RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8FIZ_0011/AA/12:22No text annotation
homologous
HL_4LFB_001
HL_73535.1
HL_8FIZ_0031/AA/158:163GNRA
homologous
HL_4LFB_003
HL_34789.2
HL_8FIZ_0041/AA/184:193No text annotation
HL_8FIZ_0061/AA/259:267GNRA related
homologous
HL_5J7L_006
NA
HL_8FIZ_0071/AA/296:301GNRA
homologous
HL_5J7L_007
NA
HL_8FIZ_0081/AA/320:333No text annotation
homologous
HL_5J7L_008
NA
HL_8FIZ_0091/AA/342:347UNCG
homologous
HL_5J7L_009
NA
HL_8FIZ_0101/AA/379:384GNRA
homologous
HL_5J7L_010
NA
HL_8FIZ_0111/AA/419:424UNCG
homologous
HL_4LFB_011
HL_61337.2
HL_8FIZ_0131/AA/522:527No text annotation
geometric
HL_4WF9_003
HL_75660.7
HL_8FIZ_0141/AA/617:623GNRA-like with tWH
homologous
HL_5J7L_014
NA
HL_8FIZ_0151/AA/689:698No text annotation
homologous
HL_5J7L_015
NA
HL_8FIZ_0161/AA/726:731GNRA
homologous
HL_4LFB_016
HL_34789.2
HL_8FIZ_0171/AA/786:796No text annotation
homologous
HL_6CZR_088
NA
HL_8FIZ_0191/AA/862:867GNRA
homologous
HL_4LFB_019
HL_34789.2
HL_8FIZ_0201/AA/897:902GNRA
homologous
HL_4LFB_020
HL_34789.2
HL_8FIZ_0211/AA/963:972No text annotation
homologous
HL_5J7L_021
NA
HL_8FIZ_0221/AA/1012:1017No text annotation
geometric
HL_5U3G_001
HL_75660.7
HL_8FIZ_0231/AA/1076:1081GNRA
homologous
HL_4LFB_024
HL_34789.2
HL_8FIZ_0241/AA/1089:1096T-loop related
homologous
HL_4LFB_025
HL_63894.2
HL_8FIZ_0261/AA/1165:1171GNRA
homologous
HL_5J7L_026
NA
HL_8FIZ_0271/AA/1265:1270Externally structured
geometric
HL_8C3A_022
NA
HL_8FIZ_1061/AA/1309:1328No text annotation
HL_8FIZ_0281/AA/1310:1327No text annotation
HL_8FIZ_0291/AA/1356:1366No text annotation
homologous
HL_5J7L_029
NA
HL_8FIZ_0301/AA/1449:1454UNCG
homologous
HL_4LFB_031
HL_61337.2
HL_8FIZ_0311/AA/1515:1520GNRA
homologous
HL_4LFB_032
HL_34789.2
HL_8FIZ_0321/BA/59:68No text annotation
homologous
HL_5J7L_134
NA
HL_8FIZ_0331/BA/87:95No text annotation
homologous
HL_5J7L_135
NA
HL_8FIZ_0341/BA/123:128No text annotation
homologous
HL_4WF9_003
HL_75660.7
HL_8FIZ_0361/BA/158:168No text annotation
homologous
HL_5J7L_138
NA
HL_8FIZ_0371/BA/194:201No text annotation
geometric
HL_4WF9_006
HL_48677.1
HL_8FIZ_0381/BA/225:230No text annotation
homologous
HL_5J7L_140
NA
HL_8FIZ_0391/BA/246:252No text annotation
homologous
HL_7A0S_008
HL_76371.2
HL_8FIZ_0401/BA/305:312T-loop with 1 bulged base
homologous
HL_7A0S_010
HL_13999.2
HL_8FIZ_0411/BA/319:323No text annotation
homologous
HL_7A0S_011
HL_75660.7
HL_8FIZ_0421/BA/327:335T-loop with unstacked turn
homologous
HL_5J7L_144
NA
HL_8FIZ_0431/BA/382:392No text annotation
homologous
HL_5J7L_145
NA
HL_8FIZ_0441/BA/410:417Pseudoknot geometry
homologous
HL_7A0S_014
HL_30680.5
HL_8FIZ_0451/BA/462:467GNRA
homologous
HL_4WF9_015
HL_34789.2
HL_8FIZ_0461/BA/487:493GNRA
homologous
HL_5J7L_148
NA
HL_8FIZ_0481/BA/566:575T-loop with 2 stacked bulged bases
geometric
HL_4WF9_018
HL_33597.2
HL_8FIZ_0491/BA/611:617No text annotation
HL_8FIZ_0501/BA/629:634GNRA
homologous
HL_5J7L_152
NA
HL_8FIZ_0511/BA/641:647No text annotation
homologous
HL_5J7L_153
NA
HL_8FIZ_0521/BA/712:719GNRA wlth tandem sheared
homologous
HL_5J7L_154
NA
HL_8FIZ_0531/BA/742:755No text annotation
HL_8FIZ_0541/BA/779:785No text annotation
homologous
HL_5J7L_156
NA
HL_8FIZ_0551/BA/826:831No text annotation
homologous
HL_7RQB_025
NA
HL_8FIZ_0571/BA/955:962GNRA
homologous
HL_7A0S_026
HL_34789.2
HL_8FIZ_0581/BA/978:985No text annotation
homologous
HL_5J7L_160
NA
HL_8FIZ_0601/BA/1170:1179No text annotation
homologous
HL_5J7L_213
NA
HL_8FIZ_0611/BA/1222:1227GNRA
homologous
HL_5J7L_164
NA
HL_8FIZ_0621/BA/1281:1289T-loop with 2 stacked bulged bases
homologous
HL_5J7L_165
NA
HL_8FIZ_0631/BA/1324:1330Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_166
NA
HL_8FIZ_0641/BA/1363:1368GNRA
homologous
HL_7RQB_035
NA
