RNA 3D Hub //

8C8Z Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8C8Z_0011/A/59:68No text annotation
homologous
HL_5J7L_134
HL_35677.3
HL_8C8Z_0021/A/87:95No text annotation
homologous
HL_5J7L_135
HL_80241.1
HL_8C8Z_0031/A/123:128No text annotation
homologous
HL_4WF9_003
HL_75660.5
HL_8C8Z_0041/A/136:143No text annotation
geometric
HL_7KI3_001
HL_75660.5
HL_8C8Z_0051/A/158:168No text annotation
homologous
HL_5J7L_138
HL_68257.1
HL_8C8Z_0061/A/194:201No text annotation
homologous
HL_9DFE_005
HL_30068.2
HL_8C8Z_0071/A/225:230No text annotation
homologous
HL_5J7L_140
HL_62934.1
HL_8C8Z_0081/A/246:252No text annotation
homologous
HL_4WF9_008
HL_37369.2
HL_8C8Z_0091/A/305:312T-loop with 1 bulged base
homologous
HL_7A0S_010
HL_01609.3
HL_8C8Z_0101/A/319:323No text annotation
homologous
HL_5J7L_143
HL_75660.5
HL_8C8Z_0111/A/327:335T-loop with unstacked turn
homologous
HL_5J7L_144
HL_27670.2
HL_8C8Z_0121/A/380:394No text annotation
geometric
HL_7A0S_011
HL_75660.5
HL_8C8Z_0131/A/410:417Pseudoknot geometry
homologous
HL_7A0S_014
HL_30680.3
HL_8C8Z_0141/A/462:467GNRA
homologous
HL_4WF9_015
HL_37824.8
HL_8C8Z_0151/A/487:493GNRA
homologous
HL_5J7L_148
HL_37824.8
HL_8C8Z_0161/A/543:550No text annotation
geometric
HL_2Y8W_001
HL_81100.2
HL_8C8Z_0171/A/566:575No text annotation
homologous
HL_7RQB_018
NA
HL_8C8Z_0181/A/611:617No text annotation
homologous
HL_5J7L_151
HL_80922.2
HL_8C8Z_0191/A/629:634GNRA
homologous
HL_5J7L_152
HL_37824.8
HL_8C8Z_0201/A/641:647No text annotation
homologous
HL_5J7L_153
HL_13529.1
HL_8C8Z_0221/A/824:833No text annotation
HL_8C8Z_0231/A/953:964No text annotation
HL_8C8Z_0241/A/978:985No text annotation
homologous
HL_7RQB_028
NA
HL_8C8Z_0251/A/1172:1177No text annotation
geometric
HL_7RQB_011
NA
HL_8C8Z_0261/A/1222:1227GNRA
homologous
HL_5J7L_164
HL_37824.8
HL_8C8Z_0271/A/1281:1289T-loop with 2 stacked bulged bases
homologous
HL_5J7L_165
HL_28252.9
HL_8C8Z_0281/A/1324:1330Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_166
HL_57176.2
HL_8C8Z_0291/A/1363:1368GNRA
homologous
HL_5J7L_167
HL_37824.8
HL_8C8Z_0301/A/1389:1398No text annotation
homologous
HL_5J7L_168
HL_81545.2
HL_8C8Z_0311/A/1451:1459Mini UNCG with extended bulge
homologous
HL_5J7L_169
HL_22622.1
HL_8C8Z_0321/A/1491:1499No text annotation
geometric
HL_4WF9_011
HL_75660.5
HL_8C8Z_0331/A/1533:1538UNCG
homologous
HL_5J7L_171
HL_34617.5
HL_8C8Z_0341/A/1565:1568No text annotation
homologous
HL_7RQB_039
NA
HL_8C8Z_0351/A/1612:1619No text annotation
homologous
HL_4WF9_038
HL_89567.2
HL_8C8Z_0361/A/1630:1636GNRA
homologous
HL_5J7L_174
HL_37824.8
HL_8C8Z_0371/A/1728:1731Mini UNCG
geometric
HL_4WF9_037
HL_48778.2
HL_8C8Z_0381/A/1752:1756No text annotation
homologous
HL_7RQB_044
NA
HL_8C8Z_0391/A/2027:2036No text annotation
homologous
HL_4WF9_047
HL_61996.3
HL_8C8Z_0411/A/2209:2215No text annotation
HL_8C8Z_0421/A/2246:2258No text annotation
HL_8C8Z_0431/A/2264:2276No text annotation
homologous
HL_5J7L_187
