RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_3JAP_0041/2/7:17No text annotation
homologous
HL_8C3A_192
NA
HL_3JAP_0051/2/70:81No text annotation
geometric
HL_5J7L_143
NA
HL_3JAP_0131/2/392:403No text annotation
homologous
HL_4V88_195
NA
HL_3JAP_0181/2/551:571No text annotation
HL_3JAP_0411/2/899:908No text annotation
homologous
HL_8P9A_209
HL_38491.2
HL_3JAP_0281/2/1187:1196No text annotation
homologous
HL_4V88_212
NA
HL_3JAP_0361/2/1592:1600No text annotation
homologous
HL_4V88_220
NA

Problematic loops

#loop idProblemSequence
HL_3JAP_001tRNA D-loop
HL_3JAP_002tRNA anticodon loop
HL_3JAP_003T-loop with 2 stacked bulged bases
HL_3JAP_006GNRA related
HL_3JAP_007No text annotation
HL_3JAP_008UNCG
HL_3JAP_009T-loop with 1 bulged base
HL_3JAP_010UNCG variation
HL_3JAP_011GNRA related
HL_3JAP_012No text annotation
HL_3JAP_014UNCG
HL_3JAP_015No text annotation
HL_3JAP_040No text annotation
HL_3JAP_039No text annotation
HL_3JAP_016No text annotation
HL_3JAP_017No text annotation
HL_3JAP_019No text annotation
HL_3JAP_020No text annotation
HL_3JAP_021Pseudoknot geometry
HL_3JAP_022No text annotation
HL_3JAP_023GNRA
HL_3JAP_024No text annotation
HL_3JAP_025No text annotation
HL_3JAP_026GNRA
HL_3JAP_027GNRA
HL_3JAP_029No text annotation
HL_3JAP_042No text annotation
HL_3JAP_030GNRA
HL_3JAP_031No text annotation
HL_3JAP_032No text annotation
HL_3JAP_033GNRA
HL_3JAP_034GNRA
HL_3JAP_035No text annotation
HL_3JAP_037No text annotation
HL_3JAP_038GNRA variation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_3JAP_0981/2/24:27,
1/2/598:600		No text annotation
IL_3JAP_0041/2/42:48,
1/2/430:432		No text annotation
homologous
IL_4V88_387
NA
IL_3JAP_0881/2/64:69,
1/2/82:85		Double sheared
geometric
IL_5J7L_256
NA
IL_3JAP_0111/2/117:121,
1/2/294:298		No text annotation
IL_3JAP_0141/2/142:148,
1/2/164:171		tWH-tWH-tHW-tHW
homologous
IL_4V88_394
NA
IL_3JAP_0221/2/310:315,
1/2/347:354		Kink-turn with non-sequential stacking
homologous
IL_4V88_402
NA
IL_3JAP_0241/2/362:364,
1/2/375:380		No text annotation
homologous
IL_4V88_404
NA
IL_3JAP_0261/2/438:440,
1/2/462:463		Single bulged U
geometric
IL_4LFB_014
IL_97561.5
IL_3JAP_0281/2/446:447,
1/2/457:459		Single bulged G
geometric
IL_5J7L_019
NA
IL_3JAP_0311/2/517:519,
1/2/531:532		Minor groove platform
homologous
IL_4V88_412
NA
IL_3JAP_0321/2/549:550,
1/2/572:587		No text annotation
IL_3JAP_0331/2/615:621,
1/2/1103:1104		No text annotation
homologous
IL_4V88_416
NA
IL_3JAP_0341/2/623:625,
1/2/972:974		Isolated non-canonical cWW pair
homologous
IL_4V88_417
NA
IL_3JAP_1011/2/751:776,
1/2/783:797		No text annotation
IL_3JAP_0931/2/867:869,
1/2/956:959		Isolated non-canonical cWW pair
homologous
IL_8P9A_418
IL_01003.4
IL_3JAP_0431/2/873:877,
1/2/949:952		Tandem non-canonical cWW pairs
homologous
IL_4V88_431
NA
IL_3JAP_0461/2/1033:1035,
1/2/1094:1100		No text annotation
homologous
IL_4V88_437
NA
IL_3JAP_0501/2/1110:1117,
1/2/1128:1133		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_4V88_440
NA
IL_3JAP_0511/2/1143:1145,
1/2/1630:1631		Single stack bend
geometric
IL_4V84_420
NA
IL_3JAP_0521/2/1145:1146,
1/2/1628:1630		Single bulged A
geometric
IL_6CZR_147
NA
IL_3JAP_0541/2/1156:1159,
1/2/1615:1619		C-loop
homologous
IL_4V88_443
NA
IL_3JAP_1031/2/1232:1233,
1/2/1249:1251		Single base bend
geometric
IL_5IBB_340
IL_15011.3
IL_3JAP_0611/2/1267:1269,
1/2/1438:1439		Single bulged U
homologous
IL_4V88_449
NA
IL_3JAP_0951/2/1271:1275,
1/2/1434:1436		Isolated cWS basepair
geometric
IL_4LFB_044
IL_82453.1
IL_3JAP_0961/2/1271:1277,
1/2/1428:1436		No text annotation
homologous
IL_8P9A_439
IL_99893.1
IL_3JAP_0641/2/1279:1280,
1/2/1424:1426		Single bulged A
homologous
IL_4V88_452
NA
IL_3JAP_0701/2/1387:1389,
1/2/1405:1410		Major groove platform; stack outside cWW
homologous
IL_4V88_458
NA
IL_3JAP_0721/2/1486:1492,
1/2/1511:1516		180 degree turn
homologous
IL_4V88_460
NA
IL_3JAP_0761/2/1636:1639,
1/2/1758:1762		No text annotation
homologous
IL_4V88_464
NA
IL_3JAP_0781/2/1642:1645,
1/2/1751:1755		Tandem non-canonical cWW pairs
geometric
IL_5J7L_033
NA
IL_3JAP_0831/2/1667:1670,
1/2/1727:1730		Double sheared
homologous
IL_4V88_471
NA

