RNA 3D Hub //

4D61 Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_4D61_0011/1/7:17No text annotation
homologous
HL_4V88_186
NA
HL_4D61_0021/1/63:85No text annotation
HL_4D61_0031/1/156:162GNRA related
homologous
HL_4V88_188
NA
HL_4D61_0391/1/197:202No text annotation
HL_4D61_0061/1/322:329T-loop with 2 stacked bulged bases
geometric
HL_5TBW_005
NA
HL_4D61_0071/1/377:387No text annotation
geometric
HL_4WSM_226
NA
HL_4D61_0081/1/416:421No text annotation
homologous
HL_4V88_194
NA
HL_4D61_0091/1/441:452No text annotation
homologous
HL_4V88_195
NA
HL_4D61_0101/1/462:467UNCG
homologous
HL_4V88_196
NA
HL_4D61_0111/1/498:504No text annotation
geometric
HL_5NFV_001
HL_69752.2
HL_4D61_0121/1/539:544No text annotation
geometric
HL_5NFV_001
HL_69752.2
HL_4D61_0401/1/565:585No text annotation
HL_4D61_0131/1/569:581No text annotation
HL_4D61_0141/1/618:623GNRA variation
homologous
HL_4V88_200
NA
HL_4D61_0151/1/820:828No text annotation
homologous
HL_4V88_203
NA
HL_4D61_0161/1/833:841No text annotation
geometric
HL_5TBW_006
NA
HL_4D61_0171/1/884:902No text annotation
homologous
HL_8P9A_208
NA
HL_4D61_0181/1/957:966No text annotation
homologous
HL_4V88_206
NA
HL_4D61_0191/1/994:999GNRA
homologous
HL_4V88_207
NA
HL_4D61_0411/1/1052:1066No text annotation
HL_4D61_0201/1/1054:1064No text annotation
homologous
HL_4V88_208
NA
HL_4D61_0421/1/1110:1123No text annotation
HL_4D61_0211/1/1112:1121No text annotation
HL_4D61_0221/1/1141:1146GNRA
homologous
HL_4V88_210
NA
HL_4D61_0231/1/1178:1183GNRA
homologous
HL_4V88_211
NA
HL_4D61_0241/1/1245:1254No text annotation
homologous
HL_4V88_212
NA
HL_4D61_0251/1/1294:1305No text annotation
HL_4D61_0431/1/1352:1359GNRA with extra cWW
geometric
HL_8KAL_001
HL_04259.3
HL_4D61_0261/1/1353:1358GNRA
homologous
HL_4V88_214
NA
HL_4D61_0271/1/1366:1373No text annotation
homologous
HL_4V88_215
NA
HL_4D61_0281/1/1420:1427No text annotation
HL_4D61_0441/1/1460:1466GNRA
geometric
HL_5TBW_059
NA
HL_4D61_0301/1/1565:1570GNRA
homologous
HL_4V88_218
NA
HL_4D61_0311/1/1614:1625No text annotation
homologous
HL_8P9A_222
HL_67079.1
HL_4D61_0321/1/1658:1666No text annotation
homologous
HL_4V88_220
NA
HL_4D61_0451/1/1761:1771No text annotation
HL_4D61_0331/1/1763:1769GNRA
geometric
HL_3SUX_002
HL_37824.8
HL_4D61_0341/1/1847:1852GNRA variation
homologous
HL_4V88_222
NA
HL_4D61_0351/j/6051:6076No text annotation
HL_4D61_0361/j/6110:6115No text annotation
HL_4D61_0371/j/6141:6147No text annotation
HL_4D61_0381/j/6183:6194No text annotation

Problematic loops

#loop idProblemSequence
HL_4D61_004No text annotation
HL_4D61_005No text annotation
HL_4D61_029tRNA anticodon loop