HL_8FIZ_0651/BA/1389:1398No text annotation
homologous
HL_5J7L_168
NA
HL_8FIZ_0661/BA/1451:1459Mini UNCG with extended bulge
homologous
HL_5J7L_169
NA
HL_8FIZ_0671/BA/1492:1498Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_170
NA
HL_8FIZ_0691/BA/1565:1568Mini UNCG
homologous
HL_5J7L_172
NA
HL_8FIZ_0701/BA/1612:1619No text annotation
homologous
HL_7RQB_040
NA
HL_8FIZ_0711/BA/1630:1636GNRA
homologous
HL_5J7L_174
NA
HL_8FIZ_0721/BA/1691:1696No text annotation
homologous
HL_7RQB_042
NA
HL_8FIZ_0741/BA/1752:1756No text annotation
homologous
HL_5J7L_177
NA
HL_8FIZ_0751/BA/1777:1787No text annotation
homologous
HL_5J7L_178
NA
HL_8FIZ_0761/BA/1806:1811GNRA related
homologous
HL_5J7L_179
NA
HL_8FIZ_0771/BA/1868:1873GNRA variation
homologous
HL_5J7L_180
NA
HL_8FIZ_0781/BA/1910:1920No text annotation
geometric
HL_2Y9H_003
HL_75660.7
HL_8FIZ_0791/BA/1949:1957No text annotation
homologous
HL_5J7L_182
NA
HL_8FIZ_0801/BA/2027:2036No text annotation
homologous
HL_4WF9_047
HL_78372.1
HL_8FIZ_0821/BA/2209:2215No text annotation
homologous
HL_5J7L_185
NA
HL_8FIZ_0831/BA/2248:2256No text annotation
homologous
HL_7A0S_052
HL_11974.2
HL_8FIZ_0841/BA/2264:2276No text annotation
homologous
HL_5J7L_187
NA
HL_8FIZ_1081/BA/2304:2312No text annotation
homologous
HL_9DFE_198
HL_02452.1
HL_8FIZ_0861/BA/2324:2331Pseudoknot geometry
homologous
HL_5J7L_189
NA
HL_8FIZ_0871/BA/2356:2361GNRA
homologous
HL_5J7L_190
NA
HL_8FIZ_0881/BA/2374:2379GNRA
homologous
HL_5J7L_191
NA
HL_8FIZ_0891/BA/2404:2413No text annotation
homologous
HL_5J7L_192
NA
HL_8FIZ_0901/BA/2471:2479No text annotation
homologous
HL_4WF9_056
HL_52011.1
HL_8FIZ_0911/BA/2528:2535No text annotation
homologous
HL_7RQB_061
NA
HL_8FIZ_0921/BA/2551:2557No text annotation
homologous
HL_4WF9_058
HL_48677.1
HL_8FIZ_0931/BA/2594:2599GNRA
homologous
HL_7RQB_063
NA
HL_8FIZ_0951/BA/2701:2706Ribsomal LSU H95
homologous
HL_5J7L_198
NA
HL_8FIZ_0961/BA/2745:2759No text annotation
homologous
HL_5J7L_199
NA
HL_8FIZ_0981/BA/2819:2827No text annotation
homologous
HL_5J7L_201
NA
HL_8FIZ_0991/BA/2856:2861GNRA
homologous
HL_7A0S_068
HL_34789.2
HL_8FIZ_1011/BB/32:40tRNA anticodon loop
homologous
HL_6UFG_007
HL_81376.2
HL_8FIZ_1071/BC/34:48No text annotation
homologous
HL_5J7L_215
NA
HL_8FIZ_1031/BC/38:44No text annotation
geometric
HL_5NFV_001
HL_69752.4
HL_8FIZ_1041/BC/86:90Mini UNCG
homologous
HL_5J7L_204
NA

Problematic loops

#loop idProblemSequence
HL_8FIZ_002No text annotation
HL_8FIZ_005UNCG
HL_8FIZ_012No text annotation
HL_8FIZ_018No text annotation
HL_8FIZ_105No text annotation
HL_8FIZ_025No text annotation
HL_8FIZ_035No text annotation
HL_8FIZ_047Externally structured
HL_8FIZ_056No text annotation
HL_8FIZ_059No text annotation
HL_8FIZ_068UNCG
HL_8FIZ_073No text annotation
HL_8FIZ_081No text annotation
HL_8FIZ_085No text annotation
HL_8FIZ_094GNRA
HL_8FIZ_097Mini UNCG
HL_8FIZ_100No text annotation
HL_8FIZ_102T-loop with 2 stacked bulged bases

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8FIZ_0011/AA/30:32,
1/AA/552:553		Single bulged G
homologous
IL_5J7L_001
NA
IL_8FIZ_0021/AA/44:45,
1/AA/396:398		Single bulged A
homologous
IL_5J7L_002
NA
IL_8FIZ_0031/AA/47:52,
1/AA/359:361		No text annotation
homologous
IL_5J7L_003
NA
IL_8FIZ_0041/AA/54:56,
1/AA/356:357		Minor groove platform
homologous
IL_4LFB_004
IL_34520.2
IL_8FIZ_0051/AA/63:66,
1/AA/103:104		Multiple bulged bases
homologous
IL_5J7L_005
NA
IL_8FIZ_0061/AA/67:69,
1/AA/99:102		Minor groove platform with extra cWW
homologous
IL_5J7L_006
NA
IL_8FIZ_0071/AA/70:73,
1/AA/97:98		Minor groove platform
homologous
IL_5J7L_007
NA
IL_8FIZ_0081/AA/128:131,
1/AA/231:233		Isolated non-canonical cWW pair
homologous
IL_5J7L_009
NA
IL_8FIZ_0091/AA/132:136,
1/AA/227:230		No text annotation
homologous
