RNA 3D Hub //

8P09 Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8P09_0011/1/14:22No text annotation
homologous
HL_3WFS_001
NA
HL_8P09_0021/1/31:39tRNA anticodon loop
homologous
HL_6CFJ_107
HL_06059.7
HL_8P09_0031/1/53:61T-loop with 2 stacked bulged bases
homologous
HL_6PMO_005
NA
HL_8P09_0041/2/7:17No text annotation
homologous
HL_8C3A_192
NA
HL_8P09_0051/2/69:80No text annotation
HL_8P09_0061/2/156:162GNRA related
homologous
HL_8C3A_194
NA
HL_8P09_0071/2/194:201No text annotation
HL_8P09_0091/2/279:286T-loop with 1 bulged base
homologous
HL_4V88_191
NA
HL_8P09_0101/2/312:319No text annotation
HL_8P09_0111/2/367:377No text annotation
HL_8P09_0121/2/406:411GNRA variation
homologous
HL_8C3A_200
NA
HL_8P09_0131/2/431:442No text annotation
homologous
HL_4V88_195
NA
HL_8P09_0141/2/452:457UNCG
homologous
HL_8C3A_202
NA
HL_8P09_0151/2/488:494No text annotation
homologous
HL_8C3A_203
NA
HL_8P09_0161/2/529:534GNRA
geometric
HL_4V9F_009
HL_37824.8
HL_8P09_0171/2/559:571No text annotation
homologous
HL_4V88_199
NA
HL_8P09_0181/2/608:613GNRA variation
homologous
HL_8C3A_206
NA
HL_8P09_0211/2/816:824No text annotation
homologous
HL_4V88_203
NA
HL_8P09_0221/2/829:837No text annotation
geometric
HL_4V88_190
NA
HL_8P09_0231/2/881:897No text annotation
homologous
HL_8C3A_210
NA
HL_8P09_0241/2/953:962No text annotation
homologous
HL_4V88_206
NA
HL_8P09_0251/2/990:995GNRA
homologous
HL_4V88_207
NA
HL_8P09_0261/2/1050:1060No text annotation
homologous
HL_4V88_208
NA
HL_8P09_0271/2/1109:1116No text annotation
HL_8P09_0281/2/1137:1142GNRA
homologous
HL_4V88_210
NA
HL_8P09_0291/2/1174:1179GNRA
homologous
HL_4V88_211
NA
HL_8P09_0301/2/1241:1250No text annotation
homologous
HL_8P9A_215
HL_50779.4
HL_8P09_0311/2/1291:1300Anticodon loop related
homologous
HL_8C3A_218
NA
HL_8P09_0321/2/1349:1354GNRA
homologous
HL_4V88_214
NA
HL_8P09_0331/2/1362:1369T-loop related
homologous
HL_8C3A_220
NA
HL_8P09_0341/2/1417:1422Mini UNCG
geometric
HL_4YAZ_004
HL_48778.2
HL_8P09_0351/2/1456:1462No text annotation
homologous
HL_8C3A_222
NA
HL_8P09_0361/2/1560:1565GNRA
homologous
HL_4V88_218
NA
HL_8P09_0371/2/1609:1620No text annotation
homologous
HL_4V88_219
NA
HL_8P09_0381/2/1653:1661No text annotation
homologous
HL_4V88_220
NA
HL_8P09_0401/2/1841:1846GNRA variation
homologous
HL_8C3A_227
NA

Problematic loops

#loop idProblemSequence
HL_8P09_008No text annotation
HL_8P09_019No text annotation
HL_8P09_020No text annotation
HL_8P09_041No text annotation
HL_8P09_039No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8P09_0011/2/23:25,
1/2/639:641		Isolated non-canonical cWW pair
geometric
IL_3MEI_002
IL_87907.2
IL_8P09_0021/2/34:36,
1/2/509:511		Isolated non-canonical cWW pair
homologous
IL_8C3A_393
NA
IL_8P09_0031/2/37:40,
1/2/504:508		Double sheared
geometric
IL_4WF9_016
IL_09705.15
IL_8P09_0041/2/41:47,
