RNA 3D Hub //

7D4I Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_7D4I_0021/5A/4:9No text annotation
geometric
HL_4WF9_003
HL_75660.7
HL_7D4I_0051/SA/64:86No text annotation
HL_7D4I_0091/SA/243:250T-loop with 1 bulged base
homologous
HL_4V88_191
NA
HL_7D4I_0111/SA/330:338GNRA related
homologous
HL_4V88_193
NA
HL_7D4I_0121/SA/450:456No text annotation
homologous
HL_4V88_197
NA
HL_7D4I_0131/SA/491:496No text annotation
geometric
HL_5NFV_001
HL_69752.4
HL_7D4I_0141/SA/520:532No text annotation
geometric
HL_4V88_199
NA
HL_7D4I_0151/SA/561:566No text annotation
geometric
HL_5NFV_001
HL_69752.4
HL_7D4I_0171/SA/764:772No text annotation
homologous
HL_4V88_203
NA
HL_7D4I_0201/SA/900:909No text annotation
homologous
HL_4V88_206
NA
HL_7D4I_0211/SA/937:942GNRA
homologous
HL_4V88_207
NA
HL_7D4I_0221/SA/1055:1064No text annotation
geometric
HL_4V88_198
NA
HL_7D4I_0231/SA/1129:1139No text annotation
HL_7D4I_0261/SA/1501:1506GNRA
homologous
HL_4V88_218
NA
HL_7D4I_0281/SA/1594:1602No text annotation
HL_7D4I_0291/SA/1629:1636Purine riboswitch
geometric
HL_4LX6_002
HL_46333.1

Problematic loops

#loop idProblemSequence
HL_7D4I_001No text annotation
HL_7D4I_003No text annotation
HL_7D4I_004No text annotation
HL_7D4I_006GNRA related
HL_7D4I_007No text annotation
HL_7D4I_008UNCG
HL_7D4I_010No text annotation
HL_7D4I_016Mini UNCG
HL_7D4I_018No text annotation
HL_7D4I_019No text annotation
HL_7D4I_024No text annotation
HL_7D4I_025No text annotation
HL_7D4I_027No text annotation
HL_7D4I_030No text annotation
HL_7D4I_031No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_7D4I_0021/3A/11:13,
1/SA/1112:1113		Single stack bend
geometric
IL_5J7L_032
NA
IL_7D4I_0031/3A/47:51,
1/5A/465:471		No text annotation
IL_7D4I_0041/3A/78:85,
1/3A/325:329		No text annotation
IL_7D4I_0661/3A/85:96,
1/3A/320:325		No text annotation
IL_7D4I_0051/3A/97:98,
1/3A/317:319		No text annotation
IL_7D4I_0061/3A/111:115,
1/3A/252:259		No text annotation
IL_7D4I_0071/3A/200:207,
1/3A/242:249		No text annotation
IL_7D4I_0081/5A/17:18,
1/5A/62:64		Single bulged G
geometric
IL_3NDB_004
NA
IL_7D4I_0121/SA/35:37,
1/SA/471:473		Isolated non-canonical cWW pair
homologous
IL_4V88_385
NA
IL_7D4I_0131/SA/37:41,
1/SA/466:471		Triple sheared related
geometric
IL_4V88_386
NA
IL_7D4I_0141/SA/50:52,
1/SA/428:429		Minor groove platform
homologous
IL_4V88_388
NA
IL_7D4I_0151/SA/58:63,
1/SA/87:89		No text annotation
homologous
IL_4V88_389
NA
IL_7D4I_0161/SA/109:112,
1/SA/302:305		Tandem non-canonical cWW pairs
homologous
IL_4V88_391
NA
IL_7D4I_0171/SA/113:116,
1/SA/300:301		Multiple bulged bases
homologous
IL_4V88_392
NA
IL_7D4I_0181/SA/117:122,
1/SA/295:299		No text annotation
homologous
IL_4V88_393
NA
IL_7D4I_0191/SA/143:149,
1/SA/165:172		tWH-tWH-tHW-tHW
homologous
IL_4V88_394
NA
IL_7D4I_0221/SA/204:209,
1/SA/256:263		No text annotation
IL_7D4I_0231/SA/265:267,
1/SA/288:289		Single bulged A
homologous
IL_4V88_399
NA
IL_7D4I_0241/SA/270:273,
1/SA/283:285		No text annotation
homologous
IL_4V88_400
NA
IL_7D4I_0281/SA/439:441,
1/SA/463:464		Single bulged U
homologous
IL_4V88_407
NA
IL_7D4I_0291/SA/443:447,
1/SA/460:461		C-loop
geometric
IL_4LFB_015
IL_26900.1
IL_7D4I_0301/SA/447:448,
1/SA/458:460		Single bulged G
geometric
IL_5J7L_019
NA
IL_7D4I_0311/SA/480:482,
1/SA/505:508		Other IL
geometric
IL_4V88_476
NA
IL_7D4I_0321/SA/514:516,
1/SA/536:543		Isolated tHS basepair with bulges
geometric
IL_7RQB_082
NA
IL_7D4I_0681/SA/517:518,
1/SA/533:535		Minor groove platform
homologous
IL_8C3A_501
NA
IL_7D4I_0341/SA/518:520,
1/SA/532:533		Minor groove platform
geometric
IL_4V88_412
NA
IL_7D4I_0351/SA/551:552,
1/SA/584:587		No text annotation
geometric
IL_5J7L_341
NA
IL_7D4I_0361/SA/552:559,
1/SA/568:584		No text annotation
IL_7D4I_0371/SA/624:626,
1/SA/973:975		Isolated non-canonical cWW pair
homologous
IL_4V88_417
NA
IL_7D4I_0381/SA/627:631,
1/SA/969:972		No text annotation
IL_7D4I_0401/SA/646:648,
1/SA/686:688		Isolated non-canonical cWW pair
homologous
IL_4V88_419
NA
IL_7D4I_0421/SA/746:751,
1/SA/798:805		No text annotation
IL_7D4I_0441/SA/865:866,
1/SA/962:965		Major groove platform; stack outside cWW
geometric
IL_4V88_428
NA
IL_7D4I_0741/SA/868:870,
1/SA/957:960		Isolated cWH basepair
homologous
IL_8CRE_432
IL_10892.2
IL_7D4I_0461/SA/871:873,
1/SA/954:956		Isolated non-canonical cWW pair
geometric
IL_5TBW_068
NA
IL_7D4I_0471/SA/874:878,
1/SA/950:953		Tandem non-canonical cWW pairs
homologous
IL_4V88_431
NA
IL_7D4I_0481/SA/885:888,
1/SA/924:927		Tandem non-canonical cWW pairs
homologous
IL_4V88_432
NA
IL_7D4I_0491/SA/893:899,
1/SA/910:919		Kink-turn related
homologous
IL_8C3A_440
NA
IL_7D4I_0501/SA/1041:1044,
1/SA/1074:1077		Tandem non-canonical cWW pairs
homologous
IL_4V88_438
NA
IL_7D4I_0511/SA/1051:1053,
1/SA/1066:1067		Single stack bend
geometric
IL_4C7O_002
IL_15011.2
IL_7D4I_0521/SA/1157:1160,
1/SA/1617:1621		C-loop
homologous
IL_4V88_443
NA
IL_7D4I_0531/SA/1173:1176,
1/SA/1463:1466		Double sheared
geometric
IL_4ZNP_002
IL_58355.2
IL_7D4I_0571/SA/1495:1498,
1/SA/1509:1512		Tandem non-canonical cWW pairs
homologous
IL_4V88_461
NA
IL_7D4I_0591/SA/1650:1652,
1/SA/1748:1750		Isolated non-canonical cWW pair
homologous
IL_4V88_467
NA
IL_7D4I_0601/SA/1653:1657,
1/SA/1744:1747		Tandem non-canonical cWW pairs
geometric
IL_5J7L_283
NA