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_4D61_0011/1/23:26,
1/1/648:651		Tandem non-canonical cWW pairs
geometric
IL_5C5W_001
IL_77658.1
IL_4D61_0021/1/34:36,
1/1/519:521		Isolated non-canonical cWW pair
homologous
IL_4V88_385
NA
IL_4D61_0871/1/34:40,
1/1/514:521		No text annotation
IL_4D61_0031/1/36:40,
1/1/514:519		Triple sheared related
homologous
IL_4V88_386
NA
IL_4D61_0041/1/41:47,
1/1/479:481		No text annotation
homologous
IL_4V88_387
NA
IL_4D61_0051/1/49:51,
1/1/476:477		Minor groove platform
homologous
IL_4V88_388
NA
IL_4D61_0061/1/56:62,
1/1/86:89		No text annotation
IL_4D61_0071/1/108:112,
1/1/349:353		No text annotation
IL_4D61_0081/1/112:115,
1/1/348:349		Multiple bulged bases
homologous
IL_4V88_392
NA
IL_4D61_0881/1/116:121,
1/1/343:347		No text annotation
homologous
IL_8P9A_382
IL_29223.1
IL_4D61_0101/1/146:151,
1/1/167:174		No text annotation
IL_4D61_0111/1/152:154,
1/1/164:166		Isolated non-canonical cWW contact
homologous
IL_4V88_395
NA
IL_4D61_0891/1/187:192,
1/1/207:212		No text annotation
IL_4D61_0131/1/317:319,
1/1/332:333		No text annotation
IL_4D61_0901/1/317:321,
1/1/330:333		No text annotation
IL_4D61_0141/1/359:364,
1/1/396:403		Kink-turn with non-sequential stacking
homologous
IL_4V88_402
NA
IL_4D61_0151/1/366:371,
1/1/393:394		No text annotation
geometric
IL_4ERD_001
IL_84476.1
IL_4D61_0161/1/411:413,
1/1/424:429		No text annotation
IL_4D61_0171/1/437:439,
1/1/454:456		Isolated cWH basepair
homologous
IL_4V88_405
NA
IL_4D61_0181/1/459:461,
1/1/468:470		Isolated near basepair
homologous
IL_4V88_406
NA
IL_4D61_0191/1/487:489,
1/1/511:512		Single bulged U
homologous
IL_4V88_407
NA
IL_4D61_0201/1/491:495,
1/1/508:509		C-loop
geometric
IL_4LFB_015
IL_03109.3
IL_4D61_0211/1/495:496,
1/1/506:508		Single bulged G
geometric
IL_5J7L_019
IL_00225.14
IL_4D61_0221/1/530:531,
1/1/553:555		Single bulged A
homologous
IL_4V88_409
NA
IL_4D61_0231/1/535:539,
1/1/544:549		No text annotation
IL_4D61_0241/1/565:569,
1/1/581:585		No text annotation
IL_4D61_0251/1/599:608,
1/1/635:637		Isolated non-canonical cWW pair
geometric
IL_4V88_470
NA
IL_4D61_0261/1/611:617,
1/1/624:632		Kink-turn related
homologous
IL_4V88_415
NA
IL_4D61_0271/1/663:665,
1/1/1162:1164		Isolated cWH basepair
geometric
IL_406D_002
IL_10167.6
IL_4D61_0281/1/673:675,
1/1/1030:1032		Isolated non-canonical cWW pair
homologous
IL_4V88_417
NA
IL_4D61_0291/1/676:680,
1/1/1025:1029		tSH-tHW-tHS
homologous
IL_4V88_418
NA
IL_4D61_0301/1/692:694,
1/1/738:739		Multiple bulged bases
geometric
IL_7Q80_001
IL_84476.1
IL_4D61_0311/1/752:754,
1/1/790:791		No text annotation
IL_4D61_0321/1/802:803,
1/1/860:863		Major groove minor groove platform; mini C-loop
