RNA 3D Hub //

8S8H Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8S8H_0021/1/31:39tRNA anticodon loop
homologous
HL_9DFC_104
NA
HL_8S8H_0031/1/53:61T-loop with 2 stacked bulged bases
homologous
HL_5HR6_003
HL_33597.1
HL_8S8H_0041/2/7:17No text annotation
homologous
HL_8C3A_192
NA
HL_8S8H_0051/2/70:81Externally structured
geometric
HL_8C3A_022
NA
HL_8S8H_0061/2/153:159GNRA related
homologous
HL_8C3A_194
NA
HL_8S8H_0091/2/242:249T-loop with 1 bulged base
homologous
HL_8C3A_197
NA
HL_8S8H_0111/2/329:337GNRA related
homologous
HL_8C3A_199
NA
HL_8S8H_0121/2/367:372GNRA variation
homologous
HL_8C3A_200
NA
HL_8S8H_0131/2/392:403No text annotation
homologous
HL_8C3A_201
NA
HL_8S8H_0151/2/449:455No text annotation
homologous
HL_8P9A_201
HL_89167.1
HL_8S8H_0171/2/519:531No text annotation
homologous
HL_8C3A_205
NA
HL_8S8H_0181/2/568:573GNRA variation
homologous
HL_8C3A_206
NA
HL_8S8H_0211/2/764:772No text annotation
homologous
HL_8C3A_208
NA
HL_8S8H_0241/2/899:908No text annotation
homologous
HL_8C3A_211
NA
HL_8S8H_0251/2/936:941GNRA
homologous
HL_8P9A_210
HL_34789.1
HL_8S8H_0261/2/995:1007No text annotation
geometric
HL_4V9F_003
HL_75660.6
HL_8S8H_0271/2/1054:1063No text annotation
homologous
HL_8P9A_212
HL_91620.1
HL_8S8H_0281/2/1083:1088GNRA
homologous
HL_8C3A_215
NA
HL_8S8H_0291/2/1120:1125GNRA
homologous
HL_8C3A_216
NA
HL_8S8H_0301/2/1187:1196No text annotation
homologous
HL_8P9A_215
HL_97521.1
HL_8S8H_0311/2/1237:1246GNRA wlth extra near cWW
homologous
HL_8P9A_216
HL_45359.1
HL_8S8H_0321/2/1295:1300GNRA
homologous
HL_8P9A_217
HL_34789.1
HL_8S8H_0331/2/1308:1315T-loop related
homologous
HL_8C3A_220
NA
HL_8S8H_0351/2/1394:1400No text annotation
homologous
HL_8C3A_222
NA
HL_8S8H_0361/2/1499:1504GNRA
homologous
HL_8C3A_223
NA
HL_8S8H_0371/2/1548:1559No text annotation
homologous
HL_8C3A_224
NA
HL_8S8H_0381/2/1592:1600No text annotation
homologous
HL_8P9A_223
NA
HL_8S8H_0391/2/1688:1709No text annotation
HL_8S8H_0401/2/1776:1781GNRA variation
homologous
HL_8C3A_227
NA

