RNA 3D Hub //

3J81 Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_3J81_0371/1/13:22No text annotation
geometric
HL_2Y9H_004
HL_48417.5
HL_3J81_0381/1/31:39tRNA anticodon loop
geometric
HL_4TUE_034
HL_06059.5
HL_3J81_0391/1/53:61No text annotation
HL_3J81_0011/2/7:17No text annotation
homologous
HL_8C3A_192
NA
HL_3J81_0021/2/70:81No text annotation
geometric
HL_2ZNI_001
HL_75660.5
HL_3J81_0031/2/151:161No text annotation
HL_3J81_0041/2/189:194No text annotation
homologous
HL_4V88_189
NA
HL_3J81_0051/2/229:234UNCG
geometric
HL_5J7L_030
HL_34617.5
HL_3J81_0061/2/242:249T-loop with 1 bulged base
homologous
HL_4V88_191
NA
HL_3J81_0071/2/275:278Mini UNCG
homologous
HL_4V88_192
NA
HL_3J81_0081/2/329:337GNRA related
homologous
HL_4V88_193
NA
HL_3J81_0091/2/367:372No text annotation
homologous
HL_4V88_194
NA
HL_3J81_0101/2/392:403No text annotation
homologous
HL_4V88_195
NA
HL_3J81_0111/2/413:418UNCG
homologous
HL_8C3A_202
NA
HL_3J81_0121/2/449:455No text annotation
homologous
HL_4V88_197
NA
HL_3J81_0131/2/490:495Externally structured
geometric
HL_5TBW_022
NA
HL_3J81_0141/2/519:531No text annotation
homologous
HL_4V88_199
NA
HL_3J81_0151/2/568:573GNRA variation
homologous
HL_4V88_200
NA
HL_3J81_0161/2/715:724No text annotation
HL_3J81_0171/2/764:772No text annotation
homologous
HL_4V88_203
NA
HL_3J81_0181/2/777:782No text annotation
HL_3J81_0191/2/828:842Pseudoknot geometry
homologous
HL_4V88_205
NA
HL_3J81_0421/2/899:908No text annotation
homologous
HL_8P9A_209
HL_75293.5
HL_3J81_0211/2/936:941GNRA
homologous
HL_4V88_207
NA
HL_3J81_0221/2/996:1006No text annotation
homologous
HL_4V88_208
NA
HL_3J81_0411/2/1052:1065No text annotation
HL_3J81_0231/2/1055:1063No text annotation
HL_3J81_0241/2/1083:1088GNRA
homologous
HL_4V88_210
NA
HL_3J81_0251/2/1120:1125GNRA
homologous
HL_4V88_211
NA
HL_3J81_0261/2/1187:1196No text annotation
homologous
HL_4V88_212
NA
HL_3J81_0431/2/1223:1258No text annotation
HL_3J81_0281/2/1295:1300GNRA
homologous
HL_4V88_214
NA
HL_3J81_0291/2/1308:1315No text annotation
homologous
HL_4V88_215
NA
HL_3J81_0301/2/1358:1363No text annotation
geometric
HL_5NFV_001
HL_69752.2
HL_3J81_0311/2/1393:1402No text annotation
HL_3J81_0321/2/1499:1504UNCG variation
geometric
HL_2CZJ_007
NA
HL_3J81_0441/2/1548:1559No text annotation
homologous
HL_8CRE_223
HL_67079.1
HL_3J81_0341/2/1592:1600No text annotation
homologous
HL_4V88_220
NA
HL_3J81_0361/2/1776:1781GNRA variation
homologous
HL_4V88_222
NA

Problematic loops

#loop idProblemSequence
HL_3J81_040No text annotation
HL_3J81_020No text annotation
HL_3J81_027No text annotation
HL_3J81_033No text annotation
HL_3J81_035No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_3J81_0021/2/24:26,
1/2/599:600		Single bulged C
homologous
IL_8C3A_392
NA
