RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_9NJV_0011/R1/59:68No text annotation
homologous
HL_5J7L_134
NA
HL_9NJV_0021/R1/87:95No text annotation
homologous
HL_5J7L_135
NA
HL_9NJV_0031/R1/123:128No text annotation
homologous
HL_5J7L_136
NA
HL_9NJV_0041/R1/153:172No text annotation
HL_9NJV_0051/R1/194:201No text annotation
homologous
HL_5J7L_139
NA
HL_9NJV_0061/R1/225:230No text annotation
homologous
HL_5J7L_140
NA
HL_9NJV_0071/R1/246:252No text annotation
homologous
HL_5J7L_141
NA
HL_9NJV_0081/R1/305:312T-loop with 2 stacked bulged bases
homologous
HL_5J7L_142
NA
HL_9NJV_0091/R1/327:335T-loop with unstacked turn
homologous
HL_5J7L_144
NA
HL_9NJV_0101/R1/382:392No text annotation
homologous
HL_5J7L_145
NA
HL_9NJV_0111/R1/410:417Pseudoknot geometry
homologous
HL_7A0S_014
HL_30680.4
HL_9NJV_0121/R1/462:467GNRA
homologous
HL_4WF9_015
HL_34789.1
HL_9NJV_0131/R1/487:493GNRA
homologous
HL_5J7L_148
NA
HL_9NJV_0151/R1/566:575T-loop with 2 stacked bulged bases
homologous
HL_5J7L_150
NA
HL_9NJV_0161/R1/611:617No text annotation
geometric
HL_2ZZM_002
NA
HL_9NJV_0171/R1/629:634GNRA
homologous
HL_5J7L_152
NA
HL_9NJV_0181/R1/641:647No text annotation
homologous
HL_5J7L_153
NA
HL_9NJV_0191/R1/712:719GNRA wlth tandem sheared
homologous
HL_5J7L_154
NA
HL_9NJV_0201/R1/744:753No text annotation
homologous
HL_7A0S_022
HL_50204.1
HL_9NJV_0211/R1/779:785No text annotation
homologous
HL_5J7L_156
NA
HL_9NJV_0221/R1/826:831No text annotation
homologous
HL_9DFE_023
HL_27530.1
HL_9NJV_0231/R1/875:902No text annotation
HL_9NJV_0241/R1/954:963GNRA with extra cWH
geometric
HL_7QR8_003
NA
HL_9NJV_0251/R1/978:985No text annotation
homologous
HL_5J7L_160
NA
HL_9NJV_0281/R1/1222:1227GNRA
homologous
HL_7A0S_031
HL_34789.1
HL_9NJV_0291/R1/1281:1289T-loop with 2 stacked bulged bases
homologous
HL_5J7L_165
NA
HL_9NJV_0301/R1/1324:1330Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_166
NA
HL_9NJV_0311/R1/1363:1368GNRA
homologous
HL_5J7L_167
NA
HL_9NJV_0321/R1/1389:1398No text annotation
homologous
HL_5J7L_168
NA
HL_9NJV_0331/R1/1451:1459Mini UNCG with extended bulge
homologous
HL_5J7L_169
NA
HL_9NJV_0341/R1/1492:1498Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_170
NA
HL_9NJV_0361/R1/1565:1568Mini UNCG
homologous
HL_5J7L_172
NA
HL_9NJV_0371/R1/1612:1619No text annotation
homologous
HL_5J7L_173
NA
HL_9NJV_0381/R1/1630:1636GNRA
homologous
HL_5J7L_174
NA
HL_9NJV_0391/R1/1691:1696UNCG
homologous
HL_5J7L_175
NA
HL_9NJV_0401/R1/1727:1733No text annotation
homologous
HL_5J7L_214
NA
HL_9NJV_0411/R1/1752:1756No text annotation
homologous
HL_5J7L_177
NA
HL_9NJV_0421/R1/1777:1787No text annotation
homologous
HL_4WF9_043
HL_87681.1
HL_9NJV_0431/R1/1806:1811GNRA related
homologous
HL_5J7L_179
NA
HL_9NJV_0451/R1/1910:1920No text annotation
HL_9NJV_0461/R1/1949:1957No text annotation
homologous
HL_5J7L_182
NA
HL_9NJV_0471/R1/2027:2036No text annotation
homologous
HL_5J7L_183
NA
HL_9NJV_0491/R1/2209:2215No text annotation
homologous
HL_4WF9_048
HL_81964.1
HL_9NJV_0501/R1/2248:2256No text annotation
homologous
HL_4WF9_049
HL_11974.1
HL_9NJV_0511/R1/2264:2276No text annotation
homologous
HL_5J7L_187
NA
HL_9NJV_0521/R1/2304:2312No text annotation
homologous
HL_5J7L_219
NA
HL_9NJV_0531/R1/2324:2331Pseudoknot geometry
homologous
HL_5J7L_189
NA
HL_9NJV_0541/R1/2356:2361GNRA
homologous
HL_5J7L_190
NA
HL_9NJV_0551/R1/2374:2379GNRA
homologous
HL_5J7L_191
NA
HL_9NJV_0561/R1/2404:2413No text annotation
homologous
HL_5J7L_192
NA
HL_9NJV_0571/R1/2471:2479No text annotation
homologous
HL_7A0S_059
HL_52011.1
HL_9NJV_0581/R1/2528:2535GNRA variation
homologous
HL_5J7L_194
