RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8BHN_0011/0/59:68No text annotation
homologous
HL_5J7L_134
HL_35677.3
HL_8BHN_0021/0/87:95No text annotation
homologous
HL_5J7L_135
HL_80241.1
HL_8BHN_0031/0/123:128No text annotation
homologous
HL_4WF9_003
HL_75660.5
HL_8BHN_0041/0/137:142UNCG
geometric
HL_6QN3_003
HL_34617.5
HL_8BHN_0051/0/158:168No text annotation
homologous
HL_5J7L_138
HL_68257.1
HL_8BHN_0061/0/194:201No text annotation
homologous
HL_7RQB_006
NA
HL_8BHN_0071/0/225:230No text annotation
homologous
HL_5J7L_140
HL_62934.1
HL_8BHN_0081/0/246:252No text annotation
homologous
HL_7RQB_008
NA
HL_8BHN_0091/0/305:312T-loop with 1 bulged base
homologous
HL_7A0S_010
HL_01609.3
HL_8BHN_0101/0/319:323No text annotation
homologous
HL_5J7L_143
HL_75660.5
HL_8BHN_0111/0/327:335T-loop with unstacked turn
homologous
HL_5J7L_144
HL_27670.2
HL_8BHN_0121/0/382:392No text annotation
homologous
HL_5J7L_145
HL_91503.7
HL_8BHN_0131/0/410:417Pseudoknot geometry
homologous
HL_7A0S_014
HL_30680.3
HL_8BHN_0141/0/462:467GNRA
homologous
HL_4WF9_015
HL_37824.7
HL_8BHN_0151/0/487:493GNRA
homologous
HL_5J7L_148
HL_37824.7
HL_8BHN_0161/0/543:550No text annotation
HL_8BHN_0171/0/566:575T-loop with 2 stacked bulged bases
geometric
HL_5J7L_150
HL_28252.8
HL_8BHN_0181/0/611:617No text annotation
homologous
HL_5J7L_151
HL_80922.2
HL_8BHN_0191/0/629:634GNRA
homologous
HL_4WF9_020
HL_37824.7
HL_8BHN_0201/0/641:647No text annotation
homologous
HL_5J7L_153
HL_13529.1
HL_8BHN_0211/0/712:719GNRA wlth tandem sheared
homologous
HL_5J7L_154
HL_81538.2
HL_8BHN_0221/0/744:753No text annotation
homologous
HL_7A0S_022
HL_88205.2
HL_8BHN_0231/0/779:785No text annotation
homologous
HL_7RQB_024
NA
HL_8BHN_0241/0/826:831No text annotation
homologous
HL_7RQB_025
NA
HL_8BHN_1081/0/955:962GNRA
homologous
HL_7A0S_026
HL_37824.7
HL_8BHN_0261/0/978:985No text annotation
homologous
HL_5J7L_160
HL_42998.2
HL_8BHN_0281/0/1172:1177No text annotation
geometric
HL_4V88_198
NA
HL_8BHN_0291/0/1222:1227GNRA
homologous
HL_7A0S_031
HL_37824.7
HL_8BHN_0301/0/1281:1289T-loop with 2 stacked bulged bases
homologous
HL_5J7L_165
HL_28252.8
HL_8BHN_0311/0/1324:1330Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_166
HL_57176.2
HL_8BHN_0321/0/1363:1368GNRA
homologous
HL_7RQB_035
NA
HL_8BHN_0331/0/1389:1398No text annotation
homologous
HL_5J7L_168
HL_81545.2
HL_8BHN_0341/0/1451:1459Mini UNCG with extended bulge
homologous
HL_5J7L_169
HL_22622.1
HL_8BHN_0351/0/1492:1498Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_170
HL_57176.2
HL_8BHN_0361/0/1533:1538UNCG
homologous
HL_5J7L_171
HL_34617.5
HL_8BHN_0371/0/1565:1568Mini UNCG
homologous
HL_5J7L_172
HL_48778.2
HL_8BHN_0381/0/1612:1619No text annotation
homologous
HL_4WF9_038
HL_89567.2
HL_8BHN_0391/0/1630:1636GNRA
homologous
HL_5J7L_174
HL_37824.7
HL_8BHN_0401/0/1691:1696UNCG
geometric
HL_7A0S_042
HL_34617.5
HL_8BHN_1091/0/1727:1733No text annotation
homologous
HL_5J7L_214
HL_08100.1
HL_8BHN_0411/0/1728:1731No text annotation
homologous
HL_5J7L_176
HL_32346.4
HL_8BHN_0421/0/1752:1756No text annotation
homologous
HL_7RQB_044
NA
HL_8BHN_0431/0/1777:1787No text annotation
homologous
HL_4WF9_043
HL_01962.2
HL_8BHN_0441/0/1806:1811GNRA related
homologous
HL_5J7L_179
HL_04783.2
HL_8BHN_0451/0/1868:1873GNRA with GA tSW pair
geometric
HL_6MJ0_008
HL_37824.7
HL_8BHN_0461/0/1910:1920No text annotation
geometric
HL_5TBW_049
NA
HL_8BHN_0471/0/1949:1957No text annotation
homologous
HL_5J7L_182
HL_20167.2
HL_8BHN_0481/0/2027:2036No text annotation
homologous
HL_4WF9_047
HL_61996.2
HL_8BHN_0501/0/2209:2215No text annotation
homologous
HL_5J7L_185
HL_49922.4
HL_8BHN_0511/0/2248:2256No text annotation
homologous
HL_7A0S_052
HL_85367.2
HL_8BHN_0521/0/2264:2276No text annotation
homologous
HL_5J7L_187
HL_91939.2
HL_8BHN_1111/0/2304:2312No text annotation
homologous
HL_5J7L_219
HL_50860.2
HL_8BHN_0541/0/2324:2331Pseudoknot geometry
homologous
HL_5J7L_189
HL_93324.4
HL_8BHN_0551/0/2356:2361GNRA
homologous
HL_5J7L_190
HL_37824.7
HL_8BHN_0561/0/2374:2379GNRA
homologous
HL_5J7L_191
HL_37824.7
