RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8PPL_0011/A2/7:17No text annotation
homologous
HL_8C3A_192
NA
HL_8PPL_0021/A2/69:80No text annotation
geometric
HL_2ZZM_002
HL_33487.1
HL_8PPL_0031/A2/156:162GNRA related
homologous
HL_4V88_188
NA
HL_8PPL_0051/A2/288:295T-loop with 1 bulged base
homologous
HL_4V88_191
NA
HL_8PPL_0071/A2/377:387No text annotation
HL_8PPL_0081/A2/416:421No text annotation
homologous
HL_4V88_194
NA
HL_8PPL_0091/A2/441:452No text annotation
homologous
HL_4V88_195
NA
HL_8PPL_0381/A2/462:467UNCG
homologous
HL_8C3A_202
NA
HL_8PPL_0111/A2/498:504No text annotation
homologous
HL_4V88_197
NA
HL_8PPL_0131/A2/569:581No text annotation
geometric
HL_4V88_199
NA
HL_8PPL_0141/A2/618:623GNRA variation
homologous
HL_8C3A_206
NA
HL_8PPL_0151/A2/820:828No text annotation
homologous
HL_4V88_203
NA
HL_8PPL_0161/A2/833:841No text annotation
HL_8PPL_0391/A2/957:966No text annotation
homologous
HL_8C3A_211
NA
HL_8PPL_0191/A2/994:999GNRA
homologous
HL_4V88_207
NA
HL_8PPL_0201/A2/1054:1064No text annotation
homologous
HL_4V88_208
NA
HL_8PPL_0211/A2/1112:1121Mini UNCG
geometric
HL_5T16_002
HL_12626.2
HL_8PPL_0221/A2/1141:1146GNRA
homologous
HL_4V88_210
NA
HL_8PPL_0231/A2/1178:1183GNRA
homologous
HL_8C3A_216
NA
HL_8PPL_0241/A2/1245:1254No text annotation
homologous
HL_8P9A_215
HL_97521.1
HL_8PPL_0251/A2/1295:1304Anticodon loop related
homologous
HL_8C3A_218
NA
HL_8PPL_0261/A2/1353:1358GNRA
homologous
HL_4V88_214
NA
HL_8PPL_0271/A2/1366:1373No text annotation
homologous
HL_4V88_215
NA
HL_8PPL_0281/A2/1417:1422Mini UNCG
geometric
HL_5SWD_005
HL_90436.3
HL_8PPL_0291/A2/1460:1466No text annotation
homologous
HL_8C3A_222
NA
HL_8PPL_0301/A2/1565:1570GNRA
homologous
HL_8C3A_223
NA
HL_8PPL_0401/A2/1614:1625No text annotation
homologous
HL_8C3A_224
NA
HL_8PPL_0321/A2/1658:1666No text annotation
homologous
HL_4V88_220
NA
HL_8PPL_0341/A2/1847:1852GNRA variation
homologous
HL_8C3A_227
NA
HL_8PPL_0351/Iw/13:21tRNA D-loop
homologous
HL_6JXM_001
HL_20490.1
HL_8PPL_0361/Iw/30:38tRNA anticodon loop
homologous
HL_4TUE_034
NA
HL_8PPL_0371/Iw/52:60No text annotation
homologous
HL_1YFG_003
NA

Problematic loops

#loop idProblemSequence
HL_8PPL_004GNRA
HL_8PPL_006Mini UNCG
HL_8PPL_010No text annotation
HL_8PPL_012GNRA
HL_8PPL_017No text annotation
HL_8PPL_018No text annotation
HL_8PPL_031No text annotation
HL_8PPL_033No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8PPL_1061/A2/23:25,
1/A2/649:651		Isolated non-canonical cWW pair
geometric
IL_4M4O_001
IL_01003.4
IL_8PPL_1071/A2/34:36,
1/A2/519:521		Isolated non-canonical cWW pair
homologous
IL_8C3A_393
NA
IL_8PPL_0031/A2/37:40,
1/A2/514:518		Double sheared
geometric
IL_4WF9_016
IL_58355.2
IL_8PPL_0041/A2/41:47,
1/A2/479:481		No text annotation
homologous
IL_4V88_387
NA
IL_8PPL_0051/A2/49:51,
1/A2/476:477		Minor groove platform
homologous
IL_4V88_388
NA
IL_8PPL_0061/A2/57:62,
1/A2/86:88		No text annotation
geometric
IL_4V88_389
NA
IL_8PPL_1081/A2/63:68,