NA
HL_9NJV_0591/R1/2551:2557No text annotation
homologous
HL_5J7L_195
NA
HL_9NJV_0601/R1/2594:2599GNRA
homologous
HL_7A0S_062
HL_34789.1
HL_9NJV_0611/R1/2658:2663GNRA
homologous
HL_9DFE_062
HL_34789.1
HL_9NJV_0621/R1/2701:2706Ribsomal LSU H95
homologous
HL_5J7L_198
NA
HL_9NJV_0631/R1/2745:2759No text annotation
homologous
HL_5J7L_199
NA
HL_9NJV_0641/R1/2795:2801UNCG variation
homologous
HL_5J7L_200
NA
HL_9NJV_0651/R1/2819:2827No text annotation
homologous
HL_5J7L_201
NA
HL_9NJV_0661/R1/2856:2861GNRA
homologous
HL_7A0S_068
HL_34789.1
HL_9NJV_0671/R2/34:48No text annotation
homologous
HL_5J7L_215
NA
HL_9NJV_0681/R2/86:90Mini UNCG
homologous
HL_5J7L_204
NA
HL_9NJV_0691/R3/12:22No text annotation
homologous
HL_4LFB_001
HL_31940.1
HL_9NJV_0701/R3/75:95No text annotation
HL_9NJV_0711/R3/158:163GNRA
homologous
HL_5J7L_003
NA
HL_9NJV_0721/R3/186:191GNRA
homologous
HL_5J7L_004
NA
HL_9NJV_0731/R3/200:217No text annotation
HL_9NJV_0741/R3/259:267GNRA related
homologous
HL_5J7L_006
NA
HL_9NJV_0751/R3/296:301GNRA
homologous
HL_5J7L_007
NA
HL_9NJV_0761/R3/319:334No text annotation
HL_9NJV_0771/R3/342:347UNCG
homologous
HL_6CZR_080
NA
HL_9NJV_0781/R3/377:386No text annotation
HL_9NJV_0791/R3/419:424UNCG
homologous
HL_4LFB_011
HL_61337.1
HL_9NJV_0811/R3/522:527GNRA variation
homologous
HL_4LFB_033
HL_34789.1
HL_9NJV_0821/R3/617:623GNRA-like with tWH
homologous
HL_4LFB_014
HL_92337.1
HL_9NJV_0831/R3/689:698No text annotation
homologous
HL_4LFB_015
HL_38491.1
HL_9NJV_0841/R3/726:731GNRA
homologous
HL_4LFB_016
HL_34789.1
HL_9NJV_0851/R3/786:796No text annotation
homologous
HL_5J7L_017
NA
HL_9NJV_0871/R3/862:867GNRA
homologous
HL_4LFB_019
HL_34789.1
HL_9NJV_0881/R3/897:902GNRA
homologous
HL_4LFB_020
HL_34789.1
HL_9NJV_0891/R3/963:972No text annotation
homologous
HL_4LFB_021
HL_97521.1
HL_9NJV_0901/R3/1012:1017GNRA
homologous
HL_4LFB_022
HL_34789.1
HL_9NJV_0921/R3/1076:1081GNRA
homologous
HL_5J7L_023
NA
HL_9NJV_0931/R3/1089:1096T-loop related
homologous
HL_4LFB_025
HL_63894.1
HL_9NJV_0941/R3/1134:1140No text annotation
homologous
HL_4LFB_026
HL_92935.1
HL_9NJV_0951/R3/1165:1171GNRA
homologous
HL_4LFB_027
HL_34789.1
HL_9NJV_0961/R3/1265:1270GNRA
homologous
HL_5J7L_027
NA
HL_9NJV_0971/R3/1314:1323T-loop with 3 stacked bulged bases
homologous
HL_5J7L_028
NA
HL_9NJV_0981/R3/1356:1366No text annotation
homologous
HL_4LFB_030
HL_86432.1
HL_9NJV_0991/R3/1449:1454UNCG
homologous
HL_5J7L_030
NA
HL_9NJV_1001/R3/1515:1520GNRA
homologous
HL_5J7L_031
NA
HL_9NJV_1011/T/12:22tRNA D-loop
homologous
HL_7MRL_001
NA
HL_9NJV_1021/T/31:39tRNA anticodon loop
homologous
HL_5E81_212
NA
HL_9NJV_1031/T/53:61T-loop with 2 stacked bulged bases
homologous
HL_3WQY_003
HL_33597.1

Problematic loops

#loop idProblemSequence
HL_9NJV_014No text annotation
HL_9NJV_026GNRA wlth tandem sheared
HL_9NJV_027No text annotation
HL_9NJV_035UNCG
HL_9NJV_044No text annotation
HL_9NJV_048No text annotation
HL_9NJV_080No text annotation
HL_9NJV_086No text annotation
HL_9NJV_091No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_9NJV_0011/R1/2:4,
1/R1/2900:2901		Single stack bend
geometric
IL_7A0S_054
IL_15011.1
IL_9NJV_0021/R1/4:5,
1/R1/2898:2900		Single stack bend
geometric
IL_8CRE_075
NA
IL_9NJV_0041/R1/24:30,
1/R1/510:516		Triple sheared with non-canonical cWW
homologous
IL_5J7L_245
NA
IL_9NJV_0051/R1/36:37,
1/R1/442:444		Single bulged A
homologous
IL_7A0S_002
IL_14190.1
IL_9NJV_0061/R1/43:44,
1/R1/434:436		Minor groove platform
homologous
IL_5J7L_247
NA
IL_9NJV_0071/R1/81:85,
1/R1/97:105		No text annotation
homologous
IL_5J7L_248
NA
IL_9NJV_0081/R1/183:184,
1/R1/212:214		Single stack bend
