RNA 3D Hub //

6GC6 Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_6GC6_0011/A/59:68No text annotation
homologous
HL_5J7L_134
HL_35677.3
HL_6GC6_0021/A/87:95No text annotation
homologous
HL_5J7L_135
HL_80241.1
HL_6GC6_0031/A/123:128No text annotation
homologous
HL_4WF9_003
HL_75660.5
HL_6GC6_0041/A/137:142No text annotation
homologous
HL_5J7L_137
HL_32392.1
HL_6GC6_0051/A/158:168No text annotation
homologous
HL_5J7L_138
HL_68257.1
HL_6GC6_0061/A/194:201No text annotation
homologous
HL_4WF9_006
HL_30068.2
HL_6GC6_0071/A/225:230No text annotation
homologous
HL_5J7L_140
HL_62934.1
HL_6GC6_0081/A/246:252No text annotation
homologous
HL_4WF9_008
HL_37369.2
HL_6GC6_0091/A/305:312T-loop with 2 stacked bulged bases
homologous
HL_5J7L_142
HL_01609.3
HL_6GC6_0101/A/319:323No text annotation
homologous
HL_7A0S_011
HL_75660.5
HL_6GC6_0111/A/327:335T-loop with unstacked turn
homologous
HL_5J7L_144
HL_27670.2
HL_6GC6_0121/A/382:392No text annotation
HL_6GC6_0131/A/410:417Pseudoknot geometry
homologous
HL_4WF9_014
HL_30680.3
HL_6GC6_0141/A/462:467GNRA
homologous
HL_4WF9_015
HL_37824.7
HL_6GC6_0151/A/487:493GNRA
homologous
HL_5J7L_148
HL_37824.7
HL_6GC6_0161/A/543:550No text annotation
homologous
HL_7RQB_017
NA
HL_6GC6_0171/A/566:575No text annotation
homologous
HL_7RQB_018
NA
HL_6GC6_0181/A/611:617No text annotation
homologous
HL_5J7L_151
HL_80922.2
HL_6GC6_0191/A/629:634GNRA
homologous
HL_5J7L_152
HL_37824.7
HL_6GC6_0201/A/641:647No text annotation
homologous
HL_5J7L_153
HL_13529.1
HL_6GC6_0211/A/712:719GNRA wlth tandem sheared
homologous
HL_5J7L_154
HL_81538.2
HL_6GC6_0221/A/744:753No text annotation
homologous
HL_4WF9_023
HL_88205.2
HL_6GC6_0231/A/779:785UNCG variation
geometric
HL_1P6V_001
HL_53890.2
HL_6GC6_0241/A/826:831No text annotation
homologous
HL_7RQB_025
NA
HL_6GC6_0261/A/955:962GNRA
homologous
HL_7A0S_026
HL_37824.7
HL_6GC6_0271/A/978:985No text annotation
homologous
HL_5J7L_160
HL_42998.2
HL_6GC6_0601/A/1172:1177No text annotation
HL_6GC6_0291/A/1222:1227GNRA
homologous
HL_5J7L_164
HL_37824.7
HL_6GC6_0301/A/1281:1289T-loop with 2 stacked bulged bases
homologous
HL_7A0S_032
HL_28252.8
HL_6GC6_0311/A/1324:1330Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_166
HL_57176.2
HL_6GC6_0321/A/1363:1368GNRA
homologous
HL_5J7L_167
HL_37824.7
HL_6GC6_0331/A/1389:1398No text annotation
homologous
HL_4WF9_035
HL_81545.2
HL_6GC6_0341/A/1451:1459No text annotation
geometric
HL_6U8D_003
HL_32346.4
HL_6GC6_0351/A/1492:1498Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_170
HL_57176.2
HL_6GC6_0361/A/1533:1538UNCG
homologous
HL_5J7L_171
HL_34617.5
HL_6GC6_0371/A/1565:1568Mini UNCG
homologous
HL_5J7L_172
HL_48778.2
HL_6GC6_0381/A/1612:1619No text annotation
homologous
HL_4WF9_038
HL_89567.2
