RNA 3D Hub //

6V3A Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_6V3A_0011/AN1/66:75No text annotation
homologous
HL_5J7L_134
NA
HL_6V3A_0021/AN1/93:104No text annotation
HL_6V3A_0031/AN1/130:135No text annotation
homologous
HL_5J7L_136
NA
HL_6V3A_0041/AN1/144:149No text annotation
geometric
HL_1WZ2_007
HL_75660.6
HL_6V3A_0051/AN1/165:175No text annotation
homologous
HL_5J7L_138
NA
HL_6V3A_0061/AN1/201:208No text annotation
homologous
HL_4WF9_006
HL_48677.1
HL_6V3A_0071/AN1/232:237No text annotation
geometric
HL_1WZ2_007
HL_75660.6
HL_6V3A_0081/AN1/253:259No text annotation
homologous
HL_4WF9_008
HL_76371.1
HL_6V3A_0091/AN1/307:314T-loop with 1 bulged base
homologous
HL_7A0S_010
HL_13999.1
HL_6V3A_0101/AN1/321:325No text annotation
homologous
HL_5J7L_143
NA
HL_6V3A_0111/AN1/329:337T-loop with unstacked turn
homologous
HL_5J7L_144
NA
HL_6V3A_0121/AN1/381:391No text annotation
homologous
HL_5J7L_145
NA
HL_6V3A_0131/AN1/409:416Pseudoknot geometry
homologous
HL_7A0S_014
HL_30680.4
HL_6V3A_0141/AN1/461:466GNRA
homologous
HL_7RQB_015
NA
HL_6V3A_0151/AN1/486:492GNRA
homologous
HL_5J7L_148
NA
HL_6V3A_0161/AN1/543:546Mini UNCG
geometric
HL_4V88_192
NA
HL_6V3A_0171/AN1/564:573T-loop with 2 stacked bulged bases
homologous
HL_5J7L_150
NA
HL_6V3A_0181/AN1/609:615No text annotation
homologous
HL_5J7L_151
NA
HL_6V3A_0191/AN1/627:632GNRA
homologous
HL_5J7L_152
NA
HL_6V3A_0201/AN1/639:645No text annotation
homologous
HL_7RQB_021
NA
HL_6V3A_0211/AN1/710:717No text annotation
homologous
HL_7RQB_022
NA
HL_6V3A_0221/AN1/742:751No text annotation
geometric
HL_4WF9_023
HL_50204.1
HL_6V3A_0231/AN1/777:783No text annotation
homologous
HL_5J7L_156
NA
HL_6V3A_0241/AN1/824:829No text annotation
homologous
HL_7RQB_025
NA
HL_6V3A_0251/AN1/882:890No text annotation
HL_6V3A_1061/AN1/952:959GNRA
homologous
HL_5J7L_211
NA
HL_6V3A_0271/AN1/975:982No text annotation
homologous
HL_5J7L_160
NA
HL_6V3A_0301/AN1/1166:1176No text annotation
HL_6V3A_0311/AN1/1217:1222GNRA
homologous
HL_7A0S_031
HL_34789.1
HL_6V3A_0321/AN1/1276:1284T-loop with 2 stacked bulged bases
homologous
HL_5J7L_165
NA
HL_6V3A_0331/AN1/1319:1325Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_166
NA
HL_6V3A_0341/AN1/1358:1363GNRA
homologous
HL_5J7L_167
NA
HL_6V3A_0351/AN1/1384:1393No text annotation
homologous
HL_5J7L_168
NA
HL_6V3A_0361/AN1/1446:1454Mini UNCG with extended bulge
geometric
HL_5J7L_169
NA
HL_6V3A_0381/AN1/1563:1566Mini UNCG
homologous
HL_5J7L_172
NA
HL_6V3A_0391/AN1/1610:1617No text annotation
homologous
HL_7RQB_040
NA
HL_6V3A_0401/AN1/1628:1634GNRA
homologous
HL_5J7L_174
NA
HL_6V3A_0411/AN1/1689:1694UNCG
geometric
HL_5LYS_002
HL_61337.1
HL_6V3A_0421/AN1/1723:1729UNCG variation
geometric
HL_6VMY_004
NA
HL_6V3A_0431/AN1/1748:1752No text annotation
homologous
HL_7RQB_044
NA
HL_6V3A_0441/AN1/1773:1783No text annotation
homologous
HL_4WF9_043
HL_87681.1
HL_6V3A_0451/AN1/1802:1807GNRA
homologous
HL_7RQB_046
NA
HL_6V3A_0471/AN1/1906:1916No text annotation
HL_6V3A_0481/AN1/1945:1953No text annotation
homologous
HL_5J7L_182
NA
HL_6V3A_0491/AN1/2023:2032No text annotation
homologous
HL_5J7L_183
NA
HL_6V3A_0511/AN1/2205:2211No text annotation
homologous
HL_5J7L_185
NA
HL_6V3A_0521/AN1/2244:2252No text annotation
homologous
HL_4WF9_049
HL_11974.1
HL_6V3A_0531/AN1/2260:2272No text annotation
homologous
HL_5J7L_187
NA
HL_6V3A_0541/AN1/2299:2309No text annotation
homologous
HL_7RQB_055
NA
HL_6V3A_0551/AN1/2320:2327Pseudoknot geometry
homologous
HL_5J7L_189
NA
HL_6V3A_0561/AN1/2351:2358GNRA with extra cWW
homologous
HL_4WF9_053
HL_45359.1
HL_6V3A_0571/AN1/2370:2375GNRA
homologous
HL_5J7L_191
NA
HL_6V3A_0581/AN1/2400:2409No text annotation
homologous
HL_5J7L_192
NA
HL_6V3A_0591/AN1/2467:2475No text annotation
HL_6V3A_0601/AN1/2524:2531GNRA variation
homologous
HL_5J7L_194
NA
HL_6V3A_0611/AN1/2547:2553No text annotation
homologous
HL_4WF9_058
