RNA 3D Hub //

6P4H Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_6P4H_0011/1/6444:6460No text annotation
HL_6P4H_0021/1/6497:6502Mini UNCG
geometric
HL_1ZBH_001
HL_56334.1
HL_6P4H_0031/1/6521:6527No text annotation
HL_6P4H_0041/1/6560:6570No text annotation
geometric
HL_4V83_139
NA
HL_6P4H_0051/1/6580:6595No text annotation
HL_6P4H_0061/2/7:17No text annotation
homologous
HL_4V88_186
NA
HL_6P4H_0071/2/69:80No text annotation
geometric
HL_2ZZM_002
HL_13963.3
HL_6P4H_0081/2/156:162GNRA related
homologous
HL_4V88_188
NA
HL_6P4H_0091/2/197:202GNRA
geometric
HL_3RG5_007
HL_37824.8
HL_6P4H_0101/2/288:295T-loop with 1 bulged base
geometric
HL_4V88_191
NA
HL_6P4H_0121/2/377:387tRNA D-loop
geometric
HL_5AXM_001
HL_20811.4
HL_6P4H_0131/2/416:421No text annotation
homologous
HL_4V88_194
NA
HL_6P4H_0141/2/441:452No text annotation
homologous
HL_4V88_195
NA
HL_6P4H_0151/2/462:467UNCG
homologous
HL_4V88_196
NA
HL_6P4H_0161/2/498:504No text annotation
homologous
HL_4V88_197
NA
HL_6P4H_0171/2/539:544GNRA
geometric
HL_7RQB_016
NA
HL_6P4H_0181/2/569:581No text annotation
geometric
HL_4V88_199
NA
HL_6P4H_0191/2/618:623GNRA variation
homologous
HL_4V88_200
NA
HL_6P4H_0201/2/820:828No text annotation
homologous
HL_4V88_203
NA
HL_6P4H_0401/2/885:901Pseudoknot geometry
geometric
HL_4GXY_003
HL_65794.5
HL_6P4H_0231/2/957:966No text annotation
homologous
HL_4V88_206
NA
HL_6P4H_0241/2/994:999GNRA
homologous
HL_4V88_207
NA
HL_6P4H_0251/2/1054:1064No text annotation
homologous
HL_4V88_208
NA
HL_6P4H_0261/2/1114:1119No text annotation
geometric
HL_2Y8W_001
HL_81100.2
HL_6P4H_0271/2/1141:1146GNRA
homologous
HL_4V88_210
NA
HL_6P4H_0281/2/1178:1183GNRA
homologous
HL_4V88_211
NA
HL_6P4H_0291/2/1245:1254No text annotation
homologous
HL_4V88_212
NA
HL_6P4H_0411/2/1295:1304No text annotation
homologous
HL_8P9A_216
HL_81538.2
HL_6P4H_0311/2/1353:1358GNRA
homologous
HL_4V88_214
NA
HL_6P4H_0321/2/1366:1373No text annotation
homologous
HL_4V88_215
NA
HL_6P4H_0341/2/1460:1466GNRA
homologous
HL_4V88_217
NA
HL_6P4H_0351/2/1565:1570GNRA
homologous
HL_4V88_218
NA
HL_6P4H_0361/2/1614:1625No text annotation
homologous
HL_4V88_219
NA
HL_6P4H_0371/2/1658:1666No text annotation
homologous
HL_4V88_220
NA
HL_6P4H_0391/2/1847:1852GNRA variation
homologous
HL_4V88_222
NA

Problematic loops

#loop idProblemSequence
HL_6P4H_011No text annotation
HL_6P4H_021No text annotation
HL_6P4H_022No text annotation
HL_6P4H_030No text annotation
HL_6P4H_033No text annotation
HL_6P4H_038No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_6P4H_0961/1/6424:6437,
1/1/6467:6476		No text annotation
IL_6P4H_0011/1/6491:6494,
1/1/6505:6513		No text annotation
IL_6P4H_0971/1/6492:6495,
1/1/6504:6512		No text annotation
IL_6P4H_1091/1/6518:6519,
1/1/6529:6531		Single stack bend
geometric
IL_8P9A_298
IL_90729.1