HL_6GC6_0561/A/1628:1638No text annotation
HL_6GC6_0391/A/1630:1636GNRA
homologous
HL_5J7L_174
HL_37824.7
HL_6GC6_0401/A/1691:1696UNCG
geometric
HL_4PMI_004
HL_34617.5
HL_6GC6_0411/A/1727:1733No text annotation
geometric
HL_5J7L_214
HL_08100.1
HL_6GC6_0421/A/1752:1756No text annotation
homologous
HL_5J7L_177
HL_80709.3
HL_6GC6_0611/A/1777:1787No text annotation
homologous
HL_4WF9_043
HL_01962.2
HL_6GC6_0431/A/1778:1787No text annotation
HL_6GC6_0441/A/1806:1811GNRA related
homologous
HL_5J7L_179
HL_04783.2
HL_6GC6_0461/A/2027:2036No text annotation
homologous
HL_4WF9_047
HL_61996.2
HL_6GC6_0481/A/2658:2663GNRA
geometric
HL_4WF9_016
HL_37824.7
HL_6GC6_0491/A/2701:2706Ribsomal LSU H95
homologous
HL_7A0S_064
HL_65794.5
HL_6GC6_0501/A/2745:2759No text annotation
homologous
HL_7RQB_066
NA
HL_6GC6_0511/A/2796:2799Mini UNCG
geometric
HL_4V88_192
NA
HL_6GC6_0521/A/2819:2827No text annotation
homologous
HL_5J7L_201
HL_64690.6
HL_6GC6_0531/A/2856:2861GNRA
homologous
HL_7A0S_068
HL_37824.7

Problematic loops

#loop idProblemSequence
HL_6GC6_054No text annotation
HL_6GC6_025No text annotation
HL_6GC6_028No text annotation
HL_6GC6_055No text annotation
HL_6GC6_057No text annotation
HL_6GC6_058No text annotation
HL_6GC6_059No text annotation
HL_6GC6_045No text annotation
HL_6GC6_047No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_6GC6_0011/A/24:30,
1/A/510:516		Triple sheared with non-canonical cWW
homologous
IL_4WF9_001
IL_04021.2
IL_6GC6_0021/A/36:37,
1/A/442:444		Single bulged A
homologous
IL_4WF9_002
IL_31462.6
IL_6GC6_0861/A/43:44,
1/A/434:436		Minor groove platform
homologous
IL_5J7L_247
IL_51454.3
IL_6GC6_0721/A/82:85,
1/A/97:104		No text annotation
IL_6GC6_0051/A/188:194,
1/A/201:208		8x7 Sarcin-Ricin; G-bulge
geometric
IL_7A0S_006
IL_04346.10
IL_6GC6_0061/A/239:245,
1/A/253:258		7x6 Sarcin-Ricin; G-bulge
homologous
IL_7RQB_007
NA
IL_6GC6_0071/A/269:271,
1/A/366:370		No text annotation
homologous
IL_5J7L_252
IL_47972.1
IL_6GC6_0081/A/274:281,
1/A/359:363		No text annotation
homologous
IL_5J7L_253
IL_77870.1
IL_6GC6_0091/A/292:295,
1/A/343:348		No text annotation
IL_6GC6_0101/A/481:484,
1/A/496:509		No text annotation
homologous
IL_5J7L_255
IL_81516.2
IL_6GC6_0111/A/536:539,
1/A/554:557		Double sheared
homologous
IL_5J7L_256
IL_09705.15
IL_6GC6_0121/A/564:566,
1/A/575:577		Isolated non-canonical cWW pair
geometric
IL_4E59_001
IL_87907.2
IL_6GC6_0131/A/606:610,
1/A/618:622		AAA cross-strand stack
homologous
IL_5J7L_258
IL_66798.2
IL_6GC6_0141/A/672:674,
1/A/806:808		No text annotation
homologous
IL_7RQB_017
NA
IL_6GC6_0151/A/674:678,
1/A/799:806		tHW-tHW cross-strand stack
geometric
IL_7RQB_018
NA
IL_6GC6_0161/A/697:698,
1/A/763:765		Single bulged A
geometric
IL_7A0S_016
IL_31462.6
IL_6GC6_0171/A/702:703,
1/A/728:730		Single bulged G