IL_3J81_0031/2/35:41,
1/2/465:472		No text annotation
IL_3J81_0041/2/42:48,
1/2/430:432		No text annotation
homologous
IL_4V88_387
NA
IL_3J81_1131/2/50:52,
1/2/427:428		Minor groove platform
homologous
IL_8P9A_377
IL_51454.2
IL_3J81_0061/2/58:63,
1/2/87:89		No text annotation
homologous
IL_4V88_389
NA
IL_3J81_0961/2/64:69,
1/2/82:86		No text annotation
homologous
IL_8P9A_379
IL_21667.1
IL_3J81_0081/2/109:112,
1/2/301:304		Tandem non-canonical cWW pairs
homologous
IL_4V88_391
NA
IL_3J81_1141/2/113:116,
1/2/299:300		Multiple bulged bases
homologous
IL_8P9A_381
IL_82107.4
IL_3J81_0101/2/117:122,
1/2/294:298		No text annotation
geometric
IL_4V88_393
NA
IL_3J81_0111/2/143:145,
1/2/170:171		No text annotation
IL_3J81_0121/2/145:149,
1/2/163:170		No text annotation
IL_3J81_0131/2/149:151,
1/2/161:163		Isolated non-canonical cWW pair
geometric
IL_4AOB_005
IL_87907.2
IL_3J81_0141/2/185:188,
1/2/195:198		Double sheared
homologous
IL_4V88_396
NA
IL_3J81_0151/2/203:205,
1/2/258:262		Major groove platform with extra cWW
geometric
IL_4V88_397
NA
IL_3J81_0161/2/205:207,
1/2/256:258		Isolated non-canonical cWW pair
homologous
IL_4V88_398
NA
IL_3J81_0171/2/264:266,
1/2/287:288		Single bulged A
homologous
IL_4V88_399
NA
IL_3J81_1151/2/269:272,
1/2/282:284		No text annotation
homologous
IL_8CRE_406
IL_15698.3
IL_3J81_0191/2/274:275,
1/2/278:280		Single bulged U
homologous
IL_8C3A_409
NA
IL_3J81_0201/2/310:315,
1/2/347:354		Kink-turn with non-sequential stacking
homologous
IL_4V88_402
NA
IL_3J81_1161/2/317:322,
1/2/344:345		No text annotation
homologous
IL_8P9A_392
IL_47074.2
IL_3J81_0221/2/362:364,
1/2/375:380		No text annotation
homologous
IL_4V88_404
NA
IL_3J81_0231/2/388:390,
1/2/405:407		Isolated cWH basepair
homologous
IL_4V88_405
NA
IL_3J81_0241/2/410:412,
1/2/419:421		Isolated near basepair
homologous
IL_4V88_406
NA
IL_3J81_0251/2/438:440,
1/2/462:463		Single bulged U
homologous
IL_4V88_407
NA
IL_3J81_0261/2/442:446,
1/2/459:460		C-loop
geometric
IL_5J7L_018
IL_03109.3
IL_3J81_0271/2/446:447,
1/2/457:459		Single bulged G
geometric
IL_5J7L_019
IL_00225.13
IL_3J81_0991/2/547:556,
1/2/586:589		No text annotation
IL_3J81_0311/2/549:556,
1/2/586:587		SSU/LSU pseudoknot
geometric
IL_4V88_413
NA
IL_3J81_0321/2/556:558,
1/2/585:586		Single bulged U
geometric
IL_5TBW_146
NA
IL_3J81_0331/2/561:567,
1/2/574:582		Kink-turn related
homologous
IL_4V88_415
NA
IL_3J81_0341/2/615:621,
1/2/1103:1104		No text annotation
homologous
IL_4V88_416
NA
IL_3J81_0351/2/623:625,
1/2/972:974		Isolated non-canonical cWW pair
homologous
IL_4V88_417
NA
IL_3J81_0361/2/626:630,
1/2/967:971		tSH-tHW-tHS
homologous
IL_4V88_418
NA
IL_3J81_1001/2/642:643,
1/2/690:692		Single stack bend
geometric
IL_8C3A_076
NA
IL_3J81_0371/2/650:657,
1/2/676:683		No text annotation
