RNA 3D Hub //

8CBJ Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8CBJ_0011/2/7:17No text annotation
geometric
HL_4V88_186
NA
HL_8CBJ_0031/2/154:160GNRA related
geometric
HL_4V88_188
NA
HL_8CBJ_0061/2/243:250T-loop with 1 bulged base
geometric
HL_4V88_191
NA
HL_8CBJ_0081/2/330:338GNRA related
geometric
HL_4V88_193
NA
HL_8CBJ_0091/2/368:373No text annotation
geometric
HL_5U3G_001
HL_75660.8
HL_8CBJ_0101/2/393:404No text annotation
geometric
HL_4V88_195
NA
HL_8CBJ_0111/2/414:419UNCG
geometric
HL_4LFB_009
HL_61337.4
HL_8CBJ_0121/2/450:456No text annotation
geometric
HL_5NFV_001
HL_69752.4
HL_8CBJ_0141/2/520:532No text annotation
geometric
HL_4V88_199
NA
HL_8CBJ_0151/2/552:572No text annotation
HL_8CBJ_0171/2/764:772No text annotation
geometric
HL_4V88_203
NA
HL_8CBJ_0181/2/777:783No text annotation
geometric
HL_4V88_204
NA
HL_8CBJ_0211/2/937:942GNRA
geometric
HL_1G1X_005
NA
HL_8CBJ_0241/2/1084:1089GNRA
geometric
HL_4V88_210
NA
HL_8CBJ_0251/2/1121:1126GNRA
geometric
HL_4LFB_020
HL_34789.4
HL_8CBJ_0281/2/1296:1301GNRA
geometric
HL_7RQB_063
NA