1/2/469:471		No text annotation
homologous
IL_4V88_387
NA
IL_8P09_0051/2/49:51,
1/2/466:467		Minor groove platform
homologous
IL_4V88_388
NA
IL_8P09_0061/2/57:62,
1/2/86:88		No text annotation
homologous
IL_4V88_389
NA
IL_8P09_0071/2/63:68,
1/2/81:85		No text annotation
homologous
IL_4V88_390
NA
IL_8P09_0081/2/108:110,
1/2/341:343		Isolated non-canonical cWW pair
geometric
IL_1T0E_002
IL_28037.2
IL_8P09_0091/2/110:112,
1/2/339:341		Isolated non-canonical cWW pair
geometric
IL_4WF9_042
IL_87907.2
IL_8P09_0101/2/112:115,
1/2/338:339		Multiple bulged bases
homologous
IL_8C3A_400
NA
IL_8P09_0111/2/116:121,
1/2/333:337		No text annotation
homologous
IL_8C3A_401
NA
IL_8P09_0121/2/145:151,
1/2/167:174		No text annotation
homologous
IL_8C3A_402
NA
IL_8P09_0131/2/152:154,
1/2/164:166		Isolated cWH basepair
geometric
IL_3R1C_032
NA
IL_8P09_0141/2/187:191,
1/2/204:208		Double sheared with non-canonical cWW
geometric
IL_4WFL_001
IL_17948.2
IL_8P09_0151/2/192:194,
1/2/201:203		Isolated non-canonical cWW pair
geometric
IL_5Z1I_004
NA
IL_8P09_0161/2/213:216,
1/2/293:300		Tandem non-canonical cWW pairs
geometric
IL_1GID_008
NA
IL_8P09_0181/2/303:305,
1/2/326:327		Single bulged A
homologous
IL_4V88_399
NA
IL_8P09_0191/2/308:310,
1/2/321:323		Isolated near basepair
geometric
IL_3NJ7_004
IL_42997.3
IL_8P09_0201/2/349:354,
1/2/386:393		Kink-turn with non-sequential stacking
homologous
IL_8C3A_410
NA
IL_8P09_0211/2/356:361,
1/2/383:384		No text annotation
geometric
IL_5Y58_001
IL_59877.1
IL_8P09_0221/2/401:403,
1/2/414:419		No text annotation
homologous
IL_4V88_404
NA
IL_8P09_0231/2/427:429,
1/2/444:446		Isolated cWH basepair
homologous
IL_8C3A_413
NA
IL_8P09_0241/2/449:451,
1/2/458:460		Isolated non-canonical cWW pair
homologous
IL_8C3A_414
NA
IL_8P09_0251/2/477:479,
1/2/501:502		Single bulged U
homologous
IL_4V88_407
NA
IL_8P09_0261/2/481:485,
1/2/498:499		C-loop
homologous
IL_8C3A_416
NA
IL_8P09_0271/2/485:486,
1/2/496:498		Single bulged G
geometric
IL_5J7L_019
IL_00225.14
IL_8P09_0281/2/519:521,
1/2/543:546		No text annotation
geometric
IL_4P3T_002
NA
IL_8P09_0291/2/522:524,
1/2/539:542		No text annotation
geometric
IL_4N0T_004
IL_99358.1
IL_8P09_0301/2/525:527,
1/2/536:538		Isolated non-canonical cWW pair
geometric
IL_4V88_417
NA
IL_8P09_0311/2/553:555,
1/2/575:582		No text annotation
geometric
IL_8VTW_081
NA
IL_8P09_0321/2/556:559,
1/2/571:574		Tandem non-canonical cWW pairs
geometric
IL_402D_001
IL_77658.1
IL_8P09_0331/2/589:596,
1/2/626:627		SSU/LSU pseudoknot
homologous
IL_4V88_413
NA
IL_8P09_0341/2/596:598,
1/2/625:626		Single bulged U
geometric
IL_7RQB_080
NA
IL_8P09_0351/2/601:607,
1/2/614:622		Kink-turn related
homologous
IL_4V88_415
NA
IL_8P09_0361/2/653:655,
1/2/1158:1160		Isolated non-canonical cWW pair
geometric
IL_1Y27_001
IL_87907.2
IL_8P09_0371/2/655:661,
1/2/1157:1158		No text annotation
