deoxyriboabasic moiety (referred to herein as “dAb”) or riboabasic moiety (referred to herein as “rAb”). In some embodiments each of Z and/or Z′ includes two covalently linked abasic moieties and is for example dAb-dAb or rAb-rAb or dAb-rAb or rAb-dAb, wherein each moiety is covalently attached to an adjacent moiety, preferably via a phospho-based bond. In some embodiments the phospho-based bond includes a phosphorothioate, a phosphonoacetate or a phosphodiester bond. In preferred embodiments the phospho-based bond includes a phosphodiester bond.

In some embodiments each of Z and/or Z′ independently includes an alkyl moiety, optionally propane [(CH2)3] moiety (C3) or a derivative thereof including propanol (C3-OH) and phospho derivative of propanediol (“C3-3′Pi”). In some embodiments each of Z and/or Z′ includes two alkyl moieties and in some examples is C3-C3-OH. The 3′ terminus of the antisense strand and/or the 3′ terminus of the sense strand is covalently attached to a C3 moiety via a phospho-based bond and the C3 moiety is covalently conjugated a C3-OH moiety via a phospho-based bond. In some embodiments the phospho-based bonds include a phosphorothioate, a phosphonoacetate or a phosphodiester bond. In preferred embodiments the phospho-based bond includes a phosphodiester bond.

In one specific embodiment of Structure A1 or Structure A2, Z includes C3-C3-OH (a propyl moiety covalently linked to a propanol moiety via a phosphodiester bond). In some embodiments Z includes a propanol moiety covalently attached to the 3′ terminus of the antisense strand via a phosphodiester bond. In some embodiments the C3-C3-OH overhang is covalently attached to the 3′ terminus of (N)x or (N′)y via covalent linkage, for example a phosphodiester linkage. In some embodiments the linkage between a first C3 and a second C3 is a phosphodiester linkage.

In various embodiments the alkyl moiety is a C3 alkyl (“C3”) to C6 alkyl (“C6”) (e.g. C3, C4, C5 or C6) moiety including a terminal hydroxyl, a terminal amino, terminal phosphate group.

In some embodiments the alkyl moiety is a C3 alkyl moiety. In some embodiments the C3 alkyl moiety includes propanol, propylphosphate, propylphosphorothioate or a combination thereof.

The C3 alkyl moiety may be covalently linked to the 3′ terminus of (N′)y and or the 3′ terminus of (N)x via a phosphodiester bond. In some embodiments the alkyl moiety includes propanol, propyl phosphate (trimethyl phosphate) or propyl phosphorothioate (trimethyl phosphorothioate).

In some embodiments each of Z and Z′ is independently selected from propanol, propyl phosphate (trimethyl phosphate), propyl phosphorothioate (trimethyl phosphorothioate), combinations thereof or multiples thereof.

In some embodiments each of Z and Z′ is independently selected from propyl phosphate (trimethyl phosphate), propyl phosphorothioate (trimethyl phosphorothioate), propyl phospho-propanol; propyl phospho-propyl phosphorothioate; propylphospho-propyl phosphate; (propyl phosphate)3, (propyl phosphate)2-propanol, (propyl phosphate)2-propyl phosphorothioate. Any propane or propanol conjugated moiety can be included in Z or Z′.

In additional embodiments each of Z and/or Z′ includes a combination of an abasic moiety and an unmodified deoxyribonucleotide or ribonucleotide or a combination of a hydrocarbon moiety and an unmodified deoxyribonucleotide or ribonucleotide or a combination of an abasic moiety (deoxyribo or ribo) and a hydrocarbon moiety. In such embodiments, each of Z and/or Z′ includes C3-rAb or C3-dAb wherein each moiety is covalently bond to the adjacent moiety via a phospho-based bond, preferably a phosphodiester, phosphorothioate or phosphonoacetate bond.

In certain embodiments nucleic acid molecules as disclosed herein include a sense oligonucleotide sequence selected from any one of Tables A1-B8.

In some embodiments, provided is a tandem structure and a triple armed structure, also known as RNAstar. Such structures are disclosed in PCT patent publication WO 2007/091269. A tandem oligonucleotide comprises at least two siRNA compounds.

A triple-stranded oligonucleotide may be an oligoribonucleotide having the general structure:

5′ oligo1 (sense)
LINKER A
Oligo2 (sense) 3′

3′ oligo1 (antisense)
LINKER B
Oligo3 (sense) 5′

3′ ligo3 (antisense)
LINKER C
oligo2 (antisense) 5′

or

5′ oligo1 (sense)
LINKER A
Oligo2 (antisense) 3′

3′ oligo1 (antisense)
LINKER B
Oligo3 (sense) 5′

3′ oligo3 (antisense)
LINKER C
oligo2 (sense) 5′

or

5′ oligo1 (sense)
LINKER A
oligo3 (antisense) 3′

3′ oligo1 (antisense)
LINKER B
oligo2 (sense) 5′

5′ oligo3 (sense)
LINKER C
oligo2 (antisense) 3′

wherein one or more of linker A, linker B or linker C is present; any combination of two or more oligonucleotides and one or more of linkers A-C is possible, so long as the polarity of the strands and the general structure of the molecule remains. Further, if two or more of linkers A-C are present, they may be identical or different.

In some embodiments a “gapped” RNAstar compound is preferred wherein the compound consists of four ribonucleotide strands forming three siRNA duplexes having the general structure as follows:

embedded image

wherein each of oligo A, oligo B, oligo C, oligo D, oligo E and oligo F represents at least 19 consecutive ribonucleotides, wherein from 19 to 40 of such consecutive ribonucleotides, in each of oligo A, B, C, D, E and F comprise a strand of a siRNA duplex, wherein each ribonucleotide may be modified or unmodified;

wherein strand 1 comprises oligo A which is either a sense portion or an antisense portion of a first siRNA duplex of the compound, strand 2 comprises oligo B which is complementary to at least 19 nucleotides in oligo A, and oligo A and oligo B together form a first siRNA duplex that targets a first target mRNA;

wherein strand 1 further comprises oligo C which is either a sense portion or an antisense strand portion of a second siRNA duplex of the compound, strand 3 comprises oligo D which is complementary to at least 19 nucleotides in oligo C and oligo C and oligo D together form a second siRNA duplex that targets a second target mRNA;

wherein strand 4 comprises oligo E which is either a sense portion or an antisense strand portion of a third siRNA duplex of the compound, strand 2 further comprises oligo F which is complementary to at least 19 nucleotides in oligo E and oligo E and oligo F together form a third siRNA duplex that targets a third target mRNA; and

wherein linker A is a moiety that covalently links oligo A and oligo C; linker B is a moiety that covalently links oligo B and oligo F, and linker A and linker B can be the same or different.

In some embodiments the first, second and third siRNA duplex target the same gene, In other embodiments two of the first, second or third siRNA duplexes target the same mRNA and the third siRNA duplex targets a different mRNA. In some embodiments each of the first, second and third duplex targets a different mRNA.

In another aspect, provided are methods for reducing the expression of TIMP1 and TIMP2 in a cell by introducing into a cell a nucleic acid molecule as provided herein in an amount sufficient to reduce expression of TIMP1 and TIMP2. In one embodiment, the cell is hepatocellular stellate cell. In another embodiment, the cell is a stellate cell in renal or pulmonary tissue. In certain embodiments, the method is performed in vitro, in other embodiments, the method is performed in vivo.

In yet another aspect, provided are methods for treating an individual suffering from a disease associated with TIMP1 and/or TIMP2. The methods include administering to the individual a nucleic acid molecule such as provided herein in an amount sufficient to reduce expression of TIMP1 or TIMP2. In certain embodiments the disease associated with TIMP1 or TIMP2 is a disease selected from the group consisting of liver fibrosis, cirrhosis, pulmonary fibrosis including lung fibrosis (including ILF), any condition causing kidney fibrosis (e.g., CKD including ESRD), peritoneal fibrosis, chronic hepatic damage, fibrillogenesis, fibrotic diseases in other organs, abnormal scarring (keloids) associated with all possible types of skin injury accidental and jatrogenic (operations); scleroderma; cardiofibrosis, fibrosis in the brain; failure of glaucoma filtering operation; and intestinal adhesions. The compounds are useful in treating organ specific indications including those shown in Table I below:

TABLE I

Organ
Indication

Skin
Pathologic scarring as keloid and hypertrophic scar

Surgical scarring

Injury scarring

keloid, or nephrogenic fibrosing dermatopathy

Peritoneum
Peritoneal fibrosis

Adhesions

Peritoneal Sclerosis associated with continual ambulatory peritoneal dialysis

(CAPD)

Liver
Cirrhosis including post-hepatitis C cirrhosis, primary biliary cirrhosis

Liver fibrosis, e.g. Prevention of Liver Fibrosis in Hepatitis C carriers

schistomasomiasis

cholangitis

Liver cirrhosis due to Hepatitis C post liver transplant or Non-Alcoholic

Steatohepatitis (NASH)

Pancreas
inter(peri)lobular fibrosis (as in alcoholic chronic pancreatitis), periductal

fibrosis (as in hereditary pancreatitis), periductal and interlobular fibrosis (as

in autoimmune pancreatitis), diffuse inter- and intralobular fibrosis (as in

obstructive chronic pancreatitis)

Kidney
Chronic Kidney Disease (CKD) of any etiology. Treatment of early stage

CKD (elevated SCr) in diabetic patients (“prevent” further deterioration in

renal function)

kidney fibrosis associated with lupus glomeruloschelerosis

Diabetic Nephropathy

Heart
Congestive heart failure,

Endomyocardial fibrosis,

cardiofibrosis

fibrosis associated with myocardial infarction

Lung
Asthma, Idiopathic pulmonary fibrosis (IPF); Radiation fibrosis, a sequel of

radiation pneumonitis (e.g. due to cancer treating radiation)

Interstitial lung fibrosis (ILF)

Radiation Pneumonitis leading to Pulmonary Fibrosis (e.g. due to cancer

treating radiation)

Bone marrow
Myeloproliferative disorders: Myelofibrosis (MF), Polycythemia vera (PV),

Essential thrombocythemia (ET)

idiopathic myelofibrosis

drug induced myelofibrosis.

Eye
Anterior segment: Corneal opacification e,g, following inherited dystrophies,

herpetic keratitis or pterygia; Glaucoma

Posterior segment fibrosis and traction retinal detachment, a complication of

advanced diabetic retinopathy (DR); Fibrovascular scarring and gliosis in the

retina;

Under the retina fibrosis for example subsequent to subretinal hemorrhage

associated with neovascular AMD

Retro-orbital fibrosis, postcataract surgery, proliferative vitreoretinopathy.

Ocular cicatricial pemphigoid

Intestine
Intestinal fibrosis, Crohn's disease

Vocal cord
Vocal cord scarring, vocal cord mucosal fibrosis, laryngeal fibrosis

Vasculature
Atherosclerosis, postangioplasty arterial restenosis

Brain
Fibrosis associated with brain (cerebral) infarction

Multisystemic
Scleroderma systemic sclerosis; multifocal fibrosclerosis; sclerodermatous

graft-versus-host disease in bone marrow transplant recipients, and

nephrogenic systemic fibrosis (exposure to gadolinium-based contrast agents

(GBCAs), 30% of MRIs)

Malignancies
Metastatic and invasive cancer by inhibiting function of activated tumor

of various
associated myofibroblasts

origin

In some embodiments the preferred indications include, Liver cirrhosis due to Hepatitis C post liver transplant; Liver cirrhosis due to Non-Alcoholic Steatohepatitis (NASH); Idiopathic Pulmonary Fibrosis (IPF); Radiation Pneumonitis leading to Pulmonary Fibrosis; Diabetic Nephropathy; Peritoneal Sclerosis associated with continual ambulatory peritoneal dialysis (CAPD) and Ocular cicatricial pemphigoid.

Fibrotic Liver indications include Alcoholic Cirrhosis, Hepatitis B cirrhosis, Hepatitis C cirrhosis, Hepatitis C (Hep C) cirrhosis post orthotopic liver transplant (OLTX), NASH/NAFLD wherein NASH is an extreme form of nonalcoholic fatty liver disease (NAFLD), Primary biliary cirrhosis (PBC), Primary sclerosing cholangitis (PSC), Biliary atresia, alpha1 antitrypsin deficiency (A1AD), Copper storage diseases (Wilson's disease), Fructosemia, Galactosemia, Glycogen storage diseases (especially types III, IV, VI, IX, and X), Iron-overload syndromes (hemochromatosis), Lipid abnormalities (e.g., Gaucher's disease). Peroxisomal disorders (eg, Zellweger syndrome), Tyrosinemia, Congenital hepatic fibrosis, Bacterial Infections (eg, brucellosis), Parasitic (eg, echinococcosis), Budd-Chiari syndrome (hepatic veno-occlusive disease).

Pulmonary Indications include Idiopathic Pulmonary Fibrosis, Silicosis, Pneumoconiosis, Bronchopulmonary Dysplasia in newborn following neonatal respiratory distress syndrome, Bleomycin/chemotherapeutic induced lung injury, Brochiolitis Obliterans (BOS) post lung transplant, Chronic obstructive pulmonary disorder (COPD), Cystic Fibrosis, Asthma.

Cardiac indications include Cardiomyopathy, Atherosclerosis (Bergers disease, etc), Endomyocardial fibrosis, Atrial Fibrillation, Scarring post Myocardial Infarction (MI).

Other Thoracic indications include Radiation-induced capsule tissue reactions around textured breast implants and Oral submucosal fibrosis.

Renal indications include Autosomal Dominant Polycystic Kidney Disease (ADPKD), Diabetic nephropathy (diabetic glomerulosclerosis), FSGS (collapsing vs. other histologic variants), IgA Nephropathy (Berger Disease), Lupus Nephritis, Wegner's, Scleroderma, Goodpasture Syndrome, tubulointerstitial fibrosis: drug induced (protective) pencillins, cephalosporins, analgesic nephropathy, Membranoproliferative glomerulonephritis (MPGN), Henoch-Schonlein Purpura, Congenital nephropathies: Medullary Cystic Disease, Nail-Patella Syndrome and Alport Syndrome.

Bone Marrow indications include lympangiolyomyositosis (LAM), Chronic graft vs. host disease, Polycythemia vera, Essential thrombocythemia, Myelofibrosis.

Ocular indications include Retinopathy of Prematurity (RoP), Ocular cicatricial pemphigoid, Lacrimal gland fibrosis, Retinal attachment surgery, Corneal opacity, Herpetic keratitis, Pterygia, Glaucoma, Age-related macular degeneration (AMD/ARMD), Retinal fibrosis associated Diabetes mellitus (DM) retinopathy.

Brain indications include fibrosis associated with brain infarction.

Gynecological indications include Endometriosis add on to hormonal therapy for prevention of scarring, post STD fibrosis/salphingitis.

Systemic indications include Dupuytren's disease, palmar fibromatosis, Peyronie's disease, Ledderhose disease, keloids, multifocal fibrosclerosis, nephrogenic systemic fibrosis, nephrogenic myelofibrosis (anemia).

Injury Associated Fibrotic Diseases include Burn (chemical included) induced skin & soft tissue scarring and contraction, Radiation induce skin & organ scarring post cancer therapeutic radiation treatment, Keloid (skin).

Surgical indications include peritoneal fibrosis post peritoneal dialysis catheter, corneal implant, cochlear implant, other implants, silicone implants in breasts, chronic sinusitis; adhesions, pseudointimal hyperplasia of dialysis grafts.

Other indications include Chronic Pancreatitis.

In some embodiments the methods include administering to the individual a nucleic acid molecule such as provided herein in an amount sufficient to reduce expression of TIMP1. In some embodiments the methods include administering to the individual a nucleic acid molecule such as provided herein in an amount sufficient to reduce expression of TIMP2. In some embodiments the methods include administering to the individual nucleic acid molecules such as provided herein in an amount sufficient to reduce expression of TIMP1. In some embodiments the methods include administering to the individual nucleic acid molecules such as provided herein in an amount sufficient to reduce expression of TIMP2. In some embodiments provided is a nucleic acid disclosed herein for the treatment of a fibrotic disease selected from a disease or disorder set forth in Table I. In another embodiment provided is a nucleic acid molecule for use in therapy. In some embodiments therapy comprises treatment of a fibrotic disease or disorder set forth in Table I. In some embodiments provided is use of a nucleic acid molecule disclosed herein for the preparation of a medicament useful in treating a fibrotic disease or disorder set forth in Table I. In some embodiments the nucleic acid molecule is set forth in Table C, e.g. TIMP1-A, TIMP1-B, TIMP1-C. In some embodiments the nucleic acid molecule is set forth in Table D, e.g. TIMP2-A, TIMP2-B, TIMP2-C, TIMP2-D, TIMP2-E. In some embodiments the sense and antisense sequences of the nucleic acid molecule are selected from the sequence pairs set forth in any one of Table A3, Table A4, Table A7 or Table A8. In some embodiments the sense and antisense sequences of the nucleic acid molecule are selected from the sequence pairs set forth in any one of Table B3, Table B4, Table B7 or Table B8.

In one aspect, provided are pharmaceutical compositions that include a nucleic acid molecule (e.g., an siNA molecule) as described herein in a pharmaceutically acceptable carrier. In certain embodiments, the pharmaceutical formulation includes, or involves, a delivery system suitable for delivering nucleic acid molecules (e.g., siNA molecules) to an individual such as a patient; for example delivery systems described in more detail below.

In a related aspect, provided are compositions or kits that include a nucleic acid molecule (e.g., an siNA molecule) packaged for use by a patient. The package may be labeled or include a package label or insert that indicates the content of the package and provides certain information regarding how the nucleic acid molecule (e.g., an siNA molecule) should be or can be used by a patient, for example the label may include dosing information and/or indications for use. In certain embodiments the contents of the label will bear a notice in a form prescribed by a government agency, for example the United States Food and Drug Administration (FDA). In certain embodiments, the label may indicate that the nucleic acid molecule (e.g., an siNA molecule) is suitable for use in treating a patient suffering from a disease associated with TIMP1 or TIMP2; for example, the label may indicate that the nucleic acid molecule (e.g., an siNA molecule) is suitable for use in treating fibroids; or for example the label may indicate that the nucleic acid molecule (e.g., an siNA molecule) is suitable for use in treating a disease selected from the group consisting of fibrosis, liver fibrosis, cirrhosis, pulmonary fibrosis, kidney fibrosis, peritoneal fibrosis, chronic hepatic damage, and fibrillogenesis.

As used herein, the term “tissue inhibitor of metalloproteinases 1” or “TIMP1” are used interchangeably and refer to any tissue inhibitor of metalloproteinases 1 peptide, or polypeptide having any TIMP1 protein activity. Tissue inhibitor of metalloproteinases 1 is a natural inhibitor of matrix metalloproteinases. In certain preferred embodiments, “TIMP1” refers to human TIMP1. Tissue inhibitor of metalloproteinases 1 (or more particularly human TIMP1) may have an amino acid sequence that is the same, or substantially the same, as SEQ ID NO. 3 (FIG. 1C).

As used herein, the term “tissue inhibitor of metalloproteinases 2” or “TIMP2” are used interchangeably and refer to any tissue inhibitor of metalloproteinases 2 peptide, or polypeptide having any TIMP2 protein activity. Tissue inhibitor of metalloproteinases 2 (or more particularly human TIMP2) may have an amino acid sequence that is the same, or substantially the same, as SEQ ID NO. 4 (FIG. 1D).

As used herein the term “nucleotide sequence encoding TIMP1 and TIMP2” means a nucleotide sequence that codes for a TIMP1 and TIMP2 protein or portion thereof. The term “nucleotide sequence encoding TIMP1 and TIMP2” is also meant to include TIMP1 and TIMP2 coding sequences such as TIMP1 and TIMP2 isoforms, mutant TIMP1 and TIMP2 genes, splice variants of TIMP1 and TIMP2 genes, and TIMP1 and TIMP2 gene polymorphisms. A nucleic acid sequence encoding TIMP1 and TIMP2 includes mRNA sequences encoding TIMP1 and TIMP2, which can also be referred to as “TIMP1 and TIMP2 mRNA.” Exemplary sequences of human TIMP1 mRNA and TIMP2 mRNA are set forth as SEQ ID. NO. 1 and SEQ ID NO:2, respectively.

As used herein, the term “nucleic acid molecule” or “nucleic acid” are used interchangeably and refer to an oligonucleotide, nucleotide or polynucleotide. Variations of “nucleic acid molecule” are described in more detail herein. A nucleic acid molecule encompasses both modified nucleic acid molecules and unmodified nucleic acid molecules as described herein. A nucleic acid molecule may include deoxyribonucleotides, ribonucleotides, modified nucleotides or nucleotide analogs in any combination.

As used herein, the term “nucleotide” refers to a chemical moiety having a sugar (or an analog thereof, or a modified sugar), a nucleotide base (or an analog thereof, or a modified base), and a phosphate group (or analog thereof, or a modified phosphate group). A nucleotide encompasses both modified nucleotides or unmodified nucleotides as described herein. As used herein, nucleotides may include deoxyribonucleotides (e.g., unmodified deoxyribonucleotides), ribonucleotides (e.g., unmodified ribonucleotides), and modified nucleotide analogs including, inter alia, locked nucleic acids and unlocked nucleic acids, peptide nucleic acids, L-nucleotides (also referred to as mirror nucleotides), ethylene-bridged nucleic acid (ENA), arabinoside, PACE, nucleotides with a 6 carbon sugar, as well as nucleotide analogs (including abasic nucleotides) often considered to be non-nucleotides. In some embodiments, nucleotides may be modified in the sugar, nucleotide base and/or in the phosphate group with any modification known in the art, such as modifications described herein. A “polynucleotide” or “oligonucleotide” as used herein refer to a chain of linked nucleotides; polynucleotides and oligonucleotides may likewise have modifications in the nucleotide sugar, nucleotide bases and phosphate backbones as are well known in the art and/or are disclosed herein.

As used herein, the term “short interfering nucleic acid”, “siNA”, or “short interfering nucleic acid molecule” refers to any nucleic acid molecule capable of modulating gene expression or viral replication. Preferably siNA inhibits or down regulates gene expression or viral replication. siNA includes without limitation nucleic acid molecules that are capable of mediating sequence specific RNAi, for example short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), short hairpin RNA (shRNA), short interfering oligonucleotide, short interfering nucleic acid, short interfering modified oligonucleotide, chemically-modified siRNA, post-transcriptional gene silencing RNA (ptgsRNA), and others. As used herein, “short interfering nucleic acid”, “siNA”, or “short interfering nucleic acid molecule” has the meaning described in more detail elsewhere herein.

As used herein, the term “complementary” means that a nucleic acid can form hydrogen bond(s) with another nucleic acid sequence by either traditional Watson-Crick or other non-traditional types. In reference to the nucleic molecules disclosed herein, the binding free energy for a nucleic acid molecule with its complementary sequence is sufficient to allow the relevant function of the nucleic acid to proceed, e.g., RNAi activity. Determination of binding free energies for nucleic acid molecules is well known in the art (see, e.g., Turner et al., 1987, CSH Symp. Quant. Biol. LII pp. 123-133; Frier et al., 1986, Proc. Nat. Acad. Sci. USA 83:9373-9377; Turner et al., 1987, J. Am. Chem. Soc. 109:3783-3785). A percent complementarity indicates the percentage of contiguous residues in a nucleic acid molecule that can form hydrogen bonds (e.g., Watson-Crick base pairing) with a second nucleic acid sequence (e.g., 5, 6, 7, 8, 9, or 10 nucleotides out of a total of 10 nucleotides in the first oligonucleotide being based paired to a second nucleic acid sequence having 10 nucleotides represents 50%, 60%, 70%, 80%, 90%, and 100% complementary respectively). “Fully complementary” means that all the contiguous residues of a nucleic acid sequence will hydrogen bond with the same number of contiguous residues in a second nucleic acid sequence. In one embodiment, a nucleic acid molecule disclosed herein includes about 15 to about 35 or more (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34 or 35 or more) nucleotides that are complementary to one or more target nucleic acid molecules or a portion thereof.

As used herein, the term “sense region” refers to a nucleotide sequence of a siNA molecule complementary (partially or fully) to an antisense region of the siNA molecule. The sense strand of a siNA molecule can include a nucleic acid sequence having homology with a target nucleic acid sequence. As used herein, “sense strand” refers to nucleic acid molecule that includes a sense region and may also include additional nucleotides.

As used herein, the term “antisense region” refers to a nucleotide sequence of a siNA molecule complementary (partially or fully) to a target nucleic acid sequence. The antisense strand of a siNA molecule can optionally include a nucleic acid sequence complementary to a sense region of the siNA molecule. As used herein, “antisense strand” refers to nucleic acid molecule that includes an antisense region and may also include additional nucleotides.

As used herein, the term “RNA” refers to a molecule that includes at least one ribonucleotide residue.

As used herein, the term “duplex region” refers to the region in two complementary or substantially complementary oligonucleotides that form base pairs with one another, either by Watson-Crick base pairing or any other manner that allows for a duplex between oligonucleotide strands that are complementary or substantially complementary. For example, an oligonucleotide strand having 21 nucleotide units can base pair with another oligonucleotide of 21 nucleotide units, yet only 19 bases on each strand are complementary or substantially complementary, such that the “duplex region” consists of 19 base pairs. The remaining base pairs may, for example, exist as 5′ and 3′ overhangs. Further, within the duplex region, 100% complementarity is not required; substantial complementarity is allowable within a duplex region. Substantial complementarity refers to complementarity between the strands such that they are capable of annealing under biological conditions. Techniques to empirically determine if two strands are capable of annealing under biological conditions are well know in the art. Alternatively, two strands can be synthesized and added together under biological conditions to determine if they anneal to one another.

As used herein, the terms “non-pairing nucleotide analog” means a nucleotide analog which includes a non-base pairing moiety including but not limited to: 6 des amino adenosine (Nebularine), 4-Me-indole, 3-nitropyrrole, 5-nitroindole, Ds, Pa, N3-Me ribo U, N3-Me riboT, N3-Me dC, N3-Me-dT, N1-Me-dG, N1-Me-dA, N3-ethyl-dC, N3-Me dC. In some embodiments the non-base pairing nucleotide analog is a ribonucleotide. In other embodiments it is a deoxyribonucleotide.

As used herein, the term, “terminal functional group” includes without limitation a halogen, alcohol, amine, carboxylic, ester, amide, aldehyde, ketone, ether groups.

An “abasic nucleotide” or “abasic nucleotide analog” is as used herein may also be often referred to herein and in the art as a pseudo-nucleotide or an unconventional moiety. While a nucleotide is a monomeric unit of nucleic acid, generally consisting of a ribose or deoxyribose sugar, a phosphate, and a base (adenine, guanine, thymine, or cytosine in DNA; adenine, guanine, uracil, or cytosine in RNA). an abasic or pseudo-nucleotide lacks a base, and thus is not strictly a nucleotide as the term is generally used in the art. Abasic deoxyribose moieties include for example, abasic deoxyribose-3′-phosphate; 1,2-dideoxy-D-ribofuranose-3-phosphate; 1,4-anhydro-2-deoxy-D-ribitol-3-phosphate. Inverted abasic deoxyribose moieties include inverted deoxyriboabasic; 3′,5′ inverted deoxyabasic 5′-phosphate.

The term “capping moiety” (z″) as used herein includes a moiety which can be covalently linked to the 5′ terminus of (N′)y and includes abasic ribose moiety, abasic deoxyribose moiety, modifications abasic ribose and abasic deoxyribose moieties including 2′ O alkyl modifications; inverted abasic ribose and abasic deoxyribose moieties and modifications thereof; C6-imino-Pi; a mirror nucleotide including L-DNA and L-RNA; 5′OMe nucleotide; and nucleotide analogs including 4′,5′-methylene nucleotide; 1-(P3-D-erythrofuranosyl)nucleotide; 4′-thio nucleotide, carbocyclic nucleotide; 5′-amino-alkyl phosphate; 1,3-diamino-2-propyl phosphate, 3-aminopropyl phosphate; 6-aminohexyl phosphate; 12-aminododecyl phosphate; hydroxypropyl phosphate; 1,5-anhydrohexitol nucleotide; alpha-nucleotide; threo-pentofuranosyl nucleotide; acyclic 3′,4′-seco nucleotide; 3,4-dihydroxybutyl nucleotide; 3,5-dihydroxypentyl nucleotide, 5′-5′-inverted abasic moiety; 1,4-butanediol phosphate; 5′-amino; and bridging or non bridging methylphosphonate and 5′-mercapto moieties.

Certain capping moieties may be abasic ribose or abasic deoxyribose moieties; inverted abasic ribose or abasic deoxyribose moieties; C6-amino-Pi; a mirror nucleotide including L-DNA and L-RNA. The nucleic acid molecules as disclosed herein may be synthesized using one or more inverted nucleotides, for example inverted thymidine or inverted adenine (for example see Takei, et al., 2002. JBC 277(26):23800-06).

The term “unconventional moiety” as used herein refers to non-nucleotide moieties including an abasic moiety, an inverted abasic moiety, a hydrocarbon (alkyl) moiety and derivatives thereof, and further includes a deoxyribonucleotide, a modified deoxyribonucleotide, a mirror nucleotide (L-DNA or L-RNA), a non-base pairing nucleotide analog and a nucleotide joined to an adjacent nucleotide by a 2′-5′ internucleotide phosphate bond; bridged nucleic acids including LNA and ethylene bridged nucleic acids, linkage modified (e.g. PACE) and base modified nucleotides as well as additional moieties explicitly disclosed herein as unconventional moieties.

As used herein, the term “inhibit”, “down-regulate”, or “reduce” with respect to gene expression means the expression of the gene, or level of RNA molecules or equivalent RNA molecules encoding one or more proteins or protein subunits (e.g., mRNA), or activity of one or more proteins or protein subunits, is reduced below that observed in the absence of an inhibitory factor (such as a nucleic acid molecule, e.g., an siNA, for example having structural features as described herein); for example the expression may be reduced to 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, 5% or less than that observed in the absence of an inhibitor.

BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A-1D show exemplary polynucleotide and polypeptide sequences. FIG. 1A shows mRNA sequence of human TIMP1 (NM_003254.2 GI:73858576; SEQ ID NO:1). FIG. 1B shows mRNA sequence of TIMP2 (NM_003255.4 GI:738585774; SEQ ID NO:2). FIG. 1C shows polypeptide sequence of human TIMP1 (NP_003245.1 GI:4507509; SEQ ID NO:3). FIG. 1D shows polypeptide sequence of human TIMP2 (NP_003246.1 GI:4507511; SEQ ID NO:4).

FIG. 2 shows knock down efficacy as determined by qPCR of TIMP1-A, TIMP1-B or TIMP1-C siRNAs (Table C) for TIMP1. The siRNA compounds were capable of knocking down the target TIMP1 gene.

FIG. 3 shows knock down efficacy as determined by qPCR TIMP2-A, TIMP2-B, TIMP2-C, TIMP2-D and TIMP2-E siRNAs (Table D). The siRNA compounds were capable of knocking down the target TIMP2 gene.

FIG. 4 shows the results of an in vivo assay testing the efficacy of siTIMP1 and siTIMP2 in treating liver fibrosis. Analysis of the liver fibrosis area was performed using Sirius red staining. The fibrotic area was calculated as the mean of 4 liver sections. The bar graph summarizes the digital quantification of staining for each group.

DETAILED DESCRIPTION OF THE INVENTION

RNA Interference and siNA Nucleic Acid Molecules

RNA interference refers to the process of sequence-specific post-transcriptional gene silencing in animals mediated by short interfering RNAs (siRNAs) (Zamore et al., 2000, Cell, 101, 25-33; Fire et al., 1998, Nature, 391, 806; Hamilton et al., 1999, Science, 286, 950-951; Lin et al., 1999, Nature, 402, 128-129; Sharp, 1999, Genes & Dev., 13:139-141; and Strauss, 1999, Science, 286, 886). The corresponding process in plants (Heifetz et al., International PCT Publication No. WO 99/61631) is often referred to as post-transcriptional gene silencing (PTGS) or RNA silencing. The process of post-transcriptional gene silencing is thought to be an evolutionarily-conserved cellular defense mechanism used to prevent the expression of foreign genes (Fire et al., 1999, Trends Genet., 15, 358). Such protection from foreign gene expression may have evolved in response to the production of double-stranded RNAs (dsRNAs) derived from viral infection or from the random integration of transposon elements into a host genome via a cellular response that specifically destroys homologous single-stranded RNA or viral genomic RNA. The presence of dsRNA in cells triggers the RNAi response through a mechanism that has yet to be fully characterized. This mechanism appears to be different from other known mechanisms involving double stranded RNA-specific ribonucleases, such as the interferon response that results from dsRNA-mediated activation of protein kinase PKR and 2′,5′-oligoadenylate synthetase resulting in non-specific cleavage of mRNA by ribonuclease L (see for example U.S. Pat. Nos. 6,107,094; 5,898,031; Clemens et al., 1997, J. Interferon & Cytokine Res., 17, 503-524; Adah et al., 2001, Curr. Med. Chem., 8, 1189).

The presence of long dsRNAs in cells stimulates the activity of a ribonuclease III enzyme referred to as dicer (Bass, 2000, Cell, 101, 235; Zamore et al., 2000, Cell, 101, 25-33; Hammond et al., 2000, Nature, 404, 293). Dicer is involved in the processing of the dsRNA into short pieces of dsRNA known as short interfering RNAs (siRNAs) (Zamore et al., 2000, Cell, 101, 25-33; Bass, 2000, Cell, 101, 235; Berstein et al., 2001, Nature, 409, 363). Short interfering RNAs derived from dicer activity are typically about 21 to about 23 nucleotides in length and include about 19 base pair duplexes (Zamore et al., 2000, Cell, 101, 25-33; Elbashir et al., 2001, Genes Dev., 15, 188). Dicer has also been implicated in the excision of 21- and 22-nucleotide small temporal RNAs (stRNAs) from precursor RNA of conserved structure that are implicated in translational control (Hutvagner et al., 2001, Science, 293, 834). The RNAi response also features an endonuclease complex, commonly referred to as an RNA-induced silencing complex (RISC), which mediates cleavage of single-stranded RNA having sequence complementary to the antisense strand of the siRNA duplex. Cleavage of the target RNA takes place in the middle of the region complementary to the antisense strand of the siRNA duplex (Elbashir et al., 2001, Genes Dev., 15, 188).

RNAi has been studied in a variety of systems. Fire et al., 1998, Nature, 391, 806, were the first to observe RNAi in C. elegans. Bahramian and Zarbl, 1999, Molecular and Cellular Biology, 19, 274-283 and Wianny and Goetz, 1999, Nature Cell Biol., 2, 70, describe RNAi mediated by dsRNA in mammalian systems. Hammond et al., 2000, Nature, 404, 293, describe RNAi in Drosophila cells transfected with dsRNA. Elbashir et al., 2001, Nature, 411, 494 and Tuschl et al., International PCT Publication No. WO 01/75164, describe RNAi induced by introduction of duplexes of synthetic 21-nucleotide RNAs in cultured mammalian cells including human embryonic kidney and HeLa cells. Recent work in Drosophila embryonic lysates (Elbashir et al., 2001, EMBO J., 20, 6877 and Tuschl et al., International PCT Publication No. WO 01/75164) has revealed certain requirements for siRNA length, structure, chemical composition, and sequence that are essential to mediate efficient RNAi activity.

Nucleic acid molecules (for example having structural features as disclosed herein) may inhibit or down regulate gene expression or viral replication by mediating RNA interference “RNAi” or gene silencing in a sequence-specific manner; see e.g., Zamore et al., 2000, Cell, 101, 25-33; Bass, 2001, Nature, 411, 428-429; Elbashir et al., 2001, Nature, 411, 494-498; and Kreutzer et al., International PCT Publication No. WO 00/44895; Zernicka-Goetz et al., International PCT Publication No. WO 01/36646; Fire, International PCT Publication No. WO 99/32619; Plaetinck et al., International PCT Publication No. WO 00/01846; Mello and Fire, International PCT Publication No. WO 01/29058; Deschamps-Depaillette, International PCT Publication No. WO 99/07409; and Li et al., International PCT Publication No. WO 00/44914; Allshire, 2002, Science, 297, 1818-1819; Volpe et al., 2002, Science, 297, 1833-1837; Jenuwein, 2002, Science, 297, 2215-2218; and Hall et al., 2002, Science, 297, 2232-2237; Hutvagner and Zamore, 2002, Science, 297, 2056-60; McManus et al., 2002, RNA, 8, 842-850; Reinhart et al., 2002, Gene & Dev., 16, 1616-1626; and Reinhart & Bartel, 2002, Science, 297, 1831).

An siNA nucleic acid molecule can be assembled from two separate polynucleotide strands, where one strand is the sense strand and the other is the antisense strand in which the antisense and sense strands are self-complementary (i.e. each strand includes nucleotide sequence that is complementary to nucleotide sequence in the other strand); such as where the antisense strand and sense strand form a duplex or double stranded structure having any length and structure as described herein for nucleic acid molecules as provided, for example wherein the double stranded region (duplex region) is about 15 to about 49 (e.g., about 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, or 49 base pairs); the antisense strand includes nucleotide sequence that is complementary to nucleotide sequence in a target nucleic acid molecule (i.e., TIMP1 and TIMP2 mRNA) or a portion thereof and the sense strand includes nucleotide sequence corresponding to the target nucleic acid sequence or a portion thereof (e.g., about 17 to about 49 or more nucleotides of the nucleic acid molecules herein are complementary to the target nucleic acid or a portion thereof).

In certain aspects and embodiments a nucleic acid molecule (e.g., a siNA molecule) provided herein may be a “RISC length” molecule or may be a Dicer substrate as described in more detail below.

An siNA nucleic acid molecule may include separate sense and antisense sequences or regions, where the sense and antisense regions are covalently linked by nucleotide or non-nucleotide linkers molecules as is known in the art, or are alternately non-covalently linked by ionic interactions, hydrogen bonding, van der Waals interactions, hydrophobic interactions, and/or stacking interactions. Nucleic acid molecules may include a nucleotide sequence that is complementary to nucleotide sequence of a target gene. Nucleic acid molecules may interact with nucleotide sequence of a target gene in a manner that causes inhibition of expression of the target gene.

Alternatively, an siNA nucleic acid molecule is assembled from a single polynucleotide, where the self-complementary sense and antisense regions of the nucleic acid molecules are linked by means of a nucleic acid based or non-nucleic acid-based linker(s), i.e., the antisense strand and the sense strand are part of one single polynucleotide that having an antisense region and sense region that fold to form a duplex region (for example to form a “hairpin” structure as is well known in the art). Such siNA nucleic acid molecules can be a polynucleotide with a duplex, asymmetric duplex, hairpin or asymmetric hairpin secondary structure, having self-complementary sense and antisense regions, wherein the antisense region includes nucleotide sequence that is complementary to nucleotide sequence in a separate target nucleic acid molecule or a portion thereof and the sense region having nucleotide sequence corresponding to the target nucleic acid sequence (e.g., a sequence of TIMP1 and TIMP2 mRNA). Such siNA nucleic acid molecules can be a circular single-stranded polynucleotide having two or more loop structures and a stem comprising self-complementary sense and antisense regions, wherein the antisense region includes nucleotide sequence that is complementary to nucleotide sequence in a target nucleic acid molecule or a portion thereof and the sense region having nucleotide sequence corresponding to the target nucleic acid sequence or a portion thereof, and wherein the circular polynucleotide can be processed either in vivo or in vitro to generate an active nucleic acid molecule capable of mediating RNAi.

The following nomenclature is often used in the art to describe lengths and overhangs of siNA molecules and may be used throughout the specification and Examples. Names given to duplexes indicate the length of the oligomers and the presence or absence of overhangs. For example, a “21+2” duplex contains two nucleic acid strands both of which are 21 nucleotides in length, also termed a 21-mer siRNA duplex or a 21-mer nucleic acid and having a 2 nucleotides 3′-overhang. A “21−2” design refers to a 21-mer nucleic acid duplex with a 2 nucleotides 5′-overhang. A 21−0 design is a 21-mer nucleic acid duplex with no overhangs (blunt). A “21+2UU” is a 21-mer duplex with 2-nucleotides 3′-overhang and the terminal 2 nucleotides at the 3′-ends are both U residues (which may result in mismatch with target sequence). The aforementioned nomenclature can be applied to siNA molecules of various lengths of strands, duplexes and overhangs (such as 19−0, 21+2, 27+2, and the like). In an alternative but similar nomenclature, a “25/27” is an asymmetric duplex having a 25 base sense strand and a 27 base antisense strand with a 2-nucleotides 3′-overhang. A “27/25” is an asymmetric duplex having a 27 base sense strand and a 25 base antisense strand.

Chemical Modifications

In certain aspects and embodiments, nucleic acid molecules (e.g., siNA molecules) as provided herein include one or more modifications (or chemical modifications). In certain embodiments, such modifications include any changes to a nucleic acid molecule or polynucleotide that would make the molecule different than a standard ribonucleotide or RNA molecule (i.e., that includes standard adenine, cytosine, uracil, or guanine moieties); which may be referred to as an “unmodified” ribonucleotide or unmodified ribonucleic acid. Traditional DNA bases and polynucleotides having a 2′-deoxy sugar represented by adenine, cytosine, thymine, or guanine moieties may be referred to as an “unmodified deoxyribonucleotide” or “unmodified deoxyribonucleic acid”; accordingly, the term “unmodified nucleotide” or “unmodified nucleic acid” as used herein refers to an “unmodified ribonucleotide” or “unmodified ribonucleic acid” unless there is a clear indication to the contrary. Such modifications can be in the nucleotide sugar, nucleotide base, nucleotide phosphate group and/or the phosphate backbone of a polynucleotide.

In certain embodiments modifications as disclosed herein may be used to increase RNAi activity of a molecule and/or to increase the in vivo stability of the molecules, particularly the stability in serum, and/or to increase bioavailability of the molecules. Non-limiting examples of modifications include without limitation internucleotide or internucleoside linkages; deoxyribonucleotides or dideoxyribonucleotides at any position and strand of the nucleic acid molecule; nucleic acid (e.g., ribonucleic acid) with a modification at the 2′-position preferably selected from an amino, fluoro, methoxy, alkoxy and alkyl; 2′-deoxyribonucleotides, 2′-O-methyl ribonucleotides, 2′-deoxy-2′-fluoro ribonucleotides, “universal base” nucleotides, “acyclic” nucleotides, 5-C-methyl nucleotides, biotin group, and terminal glyceryl and/or inverted deoxy abasic residue incorporation, sterically hindered molecules, such as fluorescent molecules and the like. Other nucleotides modifiers could include 3′-deoxyadenosine (cordycepin), 3′-azido-3′-deoxythymidine (AZT), 2′,3′-dideoxyinosine (ddI), 2′,3′-dideoxy-3′-thiacytidine (3TC), 2′,3′-didehydro-2′,3′-dideoxythymidine (d4T) and the monophosphate nucleotides of 3′-azido-3′-deoxythymidine (AZT), 2′,3′-dideoxy-3′-thiacytidine (3TC) and 2′,3′-didehydro-2′,3′-dideoxythymidine (d4T). Further details on various modifications are described in more detail below.

Modified nucleotides include those having a Northern conformation (e.g., Northern pseudorotation cycle, see for example Saenger, Principles of Nucleic Acid Structure, Springer-Verlag ed., 1984). Non-limiting examples of nucleotides having a northern configuration include locked nucleic acid (LNA) nucleotides (e.g., 2′-O, 4′-C-methylene-(D-ribofuranosyl) nucleotides); 2′-methoxyethoxy (MOE) nucleotides; 2′-methyl-thio-ethyl, 2′-deoxy-2′-fluoro nucleotides, 2′-deoxy-2′-chloro nucleotides, 2′-azido nucleotides, and 2′-O-methyl nucleotides. Locked nucleic acids, or LNA's are described, for example, in Elman et al., 2005; Kurreck et al., 2002; Crinelli et al., 2002; Braasch and Corey, 2001; Bondensgaard et al., 2000; Wahlestedt et al., 2000; and International Patent Publication Nos. WO 00/47599, WO 99/14226, and WO 98/39352 and WO 2004/083430. In one embodiment, an LNA is incorporated at the 5′ terminus of the sense strand.

Chemical modifications also include unlocked nucleic acids, or UNAs, which are non-nucleotide, acyclic analogues, in which the C2′-C3′ bond is not present (although UNAs are not truly nucleotides, they are expressly included in the scope of “modified” nucleotides or modified nucleic acids as contemplated herein). In particular embodiments, nucleic acid molecules with an overhang may be modified to have UNAs at the overhang positions (i.e., 2 nucleotide overhand). In other embodiments, UNAs are included at the 3′- or 5′-ends. A UNA may be located anywhere along a nucleic acid strand, i.e. at position 7. Nucleic acid molecules may contain one or more than UNA. Exemplary UNAs are disclosed in Nucleic Acids Symposium Series No. 52 p. 133-134 (2008). In certain embodiments a nucleic acid molecule (e.g., a siNA molecule) as described herein include one or more UNAs; or one UNA. In some embodiments, a nucleic acid molecule (e.g., a siNA molecule) as described herein that has a 3′-overhang include one or two UNAs in the 3′ overhang. In some embodiments a nucleic acid molecule (e.g., a siNA molecule) as described herein includes a UNA (for example one UNA) in the antisense strand; for example in position 6 or position 7 of the antisense strand. Chemical modifications also include non-pairing nucleotide analogs, for example as disclosed herein. Chemical modifications further include unconventional moieties as disclosed herein.

Chemical modifications also include terminal modifications on the 5′ and/or 3′ part of the oligonucleotides and are also known as capping moieties. Such terminal modifications are selected from a nucleotide, a modified nucleotide, a lipid, a peptide, and a sugar.

Chemical modifications also include six membered “six membered ring nucleotide analogs.” Examples of six-membered ring nucleotide analogs are disclosed in Allart, et al (Nucleosides & Nucleotides, 1998, 17:1523-1526; and Perez-Perez, et al., 1996, Bioorg. and Medicinal Chem Letters 6:1457-1460) Oligonucleotides including 6-membered ring nucleotide analogs including hexitol and altritol nucleotide monomers are disclosed in International patent application publication No. WO 2006/047842.

Chemical modifications also include “mirror” nucleotides which have a reversed chirality as compared to normal naturally occurring nucleotide; that is a mirror nucleotide may be an “L-nucleotide” analogue of naturally occurring D-nucleotide (see U.S. Pat. No. 6,602,858). Mirror nucleotides may further include at least one sugar or base modification and/or a backbone modification, for example, as described herein, such as a phosphorothioate or phosphonate moiety. U.S. Pat. No. 6,602,858 discloses nucleic acid catalysts including at least one L-nucleotide substitution. Mirror nucleotides include for example L-DNA (L-deoxyriboadenosine-3′-phosphate (mirror dA); L-deoxyribocytidine-3′-phosphate (mirror dC); L-deoxyriboguanosine-3′-phosphate (mirror dG); L-deoxyribothymidine-3′-phosphate (mirror image dT)) and L-RNA (L-riboadenosine-3′-phosphate (mirror rA); L-ribocytidine-3′-phosphate (mirror rC); L-riboguanosine-3′-phosphate (mirror rG); L-ribouracil-3′-phosphate (mirror dU).

In some embodiments, modified ribonucleotides include modified deoxyribonucleotides, for example 5′OMe DNA (5-methyl-deoxyriboguanosine-3′-phosphate) which may be useful as a nucleotide in the 5′ terminal position (position number 1); PACE (deoxyriboadenine 3′ phosphonoacetate, deoxyribocytidine 3′ phosphonoacetate, deoxyriboguanosine 3′ phosphonoacetate, deoxyribothymidine 3′ phosphonoacetate.

Modifications may be present in one or more strands of a nucleic acid molecule disclosed herein, e.g., in the sense strand, the antisense strand, or both strands. In certain embodiments, the antisense strand may include modifications and the sense strand my only include unmodified RNA.

Nucleobases

Nucleobases of the nucleic acid disclosed herein may include unmodified ribonucleotides (purines and pyrimidines) such as adenine, guanine, cytosine, uridine. The nucleobases in one or both strands can be modified with natural and synthetic nucleobases such as thymine, xanthine, hypoxanthine, inosine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, any “universal base” nucleotides; 2-propyl and other alkyl derivatives of adenine and guanine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, amino, thiol, thioalkyl, hydroxyl and other 8-substituted adenines and guanines, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine, deazapurines, heterocyclic substituted analogs of purines and pyrimidines, e.g., aminoethyoxy phenoxazine, derivatives of purines and pyrimidines (e.g., 1-alkyl-, 1-alkenyl-, heteroaromatic- and 1-alkynyl derivatives) and tautomers thereof, 8-oxo-N⁶-methyladenine, 7-diazaxanthine, 5-methylcytosine, 5-methyluracil, 5-(1-propynyl)uracil, 5-(1-propynyl) cytosine and 4,4-ethanocytosine). Other examples of suitable bases include non-purinyl and non-pyrimidinyl bases such as 2-aminopyridine and triazines.

Sugar Moieties

Sugar moieties in nucleic acid disclosed herein may include 2′-hydroxyl-pentofuranosyl sugar moiety without any modification. Alternatively, sugar moieties can be modified such as, 2′-deoxy-pentofuranosyl sugar moiety, D-ribose, hexose, modification at the 2′ position of the pentofuranosyl sugar moiety such as 2′-O-alkyl (including 2′-O-methyl and 2′-O-ethyl), i.e., 2′-alkoxy, 2′-amino, 2′-O-allyl, 2′-S-alkyl, 2′-halogen (including 2′-fluoro, chloro, and bromo), 2′-methoxyethoxy, 2′-O-methoxyethyl, 2′-O-2-methoxyethyl, 2′-allyloxy (—OCH₂CH═CH₂), 2′-propargyl, 2′-propyl, ethynyl, propenyl, CF, cyano, imidazole, carboxylate, thioate, C₁to C₁₀lower alkyl, substituted lower alkyl, alkaryl or aralkyl, OCF₃, OCN, O-, S-, or N-alkyl; O-, S, or N-alkenyl; SOCH₃; SO₂CH₃; ONO₂; NO₂, N₃; heterozycloalkyl; heterozycloalkaryl; aminoalkylamino; polyalkylamino or substituted silyl, as, among others, for example as described in European patents EP 0 586 520 B1 or EP 0 618 925 B1.

Alkyl group includes saturated aliphatic groups, including straight-chain alkyl groups (e.g., methyl, ethyl, propyl, butyl, pentyl, hexyl, heptyl, octyl, nonyl, decyl, etc.), branched-chain alkyl groups (isopropyl, tert-butyl, isobutyl, etc.), cycloalkyl (alicyclic) groups (cyclopropyl, cyclopentyl, cyclohexyl, cycloheptyl, cyclooctyl), alkyl substituted cycloalkyl groups, and cycloalkyl substituted alkyl groups. In certain embodiments, a straight chain or branched chain alkyl has 6 or fewer carbon atoms in its backbone (e.g., C₁-C₆for straight chain, C₃-C₆for branched chain), and more preferably 4 or fewer. Likewise, preferred cycloalkyls may have from 3-8 carbon atoms in their ring structure, and more preferably have 5 or 6 carbons in the ring structure. The term C₁-C₆includes alkyl groups containing 1 to 6 carbon atoms. The alkyl group can be substituted alkyl group such as alkyl moieties having substituents replacing a hydrogen on one or more carbons of the hydrocarbon backbone. Such substituents can include, for example, alkenyl, alkynyl, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, cyano, amino (including alkyl amino, dialkylamino, arylamino, diarylamino, and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety.

Alkoxy group includes substituted and unsubstituted alkyl, alkenyl, and alkynyl groups covalently linked to an oxygen atom. Examples of alkoxy groups include methoxy, ethoxy, isopropyloxy, propoxy, butoxy, and pentoxy groups. Examples of substituted alkoxy groups include halogenated alkoxy groups. The alkoxy groups can be substituted with groups such as alkenyl, alkynyl, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, cyano, amino (including alkyl amino, dialkylamino, arylamino, diarylamino, and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moieties. Examples of halogen substituted alkoxy groups include, but are not limited to, fluoromethoxy, difluoromethoxy, trifluoromethoxy, chloromethoxy, dichloromethoxy, trichloromethoxy, etc.

In some embodiments, the pentafuronosyl ring may be replaced with acyclic derivatives lacking the C2′-C3′-bond of the pentafuronosyl ring. For example, acyclonucleotides may substitute a 2-hydroxyethoxymethyl group for-the 2′-deoxyribofuranosyl sugar normally present in dNMPs.

Halogens include fluorine, bromine, chlorine, iodine.

Backbone

The nucleoside subunits of the nucleic acid disclosed herein may be linked to each other by phosphodiester bond. The phosphodiester bond may be optionally substituted with other linkages. For example, phosphorothioate, thiophosphate-D-ribose entities, triester, thioate, 2′-5′ bridged backbone (may also be referred to as 5′-2′), PACE, 3′-(or -5′)deoxy-3′-(or -5′)thio-phosphorothioate, phosphorodithioate, phosphoroselenates, 3′-(or -5′)deoxy phosphinates, borano phosphates, 3′-(or -5′)deoxy-3′-(or 5′-)amino phosphoramidates, hydrogen phosphonates, phosphonates, borano phosphate esters, phosphoramidates, alkyl or aryl phosphonates and phosphotriester modifications such as alkylphosphotriesters, phosphotriester phosphorus linkages, 5′-ethoxyphosphodiester, P-alkyloxyphosphotriester, methylphosphonate, and nonphosphorus containing linkages for example, carbonate, carbamate, silyl, sulfur, sulfonate, sulfonamide, formacetal, thioformacetyl, oxime, methyleneimino, methylenemethylimino, methylenehydrazo, methylenedimethylhydrazo and methyleneoxymethylimino linkages.

Nucleic acid molecules disclosed herein may include a peptide nucleic acid (PNA) backbone. The PNA backbone is includes repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The various bases such as purine, pyrimidine, natural and synthetic bases are linked to the backbone by methylene carbonyl bonds.

Terminal Phosphates

Modifications can be made at terminal phosphate groups. Non-limiting examples of different stabilization chemistries can be used, e.g., to stabilize the 3′-end of nucleic acid sequences, including (1) [3-3′]-inverted deoxyribose; (2) deoxyribonucleotide; (3) [5′-3′]-3′-deoxyribonucleotide; (4) [5′-3′]-ribonucleotide; (5) [5′-3′]-3′-O-methyl ribonucleotide; (6) 3′-glyceryl; (7) [3′-5′]-3′-deoxyribonucleotide; (8) [3′-3′]-deoxyribonucleotide; (9) [5′-2′]-deoxyribonucleotide; and (10) [5-3′]-dideoxyribonucleotide. In addition to unmodified backbone chemistries can be combined with one or more different backbone modifications described herein.

Exemplary chemically modified terminal phosphate groups include those shown below:

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Conjugates

Modified nucleotides and nucleic acid molecules (e.g., siNA molecules) as provided herein may include conjugates, for example, a conjugate covalently attached to the chemically-modified nucleic acid molecule. Non-limiting examples of conjugates include conjugates and ligands described in Vargeese et al., U.S. Ser. No. 10/427,160. The conjugate may be covalently attached to a nucleic acid molecule (such as an siNA molecule) via a biodegradable linker. The conjugate molecule may be attached at the 3′-end of either the sense strand, the antisense strand, or both strands of the chemically-modified nucleic acid molecule.

The conjugate molecule may be attached at the 5′-end of either the sense strand, the antisense strand, or both strands of the chemically-modified nucleic acid molecule. The conjugate molecule may be attached both the 3′-end and 5′-end of either the sense strand, the antisense strand, or both strands of the chemically-modified nucleic acid molecule, or any combination thereof. In one embodiment, a conjugate molecule may include a molecule that facilitates delivery of a chemically-modified nucleic acid molecule into a biological system, such as a cell. In another embodiment, the conjugate molecule attached to the chemically-modified nucleic acid molecule is a polyethylene glycol, human serum albumin, or a ligand for a cellular receptor that can mediate cellular uptake. Examples of specific conjugate molecules contemplated by herein that can be attached to chemically-modified nucleic acid molecules are described in Vargeese et al., U.S. Ser. No. 10/201,394.

Linkers

A nucleic acid molecule provided herein (e.g., an siNA) molecule may include a nucleotide, non-nucleotide, or mixed nucleotide/non-nucleotide linker that joins the sense region of the nucleic acid to the antisense region of the nucleic acid. A nucleotide linker can be a linker of ≧2 nucleotides in length, for example about 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides in length. The nucleotide linker can be a nucleic acid aptamer. By “aptamer” or “nucleic acid aptamer” as used herein refers to a nucleic acid molecule that binds specifically to a target molecule wherein the nucleic acid molecule has sequence that includes a sequence recognized by the target molecule in its natural setting. Alternately, an aptamer can be a nucleic acid molecule that binds to a target molecule (such as TIMP1 and TIMP2 mRNA) where the target molecule does not naturally bind to a nucleic acid. For example, the aptamer can be used to bind to a ligand-binding domain of a protein, thereby preventing interaction of the naturally occurring ligand with the protein. This is a non-limiting example and those in the art will recognize that other embodiments can be readily generated using techniques generally known in the art. See e.g., Gold et al.; 1995, Annu. Rev. Biochem., 64, 763; Brody and Gold, 2000, J. Biotechnol., 74, 5; Sun, 2000, Curr. Opin. Mol. Ther., 2, 100; Kusser, 2000, J. Biotechnol., 74, 27; Hermann and Patel, 2000, Science, 287, 820; and Jayasena, 1999, Clinical Chemistry, 45, 1628.

A non-nucleotide linker may include an abasic nucleotide, polyether, polyamine, polyamide, peptide, carbohydrate, lipid, polyhydrocarbon, or other polymeric compounds (e.g. polyethylene glycols such as those having between 2 and 100 ethylene glycol units). Specific examples include those described by Seela and Kaiser, Nucleic Acids Res. 1990, 18:6353 and Nucleic Acids Res. 1987, 15:3113; Cload and Schepartz, J. Am. Chem. Soc. 1991, 113:6324; Richardson and Schepartz, J. Am. Chem. Soc. 1991, 113:5109; Ma et al., Nucleic Acids Res. 1993, 21:2585 and Biochemistry 1993, 32:1751; Durand et al., Nucleic Acids Res. 1990, 18:6353; McCurdy et al., Nucleosides & Nucleotides 1991, 10:287; Jschke et al., Tetrahedron Lett. 1993, 34:301; Ono et al., Biochemistry 1991, 30:9914; Arnold et al., International Publication No. WO 89/02439; Usman et al., International Publication No. WO 95/06731; Dudycz et al., International Publication No. WO 95/11910 and Ferentz and Verdine, J. Am. Chem. Soc. 1991, 113:4000.

5′ Ends, 3′ Ends and Overhangs

Nucleic acid molecules disclosed herein (e.g., siNA molecules) may be blunt-ended on both sides, have overhangs on both sides or a combination of blunt and overhang ends. Overhangs may occur on either the 5′- or 3′-end of the sense or antisense strand.

5′- and/or 3′-ends of double stranded nucleic acid molecules (e.g., siNA) may be blunt ended or have an overhang. The 5′-end may be blunt ended and the 3′-end has an overhang in either the sense strand or the antisense strand. In other embodiments, the 3′-end may be blunt ended and the 5′-end has an overhang in either the sense strand or the antisense strand. In yet other embodiments, both the 5′- and 3′-end are blunt ended or both the 5′- and 3′-ends have overhangs.

The 5′- and/or 3′-end of one or both strands of the nucleic acid may include a free hydroxyl group. The 5′- and/or 3′-end of any nucleic acid molecule strand may be modified to include a chemical modification. Such modification may stabilize nucleic acid molecules, e.g., the 3′-end may have increased stability due to the presence of the nucleic acid molecule modification. Examples of end modifications (e.g., terminal caps) include, but are not limited to, abasic, deoxy abasic, inverted (deoxy) abasic, glyceryl, dinucleotide, acyclic nucleotide, amino, fluoro, chloro, bromo, CN, CF, methoxy, imidazole, carboxylate, thioate, C₁to C₁₀lower alkyl, substituted lower alkyl, alkaryl or aralkyl, OCF₃, OCN, O-, S-, or N-alkyl; O-, S-, or N-alkenyl; SOCH₃; SO₂CH₃; ONO₂; NO₂, N₃; heterocycloalkyl; heterocycloalkaryl; aminoalkylamino; polyalkylamino or substituted silyl, as, among others, described in European patents EP 586,520 and EP 618,925 and other modifications disclosed herein.

Nucleic acid molecules include those with blunt ends, i.e., ends that do not include any overhanging nucleotides. A nucleic acid molecule can include one or more blunt ends. The blunt ended nucleic acid molecule has a number of base pairs equal to the number of nucleotides present in each strand of the nucleic acid molecule. The nucleic acid molecule can include one blunt end, for example where the 5′-end of the antisense strand and the 3′-end of the sense strand do not have any overhanging nucleotides. Nucleic acid molecule may include one blunt end, for example where the 3′-end of the antisense strand and the 5′-end of the sense strand do not have any overhanging nucleotides. A nucleic acid molecule may include two blunt ends, for example where the 3′-end of the antisense strand and the 5′-end of the sense strand as well as the 5′-end of the antisense strand and 3′-end of the sense strand do not have any overhanging nucleotides. Other nucleotides present in a blunt ended nucleic acid molecule can include, for example, mismatches, bulges, loops, or wobble base pairs to modulate the activity of the nucleic acid molecule to mediate RNA interference.

In certain embodiments of the nucleic acid molecules (e.g., siNA molecules) provided herein, at least one end of the molecule has an overhang of at least one nucleotide (for example 1 to 8 overhang nucleotides). For example, one or both strands of a double stranded nucleic acid molecule disclosed herein may have an overhang at the 5′-end or at the 3′-end or both. An overhang may be present at either or both the sense strand and antisense strand of the nucleic acid molecule. The length of the overhang may be as little as one nucleotide and as long as 1 to 8 or more nucleotides (e.g., 1, 2, 3, 4, 5, 6, 7 or 8 nucleotides; in some preferred embodiments an overhang is 2, 3, 4, 5, 6, 7 or 8 nucleotides; for example an overhang may be 2 nucleotides. The nucleotide(s) forming the overhang may be include deoxyribonucleotide(s), ribonucleotide(s), natural and non-natural nucleobases or any nucleotide modified in the sugar, base or phosphate group such as disclosed herein. A double stranded nucleic acid molecule may have both 5′- and 3′-overhangs. The overhangs at the 5′- and 3′-end may be of different lengths. An overhang may include at least one nucleic acid modification which may be deoxyribonucleotide. One or more deoxyribonucleotides may be at the 5′-terminal. The 3′-end of the respective counter-strand of the nucleic acid molecule may not have an overhang, more preferably not a deoxyribonucleotide overhang. The one or more deoxyribonucleotide may be at the 3′-terminal. The 5′-end of the respective counter-strand of the dsRNA may not have an overhang, more preferably not a deoxyribonucleotide overhang. The overhang in either the 5′- or the 3′-end of a strand may be 1 to 8 (e.g., about 1, 2, 3, 4, 5, 6, 7 or 8) unpaired nucleotides, preferably, the overhang is 2-3 unpaired nucleotides; more preferably 2 unpaired nucleotides. Nucleic acid molecules may include duplex nucleic acid molecules with overhanging ends of about 1 to about 20 (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 1, 15, 16, 17, 18, 19 or 20); preferably 1-8 (e.g., about 1, 2, 3, 4, 5, 6, 7 or 8) nucleotides, for example, about 21-nucleotide duplexes with about 19 base pairs and 3′-terminal mononucleotide, dinucleotide, or trinucleotide overhangs. Nucleic acid molecules herein may include duplex nucleic acid molecules with blunt ends, where both ends are blunt, or alternatively, where one of the ends is blunt. Nucleic acid molecules disclosed herein can include one or more blunt ends, i.e. where a blunt end does not have any overhanging nucleotides. In one embodiment, the blunt ended nucleic acid molecule has a number of base pairs equal to the number of nucleotides present in each strand of the nucleic acid molecule. The nucleic acid molecule may include one blunt end, for example where the 5′-end of the antisense strand and the 3′-end of the sense strand do not have any overhanging nucleotides. The nucleic acid molecule may include one blunt end, for example where the 3′-end of the antisense strand and the 5′-end of the sense strand do not have any overhanging nucleotides. A nucleic acid molecule may include two blunt ends, for example where the 3′-end of the antisense strand and the 5′-end of the sense strand as well as the 5′-end of the antisense strand and 3′-end of the sense strand do not have any overhanging nucleotides. In certain preferred embodiments the nucleic acid compounds are blunt ended. Other nucleotides present in a blunt ended siNA molecule can include, for example, mismatches, bulges, loops, or wobble base pairs to modulate the activity of the nucleic acid molecule to mediate RNA interference.

In many embodiments one or more, or all, of the overhang nucleotides of a nucleic acid molecule (e.g., a siNA molecule) as described herein includes are modified such as described herein; for example one or more, or all, of the nucleotides may be 2′-deoxyribonucleotides.

Amount, Location and Patterns of Modifications.

Nucleic acid molecules (e.g., siNA molecules) disclosed herein may include modified nucleotides as a percentage of the total number of nucleotides present in the nucleic acid molecule. As such, a nucleic acid molecule may include about 5% to about 100% modified nucleotides (e.g., about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% modified nucleotides). The actual percentage of modified nucleotides present in a given nucleic acid molecule will depend on the total number of nucleotides present in the nucleic acid. If the nucleic acid molecule is single stranded, the percent modification can be based upon the total number of nucleotides present in the single stranded nucleic acid molecule. Likewise, if the nucleic acid molecule is double stranded, the percent modification can be based upon the total number of nucleotides present in the sense strand, antisense strand, or both the sense and antisense strands.

Nucleic acid molecules disclosed herein may include unmodified RNA as a percentage of the total nucleotides in the nucleic acid molecule. As such, a nucleic acid molecule may include about 5% to about 100% modified nucleotides (e.g., about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% of total nucleotides present in a nucleic acid molecule.

A nucleic acid molecule (e.g., an siNA molecule) may include a sense strand that includes about 1 to about 5, specifically about 1, 2, 3, 4, or 5 phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, or more) 2′-deoxy, 2′-O-methyl, 2′-deoxy-2′-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3-end, the 5′-end, or both of the 3′- and 5′-ends of the sense strand; and wherein the antisense strand includes about 1 to about 5 or more, specifically about 1, 2, 3, 4, 5, or more phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2′-deoxy, 2′-O-methyl, 2′-deoxy-2′-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends of the antisense strand. A nucleic acid molecule may include about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more, pyrimidine nucleotides of the sense and/or antisense nucleic acid strand are chemically-modified with 2′-deoxy, 2′-O-methyl and/or 2′-deoxy-2′-fluoro nucleotides, with or without about 1 to about 5 or more, for example about 1, 2, 3, 4, 5, or more phosphorothioate internucleotide linkages and/or a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends, being present in the same or different strand.

A nucleic acid molecule may include about 1 to about 5 or more (specifically about 1, 2, 3, 4, 5 or more) phosphorothioate internucleotide linkages in each strand of the nucleic acid molecule.

A nucleic acid molecule may include 2′-5′ internucleotide linkages, for example at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends of one or both nucleic acid sequence strands. In addition, the 2′-5′ internucleotide linkage(s) can be present at various other positions within one or both nucleic acid sequence strands, for example, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more including every internucleotide linkage of a pyrimidine nucleotide in one or both strands of the siNA molecule can include a 2′-5′ internucleotide linkage, or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more including every internucleotide linkage of a purine nucleotide in one or both strands of the siNA molecule can include a 2′-5′ internucleotide linkage.

A chemically-modified short interfering nucleic acid (siNA) molecule may include an antisense region, wherein any (e.g., one or more or all) pyrimidine nucleotides present in the antisense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and wherein any (e.g., one or more or all) purine nucleotides present in the antisense region are 2′-deoxy purine nucleotides (e.g., wherein all purine nucleotides are 2′-deoxy purine nucleotides or alternately a plurality of purine nucleotides are 2′-deoxy purine nucleotides).

A chemically-modified short interfering nucleic acid (siNA) molecule may include an antisense region, wherein any (e.g., one or more or all) pyrimidine nucleotides present in the antisense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and wherein any (e.g., one or more or all) purine nucleotides present in the antisense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides).

A chemically-modified short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) against TIMP1 and TIMP2 inside a cell or reconstituted in vitro system may include a sense region, wherein one or more pyrimidine nucleotides present in the sense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and one or more purine nucleotides present in the sense region are 2′-deoxy purine nucleotides (e.g., wherein all purine nucleotides are 2′-deoxy purine nucleotides or alternately a plurality of purine nucleotides are 2′-deoxy purine nucleotides), and an antisense region, wherein one or more pyrimidine nucleotides present in the antisense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and one or more purine nucleotides present in the antisense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides). The sense region and/or the antisense region can have a terminal cap modification, such as any modification, that is optionally present at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the sense and/or antisense sequence. The sense and/or antisense region can optionally further include a 3′-terminal nucleotide overhang having about 1 to about 4 (e.g., about 1, 2, 3, or 4) 2′-deoxyribonucleotides. The overhang nucleotides can further include one or more (e.g., about 1, 2, 3, 4 or more) phosphorothioate, phosphonoacetate, and/or thiophosphonoacetate internucleotide linkages. The purine nucleotides in the sense region may alternatively be 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides) and one or more purine nucleotides present in the antisense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides). One or more purine nucleotides in the sense region may alternatively be purine ribonucleotides (e.g., wherein all purine nucleotides are purine ribonucleotides or alternately a plurality of purine nucleotides are purine ribonucleotides) and any purine nucleotides present in the antisense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides). One or more purine nucleotides in the sense region and/or present in the antisense region may alternatively selected from the group consisting of 2′-deoxy nucleotides, locked nucleic acid (LNA) nucleotides, 2′-methoxyethyl nucleotides, 4′-thionucleotides, and 2′-O-methyl nucleotides (e.g., wherein all purine nucleotides are selected from the group consisting of 2′-deoxy nucleotides, locked nucleic acid (LNA) nucleotides, 2′-methoxyethyl nucleotides, 4′-thionucleotides, and 2′-O-methyl nucleotides or alternately a plurality of purine nucleotides are selected from the group consisting of 2′-deoxy nucleotides, locked nucleic acid (LNA) nucleotides, 2′-methoxyethyl nucleotides, 4′-thionucleotides, and 2′-O-methyl nucleotides).

In some embodiments, a nucleic acid molecule (e.g., a siNA molecule) as described herein includes a modified nucleotide (for example one modified nucleotide) in the antisense strand; for example in position 6 or position 7 of the antisense strand.

Modification Patterns and Alternating Modifications

Nucleic acid molecules (e.g., siNA molecules) provided herein may have patterns of modified and unmodified nucleic acids. A pattern of modification of the nucleotides in a contiguous stretch of nucleotides may be a modification contained within a single nucleotide or group of nucleotides that are covalently linked to each other via standard phosphodiester bonds or, at least partially, through phosphorothioate bonds. Accordingly, a “pattern” as contemplated herein, does not necessarily need to involve repeating units, although it may. Examples of modification patterns that may be used in conjunction with the nucleic acid molecules (e.g., siNA molecules) provided herein include those disclosed in Giese, U.S. Pat. No. 7,452,987. For example, nucleic acid molecules (e.g., siNA molecules) provided herein include those having modification patters such as, similar to, or the same as, the patterns shown diagrammatically in FIG. 2 of the Giese U.S. Pat. No. 7,452,987.

A modified nucleotide or group of modified nucleotides may be at the 5′-end or 3′-end of the sense or antisense strand, a flanking nucleotide or group of nucleotides is arrayed on both sides of the modified nucleotide or group, where the flanking nucleotide or group either is unmodified or does not have the same modification of the preceding nucleotide or group of nucleotides. The flanking nucleotide or group of nucleotides may, however, have a different modification. This sequence of modified nucleotide or group of modified nucleotides, respectively, and unmodified or differently modified nucleotide or group of unmodified or differently modified nucleotides may be repeated one or more times.