HL_8BHN_0571/0/2404:2413No text annotation
homologous
HL_5J7L_192
HL_53454.2
HL_8BHN_0581/0/2471:2479No text annotation
homologous
HL_4WF9_056
HL_32735.2
HL_8BHN_0591/0/2528:2535No text annotation
homologous
HL_5J7L_194
HL_31585.4
HL_8BHN_0601/0/2551:2557No text annotation
homologous
HL_4WF9_058
HL_30068.2
HL_8BHN_0611/0/2594:2599GNRA
homologous
HL_7RQB_063
NA
HL_8BHN_0621/0/2658:2663GNRA
geometric
HL_7RQB_064
NA
HL_8BHN_0631/0/2701:2706Ribsomal LSU H95
homologous
HL_5J7L_198
HL_65794.5
HL_8BHN_0641/0/2745:2759No text annotation
homologous
HL_5J7L_199
HL_74055.2
HL_8BHN_0651/0/2795:2801Other HL
homologous
HL_5J7L_200
HL_08100.1
HL_8BHN_0661/0/2819:2827No text annotation
homologous
HL_5J7L_201
HL_64690.6
HL_8BHN_0671/0/2856:2861GNRA
homologous
HL_7A0S_068
HL_37824.7
HL_8BHN_0681/1/38:44No text annotation
geometric
HL_5NFV_001
HL_69752.2
HL_8BHN_0691/1/86:90Mini UNCG
homologous
HL_5J7L_204
HL_48778.2
HL_8BHN_0701/2/12:22No text annotation
homologous
HL_4LFB_001
HL_89881.5
HL_8BHN_0711/2/76:93No text annotation
HL_8BHN_0721/2/158:163GNRA
homologous
HL_5J7L_003
HL_37824.7
HL_8BHN_0731/2/186:191GNRA
homologous
HL_5J7L_004
HL_37824.7
HL_8BHN_0741/2/207:212UNCG
homologous
HL_5J7L_005
HL_34617.5
HL_8BHN_0751/2/259:267GNRA related
homologous
HL_5J7L_006
HL_84299.4
HL_8BHN_0761/2/296:301GNRA
homologous
HL_5J7L_007
HL_37824.7
HL_8BHN_0771/2/320:333No text annotation
homologous
HL_4LFB_008
HL_81205.3
HL_8BHN_1141/2/342:347UNCG
homologous
HL_4LFB_009
HL_34617.5
HL_8BHN_0791/2/379:384GNRA
homologous
HL_4LFB_010
HL_37824.7
HL_8BHN_0801/2/419:424UNCG
homologous
HL_5J7L_011
HL_34617.5
HL_8BHN_0811/2/462:470GNRA related
homologous
HL_5J7L_012
HL_81538.2
HL_8BHN_0821/2/522:527No text annotation
geometric
HL_4WF9_003
HL_75660.5
HL_8BHN_0831/2/617:623No text annotation
homologous
HL_6CZR_085
NA
HL_8BHN_0841/2/689:698No text annotation
geometric
HL_4LFB_015
HL_75293.5
HL_8BHN_0851/2/726:731GNRA
homologous
HL_5J7L_016
HL_37824.7
HL_8BHN_0861/2/786:796No text annotation
homologous
HL_5J7L_017
HL_75293.5
HL_8BHN_0871/2/842:845No text annotation
geometric
HL_8K2Z_002
NA
HL_8BHN_0881/2/862:867GNRA
homologous
HL_4LFB_019
HL_37824.7
HL_8BHN_0891/2/897:902GNRA
homologous
HL_4LFB_020
HL_37824.7
HL_8BHN_0901/2/963:972No text annotation
homologous
HL_5J7L_021
HL_50779.4
HL_8BHN_0911/2/1003:1037No text annotation
HL_8BHN_0921/2/1076:1081GNRA
homologous
HL_5J7L_023
HL_37824.7
HL_8BHN_0931/2/1089:1096T-loop related
homologous
HL_4LFB_025
HL_77436.5
HL_8BHN_0941/2/1134:1140No text annotation
homologous
HL_5J7L_025
HL_87954.2
HL_8BHN_0951/2/1165:1171GNRA
homologous
HL_5J7L_026
HL_93535.1
HL_8BHN_0961/2/1265:1270GNRA
homologous
HL_5J7L_027
HL_37824.7
HL_8BHN_0971/2/1314:1323T-loop with 3 stacked bulged bases
homologous
HL_4LFB_029
HL_02887.3
HL_8BHN_0981/2/1356:1366No text annotation
homologous
HL_4LFB_030
HL_06226.4
HL_8BHN_0991/2/1449:1454UNCG
homologous
HL_4LFB_031
HL_34617.5
HL_8BHN_1001/2/1515:1520GNRA variation
geometric
HL_4V88_222
NA
HL_8BHN_1011/4/12:22tRNA D-loop
homologous
HL_4TUE_033
HL_93616.2
HL_8BHN_1021/4/31:39tRNA anticodon loop
homologous
HL_4WT8_216
HL_06059.6
HL_8BHN_1031/4/53:61T-loop with 2 stacked bulged bases
homologous
HL_5AH5_008
HL_28252.8
HL_8BHN_1041/5/13:22tRNA D-loop
geometric
HL_4V90_032
HL_20811.4
HL_8BHN_1051/5/31:39tRNA anticodon loop
homologous
HL_7U2I_104
HL_06059.6
HL_8BHN_1061/5/53:61T-loop with 2 stacked bulged bases
homologous
HL_5WT1_003
HL_28252.8

Problematic loops

#loop idProblemSequence
HL_8BHN_107No text annotation
HL_8BHN_025tRNA anticodon loop
HL_8BHN_027No text annotation
HL_8BHN_110No text annotation
HL_8BHN_049No text annotation
HL_8BHN_053No text annotation
HL_8BHN_078No text annotation
HL_8BHN_112No text annotation
HL_8BHN_113No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8BHN_0011/0/24:30,
1/0/510:516		Triple sheared with non-canonical cWW
homologous
IL_4WF9_001
IL_04021.2
IL_8BHN_0021/0/36:37,
1/0/442:444		Single bulged A
homologous
IL_7RQB_002
NA
IL_8BHN_0031/0/43:44,
1/0/434:436		Minor groove platform
homologous
IL_5J7L_247
IL_51454.3
IL_8BHN_0041/0/81:85,
1/0/97:105		No text annotation
