RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_7MQA_0011/L1/8:16Pseudoknot geometry
geometric
HL_3IGI_005
HL_93324.4
HL_7MQA_0021/L1/69:80No text annotation
geometric
HL_361D_002
HL_13963.3
HL_7MQA_0031/L1/156:162GNRA related
homologous
HL_4V88_188
NA
HL_7MQA_0041/L1/288:295T-loop with 1 bulged base
geometric
HL_4V88_191
NA
HL_7MQA_0051/L1/323:327Mini UNCG
homologous
HL_4V88_192
NA
HL_7MQA_0061/L1/377:387No text annotation
HL_7MQA_0071/L1/416:421No text annotation
homologous
HL_4V88_194
NA
HL_7MQA_0081/L1/441:452No text annotation
homologous
HL_4V88_195
NA
HL_7MQA_0341/L1/462:467UNCG
homologous
HL_8P9A_200
HL_34617.5
HL_7MQA_0101/L1/498:504No text annotation
homologous
HL_4V88_197
NA
HL_7MQA_0111/L1/539:544No text annotation
geometric
HL_5U3G_001
HL_75660.5
HL_7MQA_0121/L1/569:581No text annotation
homologous
HL_4V88_199
NA
HL_7MQA_0131/L1/610:615No text annotation
geometric
HL_2Y9H_003
HL_75660.5
HL_7MQA_0151/L1/820:828No text annotation
homologous
HL_4V88_203
NA
HL_7MQA_0351/L1/957:966No text annotation
homologous
HL_8C3A_211
NA
HL_7MQA_0191/L1/994:999GNRA
homologous
HL_4V88_207
NA
HL_7MQA_0201/L1/1054:1064No text annotation
geometric
HL_5TBW_006
NA
HL_7MQA_0211/L1/1112:1121No text annotation
geometric
HL_5TBW_006
NA
HL_7MQA_0221/L1/1141:1146GNRA
homologous
HL_4V88_210
NA
HL_7MQA_0231/L1/1192:1197Mini UNCG
geometric
HL_2F8K_001
HL_48778.2
HL_7MQA_0241/L1/1295:1304Anticodon loop related
homologous
HL_4V88_213
NA
HL_7MQA_0251/L1/1353:1358GNRA
homologous
HL_4V88_214
NA
HL_7MQA_0261/L1/1366:1373No text annotation
homologous
HL_4V88_215
NA
HL_7MQA_0271/L1/1460:1466GNRA
homologous
HL_4V88_217
NA
HL_7MQA_0281/L1/1565:1570GNRA
homologous
HL_4V88_218
NA
HL_7MQA_0291/L1/1658:1666No text annotation
HL_7MQA_0301/L1/1763:1769No text annotation
HL_7MQA_0311/L1/1847:1852Mini UNCG
geometric
HL_6AAX_001
HL_56334.1
HL_7MQA_0321/L2/133:140No text annotation
HL_7MQA_0331/L2/177:183No text annotation

Problematic loops

#loop idProblemSequence
HL_7MQA_009No text annotation
HL_7MQA_014No text annotation
HL_7MQA_016No text annotation
HL_7MQA_017No text annotation
HL_7MQA_018No text annotation
HL_7MQA_036No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_7MQA_1011/L1/23:25,
1/L1/649:651		Isolated non-canonical cWW pair
geometric
IL_5UNE_006
IL_87907.2
IL_7MQA_1021/L1/34:36,
1/L1/519:521		Isolated non-canonical cWW pair
homologous
IL_8C3A_393
NA
IL_7MQA_0031/L1/37:40,
1/L1/514:518		No text annotation
IL_7MQA_0041/L1/49:51,
1/L1/476:477		Minor groove platform
homologous
IL_4V88_388
NA
IL_7MQA_0051/L1/57:62,
1/L1/86:88		No text annotation