homologous
IL_8C3A_426
NA
IL_8P09_0381/2/663:665,
1/2/1026:1028		Isolated non-canonical cWW pair
homologous
IL_8C3A_427
NA
IL_8P09_0391/2/666:670,
1/2/1021:1025		tSH-tHW-tHS
homologous
IL_8C3A_428
NA
IL_8P09_0411/2/683:685,
1/2/730:731		Decoding loop related
geometric
IL_2O3X_003
IL_31737.3
IL_8P09_0421/2/741:743,
1/2/791:792		Single stack bend
geometric
IL_7A0S_054
IL_26793.1
IL_8P09_1041/2/743:751,
1/2/785:791		No text annotation
IL_8P09_0431/2/798:799,
1/2/856:859		Major groove minor groove platform; mini C-loop
homologous
IL_4V88_423
NA
IL_8P09_0441/2/801:803,
1/2/852:854		Isolated non-canonical cWW pair
homologous
IL_8C3A_431
NA
IL_8P09_0451/2/803:811,
1/2/845:852		No text annotation
geometric
IL_4V88_425
NA
IL_8P09_0461/2/869:870,
1/2/907:910		Single stack bend
geometric
IL_5J7L_044
IL_26793.1
IL_8P09_1051/2/869:872,
1/2/906:910		No text annotation
IL_8P09_0471/2/870:872,
1/2/906:907		Single stack bend
geometric
IL_5TBW_070
NA
IL_8P09_0481/2/872:875,
1/2/903:906		No text annotation
IL_8P09_0511/2/918:919,
1/2/1015:1018		Major groove platform; stack outside cWW
homologous
IL_4V88_428
NA
IL_8P09_1061/2/921:923,
1/2/1010:1013		Isolated cWH basepair
homologous
IL_8C3A_510
NA
IL_8P09_1111/2/924:927,
1/2/1006:1009		Tandem non-canonical cWW pairs
homologous
IL_8P9A_419
IL_85033.2
IL_8P09_0541/2/927:931,
1/2/1003:1006		Tandem non-canonical cWW pairs
homologous
IL_4V88_431
NA
IL_8P09_0551/2/937:941,
1/2/977:981		No text annotation
geometric
IL_5TBW_121
NA
IL_8P09_0561/2/948:952,
1/2/963:970		Kink-turn
homologous
IL_4V88_434
NA
IL_8P09_0571/2/1038:1043,
1/2/1067:1069		Other IL
homologous
IL_4V88_435
NA
IL_8P09_0581/2/1043:1047,
1/2/1063:1067		tSH-tHW-tHS
geometric
IL_4V88_436
NA
IL_8P09_0591/2/1087:1089,
1/2/1148:1154		No text annotation
homologous
IL_8C3A_443
NA
IL_8P09_0601/2/1094:1097,
1/2/1127:1130		Tandem non-canonical cWW pairs
homologous
IL_8C3A_444
NA
IL_8P09_0611/2/1097:1099,
1/2/1125:1127		Isolated non-canonical cWW pair
geometric
IL_1MFQ_003
IL_87907.2
IL_8P09_0621/2/1104:1106,
1/2/1119:1120		Minor groove platform
geometric
IL_7RQB_032
NA
IL_8P09_0631/2/1164:1171,
1/2/1182:1187		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_4V88_440
NA
IL_8P09_0641/2/1199:1200,
1/2/1689:1691		Single bulged A
homologous
IL_8C3A_447
NA
IL_8P09_0651/2/1202:1204,
1/2/1686:1687		Single bulged G
homologous
IL_8C3A_448
NA
IL_8P09_0661/2/1210:1213,
1/2/1676:1680		C-loop
homologous
IL_4V88_443
NA
IL_8P09_0671/2/1226:1228,
1/2/1521:1523		Isolated non-canonical cWW pair
homologous
IL_8C3A_450
NA
IL_8P09_0681/2/1231:1232,
1/2/1516:1518		Minor groove platform
homologous
IL_4V88_445
NA
IL_8P09_1121/2/1266:1268,
1/2/1506:1507		Intercalated cWW
geometric
IL_4WF9_047
IL_31737.3
IL_8P09_0701/2/1277:1283,
1/2/1310:1312		No text annotation
IL_8P09_1071/2/1277:1286,
1/2/1305:1312		No text annotation