HL_91939.2
HL_8C8Z_0441/A/2303:2313No text annotation
homologous
HL_7RQB_055
NA
HL_8C8Z_0451/A/2324:2331Pseudoknot geometry
homologous
HL_7RQB_056
NA
HL_8C8Z_0461/A/2356:2361GNRA
homologous
HL_5J7L_190
HL_37824.8
HL_8C8Z_0471/A/2374:2379GNRA
homologous
HL_7A0S_057
HL_37824.8
HL_8C8Z_0481/A/2404:2413No text annotation
homologous
HL_4WF9_055
HL_53454.2
HL_8C8Z_0491/A/2658:2663GNRA
geometric
HL_5FQ5_003
HL_37824.8
HL_8C8Z_0501/A/2701:2706Ribsomal LSU H95
homologous
HL_5J7L_198
HL_65794.5
HL_8C8Z_0511/A/2745:2759No text annotation
homologous
HL_5J7L_199
HL_74055.2
HL_8C8Z_0521/A/2796:2799Mini UNCG
geometric
HL_4V88_192
NA
HL_8C8Z_0531/A/2819:2827No text annotation
homologous
HL_5J7L_201
HL_64690.6
HL_8C8Z_0541/A/2856:2861GNRA
homologous
HL_7A0S_068
HL_37824.8
HL_8C8Z_0551/B/38:44No text annotation
homologous
HL_5J7L_203
HL_47787.2
HL_8C8Z_0561/B/86:90Mini UNCG
homologous
HL_5J7L_204
HL_48778.2

Problematic loops

#loop idProblemSequence
HL_8C8Z_021No text annotation
HL_8C8Z_040No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8C8Z_0011/A/24:30,
1/A/510:516		Triple sheared with non-canonical cWW
geometric
IL_7RQB_001
NA
IL_8C8Z_0021/A/36:37,
1/A/442:444		Single bulged A
homologous
IL_7RQB_002
NA
IL_8C8Z_0031/A/43:44,
1/A/434:436		Minor groove platform
homologous
IL_5J7L_247
IL_51454.3
IL_8C8Z_0861/A/82:85,
1/A/97:104		No text annotation
IL_8C8Z_0051/A/183:184,
1/A/212:214		Single stack bend
homologous
IL_7A0S_005
IL_90729.1
IL_8C8Z_0061/A/188:194,
1/A/201:208		8x7 Sarcin-Ricin; G-bulge
geometric
IL_7A0S_006
IL_04346.10
IL_8C8Z_0071/A/239:245,
1/A/253:258		7x6 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_251
IL_26307.2
IL_8C8Z_0081/A/269:271,
1/A/366:370		No text annotation
homologous
IL_5J7L_252
IL_47972.1
IL_8C8Z_0091/A/273:275,
1/A/363:364		Single stack bend
geometric
IL_7A0S_054
IL_26793.1
IL_8C8Z_0871/A/273:281,
1/A/359:364		No text annotation
IL_8C8Z_0101/A/275:281,
1/A/359:363		No text annotation
IL_8C8Z_0111/A/293:295,
1/A/343:347		No text annotation
homologous
IL_5J7L_254
IL_69440.3
IL_8C8Z_0121/A/481:484,
1/A/496:509		No text annotation
geometric
IL_5J7L_255
IL_81516.2
IL_8C8Z_0131/A/536:539,
1/A/554:557		Double sheared
homologous
IL_5J7L_256
IL_09705.15
IL_8C8Z_0141/A/564:566,
1/A/575:577		Isolated non-canonical cWW pair
geometric
IL_4ZC7_004
IL_87907.2
IL_8C8Z_0151/A/606:610,
1/A/618:622		AAA cross-strand stack
homologous
IL_5J7L_258
IL_66798.2
IL_8C8Z_0161/A/672:674,
1/A/806:808		Isolated non-canonical cWW pair
geometric
IL_4YHW_001
IL_87907.2
IL_8C8Z_0171/A/674:678,
1/A/799:806		tHW-tHW cross-strand stack
homologous
IL_7RQB_018
NA
IL_8C8Z_0181/A/844:847,
1/A/933:934		Other IL
geometric
IL_5J7L_267
IL_90729.1
IL_8C8Z_0881/A/844:848,
1/A/930:934		No text annotation
geometric
IL_5J7L_399
IL_96236.1
IL_8C8Z_0191/A/847:848,
1/A/930:933		Stack outside cWW
homologous
IL_5J7L_268
IL_56987.1
IL_8C8Z_0201/A/850:851,
1/A/926:928		Single stack bend
homologous
