RNA 3D Hub //

5NGM Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_5NGM_1021/AA/59:68Pseudoknot with intercalation
homologous
HL_4WF9_067
HL_93438.2
HL_5NGM_0021/AA/87:95No text annotation
homologous
HL_7RQB_002
NA
HL_5NGM_0031/AA/122:127No text annotation
homologous
HL_4WF9_003
HL_75660.5
HL_5NGM_0041/AA/136:143GNRA wlth tandem sheared
homologous
HL_4WF9_004
HL_81538.2
HL_5NGM_0051/AA/159:169No text annotation
HL_5NGM_0061/AA/197:204No text annotation
geometric
HL_5J7L_139
HL_30068.2
HL_5NGM_0071/AA/228:233No text annotation
homologous
HL_4WF9_007
HL_53890.2
HL_5NGM_0081/AA/249:255No text annotation
homologous
HL_7A0S_008
HL_37369.2
HL_5NGM_0091/AA/283:288No text annotation
geometric
HL_5TBW_012
NA
HL_5NGM_0101/AA/348:355T-loop with 2 stacked bulged bases
homologous
HL_5J7L_142
HL_01609.3
HL_5NGM_0111/AA/362:366No text annotation
homologous
HL_4WF9_011
HL_75660.5
HL_5NGM_0121/AA/370:378T-loop with unstacked turn
homologous
HL_7RQB_012
NA
HL_5NGM_1031/AA/428:438No text annotation
homologous
HL_5J7L_145
HL_91503.7
HL_5NGM_0141/AA/456:463No text annotation
homologous
HL_7RQB_014
NA
HL_5NGM_0151/AA/508:513GNRA
homologous
HL_4WF9_015
HL_37824.8
HL_5NGM_0161/AA/533:538GNRA
homologous
HL_7RQB_016
NA
HL_5NGM_0171/AA/587:594No text annotation
homologous
HL_4WF9_017
HL_50318.1
HL_5NGM_0181/AA/609:618T-loop with 2 stacked bulged bases
homologous
HL_4WF9_018
HL_28252.9
HL_5NGM_0191/AA/655:661No text annotation
geometric
HL_5U3G_001
HL_75660.5
HL_5NGM_0201/AA/674:679GNRA
homologous
HL_5J7L_152
HL_37824.8
HL_5NGM_0211/AA/686:692No text annotation
homologous
HL_7RQB_021
NA
HL_5NGM_0221/AA/757:764No text annotation
geometric
HL_4WF9_003
HL_75660.5
HL_5NGM_0231/AA/789:798No text annotation
homologous
HL_4WF9_023
HL_88205.2
HL_5NGM_1041/AA/824:830No text annotation
homologous
HL_4WF9_024
HL_87954.2
HL_5NGM_0251/AA/871:876No text annotation
homologous
HL_4WF9_025
HL_55195.3
HL_5NGM_0271/AA/999:1006GNRA
homologous
HL_4WF9_027
HL_37824.8
HL_5NGM_0281/AA/1022:1029No text annotation
homologous
HL_5J7L_160
HL_42998.2
HL_5NGM_0291/AA/1103:1123No text annotation
HL_5NGM_0301/AA/1214:1218Mini UNCG
geometric
HL_4YAZ_004
HL_48778.2
HL_5NGM_0311/AA/1260:1265GNRA
homologous
HL_4WF9_031
HL_37824.8
HL_5NGM_0321/AA/1318:1326T-loop with 2 stacked bulged bases
homologous
HL_4WF9_032
HL_28252.9
HL_5NGM_0331/AA/1361:1367No text annotation
homologous
HL_7RQB_034
NA
HL_5NGM_0341/AA/1400:1405GNRA
homologous
HL_5J7L_167
HL_37824.8
HL_5NGM_0351/AA/1426:1435No text annotation
homologous
HL_4WF9_035
HL_81545.2
HL_5NGM_0361/AA/1535:1541Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_170
HL_57176.2
HL_5NGM_0371/AA/1612:1615Mini UNCG
homologous
HL_7A0S_039
HL_48778.2
HL_5NGM_0381/AA/1656:1663No text annotation
homologous
HL_7RQB_040
NA
HL_5NGM_0391/AA/1673:1681GNRA with extra cWW
homologous
HL_4WF9_039
