RNA 3D Hub //

9H3O Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_9H3O_0011/A/59:68No text annotation
homologous
HL_5J7L_134
HL_35677.3
HL_9H3O_0021/A/87:95No text annotation
homologous
HL_5J7L_135
HL_80241.1
HL_9H3O_0031/A/123:128No text annotation
homologous
HL_5J7L_136
HL_82710.2
HL_9H3O_0041/A/135:144No text annotation
HL_9H3O_0051/A/158:168No text annotation
homologous
HL_5J7L_138
HL_68257.1
HL_9H3O_0061/A/195:200No text annotation
HL_9H3O_0071/A/225:230No text annotation
homologous
HL_5J7L_140
HL_62934.1
HL_9H3O_0081/A/246:252No text annotation
homologous
HL_4WF9_008
HL_37369.2
HL_9H3O_0091/A/305:312T-loop with 2 stacked bulged bases
homologous
HL_4WF9_010
HL_01609.3
HL_9H3O_0101/A/319:323No text annotation
homologous
HL_4WF9_011
HL_75660.5
HL_9H3O_0111/A/327:335T-loop with unstacked turn
homologous
HL_5J7L_144
HL_27670.2
HL_9H3O_0121/A/381:393No text annotation
HL_9H3O_0131/A/410:417No text annotation
homologous
HL_9DFE_013
HL_30680.3
HL_9H3O_0141/A/462:467GNRA
homologous
HL_7A0S_015
HL_37824.8
HL_9H3O_0151/A/487:493GNRA
homologous
HL_5J7L_148
HL_37824.8
HL_9H3O_0161/A/543:550No text annotation
geometric
HL_2Y8W_001
HL_81100.2
HL_9H3O_0171/A/566:575T-loop with 2 stacked bulged bases
homologous
HL_9DFE_016
HL_28252.9
HL_9H3O_0181/A/611:617No text annotation
homologous
HL_5J7L_151
HL_80922.2
HL_9H3O_0191/A/630:634No text annotation
HL_9H3O_0201/A/641:647GNRA
homologous
HL_4WF9_021
HL_37824.8
HL_9H3O_0211/A/779:785No text annotation
homologous
HL_5J7L_156
HL_87954.2
HL_9H3O_0221/A/826:831No text annotation
geometric
HL_6DTD_001
HL_48417.6
HL_9H3O_0231/A/955:962GNRA
homologous
HL_4WF9_027
HL_37824.8
HL_9H3O_0241/A/978:985No text annotation
homologous
HL_9DFE_026
HL_42998.2
HL_9H3O_0251/A/1092:1099No text annotation
homologous
HL_9DFE_028
NA
HL_9H3O_0261/A/1172:1177Externally structured
geometric
HL_8C3A_022
NA
HL_9H3O_0271/A/1222:1227GNRA
homologous
HL_7A0S_031
HL_37824.8
HL_9H3O_0281/A/1281:1289T-loop with 2 stacked bulged bases
homologous
HL_4WF9_032
HL_28252.9
HL_9H3O_0291/A/1324:1330Pseudoknot geometry with 3' bulge
homologous
HL_9DFE_032
HL_57176.2
HL_9H3O_0301/A/1363:1368GNRA
homologous
HL_5J7L_167
HL_37824.8
HL_9H3O_0311/A/1389:1398No text annotation
homologous
HL_9DFE_034
HL_81545.2
HL_9H3O_0321/A/1451:1459Mini UNCG with extended bulge
homologous
HL_5J7L_169
HL_22622.1
HL_9H3O_0331/A/1492:1498No text annotation
HL_9H3O_0341/A/1533:1538UNCG
homologous
HL_5J7L_171
HL_34617.5
HL_9H3O_0351/A/1565:1568Mini UNCG
homologous
HL_5J7L_172
HL_48778.2
HL_9H3O_0361/A/1612:1619No text annotation
homologous
HL_9DFE_038
HL_89567.2
HL_9H3O_0371/A/1630:1636GNRA
homologous
HL_5J7L_174
HL_37824.8
HL_9H3O_0381/A/1728:1733No text annotation
HL_9H3O_0391/A/1752:1756No text annotation
