RNA 3D Hub //

4V4Y Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_4V4Y_1201/AA/13:21No text annotation
HL_4V4Y_0021/AA/81:88No text annotation
geometric
HL_8C3A_039
NA
HL_4V4Y_0031/AA/158:163GNRA
homologous
HL_4LFB_003
HL_37824.8
HL_4V4Y_1131/AA/186:191No text annotation
homologous
HL_4LFB_004
HL_48417.6
HL_4V4Y_0051/AA/201:216Mini UNCG
homologous
HL_4LFB_005
HL_48778.2
HL_4V4Y_0061/AA/259:267GNRA related
homologous
HL_4LFB_006
HL_84299.4
HL_4V4Y_0071/AA/296:301GNRA
homologous
HL_4LFB_007
HL_37824.8
HL_4V4Y_0081/AA/320:333No text annotation
homologous
HL_6CZR_079
NA
HL_4V4Y_0091/AA/342:347UNCG
homologous
HL_4LFB_009
HL_34617.5
HL_4V4Y_0101/AA/379:384GNRA
homologous
HL_5J7L_010
HL_37824.8
HL_4V4Y_0111/AA/419:424UNCG
homologous
HL_5J7L_011
HL_34617.5
HL_4V4Y_0121/AA/458:474GNRA
homologous
HL_4LFB_012
HL_37824.8
HL_4V4Y_0131/AA/522:527No text annotation
geometric
HL_2Y8W_001
HL_81100.2
HL_4V4Y_0141/AA/617:623No text annotation
homologous
HL_6CZR_085
NA
HL_4V4Y_1141/AA/688:699No text annotation
homologous
HL_5J7L_015
HL_75293.5
HL_4V4Y_0151/AA/689:698No text annotation
homologous
HL_4LFB_015
HL_75293.5
HL_4V4Y_0161/AA/726:731GNRA
homologous
HL_5J7L_016
HL_37824.8
HL_4V4Y_0171/AA/786:796No text annotation
homologous
HL_5J7L_017
HL_75293.5
HL_4V4Y_0181/AA/838:848Mini UNCG
homologous
HL_4LFB_018
HL_48778.2
HL_4V4Y_0191/AA/862:867GNRA
homologous
HL_4LFB_019
HL_37824.8
HL_4V4Y_0201/AA/897:902GNRA
homologous
HL_4LFB_020
HL_37824.8
HL_4V4Y_0211/AA/963:972No text annotation
homologous
HL_4LFB_021
HL_50779.4
HL_4V4Y_0221/AA/1012:1017GNRA
homologous
HL_4LFB_022
HL_37824.8
HL_4V4Y_0231/AA/1028B:1032ANo text annotation
homologous
HL_4LFB_023
NA
HL_4V4Y_0241/AA/1076:1081GNRA
homologous
HL_4LFB_024
HL_37824.8
HL_4V4Y_0251/AA/1089:1096T-loop related
homologous
HL_6CZR_096
NA
HL_4V4Y_0261/AA/1134:1140No text annotation
homologous
HL_6CZR_097
NA
HL_4V4Y_0271/AA/1165:1171GNRA
homologous
HL_4LFB_027
HL_37824.8
HL_4V4Y_0281/AA/1265:1270No text annotation
HL_4V4Y_0291/AA/1314:1323T-loop with 3 stacked bulged bases
homologous
HL_4LFB_029
HL_02887.3
HL_4V4Y_0301/AA/1356:1366No text annotation
homologous
HL_6CZR_101
NA
HL_4V4Y_0311/AA/1449:1454UNCG
homologous
HL_5J7L_030
HL_34617.5
HL_4V4Y_0321/AA/1515:1520GNRA
homologous
HL_5J7L_031
HL_37824.8
HL_4V4Y_0341/AB/31:39tRNA anticodon loop
homologous
HL_6ORD_036
NA
HL_4V4Y_0361/AC/13:22No text annotation
homologous
HL_5EL4_221
NA
HL_4V4Y_0371/AC/31:39tRNA anticodon loop
homologous
HL_4TUE_034
HL_06059.7
HL_4V4Y_0381/AC/53:61T-loop with 2 stacked bulged bases
homologous
HL_4V90_034
HL_28252.9
HL_4V4Y_0391/AD/13:22No text annotation
homologous
HL_6GSL_220
NA
HL_4V4Y_0401/AD/32:38Mini UNCG
geometric
HL_4LFB_005
HL_48778.2
HL_4V4Y_0411/AD/53:61No text annotation
homologous
HL_1YFG_003
NA
HL_4V4Y_0421/BA/60:67No text annotation
HL_4V4Y_0431/BA/87:95No text annotation
homologous
HL_7RQB_002
NA
HL_4V4Y_0441/BA/123:128No text annotation
homologous
HL_4WF9_003
HL_75660.5
HL_4V4Y_0451/BA/137A:141ANo text annotation
HL_4V4Y_0461/BA/194:201No text annotation
homologous
HL_7A0S_006
HL_30068.2
HL_4V4Y_0471/BA/225:230No text annotation
homologous
HL_4WF9_007
HL_53890.2
HL_4V4Y_1211/BA/246:252No text annotation
homologous
HL_4WF9_008
HL_37369.2
HL_4V4Y_0491/BA/270J:270PNo text annotation
geometric
HL_2ZNI_001
HL_75660.5
HL_4V4Y_0501/BA/305:312No text annotation
homologous
HL_7RQB_010
NA
HL_4V4Y_0511/BA/319:323No text annotation
homologous
HL_7A0S_011
HL_75660.5
HL_4V4Y_0521/BA/327:335T-loop with unstacked turn
homologous
HL_4WF9_012
HL_27670.2