HL_20167.2
HL_5NGM_0401/AA/1735:1740UNCG
geometric
HL_4WF9_040
HL_34617.5
HL_5NGM_0411/AA/1760:1769No text annotation
HL_5NGM_0421/AA/1779:1783No text annotation
homologous
HL_4WF9_042
HL_80709.3
HL_5NGM_0431/AA/1803:1815No text annotation
homologous
HL_7A0S_045
HL_60266.1
HL_5NGM_0441/AA/1833:1838GNRA
homologous
HL_7RQB_046
NA
HL_5NGM_0451/AA/1891:1905No text annotation
HL_5NGM_1051/AA/1977:1983No text annotation
HL_5NGM_0481/AA/2054:2063No text annotation
homologous
HL_4WF9_047
HL_61996.3
HL_5NGM_1061/AA/2156:2186No text annotation
HL_5NGM_0491/AA/2169:2176No text annotation
HL_5NGM_0501/AA/2236:2242No text annotation
homologous
HL_5J7L_185
HL_49922.4
HL_5NGM_0511/AA/2275:2283No text annotation
homologous
HL_5J7L_186
HL_85367.2
HL_5NGM_0521/AA/2291:2303No text annotation
homologous
HL_4WF9_050
HL_91939.2
HL_5NGM_1121/AA/2331:2339No text annotation
HL_5NGM_0541/AA/2351:2358Pseudoknot geometry
homologous
HL_4WF9_052
HL_93324.4
HL_5NGM_0551/AA/2382:2389GNRA with extra cWW
homologous
HL_4WF9_053
HL_04259.3
HL_5NGM_0561/AA/2401:2406GNRA
homologous
HL_5J7L_191
HL_37824.8
HL_5NGM_0571/AA/2431:2440No text annotation
homologous
HL_7A0S_058
HL_53454.2
HL_5NGM_0581/AA/2498:2506No text annotation
homologous
HL_4WF9_056
HL_32735.2
HL_5NGM_0591/AA/2555:2562No text annotation
homologous
HL_5J7L_194
HL_31585.4
HL_5NGM_0601/AA/2578:2584No text annotation
homologous
HL_4WF9_058
HL_30068.2
HL_5NGM_0611/AA/2621:2626GNRA
homologous
HL_5J7L_196
HL_37824.8
HL_5NGM_0621/AA/2685:2690GNRA
homologous
HL_5J7L_197
HL_37824.8
HL_5NGM_0631/AA/2728:2733Ribsomal LSU H95
homologous
HL_5J7L_198
HL_65794.5
HL_5NGM_0641/AA/2772:2786No text annotation
homologous
HL_5J7L_199
HL_74055.2
HL_5NGM_0651/AA/2819:2824No text annotation
geometric
HL_4V88_198
NA
HL_5NGM_0661/AA/2839:2847No text annotation
homologous
HL_4WF9_064
HL_64690.6
HL_5NGM_0671/AA/2876:2881GNRA
homologous
HL_7RQB_069
NA
HL_5NGM_1071/AB/32:46No text annotation
homologous
HL_9DFE_067
HL_97756.2
HL_5NGM_0681/AB/36:42No text annotation
homologous
HL_7RQB_070
NA
HL_5NGM_0691/AB/83:88No text annotation
geometric
HL_7A0S_007
HL_53890.2
HL_5NGM_0701/Aa/13:23No text annotation
homologous
HL_4LFB_001
HL_89881.5
HL_5NGM_0711/Aa/72:97No text annotation
HL_5NGM_0721/Aa/158:163GNRA
homologous
HL_5J7L_003
HL_37824.8
HL_5NGM_0731/Aa/190:201No text annotation
HL_5NGM_0741/Aa/216:223No text annotation
HL_5NGM_0751/Aa/267:275GNRA related
homologous
HL_5J7L_006
HL_84299.4
HL_5NGM_0761/Aa/304:309GNRA
homologous
HL_5J7L_007
HL_37824.8
HL_5NGM_0771/Aa/328:341No text annotation
homologous
HL_5J7L_008
HL_81205.3
HL_5NGM_0781/Aa/350:355UNCG
homologous
HL_6CZR_080
NA
HL_5NGM_0791/Aa/386:393GNRA with extra cWW
geometric
HL_7A0S_056
HL_04259.3
HL_5NGM_0801/Aa/427:432No text annotation
geometric
HL_5U3G_001
HL_75660.5
HL_5NGM_0811/Aa/470:479No text annotation
geometric