homologous
IL_5J7L_248
IL_37015.1
IL_8BHN_0051/0/183:184,
1/0/212:214		Single stack bend
homologous
IL_7A0S_005
IL_90729.1
IL_8BHN_0061/0/188:194,
1/0/201:208		8x7 Sarcin-Ricin; G-bulge
geometric
IL_7A0S_006
IL_04346.10
IL_8BHN_0071/0/239:245,
1/0/253:258		7x6 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_251
IL_26307.2
IL_8BHN_0081/0/269:271,
1/0/366:370		No text annotation
homologous
IL_5J7L_252
IL_47972.1
IL_8BHN_0091/0/274:281,
1/0/359:363		No text annotation
homologous
IL_5J7L_253
IL_77870.1
IL_8BHN_0101/0/293:295,
1/0/343:347		No text annotation
homologous
IL_7RQB_013
NA
IL_8BHN_0111/0/481:484,
1/0/496:509		No text annotation
homologous
IL_7RQB_014
NA
IL_8BHN_0121/0/536:539,
1/0/554:557		Double sheared
homologous
IL_5J7L_256
IL_09705.15
IL_8BHN_0131/0/564:566,
1/0/575:577		Isolated non-canonical cWW pair
homologous
IL_7A0S_011
IL_07785.1
IL_8BHN_0141/0/606:610,
1/0/618:622		AAA cross-strand stack
homologous
IL_5J7L_258
IL_66798.2
IL_8BHN_0151/0/672:674,
1/0/806:808		No text annotation
homologous
IL_7RQB_017
NA
IL_8BHN_0161/0/674:678,
1/0/799:806		tHW-tHW cross-strand stack
geometric
IL_5J7L_260
IL_54041.2
IL_8BHN_0171/0/697:698,
1/0/763:765		Single bulged A
geometric
IL_4V9F_025
IL_31462.6
IL_8BHN_0181/0/702:703,
1/0/728:730		Single bulged G
homologous
IL_7RQB_020
NA
IL_8BHN_0191/0/703:707,
1/0/724:728		Triple sheared
geometric
IL_5J7L_263
IL_50730.2
IL_8BHN_0201/0/738:740,
1/0/757:758		Major groove platform
homologous
IL_5J7L_264
IL_48076.6
IL_8BHN_0211/0/775:777,
1/0/787:791		Multiple bulged bases
geometric
IL_5J7L_265
IL_06549.2
IL_8BHN_0221/0/844:847,
1/0/933:934		Other IL
geometric
IL_5J7L_267
IL_90729.1
IL_8BHN_1971/0/844:848,
1/0/930:934		No text annotation
homologous
IL_5J7L_399
IL_96236.1
IL_8BHN_0231/0/847:848,
1/0/930:933		Stack outside cWW
homologous
IL_5J7L_268
IL_56987.1
IL_8BHN_0241/0/850:851,
1/0/926:928		Single stack bend
homologous
IL_5J7L_269
IL_26793.1
IL_8BHN_0251/0/856:862,
1/0/915:921		7x7 Sarcin-Ricin with intercalated A; G-bulge
homologous
IL_5J7L_270
IL_29198.2
IL_8BHN_0261/0/862:863,
1/0/913:915		Single bulged G
geometric
IL_5J7L_271
IL_00225.13
IL_8BHN_0271/0/864:868,
1/0/909:912		C-loop
homologous
IL_5J7L_272
IL_26222.2
IL_8BHN_0281/0/870:872,
1/0/905:907		Isolated non-canonical cWW pair
homologous
IL_5J7L_273
IL_28037.2
IL_8BHN_0291/0/875:879,
1/0/898:902		Triple sheared
homologous
IL_5J7L_274
IL_17948.2
IL_8BHN_0301/0/880:883,
1/0/893:897		Decoding loop related
geometric
IL_3C3Z_002
IL_31737.3
IL_8BHN_0311/0/994:996,
1/0/1159:1160		Single bulged C
homologous
IL_5J7L_276
IL_61258.15
IL_8BHN_0321/0/998:1002,
1/0/1153:1157		UAA/GAN
homologous
IL_7A0S_033
IL_38507.2
IL_8BHN_0331/0/1004:1011,
1/0/1150:1151		SSU/LSU pseudoknot
geometric
IL_4WF9_037
IL_41203.4
IL_8BHN_0341/0/1011:1013,
1/0/1149:1150		Single bulged U
homologous
IL_5J7L_279
IL_89505.4
IL_8BHN_0351/0/1018:1024,
1/0/1140:1144		No text annotation
homologous
IL_7RQB_039
NA
IL_8BHN_1831/0/1024:1030,
1/0/1124:1140		No text annotation
homologous
IL_5J7L_281
IL_50715.3
IL_8BHN_0361/0/1031:1034,
1/0/1121:1123		Isolated non-canonical cWW pair
homologous
IL_5J7L_282
IL_57744.1
IL_8BHN_0371/0/1038:1041,
1/0/1114:1117		Tandem non-canonical cWW pairs
homologous
IL_5J7L_283
IL_85033.2
IL_8BHN_0381/0/1196:1198,
1/0/1247:1250		Isolated cWS basepair
homologous
IL_4WF9_044
IL_42997.3
IL_8BHN_0391/0/1202:1206,
1/0/1240:1243		No text annotation
homologous
IL_5J7L_287
IL_91920.1
IL_8BHN_0401/0/1208:1215,
1/0/1234:1238		Kink-turn
homologous
IL_5J7L_288
IL_70923.9
IL_8BHN_0411/0/1262:1269,
1/0/2011:2017		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
IL_04346.10
IL_8BHN_0421/0/1310:1313,
1/0/1603:1604		Major groove platform; stack outside cWW
homologous
IL_5J7L_290
IL_50694.7
IL_8BHN_0431/0/1319:1323,
1/0/1331:1333		Major groove minor groove platform with tHH
homologous
IL_4WF9_050
IL_83150.2
IL_8BHN_0441/0/1351:1355,
1/0/1376:1380		UAA/GAN
homologous
IL_5J7L_292
IL_89021.2
IL_8BHN_0451/0/1357:1361,
1/0/1370:1374		tSH-tHW-tHS
homologous
IL_5J7L_293
IL_17136.7
IL_8BHN_0461/0/1415:1416,