In some patterns, the 5′-terminal nucleotide of a strand is a modified nucleotide while in other patterns the 5′-terminal nucleotide of a strand is an unmodified nucleotide. In some patterns, the 5′-end of a strand starts with a group of modified nucleotides while in other patterns, the 5′-terminal end is an unmodified group of nucleotides. This pattern may be either on the first stretch or the second stretch of the nucleic acid molecule or on both.

Modified nucleotides of one strand of the nucleic acid molecule may be complementary in position to the modified or unmodified nucleotides or groups of nucleotides of the other strand.

There may be a phase shift between modifications or patterns of modifications on one strand relative to the pattern of modification of the other strand such that the modification groups do not overlap. In one instance, the shift is such that the modified group of nucleotides of the sense strand corresponds to the unmodified group of nucleotides of the antisense strand and vice versa.

There may be a partial shift of the pattern of modification such that the modified groups overlap. The groups of modified nucleotides in any given strand may optionally be the same length, but may be of different lengths. Similarly, groups of unmodified nucleotides in any given strand may optionally be the same length, or of different lengths.

In some patterns, the second (penultimate) nucleotide at the terminus of the strand, is an unmodified nucleotide or the beginning of group of unmodified nucleotides. Preferably, this unmodified nucleotide or unmodified group of nucleotides is located at the 5′-end of the either or both the sense and antisense strands and even more preferably at the terminus of the sense strand. An unmodified nucleotide or unmodified group of nucleotide may be located at the 5′-end of the sense strand. In a preferred embodiment the pattern consists of alternating single modified and unmodified nucleotides.

In some double stranded nucleic acid molecules include a 2′-O-methyl modified nucleotide and a non-modified nucleotide, preferably a nucleotide which is not 2′-O-methyl modified, are incorporated on both strands in an alternating fashion, resulting in a pattern of alternating 2′-O-methyl modified nucleotides and nucleotides that are either unmodified or at least do not include a 2′-O-methyl modification. In certain embodiments, the same sequence of 2′-O-methyl modification and non-modification exists on the second strand; in other embodiments the alternating 2′-O-methyl modified nucleotides are only present in the sense strand and are not present in the antisense strand; and in yet other embodiments the alternating 2′-O-methyl modified nucleotides are only present in the sense strand and are not present in the antisense strand. In certain embodiments, there is a phase shift between the two strands such that the 2′-O-methyl modified nucleotide on the first strand base pairs with a non-modified nucleotide(s) on the second strand and vice versa. This particular arrangement, i.e. base pairing of 2′-O-methyl modified and non-modified nucleotide(s) on both strands is particularly preferred in certain embodiments. In certain embodiments, the pattern of alternating 2′-O-methyl modified nucleotides exists throughout the entire nucleic acid molecule; or the entire duplex region. In other embodiments the pattern of alternating 2′-O-methyl modified nucleotides exists only in a portion of the nucleic acid; or the entire duplex region.

In “phase shift” patterns, it may be preferred if the antisense strand starts with a 2′-O-methyl modified nucleotide at the 5′ end whereby consequently the second nucleotide is non-modified, the third, fifth, seventh and so on nucleotides are thus again 2′-O-methyl modified whereas the second, fourth, sixth, eighth and the like nucleotides are non-modified nucleotides.

Exemplary Modification Locations and Patterns

While exemplary patterns are provided in more detail below, all permutations of patterns with of all possible characteristics of the nucleic acid molecules disclosed herein and those known in the art are contemplated (e.g., characteristics include, but are not limited to, length of sense strand, length of antisense strand, length of duplex region, length of hangover, whether one or both ends of a double stranded nucleic acid molecule is blunt or has an overhang, location of modified nucleic acid, number of modified nucleic acids, types of modifications, whether a double overhang nucleic acid molecule has the same or different number of nucleotides on the overhang of each side, whether a one or more than one type of modification is used in a nucleic acid molecule, and number of contiguous modified/unmodified nucleotides). With respect to all detailed examples provided below, while the duplex region is shown to be 19 nucleotides, the nucleic acid molecules provided herein can have a duplex region ranging from 1 to 49 nucleotides in length as each strand of a duplex region can independently be 17-49 nucleotides in length Exemplary patterns are provided herein.

Nucleic acid molecules may have a blunt end (when n is 0) on both ends that include a single or contiguous set of modified nucleic acids. The modified nucleic acid may be located at any position along either the sense or antisense strand. Nucleic acid molecules may include a group of about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48 or 49 contiguous modified nucleotides. Modified nucleic acids may make up 1%, 2%, 3%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98% or 100% of a nucleic acid strand. Modified nucleic acids of the examples immediately below may be in the sense strand only, the antisense strand only, or in both the sense and antisense strand.

General nucleic acid patters are shown below where X=sense strand nucleotide in the duplex region; X_a=5′-overhang nucleotide in the sense strand; X_b=3′-overhang nucleotide in the sense strand; Y=antisense strand nucleotide in the duplex region; Y_a=3′-overhang nucleotide in the antisense strand; Y_b=5′-overhang nucleotide in the antisense strand; and M=a modified nucleotide in the duplex region. Each a and b are independently 0 to 8 (e.g., 0, 1, 2, 3, 4, 5, 6, 7 or 8). Each X, Y, a and b are independently modified or unmodified. The sense and antisense strands can are each independently 17-49 nucleotides in length. The examples provided below have a duplex region of 19 nucleotides; however, nucleic acid molecules disclosed herein can have a duplex region anywhere between 17 and 49 nucleotides and where each strand is independently between 17 and 49 nucleotides in length.

5′ X_aXXXXXXXXXXXXXXXXXXXX_b

3′ Y_bYYYYYYYYYYYYYYYYYYYY_a

Further exemplary nucleic acid molecule patterns are shown below where X=unmodified sense strand nucleotides; x=an unmodified overhang nucleotide in the sense strand; Y=unmodified antisense strand nucleotides; y=an unmodified overhang nucleotide in the antisense strand; and M=a modified nucleotide. The sense and antisense strands can are each independently 17-49 nucleotides in length. The examples provided below have a duplex region of 19 nucleotides; however, nucleic acid molecules disclosed herein can have a duplex region anywhere between 17 and 49 nucleotides and where each strand is independently between 17 and 49 nucleotides in length.

5′ M_nXXXXXXXXXMXXXXXXXXXM_n

3′ M_nYYYYYYYYYYYYYYYYYYYM_n

5′ XXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYMYYYYYYYYY

5′ XXXXXXXXMMXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYMMYYYYYYYYY

5′ XXXXXXXXXMXXXXXXXXX

3′ YYYYYYYYYMYYYYYYYYY

5′ XXXXXMXXXXXXXXXXXXX

3′ YYYYYYYYYMYYYYYYYYY

5′ MXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYMYYYYYY

5′ XXXXXXXXXXXXXXXXXXM

3′ YYYYYMYYYYYYYYYYYYY

5′ XXXXXXXXXMXXXXXXXX

3′ MYYYYYYYYYYYYYYYYY

5′ XXXXXXXMXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYM

5′ XXXXXXXXXXXXXMXXXX

3′ MYYYYYYYYYYYYYYYYY

5′ MMMMMMMMMMMMMMMMMM

3′ MMMMMMMMMMMMMMMMMM

Nucleic acid molecules may have blunt ends on both ends with alternating modified nucleic acids. The modified nucleic acids may be located at any position along either the sense or antisense strand.

5′ MXMXMXMXMXMXMXMXMXM

3′ YMYMYMYMYMYMYMYMYMY

5′ XMXMXMXMXMXMXMXMXMX

3′ MYMYMYMYMYMYMYMYMYM

5′ MMXMMXMMXMMXMMXMMXM

3′ YMMYMMYMMYMMYMMYMMY

5′ XMMXMMXMMXMMXMMXMMX

3′ MMYMMYMMYMMYMMYMMYM

5′ MMMXMMMXMMMXMMMXMMM

3′ YMMMYMMMYMMMYMMMYMM

5′ XMMMXMMMXMMMXMMMXMM

3′ MMMYMMMYMMMYMMMYMMM

Nucleic acid molecules with a blunt 5′-end and 3′-end overhang end with a single modified nucleic acid.

Nucleic acid molecules with a 5′-end overhang and a blunt 3′-end with a single modified nucleic acid.

Nucleic acid molecules with overhangs on both ends and all overhangs are modified nucleic acids. In the pattern immediately below, M is n number of modified nucleic acids, where n is an integer from 0 to 8 (i.e., 0, 1, 2, 3, 4, 5, 6, 7 and 8).

5′ XXXXXXXXXXXXXXXXXXXM

3′ MYYYYYYYYYYYYYYYYYYY

Nucleic acid molecules with overhangs on both ends and some overhang nucleotides are modified nucleotides. In the patterns immediately below, M is n number of modified nucleotides, x is n number of unmodified overhang nucleotides in the sense strand, y is n number of unmodified overhang nucleotides in the antisense strand, where each n is independently an integer from 0 to 8 (i.e., 0, 1, 2, 3, 4, 5, 6, 7 and 8), and where each overhang is maximum of 20 nucleotides; preferably a maximum of 8 nucleotides (modified and/or unmodified).

5′ XXXXXXXXXXXXXXXXXXXM

3′ yYYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXXMx

3′ yYYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXXMxM

3′ yYYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXXMxMx

3′ yYYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXXMxMxM

3′ yYYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXXMxMxMx

3′ yYYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXXMxMxMxM

3′ yYYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXXMxMxMxMx

3′ yYYYYYYYYYYYYYYYYYYY

5′ MXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYYy

5′ xMXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYYy

5′ MxMXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYYy

5′ xMxMXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYYy

5′ MxMxMXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYYy

5′ xMxMxMXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYYy

5′ MxMxMxMXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYYy

5′ xMxMxMxMXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYYy

5′ xXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYYM

5′ xXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYYMy

5′ xXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYYMyM

5′ xXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYYMyMy

5′ xXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYYMyMyM

5′ xXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYYMyMyMy

5′ xXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYYMyMyMyM

5′ xXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYYMyMyMyMy

5′ XXXXXXXXXXXXXXXXXXXx

3′ MYYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXXx

3′ yMYYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXXx

3′ MyMYYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXXx

3′ yMyMYYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXXx

3′ MyMyMYYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXXx

3′ yMyMyMYYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXXx

3′ MyMyMyMYYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXXx

3′ yMyMyMyMYYYYYYYYYYYYYYYYYYY

Modified nucleotides at the 3′ end of the sense region.

5′ XXXXXXXXXXXXXXXXXXXM

3′ YYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXXMM

3′ YYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXXMMM

3′ YYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXXMMMM

3′ YYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXXMMMMM

3′ YYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXXMMMMMM

3′ YYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXXMMMMMMMM

3′ YYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXXMMMMMMMM

3′ YYYYYYYYYYYYYYYYYYY

Overhang at the 5′ end of the sense region.

5′ MXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYY

5′ MMXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYY

5′ MMMXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYY

5′ MMMMXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYY

5′ MMMMMXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYY

5′ MMMMMMXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYY

5′ MMMMMMMXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYY

5′ MMMMMMMMXXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYY

Overhang at the 3′ end of the antisense region.

5′ XXXXXXXXXXXXXXXXXXX

3′ MYYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXX

3′ MMYYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXX

3′ MMMYYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXX

3′ MMMMYYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXX

3′ MMMMMYYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXX

3′ MMMMMMYYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXX

3′ MMMMMMMYYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXX

3′ MMMMMMMMYYYYYYYYYYYYYYYYYYY

Modified nucleotide(s) within the sense region

5′ XXXXXXXXXMXXXXXXXXX

3′ YYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXX

3′ YYYYYYYYYMYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXMM

3′ YYYYYYYYYYYYYYYYYYY

5′ XXXXXXXXXXXXXXXXXXX

3′ MMYYYYYYYYYYYYYYYYYYY

Exemplary nucleic acid molecules are provided below with the equivalent general structure in line with the symbols used above. The following duplexes are in accordance with the pattern:

5′ XXXXXXXXXXXXXXXXXXXMM

3′ MMYYYYYYYYYYYYYYYYYYY

TIMP1-A siRNA to human, mouse, rat and rhesus TIMP1 having a 19 nucleotide (i.e., 19mer) duplex region and modified 2 nucleotide (i.e., deoxynucleotide) overhangs at the 3′-ends of the sense and antisense strands.

5′ CCACCUUAUACCAGCGUUATT 3′

3′ TTGGUGGAAUAUGGUCGCAAU 5′

TIMP1-B siRNA to human and rhesus TIMP1 having a 19 nucleotide (i.e., 19mer) duplex region and modified 2 nucleotide (i.e., deoxynucleotide) overhangs at the 3′-ends of the sense and antisense strands.

5′ CACUGUUGGCUGUGAGGAATT 3′

3′ TTGUGACAACCGACACUCCUU 5′

TIMP1-C siRNA to human, mouse, rat and rhesus TIMP1 having a 19 nucleotide (i.e., 19mer) duplex region and modified 2 nucleotide (i.e., deoxynucleotide) overhangs at the 3′-ends of the sense and antisense strands.

5′ GGAAUAUCUCAUUGCAGGATT 3′

3′ TTCCUUAUAGAGUAACGUCCU 5′

TIMP2-A siRNA to human TIMP2 having a 19 nucleotide (i.e., 19mer) duplex region and modified 2 nucleotide (i.e., deoxynucleotide) overhangs at the 3′-ends of the sense and antisense strands.

5′ UGCAGAUGUAGUGAUCAGGTT 3′

3′ TTACGUCUACAUCACUAGUCC 5′

TIMP2-B siRNA to human, rhesus and rabbit TIMP2 having a 19 nucleotide (i.e., 19mer) duplex region and modified 2 nucleotide (i.e., deoxynucleotide) overhangs at the 3′-ends of the sense and antisense strands.

5′ GAGGAUCCAGUAUGAGAUCTT 3′

3′ TTCUCCUAGGUCAUACUCUAG 5′

TIMP2-C siRNA to human, mouse, rat, cow, dog and pig TIMP2 having a 19 nucleotide (i.e., 19mer) duplex region and modified 2 nucleotide (i.e., deoxynucleotide) overhangs at the 3′-ends of the sense and antisense strands.

5′ GCAGAUAAAGAUGUUCAAATT 3′

3′ TTCGUCUAUUUCUACAAGUUU 5′

TIMP2-D siRNA to human TIMP2 having a 19 nucleotide (i.e., 19mer) duplex region and modified 2 nucleotide (i.e., deoxynucleotide) overhangs at the 3′-ends of the sense and antisense strands.

5′ UAUCUCAUUGCAGGAAAGGTT 3′

3′ TTAUAGAGUAACGUCCUUUCC 5′

TIMP2-E siRNA to human TIMP2 having a 19 nucleotide (i.e., 19mer) duplex region and modified 2 nucleotide (i.e., deoxynucleotide) overhangs at the 3′-ends of the sense and antisense strands.

5′ GCACAGUGUUUCCCUGUUUTT 3′

3′ TTCGUGUCACAAAGGGACAAA 5′

Nicks and Gaps in Nucleic Acid Strands

Nucleic acid molecules (e.g., siNA molecules) provided herein may have a strand, preferably the sense strand, that is nicked or gapped. As such, nucleic acid molecules may have three or more strand, for example, such as a meroduplex RNA (mdRNA) disclosed in International Patent Application No. PCT/US07/081836. Nucleic acid molecules with a nicked or gapped strand may be between about 1-49 nucleotides, or may be RISC length (e.g., about 15 to 25 nucleotides) or Dicer substrate length (e.g., about 25 to 30 nucleotides) such as disclosed herein.

Nucleic acid molecules with three or more strands include, for example, an ‘A’ (antisense) strand, ‘S1’ (second) strand, and ‘S2’ (third) strand in which the ‘S1’ and ‘S2’ strands are complementary to and form base pairs with non-overlapping regions of the ‘A’ strand (e.g., an mdRNA can have the form of A:S1S2). The S1, S2, or more strands together form what is substantially similar to a sense strand to the ‘A’ antisense strand. The double-stranded region formed by the annealing of the ‘S1’ and ‘A’ strands is distinct from and non-overlapping with the double-stranded region formed by the annealing of the ‘S2’ and ‘A’ strands. An nucleic acid molecule (e.g., an siNA molecule) may be a “gapped” molecule, meaning a “gap” ranging from 0 nucleotides up to about 10 nucleotides (e.g., 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides). Preferably, the sense strand is gapped. In some embodiments, the A:S1 duplex is separated from the A:S2 duplex by a gap resulting from at least one unpaired nucleotide (up to about 10 unpaired nucleotides) in the ‘A’ strand that is positioned between the A:S1 duplex and the A:S2 duplex and that is distinct from any one or more unpaired nucleotide at the 3′-end of one or more of the ‘A’, ‘S1’, or ‘S2 strands. The A:S1 duplex may be separated from the A:B2 duplex by a gap of zero nucleotides (i.e., a nick in which only a phosphodiester bond between two nucleotides is broken or missing in the polynucleotide molecule) between the A:S1 duplex and the A:S2 duplex-which can also be referred to as nicked dsRNA (ndsRNA). For example, A:S1S2 may be include a dsRNA having at least two double-stranded regions that combined total about 14 base pairs to about 40 base pairs and the double-stranded regions are separated by a gap of about 0 to about 10 nucleotides, optionally having blunt ends, or A:S1S2 may include a dsRNA having at least two double-stranded regions separated by a gap of up to 10 nucleotides wherein at least one of the double-stranded regions includes between about 5 base pairs and 13 base pairs.

Dicer Substrates

In certain embodiments, the nucleic acid molecules (e.g., siNA molecules) provided herein may be a precursor “Dicer substrate” molecule, e.g., double stranded nucleic acid, processed in vivo to produce an active nucleic acid molecules, for example as described in Rossi, US Patent App. No. 20050244858. In certain conditions and situations, it has been found that these relatively longer dsRNA siNA species, e.g., of from about 25 to about 30 nucleotides, can give unexpectedly effective results in terms of potency and duration of action. Without wishing to be bound by any particular theory, it is thought that the longer dsRNA species serve as a substrate for the enzyme Dicer in the cytoplasm of a cell. In addition to cleaving double stranded nucleic acid into shorter segments, Dicer may facilitate the incorporation of a single-stranded cleavage product derived from the cleaved dsRNA into the RNA-induced silencing complex (RISC complex) that is responsible for the destruction of the cytoplasmic RNA derived from the target gene.

Dicer substrates may have certain properties which enhance its processing by Dicer. Dicer substrates are of a length sufficient such that it is processed by Dicer to produce an active nucleic acid molecule and may further include one or more of the following properties: (i) the dsRNA is asymmetric, e.g., has a 3′ overhang on the first strand (antisense strand) and (ii) the dsRNA has a modified 3′ end on the antisense strand (sense strand) to direct orientation of Dicer binding and processing of the dsRNA to an active siRNA. In certain embodiments, the longest strand in the Dicer substrate may be 24-30 nucleotides.

Dicer substrates may be symmetric or asymmetric. The Dicer substrate may have a sense strand includes 22-28 nucleotides and the antisense strand may include 24-30 nucleotides; thus, in some embodiments the resulting Dicer substrate may have an overhang on the 3′ end of the antisense strand. Dicer substrate may have a sense strand 25 nucleotides in length, and the antisense strand having 27 nucleotides in length with a 2 base 3′-overhang. The overhang may be 1-3 nucleotides, for example 2 nucleotides. The sense strand may also have a 5′ phosphate.

An asymmetric Dicer substrate may further contain two deoxyribonucleotides at the 3′-end of the sense strand in place of two of the ribonucleotides. Some exemplary Dicer substrates lengths and structures are 21+0, 21+2, 21−2, 22+0, 22+1, 22−1, 23+0, 23+2, 23−2, 24+0, 24+2, 24−2, 25+0, 25+2, 25−2, 26+0, 26+2, 26−2, 27+0, 27+2, and 27−2.

The sense strand of a Dicer substrate may be between about 22 to about 30 (e.g., about 22, 23, 24, 25, 26, 27, 28, 29 or 30); about 22 to about 28; about 24 to about 30; about 25 to about 30; about 26 to about 30; about 26 and 29; or about 27 to about 28 nucleotides in length. In certain preferred embodiments Dicer substrates contain sense and antisense strands, that are at least about 25 nucleotides in length and no longer than about 30 nucleotides; between about 26 and 29 nucleotides; or 27 nucleotides in length. The sense and antisense strands may be the same length (blunt ended), different lengths (have overhangs), or a combination. The sense and antisense strands may exist on the same polynucleotide or on different polynucleotides. A Dicer substrate may have a duplex region of about 19, 20, 21, 22, 23, 24, 25 or 27 nucleotides.

Like other siNA molecules provided herein, the antisense strand of a Dicer substrate may have any sequence that anneals to the antisense strand under biological conditions, such as within the cytoplasm of a eukaryotic cell.

Dicer substrates may have any modifications to the nucleotide base, sugar or phosphate backbone as known in the art and/or as described herein for other nucleic acid molecules (such as siNA molecules). In certain embodiments, Dicer substrates may have a sense strand is modified for Dicer processing by suitable modifiers located at the 3′ end of the sense strand, i.e., the dsRNA is designed to direct orientation of Dicer binding and processing. Suitable modifiers include nucleotides such as deoxyribonucleotides, dideoxyribonucleotides, acyclonucleotides and the like and sterically hindered molecules, such as fluorescent molecules and the like. Acyclonucleotides substitute a 2-hydroxyethoxymethyl group for-the 2′-deoxyribofuranosyl sugar normally present in dNMPs. Other nucleotides modifiers that could be used in Dicer substrate siNA molecules include 3′-deoxyadenosine (cordycepin), 3′-azido-3′-deoxythymidine (AZT), 2′,3′-dideoxyinosine (ddI), 2′,3′-dideoxy-3′-thiacytidine (3TC), 2′,3′-didehydro-2′,3′-dideoxythymidine (d4T) and the monophosphate nucleotides of 3′-azido-3′-deoxythymidine (AZT), 2′,3′-dideoxy-3′-thiacytidine (3TC) and 2′,3′-didehydro-2′,3′-dideoxythymidine (d4T). In one embodiment, deoxyribonucleotides are used as the modifiers. When nucleotide modifiers are utilized, they may replace ribonucleotides (e.g., 1-3 nucleotide modifiers, or 2 nucleotide modifiers are substituted for the ribonucleotides on the 3′ end of the sense strand) such that the length of the Dicer substrate does not change. When sterically hindered molecules are utilized, they may be attached to the ribonucleotide at the 3′ end of the antisense strand. Thus, in certain embodiments the length of the strand does not change with the incorporation of the modifiers. In certain embodiments, two DNA bases in the dsRNA are substituted to direct the orientation of Dicer processing of the antisense strand. In a further embodiment of, two terminal DNA bases are substituted for two ribonucleotides on the 3′-end of the sense strand forming a blunt end of the duplex on the 3′ end of the sense strand and the 5′ end of the antisense strand, and a two-nucleotide RNA overhang is located on the 3′-end of the antisense strand. This is an asymmetric composition with DNA on the blunt end and RNA bases on the overhanging end.

In certain embodiments modifications are included in the Dicer substrate such that the modification does not prevent the nucleic acid molecule from serving as a substrate for Dicer. In one embodiment, one or more modifications are made that enhance Dicer processing of the Dicer substrate. One or more modifications may be made that result in more effective RNAi generation. One or more modifications may be made that support a greater RNAi effect. One or more modifications are made that result in greater potency per each Dicer substrate to be delivered to the cell. Modifications may be incorporated in the 3′-terminal region, the 5′-terminal region, in both the 3′-terminal and 5′-terminal region or at various positions within the sequence. Any number and combination of modifications can be incorporated into the Dicer substrate so long as the modification does not prevent the nucleic acid molecule from serving as a substrate for Dicer. Where multiple modifications are present, they may be the same or different. Modifications to bases, sugar moieties, the phosphate backbone, and their combinations are contemplated. Either 5′-terminus can be phosphorylated.

Examples of Dicer substrate phosphate backbone modifications include phosphonates, including methylphosphonate, phosphorothioate, and phosphotriester modifications such as alkylphosphotriesters, and the like. Examples of Dicer substrate sugar moiety modifications include 2′-alkyl pyrimidine, such as 2′-O-methyl, 2′-fluoro, amino, and deoxy modifications and the like (see, e.g., Amarzguioui et al., 2003). Examples of Dicer substrate base group modifications include abasic sugars, 2-O-alkyl modified pyrimidines, 4-thiouracil, 5-bromouracil, 5-iodouracil, and 5-(3-aminoallyl)-uracil and the like. Locked nucleic acids, or LNA's, could also be incorporated.

The sense strand may be modified for Dicer processing by suitable modifiers located at the 3′ end of the sense strand, i.e., the Dicer substrate is designed to direct orientation of Dicer binding and processing. Suitable modifiers include nucleotides such as deoxyribonucleotides, dideoxyribonucleotides, acyclonucleotides and the like and sterically hindered molecules, such as fluorescent molecules and the like. Acyclonucleotides substitute a 2-hydroxyethoxymethyl group for-the 2′-deoxyribofuranosyl sugar normally present in dNMPs. Other nucleotides modifiers could include 3′-deoxyadenosine (cordycepin), 3′-azido-3′-deoxythymidine (AZT), 2′,3′-dideoxyinosine (ddI), 2′,3′-dideoxy-3′-thiacytidine (3TC), 2′,3′-didehydro-2′,3′-dideoxythymidine (d4T) and the monophosphate nucleotides of 3′-azido-3′-deoxythymidine (AZT), 2′,3′-dideoxy-3′-thiacytidine (3TC) and 2′,3′-didehydro-2′,3′-dideoxythymidine (d4T). In one embodiment, deoxyribonucleotides are used as the modifiers. When nucleotide modifiers are utilized, 1-3 nucleotide modifiers, or 2 nucleotide modifiers are substituted for the ribonucleotides on the 3′ end of the sense strand. When sterically hindered molecules are utilized, they are attached to the ribonucleotide at the 3′ end of the antisense strand. Thus, the length of the strand does not change with the incorporation of the modifiers. In another embodiment, substituting two DNA bases in the Dicer substrate to direct the orientation of Dicer processing of the antisense strand is contemplated. In a further embodiment of the present invention, two terminal DNA bases are substituted for two ribonucleotides on the 3′-end of the sense strand forming a blunt end of the duplex on the 3′ end of the sense strand and the 5′ end of the antisense strand, and a two-nucleotide RNA overhang is located on the 3′-end of the antisense strand. This is an asymmetric composition with DNA on the blunt end and RNA bases on the overhanging end.

The antisense strand may be modified for Dicer processing by suitable modifiers located at the 3′ end of the antisense strand, i.e., the dsRNA is designed to direct orientation of Dicer binding and processing. Suitable modifiers include nucleotides such as deoxyribonucleotides, dideoxyribonucleotides, acyclonucleotides and the like and sterically hindered molecules, such as fluorescent molecules and the like. Acyclonucleotides substitute a 2-hydroxyethoxymethyl group for the 2′-deoxyribofuranosyl sugar normally present in dNMPs. Other nucleotide modifiers could include 3′-deoxyadenosine (cordycepin), 3′-azido-3′-deoxythymidine (AZT), 2′,3′-dideoxyinosine (ddI), 2′,3′-dideoxy-3′-thiacytidine (3TC), 2′,3′-didehydro-2′,3′-dideoxythymidine (d4T) and the monophosphate nucleotides of 3′-azido-3′-deoxythymidine (AZT), 2′,3′-dideoxy-3′-thiacytidine (3TC) and 2′,3′-didehydro-2′,3′-dideoxythymidine (d4T). In one embodiment, deoxyribonucleotides are used as the modifiers. When nucleotide modifiers are utilized, 1-3 nucleotide modifiers, or 2 nucleotide modifiers are substituted for the ribonucleotides on the 3′ end of the antisense strand. When sterically hindered molecules are utilized, they are attached to the ribonucleotide at the 3′ end of the antisense strand. Thus, the length of the strand does not change with the incorporation of the modifiers. In another embodiment, the two DNA bases in the dsRNA may be substituted to direct the orientation of Dicer processing. In a further embodiment, two terminal DNA bases are located on the 3′ end of the antisense strand in place of two ribonucleotides forming a blunt end of the duplex on the 5′ end of the sense strand and the 3′ end of the antisense strand, and a two-nucleotide RNA overhang is located on the 3′-end of the sense strand. This is an asymmetric composition with DNA on the blunt end and RNA bases on the overhanging end.

Dicer substrates with a sense and an antisense strand can be linked by a third structure. The third structure will not block Dicer activity on the Dicer substrate and will not interfere with the directed destruction of the RNA transcribed from the target gene. The third structure may be a chemical linking group. Suitable chemical linking groups are known in the art and can be used. Alternatively, the third structure may be an oligonucleotide that links the two oligonucleotides of the dsRNA is a manner such that a hairpin structure is produced upon annealing of the two oligonucleotides making up the Dicer substrate. The hairpin structure preferably does not block Dicer activity on the Dicer substrate or interfere with the directed destruction of the RNA transcribed from the target gene.

The sense and antisense strands of the Dicer substrate are not required to be completely complementary. They only need to be substantially complementary to anneal under biological conditions and to provide a substrate for Dicer that produces an siRNA sufficiently complementary to the target sequence.

Dicer substrate can have certain properties that enhance its processing by Dicer. The Dicer substrate can have a length sufficient such that it is processed by Dicer to produce an active nucleic acid molecules (e.g., siRNA) and may have one or more of the following properties: (i) the Dicer substrate is asymmetric, e.g., has a 3′ overhang on the first strand (antisense strand) and (ii) the Dicer substrate has a modified 3′ end on the second strand (sense strand) to direct orientation of Dicer binding and processing of the Dicer substrate to an active siRNA. The Dicer substrate can be asymmetric such that the sense strand includes 22-28 nucleotides and the antisense strand includes 24-30 nucleotides. Thus, the resulting Dicer substrate has an overhang on the 3′ end of the antisense strand. The overhang is 1-3 nucleotides, for example 2 nucleotides. The sense strand may also have a 5′ phosphate.

A Dicer substrate may have an overhang on the 3′ end of the antisense strand and the sense strand is modified for Dicer processing. The 5′ end of the sense strand may have a phosphate. The sense and antisense strands may anneal under biological conditions, such as the conditions found in the cytoplasm of a cell. A region of one of the strands, particularly the antisense strand, of the Dicer substrate may have a sequence length of at least 19 nucleotides, wherein these nucleotides are in the 21-nucleotide region adjacent to the 3′ end of the antisense strand and are sufficiently complementary to a nucleotide sequence of the RNA produced from the target gene. A Dicer substrate may also have one or more of the following additional properties: (a) the antisense strand has a right shift from a corresponding 21-mer (i.e., the antisense strand includes nucleotides on the right side of the molecule when compared to the corresponding 21-mer), (b) the strands may not be completely complementary, i.e., the strands may contain simple mismatch pairings and (c) base modifications such as locked nucleic acid(s) may be included in the 5′ end of the sense strand.

An antisense strand of a Dicer substrate nucleic acid molecule may be modified to include 1-9 ribonucleotides on the 5′-end to give a length of 22-28 nucleotides. When the antisense strand has a length of 21 nucleotides, then 1-7 ribonucleotides, or 2-5 ribonucleotides and or 4 ribonucleotides may be added on the 3′-end. The added ribonucleotides may have any sequence. Although the added ribonucleotides may be complementary to the target gene sequence, full complementarity between the target sequence and the antisense strands is not required. That is, the resultant antisense strand is sufficiently complementary with the target sequence. A sense strand may then have 24-30 nucleotides. The sense strand may be substantially complementary with the antisense strand to anneal to the antisense strand under biological conditions. In one embodiment, the antisense strand may be synthesized to contain a modified 3′-end to direct Dicer processing. The sense strand may have a 3′ overhang. The antisense strand may be synthesized to contain a modified 3′-end for Dicer binding and processing and the sense strand has a 3′ overhang.

TIMP1 and TIMP2

Exemplary nucleic acid sequence of target tissue inhibitors of metalloproteinase-1 and -2 (human TIMP1 and TIMP2) cDNA is disclosed in GenBank accession numbers: NM_003454 and NM_003455 and the corresponding mRNA sequence, for example as listed as SEQ ID NO: 1 and SEQ ID NO:2. One of ordinary skill in the art would understand that a given sequence may change over time and to incorporate any changes needed in the nucleic acid molecules herein accordingly.

Expression of TIMP1 and TIMP2 was shown to be increased in fibrotic liver from rats with hepatic fibrosis (Nie, et al 2004. World J. Gastroenterol. 10:86-90). TIMP1 and TIMP2 are potential targets for the treatment of fibrosis.

Methods and Compositions for Inhibiting TIMP1 and TIMP2

Provided are compositions and methods for inhibition of TIMP1 and TIMP2 expression by using small nucleic acid molecules, such as short interfering nucleic acid (siNA), interfering RNA (RNAi), short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), and short hairpin RNA (shRNA) molecules capable of mediating or that mediate RNA interference against TIMP1 and TIMP2 gene expression. The composition and methods disclosed herein are also useful in treating various fibrosis such as liver fibrosis, lung fibrosis, kidney fibrosis and fibrotic conditions shown in Table I, supra.

Nucleic acid molecule(s) and/or methods as disclosed herein may be used to down regulate the expression of gene(s) that encode RNA referred to, by example, Genbank Accession NM_003254.2 and NM_004255.4.

Compositions, methods and kits provided herein may include one or more nucleic acid molecules (e.g., siNA) and methods that independently or in combination modulate (e.g., downregulate) the expression of TIMP1 and or TIMP2 protein and/or genes encoding TIMP1 and TIMP2 proteins, proteins and/or genes encoding TIMP1 and TIMP2 associated with the maintenance and/or development of diseases, conditions or disorders associated with TIMP1 and TIMP2, such as liver fibrosis, cirrhosis, pulmonary fibrosis, kidney fibrosis, peritoneal fibrosis, chronic hepatic damage, and fibrillogenesis (e.g., genes encoding sequences comprising those sequences referred to by GenBank Accession Nos. NM-003254 and NM_003255), or a TIMP1 and TIMP2 gene family member where the genes or gene family sequences share sequence homology. The description of the various aspects and embodiments is provided with reference to exemplary genes TIMP1 and TIMP2. However, the various aspects and embodiments are also directed to other related TIMP1 and TIMP2 genes, such as homolog genes and transcript variants, and polymorphisms (e.g., single nucleotide polymorphism, (SNPs)) associated with certain TIMP1 and TIMP2 genes. As such, the various aspects and embodiments are also directed to other genes that are involved in TIMP1 and TIMP2 mediated pathways of signal transduction or gene expression that are involved, for example, in the maintenance or development of diseases, traits, or conditions described herein. These additional genes can be analyzed for target sites using the methods described for the TIMP1 and TIMP2 gene herein. Thus, the modulation of other genes and the effects of such modulation of the other genes can be performed, determined, and measured as described herein.

In one embodiment, compositions and methods provided herein include a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a TIMP1 and TIMP2 gene (e.g., human TIMP1 and TIMP2 exemplified by SEQ ID NO: 1 and SEQ ID NO:2, respectively), where the nucleic acid molecule includes about 15 to about 49 base pairs.

In one embodiment, a nucleic acid disclosed may be used to inhibit the expression of the TIMP1 and TIMP2 gene or a TIMP1 and TIMP2 gene family where the genes or gene family sequences share sequence homology. Such homologous sequences can be identified as is known in the art, for example using sequence alignments. Nucleic acid molecules can be designed to target such homologous sequences, for example using perfectly complementary sequences or by incorporating non-canonical base pairs, for example mismatches and/or wobble base pairs, that can provide additional target sequences. In instances where mismatches are identified, non-canonical base pairs (for example, mismatches and/or wobble bases) can be used to generate nucleic acid molecules that target more than one gene sequence. In a non-limiting example, non-canonical base pairs such as UU and CC base pairs are used to generate nucleic acid molecules that are capable of targeting sequences for differing TIMP1 and TIMP2 targets that share sequence homology. As such, one advantage of using siNAs disclosed herein is that a single nucleic acid can be designed to include nucleic acid sequence that is complementary to the nucleotide sequence that is conserved between the homologous genes. In this approach, a single nucleic acid can be used to inhibit expression of more than one gene instead of using more than one nucleic acid molecule to target the different genes.

Nucleic acid molecules may be used to target conserved sequences corresponding to a gene family or gene families such as TIMP1 and TIMP2 family genes. As such, nucleic acid molecules targeting multiple TIMP1 and TIMP2 targets can provide increased therapeutic effect. In addition, nucleic acid can be used to characterize pathways of gene function in a variety of applications. For example, nucleic acid molecules can be used to inhibit the activity of target gene(s) in a pathway to determine the function of uncharacterized gene(s) in gene function analysis, mRNA function analysis, or translational analysis. The nucleic acid molecules can be used to determine potential target gene pathways involved in various diseases and conditions toward pharmaceutical development. The nucleic acid molecules can be used to understand pathways of gene expression involved in, for example fibroses such as liver, kidney or pulmonary fibrosis, and/or inflammatory and proliferative traits, diseases, disorders, and/or conditions.

In one embodiment, the compositions and methods provided herein include a nucleic acid molecule having RNAi activity against TIMP1 RNA, where the nucleic acid molecule includes a sequence complementary to any RNA having TIMP1 encoding sequence. In another embodiment, a nucleic acid molecule may have RNAi activity against TIMP1 RNA, where the nucleic acid molecule includes a sequence complementary to an RNA having variant TIMP1 encoding sequence, for example other mutant TIMP1 genes known in the art to be associated with the maintenance and/or development of fibrosis. In another embodiment, a nucleic acid molecule disclosed herein includes a nucleotide sequence that can interact with nucleotide sequence of a TIMP1 gene and thereby mediate silencing of TIMP1 gene expression, for example, wherein the nucleic acid molecule mediates regulation of TIMP1 gene expression by cellular processes that modulate the chromatin structure or methylation patterns of the TIMP1 gene and prevent transcription of the TIMP1 gene.

In another embodiment the compositions and methods provided herein include a nucleic acid molecule having RNAi activity against TIMP2 RNA, where the nucleic acid molecule includes a sequence complementary to any RNA having TIMP2 encoding sequence, such as those sequences having GenBank Accession No. NM_003455. Nucleic acid molecules may have RNAi activity against TIMP2 RNA, where the nucleic acid molecule includes a sequence complementary to an RNA having variant TIMP2 encoding sequence, for example other mutant TIMP2 genes known in the art to be associated with the maintenance and/or development of fibrosis. Nucleic acid molecules disclosed herein include a nucleotide sequence that can interact with nucleotide sequence of a TIMP2 gene and thereby mediate silencing of TIMP1 gene expression, e.g., where the nucleic acid molecule mediates regulation of TIMP2 gene expression by cellular processes that modulate the chromatin structure or methylation patterns of the TIMP2 gene and prevent transcription of the TIMP2 gene.

Methods of Treatment

In one embodiment, nucleic acid molecules may be used to down regulate or inhibit the expression of TIMP1 and/or TIMP1 proteins arising from TIMP1 and/or TIMP1 haplotype polymorphisms that are associated with a disease or condition, (e.g., fibrosis). Analysis of TIMP1 and/or TIMP1 genes, or TIMP1 and/or TIMP1 protein or RNA levels can be used to identify subjects with such polymorphisms or those subjects who are at risk of developing traits, conditions, or diseases described herein. These subjects are amenable to treatment, for example, treatment with nucleic acid molecules disclosed herein and any other composition useful in treating diseases related to TIMP1 and/or TIMP1 gene expression. As such, analysis of TIMP1 and/or TIMP1 protein or RNA levels can be used to determine treatment type and the course of therapy in treating a subject. Monitoring of TIMP1 and/or TIMP1 protein or RNA levels can be used to predict treatment outcome and to determine the efficacy of compounds and compositions that modulate the level and/or activity of certain TIMP1 and/or TIMP1 proteins associated with a trait, condition, or disease.

In one embodiment, nucleic acid molecules may be used to down regulate or inhibit the expression of TIMP2 and/or TIMP2 proteins arising from TIMP2 and/or TIMP2 haplotype polymorphisms that are associated with a disease or condition, (e.g., fibrosis). Analysis of TIMP2 and/or TIMP2 genes, or TIMP2 and/or TIMP2 protein or RNA levels can be used to identify subjects with such polymorphisms or those subjects who are at risk of developing traits, conditions, or diseases described herein. These subjects are amenable to treatment, for example, treatment with nucleic acid molecules disclosed herein and any other composition useful in treating diseases related to TIMP2 and/or TIMP2 gene expression. As such, analysis of TIMP2 and/or TIMP2 protein or RNA levels can be used to determine treatment type and the course of therapy in treating a subject. Monitoring of TIMP2 and/or TIMP2 protein or RNA levels can be used to predict treatment outcome and to determine the efficacy of compounds and compositions that modulate the level and/or activity of certain TIMP2 and/or TIMP2 proteins associated with a trait, condition, or disease.

Provided are compositions and methods for inhibition of TIMP1 and TIMP2 expression by using small nucleic acid molecules as provided herein, such as short interfering nucleic acid (siNA), interfering RNA (RNAi), short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), and short hairpin RNA (shRNA) molecules capable of mediating or that mediate RNA interference against TIMP1 and TIMP2 gene expression. The composition and methods disclosed herein are also useful in treating various fibrosis such as liver fibrosis, lung fibrosis, and kidney fibrosis.

The nucleic acid molecules disclosed herein individually, or in combination or in conjunction with other drugs, can be use for preventing or treating diseases, traits, conditions and/or disorders associated with TIMP1 and TIMP2, such as liver fibrosis, cirrhosis, pulmonary fibrosis, kidney fibrosis, peritoneal fibrosis, chronic hepatic damage, and fibrillogenesis.

The nucleic acid molecules disclosed herein are able to inhibit the expression of TIMP1 or TIMP2 in a sequence specific manner. The nucleic acid molecules may include a sense strand and an antisense strand which include contiguous nucleotides that are at least partially complementary (antisense) to a TIMP1 or TIMP2 mRNA.

In some embodiments, dsRNA specific for TIMP1 or TIMP2 can be used in conjunction with other dsRNA specific for other molecular chaperones that assist in the folding of newly synthesized proteins such as, calnexin, calreticulin, BiP (Bergeron et al. Trends Biochem. Sci. 1994; 19:124-128; Herbert et al. 1995; Cold Spring Harb. Symp. Quant. Biol. 60:405-415)

Fibrosis can be treated by RNA interference using nucleic acid molecules as disclosed herein. Exemplary fibrosis include liver fibrosis, peritoneal fibrosis, lung fibrosis, kidney fibrosis, vocal cord fibrosis, intestinal fibrosis. The nucleic acid molecules disclosed herein may inhibit the expression of TIMP1 or TIMP2 in a sequence specific manner.

Treatment of fibrosis can be monitored by determining the level of extracellular collagen using suitable techniques known in the art such as, using anti-collagen I antibodies. Treatment can also be monitored by determining the level of TIMP1 or TIMP2 mRNA or the level of TIMP1 or TIMP2 protein in the cells of the affected tissue. Treatment can also be monitored by non-invasive scanning of the affected organ or tissue such as by computer assisted tomography scan, magnetic resonance elastography scans.

A method for treating or preventing TIMP1 associated disease or condition in a subject or organism may include contacting the subject or organism with a nucleic acid molecule as provided herein under conditions suitable to modulate the expression of the TIMP1 gene in the subject or organism.

A method for treating or preventing TIMP2 associated disease or condition in a subject or organism may include contacting the subject or organism with a nucleic acid molecule as provided herein under conditions suitable to modulate the expression of the TIMP2 gene in the subject or organism.

A method for treating or preventing fibrosis in a subject or organism may include contacting the subject or organism with a nucleic acid molecule under conditions suitable to modulate the expression of the TIMP1 and/or TIMP2 gene in the subject or organism.

A method for treating or preventing one or more fibroses selected from the group consisting of liver fibrosis, kidney fibrosis, and pulmonary fibrosis in a subject or organism may include contacting the subject or organism with a nucleic acid molecule under conditions suitable to modulate the expression of the TIMP1 and/or TIMP2 gene in the subject or organism.

Fibrotic Diseases

Fibrotic diseases are generally characterized by the excess deposition of a fibrous material within the extracellular matrix, which contributes to abnormal changes in tissue architecture and interferes with normal organ function.

All tissues damaged by trauma respond by the initiation of a wound-healing program. Fibrosis, a type of disorder characterized by excessive scarring, occurs when the normal self-limiting process of wound healing response is disturbed, and causes excessive production and deposition of collagen. As a result, normal organ tissue is replaced with scar tissue, which eventually leads to the functional failure of the organ.

Fibrosis may be initiated by diverse causes and in various organs. Liver cirrhosis, pulmonary fibrosis, sarcoidosis, keloids and kidney fibrosis are all chronic conditions associated with progressive fibrosis, thereby causing a continuous loss of normal tissue function.

Acute fibrosis (usually with a sudden and severe onset and of short duration) occurs as a common response to various forms of trauma including accidental injuries (particularly injuries to the spine and central nervous system), infections, surgery, ischemic illness (e.g. cardiac scarring following heart attack), burns, environmental pollutants, alcohol and other types of toxins, acute respiratory distress syndrome, radiation and chemotherapy treatments).

Fibrosis, a fibrosis related pathology or a pathology related to aberrant crosslinking of cellular proteins may all be treated by the siRNAs disclosed herein. Fibrotic diseases or diseases in which fibrosis is evident (fibrosis related pathology) include both acute and chronic forms of fibrosis of organs, including all etiological variants of the following: pulmonary fibrosis, including interstitial lung disease and fibrotic lung disease, liver fibrosis, cardiac fibrosis including myocardial fibrosis, kidney fibrosis including chronic renal failure, skin fibrosis including scleroderma, keloids and hypertrophic scars; myelofibrosis (bone marrow fibrosis); fibrosis in the brain associated with bain infarction; all types of ocular scarring including proliferative vitreoretinopathy (PVR) and scarring resulting from surgery to treat cataract or glaucoma; inflammatory bowel disease of variable etiology, macular degeneration, Grave's ophthalmopathy, drug induced ergotism, keloid scars, scleroderma, psoriasis, glioblastoma in Li-Fraumeni syndrome, sporadic glioblastoma, myleoid leukemia, acute myelogenous leukemia, myelodysplastic syndrome, myeloproferative syndrome, gynecological cancer, Kaposi's sarcoma, Hansen's disease, fibrosis associated with brain infarction and collagenous colitis.

In various embodiments, the compounds (nucleic acid molecules) as disclosed herein may be used to treat fibrotic diseases, for example as disclosed herein, as well as many other diseases and conditions apart from fibrotic diseases, for example such as disclosed herein. Other conditions to be treated include fibrotic diseases in other organs—kidney fibrosis for any reason (CKD including ESRD); lung fibrosis (including ILF); myelofibrosis, abnormal scarring (keloids) associated with all possible types of skin injury accidental and jatrogenic (operations); scleroderma; cardiofibrosis, failure of glaucoma filtering operation; intestinal adhesions.

Ocular Surgery and Fibrotic Complications

Contracture of scar tissue resulting from eye surgery may often occur. Glaucoma surgery to create new drainage channels often fails due to scarring and contraction of tissues and the generated drainage system may be blocked requiring additional surgical intervention. Current anti-scarring regimens (Mitomycin C or 5FU) are limited due to the complications involved (e.g. blindness) e.g. see Cordeiro M F, et al., Human anti-transforming growth factor-beta2 antibody: a new glaucoma anti-scarring agent Invest Ophthalmol Vis Sci. 1999 September; 40(10):2225-34. There may also be contraction of scar tissue formed after corneal trauma or corneal surgery, for example laser or surgical treatment for myopia or refractive error in which contraction of tissues may lead to inaccurate results. Scar tissue may be formed on/in the vitreous humor or the retina, for example, and may eventually causes blindness in some diabetics, and may be formed after detachment surgery, called proliferative vitreoretinopathy (PVR). PVR is the most common complication following retinal detachment and is associated with a retinal hole or break. PVR refers to the growth of cellular membranes within the vitreous cavity and on the front and back surfaces of the retina containing retinal pigment epithelial (RPE) cells. These membranes, which are essentially scar tissues, exert traction on the retina and may result in recurrences of retinal detachment, even after an initially successful retinal detachment procedure.

Scar tissue may be formed in the orbit or on eye and eyelid muscles after squint, orbital or eyelid surgery, or thyroid eye disease, and where scarring of the conjunctiva occurs as may happen after glaucoma surgery or in cicatricial disease, inflammatory disease, for example, pemphigoid, or infective disease, for example, trachoma. A further eye problem associated with the contraction of collagen-including tissues is the opacification and contracture of the lens capsule after cataract extraction. Important role for MMPs has been recognized in ocular diseases including wound healing, dry eye, sterile corneal ulceration, recurrent epithelial erosion, corneal neovascularization, pterygium, conjuctivochalasis, glaucoma, PVR, and ocular fibrosis.

Liver Fibrosis

Liver fibrosis (LF) is a generally irreversible consequence of hepatic damage of several etiologies. In the Western world, the main etiologic categories are: alcoholic liver disease (30-50%), viral hepatitis (30%), biliary disease (5-10%), primary hemochromatosis (5%), and drug-related and cryptogenic cirrhosis of, unknown etiology, (10-15%). Wilson's disease, al-antitrypsin deficiency and other rare diseases also have liver fibrosis as one of the symptoms. Liver cirrhosis, the end stage of liver fibrosis, frequently requires liver transplantation and is among the top ten causes of death in the Western world.

Kidney Fibrosis and Related Conditions.
Chronic Renal Failure (CRF)

Chronic renal failure is a gradual and progressive loss of the ability of the kidneys to excrete wastes, concentrate urine, and conserve electrolytes. CRF is slowly progressive. It most often results from any disease that causes gradual loss of kidney function, and fibrosis is the main pathology that produces CRF.

Diabetic Nephropathy

Diabetic nephropathy, hallmarks of which are glomerulosclerosis and tubulointerstitial fibrosis, is the single most prevalent cause of end-stage renal disease in the modern world, and diabetic patients constitute the largest population on dialysis. Such therapy is costly and far from optimal. Transplantation offers a better outcome but suffers from a severe shortage of donors.

Chronic Kidney Disease

Chronic kidney disease (CKD) is a worldwide public health problem and is recognized as a common condition that is associated with an increased risk of cardiovascular disease and chronic renal failure (CRF).

The Kidney Disease Outcomes Quality Initiative (K/DOQI) of the National Kidney Foundation (NKF) defines chronic kidney disease as either kidney damage or a decreased kidney glomerular filtration rate (GFR) for three or more months. Other markers of CKD are also known and used for diagnosis. In general, the destruction of renal mass with irreversible sclerosis and loss of nephrons leads to a progressive decline in GFR. Recently, the K/DOQI published a classification of the stages of CKD, as follows:

Stage 1: Kidney damage with normal or increased GFR (>90 mL/min/1.73 m2)

Stage 2: Mild reduction in GFR (60-89 mL/min/1.73 m2)

Stage 3: Moderate reduction in GFR (30-59 mL/min/1.73 m2)

Stage 4: Severe reduction in GFR (15-29 mL/min/1.73 m2)

Stage 5: Kidney failure (GFR <15 mL/min/1.73 m2 or dialysis)

In stages 1 and 2 CKD, GFR alone does not confirm the diagnosis. Other markers of kidney damage, including abnormalities in the composition of blood or urine or abnormalities in imaging tests, may be relied upon.

Pathophysiology of CKD

Approximately 1 million nephrons are present in each kidney, each contributing to the total GFR. Irrespective of the etiology of renal injury, with progressive destruction of nephrons, the kidney is able to maintain GFR by hyperfiltration and compensatory hypertrophy of the remaining healthy nephrons. This nephron adaptability allows for continued normal clearance of plasma solutes so that substances such as urea and creatinine start to show significant increases in plasma levels only after total GFR has decreased to 50%, when the renal reserve has been exhausted. The plasma creatinine value will approximately double with a 50% reduction in GFR. Therefore, a doubling in plasma creatinine from a baseline value of 0.6 mg/dL to 1.2 mg/dL in a patient actually represents a loss of 50% of functioning nephron mass.

The residual nephron hyperfiltration and hypertrophy, although beneficial for the reasons noted, is thought to represent a major cause of progressive renal dysfunction. This is believed to occur because of increased glomerular capillary pressure, which damages the capillaries and leads initially to focal and segmental glomerulosclerosis and eventually to global glomerulosclerosis. This hypothesis has been based on studies of five-sixths nephrectomized rats, which develop lesions that are identical to those observed in humans with CKD.

The two most common causes of chronic kidney disease are diabetes and hypertension. Other factors include acute insults from nephrotoxins, including contrasting agents, or decreased perfusion; Proteinuria; Increased renal ammoniagenesis with interstitial injury; Hyperlipidemia; Hyperphosphatemia with calcium phosphate deposition; Decreased levels of nitrous oxide and smoking.

In the United States, the incidence and prevalence of CKD is rising, with poor outcomes and high cost to the health system. Kidney disease is the ninth leading cause of death in the US. The high rate of mortality has led the US Surgeon General's mandate for America's citizenry, Healthy People 2010, to contain a chapter focused on CKD. The objectives of this chapter are to articulate goals and to provide strategies to reduce the incidence, morbidity, mortality, and health costs of chronic kidney disease in the United States.

The incidence rates of end-stage renal disease (ESRD) have also increased steadily internationally since 1989. The United States has the highest incident rate of ESRD, followed by Japan. Japan has the highest prevalence per million population, followed by the US.

The mortality rates associated with hemodialysis are striking and indicate that the life expectancy of patients entering into hemodialysis is markedly shortened. At every age, patients with ESRD on dialysis have significantly increased mortality when compared with nondialysis patients and individuals without kidney disease. At age 60 years, a healthy person can expect to live for more than 20 years, whereas the life expectancy of a 60-year-old patient starting hemodialysis is closer to 4 years (Aurora and Verelli, May 21, 2009. Chronic Renal Failure: Treatment & Medication. Emedicine. http://emedicine.medscape.com/article/238798-treatment).

Pulmonary Fibrosis

Interstitial pulmonary fibrosis (IPF) is scarring of the lung caused by a variety of inhaled agents including mineral particles, organic dusts, and oxidant gases, or by unknown reasons (idiopathic lung fibrosis). The disease afflicts millions of individuals worldwide, and there are no effective therapeutic approaches. A major reason for the lack of useful treatments is that few of the molecular mechanisms of disease have been defined sufficiently to design appropriate targets for therapy (Lasky J A., Brody A R. (2000), “Interstitial fibrosis and growth factors”, Environ Health Perspect.; 108 Suppl 4:751-62).

Cardiac Fibrosis

Heart failure is unique among the major cardiovascular disorders in that it alone is increasing in prevalence while there has been a striking decrease in other conditions. Some of this can be attributed to the aging of the populations of the United States and Europe. The ability to salvage patients with myocardial damage is also a major factor, as these patients may develop progression of left ventricular dysfunction due to deleterious remodelling of the heart.

The normal myocardium is composed of a variety of cells, cardiac myocytes and noncardiomyocytes, which include endothelial and vascular smooth muscle cells and fibroblasts.

Structural remodeling of the ventricular wall is a key determinant of clinical outcome in heart disease. Such remodeling involves the production and destruction of extracellular matrix proteins, cell proliferation and migration, and apoptotic and necrotic cell death. Cardiac fibroblasts are crucially involved in these processes, producing growth factors and cytokines that act as autocrine and paracrine factors, as well as extracellular matrix proteins and proteinases. Recent studies have shown that the interactions between cardiac fibroblasts and cardiomyocytes are essential for the progression of cardiac remodeling of which the net effect is deterioration in cardiac function and the onset of heart failure (Manabe I, et al., (2002), “Gene expression in fibroblasts and fibrosis: involvement in cardiac hypertrophy”, Circ Res. 13; 91(12):1103-13).

Burns and Scars

A particular problem which may arise, particularly in fibrotic disease, is contraction of tissues, for example contraction of scars. Contraction of tissues including extracellular matrix components, especially of collagen-including tissues, may occur in connection with many different pathological conditions and with surgical or cosmetic procedures. Contracture, for example, of scars, may cause physical problems, which may lead to the need for medical treatment, or it may cause problems of a purely cosmetic nature. Collagen is the major component of scar and other contracted tissue and as such is the most important structural component to consider. Nevertheless, scar and other contracted tissue also includes other structural components, especially other extracellular matrix components, for example, elastin, which may also contribute to contraction of the tissue.

Contraction of collagen-including tissue, which may also include other extracellular matrix components, frequently occurs in the healing of burns. The burns may be chemical, thermal or radiation burns and may be of the eye, the surface of the skin or the skin and the underlying tissues. It may also be the case that there are burns on internal tissues, for example, caused by radiation treatment. Contraction of burnt tissues is often a problem and may lead to physical and/or cosmetic problems, for example, loss of movement and/or disfigurement.

Skin grafts may be applied for a variety of reasons and may often undergo contraction after application. As with the healing of burnt tissues the contraction may lead to both physical and cosmetic problems. It is a particularly serious problem where many skin grafts are needed as, for example, in a serious burns case.

Contraction is also a problem in production of artificial skin. To make a true artificial skin it is necessary to have an epidermis made of epithelial cells (keratinocytes) and a dermis made of collagen populated with fibroblasts. It is important to have both types of cells because they signal and stimulate each other using growth factors. The collagen component of the artificial skin often contracts to less than one tenth of its original area when populated by fibroblasts.

Cicatricial contraction, contraction due to shrinkage of the fibrous tissue of a scar, is common. In some cases the scar may become a vicious cicatrix, a scar in which the contraction causes serious deformity. A patient's stomach may be effectively separated into two separate chambers in an hour-glass contracture by the contraction of scar tissue formed when a stomach ulcer heals. Obstruction of passages and ducts, cicatricial stenosis, may occur due to the contraction of scar tissue. Contraction of blood vessels may be due to primary obstruction or surgical trauma, for example, after surgery or angioplasty. Stenosis of other hollow visci, for examples, ureters, may also occur. Problems may occur where any form of scarring takes place, whether resulting from accidental wounds or from surgery. Conditions of the skin and tendons which involve contraction of collagen-including tissues include post-trauma conditions resulting from surgery or accidents, for example, hand or foot tendon injuries, post-graft conditions and pathological conditions, such as scleroderma, Dupuytren's contracture and epidermolysis bullosa. Scarring and contraction of tissues in the eye may occur in various conditions, for example, the sequelae of retinal detachment or diabetic eye disease (as mentioned above). Contraction of the sockets found in the skull for the eyeballs and associated structures, including extra-ocular muscles and eyelids, may occur if there is trauma or inflammatory damage. The tissues contract within the sockets causing a variety of problems including double vision and an unsightly appearance.

Other indications include Vocal cord fibrosis, Intestinal fibrosis and Fibrosis associated with brain infarction.

For further information on different types of fibrosis see: Molina V, et al., (2002), “Fibrotic diseases”, Harefuah, 141(11): 973-8, 1009; Yu L, et al., (2002), “Therapeutic strategies to halt renal fibrosis”, Curr Opin Pharmacol. 2(2):177-81; Keane W F and Lyle P A. (2003), “Recent advances in management of type 2 diabetes and nephropathy: lessons from the RENAAL study”, Am J Kidney Dis. 41(3 Suppl 2): S22-5; Bohle A, et al., (1989), “The pathogenesis of chronic renal failure”, Pathol Res Pract. 185(4):421-40; Kikkawa R, et al., (1997), “Mechanism of the progression of diabetic nephropathy to renal failure”, Kidney Int Suppl. 62:S39-40; Bataller R, and Brenner D A. (2001), “Hepatic stellate cells as a target for the treatment of liver fibrosis”, Semin Liver Dis. 21(3):437-51; Gross T J and Hunninghake G W, (2001) “Idiopathic pulmonary fibrosis”, N Engl J Med. 345(7):517-25; Frohlich E D. (2001) “Fibrosis and ischemia: the real risks in hypertensive heart disease”, Am J Hypertens; 14(6 Pt 2):194S-199S; Friedman S L. (2003), “Liver fibrosis—from bench to bedside”, J Hepatol. 38 Suppl 1:S38-53; Albanis E, et al., (2003), “Treatment of hepatic fibrosis: almost there”, Curr Gastroenterol Rep. 5(1):48-56; (Weber K T. (2000), “Fibrosis and hypertensive heart disease”, Curr Opin Cardiol. 15(4):264-72).

Delivery of Nucleic Acid Molecules and Pharmaceutical Formulations

Nucleic acid molecules may be adapted for use to prevent or treat fibrotic (e.g., liver, kidney, peritoneal, and pulmonary) diseases, traits, conditions and/or disorders, and/or any other trait, disease, disorder or condition that is related to or will respond to the levels of TIMP1 and TIMP2 in a cell or tissue. A nucleic acid molecule may include a delivery vehicle, including liposomes, for administration to a subject, carriers and diluents and their salts, and/or can be present in pharmaceutically acceptable formulations.

Nucleic acid molecules of the present invention may be delivered to the target tissue by direct application of the naked molecules prepared with a carrier or a diluent.

The terms “naked nucleic acid” or “naked dsRNA” or “naked siRNA” refers to nucleic acid molecules that are free from any delivery vehicle that acts to assist, promote or facilitate entry into the cell, including viral sequences, viral particles, liposome formulations, lipofectin or precipitating agents and the like. For example, dsRNA in PBS is “naked dsRNA”.

Nucleic acid molecules disclosed herein may be delivered or administered directly with a carrier or diluent but not any delivery vehicle that acts to assist, promote or facilitate entry to the cell, including viral vectors, viral particles, liposome formulations, lipofectin or precipitating agents and the like.

Nucleic acid molecules may be delivered or administered to a subject by direct application of the nucleic acid molecules with a carrier or diluent or any other delivery vehicle that acts to assist, promote or facilitate entry into a cell, including viral sequences, viral particular, liposome formulations, lipofectin or precipitating agents and the like. Polypeptides that facilitate introduction of nucleic acid into a desired subject such as those described in US. Application Publication No. 20070155658 (e.g., a melamine derivative such as 2,4,6-Triguanidino Traizine and 2,4,6-Tramidosarcocyl Melamine, a polyarginine polypeptide, and a polypeptide including alternating glutamine and asparagine residues).

Methods for the delivery of nucleic acid molecules are described in Akhtar et al., Trends Cell Bio., 2: 139 (1992); Delivery Strategies for Antisense Oligonucleotide Therapeutics, ed. Akhtar, (1995), Maurer et al., Mol. Membr. Biol., 16: 129-140 (1999); Hofland and Huang, Handb. Exp. Pharmacol., 137: 165-192 (1999); and Lee et al., ACS Symp. Ser., 752: 184-192 (2000); U.S. Pat. Nos. 6,395,713; 6,235,310; 5,225,182; 5,169,383; 5,167,616; 4,959217; 4,925,678; 4,487,603; and 4,486,194 and Sullivan et al., PCT WO 94/02595; PCT WO 00/03683 and PCT WO 02/08754; and U.S. Patent Application Publication No. 2003077829. These protocols can be utilized for the delivery of virtually any nucleic acid molecule. Nucleic acid molecules can be administered to cells by a variety of methods known to those of skill in the art, including, but not restricted to, encapsulation in liposomes, by iontophoresis, or by incorporation into other vehicles, such as biodegradable polymers, hydrogels, cyclodextrins (see e.g., Gonzalez et al., Bioconjugate Chem., 10: 1068-1074 (1999); Wang et al., International PCT publication Nos. WO 03/47518 and WO 03/46185), poly(lactic-co-glycolic)acid (PLGA) and PLCA microspheres (see for example U.S. Pat. No. 6,447,796 and U.S. Application Publication No. 2002130430), biodegradable nanocapsules, and bioadhesive microspheres, or by proteinaceous vectors (O'Hare and Normand, International PCT Publication No. WO 00/53722). Alternatively, the nucleic acid/vehicle combination is locally delivered by direct injection or by use of an infusion pump. Direct injection of the nucleic acid molecules as disclosed herein, whether subcutaneous, intramuscular, or intradermal, can take place using standard needle and syringe methodologies, or by needle-free technologies such as those described in Conry et al., Clin. Cancer Res., 5: 2330-2337 (1999) and Barry et al., International PCT Publication No. WO 99/31262. The molecules of as described herein can be used as pharmaceutical agents. Pharmaceutical agents may prevent, modulate the occurrence, or treat (alleviate a symptom to some extent, preferably all of the symptoms) of a disease state in a subject.

Nucleic acid molecules may be complexed with cationic lipids, packaged within liposomes, or otherwise delivered to target cells or tissues. The nucleic acid or nucleic acid complexes can be locally administered to relevant tissues ex vivo, or in vivo through direct dermal application, transdermal application, or injection, with or without their incorporation in biopolymers.

Delivery systems include surface-modified liposomes containing poly (ethylene glycol) lipids (PEG-modified, or long-circulating liposomes or stealth liposomes). These formulations offer a method for increasing the accumulation of drugs in target tissues. This class of drug carriers resists opsonization and elimination by the mononuclear phagocytic system (MPS or RES), thereby enabling longer blood circulation times and enhanced tissue exposure for the encapsulated drug (Lasic et al. Chem. Rev. 1995, 95, 2601-2627; Ishiwata et al., Chem. Pharm. Bull. 1995, 43, 1005-1011).

Nucleic acid molecules may be formulated or complexed with polyethylenimine (e.g., linear or branched PEI) and/or polyethylenimine derivatives, including for example polyethyleneimine-polyethyleneglycol-N-acetylgalactosamine (PEI-PEG-GAL) or polyethyleneimine-polyethyleneglycol-tri-N-acetylgalactosamine (PEI-PEG-triGAL) derivatives, grafted PEIs such as galactose PEI, cholesterol PEI, antibody derivatized PEI, and polyethylene glycol PEI (PEG-PEI) derivatives thereof (see for example Ogris et al., 2001, AAPA PharmSci, 3, 1-11; Furgeson et al., 2003, Bioconjugate Chem., 14, 840-847; Kunath et al., 2002, Pharmaceutical Research, 19, 810-817; Choi et al., 2001, Bull. Korean Chem. Soc., 22, 46-52; Bettinger et al., 1999, Bioconjugate Chem., 10, 558-561; Peterson et al., 2002, Bioconjugate Chem., 13, 845-854; Erbacher et al., 1999, Journal of Gene Medicine Preprint, 1, 1-18; Godbey et al., 1999., PNAS USA, 96, 5177-5181; Godbey et al., 1999, Journal of Controlled Release, 60, 149-160; Diebold et al., 1999, Journal of Biological Chemistry, 274, 19087-19094; Thomas and Klibanov, 2002, PNAS USA, 99, 14640-14645; Sagara, U.S. Pat. No. 6,586,524 and United States Patent Application Publication No. 20030077829.

Nucleic acid molecules may be complexed with membrane disruptive agents such as those described in U.S. Patent Application Publication No. 20010007666. The membrane disruptive agent or agents and the nucleic acid molecule may also be complexed with a cationic lipid or helper lipid molecule, such as those lipids described in U.S. Pat. No. 6,235,310.

The nucleic acid molecules may be administered via pulmonary delivery, such as by inhalation of an aerosol or spray dried formulation administered by an inhalation device or nebulizer, providing rapid local uptake of the nucleic acid molecules into relevant pulmonary tissues. Solid particulate compositions containing respirable dry particles of micronized nucleic acid compositions can be prepared by grinding dried or lyophilized nucleic acid compositions, and then passing the micronized composition through, for example, a 400 mesh screen to break up or separate out large agglomerates. A solid particulate composition comprising the nucleic acid compositions of contemplated herein can optionally contain a dispersant which serves to facilitate the formation of an aerosol as well as other therapeutic compounds. A suitable dispersant is lactose, which can be blended with the nucleic acid compound in any suitable ratio, such as a 1 to 1 ratio by weight.

Aerosols of liquid particles may include a nucleic acid molecules disclosed herein and can be produced by any suitable means, such as with a nebulizer (see e.g., U.S. Pat. No. 4,501,729). Nebulizers are commercially available devices which transform solutions or suspensions of an active ingredient into a therapeutic aerosol mist either by means of acceleration of a compressed gas, typically air or oxygen, through a narrow venturi orifice or by means of ultrasonic agitation. Suitable formulations for use in nebulizers include the active ingredient in a liquid carrier in an amount of up to 40% w/w preferably less than 20% w/w of the formulation. The carrier is typically water or a dilute aqueous alcoholic solution, preferably made isotonic with body fluids by the addition of, e.g., sodium chloride or other suitable salts. Optional additives include preservatives if the formulation is not prepared sterile, e.g., methyl hydroxybenzoate, anti-oxidants, flavorings, volatile oils, buffering agents and emulsifiers and other formulation surfactants. The aerosols of solid particles including the active composition and surfactant can likewise be produced with any solid particulate aerosol generator. Aerosol generators for administering solid particulate therapeutics to a subject produce particles which are respirable, as explained above, and generate a volume of aerosol containing a predetermined metered dose of a therapeutic composition at a rate suitable for human administration. One illustrative type of solid particulate aerosol generator is an insufflator. Suitable formulations for administration by insufflation include finely comminuted powders which can be delivered by means of an insufflator. In the insufflator, the powder, e.g., a metered dose thereof effective to carry out the treatments described herein, is contained in capsules or cartridges, typically made of gelatin or plastic, which are either pierced or opened in situ and the powder delivered by air drawn through the device upon inhalation or by means of a manually-operated pump. The powder employed in the insufflator consists either solely of the active ingredient or of a powder blend comprising the active ingredient, a suitable powder diluent, such as lactose, and an optional surfactant. The active ingredient typically includes from 0.1 to 100 w/w of the formulation. A second type of illustrative aerosol generator includes a metered dose inhaler. Metered dose inhalers are pressurized aerosol dispensers, typically containing a suspension or solution formulation of the active ingredient in a liquefied propellant. During use these devices discharge the formulation through a valve adapted to deliver a metered volume to produce a fine particle spray containing the active ingredient. Suitable propellants include certain chlorofluorocarbon compounds, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane and mixtures thereof. The formulation can additionally contain one or more co-solvents, for example, ethanol, emulsifiers and other formulation surfactants, such as oleic acid or sorbitan trioleate, anti-oxidants and suitable flavoring agents. Other methods for pulmonary delivery are described in, e.g., US Patent Application No. 20040037780, and U.S. Pat. Nos. 6,592,904; 6,582,728; 6,565,885. PCT Patent Publication No. WO2008/132723 discloses aerosol delivery of oligonucleotides in general, and of siRNA in particular, to the respiratory system.

Nucleic acid molecules may be administered to the central nervous system (CNS) or peripheral nervous system (PNS). Experiments have demonstrated the efficient in vivo uptake of nucleic acids by neurons. See e.g., Sommer et al., 1998, Antisense Nuc. Acid Drug Dev., 8, 75; Epa et al., 2000, Antisense Nuc. Acid Drug Dev., 10, 469; Broaddus et al., 1998, J. Neurosurg., 88(4), 734; Karle et al., 1997, Eur. J. Pharmocol., 340(2/3), 153; Bannai et al., 1998, Brain Research, 784(1,2), 304; Rajakumar et al., 1997, Synapse, 26(3), 199; Wu-pong et al., 1999, BioPharm, 12(1), 32; Bannai et al., 1998, Brain Res. Protoc., 3(1), 83; and Simantov et al., 1996, Neuroscience, 74(1), 39. Nucleic acid molecules are therefore amenable to delivery to and uptake by cells in the CNS and/or PNS.