homologous
HL_5J7L_177
HL_80709.3
HL_9H3O_0401/A/2027:2036No text annotation
homologous
HL_5J7L_183
HL_61996.3
HL_9H3O_0411/A/2471:2479No text annotation
homologous
HL_9DFE_058
HL_32735.2
HL_9H3O_0421/A/2528:2535Mini UNCG
geometric
HL_4LFB_005
HL_48778.2
HL_9H3O_0431/A/2551:2557No text annotation
homologous
HL_7A0S_061
HL_30068.2
HL_9H3O_0441/A/2594:2599GNRA
homologous
HL_4WF9_059
HL_37824.8
HL_9H3O_0451/A/2658:2663GNRA
homologous
HL_9DFE_062
HL_37824.8
HL_9H3O_0461/A/2701:2706Ribsomal LSU H95
homologous
HL_5J7L_198
HL_65794.5
HL_9H3O_0471/A/2746:2758No text annotation
HL_9H3O_0481/A/2796:2799No text annotation
geometric
HL_8C3A_004
NA
HL_9H3O_0491/A/2819:2827No text annotation
homologous
HL_5J7L_201
HL_64690.6
HL_9H3O_0501/A/2856:2861GNRA
homologous
HL_7A0S_068
HL_37824.8

Problematic loops

No problematic loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_9H3O_0011/A/24:30,
1/A/510:516		Triple sheared with non-canonical cWW
homologous
IL_7A0S_001
IL_04021.2
IL_9H3O_0021/A/36:37,
1/A/442:444		Single bulged A
homologous
IL_9DFE_002
IL_31462.7
IL_9H3O_0031/A/43:44,
1/A/434:436		Minor groove platform
homologous
IL_5J7L_247
IL_51454.3
IL_9H3O_0041/A/82:85,
1/A/97:104		No text annotation
IL_9H3O_0051/A/183:184,
1/A/212:215		No text annotation
IL_9H3O_0061/A/188:194,
1/A/201:208		8x7 Sarcin-Ricin; G-bulge
homologous
IL_7A0S_006
IL_04346.10
IL_9H3O_0071/A/237:239,
1/A/259:260		Single stack bend
geometric
IL_7A0S_054
IL_26793.1
IL_9H3O_0081/A/239:245,
1/A/253:259		No text annotation
IL_9H3O_0091/A/269:271,
1/A/366:370		No text annotation
homologous
IL_5J7L_252
IL_47972.1
IL_9H3O_0101/A/274:281,
1/A/359:363		No text annotation
homologous
IL_5J7L_253
IL_77870.1
IL_9H3O_0111/A/293:295,
1/A/343:347		No text annotation
homologous
IL_5J7L_254
IL_69440.3
IL_9H3O_0121/A/481:484,
1/A/496:509		No text annotation
homologous
IL_5J7L_255
IL_81516.2
IL_9H3O_0131/A/536:539,
1/A/554:557		Double sheared
homologous
IL_5J7L_256
IL_09705.15
IL_9H3O_0141/A/564:566,
1/A/575:577		Isolated non-canonical cWW pair
homologous
IL_4WF9_017
IL_07785.1
IL_9H3O_0151/A/606:610,
1/A/618:622		AAA cross-strand stack
homologous
IL_5J7L_258
IL_66798.2
IL_9H3O_0161/A/628:630,
1/A/634:635		Single stack bend
geometric
IL_8C3A_012
NA
IL_9H3O_0171/A/672:674,
1/A/806:808		Isolated non-canonical cWW pair
homologous
IL_7A0S_014
IL_87907.2
IL_9H3O_0181/A/674:678,
1/A/799:806		No text annotation
IL_9H3O_0191/A/775:777,
1/A/787:791		No text annotation
geometric
IL_8VTW_022
NA
IL_9H3O_0201/A/844:847,
1/A/933:934		90 degree turn
geometric
IL_5J7L_267
IL_90729.1
IL_9H3O_0211/A/844:848,
1/A/930:934		No text annotation
homologous
IL_5J7L_399
IL_96236.1
IL_9H3O_0221/A/847:848,
1/A/930:933		Stack outside cWW
homologous
IL_5J7L_268
IL_56987.1