HL_48677.1
HL_6V3A_0621/AN1/2590:2595GNRA
homologous
HL_7RQB_063
NA
HL_6V3A_0631/AN1/2654:2659GNRA
homologous
HL_7A0S_063
HL_34789.1
HL_6V3A_0641/AN1/2697:2702Ribsomal LSU H95
homologous
HL_5J7L_198
NA
HL_6V3A_0651/AN1/2741:2755No text annotation
homologous
HL_4WF9_062
HL_53269.1
HL_6V3A_0661/AN1/2792:2795No text annotation
geometric
HL_6U8D_003
HL_32346.5
HL_6V3A_0671/AN1/2815:2823No text annotation
homologous
HL_7RQB_068
NA
HL_6V3A_0681/AN1/2852:2857GNRA
homologous
HL_4WF9_065
HL_34789.1
HL_6V3A_1071/B/28:52No text annotation
HL_6V3A_0691/B/36:42No text annotation
geometric
HL_5NFV_001
HL_69752.3
HL_6V3A_0701/B/83:88No text annotation
geometric
HL_1WZ2_007
HL_75660.6
HL_6V3A_0711/sN1/14:24No text annotation
homologous
HL_4LFB_001
HL_31940.1
HL_6V3A_0721/sN1/73:94No text annotation
HL_6V3A_0731/sN1/154:159GNRA
homologous
HL_5J7L_003
NA
HL_6V3A_0741/sN1/182:187UNCG
geometric
HL_5Y85_004
HL_61337.1
HL_6V3A_0761/sN1/255:263GNRA related
homologous
HL_5J7L_006
NA
HL_6V3A_0771/sN1/292:297GNRA
homologous
HL_5J7L_007
NA
HL_6V3A_0781/sN1/316:329No text annotation
homologous
HL_5J7L_008
NA
HL_6V3A_0791/sN1/338:343UNCG
homologous
HL_4LFB_009
HL_61337.1
HL_6V3A_0801/sN1/375:380GNRA
homologous
HL_4LFB_010
HL_34789.1
HL_6V3A_1081/sN1/519:524GNRA variation
homologous
HL_5J7L_205
NA
HL_6V3A_0841/sN1/614:620GNRA-like with tWH
homologous
HL_4LFB_014
HL_92337.1
HL_6V3A_0851/sN1/686:695No text annotation
homologous
HL_4LFB_015
HL_38491.1
HL_6V3A_0861/sN1/723:728GNRA
homologous
HL_5J7L_016
NA
HL_6V3A_0871/sN1/783:793No text annotation
homologous
HL_5J7L_017
NA
HL_6V3A_0891/sN1/859:864GNRA
homologous
HL_4LFB_019
HL_34789.1
HL_6V3A_0901/sN1/894:899GNRA
homologous
HL_4LFB_020
HL_34789.1
HL_6V3A_0911/sN1/960:969No text annotation
homologous
HL_4LFB_021
HL_97521.1
HL_6V3A_0921/sN1/1009:1014GNRA
homologous
HL_4LFB_022
HL_34789.1
HL_6V3A_0941/sN1/1073:1078GNRA
homologous
HL_4LFB_024
HL_34789.1
HL_6V3A_0961/sN1/1131:1137No text annotation
homologous
HL_5J7L_025
NA
HL_6V3A_0981/sN1/1262:1267GNRA
homologous
HL_4LFB_028
HL_34789.1
HL_6V3A_0991/sN1/1311:1320T-loop with 3 stacked bulged bases
homologous
HL_4LFB_029
HL_93658.1
HL_6V3A_1001/sN1/1353:1363No text annotation
homologous
HL_4LFB_030
HL_86432.1
HL_6V3A_1021/sN1/1512:1517GNRA
homologous
HL_6CZR_103
NA
HL_6V3A_1041/v/32:40tRNA anticodon loop
homologous
HL_4TUE_034
NA

Problematic loops

#loop idProblemSequence
HL_6V3A_026No text annotation
HL_6V3A_028No text annotation
HL_6V3A_029No text annotation
HL_6V3A_110No text annotation
HL_6V3A_037Pseudoknot geometry with 3' bulge
HL_6V3A_046GNRA variation
HL_6V3A_050No text annotation
HL_6V3A_075No text annotation
HL_6V3A_081UNCG
HL_6V3A_082GNRA wlth extra near cWW
HL_6V3A_083No text annotation
HL_6V3A_088No text annotation
HL_6V3A_093Externally structured
HL_6V3A_095T-loop related
HL_6V3A_109No text annotation
HL_6V3A_097No text annotation
HL_6V3A_101No text annotation
HL_6V3A_111No text annotation
HL_6V3A_103tRNA D-loop
HL_6V3A_105No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_6V3A_0011/AN1/31:37,
1/AN1/509:515		Triple sheared with non-canonical cWW
geometric
IL_5J7L_245
NA
IL_6V3A_0021/AN1/43:44,
1/AN1/441:443		Single bulged A
homologous
IL_5J7L_246
NA
IL_6V3A_0031/AN1/50:51,
1/AN1/433:435		Minor groove platform
homologous
IL_5J7L_247
NA
IL_6V3A_0041/AN1/88:92,
1/AN1/105:112		Kink-turn
homologous
IL_7RQB_004
NA
IL_6V3A_0051/AN1/190:191,
1/AN1/219:221		Single stack bend
homologous
IL_7A0S_005
IL_15011.1
IL_6V3A_0061/AN1/195:201,
1/AN1/208:215		8x7 Sarcin-Ricin; G-bulge
geometric
IL_7A0S_006
IL_62167.1
IL_6V3A_0071/AN1/246:252,
1/AN1/260:265		7x6 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_251
NA
IL_6V3A_0081/AN1/276:282,
1/AN1/362:369		No text annotation
IL_6V3A_0091/AN1/295:297,
1/AN1/345:349		No text annotation
homologous
IL_7RQB_013
NA
IL_6V3A_0101/AN1/305:307,
1/AN1/314:316		Isolated non-canonical cWW pair