IL_3J81_1011/2/703:715,
1/2/724:735		No text annotation
IL_3J81_0381/2/746:747,
1/2/801:804		Major groove minor groove platform; mini C-loop
homologous
IL_4V88_423
NA
IL_3J81_0391/2/748:750,
1/2/798:800		Isolated non-canonical cWW pair
homologous
IL_4V88_424
NA
IL_3J81_1171/2/751:759,
1/2/790:797		No text annotation
homologous
IL_8CRE_430
IL_59049.1
IL_3J81_0411/2/816:821,
1/2/849:853		No text annotation
IL_3J81_1181/2/867:869,
1/2/956:959		Isolated non-canonical cWW pair
homologous
IL_8P9A_418
IL_57744.1
IL_3J81_0451/2/870:873,
1/2/952:955		Tandem non-canonical cWW pairs
geometric
IL_4V88_430
NA
IL_3J81_0461/2/873:877,
1/2/949:952		Tandem non-canonical cWW pairs
homologous
IL_4V88_431
NA
IL_3J81_0471/2/884:887,
1/2/923:926		Tandem non-canonical cWW pairs
homologous
IL_4V88_432
NA
IL_3J81_0481/2/892:894,
1/2/916:918		Isolated non-canonical cWW pair
geometric
IL_4E48_006
IL_87907.2
IL_3J81_1041/2/892:898,
1/2/909:918		No text annotation
homologous
IL_8P9A_422
IL_57741.1
IL_3J81_0491/2/894:898,
1/2/909:916		Kink-turn
geometric
IL_4V88_434
NA
IL_3J81_0501/2/983:993,
1/2/1009:1016		No text annotation
IL_3J81_0521/2/1033:1035,
1/2/1094:1100		No text annotation
homologous
IL_4V88_437
NA
IL_3J81_0531/2/1040:1043,
1/2/1073:1076		Tandem non-canonical cWW pairs
homologous
IL_4V88_438
NA
IL_3J81_0551/2/1050:1052,
1/2/1065:1066		Single bulged U
geometric
IL_5TBW_093
NA
IL_3J81_0561/2/1052:1054,
1/2/1064:1065		Single stack bend
geometric
IL_4V9F_005
IL_90729.1
IL_3J81_0571/2/1110:1117,
1/2/1128:1133		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_4V88_440
NA
IL_3J81_0581/2/1145:1146,
1/2/1628:1630		Single bulged A
homologous
IL_4V88_441
NA
IL_3J81_0591/2/1148:1150,
1/2/1625:1626		Single bulged G
homologous
IL_4V88_442
NA
IL_3J81_0611/2/1156:1159,
1/2/1615:1619		C-loop
homologous
IL_4V88_443
NA
IL_3J81_0621/2/1172:1174,
1/2/1462:1464		Isolated non-canonical cWW pair
homologous
IL_4V88_444
NA
IL_3J81_1061/2/1176:1178,
1/2/1457:1460		Decoding loop related
geometric
IL_2O3X_003
IL_31737.3
IL_3J81_0631/2/1177:1178,
1/2/1457:1459		Minor groove platform
homologous
IL_4V88_445
NA
IL_3J81_0641/2/1212:1214,
1/2/1446:1448		Isolated non-canonical cWW pair
homologous
IL_4V88_446
NA
IL_3J81_0651/2/1267:1269,
1/2/1438:1439		Single bulged U
geometric
IL_3MEI_001
IL_89505.4
IL_3J81_1071/2/1271:1274,
1/2/1435:1436		Multiple bulged bases
geometric
IL_1FUF_002
IL_82107.4
IL_3J81_1081/2/1275:1277,
1/2/1428:1434		No text annotation
homologous
IL_8P9A_440
IL_49061.1
IL_3J81_0681/2/1279:1280,
1/2/1424:1426		Single bulged A
homologous
IL_4V88_452
NA
IL_3J81_0691/2/1289:1291,
1/2/1322:1324		Isolated cWH basepair
homologous
IL_4V88_453
NA
IL_3J81_0701/2/1305:1307,
1/2/1316:1317		Minor groove platform
geometric
IL_4V88_388
NA