HL_4V4Y_0531/BA/383:391No text annotation
HL_4V4Y_0541/BA/411:416No text annotation
geometric
HL_2Y8W_001
HL_81100.2
HL_4V4Y_0551/BA/462:467GNRA
homologous
HL_5J7L_147
HL_37824.8
HL_4V4Y_0561/BA/487:493GNRA
homologous
HL_4WF9_016
HL_37824.8
HL_4V4Y_0571/BA/544:549No text annotation
geometric
HL_4WF9_003
HL_75660.5
HL_4V4Y_0581/BA/564:577No text annotation
HL_4V4Y_0591/BA/605:623No text annotation
HL_4V4Y_0601/BA/629:634GNRA
homologous
HL_7RQB_020
NA
HL_4V4Y_0621/BA/712:719No text annotation
homologous
HL_7RQB_022
NA
HL_4V4Y_0631/BA/744:753No text annotation
homologous
HL_7A0S_022
HL_88205.2
HL_4V4Y_0641/BA/779:785UNCG variation
homologous
HL_7A0S_023
HL_53890.2
HL_4V4Y_0651/BA/826:831No text annotation
homologous
HL_7A0S_024
HL_55195.3
HL_4V4Y_0661/BA/884:892No text annotation
homologous
HL_5J7L_158
NA
HL_4V4Y_0671/BA/955:962GNRA
homologous
HL_4WF9_027
HL_37824.8
HL_4V4Y_0681/BA/978:985No text annotation
homologous
HL_7RQB_028
NA
HL_4V4Y_0691/BA/1062:1076No text annotation
HL_4V4Y_0701/BA/1092:1099No text annotation
homologous
HL_9DFE_028
NA
HL_4V4Y_0711/BA/1170:1179No text annotation
homologous
HL_4WF9_030
NA
HL_4V4Y_0721/BA/1221:1228Externally structured
geometric
HL_8C3A_022
NA
HL_4V4Y_0731/BA/1281:1289No text annotation
homologous
HL_7RQB_033
NA
HL_4V4Y_0741/BA/1324:1330Pseudoknot geometry with 3' bulge
geometric
HL_4WF9_033
HL_57176.2
HL_4V4Y_1221/BA/1363:1368GNRA
homologous
HL_9DFE_033
HL_37824.8
HL_4V4Y_0761/BA/1389:1398No text annotation
homologous
HL_5J7L_168
HL_81545.2
HL_4V4Y_0771/BA/1450:1461No text annotation
HL_4V4Y_0781/BA/1492:1498No text annotation
HL_4V4Y_0791/BA/1533:1538UNCG
homologous
HL_5J7L_171
HL_34617.5
HL_4V4Y_0801/BA/1612:1619No text annotation
homologous
HL_4WF9_038
HL_89567.2
HL_4V4Y_1231/BA/1630A:1635Pseudoknot geometry with 3' bulge
homologous
HL_7A0S_073
HL_57176.2
HL_4V4Y_0821/BA/1691:1696UNCG
homologous
HL_5J7L_175
HL_34617.5
HL_4V4Y_0831/BA/1717:1742No text annotation
HL_4V4Y_0841/BA/1752:1756No text annotation
homologous
HL_7A0S_044
HL_80709.3
HL_4V4Y_0851/BA/1779:1785No text annotation
geometric
HL_2Y8W_001
HL_81100.2
HL_4V4Y_0861/BA/1806:1811No text annotation
geometric
HL_1WZ2_007
HL_75660.5
HL_4V4Y_0871/BA/1864:1878GNRA
homologous
HL_7RQB_047
NA
HL_4V4Y_0881/BA/1911:1919No text annotation
HL_4V4Y_0891/BA/1950:1956Mini UNCG
geometric
HL_5T16_002
HL_56334.1
HL_4V4Y_0901/BA/2027:2036No text annotation
homologous
HL_7A0S_049
HL_61996.3
HL_4V4Y_0911/BA/2143:2148No text annotation
geometric
HL_2Y8W_001
HL_81100.2
HL_4V4Y_0921/BA/2209:2215No text annotation
HL_4V4Y_0931/BA/2249:2255No text annotation
HL_4V4Y_0941/BA/2264:2276No text annotation
homologous
HL_7A0S_053
HL_91939.2
HL_4V4Y_0951/BA/2304:2312No text annotation
homologous
HL_7A0S_076
HL_50860.2
HL_4V4Y_0961/BA/2324:2331Pseudoknot geometry
homologous
HL_7RQB_056
NA
HL_4V4Y_0971/BA/2355:2362GNRA with extra cWW
homologous
HL_4WF9_053
HL_04259.3
HL_4V4Y_0981/BA/2374:2379GNRA
homologous
HL_4WF9_054
HL_37824.8
HL_4V4Y_0991/BA/2404:2413No text annotation
homologous
HL_7A0S_058
HL_53454.2
HL_4V4Y_1001/BA/2471:2479No text annotation
homologous
HL_5J7L_193
HL_32735.2
HL_4V4Y_1011/BA/2528:2535No text annotation
homologous
HL_7RQB_061
NA
HL_4V4Y_1021/BA/2551:2557No text annotation
homologous
HL_4WF9_058
HL_30068.2
HL_4V4Y_1031/BA/2594:2599GNRA
homologous
HL_5J7L_196
HL_37824.8
HL_4V4Y_1041/BA/2652:2668No text annotation
HL_4V4Y_1051/BA/2701:2706No text annotation
homologous
HL_7RQB_065
NA
HL_4V4Y_1061/BA/2746:2758No text annotation
HL_4V4Y_1071/BA/2794:2802No text annotation
geometric