geometric
IL_3SZX_001
IL_01003.1
IL_6V3A_0111/AN1/480:483,
1/AN1/495:508		No text annotation
geometric
IL_5J7L_255
NA
IL_6V3A_0121/AN1/535:538,
1/AN1/552:555		Double sheared
homologous
IL_5J7L_256
NA
IL_6V3A_0131/AN1/542:543,
1/AN1/546:548		Single bulged C
homologous
IL_7A0S_010
IL_05642.1
IL_6V3A_0141/AN1/562:564,
1/AN1/573:575		Isolated non-canonical cWW pair
geometric
IL_4WF9_017
IL_71625.1
IL_6V3A_0151/AN1/604:608,
1/AN1/616:620		AAA cross-strand stack
homologous
IL_7RQB_016
NA
IL_6V3A_0161/AN1/670:672,
1/AN1/804:806		No text annotation
homologous
IL_7RQB_017
NA
IL_6V3A_0171/AN1/672:676,
1/AN1/797:804		tHW-tHW cross-strand stack
geometric
IL_5J7L_260
NA
IL_6V3A_0181/AN1/695:696,
1/AN1/761:763		Single bulged A
geometric
IL_4V9F_025
IL_14190.1
IL_6V3A_0191/AN1/700:701,
1/AN1/726:728		Single bulged G
geometric
IL_7RQB_020
NA
IL_6V3A_0201/AN1/701:705,
1/AN1/722:726		Triple sheared
homologous
IL_4WF9_024
IL_15190.1
IL_6V3A_0211/AN1/736:738,
1/AN1/755:756		Major groove platform
homologous
IL_5J7L_264
NA
IL_6V3A_0221/AN1/740:742,
1/AN1/751:753		Isolated non-canonical cWW pair
homologous
IL_7A0S_020
IL_01003.1
IL_6V3A_0231/AN1/773:775,
1/AN1/785:789		Multiple bulged bases
geometric
IL_5TBW_033
NA
IL_6V3A_0241/AN1/841:845,
1/AN1/930:932		No text annotation
IL_6V3A_1871/AN1/841:846,
1/AN1/928:932		No text annotation
IL_6V3A_0251/AN1/845:846,
1/AN1/928:930		No text annotation
IL_6V3A_0261/AN1/848:849,
1/AN1/924:926		Single stack bend
homologous
IL_5J7L_269
NA
IL_6V3A_0271/AN1/854:860,
1/AN1/913:919		7x7 Sarcin-Ricin with intercalated A; G-bulge
homologous
IL_5J7L_270
NA
IL_6V3A_0281/AN1/860:861,
1/AN1/911:913		Minor groove platform
geometric
IL_4V9F_034
IL_34520.1
IL_6V3A_0291/AN1/862:867,
1/AN1/906:910		No text annotation
IL_6V3A_0301/AN1/868:870,
1/AN1/903:905		Isolated non-canonical cWW pair
homologous
IL_5J7L_273
NA
IL_6V3A_0311/AN1/873:877,
1/AN1/896:900		Double sheared with non-canonical cWW
homologous
IL_5J7L_274
NA
IL_6V3A_0321/AN1/878:881,
1/AN1/891:895		Tandem non-canonical cWW pairs
geometric
IL_3WBM_003
NA
IL_6V3A_0331/AN1/991:993,
1/AN1/1157:1158		Single bulged C
homologous
IL_7RQB_035
NA
IL_6V3A_0341/AN1/995:999,
1/AN1/1151:1155		UAA/GAN
homologous
IL_4WF9_036
IL_08938.1
IL_6V3A_0351/AN1/1001:1008,
1/AN1/1148:1149		SSU/LSU pseudoknot
geometric
IL_5J7L_278
NA
IL_6V3A_0361/AN1/1008:1010,
1/AN1/1147:1148		Single bulged U
homologous
IL_5J7L_279
NA
IL_6V3A_0371/AN1/1015:1021,
1/AN1/1137:1142		No text annotation
geometric
IL_7RQB_039
NA
IL_6V3A_0381/AN1/1021:1027,
1/AN1/1121:1137		No text annotation
geometric
IL_5J7L_281
NA
IL_6V3A_0391/AN1/1028:1031,
1/AN1/1118:1120		Other IL
geometric
IL_5TBW_064
NA
IL_6V3A_0401/AN1/1035:1038,
1/AN1/1111:1114		Tandem non-canonical cWW pairs
geometric
IL_5TBW_100
NA
IL_6V3A_0411/AN1/1038:1048,
1/AN1/1105:1111		No text annotation
IL_6V3A_0441/AN1/1191:1193,
1/AN1/1242:1245		Isolated cWS basepair
homologous
IL_4WF9_044
IL_42997.4
IL_6V3A_0451/AN1/1197:1201,
1/AN1/1235:1238		No text annotation
homologous
IL_5J7L_287
NA
IL_6V3A_0461/AN1/1203:1210,
1/AN1/1229:1233		Kink-turn
homologous
IL_7RQB_047
NA
IL_6V3A_0471/AN1/1257:1264,
1/AN1/2007:2013		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
NA
IL_6V3A_0481/AN1/1305:1308,
1/AN1/1601:1602		Major groove platform; stack outside cWW
homologous
IL_5J7L_290
NA
IL_6V3A_0491/AN1/1314:1318,
1/AN1/1326:1328		C-loop
homologous
IL_5J7L_291
NA
IL_6V3A_0501/AN1/1346:1350,
1/AN1/1371:1375		UAA/GAN
homologous
IL_5J7L_292
NA
IL_6V3A_0511/AN1/1352:1356,
1/AN1/1365:1369		tSH-tHW-tHS
homologous
IL_5J7L_293
NA
IL_6V3A_0531/AN1/1412:1416,
1/AN1/1575:1579		UAA/GAN
homologous
IL_5J7L_295
NA
IL_6V3A_0541/AN1/1427:1430,
1/AN1/1555:1559		Tandem non-canonical cWW pairs
homologous
IL_5J7L_296
NA
IL_6V3A_0551/AN1/1432:1435,
1/AN1/1549:1553		tSH-tHW
homologous
IL_7RQB_057
NA
IL_6V3A_0561/AN1/1445:1446,