Delivery of nucleic acid molecules to the CNS is provided by a variety of different strategies. Traditional approaches to CNS delivery that can be used include, but are not limited to, intrathecal and intracerebroventricular administration, implantation of catheters and pumps, direct injection or perfusion at the site of injury or lesion, injection into the brain arterial system, or by chemical or osmotic opening of the blood-brain barrier. Other approaches can include the use of various transport and carrier systems, for example though the use of conjugates and biodegradable polymers. Furthermore, gene therapy approaches, e.g., as described in Kaplitt et al., U.S. Pat. No. 6,180,613 and Davidson, WO 04/013280, can be used to express nucleic acid molecules in the CNS.

Delivery systems may include, for example, aqueous and nonaqueous gels, creams, multiple emulsions, microemulsions, liposomes, ointments, aqueous and nonaqueous solutions, lotions, aerosols, hydrocarbon bases and powders, and can contain excipients such as solubilizers, permeation enhancers (e.g., fatty acids, fatty acid esters, fatty alcohols and amino acids), and hydrophilic polymers (e.g., polycarbophil and polyvinylpyrolidone). In one embodiment, the pharmaceutically acceptable carrier is a liposome or a transdermal enhancer. Examples of liposomes which can be used include the following: (1) CellFectin, 1:1.5 (M/M) liposome formulation of the cationic lipid N,NI,NII,NIII-tetramethyl-N,NI,NII,NIII-tetrapalmit-y-spermine and dioleoyl phosphatidylethanolamine (DOPE) (GIBCO BRL); (2) Cytofectin GSV, 2:1 (M/M) liposome formulation of a cationic lipid and DOPE (Glen Research); (3) DOTAP (N-[1-(2,3-dioleoyloxy)-N,N,N-tri-methyl-ammoniummethylsulfate) (Boehringer Manheim); and (4) Lipofectamine, 3:1 (M/M) liposome formulation of the polycationic lipid DOSPA, the neutral lipid DOPE (GIBCO BRL) and Di-Alkylated Amino Acid (DiLA2).

Delivery systems may include patches, tablets, suppositories, pessaries, gels and creams, and can contain excipients such as solubilizers and enhancers (e.g., propylene glycol, bile salts and amino acids), and other vehicles (e.g., polyethylene glycol, fatty acid esters and derivatives, and hydrophilic polymers such as hydroxypropylmethylcellulose and hyaluronic acid).

Nucleic acid molecules may be formulated or complexed with polyethylenimine (e.g., linear or branched PEI) and/or polyethylenimine derivatives, including for example grafted PEIs such as galactose PEI, cholesterol PEI, antibody derivatized PEI, and polyethylene glycol PEI (PEG-PEI) derivatives thereof (see for example Ogris et al., 2001, AAPA PharmSci, 3, 1-11; Furgeson et al., 2003, Bioconjugate Chem., 14, 840-847; Kunath et al., 2002, Pharmaceutical Research, 19, 810-817; Choi et al., 2001, Bull. Korean Chem. Soc., 22, 46-52; Bettinger et al., 1999, Bioconjugate Chem., 10, 558-561; Peterson et al., 2002, Bioconjugate Chem., 13, 845-854; Erbacher et al., 1999, Journal of Gene Medicine Preprint, 1, 1-18; Godbey et al., 1999., PNAS USA, 96, 5177-5181; Godbey et al., 1999, Journal of Controlled Release, 60, 149-160; Diebold et al., 1999, Journal of Biological Chemistry, 274, 19087-19094; Thomas and Klibanov, 2002, PNAS USA, 99, 14640-14645; and Sagara, U.S. Pat. No. 6,586,524.

Nucleic acid molecules may include a bioconjugate, for example a nucleic acid conjugate as described in Vargeese et al., U.S. Ser. No. 10/427,160; U.S. Pat. No. 6,528,631; U.S. Pat. No. 6,335,434; U.S. Pat. No. 6,235,886; U.S. Pat. No. 6,153,737; U.S. Pat. No. 5,214,136; U.S. Pat. No. 5,138,045.

Compositions, methods and kits disclosed herein may include an expression vector that includes a nucleic acid sequence encoding at least one nucleic acid molecule as provided herein in a manner that allows expression of the nucleic acid molecule. Methods of introducing nucleic acid molecules or one or more vectors capable of expressing the strands of dsRNA into the environment of the cell will depend on the type of cell and the make up of its environment. The nucleic acid molecule or the vector construct may be directly introduced into the cell (i.e., intracellularly); or introduced extracellularly into a cavity, interstitial space, into the circulation of an organism, introduced orally, or may be introduced by bathing an organism or a cell in a solution containing dsRNA. The cell is preferably a mammalian cell; more preferably a human cell. The nucleic acid molecule of the expression vector can include a sense region and an antisense region. The antisense region can include a sequence complementary to a RNA or DNA sequence encoding TIMP1 and TIMP2 and the sense region can include a sequence complementary to the antisense region. The nucleic acid molecule can include two distinct strands having complementary sense and antisense regions. The nucleic acid molecule can include a single strand having complementary sense and antisense regions.

Nucleic acid molecules that interact with target RNA molecules and down-regulate gene encoding target RNA molecules (e.g., target RNA molecules referred to by Genbank Accession numbers herein) may be expressed from transcription units inserted into DNA or RNA vectors. Recombinant vectors can be DNA plasmids or viral vectors. Nucleic acid molecule expressing viral vectors can be constructed based on, but not limited to, adeno-associated virus, retrovirus, adenovirus, or alphavirus. The recombinant vectors capable of expressing the nucleic acid molecules can be delivered as described herein, and persist in target cells. Alternatively, viral vectors can be used that provide for transient expression of nucleic acid molecules. Such vectors can be repeatedly administered as necessary. Once expressed, the nucleic acid molecules bind and down-regulate gene function or expression via RNA interference (RNAi). Delivery of nucleic acid molecule expressing vectors can be systemic, such as by intravenous or intramuscular administration, by administration to target cells ex-planted from a subject followed by reintroduction into the subject, or by any other means that would allow for introduction into the desired target cell.

Expression vectors may include a nucleic acid sequence encoding at least one nucleic acid molecule disclosed herein, in a manner which allows expression of the nucleic acid molecule. For example, the vector may contain sequence(s) encoding both strands of a nucleic acid molecule that include a duplex. The vector can also contain sequence(s) encoding a single nucleic acid molecule that is self-complementary and thus forms a nucleic acid molecule. Non-limiting examples of such expression vectors are described in Paul et al., 2002, Nature Biotechnology, 19, 505; Miyagishi and Taira, 2002, Nature Biotechnology, 19, 497; Lee et al., 2002, Nature Biotechnology, 19, 500; and Novina et al., 2002, Nature Medicine, advance online publication doi:10.1038/nm725. Expression vectors may also be included in a mammalian (e.g., human) cell.

An expression vector may include a nucleic acid sequence encoding two or more nucleic acid molecules, which can be the same or different. Expression vectors may include a sequence for a nucleic acid molecule complementary to a nucleic acid molecule referred to by a Genbank Accession number NM_003254 (TIMP1) or NM_003255 (TIMP2).

An expression vector may encode one or both strands of a nucleic acid duplex, or a single self-complementary strand that self hybridizes into a nucleic acid duplex. The nucleic acid sequences encoding nucleic acid molecules can be operably linked in a manner that allows expression of the nucleic acid molecule (see for example Paul et al., 2002, Nature Biotechnology, 19, 505; Miyagishi and Taira, 2002, Nature Biotechnology, 19, 497; Lee et al., 2002, Nature Biotechnology, 19, 500; and Novina et al., 2002, Nature Medicine, advance online publication doi: 10.1038/nm725).

An expression vector may include one or more of the following: a) a transcription initiation region (e.g., eukaryotic pol I, II or III initiation region); b) a transcription termination region (e.g., eukaryotic pol I, II or III termination region); c) an intron and d) a nucleic acid sequence encoding at least one of the nucleic acid molecules, wherein said sequence is operably linked to the initiation region and the termination region in a manner that allows expression and/or delivery of the nucleic acid molecule. The vector can optionally include an open reading frame (ORF) for a protein operably linked on the 5′ side or the 3′-side of the sequence encoding the nucleic acid molecule; and/or an intron (intervening sequences).

Transcription of the nucleic acid molecule sequences can be driven from a promoter for eukaryotic RNA polymerase I (pol I), RNA polymerase II (pol II), or RNA polymerase III (pol III). Transcripts from pol II or pol III promoters are expressed at high levels in all cells; the levels of a given pol II promoter in a given cell type depends on the nature of the gene regulatory sequences (enhancers, silencers, etc.) present nearby. Prokaryotic RNA polymerase promoters are also used, providing that the prokaryotic RNA polymerase enzyme is expressed in the appropriate cells (Elroy-Stein and Moss, 1990, Proc. Natl. Acad. Sci. USA, 87, 6743-7; Gao and Huang 1993, Nucleic Acids Res., 21, 2867-72; Lieber et al., 1993, Methods Enzymol., 217, 47-66; Zhou et al., 1990, Mol. Cell. Biol., 10, 4529-37). Several investigators have demonstrated that nucleic acid molecules expressed from such promoters can function in mammalian cells (e.g. Kashani-Sabet et al., 1992, Antisense Res. Dev., 2, 3-15; Ojwang et al., 1992, Proc. Natl. Acad. Sci. USA, 89, 10802-6; Chen et al., 1992, Nucleic Acids Res., 20, 4581-9; Yu et al., 1993, Proc. Natl. Acad. Sci. USA, 90, 6340-4; L'Huillier et al., 1992, EMBO J., 11, 4411-8; Lisziewicz et al., 1993, Proc. Natl. Acad. Sci. U.S.A, 90, 8000-4; Thompson et al., 1995, Nucleic Acids Res., 23, 2259; Sullenger & Cech, 1993, Science, 262, 1566). More specifically, transcription units such as the ones derived from genes encoding U6 small nuclear (snRNA), transfer RNA (tRNA) and adenovirus VA RNA are useful in generating high concentrations of desired RNA molecules such as siNA in cells (Thompson et al., supra; Couture and Stinchcomb, 1996, supra; Noonberg et al., 1994, Nucleic Acid Res., 22, 2830; Noonberg et al., U.S. Pat. No. 5,624,803; Good et al., 1997, Gene Ther., 4, 45; Beigelman et al., International PCT Publication No. WO 96/18736. The above nucleic acid transcription units can be incorporated into a variety of vectors for introduction into mammalian cells, including but not restricted to, plasmid DNA vectors, viral DNA vectors (such as adenovirus or adeno-associated virus vectors), or viral RNA vectors (such as retroviral or alphavirus vectors) (see Couture and Stinchcomb, 1996 supra).

Nucleic acid molecule may be expressed within cells from eukaryotic promoters (e.g., Izant and Weintraub, 1985, Science, 229, 345; McGarry and Lindquist, 1986, Proc. Natl. Acad. Sci., USA 83, 399; Scanlon et al., 1991, Proc. Natl. Acad. Sci. USA, 88, 10591-5; Kashani-Sabet et al., 1992, Antisense Res. Dev., 2, 3-15; Dropulic et al., 1992, J. Virol., 66, 1432-41; Weerasinghe et al., 1991, J. Virol., 65, 5531-4; Ojwang et al., 1992, Proc. Natl. Acad. Sci. USA, 89, 10802-6; Chen et al., 1992, Nucleic Acids Res., 20, 4581-9; Sarver et al., 1990 Science, 247, 1222-1225; Thompson et al., 1995, Nucleic Acids Res., 23, 2259; Good et al., 1997, Gene Therapy, 4, 45. Those skilled in the art realize that any nucleic acid can be expressed in eukaryotic cells from the appropriate DNA/RNA vector. The activity of such nucleic acids can be augmented by their release from the primary transcript by a enzymatic nucleic acid (Draper et al., PCT WO 93/23569, and Sullivan et al., PCT WO 94/02595; Ohkawa et al., 1992, Nucleic Acids Symp. Ser., 27, 15-6; Taira et al., 1991, Nucleic Acids Res., 19, 5125-30; Ventura et al., 1993, Nucleic Acids Res., 21, 3249-55; Chowrira et al., 1994, J. Biol. Chem., 269, 25856.

A viral construct packaged into a viral particle would accomplish both efficient introduction of an expression construct into the cell and transcription of dsRNA construct encoded by the expression construct.

Methods for oral introduction include direct mixing of RNA with food of the organism, as well as engineered approaches in which a species that is used as food is engineered to express an RNA, then fed to the organism to be affected. Physical methods may be employed to introduce a nucleic acid molecule solution into the cell. Physical methods of introducing nucleic acids include injection of a solution containing the nucleic acid molecule, bombardment by particles covered by the nucleic acid molecule, soaking the cell or organism in a solution of the RNA, or electroporation of cell membranes in the presence of the nucleic acid molecule.

Other methods known in the art for introducing nucleic acids to cells may be used, such as lipid-mediated carrier transport, chemical mediated transport, such as calcium phosphate, and the like. Thus the nucleic acid molecules may be introduced along with components that perform one or more of the following activities: enhance RNA uptake by the cell, promote annealing of the duplex strands, stabilize the annealed strands, or other-wise increase inhibition of the target gene.

The nucleic acid molecules or the vector construct can be introduced into the cell using suitable formulations. One formulation comprises a lipid formulation such as in Lipofectamine™ 2000 (Invitrogen, CA, USA. Lipid formulations can also be administered to animals such as by intravenous, intramuscular, or intraperitoneal injection, or orally or by inhalation or other methods as are known in the art. When the formulation is suitable for administration into animals such as mammals and more specifically humans, the formulation is also pharmaceutically acceptable. Pharmaceutically acceptable formulations for administering oligonucleotides are known and can be used. In some instances, it may be preferable to formulate dsRNA in a buffer or saline solution and directly inject the formulated dsRNA into cells, as in studies with oocytes. The direct injection of dsRNA duplexes may also be done. For suitable methods of introducing dsRNA see U.S. published patent application No. 2004/0203145, 20070265220 which are incorporated herein by reference.

Polymeric nanocapsules or microcapsules facilitate transport and release of the encapsulated or bound dsRNA into the cell. They include polymeric and monomeric materials, especially including polybutylcyanoacrylate. A summary of materials and fabrication methods has been published (see Kreuter, 1991). The polymeric materials which are formed from monomeric and/or oligomeric precursors in the polymerization/nanoparticle generation step, are per se known from the prior art, as are the molecular weights and molecular weight distribution of the polymeric material which a person skilled in the field of manufacturing nanoparticles may suitably select in accordance with the usual skill.

Nucleic acid moles may be formulated as a microemulsion. A microemulsion is a system of water, oil and amphiphile which is a single optically isotropic and thermodynamically stable liquid solution. Typically microemulsions are prepared by first dispersing an oil in an aqueous surfactant solution and then adding a sufficient amount of a 4th component, generally an intermediate chain-length alcohol to form a transparent system.

Surfactants that may be used in the preparation of microemulsions include, but are not limited to, ionic surfactants, non-ionic surfactants, Brij 96, polyoxyethylene oleyl ethers, polyglycerol fatty acid esters, tetraglycerol monolaurate (ML310), tetraglycerol monooleate (MO310), hexaglycerol monooleate (PO310), hexaglycerol pentaoleate (PO500), decaglycerol monocaprate (MCA750), decaglycerol monooleate (MO750), decaglycerol sequioleate (SO750), decaglycerol decaoleate (DA0750), alone or in combination with cosurfactants. The cosurfactant, usually a short-chain alcohol such as ethanol, 1-propanol, and 1-butanol, serves to increase the interfacial fluidity by penetrating into the surfactant film and consequently creating a disordered film because of the void space generated among surfactant molecules.

Water Soluble Crosslinked Polymers

Delivery formulations can include water soluble degradable crosslinked polymers that include one or more degradable crosslinking lipid moiety, one or more PEI moiety, and/or one or more mPEG (methyl ether derivative of PEG (methoxypoly (ethylene glycol)).

Degradable lipid moieties preferably include compounds having the following structural motif:

embedded image

In the above formula, ester linkages are biodegradable groups, R represents a relatively hydrophobic “lipo” group, and the structural motif shown occurs m times where m is in the range of about 1 to about 30. For example, in certain embodiments R is selected from the group consisting of C₂-C₅₀alkyl, C₂-C₅₀heteroalkyl, C₂-C₅₀alkenyl, C₂-C₅₀heteroalkenyl, C₅-C₅₀aryl; C₂-C₅₀heteroaryl; C₂-C₅₀alkynyl, C₂-C₅₀heteroalkynyl, C₂-C₅₀carboxyalkenyl, and C₂-C₅₀carboxyheteroalkenyl. In preferred embodiments, R is a saturated or unsaturated alkyl having 4 to 30 carbons, more preferably 8 to 24 carbons or a sterol, preferably a cholesteryl moiety. In preferred embodiments, R is oleic, lauric, myristic, palmitic margaric, stearic, arachidic, behenic, or lignoceric. In a most preferred embodiment, R is oleic.

The N in formula (B) may have an electron pair or a bond to a hydrogen atom. When N has an electron pair, the recurring unit may be cationic at low pH.

The degradable crosslinking lipid moiety may be reacted with a polyethyleneimine (PEI) as shown in Scheme A below:

embedded image

In formula (A), R has the same meanings as described above. The PEI may contain recurring units of formula (B) in which x is an integer in the range of about 1 to about 100 and y is an integer in the range of about 1 to about 100.

embedded image

The reaction illustrated in Scheme A may be carried out by intermixing the PEI and the diacrylate (I) in a mutual solvent such as ethanol, methanol or dichloromethane with stirring, preferably at room temperature for several hours, then evaporating the solvent to recover the resulting polymer. While not wishing to be bound to any particular theory, it is believed that the reaction between the PEI and diacrylate (I) involves a Michael reaction between one or more amines of the PEI with double bond(s) of the diacrylate (see J. March, Advanced Organic Chemistry 3rd Ed., pp. 711-712 (1985)). The diacrylate shown in Scheme A may be prepared in the manner as described in U.S. application Ser. No. 11/216,986 (US Publication No. 2006/0258751).

The molecular weight of the PEI is preferably in the range of about 200 to 25,000 Daltons more preferably 400 to 5,000 Daltons, yet more preferably 600 to 2000 Daltons. PEI may be either branched or linear.

The molar ratio of PEI to diacrylate is preferably in the range of about 1:2 to about 1:20. The weight average molecular weight of the cationic lipopolymer may be in the range of about 500 Daltons to about 1,000,000 Daltons preferably in the range of about 2,000 Daltons to about 200,000 Daltons. Molecular weights may be determined by size exclusion chromatography using PEG standards or by agarose gel electrophoresis.

The cationic lipopolymer is preferably degradable, more preferably biodegradable, e.g., degradable by a mechanism selected from the group consisting of hydrolysis, enzyme cleavage, reduction, photo-cleavage, and sonication. While not wishing to be bound to any particular theory, but it is believed that degradation of the cationic lipopolymer of formula (II) within the cell proceeds by enzymatic cleavage and/or hydrolysis of the ester linkages.

Synthesis may be carried out by reacting the degradable lipid moiety with the PEI moiety as described above. Then the mPEG (methyl ether derivative of PEG (methoxypoly (ethylene glycol)), is added to form the degradable crosslinked polymer. In preferred embodiments, the reaction is carried out at room temperature. The reaction products may be isolated by any means known in the art including chromatographic techniques. In a preferred embodiment, the reaction product may be removed by precipitation followed by centrifugation.

Dosages

The useful dosage to be administered and the particular mode of administration will vary depending upon such factors as the cell type, or for in vivo use, the age, weight and the particular animal and region thereof to be treated, the particular nucleic acid and delivery method used, the therapeutic or diagnostic use contemplated, and the form of the formulation, for example, suspension, emulsion, micelle or liposome, as will be readily apparent to those skilled in the art. Typically, dosage is administered at lower levels and increased until the desired effect is achieved.

When lipids are used to deliver the nucleic acid, the amount of lipid compound that is administered can vary and generally depends upon the amount of nucleic acid being administered. For example, the weight ratio of lipid compound to nucleic acid is preferably from about 1:1 to about 30:1, with a weight ratio of about 5:1 to about 10:1 being more preferred.

A suitable dosage unit of nucleic acid molecules may be in the range of 0.001 to 0.25 milligrams per kilogram body weight of the recipient per day, or in the range of 0.01 to 20 micrograms per kilogram body weight per day, or in the range of 0.01 to 10 micrograms per kilogram body weight per day, or in the range of 0.10 to 5 micrograms per kilogram body weight per day, or in the range of 0.1 to 2.5 micrograms per kilogram body weight per day.

Suitable amounts of nucleic acid molecules may be introduced and these amounts can be empirically determined using standard methods. Effective concentrations of individual nucleic acid molecule species in the environment of a cell may be about 1 femtomolar, about 50 femtomolar, 100 femtomolar, 1 picomolar, 1.5 picomolar, 2.5 picomolar, 5 picomolar, 10 picomolar, 25 picomolar, 50 picomolar, 100 picomolar, 500 picomolar, 1 nanomolar, 2.5 nanomolar, 5 nanomolar, 10 nanomolar, 25 nanomolar, 50 nanomolar, 100 nanomolar, 500 nanomolar, 1 micromolar, 2.5 micromolar, 5 micromolar, 10 micromolar, 100 micromolar or more.

Dosage may be from 0.01 μg to 1 μg per kg of body weight (e.g., 0.1 μg, 0.25 μg, 0.5 μg, 0.75 μg, 1 μg, 2.5 μg, 5 μg, 10 μg, 25 μg, 50 μg, 100 μg, 250 μg, 500 μg, 1 mg, 2.5 mg, 5 mg, 10 mg, 25 mg, 50 mg, 100 mg, 250 mg, or 500 mg per kg).

Dosage levels of the order of from about 0.1 mg to about 140 mg per kilogram of body weight per day are useful in the treatment of the above-indicated conditions (about 0.5 mg to about 7 g per subject per day). The amount of active ingredient that can be combined with the carrier materials to produce a single dosage form varies depending upon the host treated and the particular mode of administration. Dosage unit forms generally contain between from about 1 mg to about 500 mg of an active ingredient.

It is understood that the specific dose level for any particular subject depends upon a variety of factors including the activity of the specific compound employed, the age, body weight, general health, sex, diet, time of administration, route of administration, and rate of excretion, drug combination and the severity of the particular disease undergoing therapy.

Pharmaceutical compositions that include the nucleic acid molecule disclosed herein may be administered once daily, qid, tid, bid, QD, or at any interval and for any duration that is medically appropriate. However, the therapeutic agent may also be dosed in dosage units containing two, three, four, five, six or more sub-doses administered at appropriate intervals throughout the day. In that case, the nucleic acid molecules contained in each sub-dose may be correspondingly smaller in order to achieve the total daily dosage unit. The dosage unit can also be compounded for a single dose over several days, e.g., using a conventional sustained release formulation which provides sustained and consistent release of the dsRNA over a several day period. Sustained release formulations are well known in the art. The dosage unit may contain a corresponding multiple of the daily dose. The composition can be compounded in such a way that the sum of the multiple units of a nucleic acid together contain a sufficient dose.

Pharmaceutical Compositions, Kits, and Containers

Also provided are compositions, kits, containers and formulations that include a nucleic acid molecule (e.g., an siNA molecule) as provided herein for reducing expression of TIMP1 and TIMP2 for administering or distributing the nucleic acid molecule to a patient. A kit may include at least one container and at least one label. Suitable containers include, for example, bottles, vials, syringes, and test tubes. The containers can be formed from a variety of materials such as glass, metal or plastic. The container can hold amino acid sequence(s), small molecule(s), nucleic acid sequence(s), cell population(s) and/or antibody(s). In one embodiment, the container holds a polynucleotide for use in examining the mRNA expression profile of a cell, together with reagents used for this purpose. In another embodiment a container includes an antibody, binding fragment thereof or specific binding protein for use in evaluating TIMP1 and TIMP2 protein expression cells and tissues, or for relevant laboratory, prognostic, diagnostic, prophylactic and therapeutic purposes; indications and/or directions for such uses can be included on or with such container, as can reagents and other compositions or tools used for these purposes. Kits may further include associated indications and/or directions; reagents and other compositions or tools used for such purpose can also be included.

The container can alternatively hold a composition that is effective for treating, diagnosis, prognosing or prophylaxing a condition and can have a sterile access port (for example the container can be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle). The active agents in the composition can be a nucleic acid molecule capable of specifically binding TIMP1 and TIMP2 and/or modulating the function of TIMP1 and TIMP2.

A kit may further include a second container that includes a pharmaceutically-acceptable buffer, such as phosphate-buffered saline, Ringer's solution and/or dextrose solution. It can further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, stirrers, needles, syringes, and/or package inserts with indications and/or instructions for use.

The units dosage ampoules or multidose containers, in which the nucleic acid molecules are packaged prior to use, may include an hermetically sealed container enclosing an amount of polynucleotide or solution containing a polynucleotide suitable for a pharmaceutically effective dose thereof, or multiples of an effective dose. The polynucleotide is packaged as a sterile formulation, and the hermetically sealed container is designed to preserve sterility of the formulation until use.

The container in which the polynucleotide including a sequence encoding a cellular immune response element or fragment thereof may include a package that is labeled, and the label may bear a notice in the form prescribed by a governmental agency, for example the Food and Drug Administration, which notice is reflective of approval by the agency under Federal law, of the manufacture, use, or sale of the polynucleotide material therein for human administration.

Federal law requires that the use of pharmaceutical compositions in the therapy of humans be approved by an agency of the Federal government. In the United States, enforcement is the responsibility of the Food and Drug Administration, which issues appropriate regulations for securing such approval, detailed in 21 U.S.C. §301-392. Regulation for biologic material, including products made from the tissues of animals is provided under 42 U.S.C. §262. Similar approval is required by most foreign countries. Regulations vary from country to country, but individual procedures are well known to those in the art and the compositions and methods provided herein preferably comply accordingly.

The dosage to be administered depends to a large extent on the condition and size of the subject being treated as well as the frequency of treatment and the route of administration. Regimens for continuing therapy, including dose and frequency may be guided by the initial response and clinical judgment. The parenteral route of injection into the interstitial space of tissues is preferred, although other parenteral routes, such as inhalation of an aerosol formulation, may be required in specific administration, as for example to the mucous membranes of the nose, throat, bronchial tissues or lungs.

As such, provided herein is a pharmaceutical product which may include a polynucleotide including a sequence encoding a cellular immune response element or fragment thereof in solution in a pharmaceutically acceptable injectable carrier and suitable for introduction interstitially into a tissue to cause cells of the tissue to express a cellular immune response element or fragment thereof, a container enclosing the solution, and a notice associated with the container in form prescribed by a governmental agency regulating the manufacture, use, or sale of pharmaceuticals, which notice is reflective of approval by the agency of manufacture, use, or sale of the solution of polynucleotide for human administration.

Indications

The nucleic acid molecules disclosed herein can be used to treat diseases, conditions or disorders associated with TIMP1 and TIMP2, such as liver fibrosis, cirrhosis, pulmonary fibrosis, kidney fibrosis, peritoneal fibrosis, chronic hepatic damage, and fibrillogenesis and any other disease or conditions that are related to or will respond to the levels of TIMP1 and TIMP2 in a cell or tissue. As such, compositions, kits and methods disclosed herein may include packaging a nucleic acid molecule disclosed herein that includes a label or package insert. The label may include indications for use of the nucleic acid molecules such as use for treatment or prevention of liver fibrosis, peritoneal fibrosis, kidney fibrosis and pulmonary fibrosis, and any other disease or conditions that are related to or will respond to the levels of TIMP1 and TIMP2 in a cell or tissue. A label may include an indication for use in reducing expression of TIMP1 and TIMP2. A “package insert” is used to refer to instructions customarily included in commercial packages of therapeutic products, that contain information about the indications, usage, dosage, administration, contraindications, other therapeutic products to be combined with the packaged product, and/or warnings concerning the use of such therapeutic products, etc.

Those skilled in the art will recognize that two or more siTIMP1 and or siTIMP2 may be combined or that other anti-fibrosis treatments, drugs and therapies known in the art can be readily combined with the nucleic acid molecules herein (e.g. siNA molecules) and are hence contemplated herein.

The methods and compositions provided herein will now be described in greater detail by reference to the following non-limiting examples.

EXAMPLES
Example 1
siRNA Sequences

siRNA sequences for TIMP-1, TIMP-2, positive control and negative control are listed in Tables C and D. 100 μM siRNA stock solution was prepared by dissolving in nucrease free water (Ambion). In the “Sequence” columns in Tables C and D, lower case letters represent unmodified ribonucleotides, “T” represents deoxyribothymidine.

TABLE C

SEQ

ID

Target
Name
Orientation
Sequence
NO:
Species
nucleotides

TIMP1
TIMP1-A
S (5′->3′)
ccaccuuauaccagcguuaTT
5
Human,
[355-373]

AS (3′->5′)
TTgguggaauauggucgcaau
6
mouse,
ORF

rat,

rhesus

TIMP1
TIMP1-B
S (5′->3′)
cacuguuggcugugaggaaTT
7
Human
[620-638]

AS (3′->5)
TTgugacaaccgacacuccuu
8
rhesus
ORF

TIMP1
TIMP1-C
S (5′->3′)
gcacaguguuucccuguuuTT
9
Human
[640-658]

AS (3′->5′)
TTcgugucacaaagggacaaa
10
mouse
ORF

rat

rhesus

TABLE D

SEQ

ID

Target
Name
Orientation
Sequence
NO
Species
nucleotides

TIMP2
TIMP2-A
S (5′->3′)
ugcagauguagugaucaggTT
11
human
[421-439]

AS (3′->5′)
TTacgucuacaucacuagucc
12

ORF

TIMP2
TIMP2-B
S (5′->3′)
gaggauccaguaugagaucTT
13
human
[502-520]

AS (3′->5′)
TTcuccuaggucauacucuag
14
rhesus
ORF

rabbit

TIMP2
TIMP2-C
S (5′->3′)
gcagauaaagauguucaaaTT
15
human
[523-541]

AS (3′->5′)
TTcgucuauuucuacaaguuu
16
mouse
ORF

rat cow

dog pig

TIMP2
TIMP2-D
S (5′->3′)
ggaauaucucauugcaggaTT
17
human
[625-643]

AS (3′->5′)
TTccuuauagaguaacguccu
18

ORF

TIMP2
TIMP2-E
S (5′->3′)
uaucucauugcaggaaaggTT
19
human
[629-647]

AS (3′->5′)
TTauagaguaacguccuuucc
20

ORF

Example 2
siRNA Delivery

HT-1080 cell (Japanese Collection of Research Bioresources) was maintained incubated in DMEM (Sigma, Cat #D6546) with 10% fetal bovine serum (FBS; Hyclone, Cat. #SH30070.03) and 1% volume/volume L-Glutamine-penicillin-streptomycin solution (Sigma, Cat. #G1146) and 1% volume/volume L-Glutamine solution (Sigma, Cat. #G7513). Before delivering siRNA, cells were seeded in 6-well plate (Nunc. #140675) at the density of 5×10³cells per well and incubated at 37° C. with 7.5% CO₂for 2 days. siRNAs for TIMP1 were transfected to the cells with VA-coupled liposome (VA-liposome) as described by Sato et al. (Sato Y. et al. Nature Biotechnology 2008. Vol. 26, p 431) and siRNAs for TIMP2 were delivered with VA-conjugated cationic polymer (VA-polymer), synthesized in-house at the ratio of 5:1 (VA-polymer:siRNA, weight per weight). The final concentration of siRNA was 50 nM. 2-hours after siRNA delivery, cell culture medium was replaced to fresh DMEM with 10% FBS and incubated for 2 overnight at 37° C. with 7.5% CO₂.

Example 3
Gene Knocking Down Assessment of siRNA by RT-PCR

After transfection as described in Example 2, total RNA was isolated with QIAshreader QIAGEN, 79654) and RNeasy Mini Kit (QIAGEN, 74104) by following manufacturer's protocol. 1 μg of the isolated total RNA was used for cDNA preparation with Hicapacity RNA-to-cDNA Master Mix (Applied Biosystems, 4390779) as indicated by manufacturer's protocol. Then, 0.05 μg of cDNA was employed for polymerase chain reaction (PCR) with ExTaq (TaKaRa, RR001B) polymerase by following supplied manual. PCR primers for detection of each gene are listed in excel file. PCR condition was as follows: 94° C. 4 min, then 4° C. 30 sec, 63° C. 30 sec, 72° C. 1 min for 23 cycles, 72° C. 5 min before termination. 15 μl of PCR products for TIMP-1 or TIMP-2 gene and 5 μl for GAPDH gene were identified by agarose gel electrophoresis.

FIG. 2 indicates knock down efficacy of siRNAs for TIMP1 as measured by qPCR. The amount of PCR product from cells transfected with TIMP-1 siRNA, e.g. TIMP1-A (SEQ ID NOS:5 and 6), TIMP1-B (SEQ ID NOS:7 and 8) or TIMP1-C(SEQ ID NOS:9 and 10), was less than that from untreated cells, therefore, those siRNA for TIMP1 gene are capable to knock down the target gene.

FIG. 3 represents knock down efficacy of siRNAs for TIMP2 as measured by qPCR: TIMP2-A (SEQ ID NOS:11 and 12), TIMP2-B (SEQ ID NOS:13 and 14), TIMP2-C(SEQ ID NOS:15 and 16), TIMP2-D (SEQ ID NOS:17 and 18) and TIMP2-E (SEQ ID NOS:19 and 20). TIMP2 siRNA showed target gene knock down and level of gene silencing was dependent on the sequence.

Example 4
Treatment of Liver Cirrhosis in Rats with siTIMP1 and siTIMP2

Liver cirrhosis animal model: Liver cirrhosis was induced in rats using the method described by Sato et al., (Sato Y. et al. Nat Biotech 2008. 26:431). Briefly, liver cirrhosis was induced in 4 week-old male SD rats by injecting them dimethylnitrosoamine (DMN) (Wako Chemicals, Japan) as follows: 0.5% DMN in phosphate-buffered saline (PBS) was administered to rats intraperitoneally at a dose of 2 ml/kg per body weight for 3 consecutive days per week. Specifically, DMN solution was injected on days 0 (start of the experiment), 2, 4, 7, 9, 11, 14, 16, 18, 21, 23, 25, 28, 30, 32, 34 and 36.

siRNA sequence for TIMP1 (“siTIMP1-A”)

(SEQ ID NO: 5)

S (5′->3′) ccaccuuauaccagcguuaTT

(SEQ ID NO: 6)

AS (3′->5′) TTgguggaauauggucgcaau

siRNA sequence for TIMP2 (“siTIMP2-C”)

(SEQ ID NO: 15)

S (5′->3′) gcagauaaagauguucaaaTT

(SEQ ID NO: 16)

AS (3′->5′) TTcgucuauuucuacaaguuu

A10 μg/μl siRNA stock solution was prepared by dissolving siRNA duplexes (siTIMP1 or siTIMP2) in nuclease free water (Ambion). For treatment of rats, siRNA was formulated with vitamin A-coupled liposome as described by Sato et al (Sato Y. et al. Nature Biotech 2008. Vol. 26, p 431). The vitamin A (VA)-liposome-siRNA formulation consisted of 0.33 μmol/ml of VA, 0.33 μmol/ml of liposome (Coatsome EL-01-D, NOF Corporation) and 0.5 μg/μl of siRNA in 5% glucose solution.

Injection Solution for siRNA Delivered at a Concentration of 0.75 mg/Kg

The liposomes were prepared at a concentration of 1 mM by addition of nuclease-free water, and left for 15 min at room temperature before use. To prepare VA-coupled liposomes, 100 nmol of vitamin A (dissolved in DMSO) was mixed with the liposomes (100 nmol) by vortex for 15 seconds at R.T.

The siRNA duplexes (150 μg) were prepared at a concentration of 10 μg/μl by addition of nuclease-free water. A 5% glucose (175 μl) solution was added to the liposomal suspension. (Total volume of 300 μl). The VA-liposome-siRNA solutions were injected to each rat to a final concentration of 0.75 ml/Kg body weight.

Injection Solution for siRNA Delivered at a Concentration of 1.5 mg/Kg

The liposomes were prepared at a concentration of 1 mM by addition of nuclease-free water, and left to stand for 15 min before use. To prepare VA-coupled liposome, 200 nmol of vitamin A (dissolved in DMSO) was mixed with the liposome (200 nmol) by vortex for 15 seconds at R.T.

The siRNA duplexes (300 μg) were prepared at a concentration of 10 μg/μl by addition of nuclease-free water. A 5% glucose (50 μl) solution was added to the liposomal suspension. (Total volume 300 μl). The VA-liposome-siRNA solutions were injected to each rat to a final concentration of 1.5 ml/Kg body weight.

siRNA Treatment

The siRNA treatment was carried out from day 28 for 5 times by intravenous injection. In detail, rats were treated with siRNA on days 28, 30, 32, 34 and 36 post DMN treatment. Rats were sacrificed on day 38 or 39. Two different siRNA species (siTIMP1-A and siTIMP2-C) and 2 different doses (0.75 mg siRNA per kg body weight, 1.5 mg siRNA per kg body weight) were tested. Details of tested groups and number of animals in each group are as follows:

- 1) Control animals: Liver cirrhosis was induced by DMN injection, and a 5% glucose was administered (n=9)
- 2) VA-Lip-siTIMP1-A 0.75 mg/Kg (n=9)
- 3) VA-Lip-siTIMP1-A 1.5 mg/Kg (n=9)
- 4) VA-Lip-siTIMP2-C 0.75 mg/Kg (n=9)
- 5) VA-Lip-siTIMP2-C 1.5 mg/Kg (n=9)
- 6) Sham (PBS was injected instead of DMN. 5% Glucose was administered instead of siRNA) (n=5)
- 7) Untreated control animals (Intact) (n=5)

Evaluation of Therapeutic Efficacy

On day 38, 2 out of 10 animals in “siTIMP2-C” group died and were not analyzed further. However, other animals were survived before the sacrifice. After rats were sacrificed, liver tissues were fixed in 10% formalin. The left lobe of the liver was embedded in paraffin for tissue slide preparation. Tissue slides were stained with Sirius red as well as hematoxylin and eosin (HE). Sirius red staining was employed to visualize collagen-deposited area and determine the level of cirrhosis. HE staining was used for nuclei and cytoplasm as counter-staining. Each slide was observed under microscope (BZ-9000, Keyence Corp. Japan) and the percentage of Sirius red-stained area per slide was determined by image analysis software attached to the microscope. At least 4 slides per each liver were prepared for image analysis, and whole area of each slide (slice of liver) was captured by camera and analyzed. Statistic analysis was carried out by t-test analysis. Results are shown in FIG. 4. Liver sections were photographed at ×32 magnification. The fibrotic areas were calculated as the mean of 4 liver sections. The bar graph summarizes the digital quantification of staining for each group. Statistical values are as follows: *=P<0.05, **=P<0.01, ***=P<0.001

FIG. 4 represents the fibrotic area in liver sections. The area of fibrosis in the “diseased rat” (group 1) was higher than “sham” (group 6) or “untreated” (group 7) groups. Therefore, DMN treatment induced collagen deposition in liver, typical of liver fibrosis. The area of fibrosis was significantly reduced by the treatment of siRNA targeting TIMP1 gene (groups 2 and 3), compared with “diseased rat” group, indicating that siRNA to TIMP1 has therapeutic efficacy in treating fibrotic diseases and disorders.

Example 5
Selecting TIMP1 and TIMP2 Nucleic Acid Molecule Sequences

Nucleic acid molecules (e.g., siNA ≦25 nucleotides) against TIMP1 and TIMP2 were designed using a proprietary database. Candidate sequences are validated by in vitro knock down assays. Details of the nucleic acids set forth in the Tables are

The Tables (A1, A2, A5, A6, B1, B2, B5, B6) include

- a. 19-mer and 18-mer siRNAs (sense and corresponding antisense sequences to form duplex siRNA) predicted to be active by a proprietary database and excludes known 19-mer siRNAs;
- b. siRNAs which target human and at least two additional species (cross species) selected from dog, rat, mouse and rabbit and are predicted to be active;
  - i. inclusion of cross-species siRNA compounds are siRNA with full match to the indicated target (“Sense”) and
  - ii. inclusion of siRNAs with mismatches relative to the target, at positions 1, 19 (5′>3′) or both.

The Tables of “preferred” siRNA (A3, A7, B3, B7) include sense and corresponding antisense sequences that were selected as follows:

- i. Selection for cross species to human (H) and rat (Rt) and inclusion of sequences with 1 MM (single mismatch (MM)) to rat target in positions other than 1/19 (5′>3′)
- ii. Addition of predicted active siRNA compounds that don't target rat but target at least two other species selected from dog, mouse and rabbit.
- iii. Addition of best siRNA targeting human or human+rhesus
- iv. Exclusion of siRNAs that target miRNA seed sequence
- v. Exclusion of siRNAs with high G/C content
- vi. Exclusion of siRNAs targeting multiple SNPs

The Tables labeled as “lowest predicted OT effect” (Tables A4, A8, B4 and B8) relate to siRNA from the “preferred” Tables having best off-target (OT) features including

- c. Column labeled “Crosses”—Indicates species specificity as follows:
  - i. H/Rt=siRNA targeting at least human and rat
  - ii. H/Rt (Rt cross—with 1 MM)=siRNA targeting at least human and rat. Target match to rat is partial and there is one mismatch at a position other than 1 or 19
  - iii. Other (w/o Rt)—siRNA targets human and other species but not rat
  - iv. H+/−Rh=siRNA targeting only human or human and Rhesus but no other species

Column labeled “# in HTS list”—Indicates the siRNA number in the preceding “Preferred” Table (A3, A7, B3, B7).

2. Selection is done in the following manner:

- i. Mismatches (MM) are identified in positions 2-18 of the guide strand. MM in positions 1 and 19 are NOT considered as mismatches.
- ii. Exclusion of siRNAs having complete match (0 MM) to other genes
- iii. Exclusion of siRNAs having 1 MM in position 17 or 18 (of AS strand) to other genes
- iv. Preference (ranking of predicted OT activity):
  - 1—has 3 MM within positions 2-16 of AS (5′>3′).
  - 2—has 2 MM to 1-4 gene targets within positions 2-16
  - 3—has 2 MM to 5-9 gene targets within (positions 2-16)
  - 4—targets 10-20 genes with 2 MM (positions 2-16)

Sequences of sense and antisense oligonucleotides useful in the preparation of siRNA molecules are disclosed in Tables A1, A2, A3, A4, A5, A6, A7, A8, B1, B2, B3, B4, B5, B6, B7, B8 (Tables A1-B8) infra. Best OT refers to least number of matches to off-target genes.

The following abbreviations are used in the Tables A1-B8 (Tables A1, A2, A3, A4, A5, A6, A7 A8, B1, B2, B3, B4, B5, B6, B7 and B8) herein: “other spec or Sp.” refers to cross species identity with other animals: D or Dg—dog, Rt—rat, Rb—rabbit, Rh—rhesus monkey, Pg—Pig, M or Ms—Mouse, Ck—Chicken, Cw—Cow; ORF: open reading frame. 19-mers, and 18+1-mers refer to oligomers of 19 and 18+1 (U at position 1 of Antisense, A at position 19 of sense strand or A at position 1 of Antisense, U at position 19 of sense strand) ribonucleic acids in length, respectively.

TABLE A1

19-mer siTIMP1

SEQ

SEQ

ID

ID

human-73858576

No.
Sense (5′>3′)
NO.
Antisense (5′>3′)
NO.
Other Sp
ORF:193-816

1
GUUUCUCAUUGCUGGAAAA
21
UUUUCCAGCAAUGAGAAAC
129
Rh
[506-524] ORF

2
CACAGUGUUUCCCUGUUUA
22
UAAACAGGGAAACACUGUG
130
Rh, M
[641-659] ORF

3
CUUUCUUCCGGACAAUGAA
23
UUCAUUGUCCGGAAGAAAG
131

[874-892] 3′UTR

4
GCUGAAGCCUGCACAGUGU
24
ACACUGUGCAGGCUUCAGC
132

[834-852] 3′UTR

5
GGAGUUUCUCAUUGCUGGA
25
UCCAGCAAUGAGAAACUCC
133
Rh
[503-521] ORF

6
GCACAGUGUUUCCCUGUUU
26
AAACAGGGAAACACUGUGC
134
Rh, Rt, M
[640-658] ORF

7
CAUCUUUCUUCCGGACAAU
27
AUUGUCCGGAAGAAAGAUG
135

[871-889] 3′UTR

8
GGCUUCACCAAGACCUACA
28
UGUAGGUCUUGGUGAAGCC
136
Rh, Rb
[603-621] ORF

9
GGCACUCAUUGCUUGUGGA
29
UCCACAAGCAAUGAGUGCC
137
Rh
[684-702] ORF

10
CUCCCAUCUUUCUUCCGGA
30
UCCGGAAGAAAGAUGGGAG
138

[867-885] 3′UTR

11
GUGUUUCCCUGUUUAUCCA
31
UGGAUAAACAGGGAAACAC
139
Rh
[645-663] ORF

12
AGUCAACCAGACCACCUUA
32
UAAGGUGGUCUGGUUGACU
140
Rh
[344-362] ORF

13
GCCCGGAGUGGAAGCUGAA
33
UUCAGCUUCCACUCCGGGC
141

[821-839] 3′UTR

14
CCACCUUAUACCAGCGUUA
34
UAACGCUGGUAUAAGGUGG
142
Rh, Rt, M
[355-373] ORF

15
CAUGGAGAGUGUCUGCGGA
35
UCCGCAGACACUCUCCAUG
143
Rh
[455-473] ORF

16
CCAAGAUGUAUAAAGGGUU
36
AACCCUUUAUACAUCUUGG
144
Rh
[388-406] ORF

17
GAGAGUGUCUGCGGAUACU
37
AGUAUCCGCAGACACUCUC
145
Rh
[459-477] ORF

18
AGAUCAAGAUGACCAAGAU
38
AUCUUGGUCAUCUUGAUCU
146
Rh, Dg
[376-394] ORF

19
CUGCAGAGUGGCACUCAUU
39
AAUGAGUGCCACUCUGCAG
147
Rh
[675-693] ORF

20
CCUGGAACAGCCUGAGCUU
40
AAGCUCAGGCUGUUCCAGG
148

[571-589] ORF

21
CACUGUUGGCUGUGAGGAA
41
UUCCUCACAGCCAACAGUG
149
Rh
[620-638] ORF

22
CCAGAAGUCAACCAGACCA
42
UGGUCUGGUUGACUUCUGG
150
Rh, Dg
[339-357] ORF

23
GAUGGACUCUUGCACAUCA
43
UGAUGUGCAAGAGUCCAUC
151

[531-549] ORF

24
AGUUUCUCAUUGCUGGAAA
44
UUUCCAGCAAUGAGAAACU
152
Rh
[505-523] ORF

25
GCUCCUCCAAGGCUCUGAA
45
UUCAGAGCCUUGGAGGAGC
153
Rh
[710-728] ORF

26
ACAGUGUUUCCCUGUUUAU
46
AUAAACAGGGAAACACUGU
154
Rh, M
[642-660] ORF

27
GUCUGCGGAUACUUCCACA
47
UGUGGAAGUAUCCGCAGAC
155
Rh
[465-483] ORF

28
CUGGAACAGCCUGAGCUUA
48
UAAGCUCAGGCUGUUCCAG
156

[572-590] ORF

29
GGGCUGUGCACCUGGCAGU
49
ACUGCCAGGUGCACAGCCC
157
Rh
[774-792] ORF

30
GUGUCUGCGGAUACUUCCA
50
UGGAAGUAUCCGCAGACAC
158
Rh
[463-481] ORF

31
AUGAGAUCAAGAUGACCAA
51
UUGGUCAUCUUGAUCUCAU
159
Rh, Dg
[373-391] ORF

32
GGAAGCUGAAGCCUGCACA
52
UGUGCAGGCUUCAGCUUCC
160

[830-848] 3′UTR

33
GAGUUUCUCAUUGCUGGAA
53
UUCCAGCAAUGAGAAACUC
161
Rh
[504-522] ORF

34
CAGACGGCCUUCUGCAAUU
54
AAUUGCAGAAGGCCGUCUG
162
Rh
[285-303] ORF

35
GCACAUCACUACCUGCAGU
55
ACUGCAGGUAGUGAUGUGC
163

[542-560] ORF

36
GGCAGUCCCUGCGGUCCCA
56
UGGGACCGCAGGGACUGCC
164

[787-805] ORF

37
GAUGUAUAAAGGGUUCCAA
57
UUGGAACCCUUUAUACAUC
165
Rh
[392-410] ORF

38
CUGGCAUCCUGUUGUUGCU
58
AGCAACAACAGGAUGCCAG
166

[217-235] ORF

39
GGACGGACCAGCUCCUCCA
59
UGGAGGAGCUGGUCCGUCC
167
Rh
[700-718] ORF

40
GAGUGGCACUCAUUGCUUG
60
CAAGCAAUGAGUGCCACUC
168
Rh
[680-698] ORF

41
AGAGUGUCUGCGGAUACUU
61
AAGUAUCCGCAGACACUCU
169
Rh
[460-478] ORF

42
ACCAGACCACCUUAUACCA
62
UGGUAUAAGGUGGUCUGGU
170
Rh
[349-367] ORF

43
CACCAAGACCUACACUGUU
63
AACAGUGUAGGUCUUGGUG
171
Rh
[608-626] ORF

44
GGCAUCCUGUUGUUGCUGU
64
ACAGCAACAACAGGAUGCC
172
Rh
[219-237] ORF

45
CCUGAAUCCUGCCCGGAGU
65
ACUCCGGGCAGGAUUCAGG
173

[811-829] ORF + 3′UTR

46
GUCAACCAGACCACCUUAU
66
AUAAGGUGGUCUGGUUGAC
174
Rh
[345-363] ORF

47
GGACACCAGAAGUCAACCA
67
UGGUUGACUUCUGGUGUCC
175
Rh
[334-352] ORF

48
AGCGUUAUGAGAUCAAGAU
68
AUCUUGAUCUCAUAACGCU
176
Rh, Dg, Rt
[367-385] ORF

49
UGCACAGUGUUUCCCUGUU
69
AACAGGGAAACACUGUGCA
177
Rh, Rt, M
[639-657] ORF

50
ACUGCAGAGUGGCACUCAU
70
AUGAGUGCCACUCUGCAGU
178
Rh
[674-692] ORF

51
CCCAUCUUUCUUCCGGACA
71
UGUCCGGAAGAAAGAUGGG
179

[869-887] 3′UTR

52
GUGAGGAAUGCACAGUGUU
72
AACACUGUGCAUUCCUCAC
180
Rh
[631-649] ORF

53
CCUCCAAGGCUCUGAAAAG
73
CUUUUCAGAGCCUUGGAGG
181
Rh
[713-731] ORF

54
CAUCACUACCUGCAGUUUU
74
AAAACUGCAGGUAGUGAUG
182

[545-563] ORF

55
AGCUGAAGCCUGCACAGUG
75
CACUGUGCAGGCUUCAGCU
183

[833-851] 3′UTR

56
GCACAGUGUCCACCCUGUU
76
AACAGGGUGGACACUGUGC
184

[844-862] 3′UTR

57
CCAGCUCCUCCAAGGCUCU
77
AGAGCCUUGGAGGAGCUGG
185
Rh
[707-725] ORF

58
CUGUUGUUGCUGUGGCUGA
78
UCAGCCACAGCAACAACAG
186
Rh
[225-243] ORF

59
UCUUCCGGACAAUGAAAUA
79
UAUUUCAUUGUCCGGAAGA
187

[877-895] 3′UTR

60
GCUCCCUGGAACAGCCUGA
80
UCAGGCUGUUCCAGGGAGC
188

[567-585] ORF

61
AUAAAGGGUUCCAAGCCUU
81
AAGGCUUGGAACCCUUUAU
189

[397-415] ORF

62
GAGUGGAAGCUGAAGCCUG
82
CAGGCUUCAGCUUCCACUC
190
Rh
[826-844] 3′UTR

63
CAAACUGCAGAGUGGCACU
83
AGUGCCACUCUGCAGUUUG
191
Rh
[671-689] ORF

64
CGGCCUUCUGCAAUUCCGA
84
UCGGAAUUGCAGAAGGCCG
192
Rh
[289-307] ORF

65
CUCCUCCAAGGCUCUGAAA
85
UUUCAGAGCCUUGGAGGAG
193
Rh
[711-729] ORF

66
CCUGCAAACUGCAGAGUGG
86
CCACUCUGCAGUUUGCAGG
194
Rh, Dg
[667-685] ORF

67
CACAUCACUACCUGCAGUU
87
AACUGCAGGUAGUGAUGUG
195

[543-561] ORF

68
UGCCCGGAGUGGAAGCUGA
88
UCAGCUUCCACUCCGGGCA
196

[820-838] 3′UTR

69
GCUUCUGGCAUCCUGUUGU
89
ACAACAGGAUGCCAGAAGC
197

[213-231] ORF

70
UUUCUUCCGGACAAUGAAA
90
UUUCAUUGUCCGGAAGAAA
198

[875-893] 3′UTR

71
UGCACAGUGUCCACCCUGU
91
ACAGGGUGGACACUGUGCA
199

[843-861] 3′UTR

72
GACCUACACUGUUGGCUGU
92
ACAGCCAACAGUGUAGGUC
200
Rh
[614-632] ORF

73
CACAGACGGCCUUCUGCAA
93
UUGCAGAAGGCCGUCUGUG
201
Rh
[283-301] ORF

74
AGGGCUUCCAGUCCCGUCA
94
UGACGGGACUGGAAGCCCU
202
Rh
[730-748] ORF

75
CCCAGAUAGCCUGAAUCCU
95
AGGAUUCAGGCUAUCUGGG
203

[802-820] ORF + 3′UTR

76
GUUGUUGCUGUGGCUGAUA
96
UAUCAGCCACAGCAACAAC
204
Rh
[227-245] ORF

77
GUCCCUGCGGUCCCAGAUA
97
UAUCUGGGACCGCAGGGAC
205

[791-809] ORF

78
CCUACACUGUUGGCUGUGA
99
UCACAGCCAACAGUGUAGG
207
Rh
[616-634] ORF

80
ACAUCACUACCUGCAGUUU
100
AAACUGCAGGUAGUGAUGU
208

[544-562] ORF

81
UCUUUCUUCCGGACAAUGA
101
UCAUUGUCCGGAAGAAAGA
209

[873-891] 3′UTR

82
CCAGAUAGCCUGAAUCCUG
102
CAGGAUUCAGGCUAUCUGG
210

[803-821] ORF + 3′UTR

83
CAGUGUUUCCCUGUUUAUC
103
GAUAAACAGGGAAACACUG
211
Rh, M
[643-661] ORF

84
CUGGCUUCUGGCAUCCUGU
104
ACAGGAUGCCAGAAGCCAG
212

[210-228] ORF

85
GACGGACCAGCUCCUCCAA
105
UUGGAGGAGCUGGUCCGUC
213
Rh
[701-719] ORF

86
UGUUGUUGCUGUGGCUGAU
106
AUCAGCCACAGCAACAACA
214
Rh
[226-244] ORF

87
GACUCUUGCACAUCACUAC
107
GUAGUGAUGUGCAAGAGUC
215

[535-553] ORF

88
CCCGCCAUGGAGAGUGUCU
108
AGACACUCUCCAUGGCGGG
216
Rh
[450-468] ORF

89
CGAGGAGUUUCUCAUUGCU
109
AGCAAUGAGAAACUCCUCG
217
Rh
[500-518] ORF

90
CACAGGUCCCACAACCGCA
110
UGCGGUUGUGGGACCUGUG
218
Rh
[480-498] ORF

91
ACACCAGAAGUCAACCAGA
111
UCUGGUUGACUUCUGGUGU
219
Rh
[336-354] ORF

92
UGUUCCCACUCCCAUCUUU
112
AAAGAUGGGAGUGGGAACA
220
Rh
[859-877] 3′UTR

93
CCCUGUUCCCACUCCCAUC
113
GAUGGGAGUGGGAACAGGG
221
Rh
[856-874] 3′UTR

94
CACCUUAUACCAGCGUUAU
114
AUAACGCUGGUAUAAGGUG
222
Rh, Rt, M
[356-374] ORF

95
CACCAGAAGUCAACCAGAC
115
GUCUGGUUGACUUCUGGUG
223
Rh
[337-355] ORF

96
UCCUCCAAGGCUCUGAAAA
116
UUUUCAGAGCCUUGGAGGA
224
Rh
[712-730] ORF

97
GAAGCCUGCACAGUGUCCA
117
UGGACACUGUGCAGGCUUC
225

[837-855] 3′UTR

98
CCUGCACAGUGUCCACCCU
118
AGGGUGGACACUGUGCAGG
226

[841-859] 3′UTR

99
CCGCCAUGGAGAGUGUCUG
119
CAGACACUCUCCAUGGCGG
227
Rh
[451-469] ORF

100
UAAAGGGUUCCAAGCCUUA
120
UAAGGCUUGGAACCCUUUA
228

[398-416] ORF

101
CAAGAUGACCAAGAUGUAU
121
AUACAUCUUGGUCAUCUUG
229
Rh
[380-398] ORF

102
GUUUUGUGGCUCCCUGGAA
122
UUCCAGGGAGCCACAAAAC
230

[559-577] ORF

103
GGAGUGGAAGCUGAAGCCU
123
AGGCUUCAGCUUCCACUCC
231
Rh
[825-843] 3′UTR

104
CUGACAUCCGGUUCGUCUA
124
UAGACGAACCGGAUGUCAG
232
Rh
[427-445] ORF

105
GCGUUAUGAGAUCAAGAUG
125
CAUCUUGAUCUCAUAACGC
233
Rh, Dg, Rt
[368-386] ORF

106
CGGACCAGCUCCUCCAAGG
126
CCUUGGAGGAGCUGGUCCG
234
Rh
[703-721] ORF

107
CAGGAUGGACUCUUGCACA
127
UGUGCAAGAGUCCAUCCUG
235

[528-546] ORF

108
CAAGAUGUAUAAAGGGUUC
128
GAACCCUUUAUACAUCUUG
236
Rh
[389-407] ORF

TABLE A2

19-mer Cross-Species siTIMP1

SEQ

SEQ

ID

ID

human-73858576

No.
Sense (5′>3′)
NO.
Antisense (5′>3′)
NO.
Other Sp
ORF:193-816

1
ACCACCUUAUACCAGCGUU
237
AACGCUGGUAUAAGGUGGU
252
Rh, Rt, M
[354-372] ORF

2
ACCGCAGCGAGGAGUUUCU
238
AGAAACUCCUCGCUGCGGU
253
Rh, Rb, Dg, Rt
[493-511] ORF

3
AGACCACCUUAUACCAGCG
239
CGCUGGUAUAAGGUGGUCU
254
Rh, Rt, M
[352-370] ORF

4
GGGCUUCACCAAGACCUAC
240
GUAGGUCUUGGUGAAGCCC
255
Rh, Rb, Dg
[602-620] ORF

5
CAACCGCAGCGAGGAGUUU
241
AAACUCCUCGCUGCGGUUG
256
Rh, Rb, Dg, Rt
[491-509] ORF

6
CAGACCACCUUAUACCAGC
242
GCUGGUAUAAGGUGGUCUG
257
Rh, Rt, M
[351-369] ORF

7
ACCUUAUACCAGCGUUAUG
243
CAUAACGCUGGUAUAAGGU
258
Rh, Rt, M
[357-375] ORF

8
CGUCAUCAGGGCCAAGUUC
244
GAACUUGGCCCUGAUGACG
259
Rh, Rb, Dg
[311-329] ORF

9
AUGCACAGUGUUUCCCUGU
245
ACAGGGAAACACUGUGCAU
260
Rh, Rt, M
[638-656] ORF

10
ACCUGGCAGUCCCUGCGGU
246
ACCGCAGGGACUGCCAGGU
261
Rh, Rb, Dg
[783-801] ORF

11
GACCACCUUAUACCAGCGU
247
ACGCUGGUAUAAGGUGGUC
262
Rh, Rt, M
[353-371] ORF

12
CCGCAGCGAGGAGUUUCUC
248
GAGAAACUCCUCGCUGCGG
263
Rh, Rb, Dg, Rt
[494-512] ORF

13
AACCGCAGCGAGGAGUUUC
249
GAAACUCCUCGCUGCGGUU
264
Rh, Rb, Dg, Rt
[492-510] ORF

14
UUAUGAGAUCAAGAUGACC
250
GGUCAUCUUGAUCUCAUAA
265
Rh, Dg, Rt
[371-389] ORF

15
ACCAGCGUUAUGAGAUCAA
251
UUGAUCUCAUAACGCUGGU
266
Rh, Rt
[364-382] ORF

TABLE A3

Preferred 19-mer siTIMP1

SEQ

SEQ

ID

ID

human-73858576

siTIMP1_pNo.
Sense (5′>3′)
NO.
Antisense (5′>3′)
NO.
length
ORF:193-816

siTIMP1_p2
GCACAGUGUUUCCCUGUUU
267
AAACAGGGAAACACUGUGC
299
19
[640-658] ORF

siTIMP1_p6
CCACCUUAUACCAGCGUUA
268
UAACGCUGGUAUAAGGUGG
300
19
[355-373] ORF

siTIMP1_p14
UGCACAGUGUUUCCCUGUU
269
AACAGGGAAACACUGUGCA
301
19
[639-657] ORF

siTIMP1_p16
CACCUUAUACCAGCGUUAU
270
AUAACGCUGGUAUAAGGUG
302
19
[356-374] ORF

siTIMP1_p17
GCGUUAUGAGAUCAAGAUG
271
CAUCUUGAUCUCAUAACGC
303
19
[368-386] ORF

siTIMP1_p19
ACCACCUUAUACCAGCGUU
272
AACGCUGGUAUAAGGUGGU
304
19
[354-372] ORF

siTIMP1_p20
ACCGCAGCGAGGAGUUUCU
273
AGAAACUCCUCGCUGCGGU
305
19
[493-511] ORF

siTIMP1_p21
ACCAGCGUUAUGAGAUCAA
274
UUGAUCUCAUAACGCUGGU
306
19
[364-382] ORF

siTIMP1_p23
CAACCGCAGCGAGGAGUUU
275
AAACUCCUCGCUGCGGUUG
307
19
[491-509] ORF

siTIMP1_p24
CAGACCACCUUAUACCAGC
276
GCUGGUAUAAGGUGGUCUG
308
19
[351-369] ORF

siTIMP1_p27
AGAUCAAGAUGACCAAGAU
277
AUCUUGGUCAUCUUGAUCU
309
19
[376-394] ORF

siTIMP1_p29
CCAGAAGUCAACCAGACCA
278
UGGUCUGGUUGACUUCUGG
310
19
[339-357] ORF

siTIMP1_p31
AUGAGAUCAAGAUGACCAA
279
UUGGUCAUCUUGAUCUCAU
311
19
[373-391] ORF

siTIMP1_p33
CCUGCAAACUGCAGAGUGG
280
CCACUCUGCAGUUUGCAGG
312
19
[667-685] ORF

siTIMP1_p38
CACAGUGUUUCCCUGUUUA
281
UAAACAGGGAAACACUGUG
313
19
[641-659] ORF

siTIMP1_p42
ACAGUGUUUCCCUGUUUAU
282
AUAAACAGGGAAACACUGU
314
19
[642-660] ORF

siTIMP1_p43
CAGUGUUUCCCUGUUUAUC
283
GAUAAACAGGGAAACACUG
315
19
[643-661] ORF

siTIMP1_p45
CUUUCUUCCGGACAAUGAA
284
UUCAUUGUCCGGAAGAAAG
316
19
[874-892] 3′UTR

siTIMP1_p49
GUUUCUCAUUGCUGGAAAA
285
UUUUCCAGCAAUGAGAAAC
317
19
[506-524] ORF

siTIMP1_p60
CAUCUUUCUUCCGGACAAU
286
AUUGUCCGGAAGAAAGAUG
318
19
[871-889] 3′UTR

siTIMP1_p71
CUCCCAUCUUUCUUCCGGA
287
UCCGGAAGAAAGAUGGGAG
319
19
[867-885] 3′UTR

siTIMP1_p73
GUGUUUCCCUGUUUAUCCA
288
UGGAUAAACAGGGAAACAC
320
19
[645-663] ORF

siTIMP1_p77
GCCCGGAGUGGAAGCUGAA
289
UUCAGCUUCCACUCCGGGC
321
19
[821-839] 3′UTR

siTIMP1_p78
CAUGGAGAGUGUCUGCGGA
290
UCCGCAGACACUCUCCAUG
322
19
[455-473] ORF

siTIMP1_p79
CCAAGAUGUAUAAAGGGUU
291
AACCCUUUAUACAUCUUGG
323
19
[388-406] ORF

siTIMP1_p85
GAGAGUGUCUGCGGAUACU
292
AGUAUCCGCAGACACUCUC
324
19
[459-477] ORF

siTIMP1_p89
CUGCAGAGUGGCACUCAUU
293
AAUGAGUGCCACUCUGCAG
325
19
[675-693] ORF

siTIMP1_p91
CCUGGAACAGCCUGAGCUU
294
AAGCUCAGGCUGUUCCAGG
326
19
[571-589] ORF

siTIMP1_p96
CACUGUUGGCUGUGAGGAA
295
UUCCUCACAGCCAACAGUG
327
19
[620-638] ORF

siTIMP1_p98
GAUGGACUCUUGCACAUCA
296
UGAUGUGCAAGAGUCCAUC
328
91
[531-549] ORF

siTIMP1_p99
AGUUUCUCAUUGCUGGAAA
297
UUUCCAGCAAUGAGAAACU
329
91
[505-523] ORF

siTIMP1_p108
GUCUGCGGAUACUUCCACA
298
UGUGGAAGUAUCCGCAGAC
330
91
[465-483] ORF

TABLE A4

19-mer siTIMP1 with lowest predicted OT effect

SEQ

SEQ

No. in

ID

ID

Table A3
Cross species
Ranking
Sense (5′>3′)
NO.
Antisense (5′>3′)
NO.