IL_4LFB_008
IL_60988.2
IL_8FIZ_0101/AA/138:141,
1/AA/222:225		Tandem non-canonical cWW pairs
geometric
IL_1MFQ_004
IL_15225.2
IL_8FIZ_0111/AA/144:146,
1/AA/176:178		Isolated cWH basepair
homologous
IL_5J7L_011
NA
IL_8FIZ_0121/AA/147:153,
1/AA/168:175		tWH-tWH-tHW-tHW
homologous
IL_5J7L_012
NA
IL_8FIZ_0141/AA/242:247,
1/AA/277:284		Kink-turn with non-sequential stacking
geometric
IL_4V88_402
NA
IL_8FIZ_0151/AA/249:252,
1/AA/274:275		No text annotation
homologous
IL_4LFB_012
IL_22002.1
IL_8FIZ_0161/AA/292:293,
1/AA/304:308		C-loop
homologous
IL_4LFB_013
IL_06671.1
IL_8FIZ_0171/AA/367:369,
1/AA/392:393		Single bulged U
homologous
IL_5J7L_017
NA
IL_8FIZ_0181/AA/371:375,
1/AA/389:390		C-loop
geometric
IL_5J7L_018
NA
IL_8FIZ_0191/AA/375:376,
1/AA/387:389		Single bulged G
homologous
IL_5J7L_019
NA
IL_8FIZ_0201/AA/409:416,
1/AA/427:433		No text annotation
homologous
IL_5J7L_020
NA
IL_8FIZ_0211/AA/440:442,
1/AA/492:497		No text annotation
homologous
IL_5J7L_021
NA
IL_8FIZ_0221/AA/446:450,
1/AA/483:488		tSH-tHW-tWW
homologous
IL_5J7L_022
NA
IL_8FIZ_0231/AA/450:455,
1/AA/477:483		No text annotation
geometric
IL_5J7L_023
NA
IL_8FIZ_0241/AA/504:511,
1/AA/540:541		SSU/LSU pseudoknot
homologous
IL_4LFB_020
IL_11411.1
IL_8FIZ_0251/AA/515:521,
1/AA/528:536		Kink-turn related
geometric
IL_4V88_415
NA
IL_8FIZ_0261/AA/569:575,
1/AA/880:881		No text annotation
homologous
IL_4LFB_022
IL_20847.1
IL_8FIZ_0271/AA/580:584,
1/AA/757:761		tSH-tHW-tHS
homologous
IL_5J7L_027
NA
IL_8FIZ_0281/AA/594:596,
1/AA/644:645		Major groove platform
homologous
IL_5J7L_028
NA
IL_8FIZ_0291/AA/597:599,
1/AA/639:643		No text annotation
homologous
IL_6CZR_361
NA
IL_8FIZ_0301/AA/605:612,
1/AA/628:633		No text annotation
homologous
IL_5J7L_030
NA
IL_8FIZ_0311/AA/654:655,
1/AA/751:754		Major groove platform; stack outside cWW
geometric
IL_7RQB_066
NA
IL_8FIZ_0321/AA/658:659,
1/AA/746:748		Single stack bend
homologous
IL_5J7L_032
NA
IL_8FIZ_0331/AA/662:666,
1/AA/740:743		Tandem non-canonical cWW pairs
homologous
IL_5J7L_033
NA
IL_8FIZ_1821/AA/673:677,
1/AA/713:717		Triple non-canonical cWW pairs
homologous
IL_4LFB_065
IL_71154.2
IL_8FIZ_0351/AA/684:688,
1/AA/699:706		No text annotation
IL_8FIZ_0361/AA/774:779,
1/AA/803:805		No text annotation
IL_8FIZ_1831/AA/774:783,
1/AA/799:805		No text annotation
IL_8FIZ_0371/AA/779:783,
1/AA/799:803		tSH-tHW-tHS
homologous
IL_5J7L_037
NA
IL_8FIZ_0381/AA/887:894,
1/AA/905:910		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_5J7L_038
NA
IL_8FIZ_0391/AA/922:923,
1/AA/1393:1395		Single bulged A
homologous
IL_5J7L_039
NA
IL_8FIZ_0401/AA/925:927,
1/AA/1390:1391		Single bulged G
homologous
IL_4LFB_036
IL_28408.2
IL_8FIZ_0411/AA/933:935,
1/AA/1380:1384		Minor groove platform
homologous
IL_5J7L_041
NA
IL_8FIZ_0421/AA/953:954,
1/AA/1226:1228		Minor groove platform
homologous
IL_4LFB_038
IL_34520.2
IL_8FIZ_0431/AA/984:987,
1/AA/1217:1220		Tandem non-canonical cWW pairs
geometric
IL_4K27_001
IL_15225.2
IL_8FIZ_0441/AA/987:990,
1/AA/1215:1217		No text annotation
geometric
IL_8C3A_070
NA
IL_8FIZ_0451/AA/993:1002,
1/AA/1038:1045		No text annotation
IL_8FIZ_0471/AA/1048:1050,
1/AA/1208:1209		Single bulged U
homologous
IL_5J7L_046
NA
IL_8FIZ_0481/AA/1052:1056,
1/AA/1204:1206		Isolated cWS basepair
homologous
IL_4LFB_044
IL_82453.1
IL_8FIZ_0491/AA/1057:1058,
1/AA/1199:1203		Minor groove platform
homologous
IL_5J7L_048
NA
IL_8FIZ_0501/AA/1060:1061,
1/AA/1195:1197		Single bulged A
geometric
IL_5J7L_049
NA
IL_8FIZ_0511/AA/1061:1063,
1/AA/1193:1195		Isolated non-canonical cWW pair
homologous
IL_4LFB_047
IL_68118.2
IL_8FIZ_0521/AA/1124:1128,
1/AA/1144:1149		No text annotation
homologous
IL_5J7L_051
NA
IL_8FIZ_0551/AA/1158:1161,
1/AA/1175:1181		No text annotation
geometric
IL_5J7L_053
NA