IL_5J7L_269
IL_26793.1
IL_8C8Z_0211/A/854:856,
1/A/922:923		Single stack bend
geometric
IL_5J7L_032
IL_26793.1
IL_8C8Z_0221/A/857:862,
1/A/915:921		No text annotation
IL_8C8Z_0231/A/862:863,
1/A/913:915		Minor groove platform
homologous
IL_7A0S_028
IL_51454.3
IL_8C8Z_0241/A/864:868,
1/A/909:912		C-loop with bulged stacked A's
homologous
IL_4WF9_033
IL_26222.2
IL_8C8Z_0251/A/870:872,
1/A/905:907		Isolated non-canonical cWW pair
homologous
IL_5J7L_273
IL_28037.2
IL_8C8Z_0261/A/875:879,
1/A/898:902		Triple sheared
homologous
IL_5J7L_274
IL_17948.2
IL_8C8Z_0271/A/994:996,
1/A/1159:1160		Single bulged C
homologous
IL_7RQB_035
NA
IL_8C8Z_0281/A/998:1002,
1/A/1153:1157		UAA/GAN
homologous
IL_4WF9_036
IL_38507.2
IL_8C8Z_0291/A/1004:1011,
1/A/1150:1151		SSU/LSU pseudoknot
homologous
IL_5J7L_278
IL_41203.4
IL_8C8Z_0301/A/1011:1013,
1/A/1149:1150		Single bulged U
geometric
IL_5J7L_279
IL_89505.4
IL_8C8Z_0311/A/1018:1024,
1/A/1140:1144		Kink-turn related
geometric
IL_4WF9_039
IL_57188.5
IL_8C8Z_0321/A/1024:1030,
1/A/1124:1140		No text annotation
IL_8C8Z_0331/A/1031:1034,
1/A/1121:1123		Isolated non-canonical cWW pair
homologous
IL_4WF9_041
IL_57744.1
IL_8C8Z_0341/A/1038:1041,
1/A/1114:1117		Tandem non-canonical cWW pairs
homologous
IL_5J7L_283
IL_85033.2
IL_8C8Z_0351/A/1196:1198,
1/A/1247:1250		Isolated cWS basepair
homologous
IL_4WF9_044
IL_42997.3
IL_8C8Z_0361/A/1202:1206,
1/A/1240:1243		No text annotation
homologous
IL_5J7L_287
IL_91920.1
IL_8C8Z_0371/A/1208:1215,
1/A/1234:1238		Kink-turn
homologous
IL_5J7L_288
IL_70923.9
IL_8C8Z_0381/A/1262:1269,
1/A/2011:2017		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
IL_04346.10
IL_8C8Z_0391/A/1310:1313,
1/A/1603:1604		Major groove platform; stack outside cWW
homologous
IL_5J7L_290
IL_50694.7
IL_8C8Z_0401/A/1319:1323,
1/A/1331:1333		Major groove minor groove platform with tHH
homologous
IL_4WF9_050
IL_83150.2
IL_8C8Z_0411/A/1351:1353,
1/A/1379:1380		Single stack bend
geometric
IL_6FZ0_001
IL_90729.1
IL_8C8Z_0901/A/1351:1355,
1/A/1376:1380		UAA/GAN
homologous
IL_7A0S_048
IL_89021.2
IL_8C8Z_0421/A/1353:1355,
1/A/1376:1379		No text annotation
IL_8C8Z_0431/A/1357:1361,
1/A/1370:1374		tSH-tHW-tHS
homologous
IL_4WF9_052
IL_17136.7
IL_8C8Z_0441/A/1415:1421,
1/A/1577:1587		No text annotation
IL_8C8Z_0921/A/1422:1424,
1/A/1575:1576		Single stack bend
geometric
IL_4WF9_089
IL_26793.1
IL_8C8Z_0461/A/1432:1435,
1/A/1557:1561		Tandem non-canonical cWW pairs
homologous
IL_5J7L_296
IL_58112.2
IL_8C8Z_0471/A/1437:1440,
1/A/1551:1555		tSH-tHW
homologous
IL_5J7L_297
IL_99646.2
IL_8C8Z_0481/A/1450:1451,
1/A/1459:1461		Single bulged U
geometric
IL_5J7L_298
IL_89505.4
IL_8C8Z_0491/A/1468:1471,
1/A/1520:1524		No text annotation
homologous
IL_5J7L_299
IL_68574.4
IL_8C8Z_0501/A/1474:1478,
1/A/1513:1517		tSH-tHW-tHS
homologous
IL_5J7L_300
IL_38862.4
IL_8C8Z_0511/A/1481:1482,
1/A/1507:1510		180 degree turn
homologous
IL_5J7L_301
IL_00881.1
IL_8C8Z_0531/A/1489:1491,