1/A2/81:85		No text annotation
homologous
IL_8P9A_379
IL_21667.2
IL_8PPL_0091/A2/108:110,
1/A2/351:353		Stack and bulge
geometric
IL_2O3X_001
IL_53541.1
IL_8PPL_0101/A2/110:112,
1/A2/349:351		Isolated non-canonical cWW pair
geometric
IL_4WF9_042
IL_01003.4
IL_8PPL_0111/A2/112:115,
1/A2/348:349		Multiple bulged bases
geometric
IL_5WLH_001
IL_71421.2
IL_8PPL_1091/A2/116:121,
1/A2/343:347		No text annotation
homologous
IL_8P9A_382
IL_31545.1
IL_8PPL_1101/A2/145:151,
1/A2/167:174		No text annotation
homologous
IL_8C3A_402
NA
IL_8PPL_1111/A2/152:154,
1/A2/164:166		No text annotation
homologous
IL_8P9A_384
IL_87720.1
IL_8PPL_0161/A2/188:192,
1/A2/207:211		Double sheared with near cWW
geometric
IL_7A0S_056
IL_87767.2
IL_8PPL_0171/A2/216:219,
1/A2/302:309		No text annotation
IL_8PPL_0181/A2/312:314,
1/A2/336:337		Single bulged A
homologous
IL_4V88_399
NA
IL_8PPL_1121/A2/317:319,
1/A2/332:333		Single stack bend
geometric
IL_5TBW_009
NA
IL_8PPL_0211/A2/359:364,
1/A2/396:403		Kink-turn with non-sequential stacking
homologous
IL_4V88_402
NA
IL_8PPL_0221/A2/366:371,
1/A2/393:394		No text annotation
homologous
IL_8C3A_411
NA
IL_8PPL_0231/A2/411:413,
1/A2/424:429		No text annotation
homologous
IL_8C3A_412
NA
IL_8PPL_0241/A2/437:439,
1/A2/454:456		Isolated cWH basepair
homologous
IL_8C3A_413
NA
IL_8PPL_1131/A2/459:461,
1/A2/468:470		Isolated non-canonical cWW pair
homologous
IL_8C3A_414
NA
IL_8PPL_1141/A2/487:489,
1/A2/511:512		Single bulged U
homologous
IL_8P9A_396
IL_97561.4
IL_8PPL_1151/A2/491:495,
1/A2/508:509		C-loop
homologous
IL_8P9A_397
IL_26900.1
IL_8PPL_0261/A2/495:496,
1/A2/506:508		Single bulged G
geometric
IL_5J7L_019
NA
IL_8PPL_0271/A2/529:530,
1/A2/554:556		Single bulged A
homologous
IL_4V88_409
NA
IL_8PPL_0281/A2/535:537,
1/A2/546:549		Isolated non-canonical cWW pair
geometric
IL_3GM7_006
IL_01003.4
IL_8PPL_0291/A2/566:569,
1/A2/581:584		tSH-tHW
geometric
IL_5UNE_005
IL_76776.1
IL_8PPL_0301/A2/599:606,
1/A2/636:637		SSU/LSU pseudoknot
geometric
IL_4V88_413
NA
IL_8PPL_0311/A2/606:608,
1/A2/635:636		Single bulged U
geometric
IL_5TBW_146
NA
IL_8PPL_0331/A2/611:617,
1/A2/624:632		Kink-turn related
homologous
IL_8C3A_425
NA
IL_8PPL_0341/A2/663:665,
1/A2/1162:1164		Isolated non-canonical cWW pair
geometric
IL_1Y27_001
IL_01003.4
IL_8PPL_0351/A2/665:671,
1/A2/1161:1162		No text annotation
geometric
IL_4LFB_022
IL_20847.1
IL_8PPL_0361/A2/673:675,
1/A2/1030:1032		Isolated non-canonical cWW pair
homologous
IL_8C3A_427
NA
IL_8PPL_0371/A2/676:680,
1/A2/1025:1029		tSH-tHW-tHS
geometric
IL_4V88_418
NA
IL_8PPL_0391/A2/692:694,
1/A2/736:738		Isolated non-canonical cWW pair
geometric
IL_4LFB_006
IL_01003.4
IL_8PPL_0401/A2/694:696,
1/A2/734:736		Isolated non-canonical cWW pair
geometric
IL_2O3X_004
IL_71625.3
IL_8PPL_0411/A2/745:747,
1/A2/795:796		Major groove platform
geometric
IL_1G1X_005
NA
IL_8PPL_1171/A2/802:803,
1/A2/860:863		No text annotation
homologous
IL_8P9A_412
IL_73108.2
IL_8PPL_0441/A2/805:807,