IL_8FIZ_1861/AA/1245:1253,
1/AA/1284:1292		No text annotation
IL_8FIZ_0561/AA/1255:1258,
1/AA/1277:1282		180 degree turn
homologous
IL_5J7L_055
NA
IL_8FIZ_0571/AA/1259:1263,
1/AA/1272:1276		Double sheared with non-canonical cWW
homologous
IL_5J7L_056
NA
IL_8FIZ_0581/AA/1353:1355,
1/AA/1367:1369		Isolated cWH basepair
geometric
IL_3R1C_032
NA
IL_8FIZ_0591/AA/1399:1401,
1/AA/1501:1504		No text annotation
geometric
IL_5J7L_058
NA
IL_8FIZ_0601/AA/1401:1405,
1/AA/1496:1501		No text annotation
homologous
IL_4LFB_057
NA
IL_8FIZ_0611/AA/1405:1407,
1/AA/1494:1496		Isolated non-canonical cWW pair
geometric
IL_5VCI_002
IL_01003.2
IL_8FIZ_0621/AA/1407:1409,
1/AA/1491:1494		Decoding loop related
geometric
IL_3C3Z_002
IL_53541.1
IL_8FIZ_0631/AA/1412:1414,
1/AA/1486:1488		Isolated non-canonical cWW pair
homologous
IL_5J7L_061
NA
IL_8FIZ_0641/AA/1416:1419,
1/AA/1481:1484		Double sheared
homologous
IL_5J7L_062
NA
IL_8FIZ_0651/AA/1430:1435,
1/AA/1466:1470		Triple sheared related
homologous
IL_5J7L_063
NA
IL_8FIZ_0661/AA/1440:1442,
1/AA/1460:1461		Single bulged A
homologous
IL_5J7L_064
NA
IL_8FIZ_0671/AA/1445:1448,
1/AA/1455:1457		No text annotation
homologous
IL_5J7L_065
NA
IL_8FIZ_0681/BA/24:30,
1/BA/510:516		Triple sheared with non-canonical cWW
homologous
IL_5J7L_245
NA
IL_8FIZ_0691/BA/36:37,
1/BA/442:444		Single bulged A
homologous
IL_5J7L_246
NA
IL_8FIZ_0701/BA/43:44,
1/BA/434:436		Minor groove platform
homologous
IL_5J7L_247
NA
IL_8FIZ_0711/BA/81:85,
1/BA/97:105		No text annotation
homologous
IL_5J7L_248
NA
IL_8FIZ_0721/BA/183:184,
1/BA/212:214		Single stack bend
homologous
IL_7A0S_005
IL_15011.2
IL_8FIZ_0731/BA/188:194,
1/BA/201:208		8x7 Sarcin-Ricin; G-bulge
homologous
IL_7A0S_006
IL_62167.2
IL_8FIZ_0741/BA/239:245,
1/BA/253:258		7x6 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_251
NA
IL_8FIZ_0751/BA/269:271,
1/BA/366:370		No text annotation
homologous
IL_5J7L_252
NA
IL_8FIZ_0771/BA/293:295,
1/BA/343:347		No text annotation
homologous
IL_5J7L_254
NA
IL_8FIZ_0781/BA/481:484,
1/BA/496:509		No text annotation
homologous
IL_5J7L_255
NA
IL_8FIZ_0791/BA/536:539,
1/BA/554:557		Double sheared
homologous
IL_5J7L_256
NA
IL_8FIZ_0801/BA/564:566,
1/BA/575:577		Isolated non-canonical cWW pair
homologous
IL_4WF9_017
IL_71625.2
IL_8FIZ_0811/BA/606:610,
1/BA/618:622		AAA cross-strand stack
homologous
IL_5J7L_258
NA
IL_8FIZ_0821/BA/672:674,
1/BA/806:808		No text annotation
homologous
IL_7RQB_017
NA
IL_8FIZ_0831/BA/674:678,
1/BA/799:806		tHW-tHW cross-strand stack
geometric
IL_5J7L_260
NA
IL_8FIZ_0841/BA/697:698,
1/BA/763:765		Single bulged A
homologous
IL_5J7L_261
NA
IL_8FIZ_0851/BA/702:703,
1/BA/728:730		Single bulged G
geometric
IL_7A0S_017
IL_28408.2
IL_8FIZ_0861/BA/703:707,
1/BA/724:728		Triple sheared
homologous
IL_7RQB_021
NA
IL_8FIZ_0871/BA/738:740,
1/BA/757:758		Major groove platform
homologous
IL_5J7L_264
NA
IL_8FIZ_0881/BA/775:777,
1/BA/787:791		Multiple bulged bases
homologous
IL_5J7L_265
NA
IL_8FIZ_0891/BA/844:847,
1/BA/933:934		90 degree turn
geometric
IL_5J7L_267
NA
IL_8FIZ_1871/BA/844:848,
1/BA/930:934		No text annotation
geometric
IL_5J7L_399
NA
IL_8FIZ_0901/BA/847:848,
1/BA/930:933		Stack outside cWW
homologous
IL_5J7L_268
NA
IL_8FIZ_0911/BA/850:851,
1/BA/926:928		Single stack bend
homologous
IL_5J7L_269
NA
IL_8FIZ_0921/BA/856:862,
1/BA/915:921		7x7 Sarcin-Ricin with intercalated A; G-bulge
geometric
IL_5J7L_270
NA
IL_8FIZ_0931/BA/862:863,
1/BA/913:915		Single bulged G
homologous
IL_5J7L_271
NA
IL_8FIZ_0941/BA/864:868,
1/BA/909:912		C-loop with bulged stacked A's
homologous
IL_5J7L_272
NA
IL_8FIZ_0951/BA/870:872,
1/BA/905:907		Isolated non-canonical cWW pair
homologous
IL_5J7L_273
NA
IL_8FIZ_0981/BA/994:996,
1/BA/1159:1160		Single bulged C
homologous
IL_5J7L_276
NA