Problematic loops

#loop idProblemSequence
IL_7D4I_001Single bulged G
IL_7D4I_009No text annotation
IL_7D4I_010No text annotation
IL_7D4I_011No text annotation
IL_7D4I_073No text annotation
IL_7D4I_020Tandem non-canonical cWW pairs
IL_7D4I_021Double sheared
IL_7D4I_025Single bulged U
IL_7D4I_026Kink-turn with non-sequential stacking
IL_7D4I_027No text annotation
IL_7D4I_067No text annotation
IL_7D4I_033Minor groove platform with extra cWW
IL_7D4I_039Single stack bend
IL_7D4I_041Single stack bend
IL_7D4I_043Tandem non-canonical cWW pairs
IL_7D4I_045No text annotation
IL_7D4I_069Double sheared with near cWW
IL_7D4I_054No text annotation
IL_7D4I_055Single stack bend
IL_7D4I_056No text annotation
IL_7D4I_058No text annotation
IL_7D4I_061Tandem non-canonical cWW pairs
IL_7D4I_075Isolated non-canonical cWW pair
IL_7D4I_070No text annotation
IL_7D4I_062Double sheared
IL_7D4I_063Isolated non-canonical cWW pair
IL_7D4I_076No text annotation
IL_7D4I_071No text annotation
IL_7D4I_064Single stack bend
IL_7D4I_072Isolated tWW contact
IL_7D4I_065No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_7D4I_0011/3A/106:111,
1/3A/259:263,
1/3A/308:309		No text annotation
J3_7D4I_0091/3A/106:111,
1/3A/259:266,
1/3A/305:309		No text annotation
J3_7D4I_0021/SA/41:48,
1/SA/431:439,
1/SA/464:466		No text annotation
J3_7D4I_0031/SA/633:635,
1/SA/861:865,
1/SA/965:966		No text annotation
homologous
J3_8P9A_071
J3_01633.1
J3_7D4I_0101/SA/633:635,
1/SA/861:866,
1/SA/962:966		No text annotation
homologous
J3_8P9A_072
J3_17385.5
J3_7D4I_0131/SA/751:763,
1/SA/773:776,
1/SA/784:798		No text annotation
J3_7D4I_0041/SA/881:884,
1/SA/928:936,
1/SA/943:947		No text annotation
homologous
J3_4V88_033
NA
J3_7D4I_0051/SA/1150:1151,
1/SA/1627:1629,
1/SA/1636:1640		No text annotation
J3_7D4I_0121/SA/1161:1164,
1/SA/1581:1587,
1/SA/1609:1616		No text annotation
homologous
J3_8C3A_038
NA
J3_7D4I_0061/SA/1168:1171,
1/SA/1468:1470,
1/SA/1574:1577		No text annotation
homologous
J3_4V88_036
NA
J3_7D4I_0081/SA/1470:1474,
1/SA/1533:1540,
1/SA/1571:1574		No text annotation
J5_7D4I_0011/SA/31:35,
1/SA/473:479,
1/SA/509:516,
1/SA/536:546,
1/SA/592:595		No text annotation
J5_7D4I_0021/SA/124:143,
1/SA/172:182,
1/SA/203:204,
1/SA/263:265,
1/SA/289:293		No text annotation

Problematic loops

#loop idProblemSequence
J3_7D4I_011No text annotation
J3_7D4I_007No text annotation

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