1/A/1499:1500		Single bulged A
geometric
IL_4P43_003
NA
IL_8C8Z_0541/A/1526:1529,
1/A/1542:1546		UAA/GAN variation
homologous
IL_5J7L_303
IL_23774.1
IL_8C8Z_0551/A/1651:1656,
1/A/2004:2006		No text annotation
homologous
IL_5J7L_304
IL_12566.4
IL_8C8Z_0561/A/1712:1718,
1/A/1742:1746		6x5 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_309
IL_88269.4
IL_8C8Z_0571/A/1720:1726,
1/A/1734:1740		No text annotation
IL_8C8Z_0581/A/1727:1728,
1/A/1731:1733		Single bulged C
geometric
IL_5J7L_311
IL_61258.15
IL_8C8Z_0591/A/2050:2052,
1/A/2617:2618		Major groove platform
homologous
IL_7RQB_078
NA
IL_8C8Z_0601/A/2053:2056,
1/A/2612:2616		No text annotation
IL_8C8Z_0611/A/2067:2069,
1/A/2442:2443		No text annotation
IL_8C8Z_0621/A/2070:2071,
1/A/2438:2441		Minor groove platform
homologous
IL_7RQB_081
NA
IL_8C8Z_0911/A/2081:2083,
1/A/2236:2239		Isolated tHS basepair with bulges
homologous
IL_4WF9_082
IL_85599.2
IL_8C8Z_0641/A/2085:2087,
1/A/2232:2234		No text annotation
homologous
IL_7RQB_083
NA
IL_8C8Z_0651/A/2202:2204,
1/A/2220:2221		Single bulged U
homologous
IL_5J7L_331
IL_89505.4
IL_8C8Z_0661/A/2350:2353,
1/A/2364:2367		Double sheared
homologous
IL_7RQB_089
NA
IL_8C8Z_0671/A/2398:2400,
1/A/2417:2418		Single stack bend
geometric
IL_7A0S_054
IL_26793.1
IL_8C8Z_0681/A/2400:2401,
1/A/2415:2417		Single stack bend
geometric
IL_7A0S_054
IL_26793.1
IL_8C8Z_0691/A/2401:2403,
1/A/2414:2415		No text annotation
IL_8C8Z_0701/A/2636:2640,
1/A/2774:2782		tSH-tHS-tHW
homologous
IL_7RQB_102
NA
IL_8C8Z_0711/A/2652:2658,
1/A/2663:2668		Sarcin-Ricin target in LSU H95; G-bulge
homologous
IL_7A0S_094
IL_16458.4
IL_8C8Z_0721/A/2680:2684,
1/A/2725:2727		C-loop
homologous
IL_5J7L_347
IL_63596.11
IL_8C8Z_0731/A/2687:2691,
1/A/2718:2722		No text annotation
homologous
IL_5J7L_348
IL_23774.1
IL_8C8Z_0741/A/2695:2696,
1/A/2711:2714		Multiple bulged bases
homologous
IL_4WF9_103
IL_42626.2
IL_8C8Z_0751/A/2737:2742,
1/A/2762:2767		UAA/GAN with extra cWW
homologous
IL_7RQB_107
NA
IL_8C8Z_0761/A/2795:2796,
1/A/2799:2801		Single bulged A
geometric
IL_7RQB_019
NA
IL_8C8Z_0771/A/2806:2811,
1/A/2889:2892		No text annotation
geometric
IL_5J7L_351
IL_29471.1
IL_8C8Z_0781/A/2838:2839,
1/A/2878:2880		Major groove intercalation
homologous
IL_5J7L_352
IL_66635.5
IL_8C8Z_0791/A/2843:2846,
1/A/2870:2874		Multiple bulged bases with non-canonical cWW
homologous
IL_5J7L_353
IL_64231.5
IL_8C8Z_0801/A/2847:2852,
1/A/2865:2869		tHS double platform
homologous
IL_5J7L_354
IL_70411.2
IL_8C8Z_0811/B/17:18,
1/B/65:67		Major groove intercalation
homologous
IL_4WF9_112
IL_31462.7
IL_8C8Z_0821/B/23:28,
1/B/56:60		No text annotation
homologous
IL_7RQB_112
NA
IL_8C8Z_0831/B/30:31,
1/B/51:54		No text annotation
IL_8C8Z_0841/B/34:38,
1/B/44:48		Symmetric double minor groove platform
geometric
IL_5J7L_358
IL_58103.11
IL_8C8Z_0851/B/71:79,
1/B/97:105		Bacterial 5S Loop E
homologous
IL_5J7L_359
IL_56455.6

Problematic loops

#loop idProblemSequence