siTIMP1_p2
H/Rt
3
GCACAGUGUUUCCCUGUUU
267
AAACAGGGAAACACUGUGC
299

siTIMP1_p6
H/Rt
2
CCACCUUAUACCAGCGUUA
268
UAACGCUGGUAUAAGGUGG
300

siTIMP1_p14
H/Rt
4
UGCACAGUGUUUCCCUGUU
269
AACAGGGAAACACUGUGCA
301

siTIMP1_p16
H/Rt
1
CACCUUAUACCAGCGUUAU
270
AUAACGCUGGUAUAAGGUG
302

siTIMP1_p17
H/Rt
2
GCGUUAUGAGAUCAAGAUG
271
CAUCUUGAUCUCAUAACGC
303

siTIMP1_p19
H/Rt
2
ACCACCUUAUACCAGCGUU
272
AACGCUGGUAUAAGGUGGU
304

siTIMP1_p20
H/Rt
3
ACCGCAGCGAGGAGUUUCU
273
AGAAACUCCUCGCUGCGGU
305

siTIMP1_p21
H/Rt
3
ACCAGCGUUAUGAGAUCAA
274
UUGAUCUCAUAACGCUGGU
306

siTIMP1_p23
H/Rt
3
CAACCGCAGCGAGGAGUUU
275
AAACUCCUCGCUGCGGUUG
307

siTIMP1_p29
Other (w/o Rt)
3
CCAGAAGUCAACCAGACCA
278
UGGUCUGGUUGACUUCUGG
310

siTIMP1_p33
Other (w/o Rt)
4
CCUGCAAACUGCAGAGUGG
280
CCACUCUGCAGUUUGCAGG
312

siTIMP1_p38
H/Rt (Rt Cross-
3
CACAGUGUUUCCCUGUUUA
281
UAAACAGGGAAACACUGUG
313

with 1MM)

siTIMP1_p42
Other (w/o Rt)
3
ACAGUGUUUCCCUGUUUAU
282
AUAAACAGGGAAACACUGU
314

siTIMP1_p43
Other (w/o Rt)
3
CAGUGUUUCCCUGUUUAUC
283
GAUAAACAGGGAAACACUG
315

siTIMP1_p45
H +/- Rh
4
CUUUCUUCCGGACAAUGAA
284
UUCAUUGUCCGGAAGAAAG
316

siTIMP1_p60
H +/- Rh
2
CAUCUUUCUUCCGGACAAU
286
AUUGUCCGGAAGAAAGAUG
318

siTIMP1_p71
H +/- Rh
4
CUCCCAUCUUUCUUCCGGA
287
UCCGGAAGAAAGAUGGGAG
319

siTIMP1_p73
H +/- Rh
3
GUGUUUCCCUGUUUAUCCA
288
UGGAUAAACAGGGAAACAC
320

siTIMP1_p78
H +/- Rh
3
CAUGGAGAGUGUCUGCGGA
290
UCCGCAGACACUCUCCAUG
322

siTIMP1_p79
H +/- Rh
3
CCAAGAUGUAUAAAGGGUU
291
AACCCUUUAUACAUCUUGG
323

siTIMP1_p85
H +/- Rh
2
GAGAGUGUCUGCGGAUACU
292
AGUAUCCGCAGACACUCUC
324

siTIMP1_p89
H +/- Rh
3
CUGCAGAGUGGCACUCAUU
293
AAUGAGUGCCACUCUGCAG
325

siTIMP1_p91
H +/- Rh
4
CCUGGAACAGCCUGAGCUU
294
AAGCUCAGGCUGUUCCAGG
326

siTIMP1_p96
H +/- Rh
4
CACUGUUGGCUGUGAGGAA
295
UUCCUCACAGCCAACAGUG
327

siTIMP1_p98
H +/- Rh
3
GAUGGACUCUUGCACAUCA
296
UGAUGUGCAAGAGUCCAUC
328

siTIMP1_p99
H +/- Rh
4
AGUUUCUCAUUGCUGGAAA
297
UUUCCAGCAAUGAGAAACU
329

siTIMP1_p108
H +/- Rh
2
GUCUGCGGAUACUUCCACA
298
UGUGGAAGUAUCCGCAGAC
330

TABLE A5

18-mer siTIMP1

SEQ

SEQ

ID

ID

human-73858576

No.
Sense (5′>3′)
NO.
Antisense (5′>3′)
NO.
Other Sp
ORF:193-816

1
GGAGAGUGUCUGCGGAUA
331
UAUCCGCAGACACUCUCC
582
Rh
[458-475] ORF

2
GCUGAAGCCUGCACAGUG
332
CACUGUGCAGGCUUCAGC
583

[834-851] 3′UTR

3
CAUCUUUCUUCCGGACAA
333
UUGUCCGGAAGAAAGAUG
584

[871-888] 3′UTR

4
CCUCCAAGGCUCUGAAAA
334
UUUUCAGAGCCUUGGAGG
585
Rh
[713-730] ORF

5
CCGCCAUGGAGAGUGUCU
335
AGACACUCUCCAUGGCGG
586
Rh
[451-468] ORF

6
GAGUGUCUGCGGAUACUU
336
AAGUAUCCGCAGACACUC
587
Rh
[461-478] ORF

7
GAGUGGCACUCAUUGCUU
337
AAGCAAUGAGUGCCACUC
588
Rh
[680-697] ORF

8
AGCUGAAGCCUGCACAGU
338
ACUGUGCAGGCUUCAGCU
589

[833-850] 3′UTR

9
AGAUCAAGAUGACCAAGA
339
UCUUGGUCAUCUUGAUCU
590
Rh, Dg
[376-393] ORF

10
GACUCUUGCACAUCACUA
340
UAGUGAUGUGCAAGAGUC
591

[535-552] ORF

11
GAGUGGAAGCUGAAGCCU
341
AGGCUUCAGCUUCCACUC
592
Rh
[826-843] 3′UTR

12
CCUGCAAACUGCAGAGUG
342
CACUCUGCAGUUUGCAGG
593
Rh, Dg
[667-684] ORF

13
CAGUGUUUCCCUGUUUAU
343
AUAAACAGGGAAACACUG
594
Rh, Ms
[643-660] ORF

14
CCCUGUUCCCACUCCCAU
344
AUGGGAGUGGGAACAGGG
595
Rh
[856-873] 3′UTR

15
CCAGAUAGCCUGAAUCCU
345
AGGAUUCAGGCUAUCUGG
596

[803-820] ORF + 3′UTR

16
GGUCCCAGAUAGCCUGAA
346
UUCAGGCUAUCUGGGACC
597

[799-816] ORF

17
GGGCUUCACCAAGACCUA
347
UAGGUCUUGGUGAAGCCC
598
Rh, Rb, Dg
[602-619] ORF

18
GCGGAUACUUCCACAGGU
348
ACCUGUGGAAGUAUCCGC
599
Rh
[469-486] ORF

19
GAGAGUGUCUGCGGAUAC
349
GUAUCCGCAGACACUCUC
600
Rh
[459-476] ORF

20
GCGUUAUGAGAUCAAGAU
350
AUCUUGAUCUCAUAACGC
601
Rh, Dg, Rt
[368-385] ORF

21
GGAACAGCCUGAGCUUAG
351
CUAAGCUCAGGCUGUUCC
602

[574-591] ORF

22
CUGAAAAGGGCUUCCAGU
352
ACUGGAAGCCCUUUUCAG
603
Rh
[724-741] ORF

23
CCAGCGUUAUGAGAUCAA
353
UUGAUCUCAUAACGCUGG
604
Rh, Rt
[365-382] ORF

24
CAACCAGACCACCUUAUA
354
UAUAAGGUGGUCUGGUUG
605
Rh
[347-364] ORF

25
GAGGAAUGCACAGUGUUU
355
AAACACUGUGCAUUCCUC
606
Rh
[633-650] ORF

26
CCAAGAUGUAUAAAGGGU
356
ACCCUUUAUACAUCUUGG
607
Rh
[388-405] ORF

27
CAGACCACCUUAUACCAG
357
CUGGUAUAAGGUGGUCUG
608
Rh, Rt, Ms
[351-368] ORF

28
AGUGGAAGCUGAAGCCUG
358
CAGGCUUCAGCUUCCACU
609
Rh
[827-844] 3′UTR

29
ACAGUGUUUCCCUGUUUA
359
UAAACAGGGAAACACUGU
610
Rh, Ms
[642-659] ORF

30
CGCCAUGGAGAGUGUCUG
360
CAGACACUCUCCAUGGCG
611
Rh
[452-469] ORF

31
CACCAGAAGUCAACCAGA
361
UCUGGUUGACUUCUGGUG
612
Rh
[337-354] ORF

32
CAGAAGUCAACCAGACCA
362
UGGUCUGGUUGACUUCUG
613
Rh
[340-357] ORF

33
CCCACUCCCAUCUUUCUU
363
AAGAAAGAUGGGAGUGGG
614
Rh
[863-880] 3′UTR

34
GCGAGGAGUUUCUCAUUG
364
CAAUGAGAAACUCCUCGC
615
Rh
[499-516] ORF

35
GCUUCACCAAGACCUACA
365
UGUAGGUCUUGGUGAAGC
616
Rh
[604-621] ORF

36
CAUCACUACCUGCAGUUU
366
AAACUGCAGGUAGUGAUG
617

[545-562] ORF

37
AGCGUUAUGAGAUCAAGA
367
UCUUGAUCUCAUAACGCU
618
Rh, Dg, Rt
[367-384] ORF

38
CUGCAGAGUGGCACUCAU
368
AUGAGUGCCACUCUGCAG
619
Rh
[675-692] ORF

39
GAAGCUGAAGCCUGCACA
369
UGUGCAGGCUUCAGCUUC
620

[831-848] 3′UTR

40
AUCACUACCUGCAGUUUU
370
AAAACUGCAGGUAGUGAU
621

[546-563] ORF

41
GCACAGUGUUUCCCUGUU
371
AACAGGGAAACACUGUGC
622
Rh, Rt, Ms
[640-657] ORF

42
CCUGGAACAGCCUGAGCU
372
AGCUCAGGCUGUUCCAGG
623

[571-588] ORF

43
GCAUCCUGUUGUUGCUGU
373
ACAGCAACAACAGGAUGC
624
Rh
[220-237] ORF

44
GUCCCAGAUAGCCUGAAU
374
AUUCAGGCUAUCUGGGAC
625

[800-817] ORF + 3′UTR

45
AGUGUUUCCCUGUUUAUC
375
GAUAAACAGGGAAACACU
626
Rh, Ms
[644-661] ORF

46
GGCUGUGAGGAAUGCACA
376
UGUGCAUUCCUCACAGCC
627
Rh
[627-644] ORF

47
AGACCACCUUAUACCAGC
377
GCUGGUAUAAGGUGGUCU
628
Rh, Rt, Ms
[352-369] ORF

48
GGAUGGACUCUUGCACAU
378
AUGUGCAAGAGUCCAUCC
629

[530-547] ORF

49
CGGACCAGCUCCUCCAAG
379
CUUGGAGGAGCUGGUCCG
630
Rh
[703-720] ORF

50
GGCCUUCUGCAAUUCCGA
380
UCGGAAUUGCAGAAGGCC
631
Rh
[290-307] ORF

51
GGGCUUCCAGUCCCGUCA
381
UGACGGGACUGGAAGCCC
632
Rh
[731-748] ORF

52
GCAGAGUGGCACUCAUUG
382
CAAUGAGUGCCACUCUGC
633
Rh
[677-694] ORF

53
CAGCGAGGAGUUUCUCAU
383
AUGAGAAACUCCUCGCUG
634
Rh, Rb, Rt
[497-514] ORF

54
CAGAUAGCCUGAAUCCUG
384
CAGGAUUCAGGCUAUCUG
635

[804-821] ORF + 3′UTR

55
GCAGCGAGGAGUUUCUCA
385
UGAGAAACUCCUCGCUGC
636
Rh, Rb, Rt
[496-513] ORF

56
CCUGCAGUUUUGUGGCUC
386
GAGCCACAAAACUGCAGG
637

[553-570] ORF

57
GUUAUGAGAUCAAGAUGA
387
UCAUCUUGAUCUCAUAAC
638
Rh, Dg, Rt
[370-387] ORF

58
CAAGAUGUAUAAAGGGUU
388
AACCCUUUAUACAUCUUG
639
Rh
[389-406] ORF

59
CCGGAGUGGAAGCUGAAG
389
CUUCAGCUUCCACUCCGG
640
Rh
[823-840] 3′UTR

60
AGGAGUUUCUCAUUGCUG
390
CAGCAAUGAGAAACUCCU
641
Rh
[502-519] ORF

61
GGCUGUGCACCUGGCAGU
391
ACUGCCAGGUGCACAGCC
642
Rh
[775-792] ORF

62
GUUUCCCUGUUUAUCCAU
392
AUGGAUAAACAGGGAAAC
643
Rh
[647-664] ORF

63
GCAGUUUUGUGGCUCCCU
393
AGGGAGCCACAAAACUGC
644

[556-573] ORF

64
GUCAACCAGACCACCUUA
394
UAAGGUGGUCUGGUUGAC
645
Rh
[345-362] ORF

65
CCAUGGAGAGUGUCUGCG
395
CGCAGACACUCUCCAUGG
646
Rh
[454-471] ORF

66
CUGGCAUCCUGUUGUUGC
396
GCAACAACAGGAUGCCAG
647

[217-234] ORF

67
CAGACGGCCUUCUGCAAU
397
AUUGCAGAAGGCCGUCUG
648
Rh
[285-302] ORF

68
ACUGCAGAGUGGCACUCA
398
UGAGUGCCACUCUGCAGU
649
Rh
[674-691] ORF

69
CGGAGUGGAAGCUGAAGC
399
GCUUCAGCUUCCACUCCG
650
Rh
[824-841] 3′UTR

70
GCCUCGGGAGCCAGGGCU
400
AGCCCUGGCUCCCGAGGC
651
Rh
[761-778] ORF

71
CCAGACCACCUUAUACCA
401
UGGUAUAAGGUGGUCUGG
652
Rh
[350-367] ORF

72
GGCUCUGAAAAGGGCUUC
402
GAAGCCCUUUUCAGAGCC
653
Rh
[720-737] ORF

73
GCUGGAAAACUGCAGGAU
403
AUCCUGCAGUUUUCCAGC
654

[516-533] ORF

74
CCUGAAUCCUGCCCGGAG
404
CUCCGGGCAGGAUUCAGG
655

[811-828] ORF + 3′UTR

75
CUGAAGCCUGCACAGUGU
405
ACACUGUGCAGGCUUCAG
656

[835-852] 3′UTR

76
GGCAUCCUGUUGUUGCUG
406
CAGCAACAACAGGAUGCC
657
Rh
[219-236] ORF

77
CCCUGCAAACUGCAGAGU
407
ACUCUGCAGUUUGCAGGG
658
Rh, Dg
[666-683] ORF

78
CUGGAAAACUGCAGGAUG
408
CAUCCUGCAGUUUUCCAG
659

[517-534] ORF

79
UCUCAUUGCUGGAAAACU
409
AGUUUUCCAGCAAUGAGA
660
Rh
[509-526] ORF

80
GUGGCUCCCUGGAACAGC
410
GCUGUUCCAGGGAGCCAC
661

[564-581] ORF

81
CCAGCUCCUCCAAGGCUC
411
GAGCCUUGGAGGAGCUGG
662
Rh
[707-724] ORF

82
AGACCUACACUGUUGGCU
412
AGCCAACAGUGUAGGUCU
663
Rh
[613-630] ORF

83
GGGACACCAGAAGUCAAC
413
GUUGACUUCUGGUGUCCC
664
Rh
[333-350] ORF

84
GGCUCCCUGGAACAGCCU
414
AGGCUGUUCCAGGGAGCC
665

[566-583] ORF

85
GUUCCCACUCCCAUCUUU
415
AAAGAUGGGAGUGGGAAC
666
Rh
[860-877] 3′UTR

86
CUCUGAAAAGGGCUUCCA
416
UGGAAGCCCUUUUCAGAG
667
Rh
[722-739] ORF

87
GGCUUCUGGCAUCCUGUU
417
AACAGGAUGCCAGAAGCC
668

[212-229] ORF

88
AGGAAUGCACAGUGUUUC
418
GAAACACUGUGCAUUCCU
669
Rh
[634-651] ORF

89
CUUCUGGCAUCCUGUUGU
419
ACAACAGGAUGCCAGAAG
670

[214-231] ORF

90
CAAACUGCAGAGUGGCAC
420
GUGCCACUCUGCAGUUUG
671
Rh
[671-688] ORF

91
AUACCAGCGUUAUGAGAU
421
AUCUCAUAACGCUGGUAU
672
Rh, Rt
[362-379] ORF

92
AGAGUGUCUGCGGAUACU
422
AGUAUCCGCAGACACUCU
673
Rh
[460-477] ORF

93
CACCAAGACCUACACUGU
423
ACAGUGUAGGUCUUGGUG
674
Rh
[608-625] ORF

94
GAUCAAGAUGACCAAGAU
424
AUCUUGGUCAUCUUGAUC
675
Rh, Dg
[377-394] ORF

95
AUGUAUAAAGGGUUCCAA
425
UUGGAACCCUUUAUACAU
676

[393-410] ORF

96
ACCAAGACCUACACUGUU
426
AACAGUGUAGGUCUUGGU
677
Rh
[609-626] ORF

97
CCGUCACCUUGCCUGCCU
427
AGGCAGGCAAGGUGACGG
678
Rh
[743-760] ORF

98
GGGAGCCAGGGCUGUGCA
428
UGCACAGCCCUGGCUCCC
679
Rh
[766-783] ORF

99
UGCACAGUGUUUCCCUGU
429
ACAGGGAAACACUGUGCA
680
Rh, Rt, Ms
[639-656] ORF

100
UGCAGAGUGGCACUCAUU
430
AAUGAGUGCCACUCUGCA
681
Rh
[676-693] ORF

101
GUGAGGAAUGCACAGUGU
431
ACACUGUGCAUUCCUCAC
682
Rh
[631-648] ORF

102
AGCGAGGAGUUUCUCAUU
432
AAUGAGAAACUCCUCGCU
683
Rh
[498-515] ORF

103
GGGCUGUGCACCUGGCAG
433
CUGCCAGGUGCACAGCCC
684
Rh
[774-791] ORF

104
ACUCAUUGCUUGUGGACG
434
CGUCCACAAGCAAUGAGU
685
Rh
[687-704] ORF

105
UGUUGUUGCUGUGGCUGA
435
UCAGCCACAGCAACAACA
686
Rh
>6-243] ORF

106
UGAGGAAUGCACAGUGUU
436
AACACUGUGCAUUCCUCA
687
Rh
[632-649] ORF

107
CCUGGCUUCUGGCAUCCU
437
AGGAUGCCAGAAGCCAGG
688

[209-226] ORF

108
GCACAGUGUCCACCCUGU
438
CAGGGUGGACACUGUGC
689

[844-861] 3′UTR

109
AAAGGGUUCCAAGCCUUA
439
UAAGGCUUGGAACCCUUU
690

[399-416] ORF

110
GCUUCUGGCAUCCUGUUG
440
CAACAGGAUGCCAGAAGC
691

[213-230] ORF

111
CCAAGACCUACACUGUUG
441
CAACAGUGUAGGUCUUGG
692
Rh
[610-627] ORF

112
AAGGGUUCCAAGCCUUAG
442
CUAAGGCUUGGAACCCUU
693

[400-417] ORF

113
UGCACAGUGUCCACCCUG
443
CAGGGUGGACACUGUGCA
694

[843-860] 3′UTR

114
GACCUACACUGUUGGCUG
444
CAGCCAACAGUGUAGGUC
695
Rh
[614-631] ORF

115
CCCAGAUAGCCUGAAUCC
445
GGAUUCAGGCUAUCUGGG
696

[802-819] ORF + 3′UTR

116
GGGUUCCAAGCCUUAGGG
446
CCCUAAGGCUUGGAACCC
697

[402-419] ORF

117
GGCUUCCAGUCCCGUCAC
447
GUGACGGGACUGGAAGCC
698
Rh
[732-749] ORF

118
AGUGUCUGCGGAUACUUC
448
GAAGUAUCCGCAGACACU
699
Rh
[462-479] ORF

119
UGACCAAGAUGUAUAAAG
449
CUUUAUACAUCUUGGUCA
700
Rh
[385-402] ORF

120
CAGCCUGAGCUUAGCUCA
450
UGAGCUAAGCUCAGGCUG
701

[578-595] ORF

121
CUUCCGGACAAUGAAAUA
451
UAUUUCAUUGUCCGGAAG
702

[878-895] 3′UTR

122
CUGUGAGGAAUGCACAGU
452
ACUGUGCAUUCCUCACAG
703
Rh
[629-646] ORF

123
GCCUGAAUCCUGCCCGGA
453
UCCGGGCAGGAUUCAGGC
704

[810-827] ORF + 3′UTR

124
ACUGCAGGAUGGACUCUU
454
AAGAGUCCAUCCUGCAGU
705

[524-541] ORF

125
GUCCCACAACCGCAGCGA
455
UCGCUGCGGUUGUGGGAC
706
Rh
[485-502] ORF

126
AUCUUUCUUCCGGACAAU
456
AUUGUCCGGAAGAAAGAU
707

[872-889] 3′UTR

127
AUAAAGGGUUCCAAGCCU
457
AGGCUUGGAACCCUUUAU
708

[397-414] ORF

128
UCCCAUCUUUCUUCCGGA
458
UCCGGAAGAAAGAUGGGA
709

[868-885] 3′UTR

129
GAAAAGGGCUUCCAGUCC
459
GGACUGGAAGCCCUUUUC
710
Rh
[726-743] ORF

130
UGGAACAGCCUGAGCUUA
460
UAAGCUCAGGCUGUUCCA
711

[573-590] ORF

131
CACCUUAUACCAGCGUUA
461
UAACGCUGGUAUAAGGUG
712
Rh, Rt, Ms
[356-373] ORF

132
CUGUUGGCUGUGAGGAAU
462
AUUCCUCACAGCCAACAG
713
Rh
[622-639] ORF

133
GCACAUCACUACCUGCAG
463
CUGCAGGUAGUGAUGUGC
714

[542-559] ORF

134
UGCUGUGGCUGAUAGCCC
464
GGGCUAUCAGCCACAGCA
715
Rh
[232-249] ORF

135
CCACUCCCAUCUUUCUUC
465
GAAGAAAGAUGGGAGUGG
716
Rh
[864-881] 3′UTR

136
CUGGCUUCUGGCAUCCUG
466
CAGGAUGCCAGAAGCCAG
717

[210-227] ORF

137
CUUCCACAGGUCCCACAA
467
UUGUGGGACCUGUGGAAG
718
Rh
[476-493] ORF

138
ACCAGCUCCUCCAAGGCU
468
AGCCUUGGAGGAGCUGGU
719
Rh
[706-723] ORF

139
CAAGAUGACCAAGAUGUA
469
UACAUCUUGGUCAUCUUG
720
Rh
[380-397] ORF

140
CCCGCCAUGGAGAGUGUC
470
GACACUCUCCAUGGCGGG
721
Rh
[450-467] ORF

141
CCCGGAGUGGAAGCUGAA
471
UUCAGCUUCCACUCCGGG
722
Rh
[822-839] 3′UTR

142
CGAGGAGUUUCUCAUUGC
472
GCAAUGAGAAACUCCUCG
723
Rh
[500-517] ORF

143
CACAUCACUACCUGCAGU
473
ACUGCAGGUAGUGAUGUG
724

[543-560] ORF

144
CUCCAAGGCUCUGAAAAG
474
CUUUUCAGAGCCUUGGAG
725
Rh
[714-731] ORF

145
UGAGAUCAAGAUGACCAA
475
UUGGUCAUCUUGAUCUCA
726
Rh, Dg
[374-391] ORF

146
GCACUCAUUGCUUGUGGA
476
UCCACAAGCAAUGAGUGC
727
Rh, Rb
[685-702] ORF

147
CAUUGCUUGUGGACGGAC
477
GUCCGUCCACAAGCAAUG
728
Rh
[690-707] ORF

148
GGACCAGCUCCUCCAAGG
478
CCUUGGAGGAGCUGGUCC
729
Rh
[704-721] ORF

149
GCCUGCACAGUGUCCACC
479
GGUGGACACUGUGCAGGC
730

[840-857] 3′UTR

150
UGUAUAAAGGGUUCCAAG
480
CUUGGAACCCUUUAUACA
731

[394-411] ORF

151
CCUGCACAGUGUCCACCC
481
GGGUGGACACUGUGCAGG
732

[841-858] 3′UTR

152
ACCUUAUACCAGCGUUAU
482
AUAACGCUGGUAUAAGGU
733
Rh, Rt, Ms
[357-374] ORF

153
CUUCCAGUCCCGUCACCU
483
AGGUGACGGGACUGGAAG
734
Rh
[734-751] ORF

154
CAGUGUCCACCCUGUUCC
484
GGAACAGGGUGGACACUG
735

[847-864] 3′UTR

155
GGAGUGGAAGCUGAAGCC
485
GGCUUCAGCUUCCACUCC
736
Rh
[825-842] 3′UTR

156
CUUAUACCAGCGUUAUGA
486
UCAUAACGCUGGUAUAAG
737
Rh, Rt
[359-376] ORF

157
CCGCAGCGAGGAGUUUCU
487
AGAAACUCCUCGCUGCGG
738
Rh, Rb, Dg, Rt
[494-511] ORF

158
CAGUUUUGUGGCUCCCUG
488
CAGGGAGCCACAAAACUG
739

[557-574] ORF

159
GUAUAAAGGGUUCCAAGC
489
GCUUGGAACCCUUUAUAC
740

[395-412] ORF

160
AAGCCUGCACAGUGUCCA
490
UGGACACUGUGCAGGCUU
741

[838-855] 3′UTR

161
AGGAUGGACUCUUGCACA
491
UGUGCAAGAGUCCAUCCU
742

[529-546] ORF

162
AUGGAGAGUGUCUGCGGA
492
UCCGCAGACACUCUCCAU
743
Rh
[456-473] ORF

163
GCCUUCUGCAAUUCCGAC
493
GUCGGAAUUGCAGAAGGC
744
Rh
[291-308] ORF

164
CUUCUGCAAUUCCGACCU
494
AGGUCGGAAUUGCAGAAG
745
Rh
[293-310] ORF

165
AGACGGCCUUCUGCAAUU
495
AAUUGCAGAAGGCCGUCU
746
Rh
[286-303] ORF

166
GCAGGAUGGACUCUUGCA
496
UGCAAGAGUCCAUCCUGC
747

[527-544] ORF

167
GCUUGUGGACGGACCAGC
497
GCUGGUCCGUCCACAAGC
748
Rh
[694-711] ORF

168
AGAAGUCAACCAGACCAC
498
GUGGUCUGGUUGACUUCU
749
Rh
[341-358] ORF

169
CUGUGCACCUGGCAGUCC
499
GGACUGCCAGGUGCACAG
750
Rh
[777-794] ORF

170
GAGGAGUUUCUCAUUGCU
500
AGCAAUGAGAAACUCCUC
751
Rh
[501-518] ORF

171
UGUUCCCACUCCCAUCUU
501
AAGAUGGGAGUGGGAACA
752
Rh
[859-876] 3′UTR

172
ACCGCAGCGAGGAGUUUC
502
GAAACUCCUCGCUGCGGU
753
Rh, Rb, Dg, Rt
[493-510] ORF

173
ACCAGAAGUCAACCAGAC
503
GUCUGGUUGACUUCUGGU
754
Rh
[338-355] ORF

174
GCAAUUCCGACCUCGUCA
504
UGACGAGGUCGGAAUUGC
755
Rh
[298-315] ORF

175
CUGCAAACUGCAGAGUGG
505
CCACUCUGCAGUUUGCAG
756
Rh
[668-685] ORF

176
GGAGCCAGGGCUGUGCAC
506
GUGCACAGCCCUGGCUCC
757
Rh
[767-784] ORF

177
CCUUCUGCAAUUCCGACC
507
GGUCGGAAUUGCAGAAGG
758
Rh
[292-309] ORF

178
CUUGCACAUCACUACCUG
508
CAGGUAGUGAUGUGCAAG
759

[539-556] ORF

179
GGAAAACUGCAGGAUGGA
509
UCCAUCCUGCAGUUUUCC
760

[519-536] ORF

180
AAUGCACAGUGUUUCCCU
510
AGGGAAACACUGUGCAUU
761
Rh
[637-654] ORF

181
CCCUGGAACAGCCUGAGC
511
GCUCAGGCUGUUCCAGGG
762

[570-587] ORF

182
GGAUGCCGCUGACAUCCG
512
CGGAUGUCAGCGGCAUCC
763
Rh
[419-436] ORF

183
GGAUACUUCCACAGGUCC
513
GGACCUGUGGAAGUAUCC
764
Rh
[471-488] ORF

184
CACUCAUUGCUUGUGGAC
514
GUCCACAAGCAAUGAGUG
765
Rh, Rb
[686-703] ORF

185
GACACCAGAAGUCAACCA
515
UGGUUGACUUCUGGUGUC
766
Rh
[335-352] ORF

186
CUACACUGUUGGCUGUGA
516
UCACAGCCAACAGUGUAG
767
Rh
[617-634] ORF

187
ACCACCUUAUACCAGCGU
517
ACGCUGGUAUAAGGUGGU
768
Rh, Rt, Ms
[354-371] ORF

188
AGAGUGGCACUCAUUGCU
518
AGCAAUGAGUGCCACUCU
769
Rh
[679-696] ORF

189
GCAAACUGCAGAGUGGCA
519
UGCCACUCUGCAGUUUGC
770
Rh
[670-687] ORF

190
GCCGCUGACAUCCGGUUC
520
GAACCGGAUGUCAGCGGC
771
Rh
[423-440] ORF

191
UGUUUCCCUGUUUAUCCA
521
UGGAUAAACAGGGAAACA
772
Rh
[646-663] ORF

192
AAGUCAACCAGACCACCU
522
AGGUGGUCUGGUUGACUU
773
Rh
[343-360] ORF

193
CCACAACCGCAGCGAGGA
523
UCCUCGCUGCGGUUGUGG
774
Rh
[488-505] ORF

194
GCCUGAGCUUAGCUCAGC
524
GCUGAGCUAAGCUCAGGC
775

[580-597] ORF

195
GUCAUCAGGGCCAAGUUC
525
GAACUUGGCCCUGAUGAC
776
Rh, Dg
[312-329] ORF

196
AACCAGACCACCUUAUAC
526
GUAUAAGGUGGUCUGGUU
777
Rh
[348-365] ORF

197
CUCCCUGGAACAGCCUGA
527
UCAGGCUGUUCCAGGGAG
778

[568-585] ORF

198
CCAAGGCUCUGAAAAGGG
528
CCCUUUUCAGAGCCUUGG
779
Rh
[716-733] ORF

199
CUCAUUGCUGGAAAACUG
529
CAGUUUUCCAGCAAUGAG
780
Rh
[510-527] ORF

200
GUGUCCACCCUGUUCCCA
530
UGGGAACAGGGUGGACAC
781

[849-866] 3′UTR

201
CCUGUUCCCACUCCCAUC
531
GAUGGGAGUGGGAACAGG
782
Rh
[857-874] 3′UTR

202
CACCUUGCCUGCCUGCCU
532
AGGCAGGCAGGCAAGGUG
783
Rh
[747-764] ORF

203
UCACCAAGACCUACACUG
533
CAGUGUAGGUCUUGGUGA
784
Rh
[607-624] ORF

204
GAAUGCACAGUGUUUCCC
534
GGGAAACACUGUGCAUUC
785
Rh
[636-653] ORF

205
AUGGACUCUUGCACAUCA
535
UGAUGUGCAAGAGUCCAU
786

[532-549] ORF

206
UGUGAGGAAUGCACAGUG
536
CACUGUGCAUUCCUCACA
787
Rh
[630-647] ORF

207
GAGCCAGGGCUGUGCACC
537
GGUGCACAGCCCUGGCUC
788
Rh
[768-785] ORF

208
UGCGGUCCCAGAUAGCCU
538
AGGCUAUCUGGGACCGCA
789

[796-813] ORF

209
CUGUUCCCACUCCCAUCU
539
AGAUGGGAGUGGGAACAG
790
Rh
[858-875] 3′UTR

210
UGGCUUCUGGCAUCCUGU
540
ACAGGAUGCCAGAAGCCA
791

[211-228] ORF

211
CGGAUACUUCCACAGGUC
541
GACCUGUGGAAGUAUCCG
792
Rh
[470-487] ORF

212
CACAGUGUCCACCCUGUU
542
AACAGGGUGGACACUGUG
793

[845-862] 3′UTR

213
GGAAUGCACAGUGUUUCC
543
GGAAACACUGUGCAUUCC
794
Rh
[635-652] ORF

214
CCAGGGCUGUGCACCUGG
544
CCAGGUGCACAGCCCUGG
795
Rh
[771-788] ORF

215
CCCUGCGGUCCCAGAUAG
545
CUAUCUGGGACCGCAGGG
796

[793-810] ORF

216
GCCUGCACCUGUGUCCCA
546
UGGGACACAGGUGCAGGC
797
Rb
[258-275] ORF

217
CAGAGUGGCACUCAUUGC
547
GCAAUGAGUGCCACUCUG
798
Rh
[678-695] ORF

218
UGCACAUCACUACCUGCA
548
UGCAGGUAGUGAUGUGCA
799

[541-558] ORF

219
GAAGUCAACCAGACCACC
549
GGUGGUCUGGUUGACUUC
800
Rh
[342-359] ORF

220
UCCCUGCGGUCCCAGAUA
550
UAUCUGGGACCGCAGGGA
801

[792-809] ORF

221
AGUGGCACUCAUUGCUUG
551
CAAGCAAUGAGUGCCACU
802
Rh
[681-698] ORF

222
GUGGCACUCAUUGCUUGU
552
ACAAGCAAUGAGUGCCAC
803
Rh
[682-699] ORF

223
CUGAAUCCUGCCCGGAGU
553
ACUCCGGGCAGGAUUCAG
804

[812-829] ORF + 3′UTR

224
CCUGCACCUGUGUCCCAC
554
GUGGGACACAGGUGCAGG
805
Rb
[259-276] ORF

225
GCCUGCCUCGGGAGCCAG
555
CUGGCUCCCGAGGCAGGC
806
Rh
[757-774] ORF

226
GGGAUGCCGCUGACAUCC
556
GGAUGUCAGCGGCAUCCC
807
Rh
[418-435] ORF

227
GCACCUGGCAGUCCCUGC
557
GCAGGGACUGCCAGGUGC
808
Rh, Dg
[781-798] ORF

228
UCCUGUUGUUGCUGUGGC
558
GCCACAGCAACAACAGGA
809
Rh
[223-240] ORF

229
UGCGGAUACUUCCACAGG
559
CCUGUGGAAGUAUCCGCA
810
Rh
[468-485] ORF

230
GACCAAGAUGUAUAAAGG
560
CCUUUAUACAUCUUGGUC
811
Rh
[386-403] ORF

231
ACUGUUGGCUGUGAGGAA
561
UUCCUCACAGCCAACAGU
812
Rh
[621-638] ORF

232
CAUUGCUGGAAAACUGCA
562
UGCAGUUUUCCAGCAAUG
813
Rh
[512-529] ORF

233
UGAAAAGGGCUUCCAGUC
563
GACUGGAAGCCCUUUUCA
814
Rh
[725-742] ORF

234
CGUCAUCAGGGCCAAGUU
564
AACUUGGCCCUGAUGACG
815
Rh, Rb, Dg
[311-328] ORF

235
ACAACCGCAGCGAGGAGU
565
ACUCCUCGCUGCGGUUGU
816
Rh
[490-507] ORF

236
UGUCCACCCUGUUCCCAC
566
GUGGGAACAGGGUGGACA
817
Rh
[850-867] 3′UTR

237
CCUGGCAGUCCCUGCGGU
567
ACCGCAGGGACUGCCAGG
818

[784-801] ORF

238
UGAAGCCUGCACAGUGUC
568
GACACUGUGCAGGCUUCA
819

[836-853] 3′UTR

239
UCCCAGAUAGCCUGAAUC
569
GAUUCAGGCUAUCUGGGA
820

[801-818] ORF + 3′UTR

240
AGCCUGAGCUUAGCUCAG
570
CUGAGCUAAGCUCAGGCU
821

[579-596] ORF

241
CACUACCUGCAGUUUUGU
571
ACAAAACUGCAGGUAGUG
822

[548-565] ORF

242
CUGCACAGUGUCCACCCU
572
AGGGUGGACACUGUGCAG
823

[842-859] 3′UTR

243
CUCGGGAGCCAGGGCUGU
573
ACAGCCCUGGCUCCCGAG
824
Rh
[763-780] ORF

244
AGCCAGGGCUGUGCACCU
574
AGGUGCACAGCCCUGGCU
825
Rh
[769-786] ORF

245
GCCAUGGAGAGUGUCUGC
575
GCAGACACUCUCCAUGGC
826
Rh
[453-470] ORF

246
AGGGCUGUGCACCUGGCA
576
UGCCAGGUGCACAGCCCU
827
Rh
[773-790] ORF

247
GAGCUUAGCUCAGCGCCG
577
CGGCGCUGAGCUAAGCUC
828
Rh
[584-601] ORF

248
AGGCUCUGAAAAGGGCUU
578
AAGCCCUUUUCAGAGCCU
829
Rh
[719-736] ORF

249
ACAUCACUACCUGCAGUU
579
AACUGCAGGUAGUGAUGU
830

[544-561] ORF

250
AACCGCAGCGAGGAGUUU
580
AAACUCCUCGCUGCGGUU
831
Rh, Rb, Dg, Rt
[492-509] ORF

251
CAGCUCCUCCAAGGCUCU
581
AGAGCCUUGGAGGAGCUG
832
Rh
[708-725] ORF

TABLE A6

18-mer Cross-Species siTIMP1

human-

SEQ

SEQ

73858576

Sense
ID
Antisense
ID
Other
ORF:

No.
(5′>3′)
NO.
(5′>3′)
NO.
Sp
193-816

1
ACCUGGCAG
833
CCGCAGGGA
839
Rh,
[783-800]

UCCCUGCGG

CUGCCAGGU

Rb,
ORF

Dg

2
CAACCGCAG
834
AACUCCUCG
840
Rh,
[491-508]

Rb,

CGAGGAGUU

CUGCGGUUG

Dg,
ORF

Rt

3
AUGCACAGU
835
CAGGGAAAC
841
Rh,
[638-655]

Rt,

GUUUCCCUG

ACUGUGCAU

Ms
ORF

4
GACCACCUU
836
CGCUGGUAU
842
Rh,
[353-370]

Rt,

AUACCAGCG

AAGGUGGUC

Ms
ORF

5
UUAUGAGAU
837
GUCAUCUUG
843
Rh,
[371-388]

Dg,

CAAGAUGAC

AUCUCAUAA

Rt
ORF

6
UAUACCAGC
838
UCUCAUAAC
844
Rh,
[361-378]

Rt

GUUAUGAGA

GCUGGUAUA

ORF

TABLE A7

Preferred 18 + A-mer siTIMP1

SEQ

SEQ

ID

ID

human-73858576

siTIMP1_pNo.
Sense (5′>3′)
NO.
Antisense (5′>3′)
NO.
length
ORF:193-816

siTIMP1_p1
GCGUUAUGAGAUCAAGAUA
845
UAUCUUGAUCUCAUAACGC
926
18 + 1
[368-385] ORF

siTIMP1_p3
CAGACCACCUUAUACCAGA
846
UCUGGUAUAAGGUGGUCUG
927
18 + 1
[351-368] ORF

siTIMP1_p4
GCACAGUGUUUCCCUGUUA
847
UAACAGGGAAACACUGUGC
928
18 + 1
[640-657] ORF

siTIMP1_p5
CAGCGAGGAGUUUCUCAUA
848
UAUGAGAAACUCCUCGCUG
929
18 + 1
[497-514] ORF

siTIMP1_p7
AUACCAGCGUUAUGAGAUA
849
UAUCUCAUAACGCUGGUAU
930
18 + 1
[362-379] ORF

siTIMP1_p8
UGCACAGUGUUUCCCUGUA
850
UACAGGGAAACACUGUGCA
931
18 + 1
[639-656] ORF

siTIMP1_p9
CACCUUAUACCAGCGUUAA
851
UUAACGCUGGUAUAAGGUG
932
18 + 1
[356-373] ORF

siTIMP1_p10
ACCUUAUACCAGCGUUAUA
852
UAUAACGCUGGUAUAAGGU
933
18 + 1
[357-374] ORF

siTIMP1_p11
CUUAUACCAGCGUUAUGAA
853
UUCAUAACGCUGGUAUAAG
934
18 + 1
[359-376] ORF

siTIMP1_p12
CCGCAGCGAGGAGUUUCUA
854
UAGAAACUCCUCGCUGCGG
935
18 + 1
[494-511] ORF

siTIMP1_p13
ACCGCAGCGAGGAGUUUCA
855
UGAAACUCCUCGCUGCGGU
936
18 + 1
[493-510] ORF

siTIMP1_p15
ACCACCUUAUACCAGCGUA
856
UACGCUGGUAUAAGGUGGU
937
18 + 1
[354-371] ORF

siTIMP1_p18
AACCGCAGCGAGGAGUUUA
857
UAAACUCCUCGCUGCGGUU
938
18 + 1
[492-509] ORF

siTIMP1_p22
UAUACCAGCGUUAUGAGAA
858
UUCUCAUAACGCUGGUAUA
939
18 + 1
[361-378] ORF

siTIMP1_p25
AGAUCAAGAUGACCAAGAA
859
UUCUUGGUCAUCUUGAUCU
940
18 + 1
[376-393] ORF

siTIMP1_p26
CCUGCAAACUGCAGAGUGA
860
UCACUCUGCAGUUUGCAGG
941
18 + 1
[667-684] ORF

siTIMP1_p28
CCCUGCAAACUGCAGAGUA
861
UACUCUGCAGUUUGCAGGG
942
18 + 1
[666-683] ORF

siTIMP1_p30
GAUCAAGAUGACCAAGAUA
862
UAUCUUGGUCAUCUUGAUC
943
18 + 1
[377-394] ORF

siTIMP1_p32
GUCAUCAGGGCCAAGUUCA
863
UGAACUUGGCCCUGAUGAC
944
18 + 1
[312-329] ORF

siTIMP1_p34
CCUGCACCUGUGUCCCACA
864
UGUGGGACACAGGUGCAGG
945
18 + 1
[259-276] ORF

siTIMP1_p35
GGGCUUCACCAAGACCUAA
865
UUAGGUCUUGGUGAAGCCC
946
18 + 1
[602-619] ORF

siTIMP1_p36
CGUCAUCAGGGCCAAGUUA
866
UAACUUGGCCCUGAUGACG
947
18 + 1
[311-328] ORF

siTIMP1_p37
CACUCAUUGCUUGUGGACA
867
UGUCCACAAGCAAUGAGUG
948
18 + 1
[686-703] ORF

siTIMP1_p39
CAGUGUUUCCCUGUUUAUA
868
UAUAAACAGGGAAACACUG
949
18 + 1
[643-660] ORF

siTIMP1_p40
ACAGUGUUUCCCUGUUUAA
869
UUAAACAGGGAAACACUGU
950
18 + 1
[642-659] ORF

siTIMP1_p41
AGUGUUUCCCUGUUUAUCA
870
UGAUAAACAGGGAAACACU
951
18 + 1
[644-661] ORF

siTIMP1_p44
CAUCUUUCUUCCGGACAAA
871
UUUGUCCGGAAGAAAGAUG
952
18 + 1
[871-888] 3′UT R

siTIMP1_p46
CCAGAUAGCCUGAAUCCUA
872
UAGGAUUCAGGCUAUCUGG
953
18 + 1
[803-820] ORF + 3′UTR

siTIMP1_p47
GGUCCCAGAUAGCCUGAAA
873
UUUCAGGCUAUCUGGGACC
954
18 + 1
[799-816] ORF

siTIMP1_p48
GGAGAGUGUCUGCGGAUAA
874
UUAUCCGCAGACACUCUCC
955
18 + 1
[458-475] ORF

siTIMP1_p50
CCGCCAUGGAGAGUGUCUA
875
UAGACACUCUCCAUGGCGG
956
18 + 1
[458-475] ORF

siTIMP1_p51
GAGUGUCUGCGGAUACUUA
876
UAAGUAUCCGCAGACACUC
957
18 + 1
[458-475] ORF

siTIMP1_p52
GAGUGGCACUCAUUGCUUA
877
UAAGCAAUGAGUGCCACUC
958
18 + 1
[680-697] ORF

siTIMP1_p53
GAGUGGAAGCUGAAGCCUA
878
UAGGCUUCAGCUUCCACUC
959
18 + 1
[826-843] 3′UTR

siTIMP1_p54
CCCUGUUCCCACUCCCAUA
879
UAUGGGAGUGGGAACAGGG
960
18 + 1
[856-873] 3′UTR

siTIMP1_p55
GCGGAUACUUCCACAGGUA
880
UACCUGUGGAAGUAUCCGC
961
18 + 1
[469-486] ORF

siTIMP1_p56
GAGAGUGUCUGCGGAUACA
881
UGUAUCCGCAGACACUCUC
962
18 + 1
[459-476] ORF

siTIMP1_p57
GGAACAGCCUGAGCUUAGA
882
UCUAAGCUCAGGCUGUUCC
963
18 + 1
[574-591] ORF

siTIMP1_p58
CAACCAGACCACCUUAUAA
883
UUAUAAGGUGGUCUGGUUG
964
18 + 1
[347-364] ORF

siTIMP1_p59
GAGGAAUGCACAGUGUUUA
884
UAAACACUGUGCAUUCCUC
965
18 + 1
[633-650] ORF

siTIMP1_p61
CCAAGAUGUAUAAAGGGUA
885
UACCCUUUAUACAUCUUGG
966
18 + 1
[388-405] ORF

siTIMP1_p62
CACCAGAAGUCAACCAGAA
886
UUCUGGUUGACUUCUGGUG
967
18 + 1
[337-354] ORF

siTIMP1_p63
CAGAAGUCAACCAGACCAA
887
UUGGUCUGGUUGACUUCUG
968
18 + 1
[340-357] ORF

siTIMP1_p64
CCCACUCCCAUCUUUCUUA
888
UAAGAAAGAUGGGAGUGGG
969
18 + 1
[863-880] 3′UTR

siTIMP1_p65
GCGAGGAGUUUCUCAUUGA
889
UCAAUGAGAAACUCCUCGC
970
18 + 1
[499-516] ORF

siTIMP1_p66
CUGCAGAGUGGCACUCAUA
890
UAUGAGUGCCACUCUGCAG
971
18 + 1
[675-692] ORF

siTIMP1_p67
GAAGCUGAAGCCUGCACAA
891
UUGUGCAGGCUUCAGCUUC
972
18 + 1
[831-848] 3′UTR

siTIMP1_p68
CCUGGAACAGCCUGAGCUA
892
UAGCUCAGGCUGUUCCAGG
973
18 + 1
[571-588] ORF

siTIMP1_p69
GCAUCCUGUUGUUGCUGUA
893
UACAGCAACAACAGGAUGC
974
18 + 1
[220-237] ORF

siTIMP1_p70
GUCCCAGAUAGCCUGAAUA
894
UAUUCAGGCUAUCUGGGAC
975
18 + 1
[800-817] ORF + 3′UTR

siTIMP1_p72
GGCUGUGAGGAAUGCACAA
895
UUGUGCAUUCCUCACAGCC
976
18 + 1
[627-644] ORF

siTIMP1_p74
GGCCUUCUGCAAUUCCGAA
896
UUCGGAAUUGCAGAAGGCC
977
18 + 1
[290-307] ORF

siTIMP1_p75
GCAGAGUGGCACUCAUUGA
897
UCAAUGAGUGCCACUCUGC
978
18 + 1
[677-694] ORF

siTIMP1_p76
CAGAUAGCCUGAAUCCUGA
898
UCAGGAUUCAGGCUAUCUG
979
18 + 1
[804-821] ORF + 3′UTR

siTIMP1_p80
CCGGAGUGGAAGCUGAAGA
899
UCUUCAGCUUCCACUCCGG
980
18 + 1
[823-840] 3′UTR

siTIMP1_p81
GGCUGUGCACCUGGCAGUA
900
UACUGCCAGGUGCACAGCC
981
18 + 1
[775-792] ORF

siTIMP1_p82
GUCAACCAGACCACCUUAA
901
UUAAGGUGGUCUGGUUGAC
982
18 + 1
[345-362] ORF

siTIMP1_p83
CCAUGGAGAGUGUCUGCGA
902
UCGCAGACACUCUCCAUGG
983
18 + 1
[454-471] ORF

siTIMP1_p84
CUGGCAUCCUGUUGUUGCA
903
UGCAACAACAGGAUGCCAG
984
18 + 1
[217-234] ORF

siTIMP1_p86
ACUGCAGAGUGGCACUCAA
904
UUGAGUGCCACUCUGCAGU
985
18 + 1
[674-691] ORF

siTIMP1_p87
CGGAGUGGAAGCUGAAGCA
905
UGCUUCAGCUUCCACUCCG
986
18 + 1
[824-841] 3′UTR

siTIMP1_p88
CCAGACCACCUUAUACCAA
906
UUGGUAUAAGGUGGUCUGG
987
18 + 1
[350-367] ORF

siTIMP1_p90
GCUGGAAAACUGCAGGAUA
907
UAUCCUGCAGUUUUCCAGC
988
18 + 1
[516-533] ORF

siTIMP1_p92
CCUGAAUCCUGCCCGGAGA
908
UCUCCGGGCAGGAUUCAGG
989
18 + 1
[811-828] ORF + 3′UTR

siTIMP1_p93
CUGAAGCCUGCACAGUGUA
909
UACACUGUGCAGGCUUCAG
990
18 + 1
[835-852] 3′UTR

siTIMP1_p94
CUGGAAAACUGCAGGAUGA
910
UCAUCCUGCAGUUUUCCAG
991
18 + 1
[517-534] ORF

siTIMP1_p95
UCUCAUUGCUGGAAAACUA
911
UAGUUUUCCAGCAAUGAGA
992
18 + 1
[509-526] ORF

siTIMP1_p97
AGACCUACACUGUUGGCUA
912
UAGCCAACAGUGUAGGUCU
993
18 + 1
[613-630] ORF

siTIMP1_p100
GGGACACCAGAAGUCAACA
913
UGUUGACUUCUGGUGUCCC
994
18 + 1
[333-350] ORF

siTIMP1_p101
GGCUCCCUGGAACAGCCUA
914
UAGGCUGUUCCAGGGAGCC
995
18 + 1
[566-583] ORF

siTIMP1_p102
GUUCCCACUCCCAUCUUUA
915
UAAAGAUGGGAGUGGGAAC
996
18 + 1
[860-877] 3′UTR

siTIMP1_p103
GGCUUCUGGCAUCCUGUUA
916
UAACAGGAUGCCAGAAGCC
997
18 + 1
[212-229] ORF

siTIMP1_p104
CUUCUGGCAUCCUGUUGUA
917
UACAACAGGAUGCCAGAAG
998
18 + 1
[214-231] ORF

siTIMP1_p105
AGAGUGUCUGCGGAUACUA
918
UAGUAUCCGCAGACACUCU
999
18 + 1
[460-477] ORF

siTIMP1_p106
CACCAAGACCUACACUGUA
919
UACAGUGUAGGUCUUGGUG
1000
18 + 1
[608-625] ORF

siTIMP1_p109
GGGAGCCAGGGCUGUGCAA
920
UUGCACAGCCCUGGCUCCC
1001
18 + 1
[766-783] ORF

siTIMP1_p110
UGCAGAGUGGCACUCAUUA
921
UAAUGAGUGCCACUCUGCA
1002
18 + 1
[676-693] ORF

siTIMP1_p111
GUGAGGAAUGCACAGUGUA
922
UACACUGUGCAUUCCUCAC
1003
18 + 1
[631-648] ORF

siTIMP1_p112
AGCGAGGAGUUUCUCAUUA
923
UAAUGAGAAACUCCUCGCU
1004
18 + 1
[498-515] ORF

siTIMP1_p113
GGGCUGUGCACCUGGCAGA
924
UCUGCCAGGUGCACAGCCC
1005
18 + 1
[774-791] ORF

siTIMP1_p114
UGUUGUUGCUGUGGCUGAA
925
UUCAGCCACAGCAACAACA
1006
18 + 1
[226-243] ORF

TABLE A8

18 + 1-mer siTIMP1 with lowest predicted Off Target (OT) effect

SEQ

SEQ

ID

ID
No. in

Cross species
Ranking
Sense (5′>3′)
NO.
Antisense (5′>3′)
NO.
Table A7

H/Rt
2
GCGUUAUGAGAUCAAGAUA
845
UAUCUUGAUCUCAUAACGC
926
siTIMP1_p1

H/Rt
3
GCACAGUGUUUCCCUGUUA
847
UAACAGGGAAACACUGUGC
928
siTIMP1_p4

H/Rt
3
CAGCGAGGAGUUUCUCAUA
848
UAUGAGAAACUCCUCGCUG
929
siTIMP1_p5

H/Rt
2
AUACCAGCGUUAUGAGAUA
849
UAUCUCAUAACGCUGGUAU
930
siTIMP1_p7

H/Rt
4
UGCACAGUGUUUCCCUGUA
850
UACAGGGAAACACUGUGCA
931
siTIMP1_p8

H/Rt
1
CACCUUAUACCAGCGUUAA
851
UUAACGCUGGUAUAAGGUG
932
siTIMP1_p9

H/Rt
1
ACCUUAUACCAGCGUUAUA
852
UAUAACGCUGGUAUAAGGU
933
siTIMP1_p10

H/Rt
1
CUUAUACCAGCGUUAUGAA
853
UUCAUAACGCUGGUAUAAG
934
siTIMP1_p11

H/Rt
2
CCGCAGCGAGGAGUUUCUA
854
UAGAAACUCCUCGCUGCGG
935
siTIMP1_p12

H/Rt
3
ACCGCAGCGAGGAGUUUCA
855
UGAAACUCCUCGCUGCGGU
936
siTIMP1_p13

H/Rt
2
ACCACCUUAUACCAGCGUA
856
UACGCUGGUAUAAGGUGGU
937
siTIMP1_p15

H/Rt
2
AACCGCAGCGAGGAGUUUA
857
UAAACUCCUCGCUGCGGUU
938
siTIMP1_p18

H/Rt
2
UAUACCAGCGUUAUGAGAA
858
UUCUCAUAACGCUGGUAUA
939
siTIMP1_p22

Other (w/o Rt)
4
CCUGCAAACUGCAGAGUGA
860
UCACUCUGCAGUUUGCAGG
941
siTIMP1_p26

Other (w/o Rt)
4
CGUCAUCAGGGCCAAGUUA
866
UAACUUGGCCCUGAUGACG
947
siTIMP1_p36

H/Rt (Rt with 1MM)
1
CACUCAUUGCUUGUGGACA
867
UGUCCACAAGCAAUGAGUG
948
siTIMP1_p37

Other (w/o Rt)
3
CAGUGUUUCCCUGUUUAUA
868
UAUAAACAGGGAAACACUG
949
siTIMP1_p39

Other (w/o Rt)
3
ACAGUGUUUCCCUGUUUAA
869
UUAAACAGGGAAACACUGU
950
siTIMP1_p40

Other (w/o Rt)
2
AGUGUUUCCCUGUUUAUCA
870
UGAUAAACAGGGAAACACU
951
siTIMP1_p41

H +/− Rh
2
CAUCUUUCUUCCGGACAAA
871
UUUGUCCGGAAGAAAGAUG
952
siTIMP1_p44

H +/− Rh
3
GGUCCCAGAUAGCCUGAAA
873
UUUCAGGCUAUCUGGGACC
954
siTIMP1_p47

H +/− Rh
2
GGAGAGUGUCUGCGGAUAA
874
UUAUCCGCAGACACUCUCC
955
siTIMP1_p48

H +/− Rh
3
CCGCCAUGGAGAGUGUCUA
875
UAGACACUCUCCAUGGCGG
956
siTIMP1_p50

H +/− Rh
3
GAGUGUCUGCGGAUACUUA
876
UAAGUAUCCGCAGACACUC
957
siTIMP1_p51

H +/− Rh
3
GAGUGGCACUCAUUGCUUA
877
UAAGCAAUGAGUGCCACUC
958
siTIMP1_p52

H +/− Rh
2
GCGGAUACUUCCACAGGUA
880
UACCUGUGGAAGUAUCCGC
961
siTIMP1_p55

H +/− Rh
2
GAGAGUGUCUGCGGAUACA
881
UGUAUCCGCAGACACUCUC
962
siTIMP1_p56

H +/− Rh
3
CAACCAGACCACCUUAUAA
883
UUAUAAGGUGGUCUGGUUG
964
siTIMP1_p58

H +/− Rh
3
CCAAGAUGUAUAAAGGGUA
885
UACCCUUUAUACAUCUUGG
966
siTIMP1_p61

H +/− Rh
4
CCCACUCCCAUCUUUCUUA
888
UAAGAAAGAUGGGAGUGGG
969
siTIMP1_p64

H +/− Rh
3
CUGCAGAGUGGCACUCAUA
890
UAUGAGUGCCACUCUGCAG
971
siTIMP1_p66

H +/− Rh
4
CCUGGAACAGCCUGAGCUA
892
UAGCUCAGGCUGUUCCAGG
973
siTIMP1_p68

H +/− Rh
3
GUCCCAGAUAGCCUGAAUA
894
UAUUCAGGCUAUCUGGGAC
975
siTIMP1_p70

H +/− Rh
4
GCAGAGUGGCACUCAUUGA
897
UCAAUGAGUGCCACUCUGC
978
siTIMP1_p75

H +/− Rh
3
CCAUGGAGAGUGUCUGCGA
903
UCGCAGACACUCUCCAUGG
983
siTIMP1_p83

H +/− Rh
4
ACUGCAGAGUGGCACUCAA
904
UUGAGUGCCACUCUGCAGU
985
siTIMP1_p86

H +/− Rh
2
CCAGACCACCUUAUACCAA
906
UUGGUAUAAGGUGGUCUGG
987
siTIMP1_p88

H +/− Rh
4
CCUGAAUCCUGCCCGGAGA
908
UCUCCGGGCAGGAUUCAGG
989
siTIMP1_p92

H +/− Rh
3
CUGAAGCCUGCACAGUGUA
909
UACACUGUGCAGGCUUCAG
990
siTIMP1_p93

H +/− Rh
4
UCUCAUUGCUGGAAAACUA
911
UAGUUUUCCAGCAAUGAGA
992
siTIMP1_p95

H +/− Rh
2
AGACCUACACUGUUGGCUA
912
UAGCCAACAGUGUAGGUCU
993
siTIMP1_p97

H +/− Rh
4
GUUCCCACUCCCAUCUUUA
915
UAAAGAUGGGAGUGGGAAC
996
siTIMP1_p102

H +/− Rh
4
CUUCUGGCAUCCUGUUGUA
917
UACAACAGGAUGCCAGAAG
998
siTIMP1_p104

H +/− Rh
2
AGAGUGUCUGCGGAUACUA
918
UAGUAUCCGCAGACACUCU
999
siTIMP1_p105

H +/− Rh
3
CACCAAGACCUACACUGUA
919
UACAGUGUAGGUCUUGGUG
1000
siTIMP1_p106

H +/− Rh
2
UGCAGAGUGGCACUCAUUA
921
UAAUGAGUGCCACUCUGCA
1002
siTIMP1_p110

H +/− Rh
4
AGCGAGGAGUUUCUCAUUA
923
UAAUGAGAAACUCCUCGCU
1004
siTIMP1_p112

TIMP2—TIMP Metallopeptidase Inhibitor 2

TABLE B1

siTIMP2 19-mers

SEQ

SEQ

human-73858577

ID

ID

ORF:303-965

Sense (5′>3′)
NO:
Antisense (5′>3′)
NO:
Other Sp

GGAAGAACUUUCUCGGUAA
1007
UUACCGAGAAAGUUCUUCC
1622
Rh
[2332-2350] 3′UTR

GGUUCUCCAGUUCAAAUUA
1008
UAAUUUGAACUGGAGAACC
1623

[62-3080] 3′UTR

CUGUGUUUAUGCUGGAAUA
1009
UAUUCCAGCAUAAACACAG
1624

[3495-3513] 3′UTR

CCUGUAUGGUGAUAUCAUA
1010
UAUGAUAUCACCAUACAGG
1625

[2789-2807] 3′UTR

GGCACAUUAUGUAAACAUA
1011
UAUGUUUACAUAAUGUGCC
1626
Rh
[2412-2430] 3′UTR

GGUGAAUUCUCAGAUGAUA
1012
UAUCAUCUGAGAAUUCACC
1627

[2165-2183] 3′UTR

CCAUGUGAUUUCAGUAUAU
1013
AUAUACUGAAAUCACAUGG
1628
Rh
[2718-2736] 3′UTR

CUCUGAGCCUUGUAGAAAU
1014
AUUUCUACAAGGCUCAGAG
1629
Rh
[1606-1624] 3′UTR

GGCUGCGAGUGCAAGAUCA
1015
UGAUCUUGCACUCGCAGCC
1630
Ck, Rb, Rt
[752-770] ORF

AGAGGAAGCCGCUCAAAUA
1016
UAUUUGAGCGGCUUCCUCU
1631

[3214-3232] 3′UTR

CUUUGGUUCUCCAGUUCAA
1017
UUGAACUGGAGAACCAAAG
1632

[58-3076] 3′UTR

CAGUAUGAGAUCAAGCAGA
1018
UCUGCUUGAUCUCAUACUG
1633
Rh, Rb, Cw,
[509-527] ORF

Dg, Ms

CUUGCAAAAUGCUUCCAAA
1019
UUUGGAAGCAUUUUGCAAG
1634

[2471-2489] 3′UTR

CUUGGUAGGUAUUAGACUU
1020
AAGUCUAAUACCUACCAAG
1635

[2906-2924] 3′UTR

CCCUCUGAGCCUUGUAGAA
1021
UUCUACAAGGCUCAGAGGG
1636
Rh
[1604-1622] 3′UTR

GGUAGGUAUUAGACUUGCA
1022
UGCAAGUCUAAUACCUACC
1637

[2909-2927] 3′UTR

GGGUCACAGAGAAGAACAU
1023
AUGUUCUUCUCUGUGACCC
1638
Rh
[831-849] ORF

GAACCUGAGUUGCAGAUAU
1024
AUAUCUGCAACUCAGGUUC
1639
Rh
[2187-2205] 3′UTR

GGAUUGAGUUGCACAGCUU
1025
AAGCUGUGCAACUCAAUCC
1640

[1853-1871] 3′UTR

GGUGAUAUCAUAUGUAACA
1026
UGUUACAUAUGAUAUCACC
1641
Rh
[2796-2814] 3′UTR

CCUGCAAGCAACUCAAAAU
1027
AUUUUGAGUUGCUUGCAGG
1642

[3343-3361] 3′UTR

GGAUAUAGAGUUUAUCUAC
1028
GUAGAUAAACUCUAUAUCC
1643

[553-571] ORF

GAUGCUUUGUAUCAUUCUU
1029
AAGAAUGAUACAAAGCAUC
1644

[3589-3607] 3′UTR

GCAAGCAACUCAAAAUAUU
1030
AAUAUUUUGAGUUGCUUGC
1645

[3346-3364] 3′UTR

CGUCUUUGGUUCUCCAGUU
1031
AACUGGAGAACCAAAGACG
1646

[55-3073] 3′UTR

CCUUUAUAUUUGAUCCACA
1032
UGUGGAUCAAAUAUAAAGG
1647

[3127-3145] 3′UTR

GUGCUGAGCAGAAAACAAA
1033
UUUGUUUUCUGCUCAGCAC
1648

[3164-3182] 3′UTR

CCAACUUCUGCUUGUAUUU
1034
AAAUACAAGCAGAAGUUGG
1649
Rh
[2207-2225] 3′UTR

CCUAUUAAUCCUCAGAAUU
1035
AAUUCUGAGGAUUAAUAGG
1650
Rh
[1572-1590] 3′UTR

CGGUAAUGAUAAGGAGAAU
1036
AUUCUCCUUAUCAUUACCG
1651

[2345-2363] 3′UTR

CGCUCAAAUACCUUCACAA
1037
UUGUGAAGGUAUUUGAGCG
1652

[3223-3241] 3′UTR

GGGCAGACUGGGAGGGUAU
1038
AUACCCUCCCAGUCUGCCC
1653
Rh
[2619-2637] 3′UTR

UGCUGAGCAGAAAACAAAA
1039
UUUUGUUUUCUGCUCAGCA
1654

[3165-3183] 3′UTR

AGCGGUCAGUGAGAAGGAA
1040
UUCCUUCUCACUGACCGCU
1655

[445-463] ORF

GGUAUUAGACUUGCACUUU
1041
AAAGUGCAAGUCUAAUACC
1656

[2913-2931] 3′UTR

GCUGGAAUAUGAAGUCUGA
1042
UCAGACUUCAUAUUCCAGC
1657
Ms
[3505-3523] 3′UTR

CCUGUGUUGUAAAGAUAAA
1043
UUUAUCUUUACAACACAGG
1658
Rh
[2380-2398] 3′UTR

GGUAAGAUGUCAUAAUGGA
1044
UCCAUUAUGACAUCUUACC
1659
Rh
[2694-2712] 3′UTR

GUGGUUUCCUGAAGCCAGU
1045
ACUGGCUUCAGGAAACCAC
1660

[2295-2313] 3′UTR

GGGUCCAAAUUAAUAUGAU
1046
AUCAUAUUAAUUUGGACCC
1661

[1077-1095] 3′UTR

GGAACACACAAGAGUUGUU
1047
AACAACUCUUGUGUGUUCC
1662

[3539-3557] 3′UTR

AGAUUACCUAGCUAAGAAA
1048
UUUCUUAGCUAGGUAAUCU
1663

[2238-2256] 3′UTR

CUGGGAACACACAAGAGUU
1049
AACUCUUGUGUGUUCCCAG
1664

[3536-3554] 3′UTR

UCCCAUGGGUCCAAAUUAA
1050
UUAAUUUGGACCCAUGGGA
1665

[1071-1089] 3′UTR

GUUCUCCAGUUCAAAUUAU
1051
AUAAUUUGAACUGGAGAAC
1666

[3063-3081] 3′UTR

CCAUGGGUCCAAAUUAAUA
1052
UAUUAAUUUGGACCCAUGG
1667

[1073-1091] 3′UTR

UGGGCGUGGUCUUGCAAAA
1053
UUUUGCAAGACCACGCCCA
1668

[2461-2479] 3′UTR

CGUGCUGAGCAGAAAACAA
1054
UUGUUUUCUGCUCAGCACG
1669

[3163-3181] 3′UTR

CGGUCAGUGAGAAGGAAGU
1055
ACUUCCUUCUCACUGACCG
1670

[447-465] ORF

CGAUAUACAGGCACAUUAU
1056
AUAAUGUGCCUGUAUAUCG
1671

[2403-2421] 3′UTR

GCAUUUUGCAGAAACUUUU
1057
AAAAGUUUCUGCAAAAUGC
1672
Rh
[1334-1352] 3′UTR

GGACCAGUCCAUGUGAUUU
1058
AAAUCACAUGGACUGGUCC
1673
Rh
[2710-2728] 3′UTR

GCUCAAAUACCUUCACAAU
1059
AUUGUGAAGGUAUUUGAGC
1674

[3224-3242] 3′UTR

CACCUUAGCCUGUUCUAUU
1060
AAUAGAACAGGCUAAGGUG
1675
Rh
[2492-2510] 3′UTR

GGAUCUCCCAGCUGGGUUA
1061
UAACCCAGCUGGGAGAUCC
1676

[1296-1314] 3′UTR

GUAUUAGACUUGCACUUUU
1062
AAAAGUGCAAGUCUAAUAC
1677

[2914-2932] 3′UTR

AGAGGAUCCAGUAUGAGAU
1063
AUCUCAUACUGGAUCCUCU
1678
Rh, Rb
[501-519] ORF

GAACCUAUGUGUUCCCUCA
1064
UGAGGGAACACAUAGGUUC
1679

[2274-2292] 3′UTR

CUGAGUUGCAGAUAUACCA
1065
UGGUAUAUCUGCAACUCAG
1680
Rh
[2191-2209] 3′UTR

CUCAAAUACCUUCACAAUA
1066
UAUUGUGAAGGUAUUUGAG
1681

[3225-3243] 3′UTR

UCCUAUUAAUCCUCAGAAU
1067
AUUCUGAGGAUUAAUAGGA
1682
Rh
[1571-1589] 3′UTR

CCAGUUCAAAUUAUUGCAA
1068
UUGCAAUAAUUUGAACUGG
1683

[3068-3086] 3′UTR

UGUUUAUGCUGGAAUAUGA
1069
UCAUAUUCCAGCAUAAACA
1684

[3498-3516] 3′UTR

GCACAGAUCUUGAUGACUU
1070
AAGUCAUCAAGAUCUGUGC
1685
Rh
[2591-2609] 3′UTR

AACCUGAGUUGCAGAUAUA
1071
UAUAUCUGCAACUCAGGUU
1686
Rh
[2188-2206] 3′UTR

CUGCAAGCAACUCAAAAUA
1072
UAUUUUGAGUUGCUUGCAG
1687

[3344-3362] 3′UTR

GGCUUUGGUGACACACUCA
1073
UGAGUGUGUCACCAAAGCC
1688

[2086-2104] 3′UTR

GUUGCAAGACUGUGUAGCA
1074
UGCUACACAGUCUUGCAAC
1689
Rh
[1360-1378] 3′UTR

GACAUUUAUGGCAACCCUA
1075
UAGGGUUGCCAUAAAUGUC
1690

[479-497] ORF

GUAUGAGAUCAAGCAGAUA
1076
UAUCUGCUUGAUCUCAUAC
1691
Rh, Rb, Cw,
[511-529] ORF

Dg, Rt, Ms

GACUUGCUGCCGUAAUUUA
1077
UAAAUUACGGCAGCAAGUC
1692

[3428-3446] 3′UTR

GAAAGAAGGAAUAUCUCAU
1078
AUGAGAUAUUCCUUCUUUC
1693

[618-636] ORF

GAGGAAAGAAGGAAUAUCU
1079
AGAUAUUCCUUCUUUCCUC
1694
Rt
[615-633] ORF

CGUGGACAAUAAACAGUAU
1080
AUACUGUUUAUUGUCCACG
1695

[3624-3642] 3′UTR

GGUGAACCUGAGUUGCAGA
1081
UCUGCAACUCAGGUUCACC
1696
Rh
[2184-2202] 3′UTR

CCUGCAUCAAGAGAAGUGA
1082
UCACUUCUCUUGAUGCAGG
1697
Rt, Ms
[876-894] ORF

AGUCCAUGUGAUUUCAGUA
1083
UACUGAAAUCACAUGGACU
1698
Rh
[2715-2733] 3′UTR

AGUAAAGGAUCUUUGAGUA
1084
UACUCAAAGAUCCUUUACU
1699

[3087-3105] 3′UTR

CCCAGAAGAAGAGCCUGAA
1085
UUCAGGCUCUUCUUCUGGG
1700
Rh, Cw, Ms, Pg
[717-735] ORF

GACAUCAGCUGUAAUCAUU
1086
AAUGAUUACAGCUGAUGUC
1701

[2864-2882] 3′UTR

CCUCAAAGACUGACAGCCA
1087
UGGCUGUCAGUCUUUGAGG
1702
Rh
[1980-1998] 3′UTR

CUCGGUCCGUGGACAAUAA
1088
UUAUUGUCCACGGACCGAG
1703

[3617-3635] 3′UTR

AGGGCAGCCUGGAACCAGU
1089
ACUGGUUCCAGGCUGCCCU
1704

[1525-1543] 3′UTR

CCGUGGACAAUAAACAGUA
1090
UACUGUUUAUUGUCCACGG
1705

[3623-3641] 3′UTR

GAAACGACAUUUAUGGCAA
1091
UUGCCAUAAAUGUCGUUUC
1706

[474-492] ORF

CCUCAGAAUUCCAGUGGGA
1092
UCCCACUGGAAUUCUGAGG
1707
Rh
[1581-1599] 3′UTR

GUCACAGAGAAGAACAUCA
1093
UGAUGUUCUUCUCUGUGAC
1708
Rh
[833-851] ORF

CCAGUGGCUAGUUCUUGAA
1094
UUCAAGAACUAGCCACUGG
1709

[1539-1557] 3′UTR

GGAACCAGUGGCUAGUUCU
1095
AGAACUAGCCACUGGUUCC
1710

[1535-1553] 3′UTR

UCCAUGUGAUUUCAGUAUA
1096
UAUACUGAAAUCACAUGGA
1711
Rh
[2717-2735] 3′UTR

AGGUAUUAGACUUGCACUU
1097
AAGUGCAAGUCUAAUACCU
1712

[2912-2930] 3′UTR

CAUUUGACCCAGAGUGGAA
1098
UUCCACUCUGGGUCAAAUG
1713

[2961-2979] 3′UTR

GCACCUGGAUUGAGUUGCA
1099
UGCAACUCAAUCCAGGUGC
1714

[1847-1865] 3′UTR

AGUUGUUGAAAGUUGACAA
1100
UUGUCAACUUUCAACAACU
1715

[3551-3569] 3′UTR

GUGGCCAACUGCAAAAAAA
1101
iTLTLTLTLTLTLJGCAGUUGGCCAC
1716

[984-1002] 3′UTR

CUCAAAGACUGACAGCCAU
1102
AUGGCUGUCAGUCUUUGAG
1717
Rh
[1981-1999] 3′UTR

GCCUCAGCUGAGUCUUUUU
1103
AAAAAGACUCAGCUGAGGC
1718
Rh
[1658-1676] 3′UTR

UGCUUUGUAUCAUUCUUGA
1104
UCAAGAAUGAUACAAAGCA
1719

[3591-3609] 3′UTR

GUUUAAGAAGGCUCUCCAU
1105
AUGGAGAGCCUUCUUAAAC
1720

[3265-3283] 3′UTR

CCAGCUAAGCAUAGUAAGA
1106
UCUUACUAUGCUUAGCUGG
1721

[2030-2048] 3′UTR

GUUGGUAAGAUGUCAUAAU
1107
AUUAUGACAUCUUACCAAC
1722
Rh
[2691-2709] 3′UTR

CACCUGUGUUGUAAAGAUA
1108
UAUCUUUACAACACAGGUG
1723
Rh
[2378-2396] 3′UTR

CAGCCUCAGCUGAGUCUUU
1109
AAAGACUCAGCUGAGGCUG
1724
Rh
[1656-1674] 3′UTR

AUGAGAUCAAGCAGAUAAA
1110
UUUAUCUGCUUGAUCUCAU
1725
Rh, Cw, Dg,
[513-531] ORF

Rt, Ms

GUUGCACAGCUUUGCUUUA
1111
UAAAGCAAAGCUGUGCAAC
1726

[1860-1878] 3′UTR

GUGGCUAGUUCUUGAAGGA
1112
UCCUUCAAGAACUAGCCAC
1727

[1542-1560] 3′UTR

GAUUGAGUUGCACAGCUUU
1113
AAAGCUGUGCAACUCAAUC
1728

[1854-1872] 3′UTR

GGAUCUUUGAGUAGGUUCG
1114
CGAACCUACUCAAAGAUCC
1729

[93-3111] 3′UTR

CGCUGGACGUUGGAGGAAA
1115
UUUCCUCCAACGUCCAGCG
1730
Rt, Ms
[603-621] ORF

CACACACGUUGGUCUUUUA
1116
UAAAAGACCAACGUGUGUG
1731

[3142-3160] 3′UTR

CUCAGUGUGGUUUCCUGAA
1117
UUCAGGAAACCACACUGAG
1732

[2289-2307] 3′UTR

AUGUUAUGUUCUAAGCACA
1118
UGUGCUUAGAACAUAACAU
1733

[3303-3321] 3′UTR

GCCACCUUAGCCUGUUCUA
1119
UAGAACAGGCUAAGGUGGC
1734
Rh
[2490-2508] 3′UTR

AAGAGUUGUUGAAAGUUGA
1120
UCAACUUUCAACAACUCUU
1735

[3548-3566] 3′UTR

CCUGAGAAGGAUAUAGAGU
1121
ACUCUAUAUCCUUCUCAGG
1736

[545-563] ORF

ACCAGUGGCUAGUUCUUGA
1122
UCAAGAACUAGCCACUGGU
1737

[1538-1556] 3′UTR

CAUCCUGCAAGCAACUCAA
1123
UUGAGUUGCUUGCAGGAUG
1738

[3340-3358] 3′UTR

GUAAUGAUAAGGAGAAUCU
1124
AGAUUCUCCUUAUCAUUAC
1739

[2347-2365] 3′UTR

GGAAUAUCUCAUUGCAGGA
1125
UCCUGCAAUGAGAUAUUCC
1740

[625-643] ORF

GGGCGUGGUCUUGCAAAAU
1126
AUUUUGCAAGACCACGCCC
1741

[2462-2480] 3′UTR

CAUCCUGAGGACAGAAAAA
1127
UUUUUCUGUCCUCAGGAUG
1742
Rh
[1921-1939] 3′UTR

UGGACUUGCUGCCGUAAUU
1128
AAUUACGGCAGCAAGUCCA
1743

[3426-3444] 3′UTR

GUGACACACUCACUUCUUU
1129
AAAGAAGUGAGUGUGUCAC
1744

[2093-2111] 3′UTR

CUGUUUUAAGAGACAUCUU
1130
AAGAUGUCUCUUAAAACAG
1745
Rh
[2135-2153] 3′UTR

GUUUAUGCUGGAAUAUGAA
1131
UUCAUAUUCCAGCAUAAAC
1746

[3499-3517] 3′UTR

GUCCAUGUGAUUUCAGUAU
1132
AUACUGAAAUCACAUGGAC
1747
Rh
[2716-2734] 3′UTR

AGGAGUUUCUCGACAUCGA
1133
UCGAUGUCGAGAAACUCCU
1748
Ck, Dg
[936-954] ORF

GAAGAACUUUCUCGGUAAU
1134
AUUACCGAGAAAGUUCUUC
1749
Rh
[2333-2351] 3′UTR

GGGUCUGGAGGGAGACGUG
1135
CACGUCUCCCUCCAGACCC
1750

[1130-1148] 3′UTR

GGAAGCCGCUCAAAUACCU
1136
AGGUAUUUGAGCGGCUUCC
1751

[3217-3235] 3′UTR

GGUCCGUGGACAAUAAACA
1137
UGUUUAUUGUCCACGGACC
1752

[3620-3638] 3′UTR

CCCUCCAACCCAUAUAACA
1138
UGUUAUAUGGGUUGGAGGG
1753

[2752-2770] 3′UTR

CCCAUGGGUCCAAAUUAAU
1139
AUUAAUUUGGACCCAUGGG
1754

[1072-1090] 3′UTR

CACACUCACUUCUUUCUCA
1140
UGAGAAAGAAGUGAGUGUG
1755

[2097-2115] 3′UTR

GCAGAAAACAAAACAGGUU
1141
AACCUGUUUUGUUUUCUGC
1756

[3171-3189] 3′UTR

CAUCAAUCCUAUUAAUCCU
1142
AGGAUUAAUAGGAUUGAUG
1757
Rh
[1565-1583] 3′UTR

CACAAUAAAUAGUGGCAAU
1143
AUUGCCACUAUUUAUUGUG
1758

[3237-3255] 3′UTR

GUUGGAGGAAAGAAGGAAU
1144
AUUCCUUCUUUCCUCCAAC
1759
Rt
[611-629] ORF

GGCCUUUAUAUUUGAUCCA
1145
UGGAUCAAAUAUAAAGGCC
1760

[3125-3143] 3′UTR

UGUUCAAAGGGCCUGAGAA
1146
UUCUCAGGCCCUUUGAACA
1761

[534-552] ORF

ACUGGGUCACAGAGAAGAA
1147
UUCUUCUCUGUGACCCAGU
1762
Rh, Rt, Ms
[828-846] ORF

GGUAAUGAUAAGGAGAAUC
1148
GAUUCUCCUUAUCAUUACC
1763

[2346-2364] 3′UTR

CACACAAGAGUUGUUGAAA
1149
UUUCAACAACUCUUGUGUG
1764

[3543-3561] 3′UTR

CUCUGGAUGGACUGGGUCA
1150
UGACCCAGUCCAUCCAGAG
1765
Rh, Rb, Cw, Dg,
[818-836] ORF

Rt, Ms, Pg

GGAACUAGGGAACCUAUGU
1151
ACAUAGGUUCCCUAGUUCC
1766
Rh
[2265-2283] 3′UTR

CUCGGUAAUGAUAAGGAGA
1152
UCUCCUUAUCAUUACCGAG
1767

[2343-2361] 3′UTR

AGGUGAAUUCUCAGAUGAU
1153
AUCAUCUGAGAAUUCACCU
1768

[2164-2182] 3′UTR

UCGGUAAUGAUAAGGAGAA
1154
UUCUCCUUAUCAUUACCGA
1769

[2344-2362] 3′UTR

GCCAAAGCGGUCAGUGAGA
1155
UCUCACUGACCGCUUUGGC
1770

[440-458] ORF

GAACCAGUGGCUAGUUCUU
1156
AAGAACUAGCCACUGGUUC
1771

[1536-1554] 3′UTR

CCCUUCUCCUUUUAGACAU
1157
AUGUCUAAAAGGAGAAGGG
1772

[1105-1123] 3′UTR

CCACCUUAGCCUGUUCUAU
1158
AUAGAACAGGCUAAGGUGG
1773
Rh
[2491-2509] 3′UTR

CCCUGAGCACCACCCAGAA
1159
UUCUGGGUGGUGCUCAGGG
1774
Rh, Pg
[705-723] ORF

UGCUGUACAGUGACCUAAA
1160
UUUAGGUCACUGUACAGCA
1775

[2672-2690] 3′UTR

CCUUAGCCUGUUCUAUUCA
1161
UGAAUAGAACAGGCUAAGG
1776
Rh
[2494-2512] 3′UTR

GAACUUUCUCGGUAAUGAU
1162
AUCAUUACCGAGAAAGUUC
1777

[2336-2354] 3′UTR

CCUAGGAAGGGAAGGAUUU
1163
AAAUCCUUCCCUUCCUAGG
1778
Rh
[2056-2074] 3′UTR

UCAGUGAGAAGGAAGUGGA
1164
UCCACUUCCUUCUCACUGA
1779

[450-468] ORF

AUAUGAAGUCUGAGACCUU
1165
AAGGUCUCAGACUUCAUAU
1780

[3511-3529] 3′UTR

GGACUCUGGAAACGACAUU
1166
AAUGUCGUUUCCAGAGUCC
1781
Rh
[466-484] ORF

CCUCUGAGCCUUGUAGAAA
1167
UUUCUACAAGGCUCAGAGG
1782
Rh
[1605-1623] 3′UTR

AGUUUAAGAAGGCUCUCCA
1168
UGGAGAGCCUUCUUAAACU
1783

[3264-3282] 3′UTR

AGGGCAGACUGGGAGGGUA
1169
UACCCUCCCAGUCUGCCCU
1784
Rh
[2618-2636] 3′UTR

GUAGAAAUGGGAGCGAGAA
1170
UUCUCGCUCCCAUUUCUAC
1785

[1617-1635] 3′UTR

GGACUUGCUGCCGUAAUUU
1171
AAAUUACGGCAGCAAGUCC
1786

[3427-3445] 3′UTR

AGAACUUUCUCGGUAAUGA
1172
UCAUUACCGAGAAAGUUCU
1787

[2335-2353] 3′UTR

GUAUCAUUCUUGAGCAAUC
1173
GAUUGCUCAAGAAUGAUAC
1788

[3597-3615] 3′UTR

CAGCUAAGCAUAGUAAGAA
1174
UUCUUACUAUGCUUAGCUG
1789

[2031-2049] 3′UTR

GGCCUGUUUUAAGAGACAU
1175
AUGUCUCUUAAAACAGGCC
1790
Rh
[2132-2150] 3′UTR

GACUGGGUCACAGAGAAGA
1176
UCUUCUCUGUGACCCAGUC
1791
Rh, Rt, Ms
[827-845] ORF

CUCUGAUGCUUUGUAUCAU
1177
AUGAUACAAAGCAUCAGAG
1792

[3585-3603] 3′UTR

GUAACAUUUACUCCUGUUU
1178
AAACAGGAGUAAAUGUUAC
1793
Rh
[2809-2827] 3′UTR

UGAGUUGCAGAUAUACCAA
1179
UUGGUAUAUCUGCAACUCA
1794
Rh
[2192-2210] 3′UTR

AUCCCAUGGGUCCAAAUUA
1180
UAAUUUGGACCCAUGGGAU
1795

[1070-1088] 3′UTR

CUCUGGAAACGACAUUUAU
1181
AUAAAUGUCGUUUCCAGAG
1796
Rh
[469-487] ORF

GAUCCAGUAUGAGAUCAAG
1182
CUUGAUCUCAUACUGGAUC
1797
Rh, Rb
[505-523] ORF

AGGUGUGGCCUUUAUAUUU
1183
AAAUAUAAAGGCCACACCU
1798

[3119-3137] 3′UTR

CCCUGUUCGCUUCCUGUAU
1184
AUACAGGAAGCGAACAGGG
1799

[2777-2795] 3′UTR

GGGAGACGUGGGUCCAAGG
1185
CCUUGGACCCACGUCUCCC
1800

[1139-1157] 3′UTR

CAUGGGUCCAAAUUAAUAU
1186
AUAUUAAUUUGGACCCAUG
1801

[1074-1092] 3′UTR

UGGGUCACAGAGAAGAACA
1187
UGUUCUUCUCUGUGACCCA
1802
Rh
[830-848] ORF

CCUCAAGGUCCCUUCCCUA
1188
UAGGGAAGGGACCUUGAGG
1803

[1786-1804] 3′UTR

UGGUUCUCCAGUUCAAAUU
1189
AAUUUGAACUGGAGAACCA
1804

[61-3079] 3′UTR

GGACCUGGUCAGCACAGAU
1190
AUCUGUGCUGACCAGGUCC
1805
Rh
[2580-2598] 3′UTR

GGAGGGAGACGUGGGUCCA
1191
UGGACCCACGUCUCCCUCC
1806

[1136-1154] 3′UTR

UCUGAUGCUUUGUAUCAUU
1192
AAUGAUACAAAGCAUCAGA
1807

[3586-3604] 3′UTR

GGGACAUGGCCCUUGUUUU
1193
AAAACAAGGGCCAUGUCCC
1808

[1407-1425] 3′UTR

GCCUGGGCGUGGUCUUGCA
1194
UGCAAGACCACGCCCAGGC
1809

[2458-2476] 3′UTR

GGCGUUUUGCAAUGCAGAU
1195
AUCUGCAUUGCAAAACGCC
1810
Cw, Rt, Ms
[409-427] ORF

GAGUAGGUUCGGUCUGAAA
1196
UUUCAGACCGAACCUACUC
1811

[3101-3119] 3′UTR

AGUUCUUCGCCUGCAUCAA
1197
UUGAUGCAGGCGAAGAACU
1812
Rh, Rb, Cw,
[867-885] ORF

Dg, Ms

ACAAAGAUUACCUAGCUAA
1198
UUAGCUAGGUAAUCUUUGU
1813

[2234-2252] 3′UTR

GAGGGAGACGUGGGUCCAA
1199
UUGGACCCACGUCUCCCUC
1814

[1137-1155] 3′UTR

CUGUUUCUGCUGAUUGUUU
1200
AAACAAUCAGCAGAAACAG
1815

[2822-2840] 3′UTR

CUGACGAUAUACAGGCACA
1201
UGUGCCUGUAUAUCGUCAG
1816

[2399-2417] 3′UTR

UGUUGAAAGUUGACAAGCA
1202
UGCUUGUCAACUUUCAACA
1817

[3554-3572] 3′UTR

GCCUAGGAAGGGAAGGAUU
1203
AAUCCUUCCCUUCCUAGGC
1818
Rh
[2055-2073] 3′UTR

GGUGACACACUCACUUCUU
1204
AAGAAGUGAGUGUGUCACC
1819

[2092-2110] 3′UTR

GAGCCUUGUAGAAAUGGGA
1205
UCCCAUUUCUACAAGGCUC
1820
Rh
[1610-1628] 3′UTR

CAGAAAACAAAACAGGUUA
1206
UAACCUGUUUUGUUUUCUG
1821

[3172-3190] 3′UTR

CGCAUGUCUCUGAUGCUUU
1207
AAAGCAUCAGAGACAUGCG
1822

[3578-3596] 3′UTR

GACAAAGAUUACCUAGCUA
1208
UAGCUAGGUAAUCUUUGUC
1823

[2233-2251] 3′UTR

CUGUAUGGUGAUAUCAUAU
1209
AUAUGAUAUCACCAUACAG
1824

[2790-2808] 3′UTR

GACUCUGGAAACGACAUUU
1210
AAAUGUCGUUUCCAGAGUC
1825
Rh
[467-485] ORF

GGUUCGGUCUGAAAGGUGU
1211
ACACCUUUCAGACCGAACC
1826

[3106-3124] 3′UTR

AGAUGAUAGGUGAACCUGA
1212
UCAGGUUCACCUAUCAUCU
1827

[2176-2194] 3′UTR

GACACUAUGGCCUGUUUUA
1213
UAAAACAGGCCAUAGUGUC
1828

[2124-2142] 3′UTR

CUGCAAAAAAAGCCUCCAA
1214
UUGGAGGCUUUUUUUGCAG
1829

[992-1010] 3′UTR

CUGUUCUAUUCAGCGGCAA
1215
UUGCCGCUGAAUAGAACAG
1830

[2501-2519] 3′UTR

GUGGGUCCAAGGUCCUCAU
1216
AUGAGGACCUUGGACCCAC
1831

[1146-1164] 3′UTR

GCCUGAGAAGGAUAUAGAG
1217
CUCUAUAUCCUUCUCAGGC
1832

[544-562] ORF

GAAACUUCCUAGGGAACUA
1218
UAGUUCCCUAGGAAGUUUC
1833

[2253-2271] 3′UTR

CGCCAGCUAAGCAUAGUAA
1219
UUACUAUGCUUAGCUGGCG
1834

[2028-2046] 3′UTR

GCCUCUGGAUGGACUGGGU
1220
ACCCAGUCCAUCCAGAGGC
1835
Rh, Rb, Cw,
[816-834] ORF

Dg, Rt, Ms

ACGAUAUACAGGCACAUUA
1221
UAAUGUGCCUGUAUAUCGU
1836

[2402-2420] 3′UTR

AGCACCACCCAGAAGAAGA
1222
UCUUCUUCUGGGUGGUGCU
1837
Rh, Pg
[710-728] ORF

CCUCCCUCAAAGACUGACA
1223
UGUCAGUCUUUGAGGGAGG
1838
Rh
[1976-1994] 3′UTR

GGAGCACUGUGUUUAUGCU
1224
AGCAUAAACACAGUGCUCC
1839

[3489-3507] 3′UTR

ACUUGCUGCCGUAAUUUAA
1225
UUAAAUUACGGCAGCAAGU
1840

[3429-3447] 3′UTR

GGUUUCCUGAAGCCAGUGA
1226
UCACUGGCUUCAGGAAACC
1841

[2297-2315] 3′UTR

GGUCAGUGAGAAGGAAGUG
1227
CACUUCCUUCUCACUGACC
1842

[448-466] ORF

GUGACGCCAGCUAAGCAUA
1228
UAUGCUUAGCUGGCGUCAC
1843

[2024-2042] 3′UTR

AUGAUAAGGAGAAUCUCUU
1229
AAGAGAUUCUCCUUAUCAU
1844

[2350-2368] 3′UTR

UAGUGUUCCCUCCCUCAAA
1230
UUUGAGGGAGGGAACACUA
1845

[1968-1986] 3′UTR

GGAGACGUGGGUCCAAGGU
1231
ACCUUGGACCCACGUCUCC
1846

[1140-1158] 3′UTR

CCUGUUCUAUUCAGCGGCA
1232
UGCCGCUGAAUAGAACAGG
1847

[2500-2518] 3′UTR

UCCAGUAUGAGAUCAAGCA
1233
UGCUUGAUCUCAUACUGGA
1848
Rh, Rb
[507-525] ORF

CAAAAUGCUUCCAAAGCCA
1234
UGGCUUUGGAAGCAUUUUG
1849
Rh
[2475-2493] 3′UTR

CACACGCAAUGAAACCGAA
1235
UUCGGUUUCAUUGCGUGUG
1850

[2431-2449] 3′UTR

CUCCAUUUGGCAUCGUUUA
1236
UAAACGAUGCCAAAUGGAG
1851

[3278-3296] 3′UTR

AGCAGGAGUUUCUCGACAU
1237
AUGUCGAGAAACUCCUGCU
1852
Ck, Dg
[933-951] ORF

GUGUGGCCUUUAUAUUUGA
1238
UCAAAUAUAAAGGCCACAC
1853

[3121-3139] 3′UTR

GGGACCUGGUCAGCACAGA
1239
UCUGUGCUGACCAGGUCCC
1854
Rh
[2579-2597] 3′UTR

CCUCAGUGUGGUUUCCUGA
1240
UCAGGAAACCACACUGAGG
1855

[2288-2306] 3′UTR

GACCCAGAGUGGAACGCGU
1241
ACGCGUUCCACUCUGGGUC
1856

[2966-2984] 3′UTR

CCACCUGUGUUGUAAAGAU
1242
AUCUUUACAACACAGGUGG
1857
Rh
[2377-2395] 3′UTR

ACCUGUGUUGUAAAGAUAA
1243
UUAUCUUUACAACACAGGU
1858
Rh
[2379-2397] 3′UTR

GUUUUGCAAUGCAGAUGUA
1244
UACAUCUGCAUUGCAAAAC
1859

[412-430] ORF

AAAAAAGCCUCCAAGGGUU
1245
AACCCUUGGAGGCUUUUUU
1860

[997-1015] 3′UTR

UAAGAAACUUCCUAGGGAA
1246
UUCCCUAGGAAGUUUCUUA
1861

[2250-2268] 3′UTR

GCAUUUGACCCAGAGUGGA
1247
UCCACUCUGGGUCAAAUGC
1862

[2960-2978] 3′UTR

CCCUCAAGGUCCCUUCCCU
1248
AGGGAAGGGACCUUGAGGG
1863

[1785-1803] 3′UTR

AGGAUCCAGUAUGAGAUCA
1249
UGAUCUCAUACUGGAUCCU
1864
Rh, Rb
[503-521] ORF

AAGAUUACCUAGCUAAGAA
1250
UUCUUAGCUAGGUAAUCUU
1865

[2237-2255] 3′UTR

CUAUGUGUUCCCUCAGUGU
1251
ACACUGAGGGAACACAUAG
1866

[2278-2296] 3′UTR

GACAGAGGAAGCCGCUCAA
1252
UUGAGCGGCUUCCUCUGUC
1867

[3211-3229] 3′UTR

UUAAGAAGGCUCUCCAUUU
1253
AAAUGGAGAGCCUUCUUAA
1868

[3267-3285] 3′UTR

UAAGGAGAAUCUCUUGUUU
1254
AAACAAGAGAUUCUCCUUA
1869

[2354-2372] 3′UTR

GUUUCCUGAAGCCAGUGAU
1255
AUCACUGGCUUCAGGAAAC
1870

[2298-2316] 3′UTR

UGAGCACCACCCAGAAGAA
1256
UUCUUCUGGGUGGUGCUCA
1871
Rh, Pg
[708-726] ORF

CUAUUAAUCCUCAGAAUUC
1257
GAAUUCUGAGGAUUAAUAG
1872
Rh
[1573-1591] 3′UTR

CUGGGCGUGGUCUUGCAAA
1258
UUUGCAAGACCACGCCCAG
1873

[2460-2478] 3′UTR

GGAGGAAAGAAGGAAUAUC
1259
GAUAUUCCUUCUUUCCUCC
1874
Rt
[614-632] ORF

CCAAGUUCUUCGCCUGCAU
1260
AUGCAGGCGAAGAACUUGG
1875
Rh, Rb, Cw,
[864-882] ORF

Dg, Ms

GUUUCUGCUGAUUGUUUUU
1261
AAAAACAAUCAGCAGAAAC
1876

[2824-2842] 3′UTR

GGUCCAAGGUCCUCAUCCC
1262
GGGAUGAGGACCUUGGACC
1877

[1149-1167] 3′UTR

AGUUGGUAAGAUGUCAUAA
1263
UUAUGACAUCUUACCAACU
1878
Rh
[2690-2708] 3′UTR

GGAAUAUGAAGUCUGAGAC
1264
GUCUCAGACUUCAUAUUCC
1879
Ms
[3508-3526] 3′UTR

GAGUGGAACGCGUGGCCUA
1265
UAGGCCACGCGUUCCACUC
1880

[2972-2990] 3′UTR

GGUUGUGGGUCUGGAGGGA
1266
UCCCUCCAGACCCACAACC
1881
Rh
[1124-1142] 3′UTR

GUUGAUUUUGUUUCCGUUU
1267
AAACGGAAACAAAAUCAAC
1882

[3454-3472] 3′UTR

CACUGUGUUUAUGCUGGAA
1268
UUCCAGCAUAAACACAGUG
1883

[3493-3511] 3′UTR

GAGCUGCGUUCCAGCCUCA
1269
UGAGGCUGGAACGCAGCUC
1884

[1645-1663] 3′UTR

GGACUGGGUCACAGAGAAG
1270
CUUCUCUGUGACCCAGUCC
1885
Rh, Rt, Ms, Pg
[826-844] ORF

AGCUAAGCAUAGUAAGAAG
1271
CUUCUUACUAUGCUUAGCU
1886

[2032-2050] 3′UTR

CACAAGAGUUGUUGAAAGU
1272
ACUUUCAACAACUCUUGUG
1887

[3545-3563] 3′UTR

GGUCAGCACAGAUCUUGAU
1273
AUCAAGAUCUGUGCUGACC
1888
Rh
[2586-2604] 3′UTR

UUCUAAAGGUGAAUUCUCA
1274
UGAGAAUUCACCUUUAGAA
1889

[2158-2176] 3′UTR

AGGGAACUAGGGAACCUAU
1275
AUAGGUUCCCUAGUUCCCU
1890
Rh
[2263-2281] 3′UTR

GGAAGUGGACUCUGGAAAC
1276
GUUUCCAGAGUCCACUUCC
1891

[460-478] ORF

CCUCCCACCUGUGUUGUAA
1277
UUACAACACAGGUGGGAGG
1892
Rh
[2373-2391] 3′UTR

CGGACGAGUGCCUCUGGAU
1278
AUCCAGAGGCACUCGUCCG
1893
Rh, Rb, Cw
[807-825] ORF

CGUGGAAGCAUUUGACCCA
1279
UGGGUCAAAUGCUUCCACG
1894
Rh
[2953-2971] 3′UTR

GCACUGUGUUUAUGCUGGA
1280
UCCAGCAUAAACACAGUGC
1895

[3492-3510] 3′UTR

AGUUGCAGAUAUACCAACU
1281
AGUUGGUAUAUCUGCAACU
1896
Rh
[2194-2212] 3′UTR

AAUGAUAAGGAGAAUCUCU
1282
AGAGAUUCUCCUUAUCAUU
1897

[2349-2367] 3′UTR

CUUGCUGCCGUAAUUUAAA
1283
UUUAAAUUACGGCAGCAAG
1898

[3430-3448] 3′UTR

GGAGAAUCUCUUGUUUCCU
1284
AGGAAACAAGAGAUUCUCC
1899

[2357-2375] 3′UTR

CCUUGGUAGGUAUUAGACU
1285
AGUCUAAUACCUACCAAGG
1900

[2905-2923] 3′UTR

GGACGUUGGAGGAAAGAAG
1286
CUUCUUUCCUCCAACGUCC
1901
Rt, Ms
[607-625] ORF

CGUUGGAGGAAAGAAGGAA
1287
UUCCUUCUUUCCUCCAACG
1902
Rt, Ms
[610-628] ORF

CUGACAUCCCUUCCUGGAA
1288
UUCCAGGAAGGGAUGUCAG
1903
Rh, Rt, Ms
[1031-1049] 3′UTR

UGACAUCCCUUCCUGGAAA
1289
UUUCCAGGAAGGGAUGUCA
1904
Rh, Rt, Ms
[1032-1050] 3′UTR

GAUAUACCAACUUCUGCUU
1290
AAGCAGAAGUUGGUAUAUC
1905
Rh
[2201-2219] 3′UTR

AGAUGGGCUGCGAGUGCAA
1291
UUGCACUCGCAGCCCAUCU
1906
Ck, Rb, Rt
[747-765] ORF

GGCUUAGUGUUCCCUCCCU
1292
AGGGAGGGAACACUAAGCC
1907

[1964-1982] 3′UTR

GUAUGGUGAUAUCAUAUGU
1293
ACAUAUGAUAUCACCAUAC
1908

[2792-2810] 3′UTR

ACCAACUUCUGCUUGUAUU
1294
AAUACAAGCAGAAGUUGGU
1909
Rh
[2206-2224] 3′UTR

CUCACUUCUUUCUCAGCCU
1295
AGGCUGAGAAAGAAGUGAG
1910

[2101-2119] 3′UTR

CUCCCACCUGUGUUGUAAA
1296
UUUACAACACAGGUGGGAG
1911
Rh
[2374-2392] 3′UTR

GGGUCUCGCUGGACGUUGG
1297
CCAACGUCCAGCGAGACCC
1912
Rt, Ms
[597-615] ORF

GAGCCUCCCUCUGAGCCUU
1298
AAGGCUCAGAGGGAGGCUC
1913
Rh
[1598-1616] 3′UTR

GCAUGUCUCUGAUGCUUUG
1299
CAAAGCAUCAGAGACAUGC
1914

[3579-3597] 3′UTR

GGCGUUUUCAUGCUGUACA
1300
UGUACAGCAUGAAAACGCC
1915
Rh
[2662-2680] 3′UTR

AUACCAACUUCUGCUUGUA
1301
UACAAGCAGAAGUUGGUAU
1916
Rh
[2204-2222] 3′UTR

GCAAUGCAGAUGUAGUGAU
1302
AUCACUACAUCUGCAUUGC
1917

[417-435] ORF

ACUUCUGCUUGUAUUUCUU
1303
AAGAAAUACAAGCAGAAGU
1918
Rh
[2210-2228] 3′UTR

UCCAGUUCAAAUUAUUGCA
1304
UGCAAUAAUUUGAACUGGA
1919

[67-3085] 3′UTR

CCUGGUCAGCACAGAUCUU
1305
AAGAUCUGUGCUGACCAGG
1920
Rh
[2583-2601] 3′UTR

UGUUGAUUUUGUUUCCGUU
1306
AACGGAAACAAAAUCAACA
1921

[3453-3471] 3′UTR

UGCAGAUAUACCAACUUCU
1307
AGAAGUUGGUAUAUCUGCA
1922
Rh
[2197-2215] 3′UTR

GCGGUCAGUGAGAAGGAAG
1308
CUUCCUUCUCACUGACCGC
1923

[446-464] ORF

GGCGUGGUCUUGCAAAAUG
1309
CAUUUUGCAAGACCACGCC
1924

[2463-2481] 3′UTR

GUCCAGCCUAGGAAGGGAA
1310
UUCCCUUCCUAGGCUGGAC
1925
Rh
[2050-2068] 3′UTR

ACUUUCUCGGUAAUGAUAA
1311
UUAUCAUUACCGAGAAAGU
1926

[2338-2356] 3′UTR

CUUCUGCUUGUAUUUCUUA
1312
UAAGAAAUACAAGCAGAAG
1927

[2211-2229] 3′UTR

CAGAGGAAGCCGCUCAAAU
1313
AUUUGAGCGGCUUCCUCUG
1928

[3213-3231] 3′UTR

GAAGGAAGUGGACUCUGGA
1314
UCCAGAGUCCACUUCCUUC
1929

[457-475] ORF

CAGUGAGAAGGAAGUGGAC
1315
GUCCACUUCCUUCUCACUG
1930

[451-469] ORF

GACUUCCCUUUCUAGGGCA
1316
UGCCCUAGAAAGGGAAGUC
1931
Rh
[2605-2623] 3′UTR

CCUCCCUCUGAGCCUUGUA
1317
UACAAGGCUCAGAGGGAGG
1932
Rh
[1601-1619] 3′UTR

CAUGCUGUACAGUGACCUA
1318
UAGGUCACUGUACAGCAUG
1933

[2670-2688] 3′UTR

GAGUGCCUCUGGAUGGACU
1319
AGUCCAUCCAGAGGCACUC
1934
Rh, Rb, Cw,
[812-830] ORF

Dg, Rt, Ms

CUGGGAGGGUAUCCAGGAA
1320
UUCCUGGAUACCCUCCCAG
1935
Rh
[2626-2644] 3′UTR

AACCGUGCUGAGCAGAAAA
1321
UUUUCUGCUCAGCACGGUU
1936

[3160-3178] 3′UTR

CAGUCCAUGUGAUUUCAGU
1322
ACUGAAAUCACAUGGACUG
1937
Rh
[2714-2732] 3′UTR

UAGACAUGGUUGUGGGUCU
1323
AGACCCACAACCAUGUCUA
1938

[1117-1135] 3′UTR

GCGCAUGUCUCUGAUGCUU
1324
AAGCAUCAGAGACAUGCGC
1939

[3577-3595] 3′UTR

AAGGUGAAUUCUCAGAUGA
1325
UCAUCUGAGAAUUCACCUU
1940

[2163-2181] 3′UTR

AGAAGAACAUCAACGGGCA
1326
UGCCCGUUGAUGUUCUUCU
1941
Rh, Rb
[840-858] ORF

ACAUACACACGCAAUGAAA
1327
UUUCAUUGCGUGUGUAUGU
1942
Rh
[2426-2444] 3′UTR

CACAGAUCUUGAUGACUUC
1328
GAAGUCAUCAAGAUCUGUG
1943
Rh
[2592-2610] 3′UTR

AGCCGCUCAAAUACCUUCA
1329
UGAAGGUAUUUGAGCGGCU
1944

[3220-3238] 3′UTR

CCAGUAUGAGAUCAAGCAG
1330
CUGCUUGAUCUCAUACUGG
1945
Rh, Rb, Cw,
[508-526] ORF

Dg, Ms

GUGAGAAGGAAGUGGACUC
1331
GAGUCCACUUCCUUCUCAC
1946

[453-471] ORF

ACCUUAGCCUGUUCUAUUC
1332
GAAUAGAACAGGCUAAGGU
1947
Rh
[2493-2511] 3′UTR

CCUGUUUCUGCUGAUUGUU
1333
AACAAUCAGCAGAAACAGG
1948

[2821-2839] 3′UTR

GCCAUUGCUUCUUGCCUGU
1334
ACAGGCAAGAAGCAAUGGC
1949

[1817-1835] 3′UTR

GCCUGGAAAUGUGCAUUUU
1335
AAAAUGCACAUUUCCAGGC
1950
Rh
[1322-1340] 3′UTR

GCACAGCUCUCUUCUCCUA
1336
UAGGAGAAGAGAGCUGUGC
1951

[3317-3335] 3′UTR

CGACAUUUAUGGCAACCCU
1337
AGGGUUGCCAUAAAUGUCG
1952

[478-496] ORF

CCUGUGCUGUGUUUUUUAU
1338
AUAAAAAACACAGCACAGG