homologous
IL_4V88_423
NA
IL_4D61_0331/1/804:807,
1/1/856:859		Tandem non-canonical cWW pairs
geometric
IL_7A0S_040
IL_77658.1
IL_4D61_0341/1/807:815,
1/1/849:856		No text annotation
geometric
IL_4V88_425
NA
IL_4D61_0351/1/877:879,
1/1/907:909		Isolated cWH basepair
homologous
IL_4V88_427
NA
IL_4D61_0361/1/922:923,
1/1/1019:1022		Major groove platform; stack outside cWW
geometric
IL_4V88_428
NA
IL_4D61_0911/1/924:926,
1/1/1015:1018		Isolated non-canonical cWW pair
homologous
IL_8P9A_418
IL_57744.1
IL_4D61_0371/1/925:927,
1/1/1014:1017		Isolated non-canonical cWW pair
geometric
IL_5J7L_009
IL_57744.1
IL_4D61_0381/1/928:931,
1/1/1010:1013		Tandem non-canonical cWW pairs
geometric
IL_4V88_430
NA
IL_4D61_0391/1/931:935,
1/1/1007:1010		Tandem non-canonical cWW pairs
homologous
IL_4V88_431
NA
IL_4D61_0401/1/942:945,
1/1/981:984		Tandem non-canonical cWW pairs
homologous
IL_4V88_432
NA
IL_4D61_0411/1/950:956,
1/1/967:976		Kink-turn related
homologous
IL_8C3A_440
NA
IL_4D61_0421/1/1042:1047,
1/1/1071:1073		Other IL
homologous
IL_4V88_435
NA
IL_4D61_0431/1/1047:1051,
1/1/1067:1071		tSH-tHW-tHS
geometric
IL_4V88_436
NA
IL_4D61_0441/1/1091:1093,
1/1/1152:1158		No text annotation
homologous
IL_4V88_437
NA
IL_4D61_0451/1/1098:1101,
1/1/1131:1134		Tandem non-canonical cWW pairs
homologous
IL_4V88_438
NA
IL_4D61_0461/1/1101:1103,
1/1/1129:1131		Isolated non-canonical cWW contact
geometric
IL_5UNE_009
IL_44465.1
IL_4D61_0471/1/1108:1110,
1/1/1123:1124		Single bulged U
homologous
IL_4V88_439
NA
IL_4D61_0481/1/1168:1175,
1/1/1186:1191		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_4V88_440
NA
IL_4D61_0921/1/1202:1204,
1/1/1694:1697		No text annotation
IL_4D61_0501/1/1206:1210,
1/1/1689:1692		Tandem non-canonical cWW pairs
geometric
IL_1D4R_001
IL_85033.2
IL_4D61_0931/1/1206:1213,
1/1/1686:1692		No text annotation
IL_4D61_0511/1/1213:1217,
1/1/1681:1686		No text annotation
IL_4D61_0941/1/1213:1218,
1/1/1680:1686		No text annotation
IL_4D61_0521/1/1230:1232,
1/1/1526:1528		Isolated non-canonical cWW pair
homologous
IL_4V88_444
NA
IL_4D61_0531/1/1235:1236,
1/1/1521:1523		Minor groove platform
homologous
IL_4V88_445
NA
IL_4D61_0951/1/1270:1272,
1/1/1510:1512		Isolated non-canonical cWW pair
homologous
IL_8C3A_452
NA
IL_4D61_0961/1/1279:1290,
1/1/1309:1318		No text annotation
IL_4D61_0551/1/1281:1290,
1/1/1309:1316		No text annotation
IL_4D61_0971/1/1290:1293,
1/1/1306:1309		No text annotation
IL_4D61_0561/1/1291:1293,
1/1/1306:1308		No text annotation
homologous
IL_4V88_448
NA
IL_4D61_0571/1/1325:1327,
1/1/1502:1503		Single bulged U
homologous
IL_4V88_449
NA
IL_4D61_0981/1/1329:1332,
1/1/1499:1500		Multiple bulged bases
geometric