IL_8C8Z_004No text annotation
IL_8C8Z_089No text annotation
IL_8C8Z_045No text annotation
IL_8C8Z_052No text annotation
IL_8C8Z_063Double sheared

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8C8Z_0011/A/30:31,
1/A/474:481,
1/A/509:510		No text annotation
homologous
J3_5J7L_036
J3_60031.2
J3_8C8Z_0111/A/32:35,
1/A/445:461,
1/A/468:473		No text annotation
homologous
J3_5J7L_067
J3_30040.2
J3_8C8Z_0021/A/56:57,
1/A/70:76,
1/A/110:114		No text annotation
homologous
J3_5J7L_037
J3_35667.2
J3_8C8Z_0121/A/297:301,
1/A/316:325,
1/A/337:341		No text annotation
homologous
J3_5J7L_068
J3_46299.2
J3_8C8Z_0031/A/1298:1303,
1/A/1625:1627,
1/A/1639:1642		No text annotation
homologous
J3_5J7L_041
J3_32852.6
J3_8C8Z_0041/A/1306:1309,
1/A/1605:1612,
1/A/1619:1622		No text annotation
J3_8C8Z_0051/A/1344:1349,
1/A/1382:1385,
1/A/1402:1403		No text annotation
homologous
J3_5J7L_043
J3_92705.1
J3_8C8Z_0131/A/1424:1429,
1/A/1564:1565,
1/A/1568:1575		No text annotation
J3_8C8Z_0061/A/2091:2093,
1/A/2196:2200,
1/A/2223:2228		Kink-turn in J3
homologous
J3_5J7L_044
J3_89368.5
J3_8C8Z_0071/A/2295:2299,
1/A/2317:2323,
1/A/2332:2337		No text annotation
homologous
J3_5J7L_071
J3_44961.1
J3_8C8Z_0081/A/2789:2791,
1/A/2805:2806,
1/A/2892:2894		No text annotation
homologous
J3_5J7L_047
J3_30104.1
J3_8C8Z_0091/A/2812:2815,
1/A/2831:2836,
1/A/2882:2888		No text annotation
homologous
J3_5J7L_048
J3_64069.1
J3_8C8Z_0101/B/10:16,
1/B/68:70,
1/B/106:110		No text annotation
homologous
J3_7A0S_014
NA
J4_8C8Z_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_8C8Z_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_8C8Z_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_8C8Z_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_8C8Z_0051/A/1310:1314,
1/A/1338:1343,
1/A/1404:1405,
1/A/1597:1604		No text annotation
homologous
J4_5J7L_022
J4_69051.6
J4_8C8Z_0061/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_8C8Z_0071/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_8C8Z_0081/A/2643:2646,
1/A/2674:2676,
1/A/2731:2735,
1/A/2769:2771		No text annotation
homologous
J4_5J7L_028
J4_77044.4
J5_8C8Z_0061/A/47:54,
1/A/116:121,
1/A/130:131,
1/A/148:150,
1/A/176:178		No text annotation
homologous
J5_5J7L_013
J5_01737.2
J5_8C8Z_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_5J7L_014
J5_43153.5
J5_8C8Z_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_8C8Z_0041/A/2074:2078,
1/A/2242:2246,
1/A/2258:2259,
1/A/2281:2282,
1/A/2427:2435		No text annotation
J5_8C8Z_0051/A/2282:2289,
1/A/2343:2347,
1/A/2370:2372,
1/A/2381:2395,
1/A/2421:2427		No text annotation
J6_8C8Z_0011/A/45:46,
1/A/179:183,
1/A/214:224,
1/A/231:235,
1/A/262:266,
1/A/426:433		No text annotation
J7_8C8Z_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_8C8Z_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

#loop idProblemSequence
J5_8C8Z_001No text annotation

Coloring options:
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