1/0/1582:1587		No text annotation
homologous
IL_5J7L_294
IL_87211.1
IL_8BHN_0471/0/1417:1421,
1/0/1577:1581		UAA/GAN
homologous
IL_5J7L_295
IL_38507.2
IL_8BHN_0481/0/1432:1435,
1/0/1557:1561		Tandem non-canonical cWW pairs
homologous
IL_5J7L_296
IL_58112.2
IL_8BHN_0491/0/1437:1440,
1/0/1551:1555		tSH-tHW
homologous
IL_5J7L_297
IL_99646.2
IL_8BHN_0501/0/1450:1451,
1/0/1459:1461		Single bulged U
geometric
IL_5J7L_298
IL_89505.4
IL_8BHN_0511/0/1468:1471,
1/0/1520:1524		No text annotation
homologous
IL_5J7L_299
IL_68574.4
IL_8BHN_0521/0/1474:1478,
1/0/1513:1517		tSH-tHW-tHS
homologous
IL_5J7L_300
IL_38862.4
IL_8BHN_0531/0/1481:1482,
1/0/1507:1510		180 degree turn
homologous
IL_5J7L_301
IL_00881.1
IL_8BHN_0541/0/1489:1491,
1/0/1499:1500		Single bulged A
homologous
IL_5J7L_302
IL_31462.6
IL_8BHN_0551/0/1526:1529,
1/0/1542:1546		UAA/GAN variation
homologous
IL_5J7L_303
IL_23774.1
IL_8BHN_0561/0/1651:1656,
1/0/2004:2006		No text annotation
homologous
IL_5J7L_304
IL_12566.4
IL_8BHN_0571/0/1663:1665,
1/0/1995:1997		Isolated tWW turn
homologous
IL_7A0S_060
IL_67095.2
IL_8BHN_0581/0/1666:1669,
1/0/1993:1994		Major groove platform; stack outside cWW
homologous
IL_4WF9_064
IL_50694.7
IL_8BHN_1841/0/1666:1674,
1/0/1990:1994		No text annotation
homologous
IL_4WF9_117
IL_22854.4
IL_8BHN_0591/0/1669:1674,
1/0/1990:1993		Intercalated tWH
geometric
IL_4WF9_065
IL_76758.2
IL_8BHN_0601/0/1686:1691,
1/0/1696:1702		tSH-tSH-tHH-tHS
homologous
IL_5J7L_308
IL_47346.2
IL_8BHN_0611/0/1712:1718,
1/0/1742:1746		6x5 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_309
IL_88269.4
IL_8BHN_0621/0/1720:1724,
1/0/1736:1740		Triple sheared
homologous
IL_5J7L_310
IL_50730.2
IL_8BHN_0631/0/1727:1728,
1/0/1731:1733		Single bulged C
homologous
IL_5J7L_311
IL_61258.15
IL_8BHN_0641/0/1770:1771,
1/0/1980:1982		Single bulged A
homologous
IL_5J7L_312
IL_31462.6
IL_8BHN_0651/0/1798:1804,
1/0/1813:1821		Kink-turn related
homologous
IL_7A0S_065
IL_17069.5
IL_8BHN_0661/0/1837:1840,
1/0/1902:1903		Minor groove platform, major groove intercalation
homologous
IL_5J7L_314
IL_95583.2
IL_8BHN_0671/0/1841:1842,
1/0/1898:1901		Major groove intercalation
homologous
IL_5J7L_315
IL_82107.4
IL_8BHN_0681/0/1846:1849,
1/0/1893:1894		Major groove minor groove platform; mini C-loop
homologous
IL_5J7L_316
IL_68140.4
IL_8BHN_1851/0/1851:1860,
1/0/1882:1891		No text annotation
homologous
IL_5J7L_387
IL_61249.1
IL_8BHN_0691/0/1864:1867,
1/0/1874:1878		UAA/GAN variation
homologous
IL_5J7L_317
IL_77691.5
IL_8BHN_0701/0/1933:1934,
1/0/1964:1967		Bulged stacked bases
homologous
IL_4WF9_076
IL_22551.4
IL_8BHN_1981/0/1934:1945,
1/0/1961:1964		No text annotation
homologous
IL_5J7L_319
IL_42218.2
IL_8BHN_0721/0/2050:2052,
1/0/2617:2618		Major groove platform
homologous
IL_5J7L_320
IL_48076.6
IL_8BHN_0731/0/2054:2056,
1/0/2612:2615		No text annotation
homologous
IL_5J7L_321
IL_83389.2
IL_8BHN_0741/0/2067:2069,
1/0/2442:2443		Single bulged U
homologous
IL_4WF9_080
IL_89505.4
IL_8BHN_0751/0/2070:2071,
1/0/2438:2441		Minor groove platform
homologous
IL_7RQB_081
NA
IL_8BHN_0761/0/2081:2083,
1/0/2236:2239		Isolated tHS basepair with bulges
homologous
IL_5J7L_325
IL_85599.2
IL_8BHN_0771/0/2085:2087,
1/0/2232:2234		No text annotation
homologous
IL_7RQB_083
NA
IL_8BHN_0781/0/2099:2101,
1/0/2189:2190		Single stack bend
geometric
IL_7KGA_003
IL_90729.1
IL_8BHN_0791/0/2101:2102,
1/0/2187:2189		Single stack bend
geometric
IL_4V9F_081
IL_26793.1
IL_8BHN_0801/0/2202:2204,
1/0/2220:2221		Single bulged U
homologous
IL_5J7L_331
IL_89505.4
IL_8BHN_0811/0/2297:2299,
1/0/2317:2321		No text annotation
geometric
IL_5J7L_332
IL_61476.2
IL_8BHN_0821/0/2350:2353,
1/0/2364:2367		Double sheared
homologous
IL_7RQB_089
NA
IL_8BHN_0831/0/2401:2403,
1/0/2414:2415		Single bulged U
homologous
IL_5J7L_334
IL_89505.4
IL_8BHN_0841/0/2453:2454,
1/0/2498:2500		Single stack bend
geometric
IL_4WF9_089
IL_26793.1
IL_8BHN_0851/0/2454:2455,
1/0/2496:2498		Major groove platform
homologous
IL_4WF9_090
IL_48076.6
IL_8BHN_0861/0/2457:2459,
1/0/2493:2494		Major groove platform
geometric
IL_4WF9_091
IL_48076.6
