RNA 3D Hub //

8C8Y Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8C8Y_0011/A/59:68No text annotation
homologous
HL_5J7L_134
NA
HL_8C8Y_0021/A/87:95No text annotation
homologous
HL_5J7L_135
NA
HL_8C8Y_0031/A/123:128No text annotation
homologous
HL_4WF9_003
HL_75660.6
HL_8C8Y_0651/A/137:142No text annotation
HL_8C8Y_0051/A/158:168No text annotation
homologous
HL_5J7L_138
NA
HL_8C8Y_0071/A/225:230No text annotation
homologous
HL_5J7L_140
NA
HL_8C8Y_0081/A/246:252No text annotation
homologous
HL_4WF9_008
HL_76371.1
HL_8C8Y_0091/A/305:312T-loop with 1 bulged base
homologous
HL_7A0S_010
HL_13999.1
HL_8C8Y_0101/A/319:323No text annotation
homologous
HL_5J7L_143
NA
HL_8C8Y_0111/A/327:335T-loop with unstacked turn
homologous
HL_5J7L_144
NA
HL_8C8Y_0121/A/381:393No text annotation
homologous
HL_4WF9_013
HL_69139.1
HL_8C8Y_0131/A/410:417Pseudoknot geometry
homologous
HL_7A0S_014
HL_30680.4
HL_8C8Y_0141/A/462:467GNRA
homologous
HL_4WF9_015
HL_34789.1
HL_8C8Y_0151/A/487:493GNRA
homologous
HL_5J7L_148
NA
HL_8C8Y_0161/A/543:550No text annotation
homologous
HL_7RQB_017
NA
HL_8C8Y_0171/A/566:575T-loop with 2 stacked bulged bases
homologous
HL_5J7L_150
NA
HL_8C8Y_0181/A/611:617No text annotation
homologous
HL_5J7L_151
NA
HL_8C8Y_0191/A/629:634GNRA
homologous
HL_5J7L_152
NA
HL_8C8Y_0631/A/641:647GNRA
homologous
HL_4WF9_021
HL_34789.1
HL_8C8Y_0221/A/744:753No text annotation
homologous
HL_4WF9_023
HL_50204.1
HL_8C8Y_0231/A/779:785No text annotation
geometric
HL_5U3G_001
NA
HL_8C8Y_0261/A/978:985No text annotation
homologous
HL_5J7L_160
NA
HL_8C8Y_0281/A/1222:1227GNRA
homologous
HL_5J7L_164
NA
HL_8C8Y_0291/A/1281:1289T-loop with 2 stacked bulged bases
homologous
HL_5J7L_165
NA
HL_8C8Y_0301/A/1324:1330Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_166
NA
HL_8C8Y_0311/A/1363:1368GNRA
homologous
HL_5J7L_167
NA
HL_8C8Y_0321/A/1389:1398No text annotation
homologous
HL_5J7L_168
NA
HL_8C8Y_0331/A/1451:1459Mini UNCG with extended bulge
homologous
HL_5J7L_169
NA
HL_8C8Y_0341/A/1492:1498Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_170
NA
HL_8C8Y_0361/A/1565:1568No text annotation
homologous
HL_7RQB_039
NA
HL_8C8Y_0371/A/1612:1619No text annotation
homologous
HL_7RQB_040
NA
HL_8C8Y_0381/A/1630:1636GNRA
homologous
HL_5J7L_174
NA
HL_8C8Y_0391/A/1691:1696No text annotation
homologous
HL_7RQB_042
NA
HL_8C8Y_0401/A/1727:1733No text annotation
homologous
HL_5J7L_214
NA
HL_8C8Y_0411/A/1752:1756No text annotation
homologous
HL_7RQB_044
NA
HL_8C8Y_0421/A/1777:1787No text annotation
homologous
HL_4WF9_043
HL_87681.1
HL_8C8Y_0431/A/1806:1811GNRA related
homologous
HL_5J7L_179
NA
HL_8C8Y_0461/A/2027:2036No text annotation
homologous
HL_4WF9_047
HL_78372.1
HL_8C8Y_0481/A/2209:2215No text annotation
homologous
HL_5J7L_185
NA
HL_8C8Y_0501/A/2264:2276No text annotation
homologous
HL_5J7L_187
NA
HL_8C8Y_0531/A/2374:2379GNRA
homologous
HL_7RQB_058
NA
HL_8C8Y_0541/A/2404:2413No text annotation
homologous
HL_7A0S_058
HL_51853.1