homologous
IL_7A0S_005
IL_15011.1
IL_9NJV_0091/R1/188:194,
1/R1/201:208		8x7 Sarcin-Ricin; G-bulge
homologous
IL_7A0S_006
IL_62167.1
IL_9NJV_0101/R1/239:245,
1/R1/253:258		7x6 Sarcin-Ricin; G-bulge
geometric
IL_1NBS_007
IL_02666.1
IL_9NJV_0111/R1/269:271,
1/R1/366:370		No text annotation
homologous
IL_5J7L_252
NA
IL_9NJV_0121/R1/273:282,
1/R1/358:364		No text annotation
IL_9NJV_0131/R1/293:295,
1/R1/343:347		No text annotation
homologous
IL_5J7L_254
NA
IL_9NJV_0141/R1/536:539,
1/R1/554:557		Double sheared
homologous
IL_5J7L_256
NA
IL_9NJV_0151/R1/564:566,
1/R1/575:577		Isolated non-canonical cWW pair
homologous
IL_7A0S_011
IL_71625.1
IL_9NJV_0161/R1/606:610,
1/R1/618:622		AAA cross-strand stack
homologous
IL_5J7L_258
NA
IL_9NJV_0171/R1/672:674,
1/R1/806:808		Isolated non-canonical cWW pair
homologous
IL_4WF9_020
IL_01003.1
IL_9NJV_0181/R1/674:678,
1/R1/799:806		tHW-tHW cross-strand stack
homologous
IL_5J7L_260
NA
IL_9NJV_0191/R1/697:698,
1/R1/763:765		Single bulged A
homologous
IL_5J7L_261
NA
IL_9NJV_0201/R1/702:703,
1/R1/728:730		Single bulged G
homologous
IL_5J7L_262
NA
IL_9NJV_0211/R1/703:707,
1/R1/724:728		Triple sheared
homologous
IL_4WF9_024
IL_15190.1
IL_9NJV_0221/R1/738:740,
1/R1/757:758		Major groove platform
homologous
IL_5J7L_264
NA
IL_9NJV_0231/R1/775:777,
1/R1/787:791		Multiple bulged bases
geometric
IL_5J7L_265
NA
IL_9NJV_0241/R1/844:847,
1/R1/933:934		90 degree turn
geometric
IL_5J7L_267
NA
IL_9NJV_0251/R1/844:848,
1/R1/930:934		No text annotation
geometric
IL_5J7L_399
NA
IL_9NJV_0261/R1/847:848,
1/R1/930:933		Stack outside cWW
homologous
IL_5J7L_268
NA
IL_9NJV_0271/R1/850:851,
1/R1/926:928		Single stack bend
homologous
IL_5J7L_269
NA
IL_9NJV_0281/R1/856:862,
1/R1/915:921		7x7 Sarcin-Ricin with intercalated A; G-bulge
homologous
IL_5J7L_270
NA
IL_9NJV_0291/R1/862:863,
1/R1/913:915		Single bulged G
homologous
IL_5J7L_271
NA
IL_9NJV_0301/R1/864:868,
1/R1/909:912		C-loop with bulged stacked A's
homologous
IL_5J7L_272
NA
IL_9NJV_0311/R1/870:872,
1/R1/905:907		Isolated non-canonical cWW pair
homologous
IL_5J7L_273
NA
IL_9NJV_0321/R1/994:996,
1/R1/1159:1160		Single bulged C
homologous
IL_7A0S_032
IL_05642.1
IL_9NJV_0331/R1/998:1002,
1/R1/1153:1157		UAA/GAN
homologous
IL_7A0S_033
IL_08938.1
IL_9NJV_0341/R1/1004:1011,
1/R1/1150:1151		SSU/LSU pseudoknot
homologous
IL_5J7L_278
NA
IL_9NJV_0351/R1/1011:1013,
1/R1/1149:1150		Single bulged U
homologous
IL_5J7L_279
NA
IL_9NJV_0361/R1/1018:1024,
1/R1/1140:1144		Kink-turn related
homologous
IL_4WF9_039
IL_57188.6
IL_9NJV_0371/R1/1024:1030,
1/R1/1124:1140		No text annotation
homologous
IL_5J7L_281
NA
IL_9NJV_0381/R1/1031:1034,
1/R1/1121:1123		Isolated non-canonical cWW pair
homologous
IL_5J7L_282
NA
IL_9NJV_0391/R1/1038:1041,
1/R1/1114:1117		Tandem non-canonical cWW pairs
homologous
IL_5J7L_283
NA
IL_9NJV_0401/R1/1043:1053,
1/R1/1106:1112		No text annotation
IL_9NJV_0431/R1/1196:1198,
1/R1/1247:1250		Isolated cWS basepair
homologous
IL_4WF9_044
IL_42997.4
IL_9NJV_0441/R1/1202:1206,
1/R1/1240:1243		No text annotation
homologous
IL_5J7L_287
NA
IL_9NJV_0451/R1/1208:1215,
1/R1/1234:1238		Kink-turn
homologous
IL_5J7L_288
NA
IL_9NJV_0461/R1/1262:1269,
1/R1/2011:2017		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
NA
IL_9NJV_0471/R1/1319:1323,
1/R1/1331:1333		C-loop
homologous
IL_5J7L_291
NA
IL_9NJV_0481/R1/1351:1353,
1/R1/1379:1380		Single stack bend with SAM intercalation
geometric
IL_6FZ0_001
NA
IL_9NJV_0491/R1/1351:1355,
1/R1/1376:1380		UAA/GAN
geometric
IL_5J7L_292
NA
IL_9NJV_0501/R1/1353:1355,
1/R1/1376:1379		No text annotation
IL_9NJV_0511/R1/1357:1361,