IL_8BHN_0871/0/2459:2461,
1/0/2489:2493		Major groove minor groove platform with extra cWW
homologous
IL_7A0S_086
IL_51387.2
IL_8BHN_0881/0/2466:2470,
1/0/2480:2484		Triple sheared
homologous
IL_4WF9_093
IL_17948.2
IL_8BHN_1911/0/2507:2508,
1/0/2580:2582		Major groove platform
homologous
IL_7A0S_088
IL_07039.3
IL_8BHN_0901/0/2510:2512,
1/0/2574:2578		Isolated non-canonical cWW with bulges
homologous
IL_5J7L_340
IL_07785.1
IL_8BHN_0911/0/2512:2513,
1/0/2571:2574		No text annotation
geometric
IL_5J7L_341
IL_42626.2
IL_8BHN_0921/0/2522:2523,
1/0/2540:2543		Major groove platform with intercalation
homologous
IL_5J7L_342
IL_02555.1
IL_8BHN_0941/0/2591:2592,
1/0/2601:2603		Single bulged A
homologous
IL_7RQB_101
NA
IL_8BHN_0951/0/2636:2640,
1/0/2774:2782		tSH-tHS-tHW
homologous
IL_5J7L_345
IL_04638.3
IL_8BHN_0961/0/2652:2658,
1/0/2663:2668		Sarcin-Ricin target in LSU H95; G-bulge
homologous
IL_7A0S_094
IL_16458.4
IL_8BHN_0971/0/2680:2684,
1/0/2725:2727		C-loop
homologous
IL_5J7L_347
IL_63596.11
IL_8BHN_0981/0/2687:2691,
1/0/2718:2722		No text annotation
homologous
IL_4WF9_102
IL_23774.1
IL_8BHN_0991/0/2695:2696,
1/0/2711:2714		Multiple bulged bases
homologous
IL_4WF9_103
IL_42626.2
IL_8BHN_1001/0/2737:2742,
1/0/2762:2767		UAA/GAN with extra cWW
homologous
IL_5J7L_350
IL_49767.8
IL_8BHN_1011/0/2806:2811,
1/0/2889:2892		No text annotation
homologous
IL_5J7L_351
IL_29471.1
IL_8BHN_1921/0/2838:2839,
1/0/2878:2880		Major groove intercalation
homologous
IL_5J7L_352
IL_66635.5
IL_8BHN_1031/0/2843:2846,
1/0/2870:2874		Multiple bulged bases with non-canonical cWW
homologous
IL_5J7L_353
IL_64231.5
IL_8BHN_1041/0/2847:2852,
1/0/2865:2869		tHS double platform
homologous
IL_5J7L_354
IL_70411.2
IL_8BHN_1051/1/17:18,
1/1/65:67		Major groove intercalation
homologous
IL_5J7L_355
IL_31462.6
IL_8BHN_1061/1/23:28,
1/1/56:60		No text annotation
homologous
IL_5J7L_356
IL_18472.4
IL_8BHN_1071/1/30:31,
1/1/51:54		Major groove minor groove platform; mini C-loop
homologous
IL_5J7L_357
IL_68140.4
IL_8BHN_1081/1/34:38,
1/1/44:48		Symmetric double minor groove platform
homologous
IL_5J7L_358
IL_58103.11
IL_8BHN_1091/1/71:79,
1/1/97:105		Bacterial 5S Loop E
homologous
IL_5J7L_359
IL_56455.6
IL_8BHN_1111/2/30:32,
1/2/552:553		Single bulged G
homologous
IL_5J7L_001
IL_00225.13
IL_8BHN_1121/2/44:45,
1/2/396:398		Single bulged A
homologous
IL_5J7L_002
IL_31462.6
IL_8BHN_1131/2/47:52,
1/2/359:361		No text annotation
homologous
IL_5J7L_003
IL_14177.2
IL_8BHN_1141/2/54:56,
1/2/356:357		Minor groove platform
homologous
IL_4LFB_004
IL_51454.3
IL_8BHN_1151/2/63:66,
1/2/103:104		Multiple bulged bases
homologous
IL_5J7L_005
IL_82107.4
IL_8BHN_1161/2/67:69,
1/2/99:102		Minor groove platform with extra cWW
homologous
IL_5J7L_006
IL_90351.1
IL_8BHN_1171/2/70:73,
1/2/97:98		Minor groove platform
homologous
IL_5J7L_007
IL_15052.4
IL_8BHN_1181/2/75:76,
1/2/93:95		Major groove intercalation
geometric
IL_5J7L_352
IL_66635.5
IL_8BHN_1191/2/128:131,
1/2/231:233		Isolated non-canonical cWW pair
homologous
IL_5J7L_009
IL_57744.1
IL_8BHN_1201/2/132:136,
1/2/227:230		No text annotation
homologous
IL_4LFB_008
IL_64231.5
IL_8BHN_1211/2/144:146,
1/2/176:178		Isolated cWH basepair
homologous
IL_5J7L_011
IL_10167.6
IL_8BHN_1221/2/147:153,
1/2/168:175		tWH-tWH-tHW-tHW
homologous
IL_5J7L_012
IL_80604.6
IL_8BHN_1231/2/203:206,
1/2/213:214		Minor groove platform
geometric
IL_3IWN_005
IL_15052.4
IL_8BHN_1241/2/242:247,
1/2/277:284		Kink-turn with non-sequential stacking
homologous
IL_5J7L_014
IL_46174.3
IL_8BHN_1251/2/249:252,
1/2/274:275		No text annotation
homologous
IL_4LFB_012
IL_47074.2
IL_8BHN_1261/2/292:293,
1/2/304:308		C-loop
homologous
IL_4LFB_013
IL_03109.3
IL_8BHN_1271/2/367:369,
1/2/392:393		Single bulged U
homologous
IL_5J7L_017
IL_89505.4
IL_8BHN_1281/2/371:375,
1/2/389:390		C-loop
homologous
IL_5J7L_018
IL_03109.3
IL_8BHN_1291/2/375:376,
1/2/387:389		Single bulged G
geometric
IL_5J7L_019
IL_00225.13
IL_8BHN_1951/2/409:416,
1/2/427:433		No text annotation
homologous
IL_5J7L_020
IL_28026.3
IL_8BHN_1311/2/440:442,
1/2/492:497		No text annotation
homologous