IL_6P4H_0031/1/6550:6552,
1/1/6601:6602		Single stack bend
geometric
IL_5TBW_070
NA
IL_6P4H_0041/2/23:25,
1/2/649:651		Isolated non-canonical cWW pair
geometric
IL_4M4O_001
IL_87907.2
IL_6P4H_0051/2/34:36,
1/2/519:521		Isolated non-canonical cWW pair
homologous
IL_4V88_385
NA
IL_6P4H_0061/2/37:40,
1/2/514:518		Double sheared
geometric
IL_4WF9_016
IL_09705.15
IL_6P4H_0071/2/41:47,
1/2/479:481		No text annotation
geometric
IL_4V88_387
NA
IL_6P4H_0081/2/49:51,
1/2/476:477		Minor groove platform
homologous
IL_4V88_388
NA
IL_6P4H_0091/2/57:62,
1/2/86:88		No text annotation
homologous
IL_4V88_389
NA
IL_6P4H_0981/2/63:68,
1/2/81:85		No text annotation
homologous
IL_8P9A_379
IL_21667.1
IL_6P4H_0111/2/108:110,
1/2/351:353		Isolated non-canonical cWW pair
geometric
IL_5WTI_002
IL_28037.2
IL_6P4H_0121/2/110:112,
1/2/349:351		No text annotation
geometric
IL_4KR9_001
NA
IL_6P4H_0131/2/112:115,
1/2/348:349		Multiple bulged bases
geometric
IL_4V88_392
NA
IL_6P4H_0141/2/116:121,
1/2/343:347		No text annotation
homologous
IL_4V88_393
NA
IL_6P4H_0161/2/145:151,
1/2/167:174		tWH-tWH-tHW-tHW
homologous
IL_4V88_394
NA
IL_6P4H_0171/2/152:154,
1/2/164:166		Isolated non-canonical cWW contact
homologous
IL_4V88_395
NA
IL_6P4H_0181/2/188:192,
1/2/207:211		Triple sheared
geometric
IL_4WFL_001
IL_17948.2
IL_6P4H_0191/2/216:219,
1/2/302:309		No text annotation
IL_6P4H_0211/2/312:314,
1/2/336:337		Single bulged A
homologous
IL_4V88_399
NA
IL_6P4H_0221/2/317:319,
1/2/332:333		Single stack bend
geometric
IL_5TBW_009
NA
IL_6P4H_0231/2/359:364,
1/2/396:403		Kink-turn with non-sequential stacking
homologous
IL_4V88_402
NA
IL_6P4H_0241/2/366:371,
1/2/393:394		No text annotation
geometric
IL_5Y58_001
IL_59877.1
IL_6P4H_0251/2/411:413,
1/2/424:429		No text annotation
homologous
IL_4V88_404
NA
IL_6P4H_0261/2/437:439,
1/2/454:456		Isolated cWH basepair
homologous
IL_4V88_405
NA
IL_6P4H_0271/2/459:461,
1/2/468:470		Isolated near basepair
homologous
IL_4V88_406
NA
IL_6P4H_0281/2/487:489,
1/2/511:512		Single bulged U
geometric
IL_4LFB_014
IL_89505.4
IL_6P4H_1101/2/491:495,
1/2/508:509		No text annotation
homologous
IL_8P9A_397
IL_03109.3
IL_6P4H_1111/2/495:496,
1/2/506:508		Single bulged G
homologous
IL_8P9A_398
IL_00225.14
IL_6P4H_0301/2/529:530,
1/2/554:556		Single bulged A
homologous
IL_4V88_409
NA
IL_6P4H_0991/2/534:537,
1/2/546:550		Other IL
geometric
IL_5J7L_327
IL_43644.1
IL_6P4H_0311/2/535:537,
1/2/546:549		Isolated non-canonical cWW with bulges
geometric
IL_4V9F_097
IL_07785.1
IL_6P4H_0321/2/563:565,
1/2/585:592		No text annotation
homologous
IL_8C3A_420
NA
IL_6P4H_0331/2/566:569,
1/2/581:584		tSH-tHW
geometric
IL_5UNE_005
IL_85033.2
IL_6P4H_0341/2/599:608,
1/2/635:637		No text annotation
IL_6P4H_0351/2/611:617,
1/2/624:632		Kink-turn related
homologous
IL_4V88_415
NA
IL_6P4H_0361/2/663:665,