1/AN1/1454:1456		Single bulged U
homologous
IL_5J7L_298
NA
IL_6V3A_0571/AN1/1468:1473,
1/AN1/1509:1514		tSH-tHW-tHS-cWW
geometric
IL_3LQX_002
IL_35186.1
IL_6V3A_0601/AN1/1649:1654,
1/AN1/2000:2002		No text annotation
homologous
IL_5J7L_304
NA
IL_6V3A_0611/AN1/1661:1663,
1/AN1/1991:1993		Isolated tWW turn
homologous
IL_4WF9_063
IL_10432.1
IL_6V3A_0621/AN1/1664:1667,
1/AN1/1989:1990		Major groove platform; stack outside cWW
geometric
IL_7RQB_066
NA
IL_6V3A_1901/AN1/1664:1672,
1/AN1/1986:1990		No text annotation
homologous
IL_4WF9_117
IL_80252.1
IL_6V3A_0631/AN1/1667:1672,
1/AN1/1986:1989		Intercalated tWH
homologous
IL_4WF9_065
IL_28217.1
IL_6V3A_0641/AN1/1684:1689,
1/AN1/1694:1700		tSH-tSH-tHH-tHS
homologous
IL_5J7L_308
NA
IL_6V3A_0651/AN1/1716:1720,
1/AN1/1732:1736		Triple sheared
homologous
IL_5J7L_310
NA
IL_6V3A_0661/AN1/1766:1767,
1/AN1/1976:1978		Single bulged A
homologous
IL_4WF9_068
IL_14190.1
IL_6V3A_0671/AN1/1794:1800,
1/AN1/1809:1817		Kink-turn related
homologous
IL_7A0S_065
IL_17069.6
IL_6V3A_0681/AN1/1833:1836,
1/AN1/1898:1899		Minor groove platform, major groove intercalation
homologous
IL_5J7L_314
NA
IL_6V3A_0691/AN1/1837:1838,
1/AN1/1894:1897		Major groove intercalation
homologous
IL_5J7L_315
NA
IL_6V3A_0701/AN1/1842:1845,
1/AN1/1889:1890		Major groove platform
geometric
IL_8DP3_001
NA
IL_6V3A_1921/AN1/1847:1856,
1/AN1/1878:1887		No text annotation
homologous
IL_5J7L_387
NA
IL_6V3A_0711/AN1/1860:1863,
1/AN1/1870:1874		No text annotation
IL_6V3A_0721/AN1/1929:1930,
1/AN1/1960:1963		Bulged stacked bases
homologous
IL_7A0S_071
IL_24886.1
IL_6V3A_0731/AN1/1930:1941,
1/AN1/1957:1960		No text annotation
geometric
IL_4WF9_077
IL_84014.1
IL_6V3A_0741/AN1/2045:2048,
1/AN1/2613:2615		No text annotation
geometric
IL_6DME_003
IL_75527.1
IL_6V3A_0751/AN1/2050:2052,
1/AN1/2608:2611		No text annotation
homologous
IL_4WF9_079
IL_80025.1
IL_6V3A_1941/AN1/2063:2065,
1/AN1/2438:2439		Single bulged U
homologous
IL_4WF9_080
IL_97561.1
IL_6V3A_0781/AN1/2066:2067,
1/AN1/2434:2437		Minor groove platform
homologous
IL_7RQB_081
NA
IL_6V3A_0791/AN1/2077:2079,
1/AN1/2232:2235		Isolated tHS basepair with bulges
homologous
IL_7RQB_082
NA
IL_6V3A_0801/AN1/2081:2083,
1/AN1/2228:2230		Isolated non-canonical cWW pair
homologous
IL_5J7L_326
NA
IL_6V3A_1961/AN1/2106:2133,
1/AN1/2150:2175		No text annotation
IL_6V3A_0851/AN1/2112:2133,
1/AN1/2150:2161		No text annotation
IL_6V3A_0871/AN1/2198:2200,
1/AN1/2216:2217		Single bulged U
homologous
IL_5J7L_331
NA
IL_6V3A_0881/AN1/2346:2349,
1/AN1/2360:2363		Double sheared
homologous
IL_7RQB_089
NA
IL_6V3A_0891/AN1/2397:2399,
1/AN1/2410:2411		Single bulged U
homologous
IL_4WF9_088
IL_97561.1
IL_6V3A_0901/AN1/2449:2450,
1/AN1/2494:2496		Single stack bend
homologous
IL_4WF9_089
IL_15011.1
IL_6V3A_0911/AN1/2450:2451,
1/AN1/2492:2494		Major groove platform
geometric
IL_4WF9_090
IL_48076.7
IL_6V3A_1971/AN1/2453:2455,
1/AN1/2489:2490		Major groove platform
homologous
IL_5J7L_393
NA
IL_6V3A_0931/AN1/2455:2457,
1/AN1/2485:2489		Major groove minor groove platform with extra cWW
geometric
IL_7RQB_094
NA
IL_6V3A_0941/AN1/2462:2466,
1/AN1/2476:2480		Double sheared with non-canonical cWW
homologous
IL_5J7L_338
NA
IL_6V3A_1981/AN1/2503:2504,
1/AN1/2576:2578		Major groove platform
homologous
IL_5J7L_394
NA
IL_6V3A_0961/AN1/2506:2508,
1/AN1/2570:2574		Isolated non-canonical cWW with bulges
homologous
IL_5J7L_340
NA
IL_6V3A_0971/AN1/2508:2509,
1/AN1/2567:2570		No text annotation
geometric
IL_5J7L_341
NA
IL_6V3A_0981/AN1/2518:2519,
1/AN1/2536:2539		Major groove platform with intercalation
homologous
IL_7A0S_091
IL_94991.1
IL_6V3A_1001/AN1/2587:2588,
1/AN1/2597:2599		No text annotation
geometric
IL_9AXU_106
IL_14190.1
IL_6V3A_1011/AN1/2632:2636,
1/AN1/2770:2778		tSH-tHS-tHW
homologous
IL_4WF9_099
IL_04638.4
IL_6V3A_1021/AN1/2647:2654,
1/AN1/2659:2665		8x7 Sarcin-Ricin; G-bulge