1/A2/856:858		Isolated non-canonical cWW pair
homologous
IL_8C3A_431
NA
IL_8PPL_1181/A2/807:815,
1/A2/849:856		No text annotation
homologous
IL_8C3A_503
NA
IL_8PPL_0461/A2/874:876,
1/A2/910:912		Isolated non-canonical cWW pair
geometric
IL_5Y85_006
IL_01003.4
IL_8PPL_0471/A2/877:879,
1/A2/907:909		Isolated non-canonical cWW pair
geometric
IL_3DIL_006
IL_01003.4
IL_8PPL_0481/A2/922:923,
1/A2/1019:1022		Major groove platform; stack outside cWW
homologous
IL_4V88_428
NA
IL_8PPL_1191/A2/925:926,
1/A2/1015:1017		Single bulged U
geometric
IL_6UFH_004
IL_97561.4
IL_8PPL_0501/A2/928:931,
1/A2/1010:1013		Tandem non-canonical cWW pairs
homologous
IL_4V88_430
NA
IL_8PPL_0511/A2/931:935,
1/A2/1007:1010		Tandem non-canonical cWW pairs
geometric
IL_4V88_431
NA
IL_8PPL_0521/A2/942:945,
1/A2/981:984		Tandem non-canonical cWW pairs
homologous
IL_4V88_432
NA
IL_8PPL_0531/A2/952:956,
1/A2/967:974		Kink-turn
homologous
IL_4V88_434
NA
IL_8PPL_0541/A2/1042:1047,
1/A2/1071:1073		Other IL
homologous
IL_4V88_435
NA
IL_8PPL_0551/A2/1047:1051,
1/A2/1067:1071		tSH-tHW-tHS
geometric
IL_5J7L_037
NA
IL_8PPL_0561/A2/1091:1093,
1/A2/1152:1158		No text annotation
homologous
IL_8C3A_443
NA
IL_8PPL_0571/A2/1098:1101,
1/A2/1131:1134		Tandem non-canonical cWW pairs
geometric
IL_4V88_438
NA
IL_8PPL_0581/A2/1101:1103,
1/A2/1129:1131		Isolated non-canonical cWW pair
geometric
IL_4WF9_083
IL_01003.4
IL_8PPL_0591/A2/1108:1110,
1/A2/1123:1124		Minor groove platform
geometric
IL_4V88_412
NA
IL_8PPL_0601/A2/1168:1175,
1/A2/1186:1191		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_4V88_440
NA
IL_8PPL_0621/A2/1203:1204,
1/A2/1694:1696		Single bulged A
homologous
IL_8C3A_447
NA
IL_8PPL_1201/A2/1206:1208,
1/A2/1691:1692		Single bulged G
homologous
IL_8C3A_448
NA
IL_8PPL_0641/A2/1214:1217,
1/A2/1681:1685		C-loop
homologous
IL_4V88_443
NA
IL_8PPL_1211/A2/1230:1232,
1/A2/1526:1528		Isolated non-canonical cWW pair
homologous
IL_8P9A_432
IL_01003.4
IL_8PPL_0671/A2/1235:1236,
1/A2/1521:1523		Minor groove platform
homologous
IL_4V88_445
NA
IL_8PPL_1221/A2/1270:1272,
1/A2/1510:1512		Isolated non-canonical cWW pair
geometric
IL_4P3T_005
NA
IL_8PPL_0681/A2/1281:1287,
1/A2/1314:1316		No text annotation
IL_8PPL_1231/A2/1281:1290,
1/A2/1309:1316		No text annotation
homologous
IL_8P9A_470
IL_28304.1
IL_8PPL_0691/A2/1287:1290,
1/A2/1309:1314		No text annotation
IL_8PPL_0701/A2/1291:1293,
1/A2/1306:1308		No text annotation
homologous
IL_4V88_448
NA
IL_8PPL_1251/A2/1325:1327,
1/A2/1502:1503		Single bulged U
homologous
IL_8C3A_455
NA
IL_8PPL_0721/A2/1329:1333,
1/A2/1498:1500		Isolated cWS basepair
homologous
IL_4V88_450
NA
IL_8PPL_1261/A2/1329:1335,
1/A2/1492:1500		No text annotation
homologous
IL_8P9A_439
IL_99893.1
IL_8PPL_0731/A2/1333:1335,
1/A2/1492:1498		Minor groove platform with extra cWW
geometric
IL_4V88_451
NA
IL_8PPL_1271/A2/1337:1338,
1/A2/1488:1490		Single bulged A
homologous
IL_8C3A_458
NA
IL_8PPL_1281/A2/1347:1349,
1/A2/1380:1382		Isolated cWH basepair