HL_4KR9_003
HL_70782.2
HL_4V4Y_1081/BA/2819:2827No text annotation
homologous
HL_7RQB_068
NA
HL_4V4Y_1091/BA/2856:2861GNRA
homologous
HL_7RQB_069
NA
HL_4V4Y_1191/BB/34:48No text annotation
homologous
HL_5J7L_215
HL_97756.2
HL_4V4Y_1101/BB/38:44No text annotation
homologous
HL_4WF9_066
HL_47787.2
HL_4V4Y_1111/BB/86:90GNRA
homologous
HL_7RQB_071
NA

Problematic loops

#loop idProblemSequence
HL_4V4Y_001No text annotation
HL_4V4Y_112No text annotation
HL_4V4Y_004No text annotation
HL_4V4Y_033No text annotation
HL_4V4Y_035T-loop with 2 stacked bulged bases
HL_4V4Y_048tRNA D-loop
HL_4V4Y_115No text annotation
HL_4V4Y_116No text annotation
HL_4V4Y_061No text annotation
HL_4V4Y_117No text annotation
HL_4V4Y_075No text annotation
HL_4V4Y_081No text annotation
HL_4V4Y_118tRNA anticodon loop

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_4V4Y_0011/A1/30:33,
1/AA/1531:1534		No text annotation
IL_4V4Y_0021/AA/30:32,
1/AA/552:553		Single bulged G
homologous
IL_5J7L_001
IL_00225.14
IL_4V4Y_0031/AA/44:46,
1/AA/395:398		Intercalated cWW
geometric
IL_7A0S_044
IL_31737.3
IL_4V4Y_0041/AA/47:52,
1/AA/359:361		No text annotation
geometric
IL_5J7L_003
IL_14177.2
IL_4V4Y_0051/AA/54:56,
1/AA/356:357		Minor groove platform
homologous
IL_4LFB_004
IL_51454.3
IL_4V4Y_0061/AA/63:66,
1/AA/103:104		Multiple bulged bases
homologous
IL_6CZR_117
NA
IL_4V4Y_0071/AA/67:69,
1/AA/99:102		Isolated non-canonical cWW pair
homologous
IL_4LFB_006
IL_87907.2
IL_4V4Y_0081/AA/129:131,
1/AA/231:232		Multiple bulged bases
homologous
IL_4LFB_007
IL_33761.2
IL_4V4Y_0091/AA/132:136,
1/AA/227:230		No text annotation
homologous
IL_4LFB_008
IL_64231.5
IL_4V4Y_0101/AA/148:153,
1/AA/168:174		tWH-tWH-tHW-tHW
homologous
IL_4LFB_009
IL_12745.1
IL_4V4Y_1531/AA/186:186,
1/AA/191:191		Isolated non-canonical cWW pair
homologous
IL_4LFB_010
IL_87907.2
IL_4V4Y_0121/AA/242:247,
1/AA/277:284		Kink-turn with non-sequential stacking
homologous
IL_5J7L_014
IL_46174.3
IL_4V4Y_0131/AA/249:252,
1/AA/274:275		No text annotation
homologous
IL_4LFB_012
IL_47074.2
IL_4V4Y_0141/AA/292:293,
1/AA/304:308		C-loop
homologous
IL_6CZR_125
NA
IL_4V4Y_0151/AA/367:369,
1/AA/392:393		Single bulged U
geometric
IL_5J7L_017
IL_89505.4
IL_4V4Y_0161/AA/371:375,
1/AA/389:390		C-loop
geometric
IL_4LFB_015
IL_03109.3
IL_4V4Y_0171/AA/375:376,
1/AA/387:389		Single bulged G
homologous
IL_4LFB_016
IL_00225.14
IL_4V4Y_0181/AA/409:416,
1/AA/427:433		No text annotation
homologous
IL_4LFB_017
IL_28026.3
IL_4V4Y_0191/AA/446:450,
1/AA/483:488		6x5 Sarcin-Ricin; G-bulge
geometric
IL_6CZR_130
NA
IL_4V4Y_0201/AA/450:455,
1/AA/477:483		No text annotation
homologous
IL_4LFB_019
IL_31561.1
IL_4V4Y_0211/AA/504:511,
1/AA/540:541		SSU/LSU pseudoknot
homologous
IL_4LFB_020
IL_41203.4
IL_4V4Y_0221/AA/515:521,
1/AA/528:536		Kink-turn related
geometric
IL_4V88_415
NA
IL_4V4Y_1551/AA/580:584,
1/AA/757:761		tSH-tHW-tHS
homologous
IL_4LFB_023
IL_17136.7
IL_4V4Y_0241/AA/594:596,
1/AA/644:645		Major groove platform
homologous
IL_4LFB_024
IL_48076.6
IL_4V4Y_0251/AA/597:598,
1/AA/640:643		Major groove minor groove platform; mini C-loop
homologous
IL_4LFB_025
IL_68140.4
IL_4V4Y_0261/AA/605:612,
1/AA/628:633		No text annotation
homologous
IL_4LFB_026
IL_78349.3
IL_4V4Y_0271/AA/654:655,
1/AA/751:754		Major groove platform; stack outside cWW
geometric
IL_4QLM_004
IL_50694.7
IL_4V4Y_0281/AA/657:658,
1/AA/747:749		Major groove platform
homologous
IL_4LFB_028
IL_48076.6
IL_4V4Y_0291/AA/662:666,
1/AA/740:743		Tandem non-canonical cWW pairs
homologous
IL_4LFB_029
IL_85033.2