homologous
IL_4V88_389
NA
IL_7MQA_0061/L1/63:68,
1/L1/81:85		No text annotation
homologous
IL_4V88_390
NA
IL_7MQA_0081/L1/108:110,
1/L1/351:353		Stack and bulge
geometric
IL_2O3X_001
IL_31737.3
IL_7MQA_0091/L1/110:112,
1/L1/349:351		Isolated non-canonical cWW pair
geometric
IL_4WF9_042
IL_87907.2
IL_7MQA_0101/L1/112:115,
1/L1/348:349		Multiple bulged bases
geometric
IL_5W1H_001
IL_82107.5
IL_7MQA_1031/L1/116:121,
1/L1/343:347		No text annotation
homologous
IL_8P9A_382
IL_29223.1
IL_7MQA_1041/L1/145:151,
1/L1/167:174		No text annotation
homologous
IL_8C3A_402
NA
IL_7MQA_1051/L1/152:154,
1/L1/164:166		No text annotation
homologous
IL_8P9A_384
IL_44465.1
IL_7MQA_0141/L1/188:192,
1/L1/207:211		No text annotation
IL_7MQA_0151/L1/216:219,
1/L1/302:309		No text annotation
IL_7MQA_0161/L1/230:233,
1/L1/282:285		Tandem non-canonical cWW pairs
geometric
IL_5TBW_100
NA
IL_7MQA_0171/L1/233:238,
1/L1/279:282		Minor groove platform related
geometric
IL_5J7L_010
IL_64231.5
IL_7MQA_0181/L1/238:240,
1/L1/277:279		Isolated non-canonical cWW pair
geometric
IL_3SZX_002
IL_87907.2
IL_7MQA_0201/L1/248:249,
1/L1/270:272		No text annotation
IL_7MQA_0211/L1/312:314,
1/L1/336:337		Single bulged A
homologous
IL_4V88_399
NA
IL_7MQA_0221/L1/317:319,
1/L1/332:333		Single stack bend
geometric
IL_5TBW_009
NA
IL_7MQA_0231/L1/322:323,
1/L1/327:329		Single bulged U
geometric
IL_5TBW_050
NA
IL_7MQA_0241/L1/359:364,
1/L1/396:403		Kink-turn with non-sequential stacking
homologous
IL_4V88_402
NA
IL_7MQA_0251/L1/366:371,
1/L1/393:394		No text annotation
geometric
IL_5Y58_001
IL_59877.1
IL_7MQA_0261/L1/411:413,
1/L1/424:429		No text annotation
homologous
IL_4V88_404
NA
IL_7MQA_0271/L1/437:439,
1/L1/454:456		Isolated non-canonical cWW pair
geometric
IL_5TBW_127
NA
IL_7MQA_1061/L1/459:461,
1/L1/468:470		Isolated non-canonical cWW pair
homologous
IL_8C3A_414
NA
IL_7MQA_1071/L1/487:489,
1/L1/511:512		Single bulged U
geometric
IL_8C3A_415
NA
IL_7MQA_1081/L1/491:495,
1/L1/508:509		C-loop
homologous
IL_8C3A_416
NA
IL_7MQA_0291/L1/495:496,
1/L1/506:508		Single bulged G
geometric
IL_5J7L_019
IL_00225.14
IL_7MQA_0301/L1/530:531,
1/L1/553:555		Single bulged A
homologous
IL_4V88_409
NA
IL_7MQA_0311/L1/534:535,
1/L1/548:550		No text annotation
IL_7MQA_0321/L1/535:537,
1/L1/546:548		Isolated non-canonical cWW pair
geometric
IL_3MEI_002
IL_87907.2
IL_7MQA_0331/L1/563:565,
1/L1/585:592		No text annotation
homologous
IL_8C3A_420
NA
IL_7MQA_0341/L1/566:569,
1/L1/581:584		Tandem non-canonical cWW pairs
geometric
IL_5C5W_003
NA
IL_7MQA_0371/L1/663:665,
1/L1/1162:1164		Isolated non-canonical cWW pair