HL_4TUE_219
HL_75293.5
HL_5NGM_0821/Aa/530:535No text annotation
geometric
HL_4WF9_003
HL_75660.5
HL_5NGM_0831/Aa/625:631No text annotation
homologous
HL_4LFB_014
HL_10453.3
HL_5NGM_0841/Aa/697:706No text annotation
homologous
HL_4LFB_015
HL_75293.5
HL_5NGM_0851/Aa/734:739GNRA
homologous
HL_4LFB_016
HL_37824.8
HL_5NGM_0861/Aa/794:804No text annotation
homologous
HL_4LFB_017
HL_75293.5
HL_5NGM_1081/Aa/849:854No text annotation
geometric
HL_4V88_198
NA
HL_5NGM_0881/Aa/871:876GNRA
homologous
HL_5J7L_019
HL_37824.8
HL_5NGM_0891/Aa/906:911GNRA
homologous
HL_6CZR_091
NA
HL_5NGM_0901/Aa/972:981No text annotation
homologous
HL_4LFB_021
HL_50779.4
HL_5NGM_0911/Aa/1021:1026No text annotation
geometric
HL_5J7L_143
HL_75660.5
HL_5NGM_0921/Aa/1038:1043No text annotation
geometric
HL_7A0S_011
HL_75660.5
HL_5NGM_0931/Aa/1087:1092GNRA
homologous
HL_5J7L_023
HL_37824.8
HL_5NGM_0941/Aa/1100:1107T-loop related
homologous
HL_4LFB_025
HL_77436.5
HL_5NGM_0951/Aa/1144:1151No text annotation
HL_5NGM_0961/Aa/1174:1182No text annotation
HL_5NGM_0971/Aa/1275:1280GNRA
homologous
HL_5J7L_027
HL_37824.8
HL_5NGM_0981/Aa/1324:1333T-loop with 3 stacked bulged bases
homologous
HL_4LFB_029
HL_02887.3
HL_5NGM_0991/Aa/1366:1376No text annotation
homologous
HL_4LFB_030
HL_06226.4
HL_5NGM_1111/Aa/1455:1468No text annotation
HL_5NGM_1001/Aa/1459:1465No text annotation
geometric
HL_5TBW_012
NA
HL_5NGM_1011/Aa/1526:1531GNRA
geometric
HL_3NVI_002
HL_37824.8

Problematic loops

#loop idProblemSequence
HL_5NGM_001No text annotation
HL_5NGM_013No text annotation
HL_5NGM_024No text annotation
HL_5NGM_026No text annotation
HL_5NGM_046No text annotation
HL_5NGM_047No text annotation
HL_5NGM_053No text annotation
HL_5NGM_087No text annotation
HL_5NGM_109No text annotation
HL_5NGM_110No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_5NGM_0011/AA/24:30,
1/AA/555:561		Triple sheared with non-canonical cWW
homologous
IL_4WF9_001
IL_04021.2
IL_5NGM_0021/AA/36:37,
1/AA/488:490		Single bulged A
homologous
IL_7RQB_002
NA
IL_5NGM_0031/AA/42:44,
1/AA/480:483		Minor groove platform with extra cWW
homologous
IL_4WF9_003
IL_90351.1
IL_5NGM_1831/AA/81:85,
1/AA/97:104		No text annotation
homologous
IL_9DFE_004
IL_01488.3
IL_5NGM_0051/AA/152:153,
1/AA/175:177		Major groove platform
geometric
IL_3NKB_002
IL_48076.6
IL_5NGM_0071/AA/186:187,
1/AA/215:217		Single stack bend
homologous
IL_5J7L_249
IL_90729.1
IL_5NGM_0081/AA/190:197,
1/AA/204:212		9x8 Sarcin-Ricin; G-bulge
homologous
IL_4WF9_008
IL_84694.2
IL_5NGM_0091/AA/241:248,
1/AA/256:262		8x7 Sarcin-Ricin; G-bulge
homologous
IL_4WF9_009
IL_04346.10
IL_5NGM_0101/AA/305:306,
1/AA/409:412		Minor groove platform
geometric
IL_7RQB_073
NA
IL_5NGM_0121/AA/319:327,
1/AA/399:400		No text annotation
IL_5NGM_0131/AA/336:338,
1/AA/386:390		No text annotation
homologous
IL_4WF9_014
IL_69440.3