IL_4V4Y_0301/AA/673:677,
1/AA/713:717		Triple non-canonical cWW pairs
homologous
IL_4LFB_065
IL_49751.4
IL_4V4Y_0311/AA/683:688,
1/AA/699:707		Kink-turn
homologous
IL_4LFB_031
IL_95727.1
IL_4V4Y_0321/AA/774:778,
1/AA/804:805		Left turn
homologous
IL_4LFB_032
IL_29346.2
IL_4V4Y_0331/AA/779:783,
1/AA/799:803		tSH-tHW-tHS
homologous
IL_4LFB_033
IL_17136.7
IL_4V4Y_0341/AA/887:894,
1/AA/905:910		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_4LFB_034
IL_41756.4
IL_4V4Y_0351/AA/922:923,
1/AA/1393:1395		Single bulged A
homologous
IL_4LFB_035
IL_31462.7
IL_4V4Y_0361/AA/925:927,
1/AA/1390:1391		Single bulged G
homologous
IL_4LFB_036
IL_00225.14
IL_4V4Y_0371/AA/933:935,
1/AA/1380:1384		Minor groove platform
homologous
IL_5J7L_041
IL_47078.3
IL_4V4Y_0381/AA/953:954,
1/AA/1226:1228		Minor groove platform
homologous
IL_4LFB_038
IL_51454.3
IL_4V4Y_0391/AA/1025:1027,
1/AA/1034:1036		No text annotation
IL_4V4Y_0401/AA/1048:1050,
1/AA/1208:1209		No text annotation
homologous
IL_6CZR_152
NA
IL_4V4Y_0411/AA/1052:1056,
1/AA/1204:1206		Isolated cWS basepair
homologous
IL_4LFB_044
IL_76319.5
IL_4V4Y_0421/AA/1057:1058,
1/AA/1199:1203		Minor groove platform
homologous
IL_6CZR_155
NA
IL_4V4Y_0431/AA/1060:1061,
1/AA/1195:1197		Single bulged U
homologous
IL_4LFB_046
IL_89505.4
IL_4V4Y_0441/AA/1061:1063,
1/AA/1193:1195		Isolated non-canonical cWW pair
geometric
IL_4LFB_047
IL_28037.2
IL_4V4Y_0451/AA/1124:1127,
1/AA/1145:1149		No text annotation
IL_4V4Y_0461/AA/1127:1132,
1/AA/1142:1145		No text annotation
IL_4V4Y_0471/AA/1247:1253,
1/AA/1284:1290		No text annotation
homologous
IL_6CZR_160
NA
IL_4V4Y_0481/AA/1255:1258,
1/AA/1277:1282		180 degree turn
homologous
IL_4LFB_052
IL_11344.2
IL_4V4Y_1641/AA/1259:1262,
1/AA/1273:1276		No text annotation
homologous
IL_6CZR_367
NA
IL_4V4Y_0501/AA/1303:1308,
1/AA/1329:1334		No text annotation
geometric
IL_5TBW_026
NA
IL_4V4Y_0511/AA/1401:1404,
1/AA/1497:1501		No text annotation
geometric
IL_4V88_464
NA
IL_4V4Y_0521/AA/1405:1409,
1/AA/1491:1496		No text annotation
homologous
IL_4LFB_058
NA
IL_4V4Y_0531/AA/1412:1414,
1/AA/1486:1488		Isolated non-canonical cWW pair
homologous
IL_4LFB_059
IL_87907.2
IL_4V4Y_0541/AA/1416:1419,
1/AA/1481:1484		No text annotation
IL_4V4Y_1571/AA/1416:1420,
1/AA/1480:1484		No text annotation
IL_4V4Y_1651/AA/1431:1435,
1/AA/1466:1469		UAA/GAN variation
homologous
IL_6CZR_170
NA
IL_4V4Y_0561/AA/1435:1437,
1/AA/1464:1466		Isolated non-canonical cWW pair
homologous
IL_6CZR_171
NA
IL_4V4Y_0571/AA/1440:1447,
1/AA/1459:1461		No text annotation
homologous
IL_4LFB_064
IL_49061.1
IL_4V4Y_0581/BA/25:30,
1/BA/510:515		No text annotation
IL_4V4Y_0591/BA/36:37,
1/BA/442:444		Single bulged A
homologous
IL_7A0S_002
IL_31462.7
IL_4V4Y_0601/BA/43:44,
1/BA/434:436		Minor groove platform
homologous
IL_5J7L_247
IL_51454.3
IL_4V4Y_0611/BA/81:85,
1/BA/97:105		Kink-turn
homologous
IL_7A0S_004
IL_94910.1
IL_4V4Y_0621/BA/183:184,
1/BA/212:215		No text annotation
IL_4V4Y_0631/BA/188:194,
1/BA/201:208		8x7 Sarcin-Ricin; G-bulge
geometric
IL_7RQB_006
NA
IL_4V4Y_0641/BA/239:245,
1/BA/253:258		7x6 Sarcin-Ricin; G-bulge
geometric
IL_7RQB_007
NA
IL_4V4Y_0661/BA/273:273A,
1/BA/363E:364		No text annotation
IL_4V4Y_1661/BA/273E:283,
1/BA/358:363A		No text annotation
IL_4V4Y_1601/BA/288:290,
1/BA/350:353		No text annotation
IL_4V4Y_0681/BA/292:295,
1/BA/343:348		No text annotation
IL_4V4Y_0691/BA/672:674,
1/BA/806:808		Isolated non-canonical cWW pair
geometric
IL_8C3A_029
NA
IL_4V4Y_1611/BA/672:678,
1/BA/799:808		No text annotation
IL_4V4Y_0701/BA/674:678,