1/2/1162:1164		Isolated non-canonical cWW pair
geometric
IL_1Y27_001
IL_87907.2
IL_6P4H_0371/2/665:671,
1/2/1161:1162		No text annotation
geometric
IL_4LFB_022
IL_38186.6
IL_6P4H_0381/2/673:675,
1/2/1030:1032		Isolated non-canonical cWW pair
homologous
IL_4V88_417
NA
IL_6P4H_0391/2/676:680,
1/2/1025:1029		tSH-tHW-tHS
homologous
IL_4V88_418
NA
IL_6P4H_1001/2/692:694,
1/2/732:734		Isolated non-canonical cWW pair
geometric
IL_4YHW_002
IL_87907.2
IL_6P4H_0421/2/752:754,
1/2/790:791		No text annotation
IL_6P4H_0431/2/802:803,
1/2/860:863		Major groove minor groove platform; mini C-loop
homologous
IL_4V88_423
NA
IL_6P4H_0441/2/805:807,
1/2/856:858		Isolated non-canonical cWW pair
homologous
IL_4V88_424
NA
IL_6P4H_1021/2/807:815,
1/2/849:856		No text annotation
homologous
IL_8C3A_503
NA
IL_6P4H_0461/2/874:876,
1/2/910:912		Isolated non-canonical cWW pair
geometric
IL_4P3U_007
IL_28037.2
IL_6P4H_0471/2/877:879,
1/2/907:909		Isolated non-canonical cWW pair
geometric
IL_3DIL_006
IL_87907.2
IL_6P4H_0481/2/922:923,
1/2/1019:1022		Major groove platform; stack outside cWW
geometric
IL_4V88_428
NA
IL_6P4H_0491/2/925:927,
1/2/1014:1017		Isolated cWH basepair
geometric
IL_3R1C_018
IL_10167.6
IL_6P4H_1041/2/928:931,
1/2/1010:1013		No text annotation
homologous
IL_8P9A_419
IL_85033.2
IL_6P4H_0511/2/931:935,
1/2/1007:1010		Tandem non-canonical cWW pairs
geometric
IL_4V88_431
NA
IL_6P4H_0521/2/942:945,
1/2/981:984		Tandem non-canonical cWW pairs
homologous
IL_4V88_432
NA
IL_6P4H_0531/2/952:956,
1/2/967:974		Kink-turn
homologous
IL_4V88_434
NA
IL_6P4H_0541/2/1042:1047,
1/2/1071:1073		Other IL
homologous
IL_4V88_435
NA
IL_6P4H_0551/2/1047:1051,
1/2/1067:1071		tSH-tHW-tHS
geometric
IL_5J7L_037
IL_17136.7
IL_6P4H_0561/2/1091:1093,
1/2/1152:1158		No text annotation
homologous
IL_4V88_437
NA
IL_6P4H_0571/2/1098:1101,
1/2/1131:1134		Tandem non-canonical cWW pairs
homologous
IL_4V88_438
NA
IL_6P4H_0581/2/1101:1103,
1/2/1129:1131		Isolated non-canonical cWW pair
geometric
IL_4V9F_105
IL_87907.2
IL_6P4H_0591/2/1108:1110,
1/2/1123:1124		Minor groove platform
geometric
IL_4V88_412
NA
IL_6P4H_0601/2/1168:1175,
1/2/1186:1191		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_4V88_440
NA
IL_6P4H_0611/2/1203:1204,
1/2/1694:1696		Single bulged A
homologous
IL_4V88_441
NA
IL_6P4H_0621/2/1206:1208,
1/2/1691:1692		Single bulged G
homologous
IL_4V88_442
NA
IL_6P4H_0631/2/1214:1217,
1/2/1681:1685		C-loop
homologous
IL_4V88_443
NA
IL_6P4H_0641/2/1230:1232,
1/2/1526:1528		Isolated non-canonical cWW pair
homologous
IL_4V88_444
NA
IL_6P4H_0651/2/1235:1236,
1/2/1521:1523		Minor groove platform
homologous
IL_4V88_445
NA
IL_6P4H_0661/2/1270:1272,
1/2/1510:1512		Isolated non-canonical cWW pair
homologous
IL_4V88_446
NA
IL_6P4H_0671/2/1281:1287,
1/2/1314:1316		No text annotation
IL_6P4H_1051/2/1281:1290,