IL_9H3O_0231/A/850:851,
1/A/926:928		Single stack bend
homologous
IL_5J7L_269
IL_26793.1
IL_9H3O_0241/A/856:862,
1/A/915:921		No text annotation
IL_9H3O_0251/A/862:863,
1/A/913:915		Minor groove platform
homologous
IL_4WF9_032
IL_51454.3
IL_9H3O_0261/A/994:996,
1/A/1159:1160		Single bulged C
homologous
IL_4WF9_035
IL_61258.15
IL_9H3O_0271/A/998:1002,
1/A/1153:1157		UAA/GAN
homologous
IL_5J7L_277
IL_38507.2
IL_9H3O_0281/A/1004:1011,
1/A/1150:1151		SSU/LSU pseudoknot
homologous
IL_4WF9_037
IL_41203.4
IL_9H3O_0291/A/1011:1013,
1/A/1149:1150		Single bulged U
homologous
IL_5J7L_279
IL_89505.4
IL_9H3O_0301/A/1018:1030,
1/A/1124:1144		No text annotation
IL_9H3O_0311/A/1030:1034,
1/A/1121:1124		No text annotation
IL_9H3O_0321/A/1038:1041,
1/A/1114:1117		Tandem non-canonical cWW pairs
homologous
IL_5J7L_283
IL_85033.2
IL_9H3O_0331/A/1043:1053,
1/A/1106:1112		No text annotation
IL_9H3O_0341/A/1055:1090,
1/A/1101:1104		No text annotation
IL_9H3O_0351/A/1196:1198,
1/A/1247:1250		Isolated cWS basepair
homologous
IL_7A0S_041
IL_42997.3
IL_9H3O_0361/A/1202:1206,
1/A/1240:1243		No text annotation
homologous
IL_5J7L_287
IL_91920.1
IL_9H3O_0371/A/1208:1215,
1/A/1234:1238		Kink-turn
homologous
IL_5J7L_288
IL_70923.9
IL_9H3O_0381/A/1262:1269,
1/A/2011:2017		8x7 Sarcin-Ricin; G-bulge
homologous
IL_9DFE_048
IL_04346.10
IL_9H3O_0391/A/1310:1313,
1/A/1603:1604		Major groove platform; stack outside cWW
homologous
IL_5J7L_290
IL_50694.7
IL_9H3O_0401/A/1319:1323,
1/A/1331:1333		C-loop
homologous
IL_7A0S_047
IL_83150.2
IL_9H3O_0411/A/1351:1355,
1/A/1376:1380		UAA/GAN
homologous
IL_7A0S_048
IL_89021.2
IL_9H3O_0421/A/1357:1361,
1/A/1370:1374		tSH-tHW-tHS
homologous
IL_4WF9_052
IL_17136.7
IL_9H3O_0431/A/1415:1417,
1/A/1581:1587		No text annotation
IL_9H3O_0441/A/1417:1422,
1/A/1576:1581		No text annotation
IL_9H3O_0451/A/1432:1435,
1/A/1557:1561		Tandem non-canonical cWW pairs
homologous
IL_5J7L_296
IL_58112.2
IL_9H3O_0461/A/1437:1440,
1/A/1551:1555		No text annotation
homologous
IL_9DFE_056
IL_99646.2
IL_9H3O_0471/A/1450:1451,
1/A/1459:1461		Single bulged U
homologous
IL_5J7L_298
IL_89505.4
IL_9H3O_0481/A/1468:1471,
1/A/1520:1524		No text annotation
homologous
IL_5J7L_299
IL_68574.4
IL_9H3O_0491/A/1474:1478,
1/A/1513:1517		tSH-tHW-tHS
homologous
IL_5J7L_300
IL_38862.4
IL_9H3O_0501/A/1481:1482,
1/A/1507:1510		180 degree turn
homologous
IL_5J7L_301
IL_00881.1
IL_9H3O_0511/A/1489:1491,
1/A/1499:1500		Single bulged A
geometric
IL_4L8H_001
IL_31462.7
IL_9H3O_0521/A/1526:1529,
1/A/1542:1546		UAA/GAN variation
homologous
IL_5J7L_303
IL_23774.1
IL_9H3O_0531/A/1651:1656,
1/A/2004:2006		No text annotation
homologous
IL_7A0S_059
IL_12566.4
IL_9H3O_0541/A/1663:1669,
1/A/1993:1997		No text annotation
IL_9H3O_0551/A/1663:1674,