1/BA/799:806		tHW-tHW cross-strand stack
geometric
IL_7A0S_015
IL_54041.2
IL_4V4Y_0711/BA/697:698,
1/BA/763:765		Single bulged A
geometric
IL_7RQB_019
NA
IL_4V4Y_0721/BA/703:707,
1/BA/724:729		Triple sheared
homologous
IL_7RQB_021
NA
IL_4V4Y_0731/BA/738:741,
1/BA/756:758		Major groove platform with extra cWW
homologous
IL_7RQB_022
NA
IL_4V4Y_0741/BA/837:838,
1/BA/940:942		Single stack bend
homologous
IL_7A0S_022
IL_90729.1
IL_4V4Y_0751/BA/844:846,
1/BA/932:934		No text annotation
IL_4V4Y_0761/BA/846:850,
1/BA/928:932		Stack outside cWW
homologous
IL_9DFE_025
IL_38507.2
IL_4V4Y_0771/BA/858:860,
1/BA/917:919		No text annotation
IL_4V4Y_0781/BA/860:862,
1/BA/915:917		No text annotation
IL_4V4Y_0791/BA/862:863,
1/BA/913:915		Minor groove platform
homologous
IL_7RQB_028
NA
IL_4V4Y_0801/BA/864:868,
1/BA/909:912		C-loop
homologous
IL_7RQB_029
NA
IL_4V4Y_0811/BA/875:879,
1/BA/898:902		Double sheared with non-canonical cWW
homologous
IL_5J7L_274
IL_17948.2
IL_4V4Y_0821/BA/880:881,
1/BA/895:897		Minor groove platform
geometric
IL_5TBW_039
NA
IL_4V4Y_0831/BA/952:954,
1/BA/963:965		No text annotation
homologous
IL_7RQB_034
NA
IL_4V4Y_0841/BA/994:996,
1/BA/1159:1160		Single bulged C
homologous
IL_7RQB_035
NA
IL_4V4Y_0851/BA/998:1002,
1/BA/1153:1157		UAA/GAN
geometric
IL_5TBW_048
NA
IL_4V4Y_0861/BA/1004:1011,
1/BA/1150:1151		SSU/LSU pseudoknot
homologous
IL_5J7L_278
IL_41203.4
IL_4V4Y_0871/BA/1011:1013,
1/BA/1149:1150		Single bulged U
geometric
IL_7A0S_035
IL_89505.4
IL_4V4Y_0881/BA/1019:1030,
1/BA/1124:1143		No text annotation
IL_4V4Y_0891/BA/1031:1034,
1/BA/1121:1123		Isolated non-canonical cWW pair
homologous
IL_4WF9_041
IL_57744.1
IL_4V4Y_0901/BA/1043:1051,
1/BA/1108:1112		No text annotation
IL_4V4Y_0911/BA/1059:1062,
1/BA/1076:1079		No text annotation
IL_4V4Y_0921/BA/1087:1091,
1/BA/1100:1102		No text annotation
IL_4V4Y_0931/BA/1197:1198,
1/BA/1247:1249		Single bulged G
geometric
IL_5J7L_001
IL_00225.14
IL_4V4Y_1671/BA/1202:1206,
1/BA/1240:1243		No text annotation
IL_4V4Y_0951/BA/1208:1215,
1/BA/1234:1238		Kink-turn
homologous
IL_7RQB_047
NA
IL_4V4Y_0961/BA/1219:1221,
1/BA/1228:1230		Intercalated cWW
geometric
IL_7A0S_044
IL_31737.3
IL_4V4Y_1681/BA/1319:1323,
1/BA/1331:1333		C-loop
homologous
IL_9DFE_050
IL_63596.11
IL_4V4Y_0981/BA/1351:1355,
1/BA/1376:1380		UAA/GAN
homologous
IL_7RQB_052
NA
IL_4V4Y_0991/BA/1357:1361,
1/BA/1370:1374		tSH-tHW-tHS
homologous
IL_7A0S_049
IL_17136.7
IL_4V4Y_1001/BA/1415:1421,
1/BA/1577:1587		No text annotation
IL_4V4Y_1621/BA/1423:1429,
1/BA/1564:1575		No text annotation
IL_4V4Y_1011/BA/1432:1435,
1/BA/1557:1561		No text annotation
IL_4V4Y_1021/BA/1437:1440,
1/BA/1551:1555		tSH-tHW
homologous
IL_7A0S_053
IL_99646.2
IL_4V4Y_1031/BA/1448:1449A,
1/BA/1462:1463		Single stack bend
homologous
IL_7RQB_058
NA
IL_4V4Y_1041/BA/1474:1478,
1/BA/1515:1517		No text annotation
IL_4V4Y_1051/BA/1478:1482,
1/BA/1507:1515		No text annotation
IL_4V4Y_1691/BA/1489:1491,
1/BA/1499:1500		Single bulged A
homologous
IL_5J7L_302
IL_31462.7
IL_4V4Y_1071/BA/1525:1531,
1/BA/1540:1546		No text annotation
IL_4V4Y_1081/BA/1651:1656,
1/BA/2004:2006		No text annotation
homologous
IL_5J7L_304
IL_12566.4
IL_4V4Y_1091/BA/1663:1665,
1/BA/1995:1997		No text annotation
IL_4V4Y_1101/BA/1686:1691,
1/BA/1696:1702		tSH-tSH-tHH-tHS
homologous
IL_4WF9_066
IL_47346.2
IL_4V4Y_1111/BA/1770:1771,
1/BA/1980:1982		Single bulged A
homologous
IL_7A0S_064
IL_31462.7
IL_4V4Y_1121/BA/1798:1804,
1/BA/1813:1821		Kink-turn related
homologous
IL_4WF9_069
IL_17069.5
IL_4V4Y_1131/BA/1837:1840,