Problematic loops

#loop idProblemSequence
IL_3JAP_001No text annotation
IL_3JAP_002Isolated non-canonical cWW pair
IL_3JAP_003No text annotation
IL_3JAP_005Minor groove platform
IL_3JAP_006No text annotation
IL_3JAP_007Single stack bend
IL_3JAP_008Double sheared with non-canonical cWW
IL_3JAP_009Tandem non-canonical cWW pairs
IL_3JAP_089Tandem non-canonical cWW pairs
IL_3JAP_010Multiple bulged bases
IL_3JAP_012Single stack bend
IL_3JAP_013Single stack bend
IL_3JAP_015Isolated non-canonical cWW contact
IL_3JAP_016Double sheared
IL_3JAP_017Major groove platform with extra cWW
IL_3JAP_018Not an internal loop
IL_3JAP_019Single stack bend
IL_3JAP_020Single bulged A
IL_3JAP_021No text annotation
IL_3JAP_023No text annotation
IL_3JAP_025Isolated cWH basepair
IL_3JAP_027C-loop
IL_3JAP_029No text annotation
IL_3JAP_030No text annotation
IL_3JAP_035tSH-tHW-tHS
IL_3JAP_099No text annotation
IL_3JAP_036No text annotation
IL_3JAP_037No text annotation
IL_3JAP_038No text annotation
IL_3JAP_100No text annotation
IL_3JAP_039Isolated non-canonical cWW pair
IL_3JAP_090No text annotation
IL_3JAP_040No text annotation
IL_3JAP_091No text annotation
IL_3JAP_092Tandem non-canonical cWW pairs
IL_3JAP_041Tandem non-canonical cWW pairs
IL_3JAP_042Tandem non-canonical cWW pairs
IL_3JAP_044Tandem non-canonical cWW pairs
IL_3JAP_045Kink-turn related
IL_3JAP_094No text annotation
IL_3JAP_102No text annotation
IL_3JAP_047No text annotation
IL_3JAP_048Single bulged U
IL_3JAP_049Single stack bend
IL_3JAP_053Single bulged G
IL_3JAP_055Tandem non-canonical cWW pairs
IL_3JAP_056Minor groove platform
IL_3JAP_057Multiple bulged bases
IL_3JAP_058Isolated non-canonical cWW pair
IL_3JAP_059No text annotation
IL_3JAP_060No text annotation
IL_3JAP_104Minor groove platform
IL_3JAP_062Tandem non-canonical cWW pairs
IL_3JAP_063Minor groove platform with extra cWW
IL_3JAP_065Isolated cWH basepair
IL_3JAP_066Minor groove platform
IL_3JAP_067Isolated non-canonical cWW pair
IL_3JAP_068Minor groove platform
IL_3JAP_105Single bulged U
IL_3JAP_069Isolated non-canonical cWW with bulges
IL_3JAP_071No text annotation
IL_3JAP_073No text annotation
IL_3JAP_106No text annotation
IL_3JAP_074No text annotation
IL_3JAP_075No text annotation
IL_3JAP_077Isolated non-canonical cWW pair
IL_3JAP_079Isolated non-canonical cWW pair
IL_3JAP_080Double sheared
IL_3JAP_081Single bulged U
IL_3JAP_082Isolated non-canonical cWW pair
IL_3JAP_084Tandem non-canonical cWW pairs
IL_3JAP_085Triple sheared
IL_3JAP_097No text annotation
IL_3JAP_086No text annotation
IL_3JAP_087Single stack bend