IL_5J7L_021
IL_33323.1
IL_8BHN_1321/2/446:450,
1/2/483:488		tSH-tHW-tWW
geometric
IL_5J7L_022
IL_88269.4
IL_8BHN_1331/2/450:455,
1/2/477:483		No text annotation
homologous
IL_5J7L_023
IL_70801.1
IL_8BHN_1341/2/504:511,
1/2/540:541		SSU/LSU pseudoknot
homologous
IL_4LFB_020
IL_41203.4
IL_8BHN_1351/2/515:521,
1/2/528:536		Kink-turn related
homologous
IL_4LFB_021
IL_54177.4
IL_8BHN_1361/2/569:575,
1/2/880:881		No text annotation
homologous
IL_4LFB_022
IL_38186.6
IL_8BHN_1371/2/580:584,
1/2/757:761		tSH-tHW-tHS
homologous
IL_5J7L_027
IL_17136.7
IL_8BHN_1381/2/594:596,
1/2/644:645		Major groove platform
homologous
IL_5J7L_028
IL_48076.6
IL_8BHN_1391/2/597:598,
1/2/640:643		Major groove minor groove platform; mini C-loop
homologous
IL_5J7L_029
IL_68140.4
IL_8BHN_1401/2/605:612,
1/2/628:633		No text annotation
homologous
IL_5J7L_030
IL_78349.3
IL_8BHN_1411/2/654:655,
1/2/751:754		Major groove platform; stack outside cWW
homologous
IL_4LFB_027
IL_50694.7
IL_8BHN_1421/2/659:660,
1/2/745:747		Single stack bend
homologous
IL_5J7L_032
IL_26793.1
IL_8BHN_1431/2/662:666,
1/2/740:743		Tandem non-canonical cWW pairs
homologous
IL_5J7L_033
IL_85033.2
IL_8BHN_1441/2/673:678,
1/2/712:717		No text annotation
homologous
IL_4LFB_030
NA
IL_8BHN_1451/2/684:689,
1/2/698:706		No text annotation
IL_8BHN_1461/2/774:778,
1/2/804:805		Left turn
homologous
IL_4LFB_032
IL_29346.2
IL_8BHN_1471/2/779:783,
1/2/799:803		tSH-tHW-tHS
homologous
IL_5J7L_037
IL_17136.7
IL_8BHN_1481/2/840:842,
1/2/845:846		No text annotation
IL_8BHN_1491/2/887:894,
1/2/905:910		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_5J7L_038
IL_41756.4
IL_8BHN_1501/2/922:923,
1/2/1393:1395		Single bulged A
homologous
IL_5J7L_039
IL_31462.6
IL_8BHN_1511/2/925:927,
1/2/1390:1391		Single bulged G
homologous
IL_4LFB_036
IL_00225.13
IL_8BHN_1521/2/933:935,
1/2/1380:1384		Minor groove platform
homologous
IL_5J7L_041
IL_47078.3
IL_8BHN_1541/2/953:954,
1/2/1226:1228		Minor groove platform
homologous
IL_4LFB_038
IL_51454.3
IL_8BHN_1551/2/993:997,
1/2/1044:1045		Minor groove platform
geometric
IL_5J7L_043
IL_47078.3
IL_8BHN_1561/2/998:999,
1/2/1041:1043		Single stack bend
homologous
IL_5J7L_044
IL_26793.1
IL_8BHN_1571/2/1048:1050,
1/2/1208:1209		Single bulged U
homologous
IL_5J7L_046
IL_89505.4
IL_8BHN_1991/2/1052:1056,
1/2/1204:1206		No text annotation
homologous
IL_6CZR_154
NA
IL_8BHN_1591/2/1057:1058,
1/2/1199:1203		Minor groove platform
homologous
IL_5J7L_048
IL_95583.2
IL_8BHN_1601/2/1060:1061,
1/2/1195:1197		Single bulged A
homologous
IL_5J7L_049
IL_31462.6
IL_8BHN_1611/2/1061:1063,
1/2/1193:1195		Isolated non-canonical cWW pair
geometric
IL_5J7L_050
IL_28037.2
IL_8BHN_1631/2/1124:1128,
1/2/1144:1149		No text annotation
homologous
IL_5J7L_051
IL_06691.1
IL_8BHN_1641/2/1129:1132,
1/2/1142:1143		Minor groove platform
homologous
IL_5J7L_052
IL_15052.4
IL_8BHN_1651/2/1247:1253,
1/2/1284:1290		No text annotation
homologous
IL_5J7L_054
IL_09129.2
IL_8BHN_1661/2/1255:1258,
1/2/1277:1282		180 degree turn
homologous
IL_5J7L_055
IL_11344.2
IL_8BHN_1671/2/1259:1263,
1/2/1272:1276		Triple sheared
homologous
IL_5J7L_056
IL_17948.2
IL_8BHN_1681/2/1399:1401,
1/2/1501:1504		No text annotation
homologous
IL_6CZR_165
NA
IL_8BHN_1691/2/1401:1404,
1/2/1497:1501		No text annotation
geometric
IL_4V88_464
NA
IL_8BHN_1701/2/1405:1407,
1/2/1494:1496		Isolated non-canonical cWW pair
geometric
IL_4WF9_020
IL_87907.2
IL_8BHN_1711/2/1407:1409,
1/2/1491:1494		Decoding loop related
geometric
IL_3C3Z_002
IL_31737.3
IL_8BHN_1721/2/1412:1414,
1/2/1486:1488		Isolated non-canonical cWW pair
homologous
IL_5J7L_061
IL_87907.2
IL_8BHN_1731/2/1416:1419,
1/2/1481:1484		Double sheared
homologous
IL_5J7L_062
IL_09705.15
IL_8BHN_1741/2/1430:1435,
1/2/1466:1470		Triple sheared related
homologous
IL_5J7L_063
IL_80231.1
IL_8BHN_1751/2/1440:1442,
1/2/1460:1461		Single bulged A
homologous
IL_5J7L_064
IL_31462.6
IL_8BHN_1761/2/1445:1448,
1/2/1455:1457		No text annotation
homologous
IL_5J7L_065
IL_31531.3

Problematic loops

#loop idProblemSequence
IL_8BHN_180No text annotation