1/2/1309:1316		No text annotation
homologous
IL_8P9A_470
IL_28304.1
IL_6P4H_0681/2/1287:1290,
1/2/1309:1314		No text annotation
IL_6P4H_0691/2/1291:1294,
1/2/1305:1308		No text annotation
IL_6P4H_0701/2/1325:1327,
1/2/1502:1503		Single bulged U
homologous
IL_4V88_449
NA
IL_6P4H_0711/2/1329:1333,
1/2/1498:1500		Isolated cWS basepair
geometric
IL_4LFB_044
IL_76319.5
IL_6P4H_1061/2/1329:1335,
1/2/1492:1500		No text annotation
homologous
IL_8P9A_439
IL_86012.1
IL_6P4H_0721/2/1333:1335,
1/2/1492:1498		Minor groove platform with extra cWW
homologous
IL_4V88_451
NA
IL_6P4H_0731/2/1337:1338,
1/2/1488:1490		Single bulged A
homologous
IL_4V88_452
NA
IL_6P4H_0741/2/1347:1349,
1/2/1380:1382		Isolated cWH basepair
homologous
IL_4V88_453
NA
IL_6P4H_0751/2/1363:1365,
1/2/1374:1375		Minor groove platform
geometric
IL_5ML7_009
IL_51454.3
IL_6P4H_0761/2/1395:1399,
1/2/1447:1450		Tandem non-canonical cWW pairs
geometric
IL_5EW4_002
IL_85033.2
IL_6P4H_0771/2/1402:1405,
1/2/1441:1444		Minor groove platform
homologous
IL_4V88_456
NA
IL_6P4H_0781/2/1412:1413,
1/2/1427:1429		Single bulged G
geometric
IL_5J7L_019
IL_00225.14
IL_6P4H_0791/2/1537:1539,
1/2/1594:1596		Isolated non-canonical cWW pair
geometric
IL_4P3T_001
NA
IL_6P4H_1071/2/1541:1550,
1/2/1582:1592		No text annotation
IL_6P4H_0801/2/1550:1558,
1/2/1577:1582		180 degree turn
geometric
IL_4LFB_052
IL_11344.2
IL_6P4H_0811/2/1560:1562,
1/2/1573:1575		Isolated non-canonical cWW pair
geometric
IL_5TBW_016
NA
IL_6P4H_0821/2/1604:1610,
1/2/1629:1635		No text annotation
homologous
IL_8C3A_469
NA
IL_6P4H_0831/2/1700:1702,
1/2/1833:1836		No text annotation
geometric
IL_4V88_463
NA
IL_6P4H_0841/2/1702:1705,
1/2/1829:1833		No text annotation
homologous
IL_4V88_464
NA
IL_6P4H_0851/2/1706:1708,
1/2/1826:1828		Isolated non-canonical cWW pair
homologous
IL_4V88_465
NA
IL_6P4H_0861/2/1708:1711,
1/2/1822:1826		No text annotation
homologous
IL_8CRE_469
IL_11399.2
IL_6P4H_0871/2/1714:1716,
1/2/1817:1819		Isolated non-canonical cWW pair
homologous
IL_4V88_467
NA
IL_6P4H_0881/2/1717:1720,
1/2/1813:1816		Double sheared
geometric
IL_4V88_468
NA
IL_6P4H_0891/2/1720:1722,
1/2/1812:1813		Single bulged U
homologous
IL_4V88_469
NA
IL_6P4H_0901/2/1729:1731,
1/2/1803:1805		Isolated non-canonical cWW pair
homologous
IL_4V88_470
NA
IL_6P4H_0911/2/1733:1736,
1/2/1798:1801		Double sheared
homologous
IL_4V88_471
NA
IL_6P4H_0921/2/1739:1741,
1/2/1793:1795		Isolated non-canonical cWW pair
geometric
IL_7A0S_107
IL_07785.1
IL_6P4H_0931/2/1742:1746,
1/2/1788:1792		Triple sheared
homologous
IL_4V88_474
NA
IL_6P4H_0941/2/1750:1751,
1/2/1782:1784		No text annotation
IL_6P4H_0951/2/1751:1752,
1/2/1780:1782		Single stack bend
geometric
IL_4C7O_002
IL_90729.1
IL_6P4H_1081/2/1751:1756,
1/2/1776:1782		No text annotation

Problematic loops

#loop idProblemSequence
IL_6P4H_002Other IL