IL_3J81_0711/2/1338:1341,
1/2/1381:1383		Isolated non-canonical cWW pair
homologous
IL_4V88_455
NA
IL_3J81_1191/2/1344:1347,
1/2/1375:1378		No text annotation
homologous
IL_8CRE_481
IL_78800.1
IL_3J81_1201/2/1352:1354,
1/2/1367:1370		Isolated non-canonical cWW pair
geometric
IL_8P9A_418
IL_57744.1
IL_3J81_0751/2/1387:1389,
1/2/1405:1410		Major groove platform; stack outside cWW
geometric
IL_4V88_458
NA
IL_3J81_1101/2/1391:1393,
1/2/1402:1403		Single stack bend
geometric
IL_8C3A_146
NA
IL_3J81_1211/2/1478:1485,
1/2/1517:1525		No text annotation
homologous
IL_8P9A_448
IL_91698.1
IL_3J81_0771/2/1486:1492,
1/2/1511:1516		180 degree turn
homologous
IL_4V88_460
NA
IL_3J81_0781/2/1493:1497,
1/2/1506:1510		No text annotation
IL_3J81_0801/2/1538:1543,
1/2/1564:1569		No text annotation
homologous
IL_4V88_462
NA
IL_3J81_0821/2/1634:1636,
1/2/1762:1765		No text annotation
geometric
IL_5J7L_058
IL_61438.4
IL_3J81_0831/2/1636:1639,
1/2/1758:1762		No text annotation
homologous
IL_4V88_464
NA
IL_3J81_0841/2/1640:1642,
1/2/1755:1757		Isolated non-canonical cWW pair
geometric
IL_1UN6_005
IL_87907.2
IL_3J81_1221/2/1642:1645,
1/2/1751:1755		No text annotation
IL_3J81_0861/2/1648:1650,
1/2/1746:1748		Isolated non-canonical cWW pair
homologous
IL_4V88_467
NA
IL_3J81_1231/2/1651:1659,
1/2/1738:1745		No text annotation
IL_3J81_1241/2/1660:1665,
1/2/1732:1737		No text annotation
IL_3J81_0891/2/1667:1670,
1/2/1727:1730		Double sheared
homologous
IL_4V88_471
NA
IL_3J81_0901/2/1673:1676,
1/2/1721:1724		Tandem non-canonical cWW pairs
homologous
IL_4V88_473
NA
IL_3J81_0911/2/1676:1680,
1/2/1717:1721		Triple sheared
geometric
IL_4V88_474
NA
IL_3J81_0931/2/1685:1688,
1/2/1709:1712		No text annotation

Problematic loops

#loop idProblemSequence
IL_3J81_094Tandem non-canonical cWW pairs
IL_3J81_095Isolated non-canonical cWW pair
IL_3J81_001Isolated non-canonical cWW pair
IL_3J81_005Minor groove platform with extra cWW
IL_3J81_007Triple sheared related
IL_3J81_009Multiple bulged bases, near cWW
IL_3J81_097No text annotation
IL_3J81_018No text annotation
IL_3J81_021No text annotation
IL_3J81_098No text annotation
IL_3J81_028Isolated cWH basepair
IL_3J81_029No text annotation
IL_3J81_030Isolated non-canonical cWW pair
IL_3J81_102Tandem non-canonical cWW pairs
IL_3J81_040No text annotation
IL_3J81_042Isolated non-canonical cWW pair
IL_3J81_103No text annotation
IL_3J81_043No text annotation
IL_3J81_044Tandem non-canonical cWW pairs
IL_3J81_105No text annotation
IL_3J81_051Isolated non-canonical cWW pair
IL_3J81_054Isolated non-canonical cWW pair
IL_3J81_060Isolated non-canonical cWW pair
IL_3J81_066Tandem non-canonical cWW pairs
IL_3J81_067No text annotation
IL_3J81_072No text annotation
IL_3J81_073No text annotation
IL_3J81_109No text annotation