homologous
IL_8P9A_470
IL_28304.1
IL_8P09_0711/2/1283:1286,
1/2/1305:1310		No text annotation
IL_8P09_0721/2/1287:1289,
1/2/1302:1304		Other IL
homologous
IL_8C3A_454
NA
IL_8P09_0731/2/1321:1323,
1/2/1498:1499		Single bulged U
homologous
IL_8C3A_455
NA
IL_8P09_0741/2/1325:1329,
1/2/1494:1496		Isolated cWS basepair
geometric
IL_4V88_450
NA
IL_8P09_1081/2/1325:1331,
1/2/1488:1496		No text annotation
homologous
IL_8P9A_439
IL_86012.1
IL_8P09_0751/2/1329:1331,
1/2/1488:1494		Minor groove platform with extra cWW
homologous
IL_4V88_451
NA
IL_8P09_0761/2/1333:1334,
1/2/1484:1486		Single bulged A
homologous
IL_8C3A_458
NA
IL_8P09_0771/2/1343:1345,
1/2/1376:1378		Isolated non-canonical cWW pair
homologous
IL_8C3A_459
NA
IL_8P09_0781/2/1359:1361,
1/2/1370:1371		Minor groove platform
homologous
IL_8C3A_460
NA
IL_8P09_0791/2/1391:1395,
1/2/1443:1446		No text annotation
homologous
IL_8C3A_461
NA
IL_8P09_0801/2/1398:1401,
1/2/1437:1440		Minor groove platform
homologous
IL_4V88_456
NA
IL_8P09_0811/2/1404:1407,
1/2/1431:1434		No text annotation
IL_8P09_0821/2/1407:1409,
1/2/1429:1431		No text annotation
IL_8P09_0831/2/1409:1412,
1/2/1425:1429		Tandem non-canonical cWW pairs
geometric
IL_1D4R_001
IL_85033.2
IL_8P09_1091/2/1409:1415,
1/2/1424:1429		No text annotation
IL_8P09_0841/2/1412:1415,
1/2/1424:1425		No text annotation
IL_8P09_0851/2/1532:1534,
1/2/1589:1591		Isolated non-canonical cWW pair
geometric
IL_4P3T_001
NA
IL_8P09_1101/2/1536:1545,
1/2/1577:1587		No text annotation
IL_8P09_0861/2/1545:1553,
1/2/1572:1577		180 degree turn
geometric
IL_5J7L_055
IL_11344.2
IL_8P09_0871/2/1555:1557,
1/2/1568:1570		Isolated non-canonical cWW pair
homologous
IL_8C3A_468
NA
IL_8P09_0881/2/1599:1605,
1/2/1624:1630		No text annotation
homologous
IL_8C3A_469
NA
IL_8P09_0891/2/1695:1697,
1/2/1827:1830		No text annotation
geometric
IL_4V88_463
NA
IL_8P09_0901/2/1697:1700,
1/2/1823:1827		No text annotation
homologous
IL_8C3A_471
NA
IL_8P09_0911/2/1701:1703,
1/2/1820:1822		Isolated non-canonical cWW pair
homologous
IL_8C3A_472
NA
IL_8P09_0921/2/1703:1707,
1/2/1815:1820		No text annotation
IL_8P09_0931/2/1709:1711,
1/2/1811:1813		Isolated non-canonical cWW pair
homologous
IL_8C3A_474
NA
IL_8P09_0941/2/1712:1717,
1/2/1806:1810		No text annotation
IL_8P09_0951/2/1724:1726,
1/2/1797:1799		Isolated non-canonical cWW pair
homologous
IL_8C3A_477
NA
IL_8P09_0961/2/1728:1731,
1/2/1792:1795		Double sheared
homologous
IL_4V88_471
NA
IL_8P09_0971/2/1734:1736,
1/2/1787:1789		Isolated non-canonical cWW pair
geometric
IL_1UN6_005
IL_87907.2
IL_8P09_0981/2/1737:1741,
1/2/1782:1786		Triple sheared
homologous
IL_8C3A_480
NA
IL_8P09_0991/2/1745:1746,
1/2/1776:1778		Multiple bulged bases
geometric
IL_7Q82_001
NA
IL_8P09_1001/2/1746:1747,
1/2/1774:1776		Single stack bend
geometric
IL_7KGA_003
IL_90729.1
IL_8P09_1011/2/1747:1748,