IL_8FIZ_0991/BA/998:1002,
1/BA/1153:1157		UAA/GAN
homologous
IL_7A0S_033
IL_08938.1
IL_8FIZ_1001/BA/1004:1011,
1/BA/1150:1151		SSU/LSU pseudoknot
geometric
IL_5J7L_278
NA
IL_8FIZ_1011/BA/1011:1013,
1/BA/1149:1150		Single bulged U
homologous
IL_5J7L_279
NA
IL_8FIZ_1021/BA/1018:1024,
1/BA/1140:1144		Kink-turn related
geometric
IL_5J7L_280
NA
IL_8FIZ_1031/BA/1024:1030,
1/BA/1124:1140		No text annotation
geometric
IL_5J7L_281
NA
IL_8FIZ_1041/BA/1031:1034,
1/BA/1121:1123		Isolated non-canonical cWW pair
geometric
IL_7A0S_038
IL_76400.1
IL_8FIZ_1881/BA/1031:1036,
1/BA/1118:1123		No text annotation
IL_8FIZ_1051/BA/1034:1036,
1/BA/1118:1121		No text annotation
geometric
IL_8GLP_064
IL_16315.2
IL_8FIZ_1061/BA/1036:1038,
1/BA/1117:1118		Single stack bend
geometric
IL_5J7L_032
NA
IL_8FIZ_1891/BA/1036:1041,
1/BA/1114:1118		No text annotation
IL_8FIZ_1071/BA/1038:1041,
1/BA/1114:1117		No text annotation
IL_8FIZ_1091/BA/1196:1198,
1/BA/1247:1250		Isolated cWS basepair
homologous
IL_4WF9_044
IL_42997.5
IL_8FIZ_1101/BA/1202:1206,
1/BA/1240:1243		No text annotation
homologous
IL_5J7L_287
NA
IL_8FIZ_1111/BA/1208:1215,
1/BA/1234:1238		Kink-turn
homologous
IL_5J7L_288
NA
IL_8FIZ_1121/BA/1262:1269,
1/BA/2011:2017		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
NA
IL_8FIZ_1131/BA/1310:1313,
1/BA/1603:1604		Major groove platform; stack outside cWW
homologous
IL_5J7L_290
NA
IL_8FIZ_1141/BA/1319:1323,
1/BA/1331:1333		C-loop
homologous
IL_5J7L_291
NA
IL_8FIZ_1151/BA/1351:1355,
1/BA/1376:1380		UAA/GAN
homologous
IL_5J7L_292
NA
IL_8FIZ_1161/BA/1357:1361,
1/BA/1370:1374		tSH-tHW-tHS
homologous
IL_5J7L_293
NA
IL_8FIZ_1181/BA/1417:1421,
1/BA/1577:1581		UAA/GAN
homologous
IL_5J7L_295
NA
IL_8FIZ_1191/BA/1430:1432,
1/BA/1561:1563		Isolated non-canonical cWW pair
geometric
IL_4V9F_105
IL_01003.2
IL_8FIZ_1201/BA/1432:1435,
1/BA/1557:1561		Tandem non-canonical cWW pairs
geometric
IL_5J7L_296
NA
IL_8FIZ_1211/BA/1437:1440,
1/BA/1551:1555		tSH-tHW
homologous
IL_5J7L_297
NA
IL_8FIZ_1221/BA/1450:1451,
1/BA/1459:1461		Single bulged U
geometric
IL_5TBW_146
NA
IL_8FIZ_1231/BA/1468:1471,
1/BA/1520:1524		No text annotation
homologous
IL_5J7L_299
NA
IL_8FIZ_1241/BA/1474:1478,
1/BA/1513:1517		tSH-tHW-tHS
homologous
IL_5J7L_300
NA
IL_8FIZ_1251/BA/1481:1482,
1/BA/1507:1510		180 degree turn
homologous
IL_5J7L_301
NA
IL_8FIZ_1261/BA/1489:1491,
1/BA/1499:1500		Single bulged A
homologous
IL_5J7L_302
NA
IL_8FIZ_1271/BA/1526:1529,
1/BA/1542:1546		UAA/GAN variation
homologous
IL_5J7L_303
NA
IL_8FIZ_1281/BA/1651:1656,
1/BA/2004:2006		No text annotation
homologous
IL_5J7L_304
NA
IL_8FIZ_1291/BA/1663:1665,
1/BA/1995:1997		Isolated tWW turn
homologous
IL_4WF9_063
IL_10432.1
IL_8FIZ_1301/BA/1666:1669,
1/BA/1993:1994		Major groove platform; stack outside cWW
homologous
IL_7RQB_066
NA
IL_8FIZ_1911/BA/1666:1674,
1/BA/1990:1994		No text annotation
homologous
IL_4WF9_117
IL_80252.1
IL_8FIZ_1311/BA/1669:1674,
1/BA/1990:1993		Intercalated tWH
geometric
IL_4WF9_065
IL_28217.1
IL_8FIZ_1321/BA/1686:1691,
1/BA/1696:1702		tSH-tSH-tHH-tHS
geometric
IL_5J7L_308
NA
IL_8FIZ_1331/BA/1712:1718,
1/BA/1742:1746		6x5 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_309
NA
IL_8FIZ_1351/BA/1727:1728,
1/BA/1731:1733		Single bulged C
geometric
IL_5J7L_311
NA
IL_8FIZ_1361/BA/1770:1771,
1/BA/1980:1982		Single bulged A
homologous
IL_4WF9_068
IL_14190.2
IL_8FIZ_1371/BA/1798:1804,
1/BA/1813:1821		Kink-turn related
homologous
IL_7A0S_065
IL_17069.6
IL_8FIZ_1381/BA/1837:1840,
1/BA/1902:1903		Minor groove platform, major groove intercalation
homologous
IL_5J7L_314
NA
IL_8FIZ_1391/BA/1841:1842,
1/BA/1898:1901		Major groove intercalation
homologous
IL_5J7L_315
NA
IL_8FIZ_1401/BA/1846:1849,
1/BA/1893:1894		Minor groove platform
geometric
IL_4KQY_004
IL_94991.2