1/R1/1370:1374		tSH-tHW-tHS
homologous
IL_5J7L_293
NA
IL_9NJV_0521/R1/1415:1416,
1/R1/1582:1587		No text annotation
homologous
IL_5J7L_294
NA
IL_9NJV_0531/R1/1417:1421,
1/R1/1577:1581		UAA/GAN
homologous
IL_5J7L_295
NA
IL_9NJV_0541/R1/1432:1435,
1/R1/1557:1561		Tandem non-canonical cWW pairs
homologous
IL_5J7L_296
NA
IL_9NJV_0551/R1/1437:1440,
1/R1/1551:1555		tSH-tHW
homologous
IL_5J7L_297
NA
IL_9NJV_0561/R1/1450:1451,
1/R1/1459:1461		Single bulged U
homologous
IL_5J7L_298
NA
IL_9NJV_0571/R1/1468:1471,
1/R1/1520:1524		No text annotation
homologous
IL_5J7L_299
NA
IL_9NJV_0581/R1/1474:1478,
1/R1/1513:1517		tSH-tHW-tHS
homologous
IL_5J7L_300
NA
IL_9NJV_0591/R1/1481:1482,
1/R1/1507:1510		180 degree turn
homologous
IL_5J7L_301
NA
IL_9NJV_0601/R1/1489:1491,
1/R1/1499:1500		Single bulged A
homologous
IL_5J7L_302
NA
IL_9NJV_0611/R1/1526:1529,
1/R1/1542:1546		UAA/GAN variation
homologous
IL_5J7L_303
NA
IL_9NJV_0621/R1/1651:1656,
1/R1/2004:2006		No text annotation
homologous
IL_5J7L_304
NA
IL_9NJV_0631/R1/1663:1665,
1/R1/1995:1997		Isolated tWW turn
homologous
IL_4WF9_063
IL_10432.1
IL_9NJV_0641/R1/1666:1669,
1/R1/1993:1994		Major groove platform; stack outside cWW
geometric
IL_4WF9_064
IL_74641.1
IL_9NJV_0651/R1/1666:1674,
1/R1/1990:1994		No text annotation
geometric
IL_4WF9_117
IL_80252.1
IL_9NJV_0661/R1/1669:1674,
1/R1/1990:1993		Intercalated tWH
homologous
IL_4WF9_065
IL_28217.1
IL_9NJV_0671/R1/1686:1691,
1/R1/1696:1702		tSH-tSH-tHH-tHS
homologous
IL_5J7L_308
NA
IL_9NJV_0681/R1/1712:1718,
1/R1/1742:1746		6x5 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_309
NA
IL_9NJV_0691/R1/1720:1724,
1/R1/1736:1740		Triple sheared
homologous
IL_5J7L_310
NA
IL_9NJV_0701/R1/1770:1771,
1/R1/1980:1982		Single bulged A
homologous
IL_5J7L_312
NA
IL_9NJV_0711/R1/1798:1804,
1/R1/1813:1821		Kink-turn related
homologous
IL_7A0S_065
IL_17069.6
IL_9NJV_0721/R1/1837:1840,
1/R1/1902:1903		Minor groove platform, major groove intercalation
homologous
IL_5J7L_314
NA
IL_9NJV_0731/R1/1841:1842,
1/R1/1898:1901		Major groove intercalation
homologous
IL_5J7L_315
NA
IL_9NJV_0741/R1/1846:1849,
1/R1/1893:1894		Major groove minor groove platform; mini C-loop
homologous
IL_5J7L_316
NA
IL_9NJV_0751/R1/1851:1860,
1/R1/1882:1891		No text annotation
homologous
IL_5J7L_387
NA
IL_9NJV_0761/R1/1864:1867,
1/R1/1874:1878		UAA/GAN related
homologous
IL_5J7L_317
NA
IL_9NJV_0771/R1/1933:1934,
1/R1/1964:1967		Bulged stacked bases
geometric
IL_5J7L_318
NA
IL_9NJV_0781/R1/1934:1945,
1/R1/1961:1964		No text annotation
homologous
IL_7A0S_072
IL_04332.3
IL_9NJV_0791/R1/2050:2052,
1/R1/2617:2618		Major groove platform
homologous
IL_5J7L_320
NA
IL_9NJV_0801/R1/2054:2056,
1/R1/2612:2615		No text annotation
homologous
IL_5J7L_321
NA
IL_9NJV_0811/R1/2067:2069,
1/R1/2442:2443		Single bulged U
homologous
IL_7A0S_075
IL_97561.1
IL_9NJV_0821/R1/2070:2071,
1/R1/2438:2441		Minor groove platform
homologous
IL_5J7L_324
NA
IL_9NJV_0831/R1/2081:2083,
1/R1/2236:2239		Isolated tHS basepair with bulges
homologous
IL_5J7L_325
NA
IL_9NJV_0841/R1/2085:2087,
1/R1/2232:2234		Isolated non-canonical cWW pair
homologous
IL_5J7L_326
NA
IL_9NJV_0901/R1/2202:2204,
1/R1/2220:2221		Single bulged U
homologous
IL_5J7L_331
NA
IL_9NJV_0911/R1/2350:2353,
1/R1/2364:2367		Double sheared
homologous
IL_5J7L_333
NA
IL_9NJV_0921/R1/2401:2403,
1/R1/2414:2415		Single bulged U
geometric
IL_5LYS_008
IL_97561.1
IL_9NJV_0931/R1/2454:2455,
1/R1/2496:2498		Major groove platform
homologous
IL_4WF9_090
IL_48076.7
IL_9NJV_0941/R1/2456:2459,
1/R1/2493:2495		No text annotation
geometric
IL_6DME_003
IL_75527.1
IL_9NJV_0951/R1/2459:2461,