1953
Rh
[2883-2901] 3′UTR

AGGAAGUGGACUCUGGAAA
1339
UUUCCAGAGUCCACUUCCU
1954

[459-477] ORF

GCUAAGCAUAGUAAGAAGU
1340
ACUUCUUACUAUGCUUAGC
1955

[2033-2051] 3′UTR

CCGUCUUUGGUUCUCCAGU
1341
ACUGGAGAACCAAAGACGG
1956

[3054-3072] 3′UTR

UUUCCUGAAGCCAGUGAUA
1342
UAUCACUGGCUUCAGGAAA
1957

[2299-2317] 3′UTR

AGACGUGGGUCCAAGGUCC
1343
GGACCUUGGACCCACGUCU
1958

[1142-1160] 3′UTR

ACAUUUAUGGCAACCCUAU
1344
AUAGGGUUGCCAUAAAUGU
1959

[480-498] ORF

GUGGACAAUAAACAGUAUU
1345
AAUACUGUUUAUUGUCCAC
1960

[3625-3643] 3′UTR

GGGAACACACAAGAGUUGU
1346
ACAACUCUUGUGUGUUCCC
1961

[3538-3556] 3′UTR

GCUCGGUCCGUGGACAAUA
1347
UAUUGUCCACGGACCGAGC
1962

[3616-3634] 3′UTR

CCGUGCUGAGCAGAAAACA
1348
UGUUUUCUGCUCAGCACGG
1963

[3162-3180] 3′UTR

CCGCUCAAAUACCUUCACA
1349
UGUGAAGGUAUUUGAGCGG
1964

[3222-3240] 3′UTR

GUUCCCUCCCUCAAAGACU
1350
AGUCUUUGAGGGAGGGAAC
1965

[1972-1990] 3′UTR

GGUCGUUGCAAGACUGUGU
1351
ACACAGUCUUGCAACGACC
1966

[1356-1374] 3′UTR

GGUGCUGGGAACACACAAG
1352
CUUGUGUGUUCCCAGCACC
1967

[3532-3550] 3′UTR

AGUAUAUACAACUCCACCA
1353
UGGUGGAGUUGUAUAUACU
1968
Rh
[2730-2748] 3′UTR

GGCAUCAGGCACCUGGAUU
1354
AAUCCAGGUGCCUGAUGCC
1969

[1839-1857] 3′UTR

AGCAGAUAAAGAUGUUCAA
1355
UUGAACAUCUUUAUCUGCU
1970
Cw, Dg, Rt,
[522-540] ORF

Ms, Pg

UGGAAUAUGAAGUCUGAGA
1356
UCUCAGACUUCAUAUUCCA
1971
Ms
[3507-3525] 3′UTR

CAGGCACCUGGAUUGAGUU
1357
AACUCAAUCCAGGUGCCUG
1972
Rh
[1844-1862] 3′UTR

AUAAGGAGAAUCUCUUGUU
1358
AACAAGAGAUUCUCCUUAU
1973

[2353-2371] 3′UTR

GCCUGUUUUAAGAGACAUC
1359
GAUGUCUCUUAAAACAGGC
1974
Rh
[2133-2151] 3′UTR

CGCUUCCUGUAUGGUGAUA
1360
UAUCACCAUACAGGAAGCG
1975

[2784-2802] 3′UTR

GCACCGUCACAGAUGCCAA
1361
UUGGCAUCUGUGACGGUGC
1976

[1262-1280] 3′UTR

GUUCCAGCCUCAGCUGAGU
1362
ACUCAGCUGAGGCUGGAAC
1977

[1652-1670] 3′UTR

GGAGGUAGGUGGCUUUGGU
1363
ACCAAAGCCACCUACCUCC
1978
Rh
[2076-2094] 3′UTR

GGAAACGACAUUUAUGGCA
1364
UGCCAUAAAUGUCGUUUCC
1979

[473-491] ORF

GCAAGAUGCACAUCACCCU
1365
AGGGUGAUGUGCAUCUUGC
1980
Rh, Dg
[660-678] ORF

UGUAGAAAUGGGAGCGAGA
1366
UCUCGCUCCCAUUUCUACA
1981
Rh
[1616-1634] 3′UTR

GGCCUAUGCAGGUGGAUUC
1367
GAAUCCACCUGCAUAGGCC
1982
Rh
[2985-3003] 3′UTR

AAGAAGAGCCUGAACCACA
1368
UGUGGUUCAGGCUCUUCUU
1983
Rh, Rb, Cw,
[722-740] ORF

Ms, Pg

GGGAGGGUAUCCAGGAAUC
1369
GAUUCCUGGAUACCCUCCC
1984
Rh
[2628-2646] 3′UTR

GUCAUAAUGGACCAGUCCA
1370
UGGACUGGUCCAUUAUGAC
1985
Rh
[2702-2720] 3′UTR

CCAAGGUCCUCAUCCCAUC
1371
GAUGGGAUGAGGACCUUGG
1986

[1152-1170] 3′UTR

AGGUGGCUUUGGUGACACA
1372
UGUGUCACCAAAGCCACCU
1987
Rh
[2082-2100] 3′UTR

AGACUGUGUAGCAGGCCUA
1373
UAGGCCUGCUACACAGUCU
1988
Rh
[1366-1384] 3′UTR

GGCCUGGAAAUGUGCAUUU
1374
AAAUGCACAUUUCCAGGCC
1989
Rh
[1321-1339] 3′UTR

GGUUAGGAUAGGAAGAACU
1375
AGUUCUUCCUAUCCUAACC
1990

[2322-2340] 3′UTR

GGCUAGUUCUUGAAGGAGC
1376
GCUCCUUCAAGAACUAGCC
1991

[1544-1562] 3′UTR

AGCUCUGUUGAUUUUGUUU
1377
AAACAAAAUCAACAGAGCU
1992

[3448-3466] 3′UTR

UGCAUUUUGCAGAAACUUU
1378
AAAGUUUCUGCAAAAUGCA
1993
Rh
[1333-1351] 3′UTR

GUCUGAAAGGUGUGGCCUU
1379
AAGGCCACACCUUUCAGAC
1994

[3112-3130] 3′UTR

CAUCCAAGGGCAGCCUGGA
1380
UCCAGGCUGCCCUUGGAUG
1995

[1519-1537] 3′UTR

UGUUUCUGCUGAUUGUUUU
1381
AAAACAAUCAGCAGAAACA
1996

[2823-2841] 3′UTR

UGCAAGCAACUCAAAAUAU
1382
AUAUUUUGAGUUGCUUGCA
1997

[3345-3363] 3′UTR

AACAUUUACUCCUGUUUCU
1383
AGAAACAGGAGUAAAUGUU
1998
Rh
[2811-2829] 3′UTR

GAAAGGUGUGGCCUUUAUA
1384
UAUAAAGGCCACACCUUUC
1999

[3116-3134] 3′UTR

UCCUGUUUCUGCUGAUUGU
1385
ACAAUCAGCAGAAACAGGA
2000

[2820-2838] 3′UTR

AUCCUAUUAAUCCUCAGAA
1386
UUCUGAGGAUUAAUAGGAU
2001
Rh
[1570-1588] 3′UTR

UCCUGAAGCCAGUGAUAUG
1387
CAUAUCACUGGCUUCAGGA
2002

[2301-2319] 3′UTR

AGGGCCUGAGAAGGAUAUA
1388
UAUAUCCUUCUCAGGCCCU
2003

[541-559] ORF

GUUGCAGAUAUACCAACUU
1389
AAGUUGGUAUAUCUGCAAC
2004
Rh
[2195-2213] 3′UTR

GGGCCUGAGAAGGAUAUAG
1390
CUAUAUCCUUCUCAGGCCC
2005

[542-560] ORF

CGGGCGUUUUCAUGCUGUA
1391
UACAGCAUGAAAACGCCCG
2006
Rh
[2660-2678] 3′UTR

ACCAGUCCAUGUGAUUUCA
1392
UGAAAUCACAUGGACUGGU
2007
Rh
[2712-2730] 3′UTR

CGUGGGUCCAAGGUCCUCA
1393
UGAGGACCUUGGACCCACG
2008

[1145-1163] 3′UTR

GCCUGGAACCAGUGGCUAG
1394
CUAGCCACUGGUUCCAGGC
2009

[1531-1549] 3′UTR

CCUUUCAUCUUGAGAGGGA
1395
UCCCUCUCAAGAUGAAAGG
2010
Rh
[1392-1410] 3′UTR

CCAGUGGGAGCCUCCCUCU
1396
AGAGGGAGGCUCCCACUGG
2011
Rh
[1591-1609] 3′UTR

AAAUGUGCAUUUUGCAGAA
1397
UUCUGCAAAAUGCACAUUU
2012
Rh, Ms
[1328-1346] 3′UTR

UGGUCAGCACAGAUCUUGA
1398
UCAAGAUCUGUGCUGACCA
2013
Rh
[2585-2603] 3′UTR

CUAUGCAGGUGGAUUCCUU
1399
AAGGAAUCCACCUGCAUAG
2014
Rh
[2988-3006] 3′UTR

AGUAAGAAGUCCAGCCUAG
1400
CUAGGCUGGACUUCUUACU
2015
Rh
[2042-2060] 3′UTR

CUCAUCCCAUGGGUCCAAA
1401
UUUGGACCCAUGGGAUGAG
2016

[1067-1085] 3′UTR

AGAGCCGGGUGGCAGCUGA
1402
UCAGCUGCCACCCGGCUCU
2017

[3194-3212] 3′UTR

GCUGGGAACACACAAGAGU
1403
ACUCUUGUGUGUUCCCAGC
2018

[3535-3553] 3′UTR

CCGGACGAGUGCCUCUGGA
1404
UCCAGAGGCACUCGUCCGG
2019
Rh, Rb, Cw
[806-824] ORF

CCCUCAGUGUGGUUUCCUG
1405
CAGGAAACCACACUGAGGG
2020

[2287-2305] 3′UTR

AGUUGCACAGCUUUGCUUU
1406
AAAGCAAAGCUGUGCAACU
2021

[1859-1877] 3′UTR

CCCAUAAGCAGGCCUCCAA
1407
UUGGAGGCCUGCUUAUGGG
2022

[958-976] ORF[3′UTR

CGGUGCUGGGAACACACAA
1408
UUGUGUGUUCCCAGCACCG
2023

[3531-3549] 3′UTR

GGUUUGUUUUUGACAUCAG
1409
CUGAUGUCAAAAACAAACC
2024
Rh
[2853-2871] 3′UTR

GACGAUAUACAGGCACAUU
1410
AAUGUGCCUGUAUAUCGUC
2025

[2401-2419] 3′UTR

CUUAGUGUUCCCUCCCUCA
1411
UGAGGGAGGGAACACUAAG
2026

[1966-1984] 3′UTR

GACACACUCACUUCUUUCU
1412
AGAAAGAAGUGAGUGUGUC
2027

[2095-2113] 3′UTR

GAAGCCGCUCAAAUACCUU
1413
AAGGUAUUUGAGCGGCUUC
2028

[3218-3236] 3′UTR

GGUCCCUUUCAUCUUGAGA
1414
UCUCAAGAUGAAAGGGACC
2029
Rh
[1388-1406] 3′UTR

CCUGGAACCAGUGGCUAGU
1415
ACUAGCCACUGGUUCCAGG
2030

[1532-1550] 3′UTR

UUCAGUAUAUACAACUCCA
1416
UGGAGUUGUAUAUACUGAA
2031
Rh
[2727-2745] 3′UTR

ACCUAUGUGUUCCCUCAGU
1417
ACUGAGGGAACACAUAGGU
2032

[2276-2294] 3′UTR

CUCCUAUUUUCAUCCUGCA
1418
UGCAGGAUGAAAAUAGGAG
2033

[3330-3348] 3′UTR

ACACACAAGAGUUGUUGAA
1419
UUCAACAACUCUUGUGUGU
2034

[3542-3560] 3′UTR

UGUCUCUGAUGCUUUGUAU
1420
AUACAAAGCAUCAGAGACA
2035

[3582-3600] 3′UTR

UAGAAAUGGGAGCGAGAAA
1421
UUUCUCGCUCCCAUUUCUA
2036

[1618-1636] 3′UTR

GAAGCAUUUGACCCAGAGU
1422
ACUCUGGGUCAAAUGCUUC
2037

[2957-2975] 3′UTR

GUUUUUGACAUCAGCUGUA
1423
UACAGCUGAUGUCAAAAAC
2038

[2858-2876] 3′UTR

GGAGUUUCUCGACAUCGAG
1424
CUCGAUGUCGAGAAACUCC
2039
Ck, Dg
[937-955] ORF

GAUAAACUGACGAUAUACA
1425
UGUAUAUCGUCAGUUUAUC
2040

[2393-2411] 3′UTR

GUGUUCCCUCCCUCAAAGA
1426
UCUUUGAGGGAGGGAACAC
2041

[1970-1988] 3′UTR

UUUGUUUCCGUUUGGAUUU
1427
AAAUCCAAACGGAAACAAA
2042

[3460-3478] 3′UTR

AGCUGAGUCUUUUUGGUCU
1428
AGACCAAAAAGACUCAGCU
2043
Rh
[1663-1681] 3′UTR

AACUUUCUCGGUAAUGAUA
1429
UAUCAUUACCGAGAAAGUU
2044

[2337-2355] 3′UTR

CCGGGUGGCAGCUGACAGA
1430
UCUGUCAGCUGCCACCCGG
2045

[3198-3216] 3′UTR

GAGUUGCACAGCUUUGCUU
1431
AAGCAAAGCUGUGCAACUC
2046

[1858-1876] 3′UTR

CCGGGACCUGGUCAGCACA
1432
UGUGCUGACCAGGUCCCGG
2047
Rh
[2577-2595] 3′UTR

CAAAGUAAAGGAUCUUUGA
1433
UCAAAGAUCCUUUACUUUG
2048

[3084-3102] 3′UTR

CAGCUCUCUUCUCCUAUUU
1434
AAAUAGGAGAAGAGAGCUG
2049

[3320-3338] 3′UTR

GACAGAAAAAGCUGGGUCU
1435
AGACCCAGCUUUUUCUGUC
2050
Rh
[1930-1948] 3′UTR

UGCAUGUGACGCCAGCUAA
1436
UUAGCUGGCGUCACAUGCA
2051

[2019-2037] 3′UTR

CCAGCCUCAGCUGAGUCUU
1437
AAGACUCAGCUGAGGCUGG
2052
Rh
[1655-1673] 3′UTR

GACCUAAAGUUGGUAAGAU
1438
AUCUUACCAACUUUAGGUC
2053

[2683-2701] 3′UTR

GGUGUGGCCUUUAUAUUUG
1439
CAAAUAUAAAGGCCACACC
2054

[3120-3138] 3′UTR

GUCCAAGGUCCUCAUCCCA
1440
UGGGAUGAGGACCUUGGAC
2055

[1150-1168] 3′UTR

UAGUAAGAAGUCCAGCCUA
1441
UAGGCUGGACUUCUUACUA
2056
Rh
[2041-2059] 3′UTR

AAGCAUAGUAAGAAGUCCA
1442
UGGACUUCUUACUAUGCUU
2057

[2036-2054] 3′UTR

AGGAUAGGAAGAACUUUCU
1443
AGAAAGUUCUUCCUAUCCU
2058

[2326-2344] 3′UTR

AGGAGAAUCUCUUGUUUCC
1444
GGAAACAAGAGAUUCUCCU
2059

[2356-2374] 3′UTR

CAAGAGUUGUUGAAAGUUG
1445
CAACUUUCAACAACUCUUG
2060

[3547-3565] 3′UTR

CCCAUGAUCCCGUGCUACA
1446
UGUAGCACGGGAUCAUGGG
2061
Rh, Rb
[779-797] ORF

CAUCCCAUGGGUCCAAAUU
1447
AAUUUGGACCCAUGGGAUG
2062

[1069-1087] 3′UTR

CUGAGCAGAAAACAAAACA
1448
UGUUUUGUUUUCUGCUCAG
2063

[3167-3185] 3′UTR

AGCAGAAAACAAAACAGGU
1449
ACCUGUUUUGUUUUCUGCU
2064

[3170-3188] 3′UTR

CUUGUUUCCUCCCACCUGU
1450
ACAGGUGGGAGGAAACAAG
2065

[2366-2384] 3′UTR

GUGGACUCUGGAAACGACA
1451
UGUCGUUUCCAGAGUCCAC
2066
Rh
[464-482] ORF

UGAUAAGGAGAAUCUCUUG
1452
CAAGAGAUUCUCCUUAUCA
2067
Rh
[2351-2369] 3′UTR

UGAGUAGGUUCGGUCUGAA
1453
UUCAGACCGAACCUACUCA
2068

[3100-3118] 3′UTR

CAUUUGGCAUCGUUUAAUU
1454
AAUUAAACGAUGCCAAAUG
2069

[3281-3299] 3′UTR

GCUUCCUGUAUGGUGAUAU
1455
AUAUCACCAUACAGGAAGC
2070

[2785-2803] 3′UTR

GAGGAUCCAGUAUGAGAUC
1456
GAUCUCAUACUGGAUCCUC
2071
Rh, Rb
[502-520] ORF

GCACAUCCUGAGGACAGAA
1457
UUCUGUCCUCAGGAUGUGC
2072
Rh
[1918-1936] 3′UTR

GCAUGAAUAAAACACUCAU
1458
AUGAGUGUUUUAUUCAUGC
2073
Rh
[1053-1071] 3′UTR

GCAACAGGCGUUUUGCAAU
1459
AUUGCAAAACGCCUGUUGC
2074
Cw, Rt, Ms
[403-421] ORF

GGGACGGCAAGAUGCACAU
1460
AUGUGCAUCUUGCCGUCCC
2075

[654-672] ORF

CUGUAAUCAUUCCUGUGCU
1461
AGCACAGGAAUGAUUACAG
2076
Rh
[2872-2890] 3′UTR

GGUCUUUUAACCGUGCUGA
1462
UCAGCACGGUUAAAAGACC
2077

[3152-3170] 3′UTR

ACAGCUCUCUUCUCCUAUU
1463
AAUAGGAGAAGAGAGCUGU
2078

[3319-3337] 3′UTR

ACCCUUGGUAGGUAUUAGA
1464
UCUAAUACCUACCAAGGGU
2079

[2903-2921] 3′UTR

GACUGGUCCAGCUCUGACA
1465
UGUCAGAGCUGGACCAGUC
2080
Rh
[1018-1036] 3′UTR

AUCCUGCAAGCAACUCAAA
1466
UUUGAGUUGCUUGCAGGAU
2081

[3341-3359] 3′UTR

CCAUGAUCCCGUGCUACAU
1467
AUGUAGCACGGGAUCAUGG
2082
Rh, Rb
[780-798] ORF

UUGUAUCAUUCUUGAGCAA
1468
UUGCUCAAGAAUGAUACAA
2083

[3595-3613] 3′UTR

GAGUCUUUUUGGUCUGCAC
1469
GUGCAGACCAAAAAGACUC
2084

[1667-1685] 3′UTR

GUUCAAAGGGCCUGAGAAG
1470
CUUCUCAGGCCCUUUGAAC
2085

[535-553] ORF

AGCCUCAGCUGAGUCUUUU
1471
AAAAGACUCAGCUGAGGCU
2086
Rh
[1657-1675] 3′UTR

GAUAAGGAGAAUCUCUUGU
1472
ACAAGAGAUUCUCCUUAUC
2087

[2352-2370] 3′UTR

ACAUCACCCUCUGUGACUU
1473
AAGUCACAGAGGGUGAUGU
2088
Rh
[669-687] ORF

GCGUGGUCUUGCAAAAUGC
1474
GCAUUUUGCAAGACCACGC
2089

[2464-2482] 3′UTR

GCCUUGGCACCGUCACAGA
1475
UCUGUGACGGUGCCAAGGC
2090
Rh
[1256-1274] 3′UTR

AGAAGAGCCUGAACCACAG
1476
CUGUGGUUCAGGCUCUUCU
2091
Rh, Rb, Cw,
[723-741] ORF

Ms, Pg

UGGCCUGUUUUAAGAGACA
1477
UGUCUCUUAAAACAGGCCA
2092
Rh
[2131-2149] 3′UTR

GGGAAGGAUUUUGGAGGUA
1478
UACCUCCAAAAUCCUUCCC
2093
Rh
[2064-2082] 3′UTR

CCCUGUGGCCAACUGCAAA
1479
UUUGCAGUUGGCCACAGGG
2094
Rh
[980-998] 3′UTR

CUUUCUCGGUAAUGAUAAG
1480
CUUAUCAUUACCGAGAAAG
2095

[2339-2357] 3′UTR

CACUCAUCCCAUGGGUCCA
1481
UGGACCCAUGGGAUGAGUG
2096

[1065-1083] 3′UTR

GGUGGCAGCUGACAGAGGA
1482
UCCUCUGUCAGCUGCCACC
2097

[3201-3219] 3′UTR

GUGAAUUCUCAGAUGAUAG
1483
CUAUCAUCUGAGAAUUCAC
2098

[2166-2184] 3′UTR

UCCUGCAAGCAACUCAAAA
1484
UUUUGAGUUGCUUGCAGGA
2099

[3342-3360] 3′UTR

CCUGUUUUAAGAGACAUCU
1485
AGAUGUCUCUUAAAACAGG
2100
Rh
[2134-2152] 3′UTR

GGGCAGCCUGGAACCAGUG
1486
CACUGGUUCCAGGCUGCCC
2101

[1526-1544] 3′UTR

GCAUCAGGCACCUGGAUUG
1487
CAAUCCAGGUGCCUGAUGC
2102

[1840-1858] 3′UTR

AGCCUGGAACCAGUGGCUA
1488
UAGCCACUGGUUCCAGGCU
2103

[1530-1548] 3′UTR

UGCACAUCACCCUCUGUGA
1489
UCACAGAGGGUGAUGUGCA
2104
Rh
[666-684] ORF

AGAUAUACCAACUUCUGCU
1490
AGCAGAAGUUGGUAUAUCU
2105
Rh
[2200-2218] 3′UTR

CUAGCUAAGAAACUUCCUA
1491
UAGGAAGUUUCUUAGCUAG
2106

[2245-2263] 3′UTR

CUCUCUUCUCCUAUUUUCA
1492
UGAAAAUAGGAGAAGAGAG
2107

[3323-3341] 3′UTR

AUCCAAGGGCAGCCUGGAA
1493
UUCCAGGCUGCCCUUGGAU
2108

[1520-1538] 3′UTR

AAAGGAUCUUUGAGUAGGU
1494
ACCUACUCAAAGAUCCUUU
2109

[90-3108] 3′UTR

CUGAGCACCACCCAGAAGA
1495
UCUUCUGGGUGGUGCUCAG
2110
Rh, Pg
[707-725] ORF

CCUGUUCUGGCAUCAGGCA
1496
UGCCUGAUGCCAGAACAGG
2111

[1831-1849] 3′UTR

UGUGUUUAUGCUGGAAUAU
1497
AUAUUCCAGCAUAAACACA
2112

[3496-3514] 3′UTR

AGGAAGAACUUUCUCGGUA
1498
UACCGAGAAAGUUCUUCCU
2113
Rh
[2331-2349] 3′UTR

AGAGCCUGAACCACAGGUA
1499
UACCUGUGGUUCAGGCUCU
2114
Rh, Rb, Cw,
[726-744] ORF

Ms, Pg

GCCAAGCAGGCAGCACUUA
1500
UAAGUGCUGCCUGCUUGGC
2115

[1276-1294] 3′UTR

GGGCUUUCUGCAUGUGACG
1501
CGUCACAUGCAGAAAGCCC
2116

[2011-2029] 3′UTR

ACCCAGAAGAAGAGCCUGA
1502
UCAGGCUCUUCUUCUGGGU
2117
Rh, Cw, Ms,
[716-734] ORF

Pg

CGCCUGCAUCAAGAGAAGU
1503
ACUUCUCUUGAUGCAGGCG
2118
Rh, Cw, Dg,
[874-892] ORF

Rt, Ms

GCAGAUAUACCAACUUCUG
1504
CAGAAGUUGGUAUAUCUGC
2119
Rh
[2198-2216] 3′UTR

UGGACCAGUCCAUGUGAUU
1505
AAUCACAUGGACUGGUCCA
2120
Rh
[2709-2727] 3′UTR

UGUAACAUUUACUCCUGUU
1506
AACAGGAGUAAAUGUUACA
2121
Rh
[2808-2826] 3′UTR

CAGCUGUAAUCAUUCCUGU
1507
ACAGGAAUGAUUACAGCUG
2122

[2869-2887] 3′UTR

GAGUUGUUGAAAGUUGACA
1508
UGUCAACUUUCAACAACUC
2123

[3550-3568] 3′UTR

AGACUGCGCAUGUCUCUGA
1509
UCAGAGACAUGCGCAGUCU
2124

[3572-3590] 3′UTR

UCCUGUGCUGUGUUUUUUA
1510
UAAAAAACACAGCACAGGA
2125
Rh
[2882-2900] 3′UTR

CCUUCUCCUUUUAGACAUG
1511
CAUGUCUAAAAGGAGAAGG
2126

[1106-1124] 3′UTR

CUAAGAAACUUCCUAGGGA
1512
UCCCUAGGAAGUUUCUUAG
2127

[2249-2267] 3′UTR

GCCAAGUUCUUCGCCUGCA
1513
UGCAGGCGAAGAACUUGGC
2128
Rh, Rb, Cw,
[863-881] ORF

Dg, Ms

GCUGGACGUUGGAGGAAAG
1514
CUUUCCUCCAACGUCCAGC
2129
Rt, Ms
[604-622] ORF

AGGCGUUUUGCAAUGCAGA
1515
UCUGCAUUGCAAAACGCCU
2130
Cw, Rt, Ms
[408-426] ORF

UGUGCAUUUUGCAGAAACU
1516
AGUUUCUGCAAAAUGCACA
2131
Rh, Rt, Ms
[1331-1349] 3′UTR

CAGCCUGGAACCAGUGGCU
1517
AGCCACUGGUUCCAGGCUG
2132

[1529-1547] 3′UTR

GCAAAAAAAGCCUCCAAGG
1518
CCUUGGAGGCUUUUUUUGC
2133

[994-1012] 3′UTR

ACCUGGAUUGAGUUGCACA
1519
UGUGCAACUCAAUCCAGGU
2134

[1849-1867] 3′UTR

CGUAAUUUAAAGCUCUGUU
1520
AACAGAGCUUUAAAUUACG
2135

[3438-3456] 3′UTR

CUGUGCUGUGUUUUUUAUU
1521
AAUAAAAAACACAGCACAG
2136
Rh
[2884-2902] 3′UTR

GGCACCAGGCCAAGUUCUU
1522
AAGAACUUGGCCUGGUGCC
2137
Rh, Rb, Rt, Ms
[855-873] ORF

CCUGUGGCCAACUGCAAAA
1523
UUUUGCAGUUGGCCACAGG
2138
Rh
[981-999] 3′UTR

GGUUUCGACUGGUCCAGCU
1524
AGCUGGACCAGUCGAAACC
2139
Rh
[1012-1030] 3′UTR

GAAUAAAACACUCAUCCCA
1525
UGGGAUGAGUGUUUUAUUC
2140
Rh
[1057-1075] 3′UTR

GAGUUGCAGAUAUACCAAC
1526
GUUGGUAUAUCUGCAACUC
2141
Rh
[2193-2211] 3′UTR

CUUCCUGUAUGGUGAUAUC
1527
GAUAUCACCAUACAGGAAG
2142

[2786-2804] 3′UTR

UUUGGUUCUCCAGUUCAAA
1528
UUUGAACUGGAGAACCAAA
2143

[59-3077] 3′UTR

GCCUGCAUCAAGAGAAGUG
1529
CACUUCUCUUGAUGCAGGC
2144
Rt, Ms
[875-893] ORF

GGCAACCCUAUCAAGAGGA
1530
UCCUCUUGAUAGGGUUGCC
2145

[488-506] ORF

AAGCGGUCAGUGAGAAGGA
1531
UCCUUCUCACUGACCGCUU
2146

[444-462] ORF

GUGGCUUUGGUGACACACU
1532
AGUGUGUCACCAAAGCCAC
2147

[2084-2102] 3′UTR

AGAUCUUGAUGACUUCCCU
1533
AGGGAAGUCAUCAAGAUCU
2148
Rh
[2595-2613] 3′UTR

GAGACGUGGGUCCAAGGUC
1534
GACCUUGGACCCACGUCUC
2149

[1141-1159] 3′UTR

UGACAUCAGCUGUAAUCAU
1535
AUGAUUACAGCUGAUGUCA
2150

[2863-2881] 3′UTR

GGGAUCUCCCAGCUGGGUU
1536
AACCCAGCUGGGAGAUCCC
2151

[1295-1313] 3′UTR

AGCACUUAGGGAUCUCCCA
1537
UGGGAGAUCCCUAAGUGCU
2152
Rh
[1287-1305] 3′UTR

GUCUUUGGUUCUCCAGUUC
1538
GAACUGGAGAACCAAAGAC
2153

[56-3074] 3′UTR

UAACCGUGCUGAGCAGAAA
1539
UUUCUGCUCAGCACGGUUA
2154

[3159-3177] 3′UTR

CUGGAUGGACUGGGUCACA
1540
UGUGACCCAGUCCAUCCAG
2155
Rh, Rb, Cw, Dg,
[820-838] ORF

Rt, Ms, Pg

GUGCUGGGAACACACAAGA
1541
UCUUGUGUGUUCCCAGCAC
2156

[3533-3551] 3′UTR

AGUGGGAGCCUCCCUCUGA
1542
UCAGAGGGAGGCUCCCACU
2157
Rh
[1593-1611] 3′UTR

GCAGGCAGCACUUAGGGAU
1543
AUCCCUAAGUGCUGCCUGC
2158
Rh
[1281-1299] 3′UTR

UAUUGGACUUGCUGCCGUA
1544
UACGGCAGCAAGUCCAAUA
2159

[3423-3441] 3′UTR

GAUCUUGAUGACUUCCCUU
1545
AAGGGAAGUCAUCAAGAUC
2160
Rh
[2596-2614] 3′UTR

ACGCCAGCUAAGCAUAGUA
1546
UACUAUGCUUAGCUGGCGU
2161

[2027-2045] 3′UTR

AGGACACUAUGGCCUGUUU
1547
AAACAGGCCAUAGUGUCCU
2162

[2122-2140] 3′UTR

GCCUGAACCACAGGUACCA
1548
UGGUACCUGUGGUUCAGGC
2163
Rh, Rb, Cw,
[729-747] ORF

Ms, Pg

UGGUUUGUUUUUGACAUCA
1549
UGAUGUCAAAAACAAACCA
2164
Rh
[2852-2870] 3′UTR

GUGGCAGCUGACAGAGGAA
1550
UUCCUCUGUCAGCUGCCAC
2165

[3202-3220] 3′UTR

CCAUCAAUCCUAUUAAUCC
1551
GGAUUAAUAGGAUUGAUGG
2166
Rh
[1564-1582] 3′UTR

GGACACUAUGGCCUGUUUU
1552
AAAACAGGCCAUAGUGUCC
2167

[2123-2141] 3′UTR

GACCUUCCGGUGCUGGGAA
1553
UUCCCAGCACCGGAAGGUC
2168

[3524-3542] 3′UTR

ACAUCCUGAGGACAGAAAA
1554
UUUUCUGUCCUCAGGAUGU
2169
Rh
[1920-1938] 3′UTR

AUGUAAACAUACACACGCA
1555
UGCGUGUGUAUGUUUACAU
2170
Rh
[2420-2438] 3 ′UTR

GCCUCCAAGGGUUUCGACU
1556
AGUCGAAACCCUUGGAGGC
2171
Rh
[1003-1021] 3′UTR

CUGCAUCAAGAGAAGUGAC
1557
GUCACUUCUCUUGAUGCAG
2172
Rt, Ms
[877-895] ORF

UGGAAGCAUUUGACCCAGA
1558
UCUGGGUCAAAUGCUUCCA
2173

[2955-2973] 3′UTR

AACACACAAGAGUUGUUGA
1559
UCAACAACUCUUGUGUGUU
2174

[3541-3559] 3′UTR

GGGAACUAGGGAACCUAUG
1560
CAUAGGUUCCCUAGUUCCC
2175
Rh
[2264-2282] 3′UTR

AUACAGGCACAUUAUGUAA
1561
UUACAUAAUGUGCCUGUAU
2176

[2407-2425] 3′UTR

GACGUGGGUCCAAGGUCCU
1562
AGGACCUUGGACCCACGUC
2177

[1143-1161] 3′UTR

GGGUUAGGAUAGGAAGAAC
1563
GUUCUUCCUAUCCUAACCC
2178

[2321-2339] 3′UTR

GGACGAGUGCCUCUGGAUG
1564
CAUCCAGAGGCACUCGUCC
2179
Rh, Rb, Cw
[808-826] ORF

AAAAAGCCUCCAAGGGUUU
1565
AAACCCUUGGAGGCUUUUU
2180

[998-1016] 3′UTR

CUUUGAGUAGGUUCGGUCU
1566
AGACCGAACCUACUCAAAG
2181

[97-3115] 3′UTR

GGCAGACUGGGAGGGUAUC
1567
GAUACCCUCCCAGUCUGCC
2182
Rh
[2620-2638] 3 ′UTR

GAAGGCUCUCCAUUUGGCA
1568
UGCCAAAUGGAGAGCCUUC
2183

[3271-3289] 3′UTR

GCCUCCCUCUGAGCCUUGU
1569
ACAAGGCUCAGAGGGAGGC
2184
Rh
[1600-1618] 3′UTR

ACAAAACAGGUUAAGAAGA
1570
UCUUCUUAACCUGUUUUGU
2185

[3178-3196] 3′UTR

CCUAUGUGUUCCCUCAGUG
1571
CACUGAGGGAACACAUAGG
2186

[2277-2295] 3′UTR

AAAGGGCCUGAGAAGGAUA
1572
UAUCCUUCUCAGGCCCUUU
2187

[539-557] ORF

GCAGACUGCGCAUGUCUCU
1573
AGAGACAUGCGCAGUCUGC
2188

[3570-3588] 3′UTR

CCCUCCCAGGCUUAGUGUU
1574
AACACUAAGCCUGGGAGGG
2189

[1956-1974] 3′UTR

CCUCCAAGGGUUUCGACUG
1575
CAGUCGAAACCCUUGGAGG
2190
Rh
[1004-1022] 3′UTR

GCUAGUUCUUGAAGGAGCC
1576
GGCUCCUUCAAGAACUAGC
2191

[1545-1563] 3′UTR

CUUGAUGACUUCCCUUUCU
1577
AGAAAGGGAAGUCAUCAAG
2192
Rh
[2599-2617] 3′UTR

AUUAAUCCUCAGAAUUCCA
1578
UGGAAUUCUGAGGAUUAAU
2193
Rh
[1575-1593] 3′UTR

GACCAGUCCAUGUGAUUUC
1579
GAAAUCACAUGGACUGGUC
2194
Rh
[2711-2729] 3′UTR

AGUGAGAAGGAAGUGGACU
1580
AGUCCACUUCCUUCUCACU
2195

[452-470] ORF

GAGAAUCUCUUGUUUCCUC
1581
GAGGAAACAAGAGAUUCUC
2196

[2358-2376] 3′UTR

GGCUCUCCAUUUGGCAUCG
1582
CGAUGCCAAAUGGAGAGCC
2197

[3274-3292] 3′UTR

CUUCUUGCCUGUUCUGGCA
1583
UGCCAGAACAGGCAAGAAG
2198

[1824-1842] 3′UTR

CUUUAUAUUUGAUCCACAC
1584
GUGUGGAUCAAAUAUAAAG
2199

[3128-3146] 3′UTR

GGGCCUGGAAAUGUGCAUU
1585
AAUGCACAUUUCCAGGCCC
2200
Rh
[1320-1338] 3′UTR

CUUUGGUGACACACUCACU
1586
AGUGAGUGUGUCACCAAAG
2201

[2088-2106] 3′UTR

CAGCCUAGGAAGGGAAGGA
1587
UCCUUCCCUUCCUAGGCUG
2202
Rh
[2053-2071] 3′UTR

CUCGCUGGACGUUGGAGGA
1588
UCCUCCAACGUCCAGCGAG
2203
Rt, Ms
[601-619] ORF

GCUUUAUCCGGGCUUGUGU
1589
ACACAAGCCCGGAUAAAGC
2204

[1873-1891] 3′UTR

UGGACUCUGGAAACGACAU
1590
AUGUCGUUUCCAGAGUCCA
2205
Rh
[465-483] ORF

GCAUCGUGGAAGCAUUUGA
1591
UCAAAUGCUUCCACGAUGC
2206
Rh
[2949-2967] 3′UTR

CCUAAAGUUGGUAAGAUGU
1592
ACAUCUUACCAACUUUAGG
2207
Rh
[2685-2703] 3′UTR

GUGGUCUUGCAAAAUGCUU
1593
AAGCAUUUUGCAAGACCAC
2208

[2466-2484] 3′UTR

CAAGGUCCCUUCCCUAGCU
1594
AGCUAGGGAAGGGACCUUG
2209

[1789-1807] 3′UTR

GCUUUGUAUCAUUCUUGAG
1595
CUCAAGAAUGAUACAAAGC
2210

[3592-3610] 3′UTR

GGGCUUCGAUCCUUGGGUG
1596
CACCCAAGGAUCGAAGCCC
2211
Rh
[1198-1216] 3′UTR

UCAUAAUGGACCAGUCCAU
1597
AUGGACUGGUCCAUUAUGA
2212
Rh
[2703-2721] 3′UTR

UAUAGUUUAAGAAGGCUCU
1598
AGAGCCUUCUUAAACUAUA
2213

[3261-3279] 3′UTR

UCGACAUCGAGGACCCAUA
1599
UAUGGGUCCUCGAUGUCGA
2214
Dg
[945-963] ORF

ACUUCUUUCUCAGCCUCCA
1600
UGGAGGCUGAGAAAGAAGU
2215

[2104-2122] 3′UTR

AUUCUCAGAUGAUAGGUGA
1601
UCACCUAUCAUCUGAGAAU
2216

[2170-2188] 3′UTR

UGAGAAGGAAGUGGACUCU
1602
AGAGUCCACUUCCUUCUCA
2217

[454-472] ORF

CAAAGCACCUGUUAAGACU
1603
AGUCUUAACAGGUGCUUUG
2218
Rh
[2523-2541] 3′UTR

GCGUUCCAGCCUCAGCUGA
1604
UCAGCUGAGGCUGGAACGC
2219

[1650-1668] 3′UTR

CCUGGGCGUGGUCUUGCAA
1605
UUGCAAGACCACGCCCAGG
2220

[2459-2477] 3′UTR

GUCUCUGAUGCUUUGUAUC
1606
GAUACAAAGCAUCAGAGAC
2221

[3583-3601] 3′UTR

CUGUGCCCUCCCAGGCUUA
1607
UAAGCCUGGGAGGGCACAG
2222

[1951-1969] 3′UTR

CCUCCAACCCAUAUAACAC
1608
GUGUUAUAUGGGUUGGAGG
2223

[2753-2771] 3′UTR

UUUGUAUCAUUCUUGAGCA
1609
UGCUCAAGAAUGAUACAAA
2224

[3594-3612] 3′UTR

GCCUUUAUAUUUGAUCCAC
1610
GUGGAUCAAAUAUAAAGGC
2225

[3126-3144] 3′UTR

AGGCCUACCAGGUCCCUUU
1611
AAAGGGACCUGGUAGGCCU
2226
Rh
[1378-1396] 3′UTR

GUUCUAAGCACAGCUCUCU
1612
AGAGAGCUGUGCUUAGAAC
2227

[3310-3328] 3′UTR

CUGUGUUUUUUAUUACCCU
1613
AGGGUAAUAAAAAACACAG
2228
Rh
[2889-2907] 3′UTR

CUAGGAAGGGAAGGAUUUU
1614
AAAAUCCUUCCCUUCCUAG
2229
Rh
[2057-2075] 3′UTR

CAGAUGGGCUGCGAGUGCA
1615
UGCACUCGCAGCCCAUCUG
2230
Ck, Rb, Rt
[746-764] ORF

CUGGCAUCAGGCACCUGGA
1616
UCCAGGUGCCUGAUGCCAG
2231

[1837-1855] 3′UTR

UGAUGCUUUGUAUCAUUCU
1617
AGAAUGAUACAAAGCAUCA
2232

[3588-3606] 3′UTR

AGUCCAGCCUAGGAAGGGA
1618
UCCCUUCCUAGGCUGGACU
2233
Rh
[2049-2067] 3′UTR

CAAAGAUUACCUAGCUAAG
1619
CUUAGCUAGGUAAUCUUUG
2234

[2235-2253] 3′UTR

AGAAGGAAGUGGACUCUGG
1620
CCAGAGUCCACUUCCUUCU
2235

[456-474] ORF

UGUACAGUGACCUAAAGUU
1621
AACUUUAGGUCACUGUACA
2236

[2675-2693] 3′UTR

TABLE B2

19-mer siTIMP2 Cross-Species

SEQ

SEQ

human-73858577

ID

ID

ORF:303-965

No.
Sense (5′>3′)
NO:
Antisense (5′>3′)
NO:
Other Sp

1
UUCGCCUGCAUCAAGAGAA
2237
UUCUCUUGAUGCAGGCGAA
2354
Rh, Cw, Dg, Ms
[872-890] ORF

2
GUGCAUUUUGCAGAAACUU
2238
AAGUUUCUGCAAAAUGCAC
2355
Rh, Rt, Ms
[1332-1350] 3′UTR

3
GGUACCAGAUGGGCUGCGA
2239
UCGCAGCCCAUCUGGUACC
2356
Rh, Ck, Rb, Rt
[741-759] ORF

4
GGUCUCGCUGGACGUUGGA
2240
UCCAACGUCCAGCGAGACC
2357
Rt, Ms
[598-616] ORF

5
UCGCCUGCAUCAAGAGAAG
2241
CUUCUCUUGAUGCAGGCGA
2358
Rh, Cw, Dg, Ms
[873-891] ORF

6
CUUCCUGGAAACAGCAUGA
2242
UCAUGCUGUUUCCAGGAAG
2359
Rh, Rb, Rt, Ms
[1040-1058] 3′UTR

7
GGGCACCAGGCCAAGUUCU
2243
AGAACUUGGCCUGGUGCCC
2360
Rh, Rb, Rt, Ms
[854-872] ORF

8
CCAGAAGAAGAGCCUGAAC
2244
GUUCAGGCUCUUCUUCUGG
2361
Rh, Rb, Cw, Ms, Pg
[718-736] ORF

9
UGGACGUUGGAGGAAAGAA
2245
UUCUUUCCUCCAACGUCCA
2362
Rt, Ms
[606-624] ORF

10
GGGCUGCGAGUGCAAGAUC
2246
GAUCUUGCACUCGCAGCCC
2363
Ck, Rb, Rt
[751-769] ORF

11
CCACCCAGAAGAAGAGCCU
2247
AGGCUCUUCUUCUGGGUGG
2364
Rh, Ck, Cw, Rt, Ms, Pg
[714-732] ORF

12
AUGGGCUGCGAGUGCAAGA
2248
UCUUGCACUCGCAGCCCAU
2365
Ck, Rb, Rt
[749-767] ORF

13
AUGGACUGGGUCACAGAGA
2249
UCUCUGUGACCCAGUCCAU
2366
Rh, Rt, Ms, Pg
[824-842] ORF

14
UGGGCUGCGAGUGCAAGAU
2250
AUCUUGCACUCGCAGCCCA
2367
Ck, Rb, Rt
[750-768] ORF

15
ACGUUGGAGGAAAGAAGGA
2251
UCCUUCUUUCCUCCAACGU
2368
Rt, Ms
[609-627] ORF

16
GACGUUGGAGGAAAGAAGG
2252
CCUUCUUUCCUCCAACGUC
2369
Rt, Ms
[608-626] ORF

17
AGGCCAAGUUCUUCGCCUG
2253
CAGGCGAAGAACUUGGCCU
2370
Rh, Rb, Cw, Dg, Ms
[861-879] ORF

18
GAAGAAGAGCCUGAACCAC
2254
GUGGUUCAGGCUCUUCUUC
2371
Rh, Rb, Cw, Ms, Pg
[721-739] ORF

19
GCACCCGCAACAGGCGUUU
2255
AAACGCCUGUUGCGGGUGC
2372
Cw, Dg, Rt, Ms
[397-415] ORF

20
UUCUUCGCCUGCAUCAAGA
2256
UCUUGAUGCAGGCGAAGAA
2373
Rh, Rb, Cw, Dg, Ms
[869-887] ORF

21
GAGCCUGAACCACAGGUAC
2257
GUACCUGUGGUUCAGGCUC
2374
Rh, Rb, Cw, Ms, Pg
[727-745] ORF

22
CUUCGCCUGCAUCAAGAGA
2258
UCUCUUGAUGCAGGCGAAG
2375
Rh, Rb, Cw, Dg, Ms
[871-889] ORF

23
UGGAAACAGCAUGAAUAAA
2259
UUUAUUCAUGCUGUUUCCA
2376
Rh, Rb, Rt, Ms
[1045-1063] 3′UTR

24
GACAUCCCUUCCUGGAAAC
2260
GUUUCCAGGAAGGGAUGUC
2377
Rh, Rt, Ms
[1033-1051] 3′UTR

25
GUUCUUCGCCUGCAUCAAG
2261
CUUGAUGCAGGCGAAGAAC
2378
Rh, Rb, Cw, Dg, Ms
[868-886] ORF

26
AAGUUCUUCGCCUGCAUCA
2262
UGAUGCAGGCGAAGAACUU
2379
Rh, Rb, Cw, Dg, Ms
[866-884] ORF

27
CCCUUCCUGGAAACAGCAU
2263
AUGCUGUUUCCAGGAAGGG
2380
Rh, Rb, Rt, Ms
[1038-1056] 3′UTR

28
CGCUCGGCCUCCUGCUGCU
2264
AGCAGCAGGAGGCCGAGCG
2381
Dg, Rt, Ms
[333-351] ORF

29
UGAACCACAGGUACCAGAU
2265
AUCUGGUACCUGUGGUUCA
2382
Rh, Rb, Cw, Ms, Pg
[732-750] ORF

30
CUGAACCACAGGUACCAGA
2266
UCUGGUACCUGUGGUUCAG
2383
Rh, Rb, Cw, Ms, Pg
[731-749] ORF

31
CAGAAGAAGAGCCUGAACC
2267
GGUUCAGGCUCUUCUUCUG
2384
Rh, Rb, Cw, Ms, Pg
[719-737] ORF

32
UCCUGGAAACAGCAUGAAU
2268
AUUCAUGCUGUUUCCAGGA
2385
Rh, Rb, Rt, Ms
[1042-1060] 3′UTR

33
GAUGGACUGGGUCACAGAG
2269
CUCUGUGACCCAGUCCAUC
2386
Rh, Rt, Ms, Pg
[823-841] ORF

34
GCCGACGCCUGCAGCUGCU
2270
AGCAGCUGCAGGCGUCGGC
2387
Cw, Dg, Rt, Ms
[371-389] ORF

35
CAGGCGUUUUGCAAUGCAG
2271
CUGCAUUGCAAAACGCCUG
2388
Cw, Rt, Ms
[407-425] ORF

36
UCAAGCAGAUAAAGAUGUU
2272
AACAUCUUUAUCUGCUUGA
2389
Cw, Dg, Rt, Ms, Pg
[519-537] ORF

37
GAACCACAGGUACCAGAUG
2273
CAUCUGGUACCUGUGGUUC
2390
Rh, Rb, Cw, Rt, Ms, Pg
[733-751] ORF

38
CACCCAGAAGAAGAGCCUG
2274
CAGGCUCUUCUUCUGGGUG
2391
Rh, Ck, Cw, Rt, Ms, Pg
[715-733] ORF

39
CCUUCCUGGAAACAGCAUG
2275
CAUGCUGUUUCCAGGAAGG
2392
Rh, Rb, Rt, Ms
[1039-1057] 3′UTR

40
CAACAGGCGUUUUGCAAUG
2276
CAUUGCAAAACGCCUGUUG
2393
Cw, Rt, Ms
[404-422] ORF

41
CACAGGUACCAGAUGGGCU
2277
AGCCCAUCUGGUACCUGUG
2394
Rh, Rb, Cw, Rt, Ms, Pg
[737-755] ORF

42
UCCCUUCCUGGAAACAGCA
2278
UGCUGUUUCCAGGAAGGGA
2395
Rh, Rb, Rt, Ms
[1037-1055] 3′UTR

43
UGAGAUCAAGCAGAUAAAG
2279
CUUUAUCUGCUUGAUCUCA
2396
Rh, Cw, Dg, Rt, Ms
[514-532] ORF

44
GGUGCACCCGCAACAGGCG
2280
CGCCUGUUGCGGGUGCACC
2397
Cw, Dg, Rt, Ms
[394-412] ORF

45
AGUGCCUCUGGAUGGACUG
2281
CAGUCCAUCCAGAGGCACU
2398
Rh, Rb, Cw, Dg, Rt, Ms
[813-831] ORF

46
AAGCAGAUAAAGAUGUUCA
2282
UGAACAUCUUUAUCUGCUU
2399
Cw, Dg, Rt, Ms, Pg
[521-539] ORF

47
UGCACCCGCAACAGGCGUU
2283
AACGCCUGUUGCGGGUGCA
2400
Cw, Dg, Rt, Ms
[396-414] ORF

48
CACCCGCAACAGGCGUUUU
2284
AAAACGCCUGUUGCGGGUG
2401
Cw, Rt, Ms
[398-416] ORF

49
CUGGACGUUGGAGGAAAGA
2285
UCUUUCCUCCAACGUCCAG
2402
Rt, Ms
[605-623] ORF

50
AUCCCUUCCUGGAAACAGC
2286
GCUGUUUCCAGGAAGGGAU
2403
Rh, Rb, Rt, Ms
[1036-1054] 3′UTR

51
ACAGGCGUUUUGCAAUGCA
2287
UGCAUUGCAAAACGCCUGU
2404
Cw, Rt, Ms
[406-424] ORF

52
GAUGGGCUGCGAGUGCAAG
2288
CUUGCACUCGCAGCCCAUC
2405
Ck, Rb, Rt
[748-766] ORF

53
AGCCUGAACCACAGGUACC
2289
GGUACCUGUGGUUCAGGCU
2406
Rh, Rb, Cw, Ms, Pg
[728-746] ORF

54
CCUCUGGAUGGACUGGGUC
2290
GACCCAGUCCAUCCAGAGG
2407
Rh, Rb, Cw, Dg, Rt, Ms, Pg
[817-835] ORF

55
CGGGCACCAGGCCAAGUUC
2291
GAACUUGGCCUGGUGCCCG
2408
Rh, Rb, Rt, Ms
[853-871] ORF

56
CAGGCCAAGUUCUUCGCCU
2292
AGGCGAAGAACUUGGCCUG
2409
Rh, Rb, Cw, Dg, Ms
[860-878] ORF

57
CAAGUUCUUCGCCUGCAUC
2293
GAUGCAGGCGAAGAACUUG
2410
Rh, Rb, Cw, Dg, Ms
[865-883] ORF

58
ACUUCAUCGUGCCCUGGGA
2294
UCCCAGGGCACGAUGAAGU
2411
Rh, Rb, Cw, Dg, Pg
[684-702] ORF

59
ACAUCCCUUCCUGGAAACA
2295
UGUUUCCAGGAAGGGAUGU
2412
Rh, Rt, Ms
[1034-1052] 3′UTR

60
UACCAGAUGGGCUGCGAGU
2296
ACUCGCAGCCCAUCUGGUA
2413
Rh, Ck, Rb, Rt
[743-761] ORF

61
GGCCAAGUUCUUCGCCUGC
2297
GCAGGCGAAGAACUUGGCC
2414
Rh, Rb, Cw, Dg, Ms
[862-880] ORF

62
CCAGAUGGGCUGCGAGUGC
2298
GCACUCGCAGCCCAUCUGG
2415
Rh, Ck, Rb, Rt
[745-763] ORF

63
GUGACUUCAUCGUGCCCUG
2299
CAGGGCACGAUGAAGUCAC
2416
Rh, Rb, Cw, Dg, Pg
[681-699] ORF

64
UCGCUGGACGUUGGAGGAA
2300
UUCCUCCAACGUCCAGCGA
2417
Rt, Ms
[602-620] ORF

65
AUCAAGCAGAUAAAGAUGU
2301
ACAUCUUUAUCUGCUUGAU
2418
Cw, Dg, Rt, Ms, Pg
[518-536] ORF

66
GUACCAGAUGGGCUGCGAG
2302
CUCGCAGCCCAUCUGGUAC
2419
Rh, Ck, Rb, Rt
[742-760] ORF

67
CGAGUGCCUCUGGAUGGAC
2303
GUCCAUCCAGAGGCACUCG
2420
Rh, Rb, Cw, Dg, Rt, Ms
[811-829] ORF

68
UCUGGAUGGACUGGGUCAC
2304
GUGACCCAGUCCAUCCAGA
2421
Rh, Rb, Cw, Dg, Rt, Ms, Pg
[819-837] ORF

69
ACCAGAUGGGCUGCGAGUG
2305
CACUCGCAGCCCAUCUGGU
2422
Rh, Ck, Rb, Rt
[744-762] ORF

70
ACAGGUACCAGAUGGGCUG
2306
CAGCCCAUCUGGUACCUGU
2423
Rh, Rb, Cw, Rt, Ms, Pg
[738-756] ORF

71
GAAGAGCCUGAACCACAGG
2307
CCUGUGGUUCAGGCUCUUC
2424
Rh, Rb, Cw, Ms, Pg
[724-742] ORF

72
GUGCACCCGCAACAGGCGU
2308
ACGCCUGUUGCGGGUGCAC
2425
Cw, Dg, Rt, Ms
[395-413] ORF

73
UGGAUGGACUGGGUCACAG
2309
CUGUGACCCAGUCCAUCCA
2426
Rh, Rt, Ms, Pg
[821-839] ORF

74
CAAGCAGAUAAAGAUGUUC
2310
GAACAUCUUUAUCUGCUUG
2427
Cw, Dg, Rt, Ms, Pg
[520-538] ORF

75
GUGCCUCUGGAUGGACUGG
2311
CCAGUCCAUCCAGAGGCAC
2428
Rh, Rb, Cw, Dg, Rt, Ms
[814-832] ORF

76
CAUCCCUUCCUGGAAACAG
2312
CUGUUUCCAGGAAGGGAUG
2429
Rh, Rb, Rt, Ms
[1035-1053] 3′UTR

77
CACCAGGCCAAGUUCUUCG
2313
CGAAGAACUUGGCCUGGUG
2430
Rh, Rb, Cw, Ms
[857-875] ORF

78
CCUGAACCACAGGUACCAG
2314
CUGGUACCUGUGGUUCAGG
2431
Rh, Rb, Cw, Ms, Pg
[730-748] ORF

79
AACCACAGGUACCAGAUGG
2315
CCAUCUGGUACCUGUGGUU
2432
Rh, Rb, Cw, Rt, Ms, Pg
[734-752] ORF

80
GUCUCGCUGGACGUUGGAG
2316
CUCCAACGUCCAGCGAGAC
2433
Rt, Ms
[599-617] ORF

81
AGAGUUUAUCUACACGGCC
2317
GGCCGUGUAGAUAAACUCU
2434
Dg, Ms, Pg
[559-577] ORF

82
UUCCUGGAAACAGCAUGAA
2318
UUCAUGCUGUUUCCAGGAA
2435
Rh, Rb, Rt, Ms
[1041-1059] 3′UTR

83
GAUAAAGAUGUUCAAAGGG
2319
CCCUUUGAACAUCUUUAUC
2436
Dg, Rt, Ms
[526-544] ORF

84
UCUUCGCCUGCAUCAAGAG
2320
CUCUUGAUGCAGGCGAAGA
2437
Rh, Rb, Cw, Dg, Ms
[870-888] ORF

85
UGGCGCUCGGCCUCCUGCU
2321
AGCAGGAGGCCGAGCGCCA
2438
Dg, Rt, Ms
[330-348] ORF

86
CCCGGUGCACCCGCAACAG
2322
CUGUUGCGGGUGCACCGGG
2439
Cw, Dg, Rt, Ms
[391-409] ORF

87
CCCGCAACAGGCGUUUUGC
2323
GCAAAACGCCUGUUGCGGG
2440
Cw, Rt, Ms
[400-418] ORF

88
CAGGGCCAAAGCGGUCAGU
2324
ACUGACCGCUUUGGCCCUG
2441
Rb, Dg
[436-454] ORF

89
AAGAGCCUGAACCACAGGU
2325
ACCUGUGGUUCAGGCUCUU
2442
Rh, Rb, Cw, Ms, Pg
[725-743] ORF

90
ACCACAGGUACCAGAUGGG
2326
CCCAUCUGGUACCUGUGGU
2443
Rh, Rb, Cw, Rt, Ms, Pg
[735-753] ORF

91
CAGGUACCAGAUGGGCUGC
2327
GCAGCCCAUCUGGUACCUG
2444
Rh, Rb, Cw, Dg, Rt, Ms, Pg
[739-757] ORF

92
CGGUGCACCCGCAACAGGC
2328
GCCUGUUGCGGGUGCACCG
2445
Cw, Dg, Rt, Ms
[393-411] ORF

93
GCUCGGCCUCCUGCUGCUG
2329
CAGCAGCAGGAGGCCGAGC
2446
Dg, Rt, Ms
[334-352] ORF

94
GACGCCUGCAGCUGCUCCC
2330
GGGAGCAGCUGCAGGCGUC
2447
Cw, Dg, Rt, Ms
[374-392] ORF

95
ACCCGCAACAGGCGUUUUG
2331
CAAAACGCCUGUUGCGGGU
2448
Cw, Rt, Ms
[399-417] ORF

96
CCGGUGCACCCGCAACAGG
2332
CCUGUUGCGGGUGCACCGG
2449
Cw, Dg, Rt, Ms
[392-410] ORF

97
UCUCGCUGGACGUUGGAGG
2333
CCUCCAACGUCCAGCGAGA
2450
Rt, Ms
[600-618] ORF

98
AACAGCAUGAAUAAAACAC
2334
GUGUUUUAUUCAUGCUGUU
2451
Rh, Rt, Ms
[1049-1067] 3′UTR

99
CCACAGGUACCAGAUGGGC
2335
GCCCAUCUGGUACCUGUGG
2452
Rh, Rb, Cw, Rt, Ms, Pg
[736-754] ORF

100
CCGACGCCUGCAGCUGCUC
2336
GAGCAGCUGCAGGCGUCGG
2453
Cw, Dg, Rt, Ms
[372-390] ORF

101
UUCAUCGUGCCCUGGGACA
2337
UGUCCCAGGGCACGAUGAA
2454
Rh, Rb, Cw, Dg, Pg
[686-704] ORF

102
CUUCAUCGUGCCCUGGGAC
2338
GUCCCAGGGCACGAUGAAG
2455
Rh, Rb, Cw, Dg, Pg
[685-703] ORF

103
CGACGCCUGCAGCUGCUCC
2339
GGAGCAGCUGCAGGCGUCG
2456
Cw, Dg, Rt, Ms
[373-391] ORF

104
UGCCUCUGGAUGGACUGGG
2340
CCCAGUCCAUCCAGAGGCA
2457
Rh, Rb, Cw, Dg, Rt, MsORF
[815-833] ORF

105
ACCAGGCCAAGUUCUUCGC
2341
GCGAAGAACUUGGCCUGGU
2458
Rh, Rb, Cw, Ms
[858-876] ORF

106
AGGUACCAGAUGGGCUGCG
2342
CGCAGCCCAUCUGGUACCU
2459
Rh, Ck, Rb, Rt
[740-758] ORF

107
CUCGGCCUCCUGCUGCUGG
2343
CCAGCAGCAGGAGGCCGAG
2460
Dg, Rt
[335-353] ORF

108
AACAGGCGUUUUGCAAUGC
2344
GCAUUGCAAAACGCCUGUU
2461
Cw, Rt, Ms
[405-423] ORF

109
UCGGCCUCCUGCUGCUGGC
2345
GCCAGCAGCAGGAGGCCGA
2462
Dg, Rt
[336-354] ORF

110
CCAGGCCAAGUUCUUCGCC
2346
GGCGAAGAACUUGGCCUGG
2463
Rh, Rb, Cw, Dg, Ms
[859-877] ORF

111
UGUGACUUCAUCGUGCCCU
2347
AGGGCACGAUGAAGUCACA
2464
Rh, Rb, Cw, Dg, Pg
[680-698] ORF

112
GACUUCAUCGUGCCCUGGG
2348
CCCAGGGCACGAUGAAGUC
2465
Rh, Rb, Cw, Dg, Pg
[683-701] ORF

113
CUGUGACUUCAUCGUGCCC
2349
GGGCACGAUGAAGUCACAG
2466
Rh, Rb, Cw, Dg, Pg
[679-697] ORF

114
UGACUUCAUCGUGCCCUGG
2350
CCAGGGCACGAUGAAGUCA
2467
Rh, Rb, Cw, Dg, Pg
[682-700] ORF

616
GCAGGAGUUUCUCGACAUC
2351
GAUGUCGAGAAACUCCUGC
2468
Dg, Ck
[934-952] ORF

617
GCACCACCCAGAAGAAGAG
2352
CUCUUCUUCUGGGUGGUGC
2469
Pg, Rh
[711-729] ORF

618
AGCUCUGACAUCCCUUCCU
2353
AGGAAGGGAUGUCAGAGCU
2470
Rh
[1027-1045] 3′UTR

TABLE B3

Preferred 19-mer siTIMP2

SEQ

SEQ

ID

ID

siTIMP2_pNo.
Sense (5′>3′)
NO:
Antisense (5′>3′)
NO:
length
position

siTIMP2_p4
GGCUGCGAGUGCAAGAUCA
2471
UGAUCUUGCACUCGCAGCC
2524
19
[752-770] ORF

siTIMP2_p16
GUAUGAGAUCAAGCAGAUA
2472
UAUCUGCUUGAUCUCAUAC
2525
19
[511-529] ORF

siTIMP2_p17
GAGGAAAGAAGGAAUAUCU
2473
AGAUAUUCCUUCUUUCCUC
2526
19
[615-633] ORF

siTIMP2_p18
CCUGCAUCAAGAGAAGUGA
2474
UCACUUCUCUUGAUGCAGG
2527
19
[876-894] ORF

siTIMP2_p20
AUGAGAUCAAGCAGAUAAA
2475
UUUAUCUGCUUGAUCUCAU
2528
19
[513-531] ORF

siTIMP2_p24
GUUGGAGGAAAGAAGGAAU
2476
AUUCCUUCUUUCCUCCAAC
2529
19
[611-629] ORF

siTIMP2_p25
ACUGGGUCACAGAGAAGAA
2477
UUCUUCUCUGUGACCCAGU
2530
19
[828-846] ORF

siTIMP2_p27
CUCUGGAUGGACUGGGUCA
2478
UGACCCAGUCCAUCCAGAG
2531
19
[818-836] ORF

siTIMP2_p29
GGCGUUUUGCAAUGCAGAU
2479
AUCUGCAUUGCAAAACGCC
2532
19
[409-427] ORF

siTIMP2_p30
GCCUCUGGAUGGACUGGGU
2480
ACCCAGUCCAUCCAGAGGC
2533
19
[816-834] ORF

siTIMP2_p33
GGAGGAAAGAAGGAAUAUC
2481
GAUAUUCCUUCUUUCCUCC
2534
19
[614-632] ORF

siTIMP2_p35
GGACUGGGUCACAGAGAAG
2482
CUUCUCUGUGACCCAGUCC
2535
19
[826-844] ORF

siTIMP2_p37
GGACGUUGGAGGAAAGAAG
2483
CUUCUUUCCUCCAACGUCC
2536
19
[607-625] ORF

siTIMP2_p38
CGUUGGAGGAAAGAAGGAA
2484
UUCCUUCUUUCCUCCAACG
2537
19
[610-628] ORF

siTIMP2_p39
CUGACAUCCCUUCCUGGAA
2485
UUCCAGGAAGGGAUGUCAG
2538
19
[1031-1049]

3′UTR

siTIMP2_p40
UGACAUCCCUUCCUGGAAA
2486
UUUCCAGGAAGGGAUGUCA
2539
19
[1032-1050]

3′UTR

siTIMP2_p41
AGAUGGGCUGCGAGUGCAA
2487
UUGCACUCGCAGCCCAUCU
2540
19
[747-765] ORF

siTIMP2_p44
GGGUCUCGCUGGACGUUGG
2488
CCAACGUCCAGCGAGACCC
2541
19
[597-615] ORF

siTIMP2_p46
GAGUGCCUCUGGAUGGACU
2489
AGUCCAUCCAGAGGCACUC
2542
19
[812-830] ORF

siTIMP2_p51
AGCAGAUAAAGAUGUUCAA
2490
UUGAACAUCUUUAUCUGCU
2543
19
[522-540] ORF

siTIMP2_p55
GCAACAGGCGUUUUGCAAU
2491
AUUGCAAAACGCCUGUUGC
2544
19
[403-421] ORF

siTIMP2_p61
GCUGGACGUUGGAGGAAAG
2492
CUUUCCUCCAACGUCCAGC
2545
19
[604-622] ORF

siTIMP2_p62
UGUGCAUUUUGCAGAAACU
2493
AGUUUCUGCAAAAUGCACA
2546
19
[1331-1349]

3′UTR

siTIMP2_p64
GGCACCAGGCCAAGUUCUU
2494
AAGAACUUGGCCUGGUGCC
2547
19
[855-873] ORF

siTIMP2_p65
GCCUGCAUCAAGAGAAGUG
2495
CACUUCUCUUGAUGCAGGC
2548
19
[875-893] ORF

siTIMP2_p67
CUGGAUGGACUGGGUCACA
2496
UGUGACCCAGUCCAUCCAG
2549
19
[820-838] ORF

siTIMP2_p68
CUGCAUCAAGAGAAGUGAC
2497
GUCACUUCUCUUGAUGCAG
2550
19
[877-895] ORF

siTIMP2_p69
CUCGCUGGACGUUGGAGGA
2498
UCCUCCAACGUCCAGCGAG
2551
19
[601-619] ORF

siTIMP2_p71
CAGAUGGGCUGCGAGUGCA
2499
UGCACUCGCAGCCCAUCUG
2552
19
[746-764] ORF

siTIMP2_p75
GUGCAUUUUGCAGAAACUU
2500
AAGUUUCUGCAAAAUGCAC
2553
19
[1332-1350]

3′UTR

siTIMP2_p76
GGUACCAGAUGGGCUGCGA
2501
UCGCAGCCCAUCUGGUACC
2554
19
[741-759] ORF

siTIMP2_p78
GGUCUCGCUGGACGUUGGA
2502
UCCAACGUCCAGCGAGACC
2555
19
[598-616] ORF

siTIMP2_p79
CUUCCUGGAAACAGCAUGA
2503
UCAUGCUGUUUCCAGGAAG
2556
19
[1040-1058]

3′UTR

siTIMP2_p82
GGGCACCAGGCCAAGUUCU
2504
AGAACUUGGCCUGGUGCCC
2557
19
[854-872] ORF

siTIMP2_p83
GUCACAGAGAAGAACAUCA
2505
UGAUGUUCUUCUCUGUGAC
2558
19
[833-851] ORF

siTIMP2_p84
AGGAGUUUCUCGACAUCGA
2506
UCGAUGUCGAGAAACUCCU
2559
19
[936-954] ORF

siTIMP2_p85
CCCAGAAGAAGAGCCUGAA
2507
UUCAGGCUCUUCUUCUGGG
2560
19
[717-735] ORF

siTIMP2_p86
GGGUCACAGAGAAGAACAU
2508
AUGUUCUUCUCUGUGACCC
2561
19
[831-849] ORF

siTIMP2_p87
CCAAGUUCUUCGCCUGCAU
2509
AUGCAGGCGAAGAACUUGG
2562
19
[864-882] ORF

siTIMP2_p88
AGCACCACCCAGAAGAAGA
2510
UCUUCUUCUGGGUGGUGCU
2563
19
[710-728] ORF

siTIMP2_p89
GUUUUGCAAUGCAGAUGUA
2511
UACAUCUGCAUUGCAAAAC
2564
19
[412-430] ORF

siTIMP2_p90
AGCAGGAGUUUCUCGACAU
2512
AUGUCGAGAAACUCCUGCU
2565
19
[933-951] ORF

siTIMP2_p91
GGAGUUUCUCGACAUCGAG
2513
CUCGAUGUCGAGAAACUCC
2566
19
[937-955] ORF

siTIMP2_p92
GCCUGAACCACAGGUACCA
2514
UGGUACCUGUGGUUCAGGC
2567
19
[729-747] ORF

siTIMP2_p93
UUCGCCUGCAUCAAGAGAA
2515
UUCUCUUGAUGCAGGCGAA
2568
19
[872-890] ORF

siTIMP2_p94
AGAGCCUGAACCACAGGUA
2516
UACCUGUGGUUCAGGCUCU
2569
19
[726-744] ORF

siTIMP2_p95
GCAGGAGUUUCUCGACAUC
2517
GAUGUCGAGAAACUCCUGC
2570
19
[934-952] ORF

siTIMP2_p96
GCACCACCCAGAAGAAGAG
2518
CUCUUCUUCUGGGUGGUGC
2571
19
[711-729] ORF

siTIMP2_p97
GGACGAGUGCCUCUGGAUG
2519
CAUCCAGAGGCACUCGUCC
2572
19
[808-826] ORF

siTIMP2_p98
GACUGGUCCAGCUCUGACA
2520
UGUCAGAGCUGGACCAGUC
2573
19
[1018-1036]

3′UTR

siTIMP2_p99
ACAUCACCCUCUGUGACUU
2521
AAGUCACAGAGGGUGAUGU
2574
19
[669-687] ORF

siTIMP2_p100
CCGGACGAGUGCCUCUGGA
2522
UCCAGAGGCACUCGUCCGG
2575
19
[806-824] ORF

siTIMP2_p101
UCGCCUGCAUCAAGAGAAG
2523
CUUCUCUUGAUGCAGGCGA
2576
19
[873-891] ORF

SiTIMP2_p102
GGAAGAACUUUCUCGGUAA
1007
UUACCGAGAAAGUUCUUCC
1622
19
[2332-2350]