IL_8FIZ_1931/BA/1851:1860,
1/BA/1882:1891		No text annotation
homologous
IL_5J7L_387
NA
IL_8FIZ_1411/BA/1864:1867,
1/BA/1874:1878		UAA/GAN related
homologous
IL_5J7L_317
NA
IL_8FIZ_1421/BA/1933:1934,
1/BA/1964:1967		Bulged stacked bases
geometric
IL_7A0S_071
IL_24886.2
IL_8FIZ_1431/BA/1934:1945,
1/BA/1961:1964		No text annotation
homologous
IL_7A0S_072
IL_04332.3
IL_8FIZ_1441/BA/2050:2052,
1/BA/2617:2618		Major groove platform
homologous
IL_5J7L_320
NA
IL_8FIZ_1451/BA/2054:2056,
1/BA/2612:2615		No text annotation
homologous
IL_4WF9_079
IL_80025.1
IL_8FIZ_1461/BA/2067:2071,
1/BA/2438:2443		No text annotation
IL_8FIZ_1471/BA/2081:2083,
1/BA/2236:2239		Isolated tHS basepair with bulges
homologous
IL_5J7L_325
NA
IL_8FIZ_1481/BA/2085:2087,
1/BA/2232:2234		No text annotation
homologous
IL_7RQB_083
NA
IL_8FIZ_1521/BA/2202:2204,
1/BA/2220:2221		Single bulged U
homologous
IL_5J7L_331
NA
IL_8FIZ_1531/BA/2350:2353,
1/BA/2364:2367		Double sheared
homologous
IL_7RQB_089
NA
IL_8FIZ_1541/BA/2401:2403,
1/BA/2414:2415		Single bulged U
homologous
IL_5J7L_334
NA
IL_8FIZ_1551/BA/2453:2455,
1/BA/2496:2500		No text annotation
homologous
IL_5J7L_335
NA
IL_8FIZ_1561/BA/2457:2459,
1/BA/2493:2494		Major groove platform
homologous
IL_7A0S_085
IL_48076.8
IL_8FIZ_1571/BA/2459:2461,
1/BA/2489:2493		Major groove minor groove platform with extra cWW
geometric
IL_5J7L_337
NA
IL_8FIZ_1581/BA/2466:2470,
1/BA/2480:2484		Double sheared with non-canonical cWW
homologous
IL_5J7L_338
NA
IL_8FIZ_1591/BA/2507:2508,
1/BA/2580:2582		Major groove platform
homologous
IL_7A0S_088
IL_46637.2
IL_8FIZ_1601/BA/2510:2512,
1/BA/2574:2578		Isolated non-canonical cWW with bulges
geometric
IL_5J7L_340
NA
IL_8FIZ_1611/BA/2512:2513,
1/BA/2571:2574		Multiple bulged bases
homologous
IL_7RQB_098
NA
IL_8FIZ_1621/BA/2522:2523,
1/BA/2540:2543		Major groove platform with intercalation
homologous
IL_7A0S_091
IL_94991.2
IL_8FIZ_1631/BA/2591:2592,
1/BA/2601:2603		Single bulged A
homologous
IL_5J7L_344
NA
IL_8FIZ_1641/BA/2636:2640,
1/BA/2774:2782		tSH-tHS-tHW
homologous
IL_7RQB_102
NA
IL_8FIZ_1651/BA/2652:2658,
1/BA/2663:2668		Sarcin-Ricin target in LSU H95; G-bulge
homologous
IL_5J7L_346
NA
IL_8FIZ_1661/BA/2680:2684,
1/BA/2725:2727		C-loop
homologous
IL_5J7L_347
NA
IL_8FIZ_1671/BA/2687:2691,
1/BA/2718:2722		UAA/GAN related, with intercalation
homologous
IL_5J7L_348
NA
IL_8FIZ_1681/BA/2695:2696,
1/BA/2711:2714		Multiple bulged bases
homologous
IL_4WF9_103
IL_44609.2
IL_8FIZ_1691/BA/2737:2742,
1/BA/2762:2767		UAA/GAN with extra cWW
homologous
IL_5J7L_350
NA
IL_8FIZ_1711/BA/2806:2811,
1/BA/2889:2892		No text annotation
homologous
IL_5J7L_351
NA
IL_8FIZ_1971/BA/2838:2839,
1/BA/2878:2880		Major groove intercalation
homologous
IL_5J7L_352
NA
IL_8FIZ_1731/BA/2843:2846,
1/BA/2870:2874		Multiple bulged bases with non-canonical cWW
homologous
IL_5J7L_353
NA
IL_8FIZ_1741/BA/2847:2852,
1/BA/2865:2869		tHS double platform
homologous
IL_5J7L_354
NA
IL_8FIZ_1751/BC/17:18,
1/BC/65:67		Major groove intercalation
homologous
IL_5J7L_355
NA
IL_8FIZ_1761/BC/23:28,
1/BC/56:60		No text annotation
homologous
IL_5J7L_356
NA
IL_8FIZ_1771/BC/30:31,
1/BC/51:54		Major groove minor groove platform; mini C-loop
geometric
IL_4PDB_002
IL_73108.2
IL_8FIZ_1781/BC/34:38,
1/BC/44:48		Symmetric double minor groove platform
homologous
IL_5J7L_358
NA
IL_8FIZ_1791/BC/71:79,
1/BC/97:105		Bacterial 5S Loop E
homologous
IL_5J7L_359
NA

Problematic loops

#loop idProblemSequence
IL_8FIZ_180Tandem non-canonical cWW pairs
IL_8FIZ_013No text annotation
IL_8FIZ_181No text annotation
IL_8FIZ_034No text annotation
IL_8FIZ_1849x7 Sarcin-Ricin with inserted C; G-bulge
IL_8FIZ_046No text annotation
IL_8FIZ_185No text annotation
IL_8FIZ_053Multiple bulged bases
IL_8FIZ_054No text annotation