geometric
IL_5TBW_116
NA
IL_6V3A_1031/AN1/2676:2680,
1/AN1/2721:2723		C-loop
homologous
IL_4WF9_101
IL_63596.12
IL_6V3A_1041/AN1/2683:2687,
1/AN1/2714:2718		UAA/GAN related, with intercalation
homologous
IL_4WF9_102
IL_82016.1
IL_6V3A_1051/AN1/2691:2692,
1/AN1/2707:2710		Multiple bulged bases
homologous
IL_5J7L_349
NA
IL_6V3A_1061/AN1/2733:2738,
1/AN1/2758:2763		UAA/GAN with extra cWW
homologous
IL_5J7L_350
NA
IL_6V3A_1071/AN1/2791:2792,
1/AN1/2795:2797		Single bulged U
geometric
IL_5TBW_050
NA
IL_6V3A_1081/AN1/2802:2807,
1/AN1/2885:2888		No text annotation
homologous
IL_5J7L_351
NA
IL_6V3A_1091/AN1/2834:2835,
1/AN1/2874:2876		Major groove intercalation
homologous
IL_5J7L_352
NA
IL_6V3A_1101/AN1/2839:2842,
1/AN1/2866:2870		Multiple bulged bases with non-canonical cWW
homologous
IL_5J7L_353
NA
IL_6V3A_1111/AN1/2843:2848,
1/AN1/2861:2865		tHS double platform
homologous
IL_5J7L_354
NA
IL_6V3A_1121/B/15:16,
1/B/63:65		Major groove intercalation
homologous
IL_4V9F_101
IL_14190.1
IL_6V3A_1131/B/20:26,
1/B/54:59		No text annotation
IL_6V3A_1141/B/28:32,
1/B/46:52		No text annotation
IL_6V3A_1991/B/28:36,
1/B/42:52		No text annotation
IL_6V3A_1151/B/32:36,
1/B/42:46		Symmetric double minor groove platform
homologous
IL_7RQB_114
NA
IL_6V3A_2001/B/69:77,
1/B/94:102		Bacterial 5S Loop E
homologous
IL_5J7L_359
NA
IL_6V3A_1161/sN1/32:34,
1/sN1/549:550		Single bulged G
homologous
IL_5J7L_001
NA
IL_6V3A_1171/sN1/46:47,
1/sN1/392:394		Single bulged A
homologous
IL_5J7L_002
NA
IL_6V3A_1181/sN1/49:54,
1/sN1/355:357		No text annotation
geometric
IL_5J7L_003
NA
IL_6V3A_1191/sN1/56:58,
1/sN1/352:353		Minor groove platform
homologous
IL_4LFB_004
IL_34520.1
IL_6V3A_1201/sN1/65:68,
1/sN1/99:100		Multiple bulged bases
homologous
IL_5J7L_005
NA
IL_6V3A_1211/sN1/69:71,
1/sN1/96:98		Isolated non-canonical cWW pair
homologous
IL_6CZR_118
NA
IL_6V3A_1221/sN1/124:127,
1/sN1/227:229		Isolated non-canonical cWW pair
homologous
IL_5J7L_009
NA
IL_6V3A_1231/sN1/128:132,
1/sN1/223:226		No text annotation
homologous
IL_4LFB_008
IL_60988.1
IL_6V3A_1241/sN1/140:142,
1/sN1/172:174		Isolated cWH basepair
homologous
IL_5J7L_011
NA
IL_6V3A_2021/sN1/143:149,
1/sN1/164:171		tWH-tWH-tHW-tHW
homologous
IL_5J7L_012
NA
IL_6V3A_1271/sN1/238:243,
1/sN1/273:280		Kink-turn with non-sequential stacking
homologous
IL_4LFB_011
IL_46174.4
IL_6V3A_1281/sN1/245:248,
1/sN1/270:271		No text annotation
homologous
IL_4LFB_012
IL_22002.1
IL_6V3A_1291/sN1/288:289,
1/sN1/300:304		C-loop
homologous
IL_6CZR_125
NA
IL_6V3A_1301/sN1/363:365,
1/sN1/388:389		Single bulged U
geometric
IL_5J7L_017
NA
IL_6V3A_1311/sN1/367:371,
1/sN1/385:386		C-loop
geometric
IL_5J7L_018
NA
IL_6V3A_1321/sN1/371:372,
1/sN1/383:385		Single bulged G
homologous
IL_5J7L_019
NA
IL_6V3A_1331/sN1/405:412,
1/sN1/423:429		No text annotation
homologous
IL_5J7L_020
NA
IL_6V3A_1341/sN1/436:438,
1/sN1/489:494		No text annotation
homologous
IL_5J7L_021
NA
IL_6V3A_1351/sN1/442:446,
1/sN1/480:485		tSH-tHW-tWW
geometric
IL_5J7L_022
NA
IL_6V3A_1361/sN1/446:449,
1/sN1/476:480		No text annotation
IL_6V3A_1381/sN1/501:508,
1/sN1/537:538		SSU/LSU pseudoknot
homologous
IL_4LFB_020
IL_11411.1
IL_6V3A_1391/sN1/512:518,
1/sN1/525:533		Kink-turn related
geometric
IL_4V88_415
NA
IL_6V3A_1401/sN1/566:572,
1/sN1/877:878		No text annotation
homologous
IL_6CZR_134
NA
IL_6V3A_1411/sN1/577:581,
1/sN1/754:758		tSH-tHW-tHS
homologous
IL_5J7L_027
NA
IL_6V3A_1421/sN1/591:593,
1/sN1/641:642		Major groove platform
homologous
IL_5J7L_028
NA
IL_6V3A_1431/sN1/594:595,
1/sN1/637:640		Major groove minor groove platform; mini C-loop
homologous
IL_5J7L_029
NA
IL_6V3A_1441/sN1/602:609,
1/sN1/625:630		No text annotation
homologous
IL_5J7L_030
NA
IL_6V3A_1451/sN1/651:652,
1/sN1/748:751		Major groove platform; stack outside cWW
homologous
IL_4LFB_027
IL_74641.1
IL_6V3A_2051/sN1/656:657,
1/sN1/742:744		Single stack bend