Problematic loops

#loop idProblemSequence
HL_8S8H_001Externally structured
HL_8S8H_007No text annotation
HL_8S8H_008No text annotation
HL_8S8H_010Mini UNCG
HL_8S8H_014UNCG
HL_8S8H_016Externally structured
HL_8S8H_019No text annotation
HL_8S8H_020No text annotation
HL_8S8H_022No text annotation
HL_8S8H_023Pseudoknot geometry
HL_8S8H_034No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8S8H_0011/2/24:26,
1/2/599:600		Single bulged C
homologous
IL_8P9A_373
IL_05642.1
IL_8S8H_0021/2/35:37,
1/2/470:472		Isolated non-canonical cWW pair
geometric
IL_8C3A_393
NA
IL_8S8H_0031/2/37:41,
1/2/465:470		Triple sheared related
homologous
IL_8C3A_394
NA
IL_8S8H_0041/2/42:48,
1/2/430:432		No text annotation
homologous
IL_8C3A_395
NA
IL_8S8H_0051/2/50:52,
1/2/427:428		Minor groove platform
homologous
IL_8P9A_377
IL_34520.1
IL_8S8H_0061/2/58:63,
1/2/87:89		No text annotation
homologous
IL_8P9A_378
IL_61299.5
IL_8S8H_0071/2/64:69,
1/2/82:86		No text annotation
homologous
IL_8C3A_398
NA
IL_8S8H_0081/2/109:112,
1/2/301:304		Tandem non-canonical cWW pairs
homologous
IL_8C3A_399
NA
IL_8S8H_0091/2/113:117,
1/2/298:300		Isolated non-canonical cWW pair
geometric
IL_6E7L_003
NA
IL_8S8H_0911/2/117:122,
1/2/294:298		No text annotation
homologous
IL_8P9A_382
IL_31545.1
IL_8S8H_0111/2/142:148,
1/2/164:171		No text annotation
homologous
IL_8C3A_402
NA
IL_8S8H_0921/2/149:152,
1/2/160:163		No text annotation
homologous
IL_8CRE_401
IL_15043.1
IL_8S8H_0141/2/203:205,
1/2/258:262		No text annotation
homologous
IL_8P9A_386
IL_36931.1
IL_8S8H_0151/2/205:207,
1/2/256:258		Isolated non-canonical cWW pair
homologous
IL_8P9A_387
IL_71625.1
IL_8S8H_0161/2/264:266,
1/2/287:288		Single bulged A
homologous
IL_8P9A_388
IL_14190.1
IL_8S8H_0171/2/269:272,
1/2/282:284		No text annotation
homologous
IL_8C3A_408
NA
IL_8S8H_0191/2/310:315,
1/2/347:354		Kink-turn with non-sequential stacking
homologous
IL_8C3A_410
NA
IL_8S8H_0201/2/317:322,
1/2/344:345		No text annotation
homologous
IL_8P9A_392
IL_01372.1
IL_8S8H_0211/2/362:364,
1/2/375:380		No text annotation
homologous
IL_8P9A_393
IL_93336.1
IL_8S8H_0221/2/388:390,
1/2/405:407		Isolated cWH basepair
homologous
IL_8C3A_413
NA
IL_8S8H_0231/2/410:412,
1/2/419:421		Isolated non-canonical cWW pair
homologous
IL_8C3A_414
NA
IL_8S8H_0241/2/438:440,
1/2/462:463		Single bulged U
homologous
IL_8P9A_396
IL_97561.1
IL_8S8H_0251/2/442:446,
1/2/459:460		C-loop
homologous
IL_8P9A_397
IL_26900.1
IL_8S8H_0261/2/446:447,
1/2/457:459		Single bulged G
homologous
IL_8P9A_398
IL_28408.1
IL_8S8H_0281/2/513:515,
1/2/535:542		No text annotation
homologous
IL_8C3A_420
NA
IL_8S8H_0291/2/516:517,
1/2/532:534		Minor groove platform
homologous
IL_8C3A_501
NA
IL_8S8H_0301/2/517:519,
1/2/531:532		Minor groove platform
homologous
IL_8P9A_401
IL_34520.1
IL_8S8H_0311/2/549:556,
1/2/586:587		SSU/LSU pseudoknot
homologous
IL_8C3A_423
NA
IL_8S8H_0321/2/556:558,
1/2/585:586		Single bulged U
homologous
IL_8C3A_424
NA
IL_8S8H_0331/2/561:567,
1/2/574:582		No text annotation
homologous
IL_8P9A_404
IL_52042.1
IL_8S8H_0341/2/615:621,
1/2/1103:1104		No text annotation
homologous
IL_8P9A_405
IL_20847.1
IL_8S8H_0351/2/623:625,
1/2/972:974		Isolated non-canonical cWW pair
homologous
IL_8C3A_427
NA
IL_8S8H_0361/2/626:631,
1/2/966:971		No text annotation
geometric
IL_8ZA4_001
NA
IL_8S8H_0401/2/745:747,
1/2/801:805		No text annotation
IL_8S8H_0411/2/748:750,
1/2/798:800		Isolated non-canonical cWW pair
homologous
IL_8C3A_431
NA
IL_8S8H_0421/2/751:759,
1/2/790:797		No text annotation
homologous
IL_8C3A_503
NA
IL_8S8H_0431/2/818:821,
1/2/849:851		Isolated non-canonical cWW pair
homologous
IL_8P9A_415
IL_71625.1
IL_8S8H_0451/2/867:869,
1/2/956:959		Isolated cWH basepair
homologous
IL_8C3A_510
NA
IL_8S8H_0461/2/870:872,
1/2/953:955		Isolated non-canonical cWW pair