1/A/1990:1997		No text annotation
IL_9H3O_0561/A/1669:1674,
1/A/1990:1993		Intercalated tWH
homologous
IL_4WF9_065
IL_76758.2
IL_9H3O_0571/A/1712:1718,
1/A/1742:1746		6x5 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_309
IL_88269.4
IL_9H3O_0581/A/1720:1724,
1/A/1736:1740		Triple sheared
homologous
IL_5J7L_310
IL_50730.2
IL_9H3O_0591/A/1725:1727,
1/A/1734:1735		Single stack bend
geometric
IL_7A0S_054
IL_26793.1
IL_9H3O_0601/A/2050:2052,
1/A/2617:2618		Major groove platform
homologous
IL_5J7L_320
IL_48076.6
IL_9H3O_0611/A/2457:2459,
1/A/2493:2494		Major groove platform
homologous
IL_7A0S_085
IL_48076.6
IL_9H3O_0621/A/2459:2461,
1/A/2489:2493		No text annotation
homologous
IL_9DFE_094
IL_51387.3
IL_9H3O_0631/A/2466:2470,
1/A/2480:2484		Double sheared with non-canonical cWW
homologous
IL_5J7L_338
IL_17948.2
IL_9H3O_0641/A/2507:2508,
1/A/2580:2582		Major groove platform
homologous
IL_7A0S_088
IL_07039.3
IL_9H3O_0651/A/2510:2512,
1/A/2574:2578		Isolated non-canonical cWW with bulges
homologous
IL_4WF9_095
IL_07785.1
IL_9H3O_0661/A/2512:2513,
1/A/2571:2574		Multiple bulged bases
homologous
IL_7A0S_090
IL_42626.2
IL_9H3O_0671/A/2522:2523,
1/A/2540:2543		Major groove platform with intercalation
homologous
IL_5J7L_342
IL_02555.1
IL_9H3O_0681/A/2591:2592,
1/A/2601:2603		Single bulged A
geometric
IL_2QUX_002
IL_31462.7
IL_9H3O_0691/A/2636:2640,
1/A/2774:2782		tSH-tHS-tHW
homologous
IL_7A0S_093
IL_04638.3
IL_9H3O_0701/A/2642:2644,
1/A/2771:2772		Single stack bend
geometric
IL_8C3A_012
NA
IL_9H3O_0711/A/2651:2658,
1/A/2663:2669		No text annotation
IL_9H3O_0721/A/2680:2684,
1/A/2725:2727		C-loop
homologous
IL_9DFE_103
IL_63596.11
IL_9H3O_0731/A/2687:2691,
1/A/2718:2722		UAA/GAN related, with intercalation
homologous
IL_5J7L_348
IL_23774.1
IL_9H3O_0741/A/2695:2696,
1/A/2711:2714		Multiple bulged bases
homologous
IL_5J7L_349
IL_42626.2
IL_9H3O_0751/A/2737:2742,
1/A/2762:2767		UAA/GAN with extra cWW
homologous
IL_5J7L_350
IL_49767.8
IL_9H3O_0761/A/2795:2796,
1/A/2799:2801		Single bulged A
geometric
IL_8C3A_031
NA
IL_9H3O_0771/A/2806:2811,
1/A/2889:2892		No text annotation
homologous
IL_5J7L_351
IL_29471.1
IL_9H3O_0781/A/2838:2839,
1/A/2878:2880		Major groove intercalation
homologous
IL_9DFE_107
IL_61258.15
IL_9H3O_0791/A/2843:2846,
1/A/2870:2874		Multiple bulged bases with non-canonical cWW
homologous
IL_5J7L_353
IL_64231.5
IL_9H3O_0801/A/2847:2852,
1/A/2865:2869		tHS double platform
homologous
IL_5J7L_354
IL_70411.2

Problematic loops

No problematic loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_9H3O_0011/A/30:31,
1/A/474:481,
1/A/509:510		No text annotation
homologous
J3_4WF9_010
J3_60031.2
J3_9H3O_0021/A/32:35,
1/A/445:461,
1/A/468:473		No text annotation
homologous