1/R1/2489:2493		Major groove minor groove platform with extra cWW
homologous
IL_7A0S_086
IL_36931.1
IL_9NJV_0961/R1/2466:2470,
1/R1/2480:2484		Double sheared with non-canonical cWW
homologous
IL_7A0S_087
IL_87767.1
IL_9NJV_0971/R1/2507:2509,
1/R1/2579:2582		Major groove platform with extra pair
geometric
IL_4AOB_003
IL_15698.4
IL_9NJV_0981/R1/2510:2512,
1/R1/2574:2578		Isolated non-canonical cWW with bulges
homologous
IL_9DFE_097
IL_68118.1
IL_9NJV_0991/R1/2512:2515,
1/R1/2569:2574		No text annotation
IL_9NJV_1001/R1/2522:2523,
1/R1/2540:2543		Major groove platform with intercalation
homologous
IL_7A0S_091
IL_94991.1
IL_9NJV_1011/R1/2591:2592,
1/R1/2601:2603		Single bulged A
homologous
IL_5J7L_344
NA
IL_9NJV_1021/R1/2636:2640,
1/R1/2774:2782		tSH-tHS-tHW
homologous
IL_5J7L_345
NA
IL_9NJV_1031/R1/2651:2658,
1/R1/2663:2669		8x7 Sarcin-Ricin; G-bulge
geometric
IL_8OI5_139
IL_62167.1
IL_9NJV_1041/R1/2680:2684,
1/R1/2725:2727		C-loop
homologous
IL_5J7L_347
NA
IL_9NJV_1051/R1/2687:2691,
1/R1/2718:2722		UAA/GAN related, with intercalation
homologous
IL_5J7L_348
NA
IL_9NJV_1061/R1/2695:2696,
1/R1/2711:2714		Multiple bulged bases
homologous
IL_5J7L_349
NA
IL_9NJV_1071/R1/2737:2742,
1/R1/2762:2767		UAA/GAN with extra cWW
homologous
IL_5J7L_350
NA
IL_9NJV_1081/R1/2806:2811,
1/R1/2889:2892		No text annotation
homologous
IL_5J7L_351
NA
IL_9NJV_1091/R1/2838:2839,
1/R1/2878:2880		Major groove intercalation
homologous
IL_5J7L_352
NA
IL_9NJV_1101/R1/2843:2846,
1/R1/2870:2874		Multiple bulged bases with non-canonical cWW
homologous
IL_5J7L_353
NA
IL_9NJV_1111/R1/2847:2852,
1/R1/2865:2869		tHS double platform
homologous
IL_5J7L_354
NA
IL_9NJV_1131/R2/17:18,
1/R2/65:67		Major groove intercalation
homologous
IL_5J7L_355
NA
IL_9NJV_1141/R2/22:28,
1/R2/56:61		No text annotation
IL_9NJV_1151/R2/30:31,
1/R2/51:54		No text annotation
homologous
IL_9DFE_112
IL_73108.1
IL_9NJV_1161/R2/71:79,
1/R2/97:105		Bacterial 5S Loop E
homologous
IL_7A0S_106
IL_71138.1
IL_9NJV_1171/R3/30:33,
1/R3/551:553		Isolated cWH basepair
geometric
IL_3R1E_001
NA
IL_9NJV_1191/R3/44:45,
1/R3/396:398		Single bulged A
homologous
IL_5J7L_002
NA
IL_9NJV_1201/R3/47:52,
1/R3/359:361		No text annotation
geometric
IL_5J7L_003
NA
IL_9NJV_1211/R3/54:56,
1/R3/356:357		Minor groove platform
homologous
IL_4LFB_004
IL_34520.1
IL_9NJV_1221/R3/63:66,
1/R3/103:104		Multiple bulged bases
homologous
IL_4LFB_005
IL_71421.1
IL_9NJV_1231/R3/67:69,
1/R3/99:102		Minor groove platform with extra cWW
homologous
IL_5J7L_006
NA
IL_9NJV_1241/R3/70:73,
1/R3/97:98		Minor groove platform
homologous
IL_5J7L_007
NA
IL_9NJV_1251/R3/128:132,
1/R3/230:233		No text annotation
IL_9NJV_1261/R3/132:136,
1/R3/227:230		No text annotation
homologous
IL_4LFB_008
IL_60988.1
IL_9NJV_1271/R3/144:146,
1/R3/176:178		Isolated cWH basepair
homologous
IL_5J7L_011
NA
IL_9NJV_1281/R3/147:153,
1/R3/168:175		tWH-tWH-tHW-tHW
homologous
IL_5J7L_012
NA
IL_9NJV_1291/R3/242:247,
1/R3/277:284		Kink-turn with non-sequential stacking
homologous
IL_5J7L_014
NA
IL_9NJV_1301/R3/249:253,
1/R3/273:275		No text annotation
IL_9NJV_1311/R3/292:293,
1/R3/304:308		C-loop
homologous
IL_4LFB_013
IL_06671.1
IL_9NJV_1321/R3/367:369,
1/R3/392:393		Single bulged U
homologous
IL_5J7L_017
NA
IL_9NJV_1331/R3/371:375,
1/R3/389:390		C-loop
homologous
IL_5J7L_018
NA
IL_9NJV_1341/R3/375:376,
1/R3/387:389		Single bulged G
homologous
IL_5J7L_019
NA
IL_9NJV_1351/R3/409:416,
1/R3/427:433		No text annotation
homologous
IL_5J7L_020
NA
IL_9NJV_1361/R3/440:442,
1/R3/492:497		No text annotation
homologous
IL_5J7L_021
NA
IL_9NJV_1371/R3/446:450,
1/R3/483:488		tSH-tHW-tWW