IL_8FIZ_076No text annotation
IL_8FIZ_096Double sheared with non-canonical cWW
IL_8FIZ_097No text annotation
IL_8FIZ_108No text annotation
IL_8FIZ_190No text annotation
IL_8FIZ_117No text annotation
IL_8FIZ_134Double sheared with non-canonical cWW
IL_8FIZ_192Triple sheared with non-canonical cWW
IL_8FIZ_194Isolated cWH basepair
IL_8FIZ_195No text annotation
IL_8FIZ_196No text annotation
IL_8FIZ_149No text annotation
IL_8FIZ_150No text annotation
IL_8FIZ_151Isolated non-canonical cWW pair
IL_8FIZ_170Single bulged A
IL_8FIZ_172Isolated non-canonical cWW pair

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8FIZ_0011/AA/46:47,
1/AA/361:367,
1/AA/393:395		No text annotation
homologous
J3_5J7L_001
NA
J3_8FIZ_0231/AA/46:52,
1/AA/359:367,
1/AA/393:395		No text annotation
homologous
J3_5J7L_050
NA
J3_8FIZ_0021/AA/586:588,
1/AA/651:654,
1/AA/754:755		No text annotation
homologous
J3_5J7L_002
NA
J3_8FIZ_0241/AA/586:588,
1/AA/651:655,
1/AA/751:755		No text annotation
homologous
J3_5J7L_051
NA
J3_8FIZ_0031/AA/672:673,
1/AA/717:725,
1/AA/732:734		No text annotation
homologous
J3_5J7L_003
NA
J3_8FIZ_0041/AA/826:829,
1/AA/857:861,
1/AA/868:874		No text annotation
homologous
J3_5J7L_004
NA
J3_8FIZ_0251/AA/936:939,
1/AA/1344:1350,
1/AA/1372:1379		No text annotation
homologous
J3_5J7L_052
NA
J3_8FIZ_0051/AA/943:946,
1/AA/1235:1237,
1/AA/1337:1340		No text annotation
homologous
J3_4LFB_003
J3_44359.1
J3_8FIZ_0061/AA/955:962,
1/AA/973:984,
1/AA/1220:1225		No text annotation
homologous
J3_5J7L_006
NA
J3_8FIZ_0261/AA/955:962,
1/AA/973:987,
1/AA/1217:1225		No text annotation
J3_8FIZ_0071/AA/990:993,
1/AA/1045:1047,
1/AA/1210:1215		No text annotation
homologous
J3_5J7L_007
NA
J3_8FIZ_0271/AA/990:1002,
1/AA/1038:1047,
1/AA/1210:1215		No text annotation
J3_8FIZ_0081/AA/1063:1068,
1/AA/1107:1113,
1/AA/1187:1193		No text annotation
homologous
J3_4LFB_007
J3_01343.1
J3_8FIZ_0091/AA/1073:1074,
1/AA/1083:1087,
1/AA/1098:1102		No text annotation
homologous
J3_6CZR_024
NA
J3_8FIZ_0101/AA/1116:1119,
1/AA/1154:1158,
1/AA/1181:1184		No text annotation
J3_8FIZ_0281/AA/1116:1119,
1/AA/1154:1161,
1/AA/1175:1184		No text annotation
J3_8FIZ_0291/AA/1237:1244,
1/AA/1293:1309,
1/AA/1328:1337		No text annotation
J3_8FIZ_0111/BA/30:31,
1/BA/474:481,
1/BA/509:510		No text annotation
homologous
J3_5J7L_036
NA
J3_8FIZ_0301/BA/30:31,
1/BA/474:484,
1/BA/496:510		No text annotation
homologous
J3_9DFE_002
J3_17917.1
J3_8FIZ_0311/BA/32:35,
1/BA/445:461,
1/BA/468:473		No text annotation
homologous
J3_5J7L_067
NA
J3_8FIZ_0121/BA/56:57,
1/BA/70:76,
1/BA/110:114		No text annotation
homologous
J3_5J7L_037
NA
J3_8FIZ_0131/BA/683:689,
1/BA/773:775,
1/BA/791:794		No text annotation
homologous
J3_5J7L_038
NA
J3_8FIZ_0141/BA/698:700,
1/BA/732:736,
1/BA/760:763		No text annotation
homologous
J3_7RQB_005
NA
J3_8FIZ_0151/BA/1298:1303,
1/BA/1625:1627,
1/BA/1639:1642		No text annotation
homologous
J3_5J7L_041
NA
J3_8FIZ_0161/BA/1306:1309,
1/BA/1605:1611,
1/BA/1620:1622		No text annotation
homologous
J3_7A0S_007
J3_47341.1
J3_8FIZ_0171/BA/1344:1349,
1/BA/1382:1385,
1/BA/1402:1403		No text annotation
homologous
J3_5J7L_043
NA
J3_8FIZ_0321/BA/1424:1429,
1/BA/1564:1565,
1/BA/1568:1574		No text annotation
homologous
J3_7A0S_019
J3_34864.3
J3_8FIZ_0181/BA/2091:2093,
1/BA/2196:2200,
1/BA/2223:2228		Kink-turn 3-way junction
homologous
J3_5J7L_044
NA
J3_8FIZ_0331/BA/2282:2284,
1/BA/2384:2395,
1/BA/2421:2427		No text annotation
homologous
J3_5J7L_070
NA
J3_8FIZ_0191/BA/2295:2299,
1/BA/2317:2323,
1/BA/2332:2337		No text annotation
J3_8FIZ_0201/BA/2517:2520,
1/BA/2545:2547,
1/BA/2561:2567		No text annotation
homologous
J3_5J7L_046
NA
J3_8FIZ_0211/BA/2812:2815,
1/BA/2831:2836,
1/BA/2882:2888		No text annotation
homologous
J3_5J7L_048