homologous
IL_5J7L_032
NA
IL_6V3A_1471/sN1/659:663,
1/sN1/737:740		Tandem non-canonical cWW pairs
homologous
IL_5J7L_033
NA
IL_6V3A_2061/sN1/670:674,
1/sN1/710:714		Triple non-canonical cWW pairs
homologous
IL_4LFB_065
IL_71154.1
IL_6V3A_2071/sN1/681:685,
1/sN1/696:703		Kink-turn
homologous
IL_5J7L_035
NA
IL_6V3A_1501/sN1/771:775,
1/sN1/801:802		Left turn
homologous
IL_5J7L_036
NA
IL_6V3A_1511/sN1/776:780,
1/sN1/796:800		tSH-tHW-tHS
homologous
IL_5J7L_037
NA
IL_6V3A_1521/sN1/884:891,
1/sN1/902:907		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_5J7L_038
NA
IL_6V3A_1531/sN1/919:920,
1/sN1/1390:1392		Single bulged A
homologous
IL_5J7L_039
NA
IL_6V3A_1541/sN1/922:924,
1/sN1/1387:1388		Single bulged G
homologous
IL_4LFB_036
IL_28408.1
IL_6V3A_1551/sN1/930:932,
1/sN1/1377:1381		Minor groove platform
homologous
IL_5J7L_041
NA
IL_6V3A_1561/sN1/950:951,
1/sN1/1223:1225		No text annotation
homologous
IL_6CZR_150
NA
IL_6V3A_1581/sN1/1006:1007,
1/sN1/1015:1017		Single stack bend
geometric
IL_5J7L_269
NA
IL_6V3A_1591/sN1/1007:1009,
1/sN1/1014:1015		No text annotation
IL_6V3A_1601/sN1/1045:1047,
1/sN1/1205:1206		Single bulged U
homologous
IL_5J7L_046
NA
IL_6V3A_1621/sN1/1049:1053,
1/sN1/1201:1203		Isolated cWS basepair
geometric
IL_4LFB_044
IL_82453.1
IL_6V3A_1631/sN1/1054:1055,
1/sN1/1196:1200		Minor groove platform
homologous
IL_5J7L_048
NA
IL_6V3A_1641/sN1/1057:1058,
1/sN1/1192:1194		Single bulged U
homologous
IL_4LFB_046
IL_97561.1
IL_6V3A_1651/sN1/1058:1060,
1/sN1/1190:1192		Isolated non-canonical cWW pair
geometric
IL_3MEI_002
NA
IL_6V3A_2111/sN1/1120:1125,
1/sN1/1141:1147		No text annotation
IL_6V3A_1691/sN1/1126:1129,
1/sN1/1139:1140		Minor groove platform
homologous
IL_5J7L_052
NA
IL_6V3A_1701/sN1/1155:1158,
1/sN1/1172:1178		No text annotation
homologous
IL_5J7L_053
NA
IL_6V3A_1711/sN1/1244:1250,
1/sN1/1281:1287		No text annotation
homologous
IL_4LFB_051
IL_12056.1
IL_6V3A_1721/sN1/1252:1255,
1/sN1/1274:1279		180 degree turn
homologous
IL_4LFB_052
IL_08849.1
IL_6V3A_1731/sN1/1256:1259,
1/sN1/1270:1273		Tandem non-canonical cWW pairs
geometric
IL_4V88_461
NA
IL_6V3A_1741/sN1/1300:1305,
1/sN1/1326:1331		No text annotation
homologous
IL_4LFB_055
IL_57885.1
IL_6V3A_1751/sN1/1396:1398,
1/sN1/1498:1501		No text annotation
geometric
IL_5J7L_058
NA
IL_6V3A_1761/sN1/1398:1401,
1/sN1/1494:1498		No text annotation
homologous
IL_5J7L_059
NA
IL_6V3A_1771/sN1/1402:1404,
1/sN1/1491:1493		Isolated non-canonical cWW pair
geometric
IL_1YZ9_001
NA
IL_6V3A_1781/sN1/1404:1406,
1/sN1/1488:1491		No text annotation
geometric
IL_4V9F_072
IL_75527.1
IL_6V3A_1791/sN1/1409:1411,
1/sN1/1483:1485		Isolated non-canonical cWW pair
homologous
IL_5J7L_061
NA
IL_6V3A_1801/sN1/1413:1416,
1/sN1/1478:1481		Double sheared
homologous
IL_5J7L_062
NA
IL_6V3A_1811/sN1/1418:1420,
1/sN1/1474:1476		Isolated non-canonical cWW pair
geometric
IL_4P3T_001
NA
IL_6V3A_1831/sN1/1427:1432,
1/sN1/1463:1467		Triple sheared related
geometric
IL_4V9F_018
IL_67427.1
IL_6V3A_1841/sN1/1436:1439,
1/sN1/1457:1459		No text annotation
geometric
IL_6DME_003
IL_75527.1
IL_6V3A_1851/sN1/1442:1445,
1/sN1/1452:1454		No text annotation
geometric
IL_5J7L_065
NA

Problematic loops

#loop idProblemSequence
IL_6V3A_042Single stack bend
IL_6V3A_043No text annotation
IL_6V3A_052No text annotation
IL_6V3A_188No text annotation
IL_6V3A_058No text annotation
IL_6V3A_189No text annotation
IL_6V3A_059No text annotation
IL_6V3A_191No text annotation
IL_6V3A_193No text annotation
IL_6V3A_076No text annotation
IL_6V3A_077Isolated non-canonical cWW pair
IL_6V3A_195No text annotation
IL_6V3A_081No text annotation
IL_6V3A_209No text annotation
IL_6V3A_082No text annotation
IL_6V3A_083Isolated non-canonical cWW pair
IL_6V3A_084No text annotation
IL_6V3A_086No text annotation
IL_6V3A_092No text annotation
IL_6V3A_095No text annotation
IL_6V3A_099No text annotation