geometric
IL_2R8S_001
IL_01003.1
IL_8S8H_0471/2/873:877,
1/2/949:952		Tandem non-canonical cWW pairs
homologous
IL_8C3A_438
NA
IL_8S8H_0481/2/885:887,
1/2/923:925		Isolated non-canonical cWW pair
geometric
IL_3HHN_004
IL_01003.1
IL_8S8H_0491/2/892:898,
1/2/909:918		Kink-turn related
homologous
IL_8C3A_440
NA
IL_8S8H_0501/2/982:993,
1/2/1009:1017		No text annotation
IL_8S8H_0511/2/1033:1035,
1/2/1094:1100		No text annotation
homologous
IL_8P9A_425
IL_82706.2
IL_8S8H_0521/2/1040:1044,
1/2/1072:1076		No text annotation
IL_8S8H_0531/2/1050:1052,
1/2/1065:1066		Single bulged U
homologous
IL_8P9A_427
IL_97561.1
IL_8S8H_0541/2/1110:1117,
1/2/1128:1133		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_8P9A_428
IL_84044.1
IL_8S8H_0551/2/1145:1146,
1/2/1628:1630		Single bulged A
homologous
IL_8C3A_447
NA
IL_8S8H_0561/2/1148:1150,
1/2/1625:1626		Single bulged G
homologous
IL_8C3A_448
NA
IL_8S8H_0931/2/1156:1159,
1/2/1615:1619		C-loop
homologous
IL_8CRE_445
IL_63596.12
IL_8S8H_0581/2/1172:1175,
1/2/1461:1464		Tandem non-canonical cWW pairs
geometric
IL_5LQT_002
NA
IL_8S8H_0591/2/1177:1178,
1/2/1457:1459		Minor groove platform
homologous
IL_8C3A_451
NA
IL_8S8H_0601/2/1212:1214,
1/2/1446:1448		Isolated non-canonical cWW pair
homologous
IL_8C3A_452
NA
IL_8S8H_0941/2/1223:1229,
1/2/1256:1258		No text annotation
IL_8S8H_0951/2/1223:1232,
1/2/1251:1258		No text annotation
homologous
IL_8P9A_470
IL_28304.1
IL_8S8H_0631/2/1229:1232,
1/2/1251:1256		No text annotation
IL_8S8H_0651/2/1267:1269,
1/2/1438:1439		Single bulged U
homologous
IL_8C3A_455
NA
IL_8S8H_0661/2/1271:1275,
1/2/1434:1436		Isolated cWS basepair
geometric
IL_4LFB_044
IL_82453.1
IL_8S8H_0671/2/1271:1277,
1/2/1428:1436		No text annotation
geometric
IL_4V88_510
NA
IL_8S8H_0681/2/1275:1277,
1/2/1428:1434		No text annotation
homologous
IL_8P9A_440
IL_93811.1
IL_8S8H_0961/2/1279:1280,
1/2/1424:1426		Single bulged A
homologous
IL_8CRE_455
IL_14190.1
IL_8S8H_0701/2/1289:1291,
1/2/1322:1324		Isolated non-canonical cWW pair
homologous
IL_8C3A_459
NA
IL_8S8H_0711/2/1305:1307,
1/2/1316:1317		Minor groove platform
homologous
IL_8C3A_460
NA
IL_8S8H_0721/2/1338:1341,
1/2/1381:1383		Isolated non-canonical cWW pair
homologous
IL_8P9A_444
IL_01003.1
IL_8S8H_0731/2/1344:1347,
1/2/1375:1378		No text annotation
homologous
IL_8C3A_462
NA
IL_8S8H_0741/2/1352:1353,
1/2/1368:1370		Single bulged U
geometric
IL_8C3A_056
NA
IL_8S8H_0751/2/1387:1389,
1/2/1405:1410		Major groove platform; stack outside cWW
geometric
IL_4V88_458
NA
IL_8S8H_0761/2/1478:1485,
1/2/1517:1525		No text annotation
homologous
IL_8C3A_466
NA
IL_8S8H_0771/2/1486:1492,
1/2/1511:1516		No text annotation
homologous
IL_8P9A_449
IL_22564.1
IL_8S8H_0781/2/1494:1496,
1/2/1507:1509		Isolated non-canonical cWW pair
homologous
IL_8C3A_468
NA
IL_8S8H_0791/2/1538:1543,
1/2/1564:1569		No text annotation
homologous
IL_8C3A_507
NA
IL_8S8H_0801/2/1634:1636,
1/2/1762:1765		No text annotation
homologous
IL_8P9A_452
IL_18228.1
IL_8S8H_0811/2/1636:1639,
1/2/1758:1762		No text annotation
homologous
IL_8C3A_471
NA
IL_8S8H_0821/2/1640:1642,
1/2/1755:1757		Isolated non-canonical cWW pair
homologous
IL_8P9A_454
IL_01003.1
IL_8S8H_0831/2/1642:1645,
1/2/1751:1755		No text annotation
IL_8S8H_0841/2/1648:1650,
1/2/1746:1748		Isolated non-canonical cWW pair
homologous
IL_8P9A_456
IL_01003.1
IL_8S8H_0851/2/1651:1656,
1/2/1741:1745		No text annotation
IL_8S8H_0861/2/1663:1665,
1/2/1732:1734		Isolated non-canonical cWW pair
homologous
IL_8C3A_477
NA
IL_8S8H_0871/2/1667:1670,
1/2/1727:1730		Double sheared
homologous
IL_8P9A_460
IL_58355.1
IL_8S8H_0881/2/1673:1676,
1/2/1721:1724		Tandem non-canonical cWW pairs
homologous
IL_8P9A_462
IL_71194.1
IL_8S8H_0891/2/1676:1680,
1/2/1717:1721		Triple sheared
homologous
IL_8C3A_480
NA