geometric
IL_1Y27_001
IL_87907.2
IL_7MQA_0381/L1/665:671,
1/L1/1161:1162		No text annotation
geometric
IL_4V88_416
NA
IL_7MQA_0391/L1/673:675,
1/L1/1030:1032		Isolated non-canonical cWW pair
homologous
IL_4V88_417
NA
IL_7MQA_0401/L1/676:680,
1/L1/1025:1029		tSH-tHW-tHS
geometric
IL_5J7L_037
IL_17136.7
IL_7MQA_1171/L1/692:694,
1/L1/738:739		Single stack bend
geometric
IL_5J7L_032
IL_26793.1
IL_7MQA_1181/L1/697:698,
1/L1/732:735		No text annotation
IL_7MQA_0441/L1/745:749,
1/L1/794:796		C-loop
geometric
IL_7RQB_104
NA
IL_7MQA_0451/L1/752:754,
1/L1/790:791		No text annotation
IL_7MQA_1091/L1/802:803,
1/L1/860:863		No text annotation
geometric
IL_8VTW_072
NA
IL_7MQA_0471/L1/805:807,
1/L1/856:858		Isolated non-canonical cWW pair
homologous
IL_4V88_424
NA
IL_7MQA_1101/L1/807:815,
1/L1/849:856		No text annotation
homologous
IL_8C3A_503
NA
IL_7MQA_0491/L1/874:876,
1/L1/910:911		No text annotation
IL_7MQA_0501/L1/877:879,
1/L1/907:909		Isolated non-canonical cWW pair
geometric
IL_4LFB_059
IL_87907.2
IL_7MQA_0511/L1/922:923,
1/L1/1019:1022		Major groove platform; stack outside cWW
homologous
IL_4V88_428
NA
IL_7MQA_1111/L1/925:926,
1/L1/1015:1017		Single bulged U
geometric
IL_6UFH_004
IL_89505.4
IL_7MQA_0531/L1/928:931,
1/L1/1010:1013		Tandem non-canonical cWW pairs
homologous
IL_4V88_430
NA
IL_7MQA_0541/L1/931:935,
1/L1/1007:1010		Tandem non-canonical cWW pairs
geometric
IL_4V88_431
NA
IL_7MQA_0551/L1/942:945,
1/L1/981:984		Tandem non-canonical cWW pairs
homologous
IL_4V88_432
NA
IL_7MQA_0561/L1/952:956,
1/L1/967:974		Kink-turn
homologous
IL_4V88_434
NA
IL_7MQA_0571/L1/1042:1047,
1/L1/1071:1073		Other IL
geometric
IL_4V88_435
NA
IL_7MQA_0581/L1/1047:1051,
1/L1/1067:1071		tSH-tHW-tHS
homologous
IL_4V88_436
NA
IL_7MQA_0591/L1/1091:1093,
1/L1/1152:1158		Decoding loop related
geometric
IL_5Z1I_002
NA
IL_7MQA_0601/L1/1098:1101,
1/L1/1131:1134		Tandem non-canonical cWW pairs
geometric
IL_4V88_438
NA
IL_7MQA_0611/L1/1101:1103,
1/L1/1129:1131		Isolated non-canonical cWW pair
geometric
IL_4WF9_083
IL_87907.2
IL_7MQA_0621/L1/1108:1110,
1/L1/1123:1124		Minor groove platform
geometric
IL_4V88_412
NA
IL_7MQA_0661/L1/1214:1217,
1/L1/1681:1685		C-loop
homologous
IL_4V88_443
NA
IL_7MQA_1121/L1/1230:1232,
1/L1/1526:1528		Isolated non-canonical cWW pair
homologous
IL_8P9A_432
IL_87907.2
IL_7MQA_0691/L1/1235:1236,
1/L1/1521:1523		Single bulged A
geometric
IL_8X5V_002
IL_31462.7
IL_7MQA_0711/L1/1270:1272,
1/L1/1510:1512		Isolated non-canonical cWW pair
homologous
IL_4V88_446
NA
IL_7MQA_0721/L1/1282:1287,
1/L1/1314:1315		No text annotation
geometric