homologous
IL_5J7L_022
NA
IL_9NJV_1381/R3/450:455,
1/R3/477:483		No text annotation
homologous
IL_5J7L_023
NA
IL_9NJV_1391/R3/504:511,
1/R3/540:541		SSU/LSU pseudoknot
homologous
IL_4LFB_020
IL_11411.1
IL_9NJV_1401/R3/515:521,
1/R3/528:536		Kink-turn related
homologous
IL_4LFB_021
IL_52042.1
IL_9NJV_1411/R3/569:575,
1/R3/880:881		No text annotation
homologous
IL_5J7L_026
NA
IL_9NJV_1421/R3/580:584,
1/R3/757:761		tSH-tHW-tHS
homologous
IL_5J7L_027
NA
IL_9NJV_1431/R3/594:596,
1/R3/644:645		Major groove platform
homologous
IL_5J7L_028
NA
IL_9NJV_1441/R3/597:598,
1/R3/640:643		Major groove minor groove platform; mini C-loop
homologous
IL_4LFB_025
IL_73108.1
IL_9NJV_1451/R3/605:612,
1/R3/628:633		No text annotation
homologous
IL_5J7L_030
NA
IL_9NJV_1461/R3/654:655,
1/R3/751:754		Major groove platform; stack outside cWW
geometric
IL_5J7L_031
NA
IL_9NJV_1471/R3/659:660,
1/R3/745:747		Single stack bend
homologous
IL_5J7L_032
NA
IL_9NJV_1481/R3/662:666,
1/R3/740:743		Tandem non-canonical cWW pairs
homologous
IL_5J7L_033
NA
IL_9NJV_1491/R3/673:677,
1/R3/713:717		Triple non-canonical cWW pairs
homologous
IL_4LFB_065
IL_71154.1
IL_9NJV_1501/R3/684:688,
1/R3/699:706		Kink-turn
homologous
IL_5J7L_035
NA
IL_9NJV_1511/R3/774:778,
1/R3/804:805		Left turn
homologous
IL_4LFB_032
IL_29346.3
IL_9NJV_1521/R3/779:783,
1/R3/799:803		tSH-tHW-tHS
homologous
IL_4LFB_033
IL_05821.1
IL_9NJV_1531/R3/887:894,
1/R3/905:910		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_5J7L_038
NA
IL_9NJV_1541/R3/922:923,
1/R3/1393:1395		Single bulged A
homologous
IL_5J7L_039
NA
IL_9NJV_1551/R3/925:927,
1/R3/1390:1391		Single bulged G
homologous
IL_5J7L_040
NA
IL_9NJV_1561/R3/933:935,
1/R3/1380:1384		Minor groove platform
homologous
IL_4LFB_037
IL_61370.1
IL_9NJV_1571/R3/953:954,
1/R3/1226:1228		No text annotation
homologous
IL_6CZR_150
NA
IL_9NJV_1581/R3/993:997,
1/R3/1044:1045		Minor groove platform
geometric
IL_5J7L_043
NA
IL_9NJV_1591/R3/1048:1050,
1/R3/1208:1209		Single bulged U
homologous
IL_5J7L_046
NA
IL_9NJV_1601/R3/1052:1056,
1/R3/1204:1206		Isolated cWS basepair
homologous
IL_4LFB_044
IL_82453.1
IL_9NJV_1611/R3/1057:1058,
1/R3/1199:1203		Minor groove platform
homologous
IL_5J7L_048
NA
IL_9NJV_1621/R3/1060:1061,
1/R3/1195:1197		Single bulged U
homologous
IL_4LFB_046
IL_97561.1
IL_9NJV_1631/R3/1061:1063,
1/R3/1193:1195		Isolated non-canonical cWW pair
homologous
IL_5J7L_050
NA
IL_9NJV_1641/R3/1124:1128,
1/R3/1144:1149		No text annotation
homologous
IL_5J7L_051
NA
IL_9NJV_1651/R3/1128:1134,
1/R3/1140:1144		No text annotation
IL_9NJV_1661/R3/1158:1161,
1/R3/1175:1181		No text annotation
geometric
IL_5J7L_053
NA
IL_9NJV_1671/R3/1247:1253,
1/R3/1284:1290		No text annotation
homologous
IL_5J7L_054
NA
IL_9NJV_1681/R3/1255:1258,
1/R3/1277:1282		180 degree turn
homologous
IL_5J7L_055
NA
IL_9NJV_1691/R3/1259:1263,
1/R3/1272:1276		Double sheared with non-canonical cWW
geometric
IL_4V9F_085
IL_87767.1
IL_9NJV_1701/R3/1303:1308,
1/R3/1329:1334		No text annotation
homologous
IL_4LFB_055
IL_57885.1
IL_9NJV_1711/R3/1399:1401,
1/R3/1501:1504		No text annotation
homologous
IL_5J7L_058
NA
IL_9NJV_1721/R3/1401:1404,
1/R3/1497:1501		No text annotation
homologous
IL_4LFB_068
IL_25873.1
IL_9NJV_1731/R3/1405:1407,
1/R3/1494:1496		Isolated non-canonical cWW pair
homologous
IL_5J7L_363
NA
IL_9NJV_1741/R3/1407:1409,
1/R3/1491:1494		Isolated non-canonical cWW pair
geometric
IL_7D7V_003
NA
IL_9NJV_1751/R3/1412:1414,
1/R3/1486:1488		Isolated non-canonical cWW pair
homologous
IL_5J7L_061
NA
IL_9NJV_1761/R3/1416:1419,
1/R3/1481:1484		Double sheared
homologous
IL_5J7L_062
NA