3′UTR

TABLE B4

19 mer siTIMP2 with lowest predicted OT effect

SEQ

SEQ

ID

ID
No. in

Cross species:
Ranking
Sense (5′>3′)
NO:
Antisense (5′>3′)
NO:
Table B3

H/Rt
4
CUCUGGAUGGACUGGGUCA
2478
UGACCCAGUCCAUCCAGAG
2531
siTIMP2_p27

H/Rt
3
GGCGUUUUGCAAUGCAGAU
2479
AUCUGCAUUGCAAAACGCC
2532
siTIMP2_p29

H/Rt
4
GCCUCUGGAUGGACUGGGU
2480
ACCCAGUCCAUCCAGAGGC
2533
siTIMP2_p30

H/Rt
4
CUGACAUCCCUUCCUGGAA
2485
UUCCAGGAAGGGAUGUCAG
2538
siTIMP2_p39

H/Rt
3
UGACAUCCCUUCCUGGAAA
2486
UUUCCAGGAAGGGAUGUCA
2539
siTIMP2_p40

H/Rt
4
AGAUGGGCUGCGAGUGCAA
2487
UUGCACUCGCAGCCCAUCU
2540
siTIMP2_p41

H/Rt
4
GAGUGCCUCUGGAUGGACU
2489
AGUCCAUCCAGAGGCACUC
2542
siTIMP2_p46

H/Rt
2
GCAACAGGCGUUUUGCAAU
2491
AUUGCAAAACGCCUGUUGC
2544
siTIMP2_p55

H/Rt
4
UGUGCAUUUUGCAGAAACU
2493
AGUUUCUGCAAAAUGCACA
2546
siTIMP2_p62

H/Rt
3
CUGCAUCAAGAGAAGUGAC
2497
GUCACUUCUCUUGAUGCAG
2550
siTIMP2_p68

H/Rt
1
CUCGCUGGACGUUGGAGGA
2498
UCCUCCAACGUCCAGCGAG
2551
siTIMP2_p69

H/Rt
4
CAGAUGGGCUGCGAGUGCA
2499
UGCACUCGCAGCCCAUCUG
2552
siTIMP2_p71

H/Rt
2
GGUACCAGAUGGGCUGCGA
2501
UCGCAGCCCAUCUGGUACC
2554
siTIMP2_p76

H/Rt
2
GGUCUCGCUGGACGUUGGA
2502
UCCAACGUCCAGCGAGACC
2555
siTIMP2_p78

H/Rt (Rt Cross 1MM)
4
GUUUUGCAAUGCAGAUGUA
2511
UACAUCUGCAUUGCAAAAC
2564
siTIMP2_p89

H/Rt (Rt Cross 1MM)
3
GGAGUUUCUCGACAUCGAG
2513
CUCGAUGUCGAGAAACUCC
2566
siTIMP2_p91

H/Rt (Rt Cross 1MM)
2
UUCGCCUGCAUCAAGAGAA
2515
UUCUCUUGAUGCAGGCGAA
2568
siTIMP2_p93

H/Rt (Rt Cross 1MM)
4
GCAGGAGUUUCUCGACAUC
2517
GAUGUCGAGAAACUCCUGC
2570
siTIMP2_p95

H/Rt (Rt Cross 1MM)
3
GGACGAGUGCCUCUGGAUG
2519
CAUCCAGAGGCACUCGUCC
2572
siTIMP2_p97

H/Rt (Rt Cross 1MM)
4
GACUGGUCCAGCUCUGACA
2520
UGUCAGAGCUGGACCAGUC
2573
siTIMP2_p98

H/Rt (Rt Cross 1MM)
2
CCGGACGAGUGCCUCUGGA
2522
UCCAGAGGCACUCGUCCGG
2575
siTIMP2_p100

TABLE B5

18-mer siTIMP2

SEQ

SEQ

ID
human-73858577
ID

No.
Sense (5′>3′)
NO:
Antisense (5>3′)
NO:
Other Sp
ORF:303-965

1
CCAUGUGAUUUCAGUAUA
2577
UAUACUGAAAUCACAUGG
3612
Rh
[2718-2735] 3′UTR

2
CUCUGAGCCUUGUAGAAA
2578
UUUCUACAAGGCUCAGAG
3613
Rh
[1606-1623] 3′UTR

3
GGUAAUGAUAAGGAGAAU
2579
AUUCUCCUUAUCAUUACC
3614

[2346-2363] 3′UTR

4
GAUGCUUUGUAUCAUUCU
2580
AGAAUGAUACAAAGCAUC
3615

[3589-3606] 3′UTR

5
GGGUCUGGAGGGAGACGU
2581
ACGUCUCCCUCCAGACCC
3616

[1130-1147] 3′UTR

6
GAUCCAGUAUGAGAUCAA
2582
UUGAUCUCAUACUGGAUC
3617
Rh, Rb
[505-522] ORF

7
CUGAGAAGGAUAUAGAGU
2583
ACUCUAUAUCCUUCUCAG
3618

[546-563] ORF

8
GUAUCAUUCUUGAGCAAU
2584
AUUGCUCAAGAAUGAUAC
3619

[3597-3614] 3′UTR

9
GCCUGAGAAGGAUAUAGA
2585
UCUAUAUCCUUCUCAGGC
3620

[544-561] ORF

10
GGCUAGUUCUUGAAGGAG
2586
CUCCUUCAAGAACUAGCC
3621

[1544-1561] 3′UTR

11
GGGUCACAGAGAAGAACA
2587
UGUUCUUCUCUGUGACCC
3622
Rh
[831-848] ORF

12
GGAUCUUUGAGUAGGUUC
2588
GAACCUACUCAAAGAUCC
3623

[93-3110] 3′UTR

13
GGAAGUGGACUCUGGAAA
2589
UUUCCAGAGUCCACUUCC
3624

[460-477] ORF

14
GAACCUGAGUUGCAGAUA
2590
UAUCUGCAACUCAGGUUC
3625
Rh
[2187-2204] 3′UTR

15
GGUCCAAGGUCCUCAUCC
2591
GGAUGAGGACCUUGGACC
3626

[1149-1166] 3′UTR

16
GUAUUAGACUUGCACUUU
2592
AAAGUGCAAGUCUAAUAC
3627

[2914-2931] 3′UTR

17
CCUGCAAGCAACUCAAAA
2593
UUUUGAGUUGCUUGCAGG
3628

[3343-3360] 3′UTR

18
GGAGGAAAGAAGGAAUAU
2594
AUAUUCCUUCUUUCCUCC
3629
Rt
[614-631] ORF

19
GGAAUAUGAAGUCUGAGA
2595
UCUCAGACUUCAUAUUCC
3630
Ms
[3508-3525] 3′UTR

20
GGACGUUGGAGGAAAGAA
2596
UUCUUUCCUCCAACGUCC
3631
Rt, Ms
[607-624] ORF

21
CAGUGAGAAGGAAGUGGA
2597
UCCACUUCCUUCUCACUG
3632

[451-468] ORF

22
AGAGGAUCCAGUAUGAGA
2598
UCUCAUACUGGAUCCUCU
3633
Rh, Rb
[501-518] ORF

23
GGUCAGUGAGAAGGAAGU
2599
ACUUCCUUCUCACUGACC
3634

[448-465] ORF

24
CUUGGUAGGUAUUAGACU
2600
AGUCUAAUACCUACCAAG
3635

[2906-2923] 3′UTR

25
GGGCAGACUGGGAGGGUA
2601
UACCCUCCCAGUCUGCCC
3636
Rh
[2619-2636] 3′UTR

26
CCAGUAUGAGAUCAAGCA
2602
GCUUGAUCUCAUACUGG
3637
Rh, Rb, Cw, Dg, Ms
[508-525] ORF

27
GGGUCUCGCUGGACGUUG
2603
CAACGUCCAGCGAGACCC
3638
Rt, Ms
[597-614] ORF

28
GCAGAUAUACCAACUUCU
2604
AGAAGUUGGUAUAUCUGC
3639
Rh
[2198-2215] 3′UTR

29
AGACGUGGGUCCAAGGUC
2605
GACCUUGGACCCACGUCU
3640

[1142-1159] 3′UTR

30
CACAGAUCUUGAUGACUU
2606
AAGUCAUCAAGAUCUGUG
3641
Rh
[2592-2609] 3′UTR

31
GGAUUGAGUUGCACAGCU
2607
AGCUGUGCAACUCAAUCC
3642

[1853-1870] 3′UTR

32
GGGUCCAAAUUAAUAUGA
2608
UCAUAUUAAUUUGGACCC
3643

[1077-1094] 3′UTR

33
GUGAGAAGGAAGUGGACU
2609
AGUCCACUUCCUUCUCAC
3644

[453-470] ORF

34
ACCUUAGCCUGUUCUAUU
2610
AAUAGAACAGGCUAAGGU
3645
Rh
[2493-2510] 3′UTR

35
GGUGCUGGGAACACACAA
2611
UUGUGUGUUCCCAGCACC
3646

[3532-3549] 3′UTR

36
GCAUGUCUCUGAUGCUUU
2612
AAAGCAUCAGAGACAUGC
3647

[3579-3596] 3′UTR

37
GCAAGCAACUCAAAAUAU
2613
AUAUUUUGAGUUGCUUGC
3648

[3346-3363] 3′UTR

38
GGCGUGGUCUUGCAAAAU
2614
AUUUUGCAAGACCACGCC
3649

[2463-2480] 3′UTR

39
CGUCUUUGGUUCUCCAGU
2615
ACUGGAGAACCAAAGACG
3650

[55-3072] 3′UTR

40
GUUCUCCAGUUCAAAUUA
2616
UAAUUUGAACUGGAGAAC
3651

[63-3080] 3′UTR

41
AGUAUGAGAUCAAGCAGA
2617
UCUGCUUGAUCUCAUACU
3652
Rh, Rb, Cw, Dg, Ms
[510-527] ORF

42
GCCUGUUUUAAGAGACAU
2618
AUGUCUCUUAAAACAGGC
3653
Rh
[2133-2150] 3′UTR

43
GGGCCUGAGAAGGAUAUA
2619
UAUAUCCUUCUCAGGCCC
3654

[542-559] ORF

44
GCCUGGAACCAGUGGCUA
2620
UAGCCACUGGUUCCAGGC
3655

[1531-1548] 3′UTR

45
CCAACUUCUGCUUGUAUU
2621
AAUACAAGCAGAAGUUGG
3656
Rh
[2207-2224] 3′UTR

46
CGAUAUACAGGCACAUUA
2622
UAAUGUGCCUGUAUAUCG
3657

[2403-2420] 3′UTR

47
GGCCUAUGCAGGUGGAUU
2623
AAUCCACCUGCAUAGGCC
3658
Rh
[2985-3002] 3′UTR

48
GGGAGGGUAUCCAGGAAU
2624
AUUCCUGGAUACCCUCCC
3659
Rh
[2628-2645] 3′UTR

49
CCUAUUAAUCCUCAGAAU
2625
AUUCUGAGGAUUAAUAGG
3660
Rh
[1572-1589] 3′UTR

50
GGGAGACGUGGGUCCAAG
2626
CUUGGACCCACGUCUCCC
3661

[1139-1156] 3′UTR

51
GCUCAAAUACCUUCACAA
2627
UUGUGAAGGUAUUUGAGC
3662

[3224-3241] 3′UTR

52
CCAAGGUCCUCAUCCCAU
2628
AUGGGAUGAGGACCUUGG
3663

[1152-1169] 3′UTR

53
AGUAAGAAGUCCAGCCUA
2629
UAGGCUGGACUUCUUACU
3664
Rh
[2042-2059] 3′UTR

54
GGACUGGGUCACAGAGAA
2630
UUCUCUGUGACCCAGUCC
3665
Rh, Rt, Ms, Pg
[826-843] ORF

55
AGCUAAGCAUAGUAAGAA
2631
UUCUUACUAUGCUUAGCU
3666

[2032-2049] 3′UTR

56
GGUUUGUUUUUGACAUCA
2632
UGAUGUCAAAAACAAACC
3667
Rh
[2853-2870] 3′UTR

57
GGAGUUUCUCGACAUCGA
2633
UCGAUGUCGAGAAACUCC
3668
Ck, Dg
[937-954] ORF

58
GAGUCUUUUUGGUCUGCA
2634
UGCAGACCAAAAAGACUC
3669

[1667-1684] 3′UTR

59
AGGAGAAUCUCUUGUUUC
2635
GAAACAAGAGAUUCUCCU
3670

[2356-2373] 3′UTR

60
CGGUAAUGAUAAGGAGAA
2636
UUCUCCUUAUCAUUACCG
3671

[2345-2362] 3′UTR

61
GGUAUUAGACUUGCACUU
2637
AAGUGCAAGUCUAAUACC
3672

[2913-2930] 3′UTR

62
CGGUCAGUGAGAAGGAAG
2638
CUUCCUUCUCACUGACCG
3673

[447-464] ORF

63
GCGGUCAGUGAGAAGGAA
2639
UUCCUUCUCACUGACCGC
3674

[446-463] ORF

64
UCCUGAAGCCAGUGAUAU
2640
AUAUCACUGGCUUCAGGA
3675

[2301-2318] 3′UTR

65
AGAAGAGCCUGAACCACA
2641
UGUGGUUCAGGCUCUUCU
3676
Rh, Rb, Cw, Ms, Pg
[723-740] ORF

66
GAAAGAAGGAAUAUCUCA
2642
UGAGAUAUUCCUUCUUUC
3677

[618-635] ORF

67
GCCGUAAUUUAAAGCUCU
2643
AGAGCUUUAAAUUACGGC
3678

[3436-3453] 3′UTR

68
CGUGGACAAUAAACAGUA
2644
UACUGUUUAUUGUCCACG
3679

[3624-3641] 3′UTR

69
GUGAAUUCUCAGAUGAUA
2645
UAUCAUCUGAGAAUUCAC
3680

[2166-2183] 3′UTR

70
GGAACACACAAGAGUUGU
2646
ACAACUCUUGUGUGUUCC
3681

[3539-3556] 3′UTR

71
GAGGAUCCAGUAUGAGAU
2647
AUCUCAUACUGGAUCCUC
3682
Rh, Rb
[502-519] ORF

72
UGAGAAGGAUAUAGAGUU
2648
AACUCUAUAUCCUUCUCA
3683

[547-564] ORF

73
GCGUGGUCUUGCAAAAUG
2649
CAUUUUGCAAGACCACGC
3684

[2464-2481] 3′UTR

74
CUGUUUUAAGAGACAUCU
2650
AGAUGUCUCUUAAAACAG
3685
Rh
[2135-2152] 3′UTR

75
CCCUCAGUGUGGUUUCCU
2651
AGGAAACCACACUGAGGG
3686

[2287-2304] 3′UTR

76
GAGUUGCAGAUAUACCAA
2652
UUGGUAUAUCUGCAACUC
3687
Rh
[2193-2210] 3′UTR

77
CUGGGAACACACAAGAGU
2653
ACUCUUGUGUGUUCCCAG
3688

[3536-3553] 3′UTR

78
GCUGAGUCUUUUUGGUCU
2654
AGACCAAAAAGACUCAGC
3689
Rh
[1664-1681] 3′UTR

79
CUGCAUCAAGAGAAGUGA
2655
UCACUUCUCUUGAUGCAG
3690
Rt, Ms
[877-894] ORF

80
GAGGAAAGAAGGAAUAUC
2656
GAUAUUCCUUCUUUCCUC
3691
Rt
[615-632] ORF

81
GCUGGACGUUGGAGGAAA
2657
UUUCCUCCAACGUCCAGC
3692
Rt, Ms
[604-621] ORF

82
GGUGUGGCCUUUAUAUUU
2658
AAAUAUAAAGGCCACACC
3693

[3120-3137] 3′UTR

83
GCAUUUUGCAGAAACUUU
2659
AAAGUUUCUGCAAAAUGC
3694
Rh
[1334-1351] 3′UTR

84
GGACCAGUCCAUGUGAUU
2660
AAUCACAUGGACUGGUCC
3695
Rh
[2710-2727] 3′UTR

85
CACCUUAGCCUGUUCUAU
2661
AUAGAACAGGCUAAGGUG
3696
Rh
[2492-2509] 3′UTR

86
UGAUAAGGAGAAUCUCUU
2662
AAGAGAUUCUCCUUAUCA
3697
Rh
[2351-2368] 3′UTR

87
CUCAAAGACUGACAGCCA
2663
UGGCUGUCAGUCUUUGAG
3698
Rh
[1981-1998] 3′UTR

88
GGGACAUGGCCCUUGUUU
2664
AAACAAGGGCCAUGUCCC
3699

[1407-1424] 3′UTR

89
CCAUCAAUCCUAUUAAUC
2665
GAUUAAUAGGAUUGAUGG
3700
Rh
[1564-1581] 3′UTR

90
GAACCAGUGGCUAGUUCU
2666
AGAACUAGCCACUGGUUC
3701

[1536-1553] 3′UTR

91
AGACAUGGUUGUGGGUCU
2667
AGACCCACAACCAUGUCU
3702

[1118-1135] 3′UTR

92
GUUUAAGAAGGCUCUCCA
2668
UGGAGAGCCUUCUUAAAC
3703

[3265-3282] 3′UTR

93
CUUCCUGUAUGGUGAUAU
2669
AUAUCACCAUACAGGAAG
3704

[2786-2803] 3′UTR

94
GGACCUGGUCAGCACAGA
2670
UCUGUGCUGACCAGGUCC
3705
Rh
[2580-2597] 3′UTR

95
GAGACGUGGGUCCAAGGU
2671
ACCUUGGACCCACGUCUC
3706

[1141-1158] 3′UTR

96
GGAACCAGUGGCUAGUUC
2672
GAACUAGCCACUGGUUCC
3707

[1535-1552] 3′UTR

97
GGGCAGCCUGGAACCAGU
2673
ACUGGUUCCAGGCUGCCC
3708

[1526-1543] 3′UTR

98
GCAUCAGGCACCUGGAUU
2674
AAUCCAGGUGCCUGAUGC
3709

[1840-1857] 3′UTR

99
GGCGUUUUGCAAUGCAGA
2675
UCUGCAUUGCAAAACGCC
3710
Cw, Rt, Ms
[409-426] ORF

100
CCUCCAACCCAUAUAACA
2676
UGUUAUAUGGGUUGGAGG
3711

[2753-2770] 3′UTR

101
GCCUUUAUAUUUGAUCCA
2677
UGGAUCAAAUAUAAAGGC
3712

[3126-3143] 3′UTR

102
GCACAGAUCUUGAUGACU
2678
AGUCAUCAAGAUCUGUGC
3713
Rh
[2591-2608] 3′UTR

103
GUCCCUUUCAUCUUGAGA
2679
UCUCAAGAUGAAAGGGAC
3714
Rh
[1389-1406] 3′UTR

104
GGAAGCAUUUGACCCAGA
2680
UCUGGGUCAAAUGCUUCC
3715

[2956-2973] 3′UTR

105
GGCAGACUGGGAGGGUAU
2681
AUACCCUCCCAGUCUGCC
3716
Rh
[2620-2637] 3′UTR

106
GCUUUGUAUCAUUCUUGA
2682
UCAAGAAUGAUACAAAGC
3717

[3592-3609] 3′UTR

107
GAGGAAGCCGCUCAAAUA
2683
UAUUUGAGCGGCUUCCUC
3718

[3215-3232] 3′UTR

108
CCUUCUCCUUUUAGACAU
2684
AUGUCUAAAAGGAGAAGG
3719

[1106-1123] 3′UTR

109
GGGCGUGGUCUUGCAAAA
2685
UUUUGCAAGACCACGCCC
3720

[2462-2479] 3′UTR

110
GCUGAGCAGAAAACAAAA
2686
UUUUGUUUUCUGCUCAGC
3721

[3166-3183] 3′UTR

111
GACCAGUCCAUGUGAUUU
2687
AAAUCACAUGGACUGGUC
3722
Rh
[2711-2728] 3′UTR

112
GAGAAUCUCUUGUUUCCU
2688
AGGAAACAAGAGAUUCUC
3723

[2358-2375] 3′UTR

113
UCCUAUUAAUCCUCAGAA
2689
UUCUGAGGAUUAAUAGGA
3724
Rh
[1571-1588] 3′UTR

114
CACAGAGAAGAACAUCAA
2690
UUGAUGUUCUUCUCUGUG
3725
Rh
[835-852] ORF

115
GCCUGCAUCAAGAGAAGU
2691
ACUUCUCUUGAUGCAGGC
3726
Rt, Ms
[875-892] ORF

116
GGUGACACACUCACUUCU
2692
AGAAGUGAGUGUGUCACC
3727

[2092-2109] 3′UTR

117
AGGAAAGAAGGAAUAUCU
2693
AGAUAUUCCUUCUUUCCU
3728
Rt
[616-633] ORF

118
CCACCUGUGUUGUAAAGA
2694
UCUUUACAACACAGGUGG
3729
Rh
[2377-2394] 3′UTR

119
GUCCAUGUGAUUUCAGUA
2695
UACUGAAAUCACAUGGAC
3730
Rh
[2716-2733] 3′UTR

120
AGUGGACUCUGGAAACGA
2696
UCGUUUCCAGAGUCCACU
3731
Rh
[463-480] ORF

121
GACAUCAGCUGUAAUCAU
2697
AUGAUUACAGCUGAUGUC
3732

[2864-2881] 3′UTR

122
GCCUGUUCUAUUCAGCGG
2698
CCGCUGAAUAGAACAGGC
3733

[2499-2516] 3′UTR

123
AGAUCAAGCAGAUAAAGA
2699
UCUUUAUCUGCUUGAUCU
3734
Cw, Dg, Rt, Ms
[516-533] ORF

124
GUCUCUGAUGCUUUGUAU
2700
AUACAAAGCAUCAGAGAC
3735

[3583-3600] 3′UTR

125
GUUCAAAGGGCCUGAGAA
2701
UUCUCAGGCCCUUUGAAC
3736

[535-552] ORF

126
GGGAACUAGGGAACCUAU
2702
AUAGGUUCCCUAGUUCCC
3737
Rh
[2264-2281] 3′UTR

127
AUGAUAAGGAGAAUCUCU
2703
AGAGAUUCUCCUUAUCAU
3738

[2350-2367] 3′UTR

128
CUUAGCCUGUUCUAUUCA
2704
UGAAUAGAACAGGCUAAG
3739
Rh
[2495-2512] 3′UTR

129
GUAAUGAUAAGGAGAAUC
2705
GAUUCUCCUUAUCAUUAC
3740

[2347-2364] 3′UTR

130
GGACGAGUGCCUCUGGAU
2706
AUCCAGAGGCACUCGUCC
3741
Rh, Rb, Cw
[808-825] ORF

131
CACAAUAAAUAGUGGCAA
2707
UUGCCACUAUUUAUUGUG
3742

[3237-3254] 3′UTR

132
GUUGGAGGAAAGAAGGAA
2708
UUCCUUCUUUCCUCCAAC
3743
Rt
[611-628] ORF

133
AGGUAUUAGACUUGCACU
2709
AGUGCAAGUCUAAUACCU
3744

[2912-2929] 3′UTR

134
ACACAAGAGUUGUUGAAA
2710
UUUCAACAACUCUUGUGU
3745

[3544-3561] 3′UTR

135
CCUAUGUGUUCCCUCAGU
2711
ACUGAGGGAACACAUAGG
3746

[2277-2294] 3′UTR

136
CAAUGCAGAUGUAGUGAU
2712
AUCACUACAUCUGCAUUG
3747

[418-435] ORF

137
GAAUAUGAAGUCUGAGAC
2713
GUCUCAGACUUCAUAUUC
3748

[3509-3526] 3′UTR

138
CCUCCAAGGGUUUCGACU
2714
AGUCGAAACCCUUGGAGG
3749
Rh
[1004-1021] 3′UTR

139
GUGGUUUCCUGAAGCCAG
2715
CUGGCUUCAGGAAACCAC
3750

[2295-2312] 3′UTR

140
UGUUCUAUUCAGCGGCAA
2716
UUGCCGCUGAAUAGAACA
3751

[2502-2519] 3′UTR

141
GAUGAUAGGUGAACCUGA
2717
UCAGGUUCACCUAUCAUC
3752

[2177-2194] 3′UTR

142
GCCUCAGCUGAGUCUUUU
2718
AAAAGACUCAGCUGAGGC
3753
Rh
[1658-1675] 3′UTR

143
AGGUGAAUUCUCAGAUGA
2719
UCAUCUGAGAAUUCACCU
3754

[2164-2181] 3′UTR

144
AGGGAGACGUGGGUCCAA
2720
UUGGACCCACGUCUCCCU
3755

[1138-1155] 3′UTR

145
AGAAGGAAGUGGACUCUG
2721
CAGAGUCCACUUCCUUCU
3756

[456-473] ORF

146
GGAAGCCGCUCAAAUACC
2722
GGUAUUUGAGCGGCUUCC
3757

[3217-3234] 3′UTR

147
GCUGUACAGUGACCUAAA
2723
UUUAGGUCACUGUACAGC
3758

[2673-2690] 3′UTR

148
GGAUAGGAAGAACUUUCU
2724
AGAAAGUUCUUCCUAUCC
3759

[2327-2344] 3′UTR

149
CCCUUCUCCUUUUAGACA
2725
UGUCUAAAAGGAGAAGGG
3760

[1105-1122] 3′UTR

150
CCACCUUAGCCUGUUCUA
2726
UAGAACAGGCUAAGGUGG
3761
Rh
[2491-2508] 3′UTR

151
GGGCUUCGAUCCUUGGGU
2727
ACCCAAGGAUCGAAGCCC
3762
Rh
[1198-1215] 3′UTR

152
AGUGUUCCCUCCCUCAAA
2728
UUUGAGGGAGGGAACACU
3763

[1969-1986] 3′UTR

153
GAACUUUCUCGGUAAUGA
2729
UCAUUACCGAGAAAGUUC
3764

[2336-2353] 3′UTR

154
GAGAAGGAAGUGGACUCU
2730
AGAGUCCACUUCCUUCUC
3765

[455-472] ORF

155
CAUCAAUCCUAUUAAUCC
2731
GGAUUAAUAGGAUUGAUG
3766
Rh
[1565-1582] 3′UTR

156
GCAGGAGUUUCUCGACAU
2732
AUGUCGAGAAACUCCUGC
3767
Ck, Dg
[934-951] ORF

157
GGGUUAGGAUAGGAAGAA
2733
UUCUUCCUAUCCUAACCC
3768

[2321-2338] 3′UTR

158
CUGAUGCUUUGUAUCAUU
2734
AAUGAUACAAAGCAUCAG
3769

[3587-3604] 3′UTR

159
CAGCCUCAGCUGAGUCUU
2735
AAGACUCAGCUGAGGCUG
3770
Rh
[1656-1673] 3′UTR

160
GGCCUGUUUUAAGAGACA
2736
UGUCUCUUAAAACAGGCC
3771
Rh
[2132-2149] 3′UTR

161
CAUACACACGCAAUGAAA
2737
UUUCAUUGCGUGUGUAUG
3772
Rh
[2427-2444] 3′UTR

162
GCACCACCCAGAAGAAGA
2738
UCUUCUUCUGGGUGGUGC
3773
Rh, Pg
[711-728] ORF

163
CUCUGAUGCUUUGUAUCA
2739
UGAUACAAAGCAUCAGAG
3774

[3585-3602] 3′UTR

164
GGGCUUUCUGCAUGUGAC
2740
GUCACAUGCAGAAAGCCC
3775

[2011-2028] 3′UTR

165
CUCUGGAAACGACAUUUA
2741
UAAAUGUCGUUUCCAGAG
3776
Rh
[469-486] ORF

166
GAUUGAGUUGCACAGCUU
2742
AAGCUGUGCAACUCAAUC
3777

[1854-1871] 3′UTR

167
GUCAGUGAGAAGGAAGUG
2743
CACUUCCUUCUCACUGAC
3778

[449-466] ORF

168
CCAGCUUGCAGGAGGAAU
2744
AUUCCUCCUGCAAGCUGG
3779

[1723-1740] 3′UTR

169
CCCUGUUCGCUUCCUGUA
2745
UACAGGAAGCGAACAGGG
3780

[2777-2794] 3′UTR

170
CAUGGGUCCAAAUUAAUA
2746
UAUUAAUUUGGACCCAUG
3781

[1074-1091] 3′UTR

171
CUCUGUUGAUUUUGUUUC
2747
GAAACAAAAUCAACAGAG
3782

[3450-3467] 3′UTR

172
GGAAGGAUUUUGGAGGUA
2748
UACCUCCAAAAUCCUUCC
3783
Rh
[2065-2082] 3′UTR

173
GGAACUAGGGAACCUAUG
2749
CAUAGGUUCCCUAGUUCC
3784
Rh
[2265-2282] 3′UTR

174
CCUGGAUUGAGUUGCACA
2750
UGUGCAACUCAAUCCAGG
3785

[1850-1867] 3′UTR

175
GCCUGGAAAUGUGCAUUU
2751
AAAUGCACAUUUCCAGGC
3786
Rh
[1322-1339] 3′UTR

176
GGCCAAAGCGGUCAGUGA
2752
UCACUGACCGCUUUGGCC
3787

[439-456] ORF

177
ACUUCUGCUUGUAUUUCU
2753
AGAAAUACAAGCAGAAGU
3788
Rh
[2210-2227] 3′UTR

178
CCCUUUCUAGGGCAGACU
2754
AGUCUGCCCUAGAAAGGG
3789
Rh
[2610-2627] 3′UTR

179
CCUGGUCAGCACAGAUCU
2755
AGAUCUGUGCUGACCAGG
3790
Rh
[2583-2600] 3′UTR

180
GGGUCCAAGGUCCUCAUC
2756
GAUGAGGACCUUGGACCC
3791

[1148-1165] 3′UTR

181
CUGUAUGGUGAUAUCAUA
2757
UAUGAUAUCACCAUACAG
3792

[2790-2807] 3′UTR

182
UGGACUUGCUGCCGUAAU
2758
AUUACGGCAGCAAGUCCA
3793

[3426-3443] 3′UTR

183
CCUGUUCGCUUCCUGUAU
2759
AUACAGGAAGCGAACAGG
3794

[2778-2795] 3′UTR

184
GUGACACACUCACUUCUU
2760
AAGAAGUGAGUGUGUCAC
3795

[2093-2110] 3′UTR

185
GGUGGAUUCCUUCAGGUC
2761
GACCUGAAGGAAUCCACC
3796
Rh
[2995-3012] 3′UTR

186
CCCAUCAAUCCUAUUAAU
2762
AUUAAUAGGAUUGAUGGG
3797
Rh
[1563-1580] 3′UTR

187
GCUAGUUCUUGAAGGAGC
2763
GCUCCUUCAAGAACUAGC
3798

[1545-1562] 3′UTR

188
GUGGGUCCAAGGUCCUCA
2764
UGAGGACCUUGGACCCAC
3799

[1146-1163] 3′UTR

189
GCUUCCAAAGCCACCUUA
2765
UAAGGUGGCUUUGGAAGC
3800
Rh
[2481-2498] 3′UTR

190
GGUCACAGAGAAGAACAU
2766
AUGUUCUUCUCUGUGACC
3801
Rh
[832-849] ORF

191
GCAUCAAGAGAAGUGACG
2767
CGUCACUUCUCUUGAUGC
3802

[879-896] ORF

192
UGGUCUUGCAAAAUGCUU
2768
AAGCAUUUUGCAAGACCA
3803

[2467-2484] 3′UTR

193
AGCAGGAGUUUCUCGACA
2769
UGUCGAGAAACUCCUGCU
3804
Ck, Dg
[933-950] ORF

194
GUUGAAAGUUGACAAGCA
2770
UGCUUGUCAACUUUCAAC
3805

[3555-3572] 3′UTR

195
GGUCUUGCAAAAUGCUUC
2771
GAAGCAUUUUGCAAGACC
3806

[2468-2485] 3′UTR

196
GUGUUUAUGCUGGAAUAU
2772
AUAUUCCAGCAUAAACAC
3807

[3497-3514] 3′UTR

197
GCAGAAAACAAAACAGGU
2773
ACCUGUUUUGUUUUCUGC
3808

[3171-3188] 3′UTR

198
ACCUAAAGUUGGUAAGAU
2774
AUCUUACCAACUUUAGGU
3809

[2684-2701] 3′UTR

199
AGCAGACUGCGCAUGUCU
2775
AGACAUGCGCAGUCUGCU
3810

[3569-3586] 3′UTR

200
AGCCUGUUCUAUUCAGCG
2776
CGCUGAAUAGAACAGGCU
3811

[2498-2515] 3′UTR

201
GGCAGCACUUAGGGAUCU
2777
AGAUCCCUAAGUGCUGCC
3812
Rh
[1284-1301] 3′UTR

202
CAUUUAUGGCAACCCUAU
2778
AUAGGGUUGCCAUAAAUG
3813

[481-498] ORF

203
GGCUCUCCAUUUGGCAUC
2779
GAUGCCAAAUGGAGAGCC
3814

[3274-3291] 3′UTR

204
UGUUUCUGCUGAUUGUUU
2780
AAACAAUCAGCAGAAACA
3815

[2823-2840] 3′UTR

205
GCUGCGAGUGCAAGAUCA
2781
UGAUCUUGCACUCGCAGC
3816
Rt
[753-770] ORF

206
CUUUCUCGGUAAUGAUAA
2782
UUAUCAUUACCGAGAAAG
3817

[2339-2356] 3′UTR

207
GUUUCCGUUUGGAUUUUU
2783
AAAAAUCCAAACGGAAAC
3818

[3463-3480] 3′UTR

208
GGGCUGCGAGUGCAAGAU
2784
AUCUUGCACUCGCAGCCC
3819
Ck, Rb, Rt
[751-768] ORF

209
CCUGAGUUGCAGAUAUAC
2785
GUAUAUCUGCAACUCAGG
3820
Rh
[2190-2207] 3′UTR

210
GUUUCCUGAAGCCAGUGA
2786
UCACUGGCUUCAGGAAAC
3821

[2298-2315] 3′UTR

211
GGAUUUUGGAGGUAGGUG
2787
CACCUACCUCCAAAAUCC
3822
Rh
[2069-2086] 3′UTR

212
GCAAAAAAAGCCUCCAAG
2788
CUUGGAGGC GC
3823

[994-1011] 3′UTR

213
CCAAGUUCUUCGCCUGCA
2789
UGCAGGCGAAGAACUUGG
3824
Rh, Rb, Cw, Dg, Ms
[864-881] ORF

214
GUUCCCUCAGUGUGGUUU
2790
AAACCACACUGAGGGAAC
3825

[2284-2301] 3′UTR

215
GGAGCACUGUGUUUAUGC
2791
GCAUAAACACAGUGCUCC
3826

[3489-3506] 3′UTR

216
UAAGAAGGCUCUCCAUUU
2792
AAAUGGAGAGCCUUCUUA
3827

[3268-3285] 3′UTR

217
GCGUUUUCAUGCUGUACA
2793
UGUACAGCAUGAAAACGC
3828
Rh
[2663-2680] 3′UTR

218
GGUUCGGUCUGAAAGGUG
2794
CACCUUUCAGACCGAACC
3829

[3106-3123] 3′UTR

219
GAUUACCUAGCUAAGAAA
2795
UUUCUUAGCUAGGUAAUC
3830

[2239-2256] 3′UTR

220
CUUUCAUCUUGAGAGGGA
2796
UCCCUCUCAAGAUGAAAG
3831

[1393-1410] 3′UTR

221
AGGGCAGCCUGGAACCAG
2797
CUGGUUCCAGGCUGCCCU
3832

[1525-1542] 3′UTR

222
GGGACACGCGGCUUCCCU
2798
AGGGAAGCCGCGUGUCCC
3833

[1228-1245] 3′UTR

223
CCUAGGAAGGGAAGGAUU
2799
AAUCCUUCCCUUCCUAGG
3834
Rh
[2056-2073] 3′UTR

224
CCAAGGGCAGCCUGGAAC
2800
GUUCCAGGCUGCCCUUGG
3835

[1522-1539] 3′UTR

225
AUAUGAAGUCUGAGACCU
2801
AGGUCUCAGACUUCAUAU
3836

[3511-3528] 3′UTR

226
GGACUCUGGAAACGACAU
2802
AUGUCGUUUCCAGAGUCC
3837
Rh
[466-483] ORF

227
CCUGAAGCCAGUGAUAUG
2803
CAUAUCACUGGCUUCAGG
3838

[2302-2319] 3′UTR

228
GGACUUGCUGCCGUAAUU
2804
AAUUACGGCAGCAAGUCC
3839

[3427-3444] 3′UTR

229
ACGGCAAGAUGCACAUCA
2805
UGAUGUGCAUCUUGCCGU
3840
Dg, Pg
[657-674] ORF

230
CAAGAGUUGUUGAAAGUU
2806
AACUUUCAACAACUCUUG
3841

[3547-3564] 3′UTR

231
GGUCAGCACAGAUCUUGA
2807
UCAAGAUCUGUGCUGACC
3842
Rh
[2586-2603] 3′UTR

232
AGGGAACUAGGGAACCUA
2808
UAGGUUCCCUAGUUCCCU
3843
Rh
[2263-2280] 3′UTR

233
CGGACGAGUGCCUCUGGA
2809
UCCAGAGGCACUCGUCCG
3844
Rh, Rb, Cw
[807-824] ORF

234
CUCCAGUUCAAAUUAUUG
2810
CAAUAAUUUGAACUGGAG
3845

[66-3083] 3′UTR

235
CAUGGUUGUGGGUCUGGA
2811
UCCAGACCCACAACCAUG
3846

[1121-1138] 3′UTR

236
AGGUGAACCUGAGUUGCA
2812
UGCAACUCAGGUUCACCU
3847
Rh
[2183-2200] 3′UTR

237
GGUGAGGUCCUGUCCUGA
2813
UCAGGACAGGACCUCACC
3848
Rh
[1742-1759] 3′UTR

238
CAGUGUGGUUUCCUGAAG
2814
CUUCAGGAAACCACACUG
3849

[2291-2308] 3′UTR

239
GAAGAAGAGCCUGAACCA
2815
UGGUUCAGGCUCUUCUUC
3850
Rh, Rb, Cw, Ms, Pg
[721-738] ORF

240
GGUAGGUGGCUUUGGUGA
2816
UCACCAAAGCCACCUACC
3851
Rh
[2079-2096] 3′UTR

241
CCCUCAAGGUCCCUUCCC
2817
GGGAAGGGACCUUGAGGG
3852

[1785-1802] 3′UTR

242
UCGCCUGCAUCAAGAGAA
2818
UUCUCUUGAUGCAGGCGA
3853
Rh, Cw, Dg, Ms
[873-890] ORF

243
AGCAUUUGACCCAGAGUG
2819
CACUCUGGGUCAAAUGCU
3854

[2959-2976] 3′UTR

244
GGGUCUUGCUGUGCCCUC
2820
GAGGGCACAGCAAGACCC
3855
Rh
[1943-1960] 3′UTR

245
GCCUCCUGCUGCUGGCGA
2821
UCGCCAGCAGCAGGAGGC
3856
Dg
[339-356] ORF

246
CAGGCUUAGUGUUCCCUC
2822
GAGGGAACACUAAGCCUG
3857

[1962-1979] 3′UTR

247
CCAGAAGAAGAGCCUGAA
2823
UUCAGGCUCUUCUUCUGG
3858
Rh, Rb, Cw, Ms, Pg
[718-735] ORF

248
GACCCAGAGUGGAACGCG
2824
CGCGUUCCACUCUGGGUC
3859

[2966-2983] 3′UTR

249
AGGUGUGGCCUUUAUAUU
2825
AAUAUAAAGGCCACACCU
3860

[3119-3136] 3′UTR

250
CAGUGGGAGCCUCCCUCU
2826
AGAGGGAGGCUCCCACUG
3861
Rh
[1592-1609] 3′UTR

251
UGGUUCUCCAGUUCAAAU
2827
AUUUGAACUGGAGAACCA
3862

[61-3078] 3′UTR

252
GGUUAAGAAGAGCCGGGU
2828
ACCCGGCUCUUCUUAACC
3863

[3186-3203] 3′UTR

253
AAGGAGAAUCUCUUGUUU
2829
AAACAAGAGAUUCUCCUU
3864

[2355-2372] 3′UTR

254
UCUGAUGCUUUGUAUCAU
2830
AUGAUACAAAGCAUCAGA
3865

[3586-3603] 3′UTR

255
CCAGGUCCCUUUCAUCUU
2831
AAGAUGAAAGGGACCUGG
3866
Rh
[1385-1402] 3′UTR

256
CACCCUCUGUGACUUCAU
2832
AUGAAGUCACAGAGGGUG
3867
Rh, Cw, Ms
[673-690] ORF

257
CCCUUGGUAGGUAUUAGA
2833
UCUAAUACCUACCAAGGG
3868

[2904-2921] 3′UTR

258
CUAUGUGUUCCCUCAGUG
2834
CACUGAGGGAACACAUAG
3869

[2278-2295] 3′UTR

259
GAGCCUGAACCACAGGUA
2835
UACCUGUGGUUCAGGCUC
3870
Rh, Rb, Cw, Ms, Pg
[727-744] ORF

260
GGCAAGUGCUCCCAUCGC
2836
GCGAUGGGAGCACUUGCC
3871

[1460-1477] 3′UTR

261
GAAUUCCAGUGGGAGCCU
2837
AGGCUCCCACUGGAAUUC
3872
Rh
[1586-1603] 3′UTR

262
GCAAUGCAGAUGUAGUGA
2838
UCACUACAUCUGCAUUGC
3873

[417-434] ORF

263
CCUGAGAAGGAUAUAGAG
2839
CUCUAUAUCCUUCUCAGG
3874

[545-562] ORF

264
ACCUGAGUUGCAGAUAUA
2840
UAUAUCUGCAACUCAGGU
3875
Rh
[2189-2206] 3′UTR

265
GACCUAAAGUUGGUAAGA
2841
UCUUACCAACUUUAGGUC
3876

[2683-2700] 3′UTR

266
GUCUUUGGUUCUCCAGUU
2842
AACUGGAGAACCAAAGAC
3877

[56-3073] 3′UTR

267
GCCUAGGAAGGGAAGGAU
2843
AUCCUUCCCUUCCUAGGC
3878
Rh
[2055-2072] 3′UTR

268
CGCAUGUCUCUGAUGCUU
2844
AAGCAUCAGAGACAUGCG
3879

[3578-3595] 3′UTR

269
CAAUCCUAUUAAUCCUCA
2845
UGAGGAUUAAUAGGAUUG
3880
Rh
[1568-1585] 3′UTR

270
AGCCUCAGCUGAGUCUUU
2846
AAAGACUCAGCUGAGGCU
3881
Rh
[1657-1674] 3′UTR

271
GCUCUGUUGAUUUUGUUU
2847
AAACAAAAUCAACAGAGC
3882

[3449-3466] 3′UTR

272
GUGGGAGCCUCCCUCUGA
2848
UCAGAGGGAGGCUCCCAC
3883
Rh
[1594-1611] 3′UTR

273
GACUCUGGAAACGACAUU
2849
AAUGUCGUUUCCAGAGUC
3884
Rh
[467-484] ORF

274
AGCAUAGUAAGAAGUCCA
2850
UGGACUUCUUACUAUGCU
3885

[2037-2054] 3′UTR

275
CAGAGGAAGCCGCUCAAA
2851
UUUGAGCGGCUUCCUCUG
3886

[3213-3230] 3′UTR

276
GUUGGUAAGAUGUCAUAA
2852
UUAUGACAUCUUACCAAC
3887
Rh
[2691-2708] 3′UTR

277
CUAUUUUCAUCCUGCAAG
2853
CUUGCAGGAUGAAAAUAG
3888

[3333-3350] 3′UTR

278
AGUUGCAGAUAUACCAAC
2854
GUUGGUAUAUCUGCAACU
3889
Rh
[2194-2211] 3′UTR

279
AAUGAUAAGGAGAAUCUC
2855
GAGAUUCUCCUUAUCAUU
3890

[2349-2366] 3′UTR

280
GGAGAAUCUCUUGUUUCC
2856
GGAAACAAGAGAUUCUCC
3891

[2357-2374] 3′UTR

281
GUAAGAUGUCAUAAUGGA
2857
UCCAUUAUGACAUCUUAC
3892
Rh
[2695-2712] 3′UTR

282
CCUUGGUAGGUAUUAGAC
2858
GUCUAAUACCUACCAAGG
3893

[2905-2922] 3′UTR

283
GGCUGGGACACGCGGCUU
2859
AAGCCGCGUGUCCCAGCC
3894

[1224-1241] 3′UTR

284
CACAAGAGUUGUUGAAAG
2860
CUUUCAACAACUCUUGUG
3895

[3545-3562] 3′UTR

285
GAGGGUCGUUGCAAGACU
2861
AGUCUUGCAACGACCCUC
3896

[1353-1370] 3′UTR

286
AAACGACAUUUAUGGCAA
2862
UUGCCAUAAAUGUCGUUU
3897

[475-492] ORF

287
UGAUGACUUCCCUUUCUA
2863
UAGAAAGGGAAGUCAUCA
3898
Rh
[2601-2618] 3′UTR

288
GGCUUAGUGUUCCCUCCC
2864
GGGAGGGAACACUAAGCC
3899

[1964-1981] 3′UTR

289
CAGAGAAGAACAUCAACG
2865
CGUUGAUGUUCUUCUCUG
3900
Rh
[837-854] ORF

290
CCAGCCUCAGCUGAGUCU
2866
AGACUCAGCUGAGGCUGG
3901
Rh
[1655-1672] 3′UTR

291
GGGACACCCUGAGCACCA
2867
UGGUGCUCAGGGUGUCCC
3902
Rh, Pg
[699-716] ORF

292
CUCACUUCUUUCUCAGCC
2868
GGCUGAGAAAGAAGUGAG
3903

[2101-2118] 3′UTR

293
GACAUCCCUUCCUGGAAA
2869
UUUCCAGGAAGGGAUGUC
3904
Rh, Rt, Ms
[1033-1050] 3′UTR

294
CCUGGCAAGUGCUCCCAU
2870
AUGGGAGCACUUGCCAGG
3905

[1457-1474] 3′UTR

295
AGAAAUGGGAGCGAGAAA
2871
UUUCUCGCUCCCAUUUCU
3906

[1619-1636] 3′UTR

296
GCAAUGAAACCGAAGCUU
2872
AAGCUUCGGUUUCAUUGC
3907

[2436-2453] 3′UTR

297
AUGUCAUAAUGGACCAGU
2873
ACUGGUCCAUUAUGACAU
3908
Rh
[2700-2717] 3′UTR

298
UGUGGUUUCCUGAAGCCA
2874
UGGCUUCAGGAAACCACA
3909

[2294-2311] 3′UTR

299
GAUAUACAGGCACAUUAU
2875
AUAAUGUGCCUGUAUAUC
3910

[2404-2421] 3′UTR

300
AAAAAAGCCUCCAAGGGU
2876
ACCCUUGGAGGCUUUUUU
3911

[997-1014] 3′UTR

301
GUAUGGUGAUAUCAUAUG
2877
CAUAUGAUAUCACCAUAC
3912

[2792-2809] 3′UTR

302
CCUGUGCUGUGUUUUUUA
2878
UAAAAAACACAGCACAGG
3913
Rh
[2883-2900] 3′UTR

303
AGGCCAAGUUCUUCGCCU
2879
AGGCGAAGAACUUGGCCU
3914
Rh, Rb, Cw, Dg, Ms
[861-878] ORF

304
UGCAGAUAUACCAACUUC
2880
GAAGUUGGUAUAUCUGCA
3915
Rh
[2197-2214] 3′UTR

305
AGAAGGAAUAUCUCAUUG
2881
CAAUGAGAUAUUCCUUCU
3916

[621-638] ORF

306
GAAGGAUUUUGGAGGUAG
2882
CUACCUCCAAAAUCCUUC
3917
Rh
[2066-2083] 3′UTR

307
GCGGCUUCCCUCCCAGUC
2883
GACUGGGAGGGAAGCCGC
3918

[1235-1252] 3′UTR

308
CUCAGAAUUCCAGUGGGA
2884
UCCCACUGGAAUUCUGAG
3919
Rh
[1582-1599] 3′UTR

309
GAUGGACUGGGUCACAGA
2885
UCUGUGACCCAGUCCAUC
3920
Rh, Rt, Ms, Pg
[823-840] ORF

310
AUAUCUCAUUGCAGGAAA
2886
UUUCCUGCAAUGAGAUAU
3921

[628-645] ORF

311
ACAUUUAUGGCAACCCUA
2887
UAGGGUUGCCAUAAAUGU
3922

[480-497] ORF

312
UUAAGAAGGCUCUCCAUU
2888
AAUGGAGAGCCUUCUUAA
3923

[3267-3284] 3′UTR

313
GCAAAAUGCUUCCAAAGC
2889
GCUUUGGAAGCAUUUUGC
3924
Rh
[2474-2491] 3′UTR

314
CUCCCUCAAAGACUGACA
2890
UGUCAGUCUUUGAGGGAG
3925
Rh
[1977-1994] 3′UTR

315
GCCUCUGGAUGGACUGGG
2891
CCCAGUCCAUCCAGAGGC
3926
Rh, Rb, Cw, Dg,
[816-833] ORF

Rt, Ms

316
CGUUGGUCUUUUAACCGU
2892
ACGGUUAAAAGACCAACG
3927

[3148-3165] 3′UTR

317
AGGAAUAUCUCAUUGCAG
2893
CUGCAAUGAGAUAUUCCU
3928

[624-641] ORF

318
GAGUUUAUCUACACGGCC
2894
GGCCGUGUAGAUAAACUC
3929
Ms, Pg
[560-577] ORF

319
UUUUCAUCCUGCAAGCAA
2895
UUGCUUGCAGGAUGAAAA
3930

[3336-3353] 3′UTR

320
CAAAGCGGUCAGUGAGAA
2896
UUCUCACUGACCGCUUUG
3931

[442-459] ORF

321
GUUUCUGCUGAUUGUUUU
2897
AAAACAAUCAGCAGAAAC
3932

[2824-2841] 3′UTR

322
AAAGGUGAAUUCUCAGAU
2898
AUCUGAGAAUUCACCUUU
3933

[2162-2179] 3′UTR

323
GAGUGCCUCUGGAUGGAC
2899
GUCCAUCCAGAGGCACUC
3934
Rh, Rb, Cw, Dg,
[812-829] ORF

Rt, Ms

324
CAAAGAUUACCUAGCUAA
2900
UUAGCUAGGUAAUCUUUG
3935

[2235-2252] 3′UTR

325
CCAGCUCUGACAUCCCUU
2901
AAGGGAUGUCAGAGCUGG
3936
Rh
[1025-1042] 3′UTR

326
GUUCUUCGCCUGCAUCAA
2902
UUGAUGCAGGCGAAGAAC
3937
Rh, Rb, Cw, Dg, Ms
[868-885] ORF

327
GGCUCCUGUGCGUGGUAC
2903
GUACCACGCACAGGAGCC
3938
Rh
[896-913] ORF

328
UAGACAUGGUUGUGGGUC
2904
GACCCACAACCAUGUCUA
3939

[1117-1134] 3′UTR

329
AGAAGUCCAGCCUAGGAA
2905
UUCCUAGGCUGGACUUCU
3940
Rh
[2046-2063] 3′UTR

330
GCAAGACUGUGUAGCAGG
2906
CCUGCUACACAGUCUUGC
3941
Rh
[1363-1380] 3′UTR

331
GCUCUCUUCUCCUAUUUU
2907
AAAAUAGGAGAAGAGAGC
3942

[3322-3339] 3′UTR

332
GGCAAGAUGCACAUCACC
2908
GGUGAUGUGCAUCUUGCC
3943
Rh, Dg
[659-676] ORF

333
GAAGAACUUUCUCGGUAA
2909
UUACCGAGAAAGUUCUUC
3944
Rh
[2333-2350] 3′UTR

334
AGAGUUGUUGAAAGUUGA
2910
UCAACUUUCAACAACUCU
3945

[3549-3566] 3′UTR

335
GUAUAUACAACUCCACCA
2911
UGGUGGAGUUGUAUAUAC
3946
Rh
[2731-2748] 3′UTR

336
GCUUAGUGUUCCCUCCCU
2912
AGGGAGGGAACACUAAGC
3947

[1965-1982] 3′UTR

337
GCUCUGACAUCCCUUCCU
2913
AGGAAGGGAUGUCAGAGC
3948
Rh
[1028-1045] 3′UTR

338
CCCAUGGGUCCAAAUUAA
2914
UUAAUUUGGACCCAUGGG
3949

[1072-1089] 3′UTR

339
UGGCCAACUGCAAAAAAA
2915
UUUUUUUGCAGUUGGCCA
3950

[985-1002] 3′UTR

340
GGACACUAUGGCCUGUUU
2916
AAACAGGCCAUAGUGUCC
3951

[2123-2140] 3′UTR

341
GCCAGCUAAGCAUAGUAA
2917
UUACUAUGCUUAGCUGGC
3952

[2029-2046] 3′UTR

342
CCAAGGGUUUCGACUGGU
2918
ACCAGUCGAAACCCUUGG
3953
Rh
[1007-1024] 3′UTR

343
AGAUGCACAUCACCCUCU
2919
AGAGGGUGAUGUGCAUCU
3954
Rh
[663-680] ORF

344
GGCAGGGCCUGGAAAUGU
2920
ACAUUUCCAGGCCCUGCC
3955

[1316-1333] 3′UTR

345
GGUCCUCAUCCCAUCCUC
2921
GAGGAUGGGAUGAGGACC
3956
Rh
[1156-1173] 3′UTR

346
CGACAUUUAUGGCAACCC
2922
GGGUUGCCAUAAAUGUCG
3957

[478-495] ORF

347
GCCUUGUAGAAAUGGGAG
2923
CUCCCAUUUCUACAAGGC
3958
Rh
[1612-1629] 3′UTR

348
CAGUCCAUGUGAUUUCAG
2924
CUGAAAUCACAUGGACUG
3959
Rh
[2714-2731] 3′UTR

349
GGAGACGUGGGUCCAAGG
2925
CCUUGGACCCACGUCUCC
3960

[1140-1157] 3′UTR

350
CAGCUUUGCUUUAUCCGG
2926
CCGGAUAAAGCAAAGCUG
3961

[1866-1883] 3′UTR

351
UGCAAGCAACUCAAAAUA
2927
UAUUUUGAGUUGCUUGCA
3962

[3345-3362] 3′UTR

352
CCUUUCUAGGGCAGACUG
2928
CAGUCUGCCCUAGAAAGG
3963
Rh
[2611-2628] 3′UTR

353
CCUGGAAAUGUGCAUUUU
2929
AAAAUGCACAUUUCCAGG
3964
Rh
[1323-1340] 3′UTR

354
AUGGCAACCCUAUCAAGA
2930
UCUUGAUAGGGUUGCCAU
3965

[486-503] ORF

355
GCCAUUGCUUCUUGCCUG
2931
CAGGCAAGAAGCAAUGGC
3966

[1817-1834] 3′UTR

356
GGAACCUAUGUGUUCCCU
2932
AGGGAACACAUAGGUUCC
3967
Rh
[2273-2290] 3′UTR

357
GAUAUACCAACUUCUGCU
2933
AGCAGAAGUUGGUAUAUC
3968
Rh
[2201-2218] 3′UTR

358
GUUUGUUUUUGACAUCAG
2934
CUGAUGUCAAAAACAAAC
3969

[2854-2871] 3′UTR

359
UGCACAGCUUUGCUUUAU
2935
AUAAAGCAAAGCUGUGCA
3970

[1862-1879] 3′UTR

360
CCUAUUUUCAUCCUGCAA
2936
UUGCAGGAUGAAAAUAGG
3971

[3332-3349] 3′UTR

361
UGCCAUUGCUUCUUGCCU
2937
AGGCAAGAAGCAAUGGCA
3972

[1816-1833] 3′UTR

362
ACCAACUUCUGCUUGUAU
2938
AUACAAGCAGAAGUUGGU
3973
Rh
[2206-2223] 3′UTR

363
GGUCCUGUCCUGAGGCUG
2939
CAGCCUCAGGACAGGACC
3974
Rh
[1747-1764] 3′UTR

364
AUGCAGAUGUAGUGAUCA
2940
UGAUCACUACAUCUGCAU
3975

[420-437] ORF

365
GCUAAGCAUAGUAAGAAG
2941
CUUCUUACUAUGCUUAGC
3976

[2033-2050] 3′UTR

366
GUUCCCUCCCUCAAAGAC
2942
GUCUUUGAGGGAGGGAAC
3977

[1972-1989] 3′UTR

367
AGCUGUAAUCAUUCCUGU
2943
ACAGGAAUGAUUACAGCU
3978

[2870-2887] 3′UTR

368
GCAUGUGACGCCAGCUAA
2944
UUAGCUGGCGUCACAUGC
3979

[2020-2037] 3′UTR

369
GCACAGCUUUGCUUUAUC
2945
GAUAAAGCAAAGCUGUGC
3980

[1863-1880] 3′UTR

370
GAGCCUCCCUCUGAGCCU
2946
AGGCUCAGAGGGAGGCUC
3981
Rh
[1598-1615] 3′UTR

371
GGCACCAGGCCAAGUUCU
2947
AGAACUUGGCCUGGUGCC
3982
Rh, Rb, Rt, Ms
[855-872] ORF

372
CAGCACAGAUCUUGAUGA
2948
UCAUCAAGAUCUGUGCUG
3983
Rh
[2589-2606] 3′UTR

373
UGUUCUAAGCACAGCUCU
2949
AGAGCUGUGCUUAGAACA
3984

[3309-3326] 3′UTR

374
UGAGCAGAAAACAAAACA
2950
UGUUUUGUUUUCUGCUCA
3985

[3168-3185] 3′UTR

375
GGGAACACACAAGAGUUG
2951
CAACUCUUGUGUGUUCCC
3986

[3538-3555] 3′UTR

376
CCCUCAAAGACUGACAGC
2952
GCUGUCAGUCUUUGAGGG
3987
Rh
[1979-1996] 3′UTR

377
CCUUGUUUUCUGCAGCUU
2953
AAGCUGCAGAAAACAAGG
3988
Rh
[1417-1434] 3′UTR

378
CUGGAAACGACAUUUAUG
2954
CAUAAAUGUCGUUUCCAG
3989

[471-488] ORF

379
GCAAGAUGCACAUCACCC
2955
GGGUGAUGUGCAUCUUGC
3990
Rh, Dg
[660-677] ORF

380
UCAGAAUUCCAGUGGGAG
2956
CUCCCACUGGAAUUCUGA
3991
Rh
[1583-1600] 3′UTR

381
UGUUGAUUUUGUUUCCGU
2957
ACGGAAACAAAAUCAACA
3992

[3453-3470] 3′UTR

382
UGCUGGAAUAUGAAGUCU
2958
AGACUUCAUAUUCCAGCA
3993
Ms
[3504-3521] 3′UTR

383
GUUGUUGAAAGUUGACAA
2959
UUGUCAACUUUCAACAAC
3994

[3552-3569] 3′UTR

384
GGUCGUUGCAAGACUGUG
2960
CACAGUCUUGCAACGACC
3995

[1356-1373] 3′UTR

385
GUAGGUAUUAGACUUGCA
2961
UGCAAGUCUAAUACCUAC
3996

[2910-2927] 3′UTR

386
CUUUGUAUCAUUCUUGAG
2962
CUCAAGAAUGAUACAAAG
3997

[3593-3610] 3′UTR

387
GGGAGCACUGUGUUUAUG
2963
CAUAAACACAGUGCUCCC
3998

[3488-3505] 3′UTR

388
UGUCUCUGAUGCUUUGUA
2964
UACAAAGCAUCAGAGACA
3999

[3582-3599] 3′UTR

389
GUUCCAGCCUCAGCUGAG
2965
CUCAGCUGAGGCUGGAAC
4000

[1652-1669] 3′UTR

390
GGUUAGGAUAGGAAGAAC
2966
GUUCUUCCUAUCCUAACC
4001

[2322-2339] 3′UTR

391
AUAUACAACUCCACCAGA
2967
UCUGGUGGAGUUGUAUAU
4002
Rh
[2733-2750] 3′UTR

392
UCUGAGCCUUGUAGAAAU
2968
AUUUCUACAAGGCUCAGA
4003
Rh
[1607-1624] 3′UTR

393
GUGAGGUCCUGUCCUGAG
2969
CUCAGGACAGGACCUCAC
4004
Rh
[1743-1760] 3′UTR

394
GGGUGGCAGCUGACAGAG
2970
CUCUGUCAGCUGCCACCC
4005

[3200-3217] 3′UTR

395
CAAGCAGACUGCGCAUGU
2971
ACAUGCGCAGUCUGCUUG
4006

[3567-3584] 3′UTR

396
CUCCCUCUGAGCCUUGUA
2972
UACAAGGCUCAGAGGGAG
4007
Rh
[1602-1619] 3′UTR

397
GGAGGUAGGUGGCUUUGG
2973
CCAAAGCCACCUACCUCC
4008
Rh
[2076-2093] 3′UTR

398
GAGCAGAAAACAAAACAG
2974
CUGUUUUGUUUUCUGCUC
4009

[3169-3186] 3′UTR

399
AGAAGGCUCUCCAUUUGG
2975
CCAAAUGGAGAGCCUUCU
4010

[3270-3287] 3′UTR

400
UAUGAAGUCUGAGACCUU
2976
AAGGUCUCAGACUUCAUA
4011

[3512-3529] 3′UTR

401
AACAUUUACUCCUGUUUC
2977
GAAACAGGAGUAAAUGUU
4012
Rh
[2811-2828] 3′UTR

402
GACGAGUGCCUCUGGAUG
2978
CAUCCAGAGGCACUCGUC
4013
Rh, Rb, Cw
[809-826] ORF

403
CUGGGUCACAGAGAAGAA
2979
UUCUUCUCUGUGACCCAG
4014
Rh
[829-846] ORF

404
CUAGGAAGGGAAGGAUUU
2980
AAAUCCUUCCCUUCCUAG
4015
Rh
[2057-2074] 3′UTR

405
CGGCUUCCCUCCCAGUCC
2981
GGACUGGGAGGGAAGCCG
4016

[1236-1253] 3′UTR

406
CCAGUGGGAGCCUCCCUC
2982
GAGGGAGGCUCCCACUGG
4017
Rh
[1591-1608] 3′UTR

407
GAGUUUCUCGACAUCGAG
2983
CUCGAUGUCGAGAAACUC
4018
Ck, Dg
[938-955] ORF

408
AGAAGAGCCGGGUGGCAG
2984
CUGCCACCCGGCUCUUCU
4019

[3191-3208] 3′UTR

409
ACAUCAGCUGUAAUCAUU
2985
AAUGAUUACAGCUGAUGU
4020

[2865-2882] 3′UTR

410
CUCAGAUGAUAGGUGAAC
2986
GUUCACCUAUCAUCUGAG
4021

[2173-2190] 3′UTR

411
GCAGGUGGAUUCCUUCAG
2987
CUGAAGGAAUCCACCUGC
4022
Rh
[2992-3009] 3′UTR

412
GCGCAUGUCUCUGAUGCU
2988
AGCAUCAGAGACAUGCGC
4023

[3577-3594] 3′UTR

413
CAGUAUAUACAACUCCAC
2989
GUGGAGUUGUAUAUACUG
4024
Rh
[2729-2746] 3′UTR

414
CAUUCUUGAGCAAUCGCU
2990
AGCGAUUGCUCAAGAAUG
4025

[3601-3618] 3′UTR

415
CCUCCUCGGCAGUGUGUG
2991
CACACACUGCCGAGGAGG
4026

[579-596] ORF

416
UCCUGUUUCUGCUGAUUG
2992
CAAUCAGCAGAAACAGGA
4027

[2820-2837] 3′UTR

417
CCCUCCUCGGCAGUGUGU
2993
ACACACUGCCGAGGAGGG
4028

[578-595] ORF

418
UACCCUUGGUAGGUAUUA
2994
UAAUACCUACCAAGGGUA
4029

[2902-2919] 3′UTR

419
GCUUCCUGUAUGGUGAUA
2995
UAUCACCAUACAGGAAGC
4030

[2785-2802] 3′UTR

420
GGACAUGGCCCUUGUUUU
2996
AAAACAAGGGCCAUGUCC
4031

[1408-1425] 3′UTR

421
GCAUGAAUAAAACACUCA
2997
UGAGUGUUUUAUUCAUGC
4032
Rh
[1053-1070] 3′UTR

422
CCUGUUUCUGCUGAUUGU
2998
ACAAUCAGCAGAAACAGG
4033

[2821-2838] 3′UTR

423
GCACAUCACCCUCUGUGA
2999
UCACAGAGGGUGAUGUGC
4034
Rh
[667-684] ORF

424
GCCGCUCAAAUACCUUCA
3000
UGAAGGUAUUUGAGCGGC
4035

[3221-3238] 3′UTR

425
GCAACAGGCGUUUUGCAA
3001
UUGCAAAACGCCUGUUGC
4036
Cw, Rt, Ms
[403-420] ORF

426
GGGACGGCAAGAUGCACA
3002
UGUGCAUCUUGCCGUCCC
4037

[654-671] ORF

427
GCCAGGCACUAUGUGUCU
3003
AGACACAUAGUGCCUGGC
4038

[1179-1196] 3′UTR

428
GACACACUCACUUCUUUC
3004
GAAAGAAGUGAGUGUGUC
4039

[2095-2112] 3′UTR

429
CUGAGACCUUCCGGUGCU
3005
AGCACCGGAAGGUCUCAG
4040

[3520-3537] 3′UTR

430
CAGAAGAAGAGCCUGAAC
3006
GUUCAGGCUCUUCUUCUG
4041
Rh, Rb, Cw, Ms, Pg
[719-736] ORF

431
GAUAGGUGAACCUGAGUU
3007
AACUCAGGUUCACCUAUC
4042

[2180-2197] 3′UTR

432
GUUCUAUUCAGCGGCAAC
3008
GUUGCCGCUGAAUAGAAC
4043

[2503-2520] 3′UTR

433
AGACUGGGAGGGUAUCCA
3009
UGGAUACCCUCCCAGUCU
4044
Rh
[2623-2640] 3′UTR

434
GGCCAACUGCAAAAAAAG
3010
CUUUUUUUGCAGUUGGCC
4045

[986-1003] 3′UTR

435
UGGCCUUUAUAUUUGAUC
3011
GAUCAAAUAUAAAGGCCA
4046

[3124-3141] 3′UTR

436
GCUGGGAACACACAAGAG
3012
CUCUUGUGUGUUCCCAGC
4047

[3535-3552] 3′UTR

437
GUGGAAGCAUUUGACCCA
3013
UGGGUCAAAUGCUUCCAC
4048

[2954-2971] 3′UTR

438
CCAUGAUCCCGUGCUACA
3014
UGUAGCACGGGAUCAUGG
4049
Rh, Rb
[780-797] ORF

439
CAGGCAGCACUUAGGGAU
3015
AUCCCUAAGUGCUGCCUG
4050
Rh
[1282-1299] 3′UTR

440
GCAAAGUAAAGGAUCUUU
3016
AAAGAUCCUUUACUUUGC
4051

[83-3100] 3′UTR

441
GUGGACAAUAAACAGUAU
3017
AUACUGUUUAUUGUCCAC
4052

[3625-3642] 3′UTR

442
UGCAAAAAAAGCCUCCAA
3018
UUGGAGGCUUUUUUUGCA
4053

[993-1010] 3′UTR

443
CAAGCAGGAGUUUCUCGA
3019
UCGAGAAACUCCUGCUUG
4054
Ck, Dg
[931-948] ORF

444
CGUUCCAGCCUCAGCUGA
3020
UCAGCUGAGGCUGGAACG
4055

[1651-1668] 3′UTR

445
CGGUCCGUGGACAAUAAA
3021
UUUAUUGUCCACGGACCG
4056

[3619-3636] 3′UTR

446
UAGGAUAGGAAGAACUUU
3022
AAAGUUCUUCCUAUCCUA
4057

[2325-2342] 3′UTR

447
AGCUGAGUCUUUUUGGUC
3023
GACCAAAAAGACUCAGCU
4058
Rh
[1663-1680] 3′UTR

448
UGGCUUUGGUGACACACU
3024
AGUGUGUCACCAAAGCCA
4059

[2085-2102] 3′UTR

449
GCCGGUGGCUGCCCUCAA
3025
UUGAGGGCAGCCACCGGC
4060
Rh
[1774-1791] 3′UTR

450
CCUGGAACCAGUGGCUAG
3026
CUAGCCACUGGUUCCAGG
4061

[1532-1549] 3′UTR

451
GCCUGUUCUGGCAUCAGG
3027
CCUGAUGCCAGAACAGGC
4062

[1830-1847] 3′UTR

452
GACAGAAAAAGCUGGGUC
3028
GACCCAGCUUUUUCUGUC
4063
Rh
[1930-1947] 3′UTR

453
CAGCCUCCAGGACACUAU
3029
AUAGUGUCCUGGAGGCUG
4064

[2114-2131] 3′UTR

454
GAAGCAUUUGACCCAGAG
3030
CUCUGGGUCAAAUGCUUC
4065

[2957-2974] 3′UTR

455
GGCAUCAGGCACCUGGAU
3031
AUCCAGGUGCCUGAUGCC
4066

[1839-1856] 3′UTR

456
AGGAUAGGAAGAACUUUC
3032
GAAAGUUCUUCCUAUCCU
4067

[2326-2343] 3′UTR

457
AGUGCAAGAUCACGCGCU
3033
AGCGCGUGAUCUUGCACU
4068
Dg, Pg
[759-776] ORF

458
CUUCGAUCCUUGGGUGCA
3034
UGCACCCAAGGAUCGAAG
4069
Rh
[1201-1218] 3′UTR

459
GUAAAGGAUCUUUGAGUA
3035
UACUCAAAGAUCCUUUAC
4070

[88-3105] 3′UTR

460
CAGGCACCUGGAUUGAGU
3036
ACUCAAUCCAGGUGCCUG
4071
Rh
[1844-1861] 3′UTR

461
AUAAGGAGAAUCUCUUGU
3037
ACAAGAGAUUCUCCUUAU
4072

[2353-2370] 3′UTR

462
UUCCCUCCCUCAAAGACU
3038
AGUCUUUGAGGGAGGGAA
4073

[1973-1990] 3′UTR

463
UCUGGAAACGACAUUUAU
3039
AUAAAUGUCGUUUCCAGA
4074

[470-487] ORF

464
GUAAGAAGUCCAGCCUAG
3040
CUAGGCUGGACUUCUUAC
4075
Rh
[2043-2060] 3′UTR

465
CAAAACAGGUUAAGAAGA
3041
UCUUCUUAACCUGUUUUG
4076

[3179-3196] 3′UTR

466
GGUUGCCAUUGCUUCUUG
3042
CAAGAAGCAAUGGCAACC
4077
Rh
[1813-1830] 3′UTR

467
AGGUCCUCAUCCCAUCCU
3043
AGGAUGGGAUGAGGACCU
4078
Rh
[1155-1172] 3′UTR

468
GUCCGUGGACAAUAAACA
3044
UGUUUAUUGUCCACGGAC
4079

[3621-3638] 3′UTR

469
UGUGUUUAUGCUGGAAUA
3045
UAUUCCAGCAUAAACACA
4080

[3496-3513] 3′UTR

470
GGGCGUUUUCAUGCUGUA
3046
UACAGCAUGAAAACGCCC
4081
Rh
[2661-2678] 3′UTR

471
GGCACCUGGAUUGAGUUG
3047
CAACUCAAUCCAGGUGCC
4082

[1846-1863] 3′UTR

472
CUGUAAUCAUUCCUGUGC
3048
GCACAGGAAUGAUUACAG
4083
Rh
[2872-2889] 3′UTR

473
GGCCUGGAAAUGUGCAUU
3049
AAUGCACAUUUCCAGGCC
4084
Rh
[1321-1338] 3′UTR

474
GGGUCGUUGCAAGACUGU
3050
ACAGUCUUGCAACGACCC
4085

[1355-1372] 3′UTR

475
CAGGCGUUUUGCAAUGCA
3051
UGCAUUGCAAAACGCCUG
4086
Cw, Rt, Ms
[407-424] ORF

476
AGGGUAUCCAGGAAUCGG
3052
CCGAUUCCUGGAUACCCU
4087

[2631-2648] 3′UTR

477
CUGGAAAUGUGCAUUUUG
3053
CAAAAUGCACAUUUCCAG
4088
Rh
[1324-1341] 3′UTR

478
GGUGGCUGCCCUCAAGGU
3054
ACCUUGAGGGCAGCCACC
4089
Rh
[1777-1794] 3′UTR

479
GGUCCAGCUCUGACAUCC
3055
GGAUGUCAGAGCUGGACC
4090
Rh
[1022-1039] 3′UTR

480
GCGGCCUGGGCGUGGUCU
3056
AGACCACGCCCAGGCCGC
4091

[2455-2472] 3′UTR

481
UGCAUUUUGCAGAAACUU
3057
AAGUUUCUGCAAAAUGCA
4092
Rh
[1333-1350] 3′UTR

482
GUCUUUUAACCGUGCUGA
3058
UCAGCACGGUUAAAAGAC
4093

[3153-3170] 3′UTR

483
CUCAAGGUCCCUUCCCUA
3059
UAGGGAAGGGACCUUGAG
4094

[1787-1804] 3′UTR

484
AUCCAGUAUGAGAUCAAG
3060
CUUGAUCUCAUACUGGAU
4095
Rh, Rb
[506-523] ORF

485
GUCUGAAAGGUGUGGCCU
3061
AGGCCACACCUUUCAGAC
4096

[3112-3129] 3′UTR

486
GACGUUGGAGGAAAGAAG
3062
CUUCUUUCCUCCAACGUC
4097
Rt, Ms
[608-625] ORF

487
CUUGUUUCCUCCCACCUG
3063
CAGGUGGGAGGAAACAAG
4098

[2366-2383] 3′UTR

488
GACCUGGUCAGCACAGAU
3064
AUCUGUGCUGACCAGGUC
4099
Rh
[2581-2598] 3′UTR

489
GUUGCAGAUAUACCAACU
3065
AGUUGGUAUAUCUGCAAC
4100
Rh
[2195-2212] 3′UTR

490
CCACACACGUUGGUCUUU
3066
AAAGACCAACGUGUGUGG
4101

[3141-3158] 3′UTR

491
CCCUCUGUGACUUCAUCG
3067
CGAUGAAGUCACAGAGGG
4102
Rh, Cw
[675-692] ORF

492
GAUCCUUGGGUGCAGGCA
3068
UGCCUGCACCCAAGGAUC
4103
Rh
[1205-1222] 3′UTR

493
CAAUGAAACCGAAGCUUG
3069
CAAGCUUCGGUUUCAUUG
4104

[2437-2454] 3′UTR

494
AGCCUUGUAGAAAUGGGA
3070
UCCCAUUUCUACAAGGCU
4105
Rh
[1611-1628] 3′UTR

495
CUGUUCGCUUCCUGUAUG
3071
CAUACAGGAAGCGAACAG
4106

[2779-2796] 3′UTR

496
AUGUGUUCCCUCAGUGUG
3072
CACACUGAGGGAACACAU
4107

[2280-2297] 3′UTR

497
CCAAGCAGGCAGCACUUA
3073
UAAGUGCUGCCUGCUUGG
4108

[1277-1294] 3′UTR

498
GCGAGUGCAAGAUCACGC
3074
GCGUGAUCUUGCACUCGC
4109

[756-773] ORF

499
AUAGUUUAAGAAGGCUCU
3075
AGAGCCUUCUUAAACUAU
4110

[3262-3279] 3′UTR

500
CAGACUGCGCAUGUCUCU
3076
AGAGACAUGCGCAGUCUG
4111

[3571-3588] 3′UTR

501
CCUGUUUUAAGAGACAUC
3077
GAUGUCUCUUAAAACAGG
4112
Rh
[2134-2151] 3′UTR

502
UCAGUAUAUACAACUCCA
3078
UGGAGUUGUAUAUACUGA
4113
Rh
[2728-2745] 3′UTR

503
CGGCAAGAUGCACAUCAC
3079
GUGAUGUGCAUCUUGCCG
4114
Rh, Ck, Dg, Pg
[658-675] ORF

504
CAUCAGCUGUAAUCAUUC
3080
GAAUGAUUACAGCUGAUG
4115

[2866-2883] 3′UTR

505
GCACCUGUUAAGACUCCU
3081
AGGAGUCUUAACAGGUGC
4116
Rh
[2527-2544] 3′UTR

506
GUCUGAGACCUUCCGGUG
3082
CACCGGAAGGUCUCAGAC
4117

[3518-3535] 3′UTR

507
CUUCUUUCUCAGCCUCCA
3083
UGGAGGCUGAGAAAGAAG
4118

[2105-2122] 3′UTR

508
GAUAAGGAGAAUCUCUUG
3084
CAAGAGAUUCUCCUUAUC
4119

[2352-2369] 3′UTR

509
AGAUAUACCAACUUCUGC
3085
GCAGAAGUUGGUAUAUCU
4120
Rh
[2200-2217] 3′UTR

510
CUAUGCAGGUGGAUUCCU
3086
AGGAAUCCACCUGCAUAG
4121
Rh
[2988-3005] 3′UTR

511
AGGAAGCCGCUCAAAUAC
3087
GUAUUUGAGCGGCUUCCU
4122

[3216-3233] 3′UTR

512
CGUGCUACAUCUCCUCCC
3088
GGGAGGAGAUGUAGCACG
4123
Rh
[789-806] ORF

513
AAAAAAGGUUUCUGCAUC
3089
GAUGCAGAAACCUUUUUU
4124

[2936-2953] 3′UTR

514
GGACACGCGGCUUCCCUC
3090
GAGGGAAGCCGCGUGUCC
4125

[1229-1246] 3′UTR

515
UAGAGUUUAUCUACACGG
3091
CCGUGUAGAUAAACUCUA
4126
Dg, Pg
[558-575] ORF

516
UCAAAGACUGACAGCCAU
3092
AUGGCUGUCAGUCUUUGA
4127
Rh
[1982-1999] 3′UTR

517
UGACAUCAGCUGUAAUCA
3093
UGAUUACAGCUGAUGUCA
4128

[2863-2880] 3′UTR

518
AGUUGCACAGCUUUGCUU
3094
AAGCAAAGCUGUGCAACU
4129

[1859-1876] 3′UTR

519
AGUGGCUAGUUCUUGAAG
3095
CUUCAAGAACUAGCCACU
4130

[1541-1558] 3′UTR

520
UGGCAACCCUAUCAAGAG
3096
CUCUUGAUAGGGUUGCCA
4131

[487-504] ORF

521
GUGGCUGCCCUCAAGGUC
3097
GACCUUGAGGGCAGCCAC
4132
Rh
[1778-1795] 3′UTR

522
GCGUUUUGCAAUGCAGAU
3098
AUCUGCAUUGCAAAACGC
4133

[410-427] ORF

523
GAUCAAGCAGAUAAAGAU
3099
AUCUUUAUCUGCUUGAUC
4134
Cw, Dg, Rt, Ms, Pg
[517-534] ORF

524
GCAGGCAGCACUUAGGGA
3100
UCCCUAAGUGCUGCCUGC
4135
Rh
[1281-1298] 3′UTR

525
CUCCAACCCAUAUAACAC
3101
GUGUUAUAUGGGUUGGAG
4136

[2754-2771] 3′UTR

526
GAACUAGGGAACCUAUGU
3102
ACAUAGGUUCCCUAGUUC
4137
Rh
[2266-2283] 3′UTR

527
GACGAUAUACAGGCACAU
3103
AUGUGCCUGUAUAUCGUC
4138

[2401-2418] 3′UTR

528
GAAAUAUUGGACUUGCUG
3104
CAGCAAGUCCAAUAUUUC
4139

[3419-3436] 3′UTR

529
GAAGCCGCUCAAAUACCU
3105
AGGUAUUUGAGCGGCUUC
4140

[3218-3235] 3′UTR

530
GGCAGCCUGGAACCAGUG
3106
CACUGGUUCCAGGCUGCC
4141

[1527-1544] 3′UTR

531
GUCUGGAGGGAGACGUGG
3107
CCACGUCUCCCUCCAGAC
4142

[1132-1149] 3′UTR

532
CAUAGUAAGAAGUCCAGC
3108
GCUGGACUUCUUACUAUG
4143

[2039-2056] 3′UTR

533
CUCCUGUUUCUGCUGAUU
3109
AAUCAGCAGAAACAGGAG
4144

[2819-2836] 3′UTR

534
CAGAAUUCCAGUGGGAGC
3110
GCUCCCACUGGAAUUCUG
4145
Rh
[1584-1601] 3′UTR

535
AGCACUGUGUUUAUGCUG
3111
CAGCAUAAACACAGUGCU
4146

[3491-3508] 3′UTR

536
GUAACAUUUACUCCUGUU
3112
AACAGGAGUAAAUGUUAC
4147
Rh
[2809-2826] 3′UTR

537
UGAGCUGCGUUCCAGCCU
3113
AGGCUGGAACGCAGCUCA
4148

[1644-1661] 3′UTR

538
AGGUGGAUUCCUUCAGGU
3114
ACCUGAAGGAAUCCACCU
4149
Rh
[2994-3011] 3′UTR

539
UUUGUUUCCGUUUGGAUU
3115
AAUCCAAACGGAAACAAA
4150

[3460-3477] 3′UTR

540
AAAGGAUCUUUGAGUAGG
3116
CCUACUCAAAGAUCCUUU
4151

[3090-3107] 3′UTR

541
GGUCUGGAGGGAGACGUG
3117
CACGUCUCCCUCCAGACC
4152

[1131-1148] 3′UTR

542
UGAGAUCAAGCAGAUAAA
3118
UUUAUCUGCUUGAUCUCA
4153
Rh, Cw, Dg, Rt, Ms
[514-531] ORF

543
GGAGGGUAUCCAGGAAUC
3119
GAUUCCUGGAUACCCUCC
4154

[2629-2646] 3′UTR

544
GAGUUGCACAGCUUUGCU
3120
AGCAAAGCUGUGCAACUC
4155

[1858-1875] 3′UTR

545
CCUUCACAAUAAAUAGUG
3121
CACUAUUUAUUGUGAAGG
4156

[3233-3250] 3′UTR

546
CUUGUUUUCUGCAGCUUC
3122
GAAGCUGCAGAAAACAAG
4157
Rh
[1418-1435] 3′UTR

547
AUUGAGUUGCACAGCUUU
3123
AAAGCUGUGCAACUCAAU
4158

[1855-1872] 3′UTR

548
UGAUUUUGUUUCCGUUUG
3124
CAAACGGAAACAAAAUCA
4159

[3456-3473] 3′UTR

549
CAGCUCUCUUCUCCUAUU
3125
AAUAGGAGAAGAGAGCUG
4160

[3320-3337] 3′UTR

550
GGCCUACCAGGUCCCUUU
3126
AAAGGGACCUGGUAGGCC
4161
Rh
[1379-1396] 3′UTR

551
UGUUAUGUUCUAAGCACA
3127
UGUGCUUAGAACAUAACA
4162

[3304-3321] 3′UTR

552
GAGCCGGGUGGCAGCUGA
3128
UCAGCUGCCACCCGGCUC
4163

[3195-3212] 3′UTR

553
GGAGGAAUCGGUGAGGUC
3129
GACCUCACCGAUUCCUCC
4164

[1733-1750] 3′UTR

554
CCUGGGACACCCUGAGCA
3130
UGCUCAGGGUGUCCCAGG
4165
Rh, Dg, Pg
[696-713] ORF

555
UGUGCAUUUUGCAGAAAC
3131
GUUUCUGCAAAAUGCACA
4166
Rh, Rt, Ms
[1331-1348] 3′UTR

556
CCCUCUGCCAGGCACUAU
3132
AUAGUGCCUGGCAGAGGG
4167

[1173-1190] 3′UTR

557
AGUCUGAGACCUUCCGGU
3133
ACCGGAAGGUCUCAGACU
4168

[3517-3534] 3′UTR

558
CAACUUCUGCUUGUAUUU
3134
AAAUACAAGCAGAAGUUG
4169
Rh
[2208-2225] 3′UTR

559
CAGCCUGGAACCAGUGGC
3135
GCCACUGGUUCCAGGCUG
4170

[1529-1546] 3′UTR

560
GCUUUGGUGACACACUCA
3136
UGAGUGUGUCACCAAAGC
4171

[2087-2104] 3′UTR

561
CGCCUGCAUCAAGAGAAG
3137
CUUCUCUUGAUGCAGGCG
4172
Rh, Cw, Dg, Rt, Ms
[874-891] ORF

562
CUCCAAGGGUUUCGACUG
3138
CAGUCGAAACCCUUGGAG
4173
Rh
[1005-1022] 3′UTR

563
UGCUGGGAACACACAAGA
3139
UCUUGUGUGUUCCCAGCA
4174

[3534-3551] 3′UTR

564
ACAUUUACUCCUGUUUCU
3140
AGAAACAGGAGUAAAUGU
4175
Rh
[2812-2829] 3′UTR

565
GGUUUCGACUGGUCCAGC
3141
GCUGGACCAGUCGAAACC
4176
Rh
[1012-1029] 3′UTR

566
CAGCUGUAAUCAUUCCUG
3142
CAGGAAUGAUUACAGCUG
4177

[2869-2886] 3′UTR

567
CCAUCUGCACAUCCUGAG
3143
CUCAGGAUGUGCAGAUGG
4178
Rh
[1912-1929] 3′UTR

568
CAUCCCAUGGGUCCAAAU
3144
AUUUGGACCCAUGGGAUG
4179

[1069-1086] 3′UTR

569
CUGUUUCUGCUGAUUGUU
3145
AACAAUCAGCAGAAACAG
4180

[2822-2839] 3′UTR

570
GUGGCUUUGGUGACACAC
3146
GUGUGUCACCAAAGCCAC
4181

[2084-2101] 3′UTR

571
GGCAGCUGACAGAGGAAG
3147
CUUCCUCUGUCAGCUGCC
4182

[3204-3221] 3′UTR

572
AGAUCUUGAUGACUUCCC
3148
GGGAAGUCAUCAAGAUCU
4183
Rh
[2595-2612] 3′UTR

573
UGCAAGACUGUGUAGCAG
3149
CUGCUACACAGUCUUGCA
4184
Rh
[1362-1379] 3′UTR

574
CAGAUGUAGUGAUCAGGG
3150
CCCUGAUCACUACAUCUG
4185

[423-440] ORF

575
CAUUUGGCAUCGUUUAAU
3151
AUUAAACGAUGCCAAAUG
4186

[3281-3298] 3′UTR

576
CAGAAAAAGCUGGGUCUU
3152
AAGACCCAGCUUUUUCUG
4187
Rh
[1932-1949] 3′UTR

577
CCCAGAGUGGAACGCGUG
3153
CACGCGUUCCACUCUGGG
4188

[2968-2985] 3′UTR

578
ACCUGUUAAGACUCCUGA
3154
UCAGGAGUCUUAACAGGU
4189
Rh
[2529-2546] 3′UTR

579
CAUCACCCUCUGUGACUU
3155
AAGUCACAGAGGGUGAUG
4190
Rh, Cw
[670-687] ORF

580
GGCUUCGAUCCUUGGGUG
3156
CACCCAAGGAUCGAAGCC
4191
Rh
[1199-1216] 3′UTR

581
CCUUGGCACCGUCACAGA
3157
UCUGUGACGGUGCCAAGG
4192
Rh
[1257-1274] 3′UTR

582
CAAGAGAAGUGACGGCUC
3158
GAGCCGUCACUUCUCUUG
4193

[883-900] ORF

583
AGCUCUCUUCUCCUAUUU
3159
AAAUAGGAGAAGAGAGCU
4194

[3321-3338] 3′UTR

584
GCAGCCUGGAACCAGUGG
3160
CCACUGGUUCCAGGCUGC
4195

[1528-1545] 3′UTR

585
UGGACUCUGGAAACGACA
3161
UGUCGUUUCCAGAGUCCA
4196
Rh
[465-482] ORF

586
CACUCACUUCUUUCUCAG
3162
CUGAGAAAGAAGUGAGUG
4197

[2099-2116] 3′UTR

587
ACCGUGCUGAGCAGAAAA
3163
UUUUCUGCUCAGCACGGU
4198

[3161-3178] 3′UTR

588
AGAAUCUCUUGUUUCCUC
3164
GAGGAAACAAGAGAUUCU
4199

[2359-2376] 3′UTR

589
ACAGCUCUCUUCUCCUAU
3165
AUAGGAGAAGAGAGCUGU
4200

[3319-3336] 3′UTR

590
UCCUCAGAAUUCCAGUGG
3166
CCACUGGAAUUCUGAGGA
4201
Rh
[1580-1597] 3′UTR

591
GGCCCUUGUUUUCUGCAG
3167
CUGCAGAAAACAAGGGCC
4202
Rh
[1414-1431] 3′UTR

592
GUGGGUCUGGAGGGAGAC
3168
GUCUCCCUCCAGACCCAC
4203
Rh
[1128-1145] 3′UTR

593
AUCUCUUGUUUCCUCCCA
3169
UGGGAGGAAACAAGAGAU
4204

[2362-2379] 3′UTR

594
GAACCACAGGUACCAGAU
3170
AUCUGGUACCUGUGGUUC
4205
Rh, Rb, Cw, Rt,
[733-750] ORF

Ms, Pg

595
GCCUCCAAGGGUUUCGAC
3171
GUCGAAACCCUUGGAGGC
4206
Rh
[1003-1020] 3′UTR

596
CAGCAUGAAUAAAACACU
3172
AGUGUUUUAUUCAUGCUG
4207
Rh
[1051-1068] 3′UTR

597
CACCCAGAAGAAGAGCCU
3173
AGGCUCUUCUUCUGGGUG
4208
Rh, Ck, Cw, Rt,
[715-732] ORF

Ms, Pg

598
UCAUAAUGGACCAGUCCA
3174
UGGACUGGUCCAUUAUGA
4209
Rh
[2703-2720] 3′UTR

599
ACAUCACCCUCUGUGACU
3175
AGUCACAGAGGGUGAUGU
4210
Rh
[669-686] ORF

600
CCUUCCUGGAAACAGCAU
3176
AUGCUGUUUCCAGGAAGG
4211
Rh, Rb, Rt, Ms
[1039-1056] 3′UTR

601
AGCCUCCAAGGGUUUCGA
3177
UCGAAACCCUUGGAGGCU
4212
Rh
[1002-1019] 3′UTR

602
UGACACACUCACUUCUUU
3178
AAAGAAGUGAGUGUGUCA
4213

[2094-2111] 3′UTR

603
UGUGGGUCUGGAGGGAGA
3179
UCUCCCUCCAGACCCACA
4214
Rh
[1127-1144] 3′UTR

604
AGGCUCUCCAUUUGGCAU
3180
AUGCCAAAUGGAGAGCCU
4215

[3273-3290] 3′UTR

605
CCAGUCCAUGUGAUUUCA
3181
UGAAAUCACAUGGACUGG
4216
Rh
[2713-2730] 3′UTR

606
GACGUGGGUCCAAGGUCC
3182
GGACCUUGGACCCACGUC
4217

[1143-1160] 3′UTR

607
GGACAGAAAAAGCUGGGU
3183
ACCCAGCUUUUUCUGUCC
4218
Rh
[1929-1946] 3′UTR

608
CUACCAGGUCCCUUUCAU
3184
AUGAAAGGGACCUGGUAG
4219
Rh
[1382-1399] 3′UTR

609
AAUCCUCAGAAUUCCAGU
3185
ACUGGAAUUCUGAGGAUU
4220
Rh
[1578-1595] 3′UTR

610
CUUUGAGUAGGUUCGGUC
3186
GACCGAACCUACUCAAAG
4221

[97-3114] 3′UTR

611
GCCGGGUGGCAGCUGACA
3187
UGUCAGCUGCCACCCGGC
4222

[3197-3214] 3′UTR

612
GCAGAAACUUUUGAGGGU
3188
ACCCUCAAAAGUUUCUGC
4223
Rh
[1341-1358] 3′UTR

613
CAGUGGCUAGUUCUUGAA
3189
UUCAAGAACUAGCCACUG
4224

[1540-1557] 3′UTR

614
GAAAUGGGAGCGAGAAAC
3190
GUUUCUCGCUCCCAUUUC
4225

[1620-1637] 3′UTR

615
GCAGACUGCGCAUGUCUC
3191
GAGACAUGCGCAGUCUGC
4226

[3570-3587] 3′UTR

616
UGUAAUCAUUCCUGUGCU
3192
AGCACAGGAAUGAUUACA
4227
Rh
[2873-2890] 3′UTR

617
UGGUAGGUAUUAGACUUG
3193
CAAGUCUAAUACCUACCA
4228

[2908-2925] 3′UTR

618
CAUUUACUCCUGUUUCUG
3194
CAGAAACAGGAGUAAAUG
4229
Rh
[2813-2830] 3′UTR

619
AUGAAGUCUGAGACCUUC
3195
GAAGGUCUCAGACUUCAU
4230

[3513-3530] 3′UTR

620
CUUGAUGACUUCCCUUUC
3196
GAAAGGGAAGUCAUCAAG
4231
Rh
[2599-2616] 3′UTR

621
CAACAGGCGUUUUGCAAU
3197
AUUGCAAAACGCCUGUUG
4232
Cw, Rt, Ms
[404-421] ORF 3′UTR

622
CCAUAAGCAGGCCUCCAA
3198
UUGGAGGCCUGCUUAUGG
4233

[959-976] ORF 3′UTR

623
GUACAGUGACCUAAAGUU
3199
AACUUUAGGUCACUGUAC
4234

[2676-2693] 3′UTR

624
GCAUAGUAAGAAGUCCAG
3200
CUGGACUUCUUACUAUGC
4235

[2038-2055] 3′UTR

625
ACACUCACUUCUUUCUCA
3201
UGAGAAAGAAGUGAGUGU
4236

[2098-2115] 3′UTR

626
AUCAAGAGGAUCCAGUAU
3202
AUACUGGAUCCUCUUGAU
4237
Rh, Rb
[497-514] ORF

627
AGUGAGAAGGAAGUGGAC
3203
GUCCACUUCCUUCUCACU
4238

[452-469] ORF

628
GCCUAUGCAGGUGGAUUC
3204
GAAUCCACCUGCAUAGGC
4239
Rh
[2986-3003] 3′UTR

629
CACCGUCACAGAUGCCAA
3205
UUGGCAUCUGUGACGGUG
4240

[1263-1280] 3′UTR

630
CUUUCUAGGGCAGACUGG
3206
CCAGUCUGCCCUAGAAAG
4241
Rh
[2612-2629] 3′UTR

631
CCCUCCCUCAAAGACUGA
3207
UCAGUCUUUGAGGGAGGG
4242

[1975-1992] 3′UTR

632
CUAAGCAUAGUAAGAAGU
3208
ACUUCUUACUAUGCUUAG
4243

[2034-2051] 3′UTR

633
CAGAUAUACCAACUUCUG
3209
CAGAAGUUGGUAUAUCUG
4244
Rh
[2199-2216] 3′UTR

634
UUGCAGAUAUACCAACUU
3210
AAGUUGGUAUAUCUGCAA
4245
Rh
[2196-2213] 3′UTR

635
GCCUCCCUCUGAGCCUUG
3211
CAAGGCUCAGAGGGAGGC
4246
Rh
[1600-1617] 3′UTR

636
GGAAAUGUGCAUUUUGCA
3212
UGCAAAAUGCACAUUUCC
4247
Rh
[1326-1343] 3′UTR

637
CUCCCAGGCUUAGUGUUC
3213
GAACACUAAGCCUGGGAG
4248

[1958-1975] 3′UTR

638
CUUUGGUGACACACUCAC
3214
GUGAGUGUGUCACCAAAG
4249

[2088-2105] 3′UTR

639
CAUCAAGAGAAGUGACGG
3215
CCGUCACUUCUCUUGAUG
4250

[880-897] ORF

640
CAGCCAUCGUUCUGCACG
3216
CGUGCAGAACGAUGGCUG
4251
Rh
[1993-2010] 3′UTR

641
CAAAGACUGACAGCCAUC
3217
GAUGGCUGUCAGUCUUUG
4252
Rh
[1983-2000] 3′UTR

642
AGCAGAAAACAAAACAGG
3218
CCUGUUUUGUUUUCUGCU
4253

[3170-3187] 3′UTR

643
GCACUUAGGGAUCUCCCA
3219
UGGGAGAUCCCUAAGUGC
4254
Rh
[1288-1305] 3′UTR

644
UGGACCAGUCCAUGUGAU
3220
AUCACAUGGACUGGUCCA
4255
Rh
[2709-2726] 3′UTR

645
AUGUGCAUUUUGCAGAAA
3221
UUUCUGCAAAAUGCACAU
4256
Rh, Ms
[1330-1347] 3′UTR

646
UGUAACAUUUACUCCUGU
3222
ACAGGAGUAAAUGUUACA
4257
Rh
[2808-2825] 3′UTR

647
GCUGUAAUCAUUCCUGUG
3223
CACAGGAAUGAUUACAGC
4258
Rh
[2871-2888] 3′UTR

648
UAAGGAGAAUCUCUUGUU
3224
AACAAGAGAUUCUCCUUA
4259

[2354-2371] 3′UTR

649
UGACAAGCAGACUGCGCA
3225
UGCGCAGUCUGCUUGUCA
4260

[3564-3581] 3′UTR

650
UCCUGUAUGGUGAUAUCA
3226
UGAUAUCACCAUACAGGA
4261

[2788-2805] 3′UTR

651
GAUAGGAAGAACUUUCUC
3227
GAGAAAGUUCUUCCUAUC
4262
Rh
[2328-2345] 3′UTR

652
CAUUCCUGUGCUGUGUUU
3228
AAACACAGCACAGGAAUG
4263
Rh
[2879-2896] 3′UTR

653
CAAGGUCCCUUCCCUAGC
3229
GCUAGGGAAGGGACCUUG
4264

[1789-1806] 3′UTR

654
CCGUCUUUGGUUCUCCAG
3230
CUGGAGAACCAAAGACGG
4265

[3054-3071] 3′UTR

655
GCUUCUUGCCUGUUCUGG
3231
CCAGAACAGGCAAGAAGC
4266

[1823-1840] 3′UTR

656
UGGGCUGCGAGUGCAAGA
3232
UCUUGCACUCGCAGCCCA
4267
Ck, Rb, Rt
[750-767] ORF

657
GAUGGGCUGCGAGUGCAA
3233
UUGCACUCGCAGCCCAUC
4268
Ck, Rb, Rt
[748-765] ORF

658
CUGUUCUGGCAUCAGGCA
3234
UGCCUGAUGCCAGAACAG
4269

[1832-1849] 3′UTR

659
GGGUAUCCAGGAAUCGGC
3235
GCCGAUUCCUGGAUACCC
4270

[2632-2649] 3′UTR

660
GCAACCCUAUCAAGAGGA
3236
UCCUCUUGAUAGGGUUGC
4271

[489-506] ORF

661
CCCAUCUGCACAUCCUGA
3237
UCAGGAUGUGCAGAUGGG
4272
Rh
[1911-1928] 3′UTR

662
UAUAGUUUAAGAAGGCUC
3238
GAGCCUUCUUAAACUAUA
4273

[3261-3278] 3′UTR

663
AGCCUGAACCACAGGUAC
3239
GUACCUGUGGUUCAGGCU
4274
Rh, Rb, Cw, Ms, Pg
[728-745] ORF

664
CGUUGCAAGACUGUGUAG
3240
CUACACAGUCUUGCAACG
4275

[1359-1376] 3′UTR

665
CGUCACAGAUGCCAAGCA
3241
UGCUUGGCAUCUGUGACG
4276

[1266-1283] 3′UTR

666
UGAGAAGGAAGUGGACUC
3242
GAGUCCACUUCCUUCUCA
4277

[454-471] ORF