IL_4V9F_009
IL_92634.2
IL_7MQA_1131/L1/1282:1290,
1/L1/1309:1315		No text annotation
IL_7MQA_0731/L1/1287:1290,
1/L1/1309:1314		No text annotation
IL_7MQA_0741/L1/1291:1293,
1/L1/1306:1308		No text annotation
homologous
IL_4V88_448
NA
IL_7MQA_0751/L1/1330:1331,
1/L1/1497:1499		Single bulged A
geometric
IL_7A0S_012
IL_31462.7
IL_7MQA_0761/L1/1335:1336,
1/L1/1491:1493		Single bulged U
geometric
IL_4O26_001
IL_89505.4
IL_7MQA_0771/L1/1337:1338,
1/L1/1488:1490		Single bulged A
geometric
IL_4V9F_090
IL_42771.1
IL_7MQA_0781/L1/1347:1349,
1/L1/1380:1382		Isolated cWH basepair
geometric
IL_4V88_453
NA
IL_7MQA_0791/L1/1395:1399,
1/L1/1447:1450		Tandem non-canonical cWW pairs
geometric
IL_5EW4_002
IL_85033.2
IL_7MQA_0801/L1/1537:1539,
1/L1/1594:1596		Isolated non-canonical cWW pair
geometric
IL_4P3T_001
NA
IL_7MQA_0811/L1/1604:1610,
1/L1/1629:1635		No text annotation
homologous
IL_8C3A_469
NA
IL_7MQA_1141/L1/1614:1616,
1/L1/1623:1625		Isolated non-canonical cWW pair
geometric
IL_4E48_006
IL_87907.2
IL_7MQA_0831/L1/1714:1716,
1/L1/1817:1819		Isolated non-canonical cWW pair
homologous
IL_4V88_467
NA
IL_7MQA_0841/L1/1717:1720,
1/L1/1813:1816		Tandem non-canonical cWW pairs
geometric
IL_5LQO_002
IL_85033.2
IL_7MQA_0851/L1/1720:1722,
1/L1/1812:1813		Single stack bend
geometric
IL_4LFB_041
IL_90729.1
IL_7MQA_0871/L1/1729:1731,
1/L1/1803:1805		Isolated non-canonical cWW pair
homologous
IL_4V88_470
NA
IL_7MQA_0881/L1/1733:1736,
1/L1/1798:1801		Double sheared
homologous
IL_4V88_471
NA
IL_7MQA_0891/L1/1739:1741,
1/L1/1793:1795		Isolated non-canonical cWW pair
geometric
IL_3SZX_003
IL_87907.2
IL_7MQA_0901/L1/1742:1746,
1/L1/1788:1792		Triple sheared
homologous
IL_4V88_474
NA
IL_7MQA_0911/L1/1750:1753,
1/L1/1779:1784		No text annotation
geometric
IL_4DB2_001
IL_68909.1
IL_7MQA_0931/L2/79:86,
1/L2/209:213		No text annotation
IL_7MQA_0941/L2/86:94,
1/L2/205:209		No text annotation
IL_7MQA_0951/L2/110:114,
1/L2/158:165		No text annotation
IL_7MQA_0961/L2/114:118,
1/L2/155:158		No text annotation
IL_7MQA_0971/L2/121:124,
1/L2/149:152		No text annotation
IL_7MQA_0981/L2/124:126,
1/L2/148:149		No text annotation
IL_7MQA_1161/L2/128:129,
1/L2/144:146		No text annotation
IL_7MQA_1001/L2/171:172,
1/L2/188:190		No text annotation

Problematic loops

#loop idProblemSequence
IL_7MQA_001Partly complementary
IL_7MQA_002Isolated non-canonical cWW pair
IL_7MQA_007Isolated non-canonical cWW pair
IL_7MQA_011No text annotation
IL_7MQA_012No text annotation
IL_7MQA_013Tandem non-canonical cWW pairs
IL_7MQA_019No text annotation
IL_7MQA_028No text annotation
IL_7MQA_035No text annotation