IL_8BHN_181Isolated non-canonical cWW pair
IL_8BHN_182No text annotation
IL_8BHN_071No text annotation
IL_8BHN_186No text annotation
IL_8BHN_187No text annotation
IL_8BHN_188Isolated non-canonical cWW pair
IL_8BHN_189No text annotation
IL_8BHN_190No text annotation
IL_8BHN_089Major groove platform with extra pair
IL_8BHN_093Isolated non-canonical cWW pair
IL_8BHN_102Isolated non-canonical cWW with bulges
IL_8BHN_110Isolated non-canonical cWW pair
IL_8BHN_193Tandem non-canonical cWW pairs
IL_8BHN_194No text annotation
IL_8BHN_130No text annotation
IL_8BHN_196No text annotation
IL_8BHN_153Isolated cWH basepair
IL_8BHN_158Tandem non-canonical cWW pairs
IL_8BHN_162Isolated non-canonical cWW pair
IL_8BHN_177Isolated non-canonical cWW pair
IL_8BHN_178No text annotation
IL_8BHN_179No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8BHN_0161/0/30:31,
1/0/474:481,
1/0/509:510		No text annotation
geometric
J3_5J7L_036
J3_60031.2
J3_8BHN_0171/0/30:31,
1/0/474:484,
1/0/496:510		No text annotation
homologous
J3_9DFE_002
J3_92134.2
J3_8BHN_0181/0/32:35,
1/0/445:461,
1/0/468:473		No text annotation
homologous
J3_5J7L_067
J3_30040.2
J3_8BHN_0191/0/56:57,
1/0/70:76,
1/0/110:114		No text annotation
homologous
J3_5J7L_037
J3_35667.2
J3_8BHN_0201/0/297:301,
1/0/316:325,
1/0/337:341		No text annotation
homologous
J3_5J7L_068
J3_46299.2
J3_8BHN_0011/0/683:689,
1/0/773:775,
1/0/791:794		No text annotation
homologous
J3_5J7L_038
J3_64189.2
J3_8BHN_0021/0/698:700,
1/0/732:736,
1/0/760:763		No text annotation
homologous
J3_7RQB_005
NA
J3_8BHN_0031/0/1298:1303,
1/0/1625:1627,
1/0/1639:1642		No text annotation
homologous
J3_5J7L_041
J3_32852.6
J3_8BHN_0041/0/1306:1309,
1/0/1605:1611,
1/0/1620:1622		No text annotation
homologous
J3_7A0S_007
J3_71677.1
J3_8BHN_0211/0/1344:1349,
1/0/1382:1385,
1/0/1402:1403		No text annotation
homologous
J3_5J7L_043
J3_92705.1
J3_8BHN_0221/0/1424:1429,
1/0/1564:1565,
1/0/1568:1574		No text annotation
homologous
J3_7A0S_019
J3_34864.2
J3_8BHN_0051/0/2091:2093,
1/0/2196:2200,
1/0/2223:2228		Kink-turn in J3
homologous
J3_5J7L_044
J3_89368.5
J3_8BHN_0231/0/2282:2284,
1/0/2384:2395,
1/0/2421:2427		No text annotation
homologous
J3_5J7L_070
J3_20992.1
J3_8BHN_0061/0/2295:2297,
1/0/2321:2323,
1/0/2332:2337		No text annotation
homologous
J3_5J7L_045
J3_61124.2
J3_8BHN_0241/0/2295:2299,
1/0/2317:2323,
1/0/2332:2337		No text annotation
homologous
J3_5J7L_071
J3_44961.1
J3_8BHN_0071/0/2517:2520,
1/0/2545:2547,
1/0/2561:2567		No text annotation
homologous
J3_5J7L_046
J3_32601.5
J3_8BHN_0251/0/2789:2791,
1/0/2805:2806,
1/0/2892:2894		No text annotation
homologous
J3_5J7L_047
J3_30104.1
J3_8BHN_0081/0/2812:2815,
1/0/2831:2836,
1/0/2882:2888		No text annotation
homologous
J3_5J7L_048
J3_64069.1
J3_8BHN_0091/1/10:16,
1/1/68:70,
1/1/106:110		No text annotation
homologous
J3_5J7L_049
J3_89095.1
J3_8BHN_0271/2/46:47,
1/2/361:367,
1/2/393:395		No text annotation
geometric
J3_4LFB_010
J3_67856.4
J3_8BHN_0281/2/46:52,
1/2/359:367,
1/2/393:395		No text annotation
homologous
J3_5J7L_050
J3_46317.4
J3_8BHN_0291/2/586:588,
1/2/651:654,
1/2/754:755		No text annotation
geometric
J3_4LFB_011
J3_56052.5
J3_8BHN_0301/2/586:588,
1/2/651:655,
1/2/751:755		No text annotation
homologous
J3_4LFB_015
J3_17385.4
J3_8BHN_0311/2/672:673,
1/2/717:725,
1/2/732:734		No text annotation
homologous
J3_5J7L_003
J3_11934.4
J3_8BHN_0101/2/826:829,
1/2/857:861,
1/2/868:874		No text annotation
homologous
J3_5J7L_004
J3_85054.4
J3_8BHN_0321/2/936:939,
1/2/1344:1350,
1/2/1372:1379		No text annotation
homologous
J3_5J7L_052
J3_25303.4
J3_8BHN_0111/2/942:946,
1/2/1235:1237,
1/2/1337:1341		No text annotation
J3_8BHN_0121/2/955:962,
1/2/973:984,
1/2/1221:1225		No text annotation
homologous
J3_4LFB_004
J3_83516.4
J3_8BHN_0131/2/988:993,
1/2/1045:1047,
1/2/1210:1217		No text annotation
J3_8BHN_0331/2/988:997,
1/2/1044:1047,
1/2/1210:1217		No text annotation
J3_8BHN_0141/2/1063:1068,
1/2/1107:1113,
1/2/1187:1193		No text annotation
homologous
J3_4LFB_007
J3_08394.3
J3_8BHN_0361/2/1073:1074,
1/2/1083:1086,
1/2/1099:1102		No text annotation
homologous
J3_4LFB_017