Problematic loops

#loop idProblemSequence
IL_8S8H_010No text annotation
IL_8S8H_012No text annotation
IL_8S8H_013Double sheared
IL_8S8H_018No text annotation
IL_8S8H_027Isolated cWH basepair
IL_8S8H_037No text annotation
IL_8S8H_038No text annotation
IL_8S8H_039No text annotation
IL_8S8H_044No text annotation
IL_8S8H_057No text annotation
IL_8S8H_061No text annotation
IL_8S8H_062No text annotation
IL_8S8H_064Other IL
IL_8S8H_069Isolated non-canonical cWW pair
IL_8S8H_090No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8S8H_0011/2/41:42,
1/2/432:438,
1/2/463:465		No text annotation
homologous
J3_8C3A_082
NA
J3_8S8H_0161/2/212:227,
1/2/236:242,
1/2/249:251		No text annotation
J3_8S8H_0031/2/632:634,
1/2/860:865,
1/2/961:965		No text annotation
homologous
J3_8P9A_072
J3_17385.5
J3_8S8H_0041/2/759:763,
1/2/773:775,
1/2/784:790		No text annotation
J3_8S8H_0051/2/880:883,
1/2/927:935,
1/2/942:946		No text annotation
homologous
J3_8P9A_074
J3_23895.1
J3_8S8H_0061/2/1036:1038,
1/2/1078:1082,
1/2/1089:1093		No text annotation
geometric
J3_4V88_034
NA
J3_8S8H_0071/2/1160:1163,
1/2/1579:1585,
1/2/1607:1614		No text annotation
homologous
J3_8C3A_038
NA
J3_8S8H_0081/2/1167:1170,
1/2/1466:1468,
1/2/1572:1575		No text annotation
homologous
J3_8C3A_039
NA
J3_8S8H_0091/2/1179:1186,
1/2/1197:1208,
1/2/1452:1456		No text annotation
homologous
J3_8C3A_040
NA
J3_8S8H_0101/2/1214:1219,
1/2/1262:1266,
1/2/1440:1446		No text annotation
homologous
J3_8C3A_041
NA
J3_8S8H_0111/2/1282:1287,
1/2/1326:1331,
1/2/1417:1422		No text annotation
homologous
J3_8P9A_080
J3_17077.1
J3_8S8H_0121/2/1291:1293,
1/2/1302:1305,
1/2/1317:1322		No text annotation
J3_8S8H_0131/2/1335:1337,
1/2/1384:1387,
1/2/1410:1413		No text annotation
geometric
J3_8C3A_043
NA
J3_8S8H_0141/2/1335:1337,
1/2/1384:1389,
1/2/1405:1413		No text annotation
homologous
J3_8C3A_086
NA
J3_8S8H_0151/2/1468:1472,
1/2/1531:1538,
1/2/1569:1572		No text annotation
homologous
J3_8C3A_044
NA
J4_8S8H_0011/1/7:10,
1/1/25:27,
1/1/43:49,
1/1/65:66		tRNA junction
homologous
J4_3WQY_001
J4_58311.1
J4_8S8H_0021/2/99:107,
1/2/306:308,
1/2/356:360,
1/2/382:383		No text annotation
homologous
J4_8P9A_021
J4_15241.2
J4_8S8H_0041/2/621:623,
1/2/974:979,
1/2/1020:1031,
1/2/1102:1103		No text annotation
homologous
J4_8P9A_022
J4_14595.1
J5_8S8H_0011/2/31:35,
1/2/472:478,
1/2/508:513,
1/2/542:545,
1/2/591:594		No text annotation
homologous
J5_8C3A_018
NA
J5_8S8H_0021/2/31:35,
1/2/472:478,
1/2/508:515,
1/2/535:545,
1/2/591:594		No text annotation
J5_8S8H_0031/2/54:57,
1/2/90:97,
1/2/385:387,
1/2/408:410,
1/2/421:425		No text annotation
homologous
J5_8C3A_020
NA
J5_8S8H_0041/2/124:141,
1/2/172:182,
1/2/201:203,
1/2/262:264,
1/2/288:292		No text annotation
J5_8S8H_0051/2/124:141,
1/2/172:182,
1/2/201:203,
1/2/262:266,
1/2/287:292		No text annotation
J5_8S8H_0061/2/635:640,
1/2/693:700,
1/2/738:744,
1/2/806:816,
1/2/853:859		No text annotation

Problematic loops

#loop idProblemSequence
J3_8S8H_002No text annotation
J4_8S8H_003No text annotation

Coloring options:
Copyright 2025 BGSU RNA group. Page generated in 0.0978 s