HL_8C8Y_0561/A/2701:2706Ribsomal LSU H95
homologous
HL_5J7L_198
NA
HL_8C8Y_0581/A/2796:2799Mini UNCG
geometric
HL_4V88_192
NA
HL_8C8Y_0591/A/2819:2827No text annotation
homologous
HL_5J7L_201
NA
HL_8C8Y_0601/A/2856:2861GNRA
homologous
HL_7A0S_068
HL_34789.1

Problematic loops

#loop idProblemSequence
HL_8C8Y_004No text annotation
HL_8C8Y_006No text annotation
HL_8C8Y_020GNRA wlth extra near cWW
HL_8C8Y_021GNRA wlth tandem sheared
HL_8C8Y_024No text annotation
HL_8C8Y_025GNRA
HL_8C8Y_027No text annotation
HL_8C8Y_035UNCG
HL_8C8Y_044No text annotation
HL_8C8Y_045Externally structured
HL_8C8Y_064No text annotation
HL_8C8Y_047No text annotation
HL_8C8Y_049Externally structured
HL_8C8Y_051No text annotation
HL_8C8Y_066No text annotation
HL_8C8Y_052GNRA
HL_8C8Y_055GNRA
HL_8C8Y_057No text annotation
HL_8C8Y_061No text annotation
HL_8C8Y_062Mini UNCG

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8C8Y_0011/A/24:30,
1/A/510:516		Triple sheared with non-canonical cWW
homologous
IL_4WF9_001
IL_22311.1
IL_8C8Y_0021/A/36:37,
1/A/442:444		Single bulged A
homologous
IL_7RQB_002
NA
IL_8C8Y_0031/A/43:44,
1/A/434:436		Minor groove platform
homologous
IL_5J7L_247
NA
IL_8C8Y_0961/A/82:85,
1/A/97:104		Kink-turn
geometric
IL_1U63_003
IL_24134.1
IL_8C8Y_0051/A/183:184,
1/A/212:214		Single stack bend
homologous
IL_7A0S_005
IL_15011.1
IL_8C8Y_0061/A/188:194,
1/A/201:208		8x7 Sarcin-Ricin; G-bulge
homologous
IL_7A0S_006
IL_62167.1
IL_8C8Y_0071/A/239:245,
1/A/253:258		7x6 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_251
NA
IL_8C8Y_0081/A/269:271,
1/A/366:370		No text annotation
homologous
IL_5J7L_252
NA
IL_8C8Y_0101/A/293:295,
1/A/343:347		No text annotation
homologous
IL_5J7L_254
NA
IL_8C8Y_0111/A/481:484,
1/A/496:509		No text annotation
geometric
IL_5J7L_255
NA
IL_8C8Y_0121/A/536:539,
1/A/554:557		Double sheared
homologous
IL_5J7L_256
NA
IL_8C8Y_0131/A/564:566,
1/A/575:577		Isolated non-canonical cWW pair
geometric
IL_5TBW_034
NA
IL_8C8Y_0141/A/606:610,
1/A/618:622		AAA cross-strand stack
homologous
IL_5J7L_258
NA
IL_8C8Y_0151/A/672:674,
1/A/806:808		Isolated non-canonical cWW pair
geometric
IL_4WF9_020
IL_01003.1
IL_8C8Y_0161/A/674:678,
1/A/799:806		tHW-tHW cross-strand stack
homologous
IL_7RQB_018
NA
IL_8C8Y_0171/A/697:698,
1/A/763:765		Single bulged A
geometric
IL_4V9F_025
IL_14190.1
IL_8C8Y_0181/A/702:703,
1/A/728:730		Single bulged G
homologous
IL_7RQB_020
NA
IL_8C8Y_0191/A/703:707,
1/A/724:728		Triple sheared
geometric
IL_4WF9_024
IL_15190.1
IL_8C8Y_0201/A/738:740,
1/A/757:758		Major groove platform
homologous
IL_4WF9_026
IL_48076.7
IL_8C8Y_0211/A/775:777,
1/A/787:791		Multiple bulged bases
geometric
IL_4V9F_030
IL_57881.1
IL_8C8Y_0221/A/844:847,
1/A/933:934		90 degree turn
geometric
IL_5J7L_267
NA
IL_8C8Y_0981/A/844:848,
1/A/930:934		No text annotation
homologous
IL_5J7L_399
NA
IL_8C8Y_0231/A/847:848,
1/A/930:933		Stack outside cWW
homologous
IL_5J7L_268
NA
IL_8C8Y_0241/A/850:851,
1/A/926:928		Single stack bend