homologous
IL_7RQB_020
NA
IL_6GC6_0751/A/702:707,
1/A/724:730		No text annotation
geometric
IL_4LFB_055
IL_85536.2
IL_6GC6_0181/A/703:707,
1/A/724:728		Triple sheared
geometric
IL_4WF9_024
IL_50730.2
IL_6GC6_0191/A/737:740,
1/A/757:759		No text annotation
geometric
IL_6DME_003
IL_55516.2
IL_6GC6_0201/A/775:777,
1/A/787:791		Multiple bulged bases
homologous
IL_5J7L_265
IL_06549.2
IL_6GC6_0211/A/844:847,
1/A/933:934		Other IL
geometric
IL_5J7L_267
IL_90729.1
IL_6GC6_0761/A/844:848,
1/A/930:934		No text annotation
geometric
IL_5J7L_399
IL_96236.1
IL_6GC6_0221/A/847:848,
1/A/930:933		Stack outside cWW
homologous
IL_5J7L_268
IL_56987.1
IL_6GC6_0231/A/850:851,
1/A/926:928		Single stack bend
homologous
IL_5J7L_269
IL_26793.1
IL_6GC6_0241/A/856:862,
1/A/915:921		7x7 Sarcin-Ricin with intercalated A; G-bulge
geometric
IL_5TBW_038
NA
IL_6GC6_0781/A/856:863,
1/A/913:921		No text annotation
IL_6GC6_0251/A/862:863,
1/A/913:915		Single bulged G
homologous
IL_5J7L_271
IL_00225.13
IL_6GC6_0871/A/994:996,
1/A/1159:1160		Single bulged C
homologous
IL_4WF9_035
IL_61258.15
IL_6GC6_0271/A/998:1002,
1/A/1153:1157		UAA/GAN
homologous
IL_4WF9_036
IL_38507.2
IL_6GC6_0281/A/1004:1011,
1/A/1150:1151		SSU/LSU pseudoknot
geometric
IL_5J7L_278
IL_41203.4
IL_6GC6_0291/A/1011:1013,
1/A/1149:1150		Single bulged U
homologous
IL_4WF9_038
IL_89505.4
IL_6GC6_0301/A/1018:1024,
1/A/1140:1144		Kink-turn related
homologous
IL_4WF9_039
IL_57188.5
IL_6GC6_0311/A/1024:1030,
1/A/1124:1140		No text annotation
homologous
IL_5J7L_281
IL_50715.3
IL_6GC6_0321/A/1196:1198,
1/A/1247:1250		Isolated cWS basepair
homologous
IL_5J7L_286
IL_42997.3
IL_6GC6_0331/A/1202:1206,
1/A/1240:1243		No text annotation
homologous
IL_5J7L_287
IL_91920.1
IL_6GC6_0341/A/1208:1215,
1/A/1234:1238		Kink-turn
homologous
IL_7RQB_047
NA
IL_6GC6_0351/A/1262:1269,
1/A/2011:2017		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
IL_04346.10
IL_6GC6_0361/A/1310:1313,
1/A/1603:1604		Major groove platform; stack outside cWW
homologous
IL_7RQB_050
NA
IL_6GC6_0371/A/1319:1323,
1/A/1331:1333		C-loop
homologous
IL_5J7L_291
IL_63596.11
IL_6GC6_0381/A/1351:1355,
1/A/1376:1380		UAA/GAN
homologous
IL_7A0S_048
IL_89021.2
IL_6GC6_0391/A/1357:1361,
1/A/1370:1374		tSH-tHW-tHS
homologous
IL_5J7L_293
IL_17136.7
IL_6GC6_0401/A/1415:1417,
1/A/1581:1587		No text annotation
IL_6GC6_0411/A/1417:1421,
1/A/1577:1581		UAA/GAN
homologous
IL_5J7L_295
IL_38507.2
IL_6GC6_0421/A/1432:1435,
1/A/1557:1561		Tandem non-canonical cWW pairs
homologous
IL_5J7L_296
IL_58112.2
IL_6GC6_0431/A/1437:1440,
1/A/1551:1555		tSH-tHW
homologous
IL_7A0S_053
IL_99646.2
IL_6GC6_0441/A/1450:1451,
1/A/1459:1461		Single bulged U
homologous
IL_5J7L_298
IL_89505.4
IL_6GC6_0451/A/1468:1471,
1/A/1520:1524		No text annotation
homologous