IL_7MQA_036Not an internal loop
IL_7MQA_041Stack and bulge
IL_7MQA_042No text annotation
IL_7MQA_043Tandem non-canonical cWW pairs
IL_7MQA_046No text annotation
IL_7MQA_048No text annotation
IL_7MQA_052Tandem non-canonical cWW pairs
IL_7MQA_063Not an internal loop
IL_7MQA_064Intercalated cWW
IL_7MQA_065Multiple bulged bases
IL_7MQA_067Not an internal loop
IL_7MQA_068Tandem non-canonical cWW pairs
IL_7MQA_070No text annotation
IL_7MQA_082Tandem non-canonical cWW pairs
IL_7MQA_086Isolated non-canonical cWW pair
IL_7MQA_115No text annotation
IL_7MQA_092Isolated non-canonical cWW pair
IL_7MQA_099No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_7MQA_0131/L1/40:47,
1/L1/479:487,
1/L1/512:514		No text annotation
J3_7MQA_0021/L1/223:229,
1/L1/286:288,
1/L1/295:298		No text annotation
J3_7MQA_0031/L1/682:685,
1/L1/917:922,
1/L1/1022:1023		No text annotation
J3_7MQA_0141/L1/682:685,
1/L1/917:923,
1/L1/1019:1023		No text annotation
J3_7MQA_0041/L1/816:819,
1/L1/829:831,
1/L1/843:848		No text annotation
J3_7MQA_0151/L1/938:941,
1/L1/985:993,
1/L1/1000:1004		No text annotation
homologous
J3_8P9A_074
J3_76375.1
J3_7MQA_0061/L1/1094:1096,
1/L1/1136:1140,
1/L1/1147:1151		No text annotation
J3_7MQA_0161/L1/1218:1221,
1/L1/1645:1651,
1/L1/1673:1680		No text annotation
homologous
J3_8P9A_076
J3_25303.4
J3_7MQA_0071/L1/1225:1228,
1/L1/1530:1532,
1/L1/1638:1641		No text annotation
homologous
J3_4V88_036
NA
J3_7MQA_0101/L1/1391:1395,
1/L1/1450:1456,
1/L1/1470:1479		No text annotation
J3_7MQA_0111/L1/1532:1536,
1/L1/1597:1604,
1/L1/1635:1638		No text annotation
homologous
J3_8C3A_044
NA
J3_7MQA_0121/L2/105:110,
1/L2/165:168,
1/L2/193:194		No text annotation
J4_7MQA_0011/L1/98:106,
1/L1/355:357,
1/L1/405:409,
1/L1/431:432		No text annotation
homologous
J4_8P9A_021
J4_15241.1
J4_7MQA_0021/L1/671:673,
1/L1/1032:1037,
1/L1/1078:1089,
1/L1/1160:1161		No text annotation
homologous
J4_8P9A_022
J4_61885.6
J4_7MQA_0031/L1/688:690,
1/L1/741:744,
1/L1/797:800,
1/L1/865:867		No text annotation
J5_7MQA_0011/L1/30:34,
1/L1/521:527,
1/L1/558:563,
1/L1/592:595,
1/L1/641:644		No text annotation
homologous
J5_8C3A_018
NA
J5_7MQA_0021/L1/30:34,
1/L1/521:527,
1/L1/558:565,
1/L1/585:595,
1/L1/641:644		No text annotation
J5_7MQA_0031/L1/53:56,
1/L1/89:96,
1/L1/434:436,
1/L1/457:459,
1/L1/470:474		No text annotation
homologous
J5_8C3A_020
NA

Problematic loops

#loop idProblemSequence
J3_7MQA_001No text annotation
J3_7MQA_005No text annotation
J3_7MQA_008No text annotation
J3_7MQA_009No text annotation

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