IL_9NJV_1771/R3/1430:1435,
1/R3/1466:1470		Triple sheared related
homologous
IL_5J7L_063
NA
IL_9NJV_1791/R3/1440:1442,
1/R3/1460:1461		Single bulged A
geometric
IL_8VMA_003
IL_14190.1
IL_9NJV_1801/R3/1445:1448,
1/R3/1455:1457		No text annotation
homologous
IL_5J7L_065
NA

Problematic loops

#loop idProblemSequence
IL_9NJV_003Isolated cWH basepair
IL_9NJV_041No text annotation
IL_9NJV_042No text annotation
IL_9NJV_085No text annotation
IL_9NJV_086Isolated tWW contact
IL_9NJV_087No text annotation
IL_9NJV_088No text annotation
IL_9NJV_089No text annotation
IL_9NJV_112Isolated cWH basepair
IL_9NJV_118Isolated cWH basepair
IL_9NJV_178Isolated cWH basepair

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_9NJV_0011/R1/30:31,
1/R1/474:484,
1/R1/496:510		No text annotation
homologous
J3_4WF9_011
J3_17917.1
J3_9NJV_0021/R1/32:35,
1/R1/445:461,
1/R1/468:473		No text annotation
homologous
J3_5J7L_067
NA
J3_9NJV_0031/R1/56:57,
1/R1/70:77,
1/R1/109:114		No text annotation
J3_9NJV_0041/R1/296:301,
1/R1/316:325,
1/R1/337:342		No text annotation
geometric
J3_4V9F_015
J3_59706.1
J3_9NJV_0051/R1/683:690,
1/R1/772:775,
1/R1/791:794		No text annotation
J3_9NJV_0061/R1/698:700,
1/R1/732:736,
1/R1/760:763		No text annotation
homologous
J3_5J7L_039
NA
J3_9NJV_0071/R1/1298:1303,
1/R1/1625:1627,
1/R1/1639:1642		No text annotation
homologous
J3_5J7L_041
NA
J3_9NJV_0081/R1/1306:1309,
1/R1/1605:1611,
1/R1/1620:1622		No text annotation
homologous
J3_5J7L_042
NA
J3_9NJV_0091/R1/1344:1349,
1/R1/1382:1385,
1/R1/1402:1403		No text annotation
homologous
J3_5J7L_043
NA
J3_9NJV_0101/R1/1424:1429,
1/R1/1564:1565,
1/R1/1568:1574		No text annotation
homologous
J3_7A0S_019
J3_34864.3
J3_9NJV_0111/R1/2091:2093,
1/R1/2196:2200,
1/R1/2223:2228		Kink-turn 3-way junction
homologous
J3_5J7L_044
NA
J3_9NJV_0121/R1/2282:2284,
1/R1/2384:2395,
1/R1/2421:2427		No text annotation
homologous
J3_5J7L_070
NA
J3_9NJV_0131/R1/2295:2299,
1/R1/2317:2323,
1/R1/2332:2337		No text annotation
homologous
J3_5J7L_071
NA
J3_9NJV_0141/R1/2517:2520,
1/R1/2545:2547,
1/R1/2561:2567		No text annotation
homologous
J3_5J7L_046
NA
J3_9NJV_0151/R1/2789:2791,
1/R1/2805:2806,
1/R1/2892:2894		No text annotation
homologous
J3_5J7L_047
NA
J3_9NJV_0161/R1/2812:2815,
1/R1/2831:2836,
1/R1/2882:2888		No text annotation
homologous
J3_5J7L_048
NA
J3_9NJV_0171/R2/10:16,
1/R2/68:70,
1/R2/106:110		No text annotation
homologous
J3_5J7L_049
NA
J3_9NJV_0181/R3/46:47,
1/R3/361:367,
1/R3/393:395		No text annotation
geometric
J3_4LFB_010
J3_58657.1
J3_9NJV_0191/R3/46:52,
1/R3/359:367,
1/R3/393:395		No text annotation
homologous
J3_5J7L_050
NA
J3_9NJV_0201/R3/586:588,
1/R3/651:654,
1/R3/754:755		No text annotation
geometric
J3_4LFB_011
J3_01633.1
J3_9NJV_0211/R3/586:588,
1/R3/651:655,
1/R3/751:755		No text annotation
homologous
J3_5J7L_051
NA
J3_9NJV_0221/R3/672:673,
1/R3/717:725,
1/R3/732:734		No text annotation
homologous
J3_5J7L_003
NA
J3_9NJV_0231/R3/826:829,
1/R3/857:861,
1/R3/868:874		No text annotation
homologous
J3_5J7L_004
NA
J3_9NJV_0241/R3/936:939,
1/R3/1344:1350,
1/R3/1372:1379		No text annotation
homologous
J3_5J7L_052
NA
J3_9NJV_0251/R3/943:946,
1/R3/1235:1237,
1/R3/1337:1340		No text annotation
homologous
J3_4LFB_003
J3_44359.1
J3_9NJV_0261/R3/955:963,
1/R3/972:984,
1/R3/1221:1225		No text annotation
J3_9NJV_0271/R3/989:993,
1/R3/1045:1047,
1/R3/1210:1216		No text annotation
J3_9NJV_0281/R3/989:997,
1/R3/1044:1047,
1/R3/1210:1216		No text annotation
J3_9NJV_0291/R3/998:1009,
1/R3/1020:1027,
1/R3/1034:1043		No text annotation
J3_9NJV_0301/R3/1063:1068,
1/R3/1107:1113,
1/R3/1187:1193		No text annotation