homologous
IL_8P9A_442
IL_10892.2
IL_8PPL_0761/A2/1363:1365,
1/A2/1374:1375		Minor groove platform
homologous
IL_8C3A_460
NA
IL_8PPL_1291/A2/1395:1399,
1/A2/1447:1450		Tandem non-canonical cWW pairs
geometric
IL_8P9A_419
IL_15225.2
IL_8PPL_0791/A2/1402:1405,
1/A2/1441:1444		Minor groove platform
geometric
IL_4V88_456
NA
IL_8PPL_0801/A2/1408:1409,
1/A2/1432:1438		Multiple bulged bases
geometric
IL_1R3E_002
IL_05670.1
IL_8PPL_0811/A2/1412:1413,
1/A2/1427:1429		Single bulged G
geometric
IL_5J7L_019
NA
IL_8PPL_0821/A2/1416:1417,
1/A2/1422:1424		Single bulged C
geometric
IL_5J7L_311
NA
IL_8PPL_0831/A2/1537:1539,
1/A2/1594:1596		Isolated non-canonical cWW pair
geometric
IL_3SZX_002
IL_01003.4
IL_8PPL_1301/A2/1541:1550,
1/A2/1582:1592		No text annotation
IL_8PPL_0841/A2/1550:1558,
1/A2/1577:1582		180 degree turn
geometric
IL_5J7L_055
NA
IL_8PPL_0851/A2/1560:1562,
1/A2/1573:1575		Isolated non-canonical cWW pair
homologous
IL_8C3A_468
NA
IL_8PPL_0861/A2/1604:1610,
1/A2/1629:1635		No text annotation
homologous
IL_8C3A_469
NA
IL_8PPL_0871/A2/1700:1702,
1/A2/1833:1836		No text annotation
homologous
IL_4V88_463
NA
IL_8PPL_0881/A2/1702:1705,
1/A2/1829:1833		No text annotation
homologous
IL_8C3A_471
NA
IL_8PPL_0891/A2/1706:1708,
1/A2/1826:1828		Isolated non-canonical cWW pair
homologous
IL_4V88_465
NA
IL_8PPL_0901/A2/1708:1711,
1/A2/1822:1826		No text annotation
IL_8PPL_0911/A2/1714:1716,
1/A2/1817:1819		Isolated non-canonical cWW pair
homologous
IL_4V88_467
NA
IL_8PPL_0921/A2/1717:1720,
1/A2/1813:1816		Double sheared
homologous
IL_8C3A_475
NA
IL_8PPL_1311/A2/1717:1722,
1/A2/1812:1816		No text annotation
IL_8PPL_0971/A2/1729:1731,
1/A2/1803:1805		Isolated non-canonical cWW pair
geometric
IL_6E7L_003
NA
IL_8PPL_0981/A2/1733:1736,
1/A2/1798:1801		Double sheared
homologous
IL_4V88_471
NA
IL_8PPL_0991/A2/1739:1741,
1/A2/1793:1795		Isolated non-canonical cWW pair
geometric
IL_4E48_002
IL_01003.4
IL_8PPL_1001/A2/1742:1746,
1/A2/1788:1792		Triple sheared
homologous
IL_8C3A_480
NA
IL_8PPL_1011/A2/1750:1751,
1/A2/1782:1784		No text annotation

Problematic loops

#loop idProblemSequence
IL_8PPL_001Partly complementary
IL_8PPL_002Isolated non-canonical cWW pair
IL_8PPL_007No text annotation
IL_8PPL_008Isolated non-canonical cWW pair
IL_8PPL_012No text annotation
IL_8PPL_013No text annotation
IL_8PPL_014No text annotation
IL_8PPL_015Tandem non-canonical cWW pairs
IL_8PPL_019No text annotation
IL_8PPL_020Single bulged U
IL_8PPL_025No text annotation
IL_8PPL_032Not an internal loop
IL_8PPL_038Stack and bulge
IL_8PPL_042No text annotation
IL_8PPL_116No text annotation
IL_8PPL_043Major groove platform
IL_8PPL_045No text annotation
IL_8PPL_049Tandem non-canonical cWW pairs
IL_8PPL_061Stack and bulge
IL_8PPL_063Intercalated cWW
IL_8PPL_065Isolated non-canonical cWW pair
IL_8PPL_066Tandem non-canonical cWW pairs
IL_8PPL_124Tandem non-canonical cWW pairs
IL_8PPL_071Isolated non-canonical cWW pair
IL_8PPL_074Isolated non-canonical cWW pair