NA
J3_8FIZ_0221/BC/10:16,
1/BC/68:70,
1/BC/106:110		No text annotation
homologous
J3_5J7L_049
NA
J4_8FIZ_0011/AA/115:122,
1/AA/239:240,
1/AA/286:289,
1/AA/311:312		No text annotation
homologous
J4_5J7L_001
NA
J4_8FIZ_0021/AA/142:144,
1/AA/178:184,
1/AA/193:198,
1/AA/219:221		No text annotation
homologous
J4_5J7L_002
NA
J4_8FIZ_0031/AA/575:577,
1/AA/764:769,
1/AA/810:821,
1/AA/879:880		No text annotation
homologous
J4_5J7L_003
NA
J4_8FIZ_0041/BA/268:269,
1/BA/370:375,
1/BA/399:406,
1/BA/421:424		No text annotation
homologous
J4_5J7L_018
NA
J4_8FIZ_0051/BA/297:301,
1/BA/316:319,
1/BA/323:325,
1/BA/337:341		No text annotation
homologous
J4_5J7L_019
NA
J4_8FIZ_0061/BA/601:604,
1/BA/624:628,
1/BA/635:638,
1/BA/650:656		No text annotation
homologous
J4_5J7L_020
NA
J4_8FIZ_0071/BA/1270:1276,
1/BA/1294:1295,
1/BA/1645:1648,
1/BA/2009:2010		No text annotation
homologous
J4_5J7L_021
NA
J4_8FIZ_0081/BA/1310:1314,
1/BA/1338:1343,
1/BA/1404:1405,
1/BA/1597:1604		No text annotation
homologous
J4_5J7L_022
NA
J4_8FIZ_0091/BA/1313:1314,
1/BA/1338:1343,
1/BA/1404:1405,
1/BA/1597:1603		No text annotation
homologous
J4_5J7L_023
NA
J4_8FIZ_0161/BA/1444:1445,
1/BA/1466:1467,
1/BA/1525:1526,
1/BA/1546:1547		No text annotation
homologous
J4_5J7L_024
NA
J4_8FIZ_0101/BA/1444:1446,
1/BA/1465:1467,
1/BA/1525:1526,
1/BA/1546:1547		No text annotation
J4_8FIZ_0111/BA/1772:1776,
1/BA/1788:1792,
1/BA/1827:1830,
1/BA/1975:1979		No text annotation
homologous
J4_5J7L_025
NA
J4_8FIZ_0121/BA/1833:1836,
1/BA/1904:1906,
1/BA/1924:1933,
1/BA/1967:1972		No text annotation
J4_8FIZ_0171/BA/2285:2289,
1/BA/2343:2347,
1/BA/2370:2372,
1/BA/2381:2383		No text annotation
homologous
J4_5J7L_027
NA
J4_8FIZ_0141/BA/2643:2646,
1/BA/2674:2676,
1/BA/2731:2735,
1/BA/2769:2771		No text annotation
homologous
J4_5J7L_028
NA
J4_8FIZ_0151/BB/7:10,
1/BB/26:28,
1/BB/44:50,
1/BB/66:67		tRNA junction
homologous
J4_4WT8_034
J4_95067.1
J5_8FIZ_0011/AA/36:39,
1/AA/403:406,
1/AA/436:440,
1/AA/497:500,
1/AA/545:548		No text annotation
homologous
J5_5J7L_001
NA
J5_8FIZ_0021/AA/36:39,
1/AA/403:406,
1/AA/436:442,
1/AA/492:500,
1/AA/545:548		No text annotation
homologous
J5_5J7L_002
NA
J5_8FIZ_0031/AA/58:61,
1/AA/106:113,
1/AA/314:316,
1/AA/337:339,
1/AA/350:354		No text annotation
homologous
J5_4LFB_002
J5_58574.1
J5_8FIZ_0041/BA/47:54,
1/BA/116:121,
1/BA/130:131,
1/BA/148:150,
1/BA/176:178		No text annotation
homologous
J5_5J7L_013
NA
J5_8FIZ_0051/BA/531:533,
1/BA/560:564,
1/BA/577:579,
1/BA/1261:1262,
1/BA/2017:2018		No text annotation
homologous
J5_5J7L_014
NA
J5_8FIZ_0061/BA/584:589,
1/BA/668:671,
1/BA/809:812,
1/BA/1195:1196,
1/BA/1250:1256		No text annotation
homologous
J5_5J7L_015
NA
J5_8FIZ_0071/BA/1674:1682,
1/BA/1706:1707,
1/BA/1751:1752,
1/BA/1756:1764,
1/BA/1988:1990		No text annotation
homologous
J5_5J7L_016
NA
J5_8FIZ_0081/BA/2057:2064,
1/BA/2446:2453,
1/BA/2500:2507,
1/BA/2582:2588,
1/BA/2606:2611		No text annotation
J5_8FIZ_0091/BA/2074:2077,
1/BA/2243:2246,
1/BA/2258:2259,
1/BA/2281:2282,
1/BA/2427:2435		No text annotation
homologous
J5_4WF9_007
J5_39529.2
J6_8FIZ_0011/BA/45:46,
1/BA/179:183,
1/BA/214:224,
1/BA/231:235,
1/BA/262:266,
1/BA/426:433		No text annotation
J6_8FIZ_0021/BA/2074:2077,
1/BA/2243:2246,
1/BA/2258:2259,
1/BA/2281:2284,
1/BA/2384:2395,
1/BA/2421:2435		No text annotation
J7_8FIZ_0011/BA/817:822,
1/BA/835:838,
1/BA/940:946,
1/BA/971:976,
1/BA/987:991,
1/BA/1163:1164,
1/BA/1185:1190		No text annotation
J8_8FIZ_0011/BA/8:15,
1/BA/525:531,
1/BA/2018:2023,
1/BA/2040:2043,
1/BA/2625:2630,
1/BA/2788:2791,
1/BA/2805:2806,
1/BA/2892:2895		No text annotation

Problematic loops

#loop idProblemSequence
J4_8FIZ_013No text annotation

Coloring options:
Copyright 2025 BGSU RNA group. Page generated in 0.0912 s