IL_1FUF_002
IL_82107.5
IL_4D61_0591/1/1333:1335,
1/1/1492:1498		Minor groove platform with extra cWW
homologous
IL_4V88_451
NA
IL_4D61_0601/1/1337:1338,
1/1/1488:1490		Single bulged A
homologous
IL_4V88_452
NA
IL_4D61_0611/1/1347:1349,
1/1/1380:1382		Isolated cWH basepair
homologous
IL_4V88_453
NA
IL_4D61_0621/1/1395:1397,
1/1/1448:1450		Isolated non-canonical cWW contact
geometric
IL_5UNE_001
IL_44465.1
IL_4D61_0631/1/1397:1399,
1/1/1447:1448		No text annotation
IL_4D61_0991/1/1401:1405,
1/1/1441:1445		No text annotation
IL_4D61_0651/1/1408:1413,
1/1/1433:1438		No text annotation
IL_4D61_1001/1/1415:1418,
1/1/1429:1431		No text annotation
IL_4D61_0671/1/1537:1539,
1/1/1594:1596		Isolated non-canonical cWW pair
geometric
IL_6OL3_002
IL_87907.2
IL_4D61_1011/1/1537:1540,
1/1/1593:1596		Tandem non-canonical cWW pairs
geometric
IL_1D4R_001
IL_85033.2
IL_4D61_1021/1/1541:1550,
1/1/1582:1592		No text annotation
IL_4D61_0681/1/1550:1558,
1/1/1577:1582		No text annotation
IL_4D61_0691/1/1559:1562,
1/1/1573:1576		Tandem non-canonical cWW pairs
homologous
IL_4V88_461
NA
IL_4D61_0701/1/1604:1610,
1/1/1629:1635		No text annotation
homologous
IL_8C3A_469
NA
IL_4D61_0711/1/1700:1702,
1/1/1833:1836		No text annotation
homologous
IL_4V88_463
NA
IL_4D61_0721/1/1702:1705,
1/1/1829:1833		No text annotation
geometric
IL_4V88_464
NA
IL_4D61_0731/1/1706:1708,
1/1/1826:1828		Isolated non-canonical cWW pair
geometric
IL_4E48_002
IL_87907.2
IL_4D61_0741/1/1708:1711,
1/1/1822:1826		Non canonical cWW and near pair
homologous
IL_4V88_466
NA
IL_4D61_1031/1/1714:1716,
1/1/1817:1819		Isolated non-canonical cWW pair
homologous
IL_8C3A_474
NA
IL_4D61_0761/1/1717:1720,
1/1/1813:1816		Double sheared
geometric
IL_4V88_468
NA
IL_4D61_0771/1/1720:1722,
1/1/1812:1813		No text annotation
IL_4D61_0781/1/1729:1731,
1/1/1803:1805		Isolated non-canonical cWW pair
homologous
IL_4V88_470
NA
IL_4D61_0791/1/1733:1736,
1/1/1798:1801		Double sheared
homologous
IL_4V88_471
NA
IL_4D61_0801/1/1739:1742,
1/1/1792:1795		Tandem non-canonical cWW pairs
geometric
IL_4V88_473
NA
IL_4D61_1041/1/1742:1746,
1/1/1788:1792		Triple sheared
homologous
IL_8C3A_480
NA
IL_4D61_1051/1/1748:1752,
1/1/1780:1786		Partly complementary
geometric
IL_6CZR_167
NA
IL_4D61_0821/1/1750:1752,
1/1/1780:1784		No text annotation
homologous
IL_4V88_475
NA
IL_4D61_1061/j/6031:6045,
1/j/6082:6094		No text annotation
IL_4D61_0831/j/6127:6129,
1/j/6157:6159		No text annotation
IL_4D61_0841/j/6130:6132,
1/j/6154:6156		No text annotation
IL_4D61_1071/j/6132:6139,
1/j/6149:6154		No text annotation
IL_4D61_1081/j/6175:6179,
1/j/6197:6201		No text annotation
IL_4D61_0861/j/6180:6183,
1/j/6194:6196		No text annotation