1/BA/1902:1903		Minor groove platform, major groove intercalation
homologous
IL_7RQB_071
NA
IL_4V4Y_1141/BA/1841:1842,
1/BA/1898:1901		Major groove intercalation
homologous
IL_4WF9_071
IL_82107.5
IL_4V4Y_1151/BA/1846:1849,
1/BA/1893:1894		Major groove minor groove platform; mini C-loop
homologous
IL_4WF9_072
IL_68140.4
IL_4V4Y_1161/BA/1851:1855,
1/BA/1887:1891		UAA/GAN with extra stack
homologous
IL_7A0S_069
IL_89021.2
IL_4V4Y_1171/BA/1856:1860,
1/BA/1882:1886		Triple sheared
homologous
IL_4WF9_074
IL_66798.2
IL_4V4Y_1181/BA/1934:1945,
1/BA/1961:1964		No text annotation
homologous
IL_7A0S_072
IL_04332.3
IL_4V4Y_1191/BA/2050:2052,
1/BA/2617:2618		Major groove platform
homologous
IL_7A0S_073
IL_48076.6
IL_4V4Y_1201/BA/2054:2056,
1/BA/2612:2615		No text annotation
homologous
IL_4WF9_079
IL_83389.2
IL_4V4Y_1211/BA/2067:2069,
1/BA/2442:2443		Single bulged U
homologous
IL_7A0S_075
IL_89505.4
IL_4V4Y_1221/BA/2070:2071,
1/BA/2438:2441		Minor groove platform
homologous
IL_5J7L_324
IL_51454.3
IL_4V4Y_1231/BA/2081:2083,
1/BA/2236:2239		Isolated tHS basepair with bulges
homologous
IL_7RQB_082
NA
IL_4V4Y_1241/BA/2085:2087,
1/BA/2232:2234		No text annotation
homologous
IL_7RQB_083
NA
IL_4V4Y_1251/BA/2108:2110,
1/BA/2179:2181		Isolated non-canonical cWW pair
geometric
IL_4KZD_003
IL_28037.2
IL_4V4Y_1261/BA/2110:2120,
1/BA/2178:2179		No text annotation
homologous
IL_3U4M_002
IL_32056.1
IL_4V4Y_1271/BA/2124:2127,
1/BA/2161:2174		No text annotation
homologous
IL_9DFE_086
NA
IL_4V4Y_1281/BA/2130:2136,
1/BA/2155:2158		No text annotation
IL_4V4Y_1291/BA/2297:2299,
1/BA/2317:2321		Isolated tHS basepair with bulges
geometric
IL_7RQB_082
NA
IL_4V4Y_1301/BA/2350:2353,
1/BA/2364:2367		Double sheared
homologous
IL_4WF9_087
IL_09705.15
IL_4V4Y_1311/BA/2401:2403,
1/BA/2414:2415		Major groove platform
homologous
IL_7RQB_090
NA
IL_4V4Y_1321/BA/2454:2455,
1/BA/2496:2498		Major groove platform
homologous
IL_7RQB_092
NA
IL_4V4Y_1631/BA/2457:2459,
1/BA/2491:2494		No text annotation
IL_4V4Y_1341/BA/2466:2470,
1/BA/2480:2484		Double sheared with non-canonical cWW
homologous
IL_5J7L_338
IL_17948.2
IL_4V4Y_1351/BA/2507:2508,
1/BA/2580:2582		Major groove platform
homologous
IL_7RQB_096
NA
IL_4V4Y_1361/BA/2510:2512,
1/BA/2574:2578		Isolated non-canonical cWW with bulges
homologous
IL_7A0S_089
IL_07785.1
IL_4V4Y_1371/BA/2512:2513,
1/BA/2571:2574		No text annotation
geometric
IL_5J7L_341
IL_42626.2
IL_4V4Y_1381/BA/2521:2522,
1/BA/2541:2544		No text annotation
IL_4V4Y_1391/BA/2591:2592,
1/BA/2601:2603		Single bulged A
homologous
IL_7RQB_101
NA
IL_4V4Y_1401/BA/2637:2640,
1/BA/2774:2781		No text annotation
IL_4V4Y_1411/BA/2680:2684,
1/BA/2725:2727		C-loop
homologous
IL_4WF9_101
IL_63596.11
IL_4V4Y_1421/BA/2686:2691,
1/BA/2718:2723		No text annotation
IL_4V4Y_1431/BA/2695:2696,
1/BA/2711:2714		Multiple bulged bases
homologous
IL_7RQB_106
NA
IL_4V4Y_1441/BA/2737:2742,
1/BA/2762:2767		UAA/GAN with extra cWW
homologous
IL_7RQB_107
NA
IL_4V4Y_1451/BA/2838:2839,
1/BA/2878:2880		Single bulged C
homologous
IL_7RQB_108
NA
IL_4V4Y_1461/BA/2843:2845,
1/BA/2871:2874		No text annotation
homologous
IL_4WF9_107
IL_31531.3
IL_4V4Y_1701/BA/2847:2852,
1/BA/2865:2869		tHS double platform
homologous
IL_5J7L_354
IL_70411.2
IL_4V4Y_1481/BB/17:18,
1/BB/65:67		Major groove intercalation
homologous
IL_7RQB_111
NA
IL_4V4Y_1711/BB/23:28,
1/BB/56:60		No text annotation
homologous
IL_9DFE_111
IL_18472.4
IL_4V4Y_1501/BB/30:31,
1/BB/51:54		No text annotation
IL_4V4Y_1511/BB/34:38,
1/BB/44:48		No text annotation
homologous
IL_8C3A_147
NA