IL_5J7L_299
IL_68574.4
IL_6GC6_0811/A/1474:1478,
1/A/1513:1517		tSH-tHW-tHS
homologous
IL_5J7L_300
IL_38862.4
IL_6GC6_0471/A/1481:1482,
1/A/1507:1510		180 degree turn
homologous
IL_5J7L_301
IL_00881.1
IL_6GC6_0481/A/1489:1491,
1/A/1499:1500		Single bulged A
homologous
IL_5J7L_302
IL_31462.6
IL_6GC6_0821/A/1526:1529,
1/A/1542:1546		UAA/GAN variation
homologous
IL_5J7L_303
IL_23774.1
IL_6GC6_0501/A/1651:1656,
1/A/2004:2006		No text annotation
homologous
IL_7A0S_059
IL_12566.4
IL_6GC6_0511/A/1663:1665,
1/A/1995:1997		Isolated tWW turn
homologous
IL_4WF9_063
IL_67095.2
IL_6GC6_0521/A/1666:1669,
1/A/1993:1994		Major groove platform; stack outside cWW
homologous
IL_7RQB_066
NA
IL_6GC6_0831/A/1666:1674,
1/A/1990:1994		No text annotation
homologous
IL_4WF9_117
IL_22854.4
IL_6GC6_0531/A/1669:1674,
1/A/1990:1993		Intercalated tWH
geometric
IL_4WF9_065
IL_76758.2
IL_6GC6_0541/A/1686:1691,
1/A/1696:1702		tSH-tSH-tHH-tHS
homologous
IL_7RQB_068
NA
IL_6GC6_0551/A/1712:1718,
1/A/1742:1746		6x5 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_309
IL_88269.4
IL_6GC6_0881/A/1720:1724,
1/A/1736:1740		Triple sheared
homologous
IL_5J7L_310
IL_50730.2
IL_6GC6_0571/A/1776:1778,
1/A/1787:1788		Single stack bend
geometric
IL_4V9F_005
IL_90729.1
IL_6GC6_0581/A/1798:1804,
1/A/1813:1821		Kink-turn related
homologous
IL_7A0S_065
IL_17069.5
IL_6GC6_0591/A/2050:2052,
1/A/2617:2618		Major groove platform
homologous
IL_5J7L_320
IL_48076.6
IL_6GC6_0601/A/2053:2057,
1/A/2611:2616		No text annotation
IL_6GC6_0611/A/2636:2640,
1/A/2774:2782		tSH-tHS-tHW
homologous
IL_7RQB_102
NA
IL_6GC6_0621/A/2652:2658,
1/A/2663:2668		Sarcin-Ricin target in LSU H95; G-bulge
homologous
IL_7A0S_094
IL_16458.4
IL_6GC6_0631/A/2680:2684,
1/A/2725:2727		C-loop
homologous
IL_5J7L_347
IL_63596.11
IL_6GC6_0641/A/2687:2691,
1/A/2718:2722		No text annotation
homologous
IL_5J7L_348
IL_23774.1
IL_6GC6_0651/A/2695:2696,
1/A/2711:2714		Multiple bulged bases
homologous
IL_4WF9_103
IL_42626.2
IL_6GC6_0661/A/2737:2742,
1/A/2762:2767		UAA/GAN with extra cWW
homologous
IL_5J7L_350
IL_49767.8
IL_6GC6_0671/A/2795:2796,
1/A/2799:2801		Single bulged A
geometric
IL_5J7L_261
IL_31462.6
IL_6GC6_0681/A/2806:2811,
1/A/2889:2892		No text annotation
geometric
IL_5J7L_351
IL_29471.1
IL_6GC6_0691/A/2838:2839,
1/A/2878:2880		Major groove intercalation
homologous
IL_5J7L_352
IL_66635.5
IL_6GC6_0701/A/2843:2846,
1/A/2870:2874		Multiple bulged bases with non-canonical cWW
homologous
IL_5J7L_353
IL_64231.5
IL_6GC6_0711/A/2847:2852,
1/A/2865:2869		tHS double platform
homologous
IL_7RQB_110
NA

Problematic loops

#loop idProblemSequence
IL_6GC6_003Minor groove platform with extra cWW
IL_6GC6_004No text annotation
IL_6GC6_073No text annotation
IL_6GC6_074No text annotation
IL_6GC6_077No text annotation