IL_3J81_074Isolated non-canonical cWW pair
IL_3J81_076No text annotation
IL_3J81_111No text annotation
IL_3J81_079Isolated non-canonical cWW pair
IL_3J81_112No text annotation
IL_3J81_081Isolated non-canonical cWW pair
IL_3J81_085No text annotation
IL_3J81_087No text annotation
IL_3J81_088No text annotation
IL_3J81_092No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_3J81_0121/2/41:42,
1/2/432:438,
1/2/463:465		No text annotation
homologous
J3_8C3A_082
NA
J3_3J81_0171/2/212:227,
1/2/236:242,
1/2/249:251		No text annotation
J3_3J81_0011/2/632:634,
1/2/860:865,
1/2/961:965		No text annotation
homologous
J3_8C3A_034
NA
J3_3J81_0181/2/760:763,
1/2/773:776,
1/2/783:789		No text annotation
J3_3J81_0021/2/879:883,
1/2/927:935,
1/2/942:947		No text annotation
J3_3J81_0031/2/1036:1038,
1/2/1078:1082,
1/2/1089:1093		No text annotation
homologous
J3_4V88_034
NA
J3_3J81_0041/2/1160:1163,
1/2/1579:1585,
1/2/1607:1614		No text annotation
J3_3J81_0051/2/1167:1170,
1/2/1466:1468,
1/2/1572:1575		No text annotation
homologous
J3_4V88_036
NA
J3_3J81_0061/2/1179:1186,
1/2/1197:1208,
1/2/1452:1456		No text annotation
homologous
J3_8C3A_040
NA
J3_3J81_0151/2/1214:1219,
1/2/1262:1266,
1/2/1440:1446		No text annotation
homologous
J3_8P9A_079
J3_87797.1
J3_3J81_0081/2/1282:1287,
1/2/1326:1331,
1/2/1417:1422		No text annotation
homologous
J3_4V88_039
NA
J3_3J81_0091/2/1291:1293,
1/2/1302:1305,
1/2/1317:1322		No text annotation
J3_3J81_0101/2/1335:1337,
1/2/1384:1387,
1/2/1410:1413		No text annotation
homologous
J3_4V88_040
NA
J3_3J81_0161/2/1335:1337,
1/2/1384:1389,
1/2/1405:1413		No text annotation
homologous
J3_8C3A_086
NA
J3_3J81_0111/2/1468:1472,
1/2/1531:1538,
1/2/1569:1572		No text annotation
homologous
J3_4V88_041
NA
J4_3J81_0011/1/7:10,
1/1/25:27,
1/1/43:49,
1/1/65:66		No text annotation
J4_3J81_0051/2/31:35,
1/2/472:486,
1/2/499:545,
1/2/591:594		No text annotation
J4_3J81_0031/2/99:107,
1/2/306:308,
1/2/356:360,
1/2/382:383		No text annotation
homologous
J4_8C3A_021
NA
J4_3J81_0041/2/621:623,
1/2/974:979,
1/2/1020:1031,
1/2/1102:1103		No text annotation
homologous
J4_8C3A_022
NA
J5_3J81_0011/2/54:57,
1/2/90:97,
1/2/385:387,
1/2/408:412,
1/2/419:425		No text annotation
J5_3J81_0021/2/124:149,
1/2/163:181,
1/2/202:203,
1/2/262:264,
1/2/288:292		No text annotation
J5_3J81_0031/2/124:149,
1/2/163:181,
1/2/202:203,
1/2/262:266,
1/2/287:292		No text annotation
J5_3J81_0051/2/635:641,
1/2/693:698,
1/2/740:744,
1/2/806:816,
1/2/853:859		No text annotation

Problematic loops

#loop idProblemSequence
J3_3J81_013No text annotation
J3_3J81_014No text annotation
J3_3J81_007No text annotation
J4_3J81_002No text annotation
J5_3J81_004No text annotation

Coloring options:
Copyright 2025 BGSU RNA group. Page generated in 0.0764 s