homologous
IL_5J7L_269
NA
IL_8C8Y_0251/A/856:862,
1/A/915:921		7x7 Sarcin-Ricin with intercalated A; G-bulge
geometric
IL_5J7L_270
NA
IL_8C8Y_0261/A/862:863,
1/A/913:915		Single bulged G
homologous
IL_5J7L_271
NA
IL_8C8Y_0291/A/994:996,
1/A/1159:1160		Single bulged C
homologous
IL_7RQB_035
NA
IL_8C8Y_0301/A/998:1002,
1/A/1153:1157		UAA/GAN
homologous
IL_5J7L_277
NA
IL_8C8Y_0311/A/1004:1011,
1/A/1150:1151		SSU/LSU pseudoknot
homologous
IL_4WF9_037
IL_11411.1
IL_8C8Y_0321/A/1011:1013,
1/A/1149:1150		Single bulged U
geometric
IL_5J7L_279
NA
IL_8C8Y_0331/A/1018:1024,
1/A/1140:1144		Kink-turn related
homologous
IL_4WF9_039
IL_57188.6
IL_8C8Y_0341/A/1024:1030,
1/A/1124:1140		No text annotation
homologous
IL_5J7L_281
NA
IL_8C8Y_0371/A/1196:1198,
1/A/1247:1250		Isolated cWS basepair
homologous
IL_4WF9_044
IL_42997.4
IL_8C8Y_0381/A/1202:1206,
1/A/1240:1243		No text annotation
homologous
IL_5J7L_287
NA
IL_8C8Y_0391/A/1208:1215,
1/A/1234:1238		Kink-turn
homologous
IL_5J7L_288
NA
IL_8C8Y_0401/A/1262:1269,
1/A/2011:2017		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
NA
IL_8C8Y_0411/A/1310:1313,
1/A/1603:1604		Major groove platform; stack outside cWW
homologous
IL_7RQB_050
NA
IL_8C8Y_0421/A/1319:1323,
1/A/1331:1333		Major groove minor groove platform with tHH
homologous
IL_4WF9_050
IL_06671.1
IL_8C8Y_0431/A/1351:1355,
1/A/1376:1380		UAA/GAN
homologous
IL_7A0S_048
IL_89021.3
IL_8C8Y_0441/A/1357:1361,
1/A/1370:1374		tSH-tHW-tHS
homologous
IL_5J7L_293
NA
IL_8C8Y_0451/A/1415:1416,
1/A/1582:1587		No text annotation
homologous
IL_5J7L_294
NA
IL_8C8Y_0461/A/1417:1421,
1/A/1577:1581		UAA/GAN
homologous
IL_5J7L_295
NA
IL_8C8Y_0471/A/1432:1435,
1/A/1557:1561		Tandem non-canonical cWW pairs
homologous
IL_5J7L_296
NA
IL_8C8Y_0481/A/1437:1440,
1/A/1551:1555		tSH-tHW
homologous
IL_5J7L_297
NA
IL_8C8Y_0491/A/1450:1451,
1/A/1459:1461		Single bulged U
geometric
IL_5J7L_298
NA
IL_8C8Y_0501/A/1468:1471,
1/A/1520:1524		No text annotation
homologous
IL_5J7L_299
NA
IL_8C8Y_0511/A/1474:1478,
1/A/1513:1517		tSH-tHW-tHS
homologous
IL_5J7L_300
NA
IL_8C8Y_0521/A/1481:1482,
1/A/1507:1510		180 degree turn
homologous
IL_5J7L_301
NA
IL_8C8Y_0531/A/1489:1491,
1/A/1499:1500		Single bulged A
homologous
IL_5J7L_302
NA
IL_8C8Y_0541/A/1526:1529,
1/A/1542:1546		UAA/GAN variation
homologous
IL_5J7L_303
NA
IL_8C8Y_0551/A/1651:1656,
1/A/2004:2006		No text annotation
homologous
IL_5J7L_304
NA
IL_8C8Y_0561/A/1663:1665,
1/A/1995:1997		Isolated tWW turn
homologous
IL_5J7L_305
NA
IL_8C8Y_0571/A/1666:1669,
1/A/1993:1994		Major groove platform; stack outside cWW
geometric
IL_7RQB_066
NA
IL_8C8Y_0991/A/1666:1674,
1/A/1990:1994		No text annotation
homologous
IL_4WF9_117
IL_80252.1
IL_8C8Y_0581/A/1669:1674,
1/A/1990:1993		Intercalated tWH
homologous
IL_4WF9_065
IL_28217.1
IL_8C8Y_0591/A/1686:1691,
1/A/1696:1702		tSH-tSH-tHH-tHS
geometric
IL_5J7L_308
NA
IL_8C8Y_0601/A/1712:1718,
1/A/1742:1746		6x5 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_309