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_3JAP_0011/2/41:42,
1/2/432:438,
1/2/463:465		No text annotation
homologous
J3_8C3A_082
NA
J3_3JAP_0131/2/212:227,
1/2/236:242,
1/2/249:251		No text annotation
J3_3JAP_0021/2/632:634,
1/2/860:865,
1/2/961:965		No text annotation
homologous
J3_8C3A_034
NA
J3_3JAP_0031/2/880:883,
1/2/927:935,
1/2/942:946		No text annotation
homologous
J3_4V88_033
NA
J3_3JAP_0041/2/1036:1038,
1/2/1078:1082,
1/2/1089:1093		No text annotation
homologous
J3_4V88_034
NA
J3_3JAP_0051/2/1160:1162,
1/2/1580:1585,
1/2/1607:1614		No text annotation
J3_3JAP_0071/2/1179:1186,
1/2/1197:1206,
1/2/1453:1456		No text annotation
J3_3JAP_0141/2/1179:1186,
1/2/1197:1208,
1/2/1452:1456		No text annotation
homologous
J3_8C3A_040
NA
J3_3JAP_0081/2/1214:1219,
1/2/1262:1266,
1/2/1440:1446		No text annotation
homologous
J3_4V88_038
NA
J3_3JAP_0111/2/1335:1337,
1/2/1384:1387,
1/2/1410:1413		No text annotation
homologous
J3_8C3A_043
NA
J3_3JAP_0151/2/1335:1337,
1/2/1384:1389,
1/2/1405:1413		No text annotation
homologous
J3_8C3A_086
NA
J3_3JAP_0121/2/1468:1472,
1/2/1531:1538,
1/2/1569:1572		No text annotation
homologous
J3_4V88_041
NA
J4_3JAP_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_3JAP_0031/2/621:623,
1/2/974:979,
1/2/1020:1031,
1/2/1102:1103		No text annotation
homologous
J4_8C3A_022
NA
J5_3JAP_0011/2/31:35,
1/2/472:482,
1/2/503:517,
1/2/532:545,
1/2/591:594		No text annotation
J5_3JAP_0021/2/54:57,
1/2/90:97,
1/2/385:387,
1/2/408:412,
1/2/419:425		No text annotation
J5_3JAP_0061/2/635:640,
1/2/693:698,
1/2/740:744,
1/2/806:816,
1/2/853:859		No text annotation

Problematic loops

#loop idProblemSequence
J3_3JAP_006No text annotation
J3_3JAP_009No text annotation
J3_3JAP_010No text annotation
J4_3JAP_001No text annotation
J5_3JAP_003No text annotation
J5_3JAP_004No text annotation
J5_3JAP_005No text annotation

Coloring options:
Copyright 2026 BGSU RNA group. Page generated in 0.0486 s