IL_4V4Y_1521/BB/71:79,
1/BB/97:105		Bacterial 5S Loop E
homologous
IL_7RQB_115
NA

Problematic loops

#loop idProblemSequence
IL_4V4Y_011No text annotation
IL_4V4Y_154No text annotation
IL_4V4Y_023tSH-tHW-tHS-cWW
IL_4V4Y_156No text annotation
IL_4V4Y_049Double sheared with non-canonical cWW
IL_4V4Y_055Triple sheared related
IL_4V4Y_065Multiple bulged bases
IL_4V4Y_158No text annotation
IL_4V4Y_159No text annotation
IL_4V4Y_067No text annotation
IL_4V4Y_094No text annotation
IL_4V4Y_097C-loop with extra cWW pair
IL_4V4Y_106No text annotation
IL_4V4Y_133No text annotation
IL_4V4Y_147No text annotation
IL_4V4Y_149No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_4V4Y_0261/AA/44:47,
1/AA/361:367,
1/AA/393:398		No text annotation
J3_4V4Y_0271/AA/44:52,
1/AA/359:367,
1/AA/393:398		No text annotation
J3_4V4Y_0011/AA/46:47,
1/AA/361:367,
1/AA/393:395		No text annotation
geometric
J3_4LFB_010
J3_67856.4
J3_4V4Y_0021/AA/586:588,
1/AA/651:654,
1/AA/754:755		No text annotation
homologous
J3_5J7L_002
J3_56052.5
J3_4V4Y_0281/AA/586:588,
1/AA/651:655,
1/AA/751:755		No text annotation
homologous
J3_4LFB_015
J3_17385.4
J3_4V4Y_0031/AA/672:673,
1/AA/717:725,
1/AA/732:734		No text annotation
homologous
J3_6CZR_017
NA
J3_4V4Y_0041/AA/826:829,
1/AA/857:861,
1/AA/868:874		No text annotation
homologous
J3_4LFB_001
J3_85054.4
J3_4V4Y_0051/AA/936:939,
1/AA/1344:1350,
1/AA/1372:1379		No text annotation
homologous
J3_4LFB_002
J3_25303.4
J3_4V4Y_0061/AA/943:946,
1/AA/1235:1237,
1/AA/1337:1340		No text annotation
homologous
J3_5J7L_005
J3_52655.4
J3_4V4Y_0071/AA/955:962,
1/AA/973:984,
1/AA/1221:1225		No text annotation
homologous
J3_4LFB_004
J3_83516.4
J3_4V4Y_0081/AA/990:997,
1/AA/1044:1047,
1/AA/1210:1215		No text annotation
homologous
J3_4LFB_016
J3_76475.2
J3_4V4Y_0091/AA/1003:1006,
1/AA/1023:1025,
1/AA/1036:1037		No text annotation
J3_4V4Y_0101/AA/1064:1068,
1/AA/1107:1113,
1/AA/1187:1192		No text annotation
J3_4V4Y_0111/AA/1073:1074,
1/AA/1083:1086,
1/AA/1099:1102		No text annotation
homologous
J3_4LFB_017
J3_79369.1
J3_4V4Y_0121/AA/1116:1118,
1/AA/1155:1161,
1/AA/1175:1184		No text annotation
homologous
J3_4LFB_018
J3_17791.2
J3_4V4Y_0131/AA/1237:1241,
1/AA/1296:1303,
1/AA/1334:1337		No text annotation
homologous
J3_5J7L_011
J3_37047.6
J3_4V4Y_0291/BA/30:31,
1/BA/474:484,
1/BA/496:510		No text annotation
geometric
J3_5TBW_062
NA
J3_4V4Y_0351/BA/32:35,
1/BA/445:461,
1/BA/468:473		No text annotation
homologous
J3_9DFE_003
J3_30040.2
J3_4V4Y_0141/BA/56:57,
1/BA/70:76,
1/BA/110:114		No text annotation
homologous
J3_7A0S_002
J3_35667.2
J3_4V4Y_0151/BA/683:687,
1/BA/775:777,
1/BA/787:794		No text annotation
J3_4V4Y_0161/BA/698:700,
1/BA/732:736,
1/BA/760:763		No text annotation
homologous
J3_7A0S_005
J3_44724.7
J3_4V4Y_0171/BA/1055:1057,
1/BA/1081:1087,
1/BA/1102:1104		No text annotation
J3_4V4Y_0311/BA/1055:1057,
1/BA/1081:1091,
1/BA/1100:1104		No text annotation
J3_4V4Y_0181/BA/1298:1303,
1/BA/1625:1627,
1/BA/1639:1642		No text annotation
homologous
J3_7A0S_006
J3_32852.6
J3_4V4Y_0191/BA/1306:1309,
1/BA/1605:1611,
1/BA/1620:1622		No text annotation
homologous
J3_7RQB_008
NA
J3_4V4Y_0321/BA/1344:1350,
1/BA/1381:1385,
1/BA/1402:1403		No text annotation
homologous
J3_9DFE_012
J3_31965.2
J3_4V4Y_0211/BA/2090:2093,
1/BA/2196:2205,
1/BA/2219:2229		No text annotation
geometric
J3_4V9F_007
J3_97609.1
J3_4V4Y_0331/BA/2282:2284,
1/BA/2384:2395,
1/BA/2421:2427		No text annotation
homologous
J3_7A0S_020
J3_20992.1
J3_4V4Y_0221/BA/2295:2297,
1/BA/2321:2323,
1/BA/2332:2337		No text annotation