NA
IL_8C8Y_0611/A/1720:1724,
1/A/1736:1740		Triple sheared
homologous
IL_5J7L_310
NA
IL_8C8Y_0621/A/1770:1771,
1/A/1980:1982		Single bulged A
homologous
IL_4WF9_068
IL_14190.1
IL_8C8Y_0631/A/1798:1804,
1/A/1813:1821		Kink-turn related
homologous
IL_7A0S_065
IL_17069.6
IL_8C8Y_0651/A/2050:2052,
1/A/2617:2618		Major groove platform
homologous
IL_5J7L_320
NA
IL_8C8Y_0661/A/2054:2056,
1/A/2612:2615		No text annotation
IL_8C8Y_0701/A/2085:2087,
1/A/2232:2234		No text annotation
homologous
IL_7RQB_083
NA
IL_8C8Y_0761/A/2202:2204,
1/A/2220:2221		Single bulged U
homologous
IL_5J7L_331
NA
IL_8C8Y_0781/A/2350:2353,
1/A/2364:2367		Double sheared
homologous
IL_7RQB_089
NA
IL_8C8Y_0791/A/2401:2403,
1/A/2414:2415		Single bulged U
geometric
IL_5LYS_008
IL_97561.1
IL_8C8Y_0801/A/2636:2640,
1/A/2774:2782		tSH-tHS-tHW
homologous
IL_7RQB_102
NA
IL_8C8Y_0821/A/2680:2684,
1/A/2725:2727		C-loop
homologous
IL_5J7L_347
NA
IL_8C8Y_0831/A/2687:2691,
1/A/2718:2722		UAA/GAN related, with intercalation
homologous
IL_5J7L_348
NA
IL_8C8Y_0841/A/2695:2696,
1/A/2711:2714		Multiple bulged bases
homologous
IL_5J7L_349
NA
IL_8C8Y_0851/A/2737:2742,
1/A/2762:2767		UAA/GAN with extra cWW
homologous
IL_5J7L_350
NA
IL_8C8Y_0861/A/2795:2796,
1/A/2799:2801		Single bulged A
geometric
IL_7RQB_019
NA
IL_8C8Y_0871/A/2806:2811,
1/A/2889:2892		No text annotation
homologous
IL_5J7L_351
NA
IL_8C8Y_0881/A/2838:2839,
1/A/2878:2880		Major groove intercalation
homologous
IL_4WF9_106
IL_78536.1
IL_8C8Y_0891/A/2843:2846,
1/A/2870:2874		Multiple bulged bases with non-canonical cWW
homologous
IL_5J7L_353
NA
IL_8C8Y_0901/A/2847:2852,
1/A/2865:2869		tHS double platform
homologous
IL_5J7L_354
NA
IL_8C8Y_0951/B/71:79,
1/B/97:105		Bacterial 5S Loop E
homologous
IL_5J7L_359
NA

Problematic loops

#loop idProblemSequence
IL_8C8Y_004No text annotation
IL_8C8Y_009No text annotation
IL_8C8Y_097Isolated non-canonical cWW pair
IL_8C8Y_027C-loop with bulged stacked A's
IL_8C8Y_028Isolated non-canonical cWW pair
IL_8C8Y_035Isolated non-canonical cWW pair
IL_8C8Y_036Tandem non-canonical cWW pairs
IL_8C8Y_064Minor groove platform, major groove intercalation
IL_8C8Y_067No text annotation
IL_8C8Y_068Multiple bulged bases
IL_8C8Y_100No text annotation
IL_8C8Y_069No text annotation
IL_8C8Y_101Tandem non-canonical cWW pairs
IL_8C8Y_071Isolated non-canonical cWW with bulges
IL_8C8Y_072No text annotation
IL_8C8Y_102No text annotation
IL_8C8Y_073No text annotation
IL_8C8Y_103No text annotation
IL_8C8Y_074Kink-turn related
IL_8C8Y_075No text annotation
IL_8C8Y_104No text annotation
IL_8C8Y_105No text annotation
IL_8C8Y_077No text annotation
IL_8C8Y_0817x6 Sarcin-Ricin; G-bulge
IL_8C8Y_091Major groove intercalation
IL_8C8Y_092No text annotation
IL_8C8Y_093No text annotation
IL_8C8Y_094Symmetric double minor groove platform

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8C8Y_0011/A/30:31,
1/A/474:481,
1/A/509:510		No text annotation
homologous
J3_5J7L_036
NA
J3_8C8Y_0121/A/32:35,