IL_8PPL_075No text annotation
IL_8PPL_077Other IL
IL_8PPL_078No text annotation
IL_8PPL_093No text annotation
IL_8PPL_094Isolated non-canonical cWW pair
IL_8PPL_095Isolated non-canonical cWW pair
IL_8PPL_096Isolated non-canonical cWW pair
IL_8PPL_132Tandem non-canonical cWW pairs
IL_8PPL_102Single stack bend
IL_8PPL_103Tandem non-canonical cWW pairs
IL_8PPL_104Tandem non-canonical cWW pairs
IL_8PPL_105Isolated non-canonical cWW pair

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8PPL_0101/A2/40:41,
1/A2/481:487,
1/A2/512:514		No text annotation
geometric
J3_4V88_078
NA
J3_8PPL_0111/A2/40:47,
1/A2/479:487,
1/A2/512:514		No text annotation
homologous
J3_8P9A_069
J3_63856.1
J3_8PPL_0211/A2/223:238,
1/A2/280:288,
1/A2/295:298		No text annotation
J3_8PPL_0131/A2/682:685,
1/A2/917:922,
1/A2/1022:1023		No text annotation
J3_8PPL_0141/A2/682:685,
1/A2/917:923,
1/A2/1019:1023		No text annotation
J3_8PPL_0011/A2/816:819,
1/A2/829:831,
1/A2/843:848		No text annotation
homologous
J3_8P9A_073
J3_97642.2
J3_8PPL_0151/A2/938:941,
1/A2/985:993,
1/A2/1000:1004		No text annotation
homologous
J3_8P9A_074
J3_23895.1
J3_8PPL_0161/A2/1094:1096,
1/A2/1136:1140,
1/A2/1147:1151		No text annotation
J3_8PPL_0041/A2/1218:1221,
1/A2/1645:1651,
1/A2/1673:1680		No text annotation
homologous
J3_4V88_035
NA
J3_8PPL_0051/A2/1225:1228,
1/A2/1530:1532,
1/A2/1638:1641		No text annotation
homologous
J3_8C3A_039
NA
J3_8PPL_0171/A2/1237:1244,
1/A2/1255:1266,
1/A2/1516:1520		No text annotation
homologous
J3_8P9A_078
J3_88451.1
J3_8PPL_0181/A2/1272:1277,
1/A2/1320:1324,
1/A2/1504:1510		No text annotation
homologous
J3_8C3A_041
NA
J3_8PPL_0081/A2/1340:1345,
1/A2/1384:1389,
1/A2/1481:1486		No text annotation
homologous
J3_8P9A_080
J3_17077.1
J3_8PPL_0191/A2/1350:1351,
1/A2/1360:1363,
1/A2/1375:1379		No text annotation
homologous
J3_8C3A_085
NA
J3_8PPL_0201/A2/1391:1395,
1/A2/1450:1456,
1/A2/1470:1479		No text annotation
J3_8PPL_0091/A2/1532:1536,
1/A2/1597:1604,
1/A2/1635:1638		No text annotation
homologous
J3_8C3A_044
NA
J4_8PPL_0011/A2/98:106,
1/A2/355:357,
1/A2/405:409,
1/A2/431:432		No text annotation
homologous
J4_8P9A_021
J4_15241.2
J4_8PPL_0021/A2/671:673,
1/A2/1032:1037,
1/A2/1078:1089,
1/A2/1160:1161		No text annotation
homologous
J4_8P9A_022
J4_14595.1
J4_8PPL_0031/Iw/7:10,
1/Iw/24:26,
1/Iw/42:48,
1/Iw/64:65		tRNA junction
homologous
J4_3WQY_001
J4_95067.1
J5_8PPL_0011/A2/30:34,
1/A2/521:527,
1/A2/558:565,
1/A2/585:595,
1/A2/641:644		No text annotation
J5_8PPL_0021/A2/53:56,
1/A2/89:96,
1/A2/434:436,
1/A2/457:459,
1/A2/470:474		No text annotation
homologous
J5_8C3A_020
NA
J5_8PPL_0031/A2/123:129,
1/A2/183:185,
1/A2/214:215,
1/A2/310:312,
1/A2/337:341		No text annotation

Problematic loops

#loop idProblemSequence
J3_8PPL_012No text annotation
J3_8PPL_002No text annotation
J3_8PPL_003No text annotation
J3_8PPL_006No text annotation
J3_8PPL_007No text annotation

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