IL_6P4H_010No text annotation
IL_6P4H_015No text annotation
IL_6P4H_020No text annotation
IL_6P4H_029C-loop with extra cWW pair
IL_6P4H_040Tandem non-canonical cWW pairs
IL_6P4H_041Not an internal loop
IL_6P4H_101No text annotation
IL_6P4H_045No text annotation
IL_6P4H_103Tandem non-canonical cWW pairs
IL_6P4H_050No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_6P4H_0181/1/6550:6555,
1/1/6575:6577,
1/1/6598:6602		No text annotation
J3_6P4H_0011/1/6552:6555,
1/1/6575:6577,
1/1/6598:6601		No text annotation
J3_6P4H_0021/2/40:41,
1/2/481:487,
1/2/512:514		No text annotation
geometric
J3_8C3A_082
NA
J3_6P4H_0161/2/40:47,
1/2/479:487,
1/2/512:514		No text annotation
homologous
J3_8P9A_069
J3_46317.4
J3_6P4H_0191/2/682:684,
1/2/918:922,
1/2/1022:1023		No text annotation
geometric
J3_8P9A_071
J3_56052.5
J3_6P4H_0201/2/682:684,
1/2/918:923,
1/2/1019:1023		No text annotation
homologous
J3_8P9A_072
J3_17385.4
J3_6P4H_0041/2/816:819,
1/2/829:831,
1/2/843:848		No text annotation
homologous
J3_4V88_032
NA
J3_6P4H_0051/2/938:941,
1/2/985:993,
1/2/1000:1004		No text annotation
homologous
J3_4V88_033
NA
J3_6P4H_0061/2/1094:1096,
1/2/1136:1140,
1/2/1147:1151		No text annotation
J3_6P4H_0071/2/1218:1221,
1/2/1645:1651,
1/2/1673:1680		No text annotation
homologous
J3_4V88_035
NA
J3_6P4H_0081/2/1225:1228,
1/2/1530:1532,
1/2/1638:1641		No text annotation
homologous
J3_4V88_036
NA
J3_6P4H_0091/2/1237:1244,
1/2/1255:1266,
1/2/1516:1520		No text annotation
homologous
J3_8C3A_040
NA
J3_6P4H_0101/2/1272:1277,
1/2/1320:1324,
1/2/1504:1510		No text annotation
homologous
J3_4V88_038
NA
J3_6P4H_0111/2/1340:1345,
1/2/1384:1389,
1/2/1481:1486		No text annotation
homologous
J3_4V88_039
NA
J3_6P4H_0121/2/1350:1351,
1/2/1360:1363,
1/2/1375:1379		No text annotation
homologous
J3_8C3A_085
NA
J3_6P4H_0131/2/1391:1395,
1/2/1450:1456,
1/2/1470:1479		No text annotation
J3_6P4H_0141/2/1532:1536,
1/2/1597:1604,
1/2/1635:1638		No text annotation
homologous
J3_4V88_041
NA
J4_6P4H_0011/2/98:106,
1/2/355:357,
1/2/405:409,
1/2/431:432		No text annotation
homologous
J4_8C3A_021
NA
J4_6P4H_0021/2/671:673,
1/2/1032:1037,
1/2/1078:1089,
1/2/1160:1161		No text annotation
homologous
J4_8P9A_022
J4_61885.6
J5_6P4H_0011/2/30:34,
1/2/521:527,
1/2/558:563,
1/2/592:595,
1/2/641:644		No text annotation
homologous
J5_8C3A_018
NA
J5_6P4H_0021/2/30:34,
1/2/521:527,
1/2/558:565,
1/2/585:595,
1/2/641:644		No text annotation
J5_6P4H_0031/2/53:56,
1/2/89:96,
1/2/434:436,
1/2/457:459,
1/2/470:474		No text annotation
homologous
J5_8C3A_020
NA
J5_6P4H_0041/2/123:129,
1/2/183:185,
1/2/214:215,
1/2/310:312,
1/2/337:341		No text annotation

Problematic loops

#loop idProblemSequence
J3_6P4H_015No text annotation
J3_6P4H_003No text annotation
J3_6P4H_017No text annotation

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