667
AUCCCUUCCUGGAAACAG
3243
CUGUUUCCAGGAAGGGAU
4278
Rh, Rb, Rt, Ms
[1036-1053] 3′UTR

668
CAAAGCACCUGUUAAGAC
3244
GUCUUAACAGGUGCUUUG
4279
Rh
[2523-2540] 3′UTR

669
AGGUCCCUUUCAUCUUGA
3245
UCAAGAUGAAAGGGACCU
4280
Rh
[1387-1404] 3′UTR

670
CCUUUUAGACAUGGUUGU
3246
ACAACCAUGUCUAAAAGG
4281

[1112-1129] 3′UTR

671
AGCCUAGGAAGGGAAGGA
3247
UCCUUCCCUUCCUAGGCU
4282
Rh
[2054-2071] 3′UTR

672
GCUUUAUCCGGGCUUGUG
3248
CACAAGCCCGGAUAAAGC
4283

[1873-1890] 3′UTR

673
CUCUUCUCCUAUUUUCAU
3249
AUGAAAAUAGGAGAAGAG
4284

[3325-3342] 3′UTR

674
CGUAAUUUAAAGCUCUGU
3250
ACAGAGCUUUAAAUUACG
4285

[3438-3455] 3′UTR

675
CCUAAAGUUGGUAAGAUG
3251
CAUCUUACCAACUUUAGG
4286
Rh
[2685-2702] 3′UTR

676
CUGUGCUGUGUUUUUUAU
3252
AUAAAAAACACAGCACAG
4287
Rh
[2884-2901] 3′UTR

677
ACCCAGAGUGGAACGCGU
3253
ACGCGUUCCACUCUGGGU
4288

[2967-2984] 3′UTR

678
GUUCUAAGCACAGCUCUC
3254
GAGAGCUGUGCUUAGAAC
4289

[3310-3327] 3′UTR

679
CUGUGUUUUUUAUUACCC
3255
GGGUAAUAAAAAACACAG
4290
Rh
[2889-2906] 3′UTR

680
GGACGGCAAGAUGCACAU
3256
AUGUGCAUCUUGCCGUCC
4291

[655-672] ORF

681
GUUGAUUUUGUUUCCGUU
3257
AACGGAAACAAAAUCAAC
4292

[3454-3471] 3′UTR

682
CUCCUUUUAGACAUGGUU
3258
AACCAUGUCUAAAAGGAG
4293

[1110-1127] 3′UTR

683
UGAUGCUUUGUAUCAUUC
3259
GAAUGAUACAAAGCAUCA
4294

[3588-3605] 3′UTR

684
CUUUAUCCGGGCUUGUGU
3260
ACACAAGCCCGGAUAAAG
4295

[1874-1891] 3′UTR

685
AUAGAGUUUAUCUACACG
3261
CGUGUAGAUAAACUCUAU
4296
Dg, Pg
[557-574] ORF

686
GGGAUCUCCCAGCUGGGU
3262
ACCCAGCUGGGAGAUCCC
4297

[1295-1312] 3′UTR

687
GUGAACCUGAGUUGCAGA
3263
UCUGCAACUCAGGUUCAC
4298
Rh
[2185-2202] 3′UTR

688
AGUGCCUCUGGAUGGACU
3264
AGUCCAUCCAGAGGCACU
4299
Rh, Rb, Cw, Dg,
[813-830] ORF

Rt, Ms

689
GAAAGUUGACAAGCAGAC
3265
GUCUGCUUGUCAACUUUC
4300

[3558-3575] 3′UTR

690
UUGCAAAAUGCUUCCAAA
3266
UUUGGAAGCAUUUUGCAA
4301
Rh
[2472-2489] 3′UTR

691
GUAAAGAUAAACUGACGA
3267
UCGUCAGUUUAUCUUUAC
4302
Rh
[2388-2405] 3′UTR

692
CCAAAGCCACCUUAGCCU
3268
AGGCUAAGGUGGCUUUGG
4303
Rh
[2485-2502] 3′UTR

693
AGAAAAAGCUGGGUCUUG
3269
CAAGACCCAGCUUUUUCU
4304
Rh
[1933-1950] 3′UTR

694
CUGCCGUAAUUUAAAGCU
3270
AGCUUUAAAUUACGGCAG
4305

[3434-3451] 3′UTR

695
UCCCUUUCAUCUUGAGAG
3271
CUCUCAAGAUGAAAGGGA
4306
Rh
[1390-1407] 3′UTR

696
GAUCUUGAUGACUUCCCU
3272
AGGGAAGUCAUCAAGAUC
4307
Rh
[2596-2613] 3′UTR

697
UCAGUGUGGUUUCCUGAA
3273
UUCAGGAAACCACACUGA
4308

[2290-2307] 3′UTR

698
GGAGCCUCCCUCUGAGCC
3274
GGCUCAGAGGGAGGCUCC
4309
Rh
[1597-1614] 3′UTR

699
UGGUAAGAUGUCAUAAUG
3275
CAUUAUGACAUCUUACCA
4310
Rh
[2693-2710] 3′UTR

700
AAGCAUUUGACCCAGAGU
3276
ACUCUGGGUCAAAUGCUU
4311

[2958-2975] 3′UTR

701
AGCUAAGAAACUUCCUAG
3277
CUAGGAAGUUUCUUAGCU
4312

[2247-2264] 3′UTR

702
CAGGUUAAGAAGAGCCGG
3278
CCGGCUCUUCUUAACCUG
4313

[3184-3201] 3′UTR

703
GACUGCGCAUGUCUCUGA
3279
UCAGAGACAUGCGCAGUC
4314

[3573-3590] 3′UTR

704
GUAGGUUCGGUCUGAAAG
3280
CUUUCAGACCGAACCUAC
4315

[3103-3120] 3′UTR

705
UGAAAGUUGACAAGCAGA
3281
UCUGCUUGUCAACUUUCA
4316

[3557-3574] 3′UTR

706
AACUUCUGCUUGUAUUUC
3282
GAAAUACAAGCAGAAGUU
4317
Rh
[2209-2226] 3′UTR

707
GACAAGCAGACUGCGCAU
3283
AUGCGCAGUCUGCUUGUC
4318

[3565-3582] 3′UTR

708
AAGUCUGAGACCUUCCGG
3284
CCGGAAGGUCUCAGACUU
4319

[3516-3533] 3′UTR

709
CUCUGACAUCCCUUCCUG
3285
CAGGAAGGGAUGUCAGAG
4320
Rh
[1029-1046] 3′UTR

710
GUAAACAUACACACGCAA
3286
UUGCGUGUGUAUGUUUAC
4321
Rh
[2422-2439] 3′UTR

711
CCUCUGGAUGGACUGGGU
3287
ACCCAGUCCAUCCAGAGG
4322
Rh, Rb, Cw, Dg,
[817-834] ORF

Rt, Ms, Pg

712
GAUGACUUCCCUUUCUAG
3288
CUAGAAAGGGAAGUCAUC
4323
Rh
[2602-2619] 3′UTR

713
CCUACCAGGUCCCUUUCA
3289
UGAAAGGGACCUGGUAGG
4324
Rh
[1381-1398] 3′UTR

714
CAAGGUCCUCAUCCCAUC
3290
GAUGGGAUGAGGACCUUG
4325

[1153-1170] 3′UTR

715
GAUCUUUGAGUAGGUUCG
3291
CGAACCUACUCAAAGAUC
4326

[3094-3111] 3′UTR

716
AGAAAUAUUGGACUUGCU
3292
AGCAAGUCCAAUAUUUCU
4327

[3418-3435] 3′UTR

717
CUGCCCUCAAGGUCCCUU
3293
AAGGGACCUUGAGGGCAG
4328
Rh
[1782-1799] 3′UTR

718
CUAGGGAACCUAUGUGUU
3294
AACACAUAGGUUCCCUAG
4329
Rh
[2269-2286] 3′UTR

719
CAAGCAGGCAGCACUUAG
3295
CUAAGUGCUGCCUGCUUG
4330

[1278-1295] 3′UTR

720
CCCACCGGGACCUGGUCA
3296
UGACCAGGUCCCGGUGGG
4331

[2573-2590] 3′UTR

721
GUUUCUGCAUCGUGGAAG
3297
CUUCCACGAUGCAGAAAC
4332
Rh
[2943-2960] 3′UTR

722
GUGACCUAAAGUUGGUAA
3298
UUACCAACUUUAGGUCAC
4333

[2681-2698] 3′UTR

723
UGGGAACACACAAGAGUU
3299
AACUCUUGUGUGUUCCCA
4334

[3537-3554] 3′UTR

724
GAAUCGGUGAGGUCCUGU
3300
ACAGGACCUCACCGAUUC
4335

[1737-1754] 3′UTR

725
CCCUCCCAGGCUUAGUGU
3301
ACACUAAGCCUGGGAGGG
4336

[1956-1973] 3′UTR

726
CCCACAUCCAAGGGCAGC
3302
GCUGCCCUUGGAUGUGGG
4337

[1515-1532] 3′UTR

727
AGCCUCCCUCUGAGCCUU
3303
AAGGCUCAGAGGGAGGCU
4338
Rh
[1599-1616] 3′UTR

728
CAUGAUCCCGUGCUACAU
3304
AUGUAGCACGGGAUCAUG
4339
Rh, Rb
[781-798] ORF

729
CAUAAUGGACCAGUCCAU
3305
AUGGACUGGUCCAUUAUG
4340
Rh
[2704-2721] 3′UTR

730
GUCACAGAUGCCAAGCAG
3306
CUGCUUGGCAUCUGUGAC
4341

[1267-1284] 3′UTR

731
UGCAUCAAGAGAAGUGAC
3307
GUCACUUCUCUUGAUGCA
4342

[878-895] ORF

732
GAGACCUUCCGGUGCUGG
3308
CCAGCACCGGAAGGUCUC
4343

[3522-3539] 3′UTR

733
UACCUAGCUAAGAAACUU
3309
AAGUUUCUUAGCUAGGUA
4344
Rh
[2242-2259] 3′UTR

734
GCUGCGUUCCAGCCUCAG
3310
CUGAGGCUGGAACGCAGC
4345

[1647-1664] 3′UTR

735
UGGUUUCCUGAAGCCAGU
3311
ACUGGCUUCAGGAAACCA
4346

[2296-2313] 3′UTR

736
GCAGAUGUAGUGAUCAGG
3312
CCUGAUCACUACAUCUGC
4347

[422-439] ORF

737
CACCUGGAUUGAGUUGCA
3313
UGCAACUCAAUCCAGGUG
4348

[1848-1865] 3′UTR

738
UUGGUUCUCCAGUUCAAA
3314
UUUGAACUGGAGAACCAA
4349

[60-3077] 3′UTR

739
CUUGGCACCGUCACAGAU
3315
AUCUGUGACGGUGCCAAG
4350
Rh
[1258-1275] 3′UTR

740
CUUCCAAAGCCACCUUAG
3316
CUAAGGUGGCUUUGGAAG
4351
Rh
[2482-2499] 3′UTR

741
GGGCCUGGAAAUGUGCAU
3317
AUGCACAUUUCCAGGCCC
4352
Rh
[1320-1337] 3′UTR

742
CACGCGGCUUCCCUCCCA
3318
UGGGAGGGAAGCCGCGUG
4353

[1232-1249] 3′UTR

743
CAAGUUCUUCGCCUGCAU
3319
AUGCAGGCGAAGAACUUG
4354
Rh, Rb, Cw, Dg, Ms
[865-882] ORF

744
CUGAAGCCAGUGAUAUGG
3320
CCAUAUCACUGGCUUCAG
4355

[2303-2320] 3′UTR

745
UUCUCAGCCUCCAGGACA
3321
UGUCCUGGAGGCUGAGAA
4356

[2110-2127] 3′UTR

746
UAUUACCCUUGGUAGGUA
3322
UACCUACCAAGGGUAAUA
4357

[2899-2916] 3′UTR

747
AGGAUCUUUGAGUAGGUU
3323
AACCUACUCAAAGAUCCU
4358

[92-3109] 3′UTR

748
GGCUUCCCUCCCAGUCCC
3324
GGGACUGGGAGGGAAGCC
4359

[1237-1254] 3′UTR

749
UCUCGGUAAUGAUAAGGA
3325
UCCUUAUCAUUACCGAGA
4360

[2342-2359] 3′UTR

750
GCUUGCAGGAGGAAUCGG
3326
CCGAUUCCUCCUGCAAGC
4361

[1726-1743] 3′UTR

751
GUGGUCUUGCAAAAUGCU
3327
AGCAUUUUGCAAGACCAC
4362

[2466-2483] 3′UTR

752
CCUCAGCUGAGUCUUUUU
3328
AAAAAGACUCAGCUGAGG
4363
Rh
[1659-1676] 3′UTR

753
AGAAGUGACGGCUCCUGU
3329
ACAGGAGCCGUCACUUCU
4364

[887-904] ORF

754
CGUGGUCUUGCAAAAUGC
3330
GCAUUUUGCAAGACCACG
4365

[2465-2482] 3′UTR

755
ACCGGGACCUGGUCAGCA
3331
UGCUGACCAGGUCCCGGU
4366

[2576-2593] 3′UTR

756
GAUCCACACACGUUGGUC
3332
GACCAACGUGUGUGGAUC
4367

[3138-3155] 3′UTR

757
UAUAUUUGAUCCACACAC
3333
GUGUGUGGAUCAAAUAUA
4368

[3131-3148] 3′UTR

758
ACCUAUGUGUUCCCUCAG
3334
CUGAGGGAACACAUAGGU
4369

[2276-2293] 3′UTR

759
GUUUUUUAUUACCCUUGG
3335
CCAAGGGUAAUAAAAAAC
4370
Rh
[2893-2910] 3′UTR

760
GAAGUGGACUCUGGAAAC
3336
GUUUCCAGAGUCCACUUC
4371

[461-478] ORF

761
CGCGGCUUCCCUCCCAGU
3337
ACUGGGAGGGAAGCCGCG
4372

[1234-1251] 3′UTR

762
CCCUAUCAAGAGGAUCCA
3338
UGGAUCCUCUUGAUAGGG
4373

[493-510] ORF

763
CCCGGACGAGUGCCUCUG
3339
CAGAGGCACUCGUCCGGG
4374
Rh, Rb, Cw
[805-822] ORF

764
CGGUUGCCAUUGCUUCUU
3340
AAGAAGCAAUGGCAACCG
4375
Rh
[1812-1829] 3′UTR

765
GCUGUGUUUUUUAUUACC
3341
GGUAAUAAAAAACACAGC
4376
Rh
[2888-2905] 3′UTR

766
CUUCCACGCCUCUGCACU
3342
AGUGCAGAGGCGUGGAAG
4377

[1432-1449] 3′UTR

767
GGACCCAUAAGCAGGCCU
3343
AGGCCUGCUUAUGGGUCC
4378
Rh
[955-972] ORF 3′UTR

768
CUGGCAAGUGCUCCCAUC
3344
GAUGGGAGCACUUGCCAG
4379

[1458-1475] 3′UTR

769
AAAGGUGUGGCCUUUAUA
3345
UAUAAAGGCCACACCUUU
4380

[3117-3134] 3′UTR

770
ACAGGCACAUUAUGUAAA
3346
UUUACAUAAUGUGCCUGU
4381

[2409-2426] 3′UTR

771
ACUUCCCUUUCUAGGGCA
3347
UGCCCUAGAAAGGGAAGU
4382
Rh
[2606-2623] 3′UTR

772
CUGUUGAUUUUGUUUCCG
3348
CGGAAACAAAAUCAACAG
4383

[3452-3469] 3′UTR

773
CAAAGGGCCUGAGAAGGA
3349
UCCUUCUCAGGCCCUUUG
4384

[538-555] ORF

774
CCUGAGCACCACCCAGAA
3350
UUCUGGGUGGUGCUCAGG
4385
Rh, Pg
[706-723] ORF

775
UCUUGAUGACUUCCCUUU
3351
AAAGGGAAGUCAUCAAGA
4386
Rh
[2598-2615] 3′UTR

776
GAGUGCAAGAUCACGCGC
3352
GCGCGUGAUCUUGCACUC
4387
Dg, Pg
[758-775] ORF

777
UUGUUUCCGUUUGGAUUU
3353
AAAUCCAAACGGAAACAA
4388

[3461-3478] 3′UTR

778
CCUCCCAGUCCCUGCCUU
3354
AAGGCAGGGACUGGGAGG
4389
Rh
[1243-1260] 3′UTR

779
AGGCCUACCAGGUCCCUU
3355
AAGGGACCUGGUAGGCCU
4390
Rh
[1378-1395] 3′UTR

780
CAAGAUGCACAUCACCCU
3356
AGGGUGAUGUGCAUCUUG
4391
Rh, Dg
[661-678] ORF

781
UGGAGGAAAGAAGGAAUA
3357
UAUUCCUUCUUUCCUCCA
4392
Rt
[613-630] ORF

782
UGACAAAGAUUACCUAGC
3358
GCUAGGUAAUCUUUGUCA
4393

[2232-2249] 3′UTR

783
GGUGGCUUUGGUGACACA
3359
UGUGUCACCAAAGCCACC
4394

[2083-2100] 3′UTR

784
UCACUUCUUUCUCAGCCU
3360
AGGCUGAGAAAGAAGUGA
4395

[2102-2119] 3′UTR

785
UAAUCAUUCCUGUGCUGU
3361
ACAGCACAGGAAUGAUUA
4396
Rh
[2875-2892] 3′UTR

786
AGUAGGUUCGGUCUGAAA
3362
UUUCAGACCGAACCUACU
4397

[3102-3119] 3′UTR

787
CGUUUUGCAAUGCAGAUG
3363
CAUCUGCAUUGCAAAACG
4398

[411-428] ORF

788
GGGCACCAGGCCAAGUUC
3364
GAACUUGGCCUGGUGCCC
4399
Rh, Rb, Rt, Ms
[854-871] ORF

789
ACAGAGAAGAACAUCAAC
3365
GUUGAUGUUCUUCUCUGU
4400
Rh
[836-853] ORF

790
CAAAAAAAGCCUCCAAGG
3366
CCUUGGAGGCUUUUUUUG
4401

[995-1012] 3′UTR

791
UUGGUAGGUAUUAGACUU
3367
AAGUCUAAUACCUACCAA
4402

[2907-2924] 3′UTR

792
GAGCACUGUGUUUAUGCU
3368
AGCAUAAACACAGUGCUC
4403

[3490-3507] 3′UTR

793
UGUACAGUGACCUAAAGU
3369
ACUUUAGGUCACUGUACA
4404

[2675-2692] 3′UTR

794
AAGAAAUAUUGGACUUGC
3370
GCAAGUCCAAUAUUUCUU
4405

[3417-3434] 3′UTR

795
CAGAAACUUUUGAGGGUC
3371
GACCCUCAAAAGUUUCUG
4406
Rh
[1342-1359] 3′UTR

796
UUCCCUUUCUAGGGCAGA
3372
UCUGCCCUAGAAAGGGAA
4407
Rh
[2608-2625] 3′UTR

797
CACAUCCAAGGGCAGCCU
3373
AGGCUGCCCUUGGAUGUG
4408

[1517-1534] 3′UTR

798
CAUCUUGAGAGGGACAUG
3374
CAUGUCCCUCUCAAGAUG
4409

[1397-1414] 3′UTR

799
GGCUUUCUGCAUGUGACG
3375
CGUCACAUGCAGAAAGCC
4410

[2012-2029] 3′UTR

800
UAGCUAAGAAACUUCCUA
3376
UAGGAAGUUUCUUAGCUA
4411

[2246-2263] 3′UTR

801
ACAUCCAAGGGCAGCCUG
3377
CAGGCUGCCCUUGGAUGU
4412

[1518-1535] 3′UTR

802
UGUUCCCUCCCUCAAAGA
3378
UCUUUGAGGGAGGGAACA
4413

[1971-1988] 3′UTR

803
GUCUUUUUGGUCUGCACC
3379
GGUGCAGACCAAAAAGAC
4414

[1669-1686] 3′UTR

804
CCAUGAGCUCCCAGCACC
3380
GGUGCUGGGAGCUCAUGG
4415

[1489-1506] 3′UTR

805
AGAUGUAGUGAUCAGGGC
3381
GCCCUGAUCACUACAUCU
4416

[424-441] ORF

806
GAGGUAGGUGGCUUUGGU
3382
ACCAAAGCCACCUACCUC
4417
Rh
[2077-2094] 3′UTR

807
AAGCCGCUCAAAUACCUU
3383
AAGGUAUUUGAGCGGCUU
4418

[3219-3236] 3′UTR

808
UGAGCCUUGUAGAAAUGG
3384
CCAUUUCUACAAGGCUCA
4419
Rh
[1609-1626] 3′UTR

809
GACGCCAGCUAAGCAUAG
3385
CUAUGCUUAGCUGGCGUC
4420

[2026-2043] 3′UTR

810
GCAGCUUCCACGCCUCUG
3386
CAGAGGCGUGGAAGCUGC
4421
Rh
[1428-1445] 3′UTR

811
AGAAUUCCAGUGGGAGCC
3387
GGCUCCCACUGGAAUUCU
4422
Rh
[1585-1602] 3′UTR

812
GAACGCGUGGCCUAUGCA
3388
UGCAUAGGCCACGCGUUC
4423
Rh
[2977-2994] 3′UTR

813
ACAGAAAAAGCUGGGUCU
3389
AGACCCAGCUUUUUCUGU
4424
Rh
[1931-1948] 3′UTR

814
AAGGAAUAUCUCAUUGCA
3390
UGCAAUGAGAUAUUCCUU
4425

[623-640] ORF

815
CAAGAGGAUCCAGUAUGA
3391
UCAUACUGGAUCCUCUUG
4426
Rh, Rb
[499-516] ORF

816
AGCUGACAGAGGAAGCCG
3392
CGGCUUCCUCUGUCAGCU
4427

[3207-3224] 3′UTR

817
AUAAAACACUCAUCCCAU
3393
AUGGGAUGAGUGUUUUAU
4428

[1059-1076] 3′UTR

818
GAAUCUCUUGUUUCCUCC
3394
GGAGGAAACAAGAGAUUC
4429

[2360-2377] 3′UTR

819
GUUAUGUUCUAAGCACAG
3395
CUGUGCUUAGAACAUAAC
4430

[3305-3322] 3′UTR

820
ACACGUUGGUCUUUUAAC
3396
GUUAAAAGACCAACGUGU
4431

[3145-3162] 3′UTR

821
GGUGCACCCGCAACAGGC
3397
GCCUGUUGCGGGUGCACC
4432
Cw, Dg, Rt, Ms
[394-411] ORF

822
UCUGCAUCGUGGAAGCAU
3398
AUGCUUCCACGAUGCAGA
4433
Rh
[2946-2963] 3′UTR

823
CUGCCAGGCACUAUGUGU
3399
ACACAUAGUGCCUGGCAG
4434

[1177-1194] 3′UTR

824
GAAGUCUGAGACCUUCCG
3400
CGGAAGGUCUCAGACUUC
4435

[3515-3532] 3′UTR

825
CUGGUCAGCACAGAUCUU
3401
AAGAUCUGUGCUGACCAG
4436
Rh
[2584-2601] 3′UTR

826
GUGCAUUUUGCAGAAACU
3402
AGUUUCUGCAAAAUGCAC
4437
Rh, Rt, Ms
[1332-1349] 3′UTR

827
UCAUCUUGAGAGGGACAU
3403
AUGUCCCUCUCAAGAUGA
4438

[1396-1413] 3′UTR

828
CACUUAGGGAUCUCCCAG
3404
CUGGGAGAUCCCUAAGUG
4439
Rh
[1289-1306] 3′UTR

829
CACGCAAUGAAACCGAAG
3405
CUUCGGUUUCAUUGCGUG
4440

[2433-2450] 3′UTR

830
GACUGACAGCCAUCGUUC
3406
GAACGAUGGCUGUCAGUC
4441
Rh
[1987-2004] 3′UTR

831
AUUGCAAAGUAAAGGAUC
3407
GAUCCUUUACUUUGCAAU
4442

[80-3097] 3′UTR

832
AGUGGAACGCGUGGCCUA
3408
UAGGCCACGCGUUCCACU
4443

[2973-2990] 3′UTR

833
GUUCGGUCUGAAAGGUGU
3409
ACACCUUUCAGACCGAAC
4444

[3107-3124] 3′UTR

834
UGCAGAUGUAGUGAUCAG
3410
CUGAUCACUACAUCUGCA
4445

[421-438] ORF

835
GUGUUCCCUCAGUGUGGU
3411
ACCACACUGAGGGAACAC
4446

[2282-2299] 3′UTR

836
UGCCGUAAUUUAAAGCUC
3412
GAGCUUUAAAUUACGGCA
4447

[3435-3452] 3′UTR

837
CUGCGGUUGCCAUUGCUU
3413
AAGCAAUGGCAACCGCAG
4448

[1809-1826] 3′UTR

838
CGGCUCCUGUGCGUGGUA
3414
UACCACGCACAGGAGCCG
4449
Rh
[895-912] ORF

839
GGGUUUCGACUGGUCCAG
3415
CUGGACCAGUCGAAACCC
4450
Rh
[1011-1028] 3′UTR

840
AGAGAAGAACAUCAACGG
3416
CCGUUGAUGUUCUUCUCU
4451
Rh, Rb, Cw
[838-855] ORF

841
AUGGACCAGUCCAUGUGA
3417
UCACAUGGACUGGUCCAU
4452
Rh
[2708-2725] 3′UTR

842
CCGUGCUACAUCUCCUCC
3418
GGAGGAGAUGUAGCACGG
4453
Rh
[788-805] ORF

843
CCAAAGCACCUGUUAAGA
3419
UCUUAACAGGUGCUUUGG
4454
Rh
[2522-2539] 3′UTR

844
CAACUGCAAAAAAAGCCU
3420
AGGCUUUUUUUGCAGUUG
4455

[989-1006] 3′UTR

845
CUUUCUCAGCCUCCAGGA
3421
UCCUGGAGGCUGAGAAAG
4456

[2108-2125] 3′UTR

846
UCUAAAGGUGAAUUCUCA
3422
UGAGAAUUCACCUUUAGA
4457
Ms
[2159-2176] 3′UTR

847
GCAGACUGGGAGGGUAUC
3423
GAUACCCUCCCAGUCUGC
4458
Rh
[2621-2638] 3′UTR

848
CUGGAACCAGUGGCUAGU
3424
ACUAGCCACUGGUUCCAG
4459

[1533-1550] 3′UTR

849
GACUGUGUAGCAGGCCUA
3425
UAGGCCUGCUACACAGUC
4460
Rh
[1367-1384] 3′UTR

850
GGCCAAGUUCUUCGCCUG
3426
CAGGCGAAGAACUUGGCC
4461
Rh, Rb, Cw, Dg, Ms
[862-879] ORF

851
GUUCGCUUCCUGUAUGGU
3427
ACCAUACAGGAAGCGAAC
4462

[2781-2798] 3′UTR

852
AAUUCCAGUGGGAGCCUC
3428
GAGGCUCCCACUGGAAUU
4463
Rh
[1587-1604] 3′UTR

853
UGCAAAAUGCUUCCAAAG
3429
CUUUGGAAGCAUUUUGCA
4464
Rh
[2473-2490] 3′UTR

854
CUGGAAUAUGAAGUCUGA
3430
UCAGACUUCAUAUUCCAG
4465
Ms
[3506-3523] 3′UTR

855
GCUGUGCCCUCCCAGGCU
3431
AGCCUGGGAGGGCACAGC
4466

[1950-1967] 3′UTR

856
CCAGAUGGGCUGCGAGUG
3432
CACUCGCAGCCCAUCUGG
4467
Rh, Ck, Rb, Rt
[745-762] ORF

857
GCGGUUGCCAUUGCUUCU
3433
AGAAGCAAUGGCAACCGC
4468

[1811-1828] 3′UTR

858
AGCUCUGUUGAUUUUGUU
3434
AACAAAAUCAACAGAGCU
4469

[3448-3465] 3′UTR

859
UAUCAUUCUUGAGCAAUC
3435
GAUUGCUCAAGAAUGAUA
4470

[3598-3615] 3′UTR

860
UGGAGGGAGACGUGGGUC
3436
GACCCACGUCUCCCUCCA
4471

[1135-1152] 3′UTR

861
AAGAAACUUCCUAGGGAA
3437
UUCCCUAGGAAGUUUCUU
4472

[2251-2268] 3′UTR

862
AAAGCUGGGUCUUGCUGU
3438
ACAGCAAGACCCAGCUUU
4473
Rh
[1937-1954] 3′UTR

863
AAUAUGAAGUCUGAGACC
3439
GGUCUCAGACUUCAUAUU
4474

[3510-3527] 3′UTR

864
UUCCUGAAGCCAGUGAUA
3440
UAUCACUGGCUUCAGGAA
4475

[2300-2317] 3′UTR

865
ACUCCUGUUUCUGCUGAU
3441
AUCAGCAGAAACAGGAGU
4476

[2818-2835] 3′UTR

866
CCAGGCUUAGUGUUCCCU
3442
AGGGAACACUAAGCCUGG
4477

[1961-1978] 3′UTR

867
CCAGAGUGGAACGCGUGG
3443
CCACGCGUUCCACUCUGG
4478

[2969-2986] 3′UTR

868
ACCAGGUCCCUUUCAUCU
3444
AGAUGAAAGGGACCUGGU
4479
Rh
[1384-1401] 3′UTR

869
CGAGUGCCUCUGGAUGGA
3445
UCCAUCCAGAGGCACUCG
4480
Rh, Rb, Cw, Dg,
[811-828] ORF

Rt, Ms

870
UAUGUGUUCCCUCAGUGU
3446
ACACUGAGGGAACACAUA
4481

[2279-2296] 3′UTR

871
GUUUUCAUGCUGUACAGU
3447
ACUGUACAGCAUGAAAAC
4482
Rh
[2665-2682] 3′UTR

872
GACUGGGAGGGUAUCCAG
3448
CUGGAUACCCUCCCAGUC
4483
Rh
[2624-2641] 3′UTR

873
GUCAGCACAGAUCUUGAU
3449
AUCAAGAUCUGUGCUGAC
4484
Rh
[2587-2604] 3′UTR

874
CGGCCUGGGCGUGGUCUU
3450
AAGACCACGCCCAGGCCG
4485

[2456-2473] 3′UTR

875
CUGCGAGUGCAAGAUCAC
3451
GUGAUCUUGCACUCGCAG
4486
Rt
[754-771] ORF

876
UGAAAGGUGUGGCCUUUA
3452
UAAAGGCCACACCUUUCA
4487

[3115-3132] 3′UTR

877
UGUUCUGGCAUCAGGCAC
3453
GUGCCUGAUGCCAGAACA
4488

[1833-1850] 3′UTR

878
GGGCUUGUGUGCAGGGCC
3454
GGCCCUGCACACAAGCCC
4489
Rh
[1882-1899] 3′UTR

879
CCACCCAGAAGAAGAGCC
3455
GGCUCUUCUUCUGGGUGG
4490
Rh, Ck, Cw, Rt,
[714-731] ORF

Ms, Pg

880
CAGCUGAGCUGCGUUCCA
3456
UGGAACGCAGCUCAGCUG
4491

[1640-1657] 3′UTR

881
UCUGGAUGGACUGGGUCA
3457
UGACCCAGUCCAUCCAGA
4492
Rh, Rb, Cw, Dg,
[819-836] ORF

Rt, Ms,

882
CCCAAGCAGGAGUUUCUC
3458
GAGAAACUCCUGCUUGGG
4493
Dg
[929-946] ORF

883
AAGGUGUGGCCUUUAUAU
3459
AUAUAAAGGCCACACCUU
4494

[3118-3135] 3′UTR

884
CCUCCCAGGCUUAGUGUU
3460
AACACUAAGCCUGGGAGG
4495

[1957-1974] 3′UTR

885
CCAACUGCAAAAAAAGCC
3461
GGCUUUUUUUGCAGUUGG
4496

[988-1005] 3′UTR

886
CUGGAUUGAGUUGCACAG
3462
CUGUGCAACUCAAUCCAG
4497

[1851-1868] 3′UTR

887
AUGGCCUGUUUUAAGAGA
3463
UCUCUUAAAACAGGCCAU
4498

[2130-2147] 3′UTR

888
UGUAUCAUUCUUGAGCAA
3464
UUGCUCAAGAAUGAUACA
4499

[3596-3613] 3′UTR

889
AGAGUUUAUCUACACGGC
3465
GCCGUGUAGAUAAACUCU
4500
Dg, Ms, Pg
[559-576] ORF

890
CGGGACCUGGUCAGCACA
3466
UGUGCUGACCAGGUCCCG
4501
Rh
[2578-2595] 3′UTR

891
AUGACAAAGAUUACCUAG
3467
CUAGGUAAUCUUUGUCAU
4502

[2231-2248] 3′UTR

892
UGAAGCCAGUGAUAUGGG
3468
CCCAUAUCACUGGCUUCA
4503

[2304-2321] 3′UTR

893
GUGGCCUUUAUAUUUGAU
3469
AUCAAAUAUAAAGGCCAC
4504

[3123-3140] 3′UTR

894
UAAGCAUAGUAAGAAGUC
3470
GACUUCUUACUAUGCUUA
4505

[2035-2052] 3′UTR

895
CUGCACAUCCUGAGGACA
3471
UGUCCUCAGGAUGUGCAG
4506
Rh
[1916-1933] 3′UTR

896
AGUUGACAAGCAGACUGC
3472
GCAGUCUGCUUGUCAACU
4507

[3561-3578] 3′UTR

897
UGAGCUCCCAGCACCUGA
3473
UCAGGUGCUGGGAGCUCA
4508

[1492-1509] 3′UTR

898
CUGUUAAGACUCCUGACC
3474
GGUCAGGAGUCUUAACAG
4509
Rh
[2531-2548] 3′UTR

899
CACAUCACCCUCUGUGAC
3475
GUCACAGAGGGUGAUGUG
4510
Rh
[668-685] ORF

900
AAAGUUGACAAGCAGACU
3476
AGUCUGCUUGUCAACUUU
4511

[3559-3576] 3′UTR

901
CCAAGUGGCAUGCAGCCC
3477
GGGCUGCAUGCCACUUGG
4512

[2550-2567] 3′UTR

902
GUACCAGAUGGGCUGCGA
3478
UCGCAGCCCAUCUGGUAC
4513
Rh, Ck, Rb, Rt
[742-759] ORF

903
UGUUUCCGUUUGGAUUUU
3479
AAAAUCCAAACGGAAACA
4514

[3462-3479] 3′UTR

904
AUCUUUGAGUAGGUUCGG
3480
CCGAACCUACUCAAAGAU
4515

[95-3112] 3′UTR

905
UGAUCCCGUGCUACAUCU
3481
AGAUGUAGCACGGGAUCA
4516
Rh, Rb
[783-800] ORF

906
ACCUGGUCAGCACAGAUC
3482
GAUCUGUGCUGACCAGGU
4517
Rh
[2582-2599] 3′UTR

907
CACUUCUUUCUCAGCCUC
3483
GAGGCUGAGAAAGAAGUG
4518

[2103-2120] 3′UTR

908
GCUGCUGCGGUUGCCAUU
3484
AAUGGCAACCGCAGCAGC
4519

[1805-1822] 3′UTR

909
CAUUGCUUCUUGCCUGUU
3485
AACAGGCAAGAAGCAAUG
4520

[1819-1836] 3′UTR

910
CUGGAGGGAGACGUGGGU
3486
ACCCACGUCUCCCUCCAG
4521

[1134-1151] 3′UTR

911
UGGUGACACACUCACUUC
3487
GAAGUGAGUGUGUCACCA
4522

[2091-2108] 3′UTR

912
GGCAGGGCUGGGACACGC
3488
GCGUGUCCCAGCCCUGCC
4523

[1219-1236] 3′UTR

913
UGAACCACAGGUACCAGA
3489
UCUGGUACCUGUGGUUCA
4524
Rh, Rb, Cw, Ms, Pg
[732-749] ORF

914
GUUAGGAUAGGAAGAACU
3490
AGUUCUUCCUAUCCUAAC
4525

[2323-2340] 3′UTR

915
AGCUUUGCUUUAUCCGGG
3491
CCCGGAUAAAGCAAAGCU
4526

[1867-1884] 3′UTR

916
CUGUCCUGAGGCUGCUGU
3492
ACAGCAGCCUCAGGACAG
4527
Rh
[1751-1768] 3′UTR

917
AUUGCUUCUUGCCUGUUC
3493
GAACAGGCAAGAAGCAAU
4528

[1820-1837] 3′UTR

918
GAGCACCACCCAGAAGAA
3494
UUCUUCUGGGUGGUGCUC
4529
Rh, Pg
[709-726] ORF

919
GUAGUGAUCAGGGCCAAA
3495
UUUGGCCCUGAUCACUAC
4530
Cw, Rt, Pg
[428-445] ORF

920
CCUGUUAAGACUCCUGAC
3496
GUCAGGAGUCUUAACAGG
4531
Rh
[2530-2547] 3′UTR

921
AGGGUUUCGACUGGUCCA
3497
UGGACCAGUCGAAACCCU
4532
Rh
[1010-1027] 3′UTR

922
UCAUCCCAUGGGUCCAAA
3498
UUUGGACCCAUGGGAUGA
4533

[1068-1085] 3′UTR

923
GCCCUUGUUUUCUGCAGC
3499
GCUGCAGAAAACAAGGGC
4534
Rh
[1415-1432] 3′UTR

924
GUUGACAAGCAGACUGCG
3500
CGCAGUCUGCUUGUCAAC
4535

[3562-3579] 3′UTR

925
AGGGAACCUAUGUGUUCC
3501
GGAACACAUAGGUUCCCU
4536
Rh
[2271-2288] 3′UTR

926
CCCAGCUGGGUUAGGGCA
3502
UGCCCUAACCCAGCUGGG
4537

[1302-1319] 3′UTR

927
GUUGGUCUUUUAACCGUG
3503
CACGGUUAAAAGACCAAC
4538

[3149-3166] 3′UTR

928
UUAUGGCAACCCUAUCAA
3504
UUGAUAGGGUUGCCAUAA
4539

[484-501] ORF

929
CUAAAGUUGGUAAGAUGU
3505
ACAUCUUACCAACUUUAG
4540
Rh
[2686-2703] 3′UTR

930
UGAAUUCUCAGAUGAUAG
3506
CUAUCAUCUGAGAAUUCA
4541

[2167-2184] 3′UTR

931
UGCAGGUGGAUUCCUUCA
3507
UGAAGGAAUCCACCUGCA
4542
Rh
[2991-3008] 3′UTR

932
CUGCGCAUGUCUCUGAUG
3508
CAUCAGAGACAUGCGCAG
4543

[3575-3592] 3′UTR

933
GAAGAACAUCAACGGGCA
3509
UGCCCGUUGAUGUUCUUC
4544
Rh, Rb
[841-858] ORF

934
GGCGCUCGGCCUCCUGCU
3510
AGCAGGAGGCCGAGCGCC
4545
Dg, Rt, Ms
[331-348] ORF

935
CUGAGGACAGAAAAAGCU
3511
AGCUUUUUCUGUCCUCAG
4546
Rh
[1925-1942] 3′UTR

936
AUCUUGAUGACUUCCCUU
3512
AAGGGAAGUCAUCAAGAU
4547
Rh
[2597-2614] 3′UTR

937
UAGGUAUUAGACUUGCAC
3513
GUGCAAGUCUAAUACCUA
4548

[2911-2928] 3′UTR

938
UGAAGUCUGAGACCUUCC
3514
GGAAGGUCUCAGACUUCA
4549

[3514-3531] 3′UTR

939
CCGUAAUUUAAAGCUCUG
3515
CAGAGCUUUAAAUUACGG
4550

[3437-3454] 3′UTR

940
AAGGCUCUCCAUUUGGCA
3516
UGCCAAAUGGAGAGCCUU
4551

[3272-3289] 3′UTR

941
UAGGGAACCUAUGUGUUC
3517
GAACACAUAGGUUCCCUA
4552
Rh
[2270-2287] 3′UTR

942
GCUCCCAGCACCUGACUC
3518
GAGUCAGGUGCUGGGAGC
4553

[1495-1512] 3′UTR

943
UGGAUUGAGUUGCACAGC
3519
GCUGUGCAACUCAAUCCA
4554

[1852-1869] 3′UTR

944
CUGCUGGCGACGCUGCUU
3520
AAGCAGCGUCGCCAGCAG
4555

[347-364] ORF

945
CUGCGUUCCAGCCUCAGC
3521
GCUGAGGCUGGAACGCAG
4556

[1648-1665] 3′UTR

946
GUGACUUCAUCGUGCCCU
3522
AGGGCACGAUGAAGUCAC
4557
Rh, Rb, Cw, Dg, Pg
[681-698] ORF

947
GCCCUGGGACACCCUGAG
3523
CUCAGGGUGUCCCAGGGC
4558
Rh, Cw, Dg, Pg
[694-711] ORF

948
UAUACAACUCCACCAGAC
3524
GUCUGGUGGAGUUGUAUA
4559
Rh
[2734-2751] 3′UTR

949
ACCUUCCGGUGCUGGGAA
3525
UUCCCAGCACCGGAAGGU
4560

[3525-3542] 3′UTR

950
GCUUUCUGCAUGUGACGC
3526
GCGUCACAUGCAGAAAGC
4561

[2013-2030] 3′UTR

951
CCACAUCCAAGGGCAGCC
3527
GGCUGCCCUUGGAUGUGG
4562

[1516-1533] 3′UTR

952
GCAGCACUUAGGGAUCUC
3528
GAGAUCCCUAAGUGCUGC
4563
Rh
[1285-1302] 3′UTR

953
UGGGUCCAAGGUCCUCAU
3529
AUGAGGACCUUGGACCCA
4564

[1147-1164] 3′UTR

954
UCUAGGGCAGACUGGGAG
3530
CUCCCAGUCUGCCCUAGA
4565
Rh
[2615-2632] 3′UTR

955
GAAGGGAAGGAUUUUGGA
3531
UCCAAAAUCCUUCCCUUC
4566
Rh
[2061-2078] 3′UTR

956
GAGGAAUCGGUGAGGUCC
3532
GGACCUCACCGAUUCCUC
4567

[1734-1751] 3′UTR

957
AUUUGACCCAGAGUGGAA
3533
UUCCACUCUGGGUCAAAU
4568

[2962-2979] 3′UTR

958
GGCGACGCUGCUUCGCCC
3534
GGGCGAAGCAGCGUCGCC
4569

[352-369] ORF

959
UUAGCCUGUUCUAUUCAG
3535
CUGAAUAGAACAGGCUAA
4570
Rh
[2496-2513] 3′UTR

960
AGCUGAGCUGCGUUCCAG
3536
CUGGAACGCAGCUCAGCU
4571

[1641-1658] 3′UTR

961
AAGUUGACAAGCAGACUG
3537
CAGUCUGCUUGUCAACUU
4572

[3560-3577] 3′UTR

962
AGCACAGAUCUUGAUGAC
3538
GUCAUCAAGAUCUGUGCU
4573
Rh
[2590-2607] 3′UTR

963
GAGGGUAUCCAGGAAUCG
3539
CGAUUCCUGGAUACCCUC
4574

[2630-2647] 3′UTR

964
AGUGUGGUUUCCUGAAGC
3540
GCUUCAGGAAACCACACU
4575

[2292-2309] 3′UTR

965
UCCUUUUAGACAUGGUUG
3541
CAACCAUGUCUAAAAGGA
4576

[1111-1128] 3′UTR

966
GUUUCCUCCCACCUGUGU
3542
ACACAGGUGGGAGGAAAC
4577

[2369-2386] 3′UTR

967
CACUAUGGCCUGUUUUAA
3543
UUAAAACAGGCCAUAGUG
4578

[2126-2143] 3′UTR

968
CCAGCUGGGUUAGGGCAG
3544
CUGCCCUAACCCAGCUGG
4579

[1303-1320] 3′UTR

969
UGCGUUCCAGCCUCAGCU
3545
AGCUGAGGCUGGAACGCA
4580

[1649-1666] 3′UTR

970
CCAGCCUAGGAAGGGAAG
3546
CUUCCCUUCCUAGGCUGG
4581
Rh
[2052-2069] 3′UTR

971
GCUGGGUCUUGCUGUGCC
3547
GGCACAGCAAGACCCAGC
4582
Rh
[1940-1957] 3′UTR

972
GUUUCUCGACAUCGAGGA
3548
UCCUCGAUGUCGAGAAAC
4583
Ck, Dg
[940-957] ORF

973
GCUGGGACACGCGGCUUC
3549
GAAGCCGCGUGUCCCAGC
4584

[1225-1242] 3′UTR

974
UACCAACUUCUGCUUGUA
3550
UACAAGCAGAAGUUGGUA
4585
Rh
[2205-2222] 3′UTR

975
UCCAAGGGCAGCCUGGAA
3551
UUCCAGGCUGCCCUUGGA
4586

[1521-1538] 3′UTR

976
CAACCCUAUCAAGAGGAU
3552
AUCCUCUUGAUAGGGUUG
4587

[490-507] ORF

977
CAGCUGAGUCUUUUUGGU
3553
ACCAAAAAGACUCAGCUG
4588
Rh
[1662-1679] 3′UTR

978
UGUUAAGACUCCUGACCC
3554
GGGUCAGGAGUCUUAACA
4589
Rh
[2532-2549] 3′UTR

979
UAUCAAGAGGAUCCAGUA
3555
UACUGGAUCCUCUUGAUA
4590
Rh, Rb
[496-513] ORF

980
GCACCAGGCCAAGUUCUU
3556
AAGAACUUGGCCUGGUGC
4591
Rh, Rb, Cw, Rt, Ms
[856-873] ORF

981
GGGCUGGGACACGCGGCU
3557
AGCCGCGUGUCCCAGCCC
4592

[1223-1240] 3′UTR

982
GGUCCCUUCCCUAGCUGC
3558
GCAGCUAGGGAAGGGACC
4593

[1792-1809] 3′UTR

983
UGAUAGGUGAACCUGAGU
3559
ACUCAGGUUCACCUAUCA
4594

[2179-2196] 3′UTR

984
AUUCCUGUGCUGUGUUUU
3560
AAAACACAGCACAGGAAU
4595
Rh
[2880-2897] 3′UTR

985
GAUGCACAUCACCCUCUG
3561
CAGAGGGUGAUGUGCAUC
4596
Rh
[664-681] ORF

986
CCAGGCACUAUGUGUCUG
3562
CAGACACAUAGUGCCUGG
4597

[1180-1197] 3′UTR

987
GCUGCUGGCGACGCUGCU
3563
AGCAGCGUCGCCAGCAGC
4598

[346-363] ORF

988
UCCAGUGGGAGCCUCCCU
3564
AGGGAGGCUCCCACUGGA
4599
Rh
[1590-1607] 3′UTR

989
AGCUCUGACAUCCCUUCC
3565
GGAAGGGAUGUCAGAGCU
4600
Rh
[1027-1044] 3′UTR

990
ACAGCUUUGCUUUAUCCG
3566
CGGAUAAAGCAAAGCUGU
4601

[1865-1882] 3′UTR

991
GGGAACCUAUGUGUUCCC
3567
GGGAACACAUAGGUUCCC
4602
Rh
[2272-2289] 3′UTR

992
CAGGAGUUUCUCGACAUC
3568
GAUGUCGAGAAACUCCUG
4603
Ck, Dg
[935-952] ORF

993
GUCCCUUCCCUAGCUGCU
3569
AGCAGCUAGGGAAGGGAC
4604

[1793-1810] 3′UTR

994
AGGUUCGGUCUGAAAGGU
3570
ACCUUUCAGACCGAACCU
4605

[3105-3122] 3′UTR

995
UGACGAUAUACAGGCACA
3571
UGUGCCUGUAUAUCGUCA
4606

[2400-2417] 3′UTR

996
AGUCUUUUUGGUCUGCAC
3572
GUGCAGACCAAAAAGACU
4607

[1668-1685] 3′UTR

997
CACCCUGAGCACCACCCA
3573
UGGGUGGUGCUCAGGGUG
4608
Rh, Pg
[703-720] ORF

998
GAGAAGAACAUCAACGGG
3574
CCCGUUGAUGUUCUUCUC
4609
Rh, Rb
[839-856] ORF

999
GAGAAGUGACGGCUCCUG
3575
CAGGAGCCGUCACUUCUC
4610

[886-903] ORF

1000
UGCGAGUGCAAGAUCACG
3576
CGUGAUCUUGCACUCGCA
4611

[755-772] ORF

1001
AAGUAAAGGAUCUUUGAG
3577
CUCAAAGAUCCUUUACUU
4612

[86-3103] 3′UTR

1002
AGGCACAUUAUGUAAACA
3578
UGUUUACAUAAUGUGCCU
4613
Rh
[2411-2428] 3′UTR

1003
CGCUCGGUCCGUGGACAA
3579
UUGUCCACGGACCGAGCG
4614

[3615-3632] 3′UTR

1004
GUUAAGAAGAGCCGGGUG
3580
CACCCGGCUCUUCUUAAC
4615

[3187-3204] 3′UTR

1005
GUGGAACGCGUGGCCUAU
3581
AUAGGCCACGCGUUCCAC
4616

[2974-2991] 3′UTR

1006
AAAGUUGGUAAGAUGUCA
3582
UGACAUCUUACCAACUUU
4617
Rh
[2688-2705] 3′UTR

1007
AGCUGCUGCGGUUGCCAU
3583
AUGGCAACCGCAGCAGCU
4618

[1804-1821] 3′UTR

1008
CUGCAUCGUGGAAGCAUU
3584
AAUGCUUCCACGAUGCAG
4619
Rh
[2947-2964] 3′UTR

1009
UACUCCUGUUUCUGCUGA
3585
UCAGCAGAAACAGGAGUA
4620

[2817-2834] 3′UTR

1010
CCUUGUAGAAAUGGGAGC
3586
GCUCCCAUUUCUACAAGG
4621
Rh
[1613-1630] 3′UTR

1011
AACCUAUGUGUUCCCUCA
3587
UGAGGGAACACAUAGGUU
4622

[2275-2292] 3′UTR

1012
UAGUUUAAGAAGGCUCUC
3588
GAGAGCCUUCUUAAACUA
4623

[3263-3280] 3′UTR

1013
UGCGCAUGUCUCUGAUGC
3589
GCAUCAGAGACAUGCGCA
4624

[3576-3593] 3′UTR

1014
AGAGAAGUGACGGCUCCU
3590
AGGAGCCGUCACUUCUCU
4625

[885-902] ORF

1015
CAAGGGUUUCGACUGGUC
3591
GACCAGUCGAAACCCUUG
4626
Rh
[1008-1025] 3′UTR

1016
UCUAAGCACAGCUCUCUU
3592
AAGAGAGCUGUGCUUAGA
4627

[3312-3329] 3′UTR

1017
AUUUGAUCCACACACGUU
3593
AACGUGUGUGGAUCAAAU
4628

[3134-3151] 3′UTR

1018
CUUCCCUCCCAGUCCCUG
3594
CAGGGACUGGGAGGGAAG
4629

[1239-1256] 3′UTR

1019
AAGAAGGCUCUCCAUUUG
3595
CAAAUGGAGAGCCUUCUU
4630

[3269-3286] 3′UTR

1020
CGGGUGGCAGCUGACAGA
3596
UCUGUCAGCUGCCACCCG
4631

[3199-3216] 3′UTR

1021
UGGGAGCCUCCCUCUGAG
3597
CUCAGAGGGAGGCUCCCA
4632
Rh
[1595-1612] 3′UTR

1022
UAUACCAACUUCUGCUUG
3598
CAAGCAGAAGUUGGUAUA
4633
Rh
[2203-2220] 3′UTR

1023
UGGAUGGACUGGGUCACA
3599
UGUGACCCAGUCCAUCCA
4634
Rh, Rt, Ms, Pg
[821-838] ORF

1024
CAGAGUGGAACGCGUGGC
3600
GCCACGCGUUCCACUCUG
4635

[2970-2987] 3′UTR

1025
UCUCUUGUUUCCUCCCAC
3601
GUGGGAGGAAACAAGAGA
4636

[2363-2380] 3′UTR

1026
CACCAUGAGCUCCCAGCA
3602
UGCUGGGAGCUCAUGGUG
4637

[1487-1504] 3′UTR

1027
AUCUGCACAUCCUGAGGA
3603
UCCUCAGGAUGUGCAGAU
4638
Rh
[1914-1931] 3′UTR

1028
CCCUUGUUUUCUGCAGCU
3604
AGCUGCAGAAAACAAGGG
4639
Rh
[1416-1433] 3′UTR

1029
CCCUUCCUGGAAACAGCA
3605
UGCUGUUUCCAGGAAGGG
4640
Rh, Rb, Rt, Ms
[1038-1055] 3′UTR

1030
ACCAUGAGCUCCCAGCAC
3606
GUGCUGGGAGCUCAUGGU
4641

[1488-1505] 3′UTR

1031
CACACGUUGGUCUUUUAA
3607
UUAAAAGACCAACGUGUG
4642

[3144-3161] 3′UTR

1032
CUGAGUCUUUUUGGUCUG
3608
CAGACCAAAAAGACUCAG
4643

[1665-1682] 3′UTR

1033
CCCUCCCAGUCCCUGCCU
3609
AGGCAGGGACUGGGAGGG
4644
Rh
[1242-1259] 3′UTR

1034
UCAGCCUCCAGGACACUA
3610
UAGUGUCCUGGAGGCUGA
4645

[2113-2130] 3′UTR

1035
UGCUUUAUCCGGGCUUGU
3611
ACAAGCCCGGAUAAAGCA
4646

[1872-1889] 3′UTR

TABLE B6

18-mer siTIMP2 Cross-Species

SEQ

SEQ

ID

ID

human-73858577

No.
Sense (5′>3′)
NO:
Antisense (5′>3′)
NO:
Other Sp
ORF:303-965

1
ACCAGAUGGGCUGCGAGU
4647
ACUCGCAGCCCAUCUGGU
4707
Rh, Ck, Rb, Rt
[744-761] ORF

2
ACAGGUACCAGAUGGGCU
4648
AGCCCAUCUGGUACCUGU
4708
Rh, Rb, Cw, Rt, Ms, Pg
[738-755] ORF

3
GAAGAGCCUGAACCACAG
4649
CUGUGGUUCAGGCUCUUC
4709
Rh, Rb, Cw, Ms, Pg
[724-741] ORF

4
UCUUCGCCUGCAUCAAGA
4650
UCUUGAUGCAGGCGAAGA
4710
Rh, Rb, Cw, Dg, Ms
[870-887] ORF

5
CGGGCACCAGGCCAAGUU
4651
AACUUGGCCUGGUGCCCG
4711
Rh, Rb, Rt, Ms
[853-870] ORF

6
CGCUCGGCCUCCUGCUGC
4652
GCAGCAGGAGGCCGAGCG
4712
Dg, Rt, Ms
[333-350] ORF

7
CAUCCCUUCCUGGAAACA
4653
UGUUUCCAGGAAGGGAUG
4713
Rh, Rb, Rt, Ms
[1035-1052] 3′UTR

8
CACCCGCAACAGGCGUUU
4654
AAACGCCUGUUGCGGGUG
4714
Cw, Rt, Ms
[398-415] ORF

9
GGCCGACGCCUGCAGCUG
4655
CAGCUGCAGGCGUCGGCC
4715
Cw, Dg, Rt, Ms
[370-387] ORF

10
GUGCCUCUGGAUGGACUG
4656
CAGUCCAUCCAGAGGCAC
4716
Rh, Rb, Cw, Dg, Rt, Ms
[814-831] ORF

11
CCUGAACCACAGGUACCA
4657
UGGUACCUGUGGUUCAGG
4717
Rh, Rb, Cw, Ms, Pg
[730-747] ORF

12
UCCUGGAAACAGCAUGAA
4658
UUCAUGCUGUUUCCAGGA
4718
Rh, Rb, Rt, Ms
[1042-1059] 3′UTR

13
GUCUCGCUGGACGUUGGA
4659
UCCAACGUCCAGCGAGAC
4719
Rt, Ms
[599-616] ORF

14
GCCGACGCCUGCAGCUGC
4660
GCAGCUGCAGGCGUCGGC
4720
Cw, Dg, Rt, Ms
[371-388] ORF

15
AACCACAGGUACCAGAUG
4661
CAUCUGGUACCUGUGGUU
4721
Rh, Rb, Cw, Rt, Ms, Pg
[734-751] ORF

16
CCCGGUGCACCCGCAACA
4662
UGUUGCGGGUGCACCGGG
4722
Cw, Dg, Rt, Ms
[391-408] ORF

17
CACAGGUACCAGAUGGGC
4663
GCCCAUCUGGUACCUGUG
4723
Rh, Rb, Cw, Rt, Ms, Pg
[737-754] ORF

18
CCCGCAACAGGCGUUUUG
4664
CAAAACGCCUGUUGCGGG
4724
Cw, Rt, Ms
[400-417] ORF

19
UCAAGCAGAUAAAGAUGU
4665
ACAUCUUUAUCUGCUUGA
4725
Cw, Dg, Rt, Ms, Pg
[519-536] ORF

20
CACCAGGCCAAGUUCUUC
4666
GAAGAACUUGGCCUGGUG
4726
Rh, Rb, Cw, Ms
[857-874] ORF

21
ACCACAGGUACCAGAUGG
4667
CCAUCUGGUACCUGUGGU
4727
Rh, Rb, Cw, Rt, Ms, Pg
[735-752] ORF

22
UCUCGCUGGACGUUGGAG
4668
CUCCAACGUCCAGCGAGA
4728
Rt, Ms
[600-617] ORF

23
CAAGCAGAUAAAGAUGUU
4669
AACAUCUUUAUCUGCUUG
4729
Cw, Dg, Rt, Ms, Pg
[520-537] ORF

24
GAUAAAGAUGUUCAAAGG
4670
CCUUUGAACAUCUUUAUC
4730
Dg, Rt, Ms
[526-543] ORF

25
GCACCCGCAACAGGCGUU
4671
AACGCCUGUUGCGGGUGC
4731
Cw, Dg, Rt, Ms
[397-414] ORF

26
CAGGCCAAGUUCUUCGCC
4672
GGCGAAGAACUUGGCCUG
4732
Rh, Rb, Cw, Dg, Ms
[860-877] ORF

27
UGCACCCGCAACAGGCGU
4673
ACGCCUGUUGCGGGUGCA
4733
Cw, Dg, Rt, Ms
[396-413] ORF

28
CAGGUACCAGAUGGGCUG
4674
CAGCCCAUCUGGUACCUG
4734
Rh, Rb, Cw, Dg, Rt, Ms, Pg
[739-756] ORF

29
GCUGGCGCUCGGCCUCCU
4675
AGGAGGCCGAGCGCCAGC
4735
Dg, Rt, Ms
[328-345] ORF

30
GCGCUCGGCCUCCUGCUG
4676
CAGCAGGAGGCCGAGCGC
4736
Dg, Rt, Ms
[332-349] ORF

31
GACGCCUGCAGCUGCUCC
4677
GGAGCAGCUGCAGGCGUC
4737
Cw, Dg, Rt, Ms
[374-391] ORF

32
UACCAGAUGGGCUGCGAG
4678
CUCGCAGCCCAUCUGGUA
4738
Rh, Ck, Rb, Rt
[743-760] ORF

33
GCUCGGCCUCCUGCUGCU
4679
AGCAGCAGGAGGCCGAGC
4739
Dg, Rt, Ms
[334-351] ORF

34
CGGUGCACCCGCAACAGG
4680
CCUGUUGCGGGUGCACCG
4740
Cw, Dg, Rt, Ms
[393-410] ORF

35
CCGGUGCACCCGCAACAG
4681
CUGUUGCGGGUGCACCGG
4741
Cw, Dg, Rt, Ms
[392-409] ORF

36
ACCCGCAACAGGCGUUUU
4682
AAAACGCCUGUUGCGGGU
4742
Cw, Rt, Ms
[399-416] ORF

37
AUCAAGCAGAUAAAGAUG
4683
CAUCUUUAUCUGCUUGAU
4743
Cw, Dg, Rt, Ms, Pg
[518-535] ORF

38
CCACAGGUACCAGAUGGG
4684
CCCAUCUGGUACCUGUGG
4744
Rh, Rb, Cw, Rt, Ms, Pg
[736-753] ORF

39
CCGACGCCUGCAGCUGCU
4685
AGCAGCUGCAGGCGUCGG
4745
Cw, Dg, Rt, Ms
[372-389] ORF

40
CUUCAUCGUGCCCUGGGA
4686
UCCCAGGGCACGAUGAAG
4746
Rh, Rb, Cw, Dg, Pg
[685-702] ORF

41
CGGCCGACGCCUGCAGCU
4687
AGCUGCAGGCGUCGGCCG
4747
Cw, Dg, Rt, Ms
[369-386] ORF

42
GUGCACCCGCAACAGGCG
4688
CGCCUGUUGCGGGUGCAC
4748
Cw, Dg, Rt, Ms
[395-412] ORF

43
CGACGCCUGCAGCUGCUC
4689
GAGCAGCUGCAGGCGUCG
4749
Cw, Dg, Rt, Ms
[373-390] ORF

44
ACCAGGCCAAGUUCUUCG
4690
CGAAGAACUUGGCCUGGU
4750
Rh, Rb, Cw, Ms
[858-875] ORF

45
UGCCUCUGGAUGGACUGG
4691
CCAGUCCAUCCAGAGGCA
4751
Rh, Rb, Cw, Dg, Rt, Ms
[815-832] ORF

46
AACAGGCGUUUUGCAAUG
4692
CAUUGCAAAACGCCUGUU
4752
Cw, Rt, Ms
[405-422] ORF

47
CUCGGCCUCCUGCUGCUG
4693
CAGCAGCAGGAGGCCGAG
4753
Dg, Rt
[335-352] ORF

48
CGGCCUCCUGCUGCUGGC
4694
GCCAGCAGCAGGAGGCCG
4754
Dg, Rt
[337-354] ORF

49
CCAGGCCAAGUUCUUCGC
4695
GCGAAGAACUUGGCCUGG
4755
Rh, Rb, Cw, Dg, Ms
[859-876] ORF

50
CUGGCGCUCGGCCUCCUG
4696
CAGGAGGCCGAGCGCCAG
4756
Dg, Rt, Ms
[329-346] ORF

51
UCGGCCUCCUGCUGCUGG
4697
CCAGCAGCAGGAGGCCGA
4757
Dg, Rt
[336-353] ORF

52
UGGCGCUCGGCCUCCUGC
4698
GCAGGAGGCCGAGCGCCA
4758
Dg, Rt, Ms
[330-347] ORF

53
AGGUACCAGAUGGGCUGC
4699
GCAGCCCAUCUGGUACCU
4759
Rh, Ck, Rb, Rt
[740-757] ORF

54
CUGUGACUUCAUCGUGCC
4700
GGCACGAUGAAGUCACAG
4760
Rh, Rb, Cw, Dg, Pg
[679-696] ORF

55
GACUUCAUCGUGCCCUGG
4701
CCAGGGCACGAUGAAGUC
4761
Rh, Rb, Cw, Dg, Pg
[683-700] ORF

56
ACGCCUGCAGCUGCUCCC
4702
GGGAGCAGCUGCAGGCGU
4762
Cw, Dg, Rt, Ms
[375-392] ORF

57
AAGAGCCUGAACCACAGG
4703
CCUGUGGUUCAGGCUCUU
4763
Rh, Rb, Cw, Ms, Pg
[725-742] ORF

58
CAGGGCCAAAGCGGUCAG
4704
CUGACCGCUUUGGCCCUG
4764
Rb, Dg
[436-453] ORF

59
UGACUUCAUCGUGCCCUG
4705
CAGGGCACGAUGAAGUCA
4765
Rh, Rb, Cw, Dg, Pg
[682-699] ORF

60
UGUGACUUCAUCGUGCCC
4706
GGGCACGAUGAAGUCACA
4766
Rh, Rb, Cw, Dg, Pg
[680-697] ORF

TABLE B7

Preferred 18 + 1-mer siTIMP2

SEQ

SEQ

ID

ID

SiTIMP2_p#
Sense (5′>3′)
NO:
Antisense (5′>3′)
NO:
Length
Position

siTIMP2_p1
GGAGGAAAGAAGGAAUAUA
4767
UAUAUUCCUUCUUUCCUCC
4815
18 + 1
[614-631] ORF

siTIMP2_p2
GGACGUUGGAGGAAAGAAA
4768
UUUCUUUCCUCCAACGUCC
4816
18 + 1
[607-624] ORF

siTIMP2 p3
GGGUCUCGCUGGACGUUGA
4769
UCAACGUCCAGCGAGACCC
4817
18 + 1
[597-614] ORF

siTIMP2 p5
GGACUGGGUCACAGAGAAA
4770
UUUCUCUGUGACCCAGUCC
4818
18 + 1
[826-843] ORF

siTIMP2 p6
CUGCAUCAAGAGAAGUGAA
4771
UUCACUUCUCUUGAUGCAG
4819
18 + 1
[877-894] ORF

siTIMP2 p7
GAGGAAAGAAGGAAUAUCA
4772
UGAUAUUCCUUCUUUCCUC
4820
18 + 1
[615-632] ORF

siTIMP2 p8
GCUGGACGUUGGAGGAAAA
4773
UUUUCCUCCAACGUCCAGC
4821
18 + 1
[604-621] ORF

siTIMP2 p9
GGCGUUUUGCAAUGCAGAA
4774
UUCUGCAUUGCAAAACGCC
4822
18 + 1
[409-426] ORF

siTIMP2_p10
GCCUGCAUCAAGAGAAGUA
4775
UACUUCUCUUGAUGCAGGC
4823
18 + 1
[875-892] ORF

siTIMP2_p11
AGGAAAGAAGGAAUAUCUA
4776
UAGAUAUUCCUUCUUUCCU
4824
18 + 1
[616-633] ORF

siTIMP2_p12
AGAUCAAGCAGAUAAAGAA
4777
UUCUUUAUCUGCUUGAUCU
4825
18 + 1
[516-533] ORF

siTIMP2_p13
GUUGGAGGAAAGAAGGAAA
4778
UUUCCUUCUUUCCUCCAAC
4826
18 + 1
[611-628] ORF

siTIMP2_p14
GCUGCGAGUGCAAGAUCAA
4779
UUGAUCUUGCACUCGCAGC
4827
18 + 1
[753-770] ORF

siTIMP2_p15
GGGCUGCGAGUGCAAGAUA
4780
UAUCUUGCACUCGCAGCCC
4828
18 + 1
[751-768] ORF

siTIMP2_p19
GACAUCCCUUCCUGGAAAA
4781
UUUUCCAGGAAGGGAUGUC
4829
18 + 1
[1033-1050] 3′UTR

siTIMP2 p21
GAUGGACUGGGUCACAGAA
4782
UUCUGUGACCCAGUCCAUC
4830
18 + 1
[823-840] ORF

siTIMP2 p22
GCCUCUGGAUGGACUGGGA
4783
UCCCAGUCCAUCCAGAGGC
4831
18 + 1
[816-833] ORF

siTIMP2_p23
GAGUGCCUCUGGAUGGACA
4784
UGUCCAUCCAGAGGCACUC
4832
18 + 1
[812-829] ORF

siTIMP2_p26
GGCACCAGGCCAAGUUCUA
4785
UAGAACUUGGCCUGGUGCC
4833
18 + 1
[855-872] ORF

siTIMP2_p28
GCAACAGGCGUUUUGCAAA
4786
UUUGCAAAACGCCUGUUGC
4834
18 + 1
[403-420] ORF

siTIMP2_p31
GACGUUGGAGGAAAGAAGA
4787
UCUUCUUUCCUCCAACGUC
4835
18 + 1
[608-625] ORF

siTIMP2_p32
GAUCAAGCAGAUAAAGAUA
4788
UAUCUUUAUCUGCUUGAUC
4836
18 + 1
[517-534] ORF

siTIMP2_p34
UGAGAUCAAGCAGAUAAAA
4789
UUUUAUCUGCUUGAUCUCA
4837
18 + 1
[514-531] ORF

siTIMP2_p36
UGUGCAUUUUGCAGAAACA
4790
UGUUUCUGCAAAAUGCACA
4838
18 + 1
[1331-1348] 3′UTR

siTIMP2_p42
GAACCACAGGUACCAGAUA
4791
UAUCUGGUACCUGUGGUUC
4839
18 + 1
[733-750] ORF

siTIMP2_p43
CACCCAGAAGAAGAGCCUA
4792
UAGGCUCUUCUUCUGGGUG
4840
18 + 1
[715-732] ORF

siTIMP2_p45
CCUUCCUGGAAACAGCAUA
4793
UAUGCUGUUUCCAGGAAGG
4841
18 + 1
[1039-1056] 3′UTR

siTIMP2_p47
UGGGCUGCGAGUGCAAGAA
4794
UUCUUGCACUCGCAGCCCA
4842
18 + 1
[750-767] ORF

siTIMP2_p48
GAUGGGCUGCGAGUGCAAA
4795
UUUGCACUCGCAGCCCAUC
4843
18 + 1
[748-765] ORF

siTIMP2_p49
AUCCCUUCCUGGAAACAGA
4796
UCUGUUUCCAGGAAGGGAU
4844
18 + 1
[1036-1053] 3′UTR

siTIMP2_p50
AGUGCCUCUGGAUGGACUA
4797
UAGUCCAUCCAGAGGCACU
4845
18 + 1
[813-830] ORF

siTIMP2_p52
UGGAGGAAAGAAGGAAUAA
4798
UUAUUCCUUCUUUCCUCCA
4846
18 + 1
[613-630] ORF

siTIMP2_p53
GGGCACCAGGCCAAGUUCA
4799
UGAACUUGGCCUGGUGCCC
4847
18 + 1
[854-871] ORF

siTIMP2_p54
GUGCAUUUUGCAGAAACUA
4800
UAGUUUCUGCAAAAUGCAC
4848
18 + 1
[1332-1349] 3′UTR

siTIMP2_p56
CCAGAUGGGCUGCGAGUGA
4801
UCACUCGCAGCCCAUCUGG
4849
18 + 1
[745-762] ORF

siTIMP2_p57
CGAGUGCCUCUGGAUGGAA
4802
UUCCAUCCAGAGGCACUCG
4850
18 + 1
[811-828] ORF

siTIMP2_p58
CUGCGAGUGCAAGAUCACA
4803
UGUGAUCUUGCACUCGCAG
4851
18 + 1
[754-771] ORF

siTIMP2_p59
UCUGGAUGGACUGGGUCAA
4804
UUGACCCAGUCCAUCCAGA
4852
18 + 1
[819-836] ORF

siTIMP2_p60
GUACCAGAUGGGCUGCGAA
4805
UUCGCAGCCCAUCUGGUAC
4853
18 + 1
[742-759] ORF

siTIMP2_p63
GUAGUGAUCAGGGCCAAAA
4806
UUUUGGCCCUGAUCACUAC
4854
18 + 1
[428-445] ORF

siTIMP2_p66
GGCGCUCGGCCUCCUGCUA
4807
UAGCAGGAGGCCGAGCGCC
4855
18 + 1
[331-348] ORF

siTIMP2_p70
UGGAUGGACUGGGUCACAA
4808
UUGUGACCCAGUCCAUCCA
4856
18 + 1
[821-838] ORF

siTIMP2_p72
CCCUUCCUGGAAACAGCAA
4809
UUGCUGUUUCCAGGAAGGG
4857
18 + 1
[1038-1055] 3′UTR

siTIMP2_p73
ACCAGAUGGGCUGCGAGUA
4810
UACUCGCAGCCCAUCUGGU
4858
18 + 1
[744-761] ORF

siTIMP2_p74
ACAGGUACCAGAUGGGCUA
4811
UAGCCCAUCUGGUACCUGU
4859
18 + 1
[738-755] ORF

siTIMP2_p77
CGGGCACCAGGCCAAGUUA
4812
UAACUUGGCCUGGUGCCCG
4860
18 + 1
[853-870] ORF

siTIMP2_p80
CAUCCCUUCCUGGAAACAA
4813
UUGUUUCCAGGAAGGGAUG
4861
18 + 1
[1035-1052] 3′UTR

siTIMP2_p81
CACCCGCAACAGGCGUUUA
4814
UAAACGCCUGUUGCGGGUG
4862
18 + 1
[398-415] ORF

TABLE B8

18 + 1-mer siTIMP2 with lowest predicted OT effect

SEQ

Cross

ID

SEQ
No. in

species:
Ranking
Sense (5′>3′)
NO:
Antisense (5′>3′)
ID NO:
Table B7

H/Rt
3
CUGCAUCAAGAGAAGUGAA
4771
UUCACUUCUCUUGAUGCAG
4819
siTIMP2_p6

H/Rt
3
GGCGUUUUGCAAUGCAGAA
4774
UUCUGCAUUGCAAAACGCC
4822
siTIMP2_p9

H/Rt
4
GGGCUGCGAGUGCAAGAUA
4780
UUCUGCAUUGCAAAACGCC
4828
siTIMP2_p15

H/Rt
4
GACAUCCCUUCCUGGAAAA
4781
UUCUGCAUUGCAAAACGCC
4829
siTIMP2_p19

H/Rt
4
GAUGGACUGGGUCACAGAA
4782
UUCUGCAUUGCAAAACGCC
4830
siTIMP2_p21

H/Rt
4
GCCUCUGGAUGGACUGGGA
4783
UUCUGCAUUGCAAAACGCC
4831
siTIMP2_p22

H/Rt
4
GAGUGCCUCUGGAUGGACA
4784
UUCUGCAUUGCAAAACGCC
4832
siTIMP2_p23

H/Rt
2
GCAACAGGCGUUUUGCAAA
4786
UUUGCAAAACGCCUGUUGC
4834
siTIMP2_p28

H/Rt
3
GACGUUGGAGGAAAGAAGA
4787
UCUUCUUUCCUCCAACGUC
4835
siTIMP2_p31

H/Rt
4
UGUGCAUUUUGCAGAAACA
4790
UGUUUCUGCAAAAUGCACA
4838
siTIMP2_p36

H/Rt
4
GAACCACAGGUACCAGAUA
4791
UAUCUGGUACCUGUGGUUC
4839
siTIMP2_p42

H/Rt
4
UGGGCUGCGAGUGCAAGAA
4794
UUCUUGCACUCGCAGCCCA
4842
siTIMP2_p47

H/Rt
4
AGUGCCUCUGGAUGGACUA
4797
UAGUCCAUCCAGAGGCACU
4845
siTIMP2_p50

H/Rt
4
CCAGAUGGGCUGCGAGUGA
4801
UCACUCGCAGCCCAUCUGG
4849
siTIMP2_p56

H/Rt
4
CGAGUGCCUCUGGAUGGAA
4802
UUCCAUCCAGAGGCACUCG
4850
siTIMP2_p57

H/Rt
2
CUGCGAGUGCAAGAUCACA
4803
UGUGAUCUUGCACUCGCAG
4851
siTIMP2_p58

H/Rt
3
GUACCAGAUGGGCUGCGAA
4805
UUCGCAGCCCAUCUGGUAC
4853
siTIMP2_p60

H/Rt
2
GUAGUGAUCAGGGCCAAAA
4806
UUUUGGCCCUGAUCACUAC
4854
siTIMP2_p63

H/Rt
3
UGGAUGGACUGGGUCACAA
4808
UUGUGACCCAGUCCAUCCA
4856
siTIMP2_p70

H/Rt
4
ACCAGAUGGGCUGCGAGUA
4810
UACUCGCAGCCCAUCUGGU
4858
siTIMP2_p73

H/Rt
4
ACAGGUACCAGAUGGGCUA
4811
UAGCCCAUCUGGUACCUGU
4859
siTIMP2_p74

H/Rt
2
CACCCGCAACAGGCGUUUA
4814
UAAACGCCUGUUGCGGGUG
4862
siTIMP2_p81

Example 6
In Vitro Testing of the siRNA Compounds for the Target Genes

Low-Throughput-Screen (LTS) for siRNA oligos directed to human and rat TIMP1 and TIMP2 gene.

About 2×10⁵human cell lines (HeLa, LX2, hHSC or PC3) endogenously expressing TIMP1 or TIMP2 gene, are inoculated in 1.5 mL growth medium in order to reach 30-50% confluence after 24 hours. Cells are transfected with Lipofectamine2000® reagent to a final concentration of 0.01-5 nM per transfected cells. Cells are incubated at 37±1° C., 5% CO₂for 48 hours. siRNA transfected cells are harvested and RNA is isolated using EZ-RNA® kit [Biological Industries (#20-410-100)].

Reverse transcription is performed as follows: Synthesis of cDNA is performed and human TIMP1 and TIMP2 mRNA levels are determined by Real Time qPCR and normalized to those of the Cyclophilin A (CYNA, PPIA) mRNA for each sample. siRNA activity is determined based on the ratio of the TIMP1 or TIMP2 mRNA quantity in siRNA-treated samples versus non-transfected control samples.

The most active sequences are selected from additional, assays.

IC50 Values for the LTS Selected TIMP1 or TIMP2 siRNA Oligos

Cells are grown as described above. The IC50 value of the tested RNAi activity is determined by constructing a dose-response curve using the activity results obtained with the various final siRNA concentrations. The dose response curve is constructed by plotting the relative amount of residual TIMP1 or TIMP2 mRNA versus the logarithm of transfected siRNA concentration. The curve is calculated by fitting the best sigmoid curve to the measured data. The method for the sigmoid fit is also known as a 3-point curve fit.

$Y = Bot + \frac{100 - Bot}{1 + 10^{(Log / C 50 - X) \times HillSlope}}$

where Y is the residual TIMP1 or TIMP2 mRNA response, X is the logarithm of transfected siRNA concentration, Bot is the Y value at the bottom plateau, Log IC50 is the X value when Y is halfway between bottom and top plateaus and HillSlope is the steepness of the curve.

The percent of inhibition of gene expression using specific siRNAs was determined using qPCR analysis of target gene in cells expressing the endogenous gene. Other siRNA compounds according to Tables A1, A2, A3, A4, A5, A6, A7, A8, B1, B2, B3, B4, B5, B6, B7, B8 (Tables A1-B8) are tested in vitro where it is shown that these siRNA compounds inhibit gene expression. Activity is shown as percent residual mRNA; accordingly, a lower value reflects better activity.

In order to test the stability of the siRNA compounds in serum, specific siRNA molecules are incubated in four different batches of human serum (100% concentration) at 37° C. for up to 24 hours. Samples are collected at 0.5, 1, 3, 6, 8, 10, 16 and 24 hours. The migration patterns as an indication of are determined at each collection time by polyacrylamide gel electrophoresis (PAGE).

Example 7
Validation of siTIMP1 and siTIMP2 Knock Down Effect at the Protein Level

The inhibitory effect of different siTIMP1 and siTIMP2 siNA molecules on TIMP1 and TIMP2 mRNA expression are validated at the protein level by measuring TIMP1 and TIMP2 in hTERT cells transfected with different siTIMP1 and siTIMP2. Transfection of hTERT cells with different siTIMP1 and siTIMP2 are performed as described above. Transfected hTERT cells are lysed and the cell lysate are clarified by centrifugation. Proteins in the clarified cell lysate are resolved by SDS polyacrylamide gel electrophoresis. The level of TIMP1 and TIMP2 protein in the cell lysate are determined using anti-TIMP or anti-TIMP2 antibodies as the primary antibody HRP conjugated antibodies (Millipore) as the secondary antibody, and subsequently detection by Supersignal West Pico Chemiluminescence kit (Pierce). Anti-actin antibody (Abcam) is used as a protein loading control.

Example 8
Downregulation of Collagen I Expression by siTIMP1 and siTIMP2 siRNA Duplexes

To determine the effect of siTIMP1 and siTIMP2, alone or in combination on collagen I expression level, collagen I mRNA level in hTERT cells treated with different siTIMP1 and or siTIMP2. Briefly, hTERT cells are transfected with different siTIMP1, and or siTIMP2 as described in Example 2. The cells are lysed after 72 hours and mRNA were isolated using RNeasy mini kit according to the manual (Qiagen). The level of collagen 1 mRNA is determined by reverse transcription coupled with quantitative PCR using TaqMan® probes. Briefly, cDNA synthesis is carried out using High-Capacity cDNA Reverse Transcription Kit (ABI) according to the manual, and subjected to TaqMan Gene Expression Assay (ABI, COL1A1 assay ID Hs01076780_g1). The level of collagen I mRNA is normalized to the level of GAPDH mRNA according to the manufacturer's instruction (ABI). The signals are normalized to the signal obtained from cells transfected with scrambled siNA.

Example 9
Immunofluorescence Staining of siTIMP1 and or siTIMP2 Treated hTERT Cells

To visualize the expression of two fibrosis markers, collagen I and alpha-smooth muscle actin (SMA), in hTERT cells transfected, the cells are stained with rabbit anti-collagen I antibody (Abcam) and mouse anti-alpha-SMA antibody (Sigma). Alexa Fluor 594 goat anti-mouse IgG and Alexa Fluor 488 goat anti-rabbit IgG (Invitrogen (Molecular Probes)) are used as secondary antibodies to visualize collagen I (green) and alpha-SMA (red). Hoescht is used to visualize nucleus (blue).

Example 10
Animal Models: Model Systems of Fibrotic Conditions

siRNAs provided herein may be tested in predictive animal models. Rat diabetic and aging models of kidney fibrosis include Zucker diabetic fatty (ZDF) rats, aged fa/fa (obese Zucker) rats, aged Sprague-Dawley (SD) rats, and Goto Kakizaki (GK) rats; GK rats are an inbred strain derived from Wistar rats, selected for spontaneous development of NIDDM (diabetes type II). Induced models of kidney fibrosis include the permanent unilateral ureteral obstruction (UUO) model which is a model of acute interstitial fibrosis occurring in healthy non-diabetic animals; renal fibrosis develops within days following the obstruction. Another induced model of kidney fibrosis is 5/6 nephrectomy model.

Two models of liver fibrosis in rats are the Bile Duct Ligation (BDL) with sham operation as controls, and CCl4 poisoning, with olive oil fed animals as controls, as described in the following references: Lotersztajn S, et al Hepatic Fibrosis: Molecular Mechanisms and Drug Targets. Annu Rev Pharmacol Toxicol. 2004 Oct. 7; Uchio K, et al., Down-regulation of connective tissue growth factor and type I collagen mRNA expression by connective tissue growth factor antisense oligonucleotide during experimental liver fibrosis. Wound Repair Regen. 2004 January-February; 12(1):60-6; Xu X Q, et al., Molecular classification of liver cirrhosis in a rat model by proteomics and bioinformatics Proteomics. 2004 October; 4(10):3235-45.

Models for ocular scarring are well known in the art e.g. Sherwood M B et al., J Glaucoma. 2004 October; 13(5):407-12. A new model of glaucoma filtering surgery in the rat; Miller M H et al., Ophthalmic Surg. 1989 May; 20(5):350-7. Wound healing in an animal model of glaucoma fistulizing surgery in the Rb; vanBockxmeer F M et al., Retina. 1985 Fall-Winter; 5(4): 239-52. Models for assessing scar tissue inhibitors; Wiedemann P et al., J Pharmacol Methods. 1984 August; 12(1): 69-78. Proliferative vitreoretinopathy: the Rb cell injection model for screening of antiproliferative drugs.

Models of cataract are described in the following publications: The role of Src family kinases in cortical cataract formation. Zhou J, Menko A S. Invest Ophthalmol Vis Sci. 2002 July; 43(7):2293-300; Bioavailability and anticataract effects of a topical ocular drug delivery system containing disulfiram and hydroxypropyl-beta-cyclodextrin on selenite-treated rats. Wang S, et al. Curr Eye Res. 2004 July; 29(1):51-8; and Long-term organ culture system to study the effects of UV-A irradiation on lens transglutaminase. Weinreb O, Dovrat A.; Curr Eye Res. 2004 July; 29(1):51-8.

The compounds disclosed herein are tested in these models of fibrotic conditions, in which it is found that they are effective in treating liver fibrosis and other fibrotic conditions. The compounds as described herein are tested in this animal model and the results show that these siRNA compounds are useful in treating and/or preventing ischemia reperfusion injury following lung transplantation.

The contents of the articles, patents, and patent applications, and all other documents and electronically available information mentioned or cited herein, are hereby incorporated by reference in their entirety to the same extent as if each individual publication was specifically and individually indicated to be incorporated by reference.

Applicants reserve the right to physically incorporate into this application any and all materials and information from any such articles, patents, patent applications, or other physical and electronic documents.

It will be readily apparent to one skilled in the art that varying substitutions and modifications can be made to the invention disclosed herein without departing from the scope and spirit of the invention. Thus, such additional embodiments are within the scope of the present invention and the following claims. The present disclosure teaches one skilled in the art to test various combinations and/or substitutions of chemical modifications described herein toward generating nucleic acid constructs with improved activity for mediating RNAi activity. Such improved activity can include improved stability, improved bioavailability, and/or improved activation of cellular responses mediating RNAi. Therefore, the specific embodiments described herein are not limiting and one skilled in the art can readily appreciate that specific combinations of the modifications described herein can be tested without undue experimentation toward identifying nucleic acid molecules with improved RNAi activity.

The inventions illustratively described herein may suitably be practiced in the absence of any element or elements, limitation or limitations, not specifically disclosed herein. Thus, for example, the terms “a” and “an” and “the” and similar referents in the context of describing the invention (especially in the context of the following claims) are to be construed to cover both the singular and the plural, unless otherwise indicated herein or clearly contradicted by context. The terms “comprising”, “having,” “including,” containing”, etc. shall be read expansively and without limitation (e.g., meaning “including, but not limited to,”). Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., “such as”) provided herein, is intended merely to better illuminate the invention and does not pose a limitation on the scope of the invention unless otherwise claimed. No language in the specification should be construed as indicating any non-claimed element as essential to the practice of the invention. Additionally, the terms and expressions employed herein have been used as terms of description and not of limitation, and there is no intention in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention claimed. Thus, it should be understood that although the present invention has been specifically disclosed by preferred embodiments and optional features, modification and variation of the inventions embodied therein herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention.

The invention has been described broadly and generically herein. Each of the narrower species and subgeneric groupings falling within the generic disclosure also form part of the invention. This includes the generic description of the invention with a proviso or negative limitation removing any subject matter from the genus, regardless of whether or not the excised material is specifically recited herein. Other embodiments are within the following claims. In addition, where features or aspects of the invention are described in terms of Markush groups, those skilled in the art will recognize that the invention is also thereby described in terms of any individual member or subgroup of members of the Markush group.

	Number	Date	Country
Parent	13246621	Sep 2011	US
Child	14927856		US

MODULATION OF TIMP1 AND TIMP2 EXPRESSION

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