IL_6GC6_026Isolated non-canonical cWW pair
IL_6GC6_079UAA/GAN with extra cWW
IL_6GC6_080No text annotation
IL_6GC6_046tSH-tHW-tHS-cWW
IL_6GC6_049Triple sheared related
IL_6GC6_084No text annotation
IL_6GC6_085No text annotation
IL_6GC6_056No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_6GC6_0011/A/56:57,
1/A/70:76,
1/A/110:114		No text annotation
homologous
J3_5J7L_037
J3_35667.2
J3_6GC6_0091/A/297:301,
1/A/316:325,
1/A/337:341		No text annotation
homologous
J3_5J7L_068
J3_46299.2
J3_6GC6_0021/A/683:689,
1/A/773:775,
1/A/791:794		No text annotation
homologous
J3_5J7L_038
J3_64189.2
J3_6GC6_0031/A/698:700,
1/A/732:736,
1/A/760:763		No text annotation
homologous
J3_7A0S_005
J3_44724.7
J3_6GC6_0041/A/1298:1303,
1/A/1625:1627,
1/A/1639:1642		No text annotation
homologous
J3_5J7L_041
J3_32852.6
J3_6GC6_0101/A/1306:1309,
1/A/1605:1611,
1/A/1620:1622		No text annotation
homologous
J3_7A0S_007
J3_71677.1
J3_6GC6_0061/A/1344:1349,
1/A/1382:1385,
1/A/1402:1403		No text annotation
homologous
J3_5J7L_043
J3_92705.1
J3_6GC6_0121/A/1424:1429,
1/A/1564:1565,
1/A/1568:1574		No text annotation
homologous
J3_7A0S_019
J3_34864.2
J3_6GC6_0071/A/2789:2791,
1/A/2805:2806,
1/A/2892:2894		No text annotation
homologous
J3_5J7L_047
J3_30104.1
J3_6GC6_0081/A/2812:2815,
1/A/2831:2836,
1/A/2882:2888		No text annotation
homologous
J3_5J7L_048
J3_64069.1
J4_6GC6_0011/A/30:35,
1/A/445:461,
1/A/468:481,
1/A/509:510		No text annotation
J4_6GC6_0021/A/30:35,
1/A/445:461,
1/A/468:484,
1/A/496:510		No text annotation
J4_6GC6_0031/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_6GC6_0041/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_6GC6_0051/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_6GC6_0061/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_6GC6_0071/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_6GC6_0081/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_6GC6_0091/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_6GC6_0101/A/1770:1776,
1/A/1788:1792,
1/A/1827:1830,
1/A/1975:1982		No text annotation
J4_6GC6_0111/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_6GC6_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
J5_01737.2
J5_6GC6_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_6GC6_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_7A0S_004
J5_74302.5
J5_6GC6_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_6GC6_0011/A/45:46,
1/A/179:184,
1/A/212:224,
1/A/231:235,
1/A/262:266,
1/A/426:433		No text annotation
J7_6GC6_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_6GC6_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
J3_6GC6_005No text annotation
J3_6GC6_011No text annotation

Coloring options:
Copyright 2025 BGSU RNA group. Page generated in 0.148 s