Problematic loops

#loop idProblemSequence
HL_8CBJ_002No text annotation
HL_8CBJ_004No text annotation
HL_8CBJ_005UNCG
HL_8CBJ_007No text annotation
HL_8CBJ_013No text annotation
HL_8CBJ_016No text annotation
HL_8CBJ_019Pseudoknot geometry
HL_8CBJ_020No text annotation
HL_8CBJ_022No text annotation
HL_8CBJ_023No text annotation
HL_8CBJ_026No text annotation
HL_8CBJ_027No text annotation
HL_8CBJ_029No text annotation
HL_8CBJ_030No text annotation
HL_8CBJ_031GNRA
HL_8CBJ_032GNRA
HL_8CBJ_033No text annotation
HL_8CBJ_034No text annotation
HL_8CBJ_035Externally structured
HL_8CBJ_036No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8CBJ_0011/2/24:26,
1/2/600:601		Single bulged C
geometric
IL_1DQH_001
NA
IL_8CBJ_0021/2/35:37,
1/2/471:473		Isolated non-canonical cWW pair
geometric
IL_4E59_001
IL_01003.4
IL_8CBJ_0031/2/37:41,
1/2/466:471		Triple sheared related
geometric
IL_4V88_386
NA
IL_8CBJ_0041/2/42:48,
1/2/431:433		No text annotation
geometric
IL_4V88_387
NA
IL_8CBJ_0051/2/50:52,
1/2/428:429		Minor groove platform
geometric
IL_4LFB_004
IL_34520.3
IL_8CBJ_0061/2/58:63,
1/2/87:89		No text annotation
geometric
IL_4V88_389
NA
IL_8CBJ_0071/2/64:69,
1/2/82:86		No text annotation
geometric
IL_4V88_390
NA
IL_8CBJ_0081/2/109:112,
1/2/302:305		Tandem non-canonical cWW pairs
geometric
IL_4V88_391
NA
IL_8CBJ_0091/2/113:116,
1/2/300:301		Multiple bulged bases
geometric
IL_4V88_392
NA
IL_8CBJ_0101/2/117:122,
1/2/295:299		No text annotation
geometric
IL_4V88_393
NA
IL_8CBJ_0111/2/144:149,
1/2/165:171		tWH-tWH-tHW-tHW
geometric
IL_4LFB_009
IL_00680.1
IL_8CBJ_0121/2/150:152,
1/2/162:164		Isolated cWH basepair
geometric
IL_6RA4_002
IL_10892.2
IL_8CBJ_0141/2/204:206,
1/2/259:263		Major groove platform with extra cWW
geometric
IL_4V88_397
NA
IL_8CBJ_0151/2/206:208,
1/2/257:259		Isolated non-canonical cWW pair
geometric
IL_3U4M_001
IL_71625.3
IL_8CBJ_0161/2/265:267,
1/2/288:289		Single bulged A
geometric
IL_4V88_399
NA
IL_8CBJ_0171/2/270:273,
1/2/283:285		No text annotation
geometric
IL_4V88_400
NA
IL_8CBJ_0191/2/311:316,
1/2/348:355		Kink-turn with non-sequential stacking
geometric
IL_4V88_402
NA
IL_8CBJ_0201/2/318:323,
1/2/345:346		No text annotation
geometric
IL_5Y58_001
IL_37738.1
IL_8CBJ_0211/2/363:365,
1/2/376:381		No text annotation
geometric
IL_4V88_404
NA
IL_8CBJ_0221/2/389:391,
1/2/406:408		Isolated cWH basepair
geometric
IL_4V88_405
NA
IL_8CBJ_0231/2/411:413,
1/2/420:422		Isolated near basepair
geometric
IL_3NJ7_004
IL_42997.5
IL_8CBJ_0241/2/439:441,
1/2/463:464		Single bulged U
geometric
IL_4V88_407
NA
IL_8CBJ_0251/2/443:447,
1/2/460:461		C-loop
geometric
IL_5J7L_018
NA
IL_8CBJ_0261/2/447:448,
1/2/458:460		Single bulged G
geometric
IL_5J7L_019
NA
IL_8CBJ_0301/2/514:516,
1/2/536:543		No text annotation
IL_8CBJ_0311/2/517:518,
1/2/533:535		Minor groove platform
geometric
IL_4V88_412
NA
IL_8CBJ_0321/2/518:520,
1/2/532:533		Minor groove platform
geometric
IL_4V88_388
NA
IL_8CBJ_0331/2/550:551,
1/2/573:588		No text annotation
IL_8CBJ_0341/2/616:622,
1/2/1104:1105		No text annotation
geometric
IL_4V88_416
NA
IL_8CBJ_0351/2/624:626,
1/2/973:975		Isolated non-canonical cWW pair
geometric
IL_4E59_001
IL_01003.4
IL_8CBJ_0361/2/627:631,
1/2/968:972		tSH-tHW-tHS
geometric
IL_4V88_418
NA
IL_8CBJ_0441/2/746:747,
1/2/802:805		Major groove minor groove platform; mini C-loop
geometric
IL_4V88_423
NA
IL_8CBJ_0451/2/748:750,
1/2/799:801		Isolated non-canonical cWW pair
geometric
IL_7A0S_078
IL_71625.3
IL_8CBJ_0461/2/751:759,
1/2/791:798		No text annotation
homologous
IL_8CRE_430
IL_59049.2
IL_8CBJ_0501/2/865:866,
1/2/962:965		Major groove platform; stack outside cWW
geometric
IL_4V88_428
NA
IL_8CBJ_0991/2/868:870,
1/2/957:960		Isolated non-canonical cWW pair
geometric
IL_4V88_507
NA
IL_8CBJ_1001/2/871:873,
1/2/954:956		Isolated non-canonical cWW pair
geometric
IL_2R8S_001
IL_01003.4
IL_8CBJ_0531/2/874:878,
1/2/950:953		Tandem non-canonical cWW pairs
geometric
IL_4V88_431
NA
IL_8CBJ_0541/2/885:888,
1/2/924:927		Tandem non-canonical cWW pairs
geometric
IL_4V88_432
NA
IL_8CBJ_0561/2/985:990,
1/2/1014:1016		Other IL
geometric
IL_4V88_435
NA
IL_8CBJ_0571/2/990:994,
1/2/1010:1014		tSH-tHW-tHS
geometric
IL_5J7L_037
NA
IL_8CBJ_0581/2/1034:1036,
1/2/1095:1101		No text annotation
geometric
IL_4V88_437
NA
IL_8CBJ_0591/2/1041:1044,
1/2/1074:1077		Tandem non-canonical cWW pairs
geometric
IL_4V88_438
NA
IL_8CBJ_0601/2/1051:1053,
1/2/1066:1067		Single bulged U
geometric
IL_4V88_439
NA
IL_8CBJ_0611/2/1111:1118,
1/2/1129:1134		8x6 Sarcin-Ricin with inserted Y; G-bulge
geometric
IL_4V88_440
NA
IL_8CBJ_0911/2/1669:1672,
1/2/1729:1732		Double sheared
geometric
IL_4V88_471
NA
IL_8CBJ_0921/2/1672:1674,
1/2/1727:1729		Isolated non-canonical cWW pair
geometric
IL_3D0U_006
IL_01003.4
IL_8CBJ_0931/2/1675:1678,
1/2/1723:1726		Tandem non-canonical cWW pairs
geometric
IL_4V88_473
NA
IL_8CBJ_0941/2/1678:1682,
1/2/1719:1723		Triple sheared
geometric
IL_4V88_474
NA