J3_79369.1
J3_8BHN_0151/2/1116:1118,
1/2/1155:1161,
1/2/1175:1184		No text annotation
homologous
J3_5J7L_054
J3_17791.2
J3_8BHN_0351/2/1237:1241,
1/2/1296:1309,
1/2/1328:1337		No text annotation
J4_8BHN_0011/0/268:269,
1/0/370:375,
1/0/399:406,
1/0/421:424		No text annotation
homologous
J4_5J7L_018
J4_45801.6
J4_8BHN_0021/0/297:301,
1/0/316:319,
1/0/323:325,
1/0/337:341		No text annotation
homologous
J4_5J7L_019
J4_71729.5
J4_8BHN_0031/0/601:604,
1/0/624:628,
1/0/635:638,
1/0/650:656		No text annotation
homologous
J4_5J7L_020
J4_60168.1
J4_8BHN_0041/0/1270:1276,
1/0/1294:1295,
1/0/1645:1648,
1/0/2009:2010		No text annotation
homologous
J4_5J7L_021
J4_64571.5
J4_8BHN_0171/0/1310:1314,
1/0/1338:1343,
1/0/1404:1405,
1/0/1597:1604		No text annotation
homologous
J4_5J7L_022
J4_69051.6
J4_8BHN_0181/0/1313:1314,
1/0/1338:1343,
1/0/1404:1405,
1/0/1597:1603		No text annotation
homologous
J4_5J7L_023
J4_10313.5
J4_8BHN_0071/0/1444:1445,
1/0/1466:1467,
1/0/1525:1526,
1/0/1546:1547		No text annotation
homologous
J4_5J7L_024
J4_24280.2
J4_8BHN_0081/0/1772:1776,
1/0/1788:1792,
1/0/1827:1830,
1/0/1975:1979		No text annotation
homologous
J4_5J7L_025
J4_61477.5
J4_8BHN_0191/0/1833:1835,
1/0/1905:1906,
1/0/1924:1933,
1/0/1967:1972		No text annotation
homologous
J4_9DFE_008
J4_93343.1
J4_8BHN_0101/0/2285:2289,
1/0/2343:2347,
1/0/2370:2372,
1/0/2381:2383		No text annotation
homologous
J4_5J7L_027
J4_04930.6
J4_8BHN_0111/0/2643:2646,
1/0/2674:2676,
1/0/2731:2735,
1/0/2769:2771		No text annotation
homologous
J4_5J7L_028
J4_77044.4
J4_8BHN_0121/2/115:122,
1/2/239:240,
1/2/286:289,
1/2/311:312		No text annotation
homologous
J4_5J7L_001
J4_35578.3
J4_8BHN_0131/2/142:144,
1/2/178:184,
1/2/193:198,
1/2/219:221		No text annotation
homologous
J4_5J7L_002
J4_01665.1
J4_8BHN_0141/2/569:577,
1/2/764:769,
1/2/810:821,
1/2/879:881		No text annotation
J4_8BHN_0201/4/6:9,
1/4/25:27,
1/4/43:49,
1/4/65:66		tRNA junction
homologous
J4_5E81_027
J4_70449.28
J4_8BHN_0211/5/7:10,
1/5/25:27,
1/5/43:49,
1/5/65:66		No text annotation
homologous
J4_7EQJ_002
J4_70449.28
J5_8BHN_0011/0/47:54,
1/0/116:121,
1/0/130:131,
1/0/148:150,
1/0/176:178		No text annotation
homologous
J5_5J7L_013
J5_01737.2
J5_8BHN_0021/0/531:533,
1/0/560:564,
1/0/577:579,
1/0/1261:1262,
1/0/2017:2018		No text annotation
homologous
J5_5J7L_014
J5_43153.5
J5_8BHN_0031/0/584:589,
1/0/668:671,
1/0/809:812,
1/0/1195:1196,
1/0/1250:1256		No text annotation
homologous
J5_5J7L_015
J5_74302.5
J5_8BHN_0041/0/1674:1682,
1/0/1706:1707,
1/0/1751:1752,
1/0/1756:1764,
1/0/1988:1990		No text annotation
homologous
J5_5J7L_016
J5_62523.6
J5_8BHN_0051/0/2057:2064,
1/0/2446:2454,
1/0/2498:2507,
1/0/2582:2588,
1/0/2606:2611		No text annotation
J5_8BHN_0061/0/2074:2077,
1/0/2243:2246,
1/0/2258:2259,
1/0/2281:2282,
1/0/2427:2435		No text annotation
homologous
J5_7A0S_007
J5_39529.1
J5_8BHN_0071/2/36:39,
1/2/403:406,
1/2/436:440,
1/2/497:500,
1/2/545:548		No text annotation
homologous
J5_5J7L_001
J5_92941.1
J5_8BHN_0081/2/36:39,
1/2/403:406,
1/2/436:442,
1/2/492:500,
1/2/545:548		No text annotation
homologous
J5_5J7L_002
J5_67416.1
J5_8BHN_0091/2/58:61,
1/2/106:113,
1/2/314:316,
1/2/337:339,
1/2/350:354		No text annotation
homologous
J5_4LFB_002
J5_59910.6
J6_8BHN_0031/0/45:46,
1/0/179:183,
1/0/214:224,
1/0/231:235,
1/0/262:266,
1/0/426:433		No text annotation
J6_8BHN_0021/0/2074:2077,
1/0/2243:2246,
1/0/2258:2259,
1/0/2281:2284,
1/0/2384:2395,
1/0/2421:2435		No text annotation
J7_8BHN_0031/0/8:15,
1/0/525:531,
1/0/2018:2023,
1/0/2040:2043,
1/0/2625:2630,
1/0/2788:2789,
1/0/2894:2895		No text annotation
J7_8BHN_0021/0/817:822,
1/0/835:838,
1/0/940:946,
1/0/971:976,
1/0/987:991,
1/0/1163:1164,
1/0/1185:1190		No text annotation

Problematic loops

#loop idProblemSequence
J3_8BHN_026No text annotation
J3_8BHN_034No text annotation
J4_8BHN_005No text annotation
J4_8BHN_006No text annotation
J4_8BHN_009No text annotation
J4_8BHN_015No text annotation
J4_8BHN_016No text annotation
J6_8BHN_001No text annotation
J7_8BHN_001No text annotation

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