Problematic loops

#loop idProblemSequence
IL_4D61_009No text annotation
IL_4D61_012No text annotation
IL_4D61_049No text annotation
IL_4D61_054Tandem non-canonical cWW pairs
IL_4D61_058Tandem non-canonical cWW pairs
IL_4D61_064No text annotation
IL_4D61_066No text annotation
IL_4D61_075Tandem non-canonical cWW pairs
IL_4D61_081No text annotation
IL_4D61_085No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_4D61_0011/1/40:41,
1/1/481:487,
1/1/512:514		No text annotation
homologous
J3_8P9A_068
J3_67856.4
J3_4D61_0021/1/681:684,
1/1/918:922,
1/1/1022:1024		No text annotation
J3_4D61_0031/1/816:819,
1/1/829:831,
1/1/843:848		No text annotation
geometric
J3_4V88_032
NA
J3_4D61_0111/1/816:820,
1/1/828:831,
1/1/843:848		No text annotation
J3_4D61_0041/1/938:941,
1/1/985:993,
1/1/1000:1004		No text annotation
homologous
J3_4V88_033
NA
J3_4D61_0121/1/1094:1096,
1/1/1136:1140,
1/1/1147:1151		No text annotation
homologous
J3_8P9A_075
J3_94999.1
J3_4D61_0061/1/1218:1221,
1/1/1645:1651,
1/1/1673:1680		No text annotation
homologous
J3_8C3A_038
NA
J3_4D61_0071/1/1237:1245,
1/1/1254:1266,
1/1/1516:1520		No text annotation
J3_4D61_0081/1/1272:1277,
1/1/1320:1324,
1/1/1504:1510		No text annotation
homologous
J3_8C3A_041
NA
J3_4D61_0091/1/1340:1345,
1/1/1384:1389,
1/1/1481:1486		No text annotation
homologous
J3_4V88_039
NA
J3_4D61_0131/1/1340:1345,
1/1/1384:1390,
1/1/1480:1486		No text annotation
geometric
J3_5J7L_008
J3_08394.3
J3_4D61_0101/1/1350:1351,
1/1/1360:1365,
1/1/1374:1379		No text annotation
J3_4D61_0141/1/1391:1395,
1/1/1450:1456,
1/1/1470:1479		No text annotation
J4_4D61_0011/1/98:106,
1/1/355:357,
1/1/405:410,
1/1/430:432		No text annotation
J4_4D61_0021/1/665:673,
1/1/1032:1037,
1/1/1078:1089,
1/1/1160:1162		No text annotation
J4_4D61_0031/1/1225:1228,
1/1/1530:1536,
1/1/1597:1610,
1/1/1629:1641		No text annotation
J5_4D61_0011/1/30:34,
1/1/521:528,
1/1/557:565,
1/1/585:595,
1/1/641:644		No text annotation
J5_4D61_0021/1/53:56,
1/1/89:96,
1/1/434:436,
1/1/457:459,
1/1/470:474		No text annotation
homologous
J5_8C3A_020
NA
J5_4D61_0031/1/123:146,
1/1/174:186,
1/1/213:220,
1/1/301:316,
1/1/334:341		No text annotation
J6_4D61_0011/1/682:694,
1/1/738:750,
1/1/793:807,
1/1/856:877,
1/1/909:922,
1/1/1022:1023		No text annotation
J6_4D61_0021/1/682:694,
1/1/738:750,
1/1/793:807,
1/1/856:877,
1/1/909:923,
1/1/1019:1023		No text annotation

Problematic loops

#loop idProblemSequence
J3_4D61_005No text annotation

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