IL_6V3A_201Isolated non-canonical cWW pair
IL_6V3A_125No text annotation
IL_6V3A_126No text annotation
IL_6V3A_203No text annotation
IL_6V3A_137Single stack bend
IL_6V3A_204No text annotation
IL_6V3A_146No text annotation
IL_6V3A_148No text annotation
IL_6V3A_149Kink-turn
IL_6V3A_210Single stack bend
IL_6V3A_157No text annotation
IL_6V3A_161Isolated non-canonical cWW pair
IL_6V3A_166Single stack bend
IL_6V3A_167No text annotation
IL_6V3A_168No text annotation
IL_6V3A_208No text annotation
IL_6V3A_182Isolated non-canonical cWW pair
IL_6V3A_186Isolated non-canonical cWW pair

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_6V3A_0011/AN1/37:38,
1/AN1/473:480,
1/AN1/508:509		No text annotation
homologous
J3_5J7L_036
NA
J3_6V3A_0261/AN1/39:42,
1/AN1/444:460,
1/AN1/467:472		No text annotation
homologous
J3_9DFE_003
J3_07616.1
J3_6V3A_0021/AN1/63:64,
1/AN1/77:83,
1/AN1/117:121		No text annotation
homologous
J3_5J7L_037
NA
J3_6V3A_0271/AN1/299:303,
1/AN1/318:327,
1/AN1/339:343		No text annotation
homologous
J3_5J7L_068
NA
J3_6V3A_0031/AN1/681:687,
1/AN1/771:773,
1/AN1/789:792		No text annotation
homologous
J3_5J7L_038
NA
J3_6V3A_0041/AN1/696:698,
1/AN1/730:734,
1/AN1/758:761		No text annotation
homologous
J3_7RQB_005
NA
J3_6V3A_0061/AN1/1293:1298,
1/AN1/1623:1625,
1/AN1/1637:1640		No text annotation
homologous
J3_5J7L_041
NA
J3_6V3A_0071/AN1/1301:1304,
1/AN1/1603:1609,
1/AN1/1618:1620		No text annotation
homologous
J3_5J7L_042
NA
J3_6V3A_0081/AN1/1339:1344,
1/AN1/1377:1380,
1/AN1/1397:1398		No text annotation
homologous
J3_5J7L_043
NA
J3_6V3A_0291/AN1/1419:1424,
1/AN1/1562:1563,
1/AN1/1566:1572		No text annotation
homologous
J3_5J7L_069
NA
J3_6V3A_0301/AN1/1439:1440,
1/AN1/1461:1466,
1/AN1/1516:1545		No text annotation
J3_6V3A_0091/AN1/2087:2089,
1/AN1/2192:2196,
1/AN1/2219:2224		Kink-turn 3-way junction
homologous
J3_5J7L_044
NA
J3_6V3A_0311/AN1/2278:2280,
1/AN1/2380:2391,
1/AN1/2417:2423		No text annotation
homologous
J3_5J7L_070
NA
J3_6V3A_0101/AN1/2291:2295,
1/AN1/2313:2319,
1/AN1/2328:2333		No text annotation
J3_6V3A_0111/AN1/2513:2516,
1/AN1/2541:2543,
1/AN1/2557:2563		No text annotation
homologous
J3_5J7L_046
NA
J3_6V3A_0121/AN1/2785:2788,
1/AN1/2800:2802,
1/AN1/2888:2890		No text annotation
J3_6V3A_0131/AN1/2810:2811,
1/AN1/2827:2832,
1/AN1/2878:2882		No text annotation
homologous
J3_7RQB_014
NA
J3_6V3A_0141/B/8:14,
1/B/66:67,
1/B/104:107		No text annotation
homologous
J3_7A0S_021
J3_47324.1
J3_6V3A_0151/sN1/48:49,
1/sN1/357:363,
1/sN1/389:391		No text annotation
homologous
J3_5J7L_001
NA
J3_6V3A_0321/sN1/48:54,
1/sN1/355:363,
1/sN1/389:391		No text annotation
homologous
J3_5J7L_050
NA
J3_6V3A_0161/sN1/583:585,
1/sN1/648:651,
1/sN1/751:752		No text annotation
geometric
J3_1KUQ_001
J3_01633.1
J3_6V3A_0381/sN1/583:585,
1/sN1/648:652,
1/sN1/748:752		No text annotation
homologous
J3_4LFB_015
J3_17385.5
J3_6V3A_0171/sN1/669:670,
1/sN1/714:722,
1/sN1/729:731		No text annotation
homologous
J3_5J7L_003
NA
J3_6V3A_0181/sN1/823:826,
1/sN1/854:858,
1/sN1/865:871		No text annotation
homologous
J3_5J7L_004
NA
J3_6V3A_0341/sN1/933:936,
1/sN1/1341:1347,
1/sN1/1369:1376		No text annotation
homologous
J3_5J7L_052
NA
J3_6V3A_0191/sN1/940:943,
1/sN1/1232:1234,
1/sN1/1334:1337		No text annotation
homologous
J3_4LFB_003
J3_44359.1
J3_6V3A_0201/sN1/952:959,
1/sN1/970:981,
1/sN1/1218:1222		No text annotation
homologous
J3_5J7L_006
NA
J3_6V3A_0211/sN1/987:995,
1/sN1/1040:1044,
1/sN1/1207:1212		No text annotation
J3_6V3A_0221/sN1/1060:1065,
1/sN1/1104:1110,
1/sN1/1184:1190		No text annotation
homologous
J3_5J7L_008
NA
J3_6V3A_0231/sN1/1070:1071,
1/sN1/1080:1083,
1/sN1/1096:1099		No text annotation
J3_6V3A_0361/sN1/1070:1071,
1/sN1/1080:1086,
1/sN1/1093:1099		No text annotation
J3_6V3A_0391/sN1/1113:1115,
1/sN1/1152:1155,
1/sN1/1178:1181		No text annotation
geometric
J3_5J7L_010
NA
J3_6V3A_0401/sN1/1113:1115,