Problematic loops

#loop idProblemSequence
IL_8CBJ_013Double sheared
IL_8CBJ_018Single bulged U
IL_8CBJ_027Single bulged A
IL_8CBJ_028Isolated cWH basepair
IL_8CBJ_029Isolated cWH basepair
IL_8CBJ_037Isolated non-canonical cWW pair
IL_8CBJ_038Isolated non-canonical cWW pair
IL_8CBJ_097No text annotation
IL_8CBJ_039No text annotation
IL_8CBJ_040Isolated cWH basepair
IL_8CBJ_098Tandem non-canonical cWW pairs with near WC pairs
IL_8CBJ_041Tandem non-canonical cWW pairs
IL_8CBJ_042Tandem non-canonical cWW pairs
IL_8CBJ_043Isolated non-canonical cWW pair
IL_8CBJ_047Isolated non-canonical cWW pair
IL_8CBJ_048Isolated non-canonical cWW pair
IL_8CBJ_049Isolated non-canonical cWW pair
IL_8CBJ_051Tandem non-canonical cWW pairs
IL_8CBJ_052Tandem non-canonical cWW pairs
IL_8CBJ_055No text annotation
IL_8CBJ_062Isolated non-canonical cWW pair
IL_8CBJ_063C-loop
IL_8CBJ_101No text annotation
IL_8CBJ_064Isolated non-canonical cWW pair
IL_8CBJ_065Minor groove platform
IL_8CBJ_066Isolated non-canonical cWW pair
IL_8CBJ_067No text annotation
IL_8CBJ_102No text annotation
IL_8CBJ_068No text annotation
IL_8CBJ_069Isolated non-canonical cWW pair
IL_8CBJ_070Single stack bend
IL_8CBJ_071Decoding loop related
IL_8CBJ_107No text annotation
IL_8CBJ_072Single bulged U
IL_8CBJ_073Isolated non-canonical cWW pair
IL_8CBJ_074Single bulged A
IL_8CBJ_103No text annotation
IL_8CBJ_075Isolated cWH basepair
IL_8CBJ_076Minor groove platform
IL_8CBJ_077Isolated non-canonical cWW pair
IL_8CBJ_078Minor groove platform
IL_8CBJ_079Isolated non-canonical cWW pair
IL_8CBJ_080Major groove platform; stack outside cWW
IL_8CBJ_081No text annotation
IL_8CBJ_082180 degree turn
IL_8CBJ_083Tandem non-canonical cWW pairs
IL_8CBJ_104No text annotation
IL_8CBJ_084No text annotation
IL_8CBJ_085No text annotation
IL_8CBJ_105No text annotation
IL_8CBJ_086No text annotation
IL_8CBJ_087Tandem non-canonical cWW pairs
IL_8CBJ_088Isolated cWH basepair
IL_8CBJ_106No text annotation
IL_8CBJ_089No text annotation
IL_8CBJ_090Isolated non-canonical cWW pair
IL_8CBJ_095Isolated non-canonical cWW pair
IL_8CBJ_096Isolated non-canonical cWW pair

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8CBJ_0111/2/41:42,
1/2/433:439,
1/2/464:466		No text annotation
geometric
J3_8C3A_082
NA
J3_8CBJ_0121/2/41:48,
1/2/431:439,
1/2/464:466		No text annotation
geometric
J3_8C3A_083
NA
J3_8CBJ_0131/2/213:228,
1/2/237:243,
1/2/250:252		No text annotation
J3_8CBJ_0141/2/633:635,
1/2/861:865,
1/2/965:966		No text annotation
geometric
J3_4V88_080
NA
J3_8CBJ_0151/2/633:635,
1/2/861:866,
1/2/962:966		No text annotation
geometric
J3_4V88_081
NA
J3_8CBJ_0011/2/760:763,
1/2/773:775,
1/2/785:790		No text annotation
geometric
J3_4V88_032
NA
J3_8CBJ_0021/2/881:884,
1/2/928:936,
1/2/943:947		No text annotation
geometric
J3_4V88_033
NA
J3_8CBJ_0031/2/1037:1039,
1/2/1079:1083,
1/2/1090:1094		No text annotation
geometric
J3_8C3A_037
NA
J3_8CBJ_0181/2/1293:1294,
1/2/1303:1306,
1/2/1318:1322		No text annotation
geometric
J3_8C3A_085
NA
J4_8CBJ_0011/2/99:107,
1/2/307:309,
1/2/357:361,
1/2/383:384		No text annotation
homologous
J4_8P9A_021
J4_15241.2
J4_8CBJ_0021/2/622:624,
1/2/975:980,
1/2/1021:1032,
1/2/1103:1104		No text annotation
homologous
J4_8P9A_022
J4_14595.1
J5_8CBJ_0011/2/31:35,
1/2/473:479,
1/2/509:516,
1/2/536:547,
1/2/591:595		No text annotation
J5_8CBJ_0021/2/54:57,
1/2/90:97,
1/2/386:388,
1/2/409:411,
1/2/422:426		No text annotation
homologous
J5_8CRE_020
J5_58574.1
J5_8CBJ_0031/2/636:641,
1/2/693:699,
1/2/739:744,
1/2/807:817,
1/2/854:860		No text annotation

Problematic loops

#loop idProblemSequence
J3_8CBJ_016No text annotation
J3_8CBJ_017No text annotation
J3_8CBJ_004No text annotation
J3_8CBJ_005No text annotation
J3_8CBJ_006No text annotation
J3_8CBJ_007No text annotation
J3_8CBJ_008No text annotation
J3_8CBJ_019No text annotation
J3_8CBJ_020No text annotation
J3_8CBJ_009No text annotation
J3_8CBJ_010No text annotation

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