homologous
J3_4LFB_007
J3_01343.1
J3_9NJV_0311/R3/1073:1074,
1/R3/1083:1087,
1/R3/1098:1102		No text annotation
homologous
J3_5J7L_009
NA
J3_9NJV_0321/R3/1116:1118,
1/R3/1155:1158,
1/R3/1181:1184		No text annotation
geometric
J3_5J7L_010
NA
J3_9NJV_0331/R3/1116:1118,
1/R3/1155:1161,
1/R3/1175:1184		No text annotation
homologous
J3_5J7L_054
NA
J3_9NJV_0341/R3/1237:1241,
1/R3/1296:1303,
1/R3/1334:1337		No text annotation
homologous
J3_5J7L_011
NA
J4_9NJV_0011/R1/47:54,
1/R1/116:121,
1/R1/130:153,
1/R1/172:178		No text annotation
J4_9NJV_0021/R1/268:269,
1/R1/370:375,
1/R1/399:406,
1/R1/421:424		No text annotation
homologous
J4_5J7L_018
NA
J4_9NJV_0031/R1/601:604,
1/R1/624:628,
1/R1/635:638,
1/R1/650:656		No text annotation
homologous
J4_5J7L_020
NA
J4_9NJV_0041/R1/1270:1276,
1/R1/1294:1295,
1/R1/1645:1648,
1/R1/2009:2010		No text annotation
homologous
J4_5J7L_021
NA
J4_9NJV_0051/R1/1310:1314,
1/R1/1338:1343,
1/R1/1404:1405,
1/R1/1597:1604		No text annotation
homologous
J4_5J7L_022
NA
J4_9NJV_0061/R1/1444:1445,
1/R1/1466:1467,
1/R1/1525:1526,
1/R1/1546:1547		No text annotation
homologous
J4_5J7L_024
NA
J4_9NJV_0071/R1/1772:1776,
1/R1/1788:1792,
1/R1/1827:1830,
1/R1/1975:1979		No text annotation
homologous
J4_5J7L_025
NA
J4_9NJV_0081/R1/1833:1835,
1/R1/1905:1906,
1/R1/1924:1933,
1/R1/1967:1972		No text annotation
homologous
J4_9DFE_008
J4_42306.1
J4_9NJV_0091/R1/2285:2289,
1/R1/2343:2347,
1/R1/2370:2372,
1/R1/2381:2383		No text annotation
homologous
J4_5J7L_027
NA
J4_9NJV_0101/R1/2643:2646,
1/R1/2674:2676,
1/R1/2731:2735,
1/R1/2769:2771		No text annotation
homologous
J4_5J7L_028
NA
J4_9NJV_0111/R3/115:122,
1/R3/239:240,
1/R3/286:289,
1/R3/311:312		No text annotation
homologous
J4_5J7L_001
NA
J4_9NJV_0121/R3/142:144,
1/R3/178:184,
1/R3/193:198,
1/R3/219:221		No text annotation
homologous
J4_5J7L_002
NA
J4_9NJV_0131/R3/575:577,
1/R3/764:769,
1/R3/810:821,
1/R3/879:880		No text annotation
homologous
J4_5J7L_003
NA
J4_9NJV_0141/T/6:9,
1/T/25:27,
1/T/43:49,
1/T/65:66		tRNA junction
homologous
J4_5E81_027
NA
J5_9NJV_0011/R1/531:533,
1/R1/560:564,
1/R1/577:579,
1/R1/1261:1262,
1/R1/2017:2018		No text annotation
homologous
J5_5J7L_014
NA
J5_9NJV_0021/R1/584:589,
1/R1/668:671,
1/R1/809:812,
1/R1/1195:1196,
1/R1/1250:1256		No text annotation
homologous
J5_5J7L_015
NA
J5_9NJV_0031/R1/1674:1682,
1/R1/1706:1707,
1/R1/1751:1752,
1/R1/1756:1764,
1/R1/1988:1990		No text annotation
homologous
J5_5J7L_016
NA
J5_9NJV_0041/R1/2057:2064,
1/R1/2446:2454,
1/R1/2498:2507,
1/R1/2582:2588,
1/R1/2606:2611		No text annotation
J5_9NJV_0051/R1/2074:2077,
1/R1/2243:2246,
1/R1/2258:2259,
1/R1/2281:2282,
1/R1/2427:2435		No text annotation
homologous
J5_4WF9_007
J5_39529.2
J5_9NJV_0061/R3/36:39,
1/R3/403:408,
1/R3/434:440,
1/R3/497:500,
1/R3/545:548		No text annotation
J5_9NJV_0071/R3/36:39,
1/R3/403:408,
1/R3/434:442,
1/R3/492:500,
1/R3/545:548		No text annotation
J5_9NJV_0081/R3/56:61,
1/R3/106:113,
1/R3/314:316,
1/R3/337:339,
1/R3/350:356		No text annotation
J6_9NJV_0011/R1/45:46,
1/R1/179:183,
1/R1/214:224,
1/R1/231:235,
1/R1/262:266,
1/R1/426:433		No text annotation
J6_9NJV_0021/R1/2074:2077,
1/R1/2243:2246,
1/R1/2258:2259,
1/R1/2281:2284,
1/R1/2384:2395,
1/R1/2421:2435		No text annotation
J7_9NJV_0011/R1/8:15,
1/R1/525:531,
1/R1/2018:2023,
1/R1/2040:2043,
1/R1/2625:2630,
1/R1/2788:2789,
1/R1/2894:2895		No text annotation
J7_9NJV_0021/R1/817:822,
1/R1/835:838,
1/R1/940:946,
1/R1/971:976,
1/R1/987:991,
1/R1/1163:1164,
1/R1/1185:1190		No text annotation

Problematic loops

No problematic loops


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