homologous
J3_7RQB_011
NA
J3_4V4Y_0231/BA/2517:2520,
1/BA/2545:2547,
1/BA/2561:2567		No text annotation
homologous
J3_7RQB_012
NA
J3_4V4Y_0241/BA/2814:2815,
1/BA/2831:2836,
1/BA/2882:2886		No text annotation
homologous
J3_7RQB_014
NA
J3_4V4Y_0361/BB/11:16,
1/BB/68:69,
1/BB/107:109		No text annotation
homologous
J3_9DFE_020
J3_12003.2
J4_4V4Y_0011/AA/115:122,
1/AA/239:240,
1/AA/286:289,
1/AA/311:312		No text annotation
homologous
J4_4LFB_001
J4_35578.3
J4_4V4Y_0021/AA/142:144,
1/AA/178:183,
1/AA/194:198,
1/AA/219:221		No text annotation
homologous
J4_4LFB_002
J4_88771.1
J4_4V4Y_0161/AA/569:577,
1/AA/764:769,
1/AA/810:821,
1/AA/879:881		No text annotation
J4_4V4Y_0051/AC/7:10,
1/AC/25:27,
1/AC/43:49,
1/AC/65:66		tRNA junction
homologous
J4_6JXM_001
J4_70449.29
J4_4V4Y_0061/AD/7:10,
1/AD/25:27,
1/AD/43:49,
1/AD/65:66		tRNA junction
homologous
J4_4V9Q_031
J4_70449.29
J4_4V4Y_0071/BA/47:54,
1/BA/116:121,
1/BA/130:131,
1/BA/148:178		No text annotation
J4_4V4Y_0081/BA/297:301,
1/BA/316:319,
1/BA/323:325,
1/BA/337:341		No text annotation
J4_4V4Y_0091/BA/1270:1276,
1/BA/1294:1295,
1/BA/1645:1648,
1/BA/2009:2010		No text annotation
homologous
J4_9DFE_003
J4_64571.5
J4_4V4Y_0101/BA/1309:1313,
1/BA/1339:1343,
1/BA/1404:1405,
1/BA/1597:1605		No text annotation
J4_4V4Y_0171/BA/1444:1445,
1/BA/1466:1473,
1/BA/1518:1530,
1/BA/1541:1547		No text annotation
J4_4V4Y_0121/BA/1772:1775,
1/BA/1789:1792,
1/BA/1827:1830,
1/BA/1975:1979		No text annotation
J4_4V4Y_0131/BA/1833:1835,
1/BA/1905:1906,
1/BA/1924:1945,
1/BA/1961:1972		No text annotation
J4_4V4Y_0141/BA/2285:2289,
1/BA/2343:2347,
1/BA/2370:2372,
1/BA/2381:2383		No text annotation
homologous
J4_7A0S_009
J4_04930.6
J4_4V4Y_0151/BA/2643:2646,
1/BA/2674:2676,
1/BA/2731:2735,
1/BA/2769:2771		No text annotation
homologous
J4_9DFE_010
J4_77044.4
J5_4V4Y_0011/AA/36:39,
1/AA/403:406,
1/AA/436:442,
1/AA/492:500,
1/AA/545:548		No text annotation
homologous
J5_4LFB_001
J5_70703.1
J5_4V4Y_0021/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_59910.6
J5_4V4Y_0081/BA/268:270C,
1/BA/270W:271,
1/BA/366:375,
1/BA/399:406,
1/BA/421:424		No text annotation
J5_4V4Y_0041/BA/584:589,
1/BA/668:671,
1/BA/809:812,
1/BA/1195:1198,
1/BA/1247:1256		No text annotation
J5_4V4Y_0091/BA/1667:1683,
1/BA/1705:1707,
1/BA/1751:1752,
1/BA/1756:1764,
1/BA/1988:1993		No text annotation
J5_4V4Y_0061/BA/2057:2064,
1/BA/2446:2455,
1/BA/2496:2507,
1/BA/2582:2588,
1/BA/2606:2611		No text annotation
J5_4V4Y_0071/BA/2074:2077,
1/BA/2243:2246,
1/BA/2258:2259,
1/BA/2281:2282,
1/BA/2427:2435		No text annotation
homologous
J5_7A0S_007
J5_39529.1
J6_4V4Y_0031/BA/45:46,
1/BA/179:183,
1/BA/215:224,
1/BA/231:235,
1/BA/262:265,
1/BA/427:433		No text annotation
J6_4V4Y_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_4V4Y_0011/BA/817:822,
1/BA/835:837,
1/BA/942:946,
1/BA/971:976,
1/BA/987:991,
1/BA/1163:1164,
1/BA/1185:1190		No text annotation
J11_4V4Y_0021/BA/8:15,
1/BA/525:533,
1/BA/560:564,
1/BA/577:579,
1/BA/1261:1269,
1/BA/2011:2023,
1/BA/2040:2043,
1/BA/2625:2630,
1/BA/2788:2793,
1/BA/2803:2811,
1/BA/2889:2895		No text annotation

Problematic loops

#loop idProblemSequence
J3_4V4Y_030No text annotation
J3_4V4Y_020No text annotation
J3_4V4Y_034No text annotation
J3_4V4Y_025No text annotation
J4_4V4Y_003No text annotation
J4_4V4Y_004tRNA junction
J4_4V4Y_011No text annotation
J5_4V4Y_003No text annotation
J5_4V4Y_005No text annotation
J6_4V4Y_001No text annotation
J11_4V4Y_001No text annotation

Coloring options:
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