1/A/445:461,
1/A/468:473		No text annotation
homologous
J3_5J7L_067
NA
J3_8C8Y_0021/A/56:57,
1/A/70:76,
1/A/110:114		No text annotation
homologous
J3_5J7L_037
NA
J3_8C8Y_0131/A/297:301,
1/A/316:325,
1/A/337:341		No text annotation
homologous
J3_5J7L_068
NA
J3_8C8Y_0031/A/683:689,
1/A/773:775,
1/A/791:794		No text annotation
homologous
J3_5J7L_038
NA
J3_8C8Y_0041/A/698:700,
1/A/732:736,
1/A/760:763		No text annotation
homologous
J3_7RQB_005
NA
J3_8C8Y_0051/A/1298:1303,
1/A/1625:1627,
1/A/1639:1642		No text annotation
homologous
J3_5J7L_041
NA
J3_8C8Y_0061/A/1306:1309,
1/A/1605:1611,
1/A/1620:1622		No text annotation
homologous
J3_7A0S_007
J3_47341.1
J3_8C8Y_0071/A/1344:1349,
1/A/1382:1385,
1/A/1402:1403		No text annotation
homologous
J3_5J7L_043
NA
J3_8C8Y_0141/A/1424:1429,
1/A/1564:1565,
1/A/1568:1574		No text annotation
homologous
J3_5J7L_069
NA
J3_8C8Y_0081/A/2091:2093,
1/A/2196:2200,
1/A/2223:2228		Kink-turn 3-way junction
homologous
J3_5J7L_044
NA
J3_8C8Y_0151/A/2330:2347,
1/A/2370:2372,
1/A/2381:2385		No text annotation
J3_8C8Y_0091/A/2789:2791,
1/A/2805:2806,
1/A/2892:2894		No text annotation
homologous
J3_5J7L_047
NA
J3_8C8Y_0101/A/2812:2815,
1/A/2831:2836,
1/A/2882:2888		No text annotation
homologous
J3_5J7L_048
NA
J3_8C8Y_0111/B/10:16,
1/B/68:70,
1/B/106:110		No text annotation
homologous
J3_5J7L_049
NA
J4_8C8Y_0011/A/268:269,
1/A/370:375,
1/A/399:406,
1/A/421:424		No text annotation
homologous
J4_5J7L_018
NA
J4_8C8Y_0021/A/297:301,
1/A/316:319,
1/A/323:325,
1/A/337:341		No text annotation
homologous
J4_5J7L_019
NA
J4_8C8Y_0031/A/601:604,
1/A/624:628,
1/A/635:638,
1/A/650:656		No text annotation
homologous
J4_5J7L_020
NA
J4_8C8Y_0041/A/1270:1276,
1/A/1294:1295,
1/A/1645:1648,
1/A/2009:2010		No text annotation
homologous
J4_5J7L_021
NA
J4_8C8Y_0051/A/1310:1314,
1/A/1338:1343,
1/A/1404:1405,
1/A/1597:1604		No text annotation
homologous
J4_5J7L_022
NA
J4_8C8Y_0061/A/1313:1314,
1/A/1338:1343,
1/A/1404:1405,
1/A/1597:1603		No text annotation
homologous
J4_5J7L_023
NA
J4_8C8Y_0071/A/1444:1445,
1/A/1466:1467,
1/A/1525:1526,
1/A/1546:1547		No text annotation
homologous
J4_5J7L_024
NA
J4_8C8Y_0081/A/1772:1776,
1/A/1788:1792,
1/A/1827:1830,
1/A/1975:1979		No text annotation
homologous
J4_5J7L_025
NA
J4_8C8Y_0111/A/2643:2646,
1/A/2674:2676,
1/A/2731:2735,
1/A/2769:2771		No text annotation
homologous
J4_5J7L_028
NA
J5_8C8Y_0011/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
NA
J5_8C8Y_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
NA
J5_8C8Y_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
NA
J5_8C8Y_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
NA
J6_8C8Y_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_8C8Y_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_8C8Y_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
J4_8C8Y_009No text annotation
J4_8C8Y_010No text annotation
J5_8C8Y_005No text annotation

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