1/sN1/1152:1158,
1/sN1/1172:1181		No text annotation
homologous
J3_4LFB_018
J3_40706.1
J3_6V3A_0251/sN1/1234:1238,
1/sN1/1293:1300,
1/sN1/1331:1334		No text annotation
homologous
J3_4LFB_009
J3_03192.1
J4_6V3A_0011/AN1/275:276,
1/AN1/369:374,
1/AN1/398:405,
1/AN1/420:423		No text annotation
homologous
J4_5J7L_018
NA
J4_6V3A_0021/AN1/299:303,
1/AN1/318:321,
1/AN1/325:327,
1/AN1/339:343		No text annotation
homologous
J4_5J7L_019
NA
J4_6V3A_0031/AN1/599:602,
1/AN1/622:626,
1/AN1/633:636,
1/AN1/648:654		No text annotation
homologous
J4_5J7L_020
NA
J4_6V3A_0041/AN1/1265:1271,
1/AN1/1289:1290,
1/AN1/1643:1646,
1/AN1/2005:2006		No text annotation
homologous
J4_7A0S_004
J4_64571.6
J4_6V3A_0051/AN1/1305:1309,
1/AN1/1333:1338,
1/AN1/1399:1400,
1/AN1/1595:1602		No text annotation
homologous
J4_5J7L_022
NA
J4_6V3A_0061/AN1/1308:1309,
1/AN1/1333:1338,
1/AN1/1399:1400,
1/AN1/1595:1601		No text annotation
homologous
J4_5J7L_023
NA
J4_6V3A_0071/AN1/1768:1772,
1/AN1/1784:1788,
1/AN1/1823:1826,
1/AN1/1971:1975		No text annotation
homologous
J4_5J7L_025
NA
J4_6V3A_0081/AN1/1829:1831,
1/AN1/1901:1902,
1/AN1/1920:1929,
1/AN1/1963:1968		No text annotation
homologous
J4_5J7L_026
NA
J4_6V3A_0091/AN1/2281:2285,
1/AN1/2339:2343,
1/AN1/2366:2368,
1/AN1/2377:2379		No text annotation
homologous
J4_5J7L_027
NA
J4_6V3A_0101/AN1/2639:2642,
1/AN1/2670:2672,
1/AN1/2727:2731,
1/AN1/2765:2767		No text annotation
J4_6V3A_0111/sN1/111:118,
1/sN1/235:236,
1/sN1/282:285,
1/sN1/307:308		No text annotation
homologous
J4_5J7L_001
NA
J4_6V3A_0121/sN1/139:140,
1/sN1/174:180,
1/sN1/189:194,
1/sN1/215:216		No text annotation
J4_6V3A_0131/sN1/572:574,
1/sN1/761:766,
1/sN1/807:818,
1/sN1/876:877		No text annotation
homologous
J4_5J7L_003
NA
J4_6V3A_0141/v/7:10,
1/v/26:28,
1/v/44:50,
1/v/66:67		tRNA junction
homologous
J4_7MRL_001
NA
J5_6V3A_0011/AN1/54:61,
1/AN1/123:128,
1/AN1/137:138,
1/AN1/155:157,
1/AN1/183:185		No text annotation
homologous
J5_5J7L_013
NA
J5_6V3A_0021/AN1/530:532,
1/AN1/558:562,
1/AN1/575:577,
1/AN1/1256:1257,
1/AN1/2013:2014		No text annotation
homologous
J5_5J7L_014
NA
J5_6V3A_0031/AN1/582:587,
1/AN1/666:669,
1/AN1/807:810,
1/AN1/1190:1191,
1/AN1/1245:1251		No text annotation
homologous
J5_5J7L_015
NA
J5_6V3A_0041/AN1/1672:1680,
1/AN1/1704:1705,
1/AN1/1747:1748,
1/AN1/1752:1760,
1/AN1/1984:1986		No text annotation
homologous
J5_5J7L_016
NA
J5_6V3A_0051/AN1/2053:2060,
1/AN1/2442:2449,
1/AN1/2496:2503,
1/AN1/2578:2584,
1/AN1/2602:2607		No text annotation
J5_6V3A_0061/AN1/2070:2073,
1/AN1/2239:2242,
1/AN1/2254:2255,
1/AN1/2277:2278,
1/AN1/2423:2431		No text annotation
homologous
J5_4WF9_007
J5_39529.2
J5_6V3A_0071/sN1/38:41,
1/sN1/399:402,
1/sN1/432:436,
1/sN1/494:497,
1/sN1/542:545		No text annotation
homologous
J5_5J7L_001
NA
J5_6V3A_0081/sN1/38:41,
1/sN1/399:402,
1/sN1/432:438,
1/sN1/489:497,
1/sN1/542:545		No text annotation
homologous
J5_5J7L_002
NA
J5_6V3A_0091/sN1/60:63,
1/sN1/102:109,
1/sN1/310:312,
1/sN1/333:335,
1/sN1/346:350		No text annotation
homologous
J5_4LFB_002
J5_58574.1
J6_6V3A_0011/AN1/52:53,
1/AN1/186:190,
1/AN1/221:231,
1/AN1/238:242,
1/AN1/269:273,
1/AN1/425:432		No text annotation
J6_6V3A_0021/AN1/2070:2073,
1/AN1/2239:2242,
1/AN1/2254:2255,
1/AN1/2277:2280,
1/AN1/2380:2391,
1/AN1/2417:2431		No text annotation
J7_6V3A_0011/AN1/15:22,
1/AN1/524:530,
1/AN1/2014:2019,
1/AN1/2036:2039,
1/AN1/2621:2626,
1/AN1/2784:2785,
1/AN1/2890:2891		No text annotation
J7_6V3A_0021/AN1/815:820,
1/AN1/833:836,
1/AN1/937:943,
1/AN1/968:973,
1/AN1/984:988,
1/AN1/1161:1162,
1/AN1/1180:1185		No text annotation

Problematic loops

#loop idProblemSequence
J3_6V3A_028No text annotation
J3_6V3A_005No text annotation
J3_6V3A_033No text annotation
J3_6V3A_035No text annotation
J3_6V3A_024No text annotation
J3_6V3A_037No text annotation

Coloring options:
Copyright 2025 BGSU RNA group. Page generated in 0.1039 s