J3_5J7L_067
J3_30040.2
J3_9H3O_0031/A/56:57,
1/A/70:76,
1/A/110:114		No text annotation
homologous
J3_5J7L_037
J3_35667.2
J3_9H3O_0041/A/683:689,
1/A/773:775,
1/A/791:794		No text annotation
homologous
J3_7A0S_004
J3_64189.2
J3_9H3O_0051/A/1298:1303,
1/A/1625:1627,
1/A/1639:1642		No text annotation
homologous
J3_5J7L_041
J3_32852.6
J3_9H3O_0061/A/1306:1309,
1/A/1605:1611,
1/A/1620:1622		No text annotation
homologous
J3_5J7L_042
J3_19545.2
J3_9H3O_0071/A/1344:1349,
1/A/1382:1385,
1/A/1402:1403		No text annotation
homologous
J3_5J7L_043
J3_92705.1
J3_9H3O_0081/A/1423:1429,
1/A/1564:1565,
1/A/1568:1575		No text annotation
J3_9H3O_0091/A/2517:2520,
1/A/2545:2547,
1/A/2561:2567		No text annotation
homologous
J3_5J7L_046
J3_32601.5
J3_9H3O_0101/A/2789:2791,
1/A/2805:2806,
1/A/2892:2894		No text annotation
homologous
J3_5J7L_047
J3_30104.1
J3_9H3O_0111/A/2812:2815,
1/A/2831:2836,
1/A/2882:2888		No text annotation
homologous
J3_5J7L_048
J3_64069.1
J4_9H3O_0011/A/268:269,
1/A/370:375,
1/A/399:406,
1/A/421:424		No text annotation
homologous
J4_5J7L_018
J4_45801.6
J4_9H3O_0021/A/297:301,
1/A/316:319,
1/A/323:325,
1/A/337:341		No text annotation
homologous
J4_5J7L_019
J4_71729.5
J4_9H3O_0031/A/601:604,
1/A/624:628,
1/A/635:638,
1/A/650:656		No text annotation
homologous
J4_5J7L_020
J4_60168.1
J4_9H3O_0041/A/1270:1276,
1/A/1294:1295,
1/A/1645:1648,
1/A/2009:2010		No text annotation
homologous
J4_5J7L_021
J4_64571.5
J4_9H3O_0051/A/1313:1314,
1/A/1338:1343,
1/A/1404:1405,
1/A/1597:1603		No text annotation
homologous
J4_5J7L_023
J4_10313.5
J4_9H3O_0061/A/1444:1445,
1/A/1466:1467,
1/A/1525:1526,
1/A/1546:1547		No text annotation
homologous
J4_5J7L_024
J4_24280.2
J4_9H3O_0071/A/2644:2646,
1/A/2674:2676,
1/A/2731:2735,
1/A/2769:2771		No text annotation
J5_9H3O_0011/A/47:54,
1/A/116:121,
1/A/130:131,
1/A/148:152,
1/A/174:178		No text annotation
J5_9H3O_0021/A/531:533,
1/A/560:564,
1/A/577:579,
1/A/1261:1262,
1/A/2017:2018		No text annotation
homologous
J5_9DFE_003
J5_43153.5
J5_9H3O_0031/A/584:589,
1/A/668:671,
1/A/809:812,
1/A/1195:1196,
1/A/1250:1256		No text annotation
homologous
J5_5J7L_015
J5_74302.5
J5_9H3O_0041/A/1674:1682,
1/A/1706:1707,
1/A/1751:1752,
1/A/1756:1764,
1/A/1988:1990		No text annotation
homologous
J5_5J7L_016
J5_62523.6
J6_9H3O_0011/A/45:46,
1/A/179:183,
1/A/215:224,
1/A/231:235,
1/A/262:266,
1/A/426:433		No text annotation
J7_9H3O_0011/A/8:15,
1/A/525:531,
1/A/2018:2023,
1/A/2040:2043,
1/A/2625:2630,
1/A/2788:2789,
1/A/2894:2895		No text annotation
J7_9H3O_0021/A/817:822,
1/A/835:838,
1/A/940:946,
1/A/971:976,
1/A/987:991,
1/A/1163:1164,
1/A/1185:1190		No text annotation

Problematic loops

No problematic loops


Coloring options:
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