1/2/1772:1774		Single stack bend
geometric
IL_5TBW_009
NA

Problematic loops

#loop idProblemSequence
IL_8P09_017Isolated non-canonical cWW pair
IL_8P09_102Isolated cWH basepair
IL_8P09_103No text annotation
IL_8P09_040Isolated non-canonical cWW pair
IL_8P09_049Isolated non-canonical cWW pair
IL_8P09_050Isolated non-canonical cWW pair
IL_8P09_052Tandem non-canonical cWW pairs
IL_8P09_053No text annotation
IL_8P09_069No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8P09_0111/2/40:41,
1/2/471:477,
1/2/502:504		No text annotation
geometric
J3_4V88_078
NA
J3_8P09_0121/2/40:47,
1/2/469:477,
1/2/502:504		No text annotation
homologous
J3_8P9A_069
J3_46317.4
J3_8P09_0131/2/220:235,
1/2/274:279,
1/2/286:289		No text annotation
J3_8P09_0141/2/672:675,
1/2/913:918,
1/2/1018:1019		No text annotation
J3_8P09_0151/2/672:675,
1/2/913:919,
1/2/1015:1019		No text annotation
J3_8P09_0011/2/812:815,
1/2/825:827,
1/2/839:844		No text annotation
homologous
J3_4V88_032
NA
J3_8P09_0021/2/934:937,
1/2/981:989,
1/2/996:1000		No text annotation
homologous
J3_4V88_033
NA
J3_8P09_0031/2/1090:1092,
1/2/1132:1136,
1/2/1143:1147		No text annotation
J3_8P09_0041/2/1214:1217,
1/2/1640:1646,
1/2/1668:1675		No text annotation
homologous
J3_4V88_035
NA
J3_8P09_0051/2/1221:1224,
1/2/1525:1527,
1/2/1633:1636		No text annotation
homologous
J3_8C3A_039
NA
J3_8P09_0061/2/1233:1240,
1/2/1251:1262,
1/2/1511:1515		No text annotation
homologous
J3_8C3A_040
NA
J3_8P09_0071/2/1268:1273,
1/2/1316:1320,
1/2/1500:1506		No text annotation
homologous
J3_4V88_038
NA
J3_8P09_0081/2/1336:1341,
1/2/1380:1385,
1/2/1477:1482		No text annotation
homologous
J3_4V88_039
NA
J3_8P09_0161/2/1346:1347,
1/2/1356:1359,
1/2/1371:1375		No text annotation
homologous
J3_8C3A_085
NA
J3_8P09_0091/2/1387:1391,
1/2/1446:1452,
1/2/1466:1475		No text annotation
J3_8P09_0101/2/1527:1531,
1/2/1592:1599,
1/2/1630:1633		No text annotation
homologous
J3_8C3A_044
NA
J4_8P09_0011/1/8:11,
1/1/25:27,
1/1/43:49,
1/1/65:66		tRNA junction
homologous
J4_7EQJ_002
J4_70449.29
J4_8P09_0021/2/98:106,
1/2/345:347,
1/2/395:399,
1/2/421:422		No text annotation
homologous
J4_8P9A_021
J4_15241.1
J4_8P09_0031/2/661:663,
1/2/1028:1033,
1/2/1074:1085,
1/2/1156:1157		No text annotation
homologous
J4_8P9A_022
J4_61885.6
J5_8P09_0011/2/30:34,
1/2/511:517,
1/2/548:553,
1/2/582:585,
1/2/631:634		No text annotation
homologous
J5_8C3A_018
NA
J5_8P09_0021/2/30:34,
1/2/511:517,
1/2/548:555,
1/2/575:585,
1/2/631:634		No text annotation
J5_8P09_0031/2/53:56,
1/2/89:96,
1/2/424:426,
1/2/447:449,
1/2/460:464		No text annotation
homologous
J5_8C3A_020
NA
J5_8P09_0051/2/675:680,
1/2/734:740,
1/2/793:796,
1/2/861:869,
1/2/910:913		No text annotation

Problematic loops

#loop idProblemSequence
J5_8P09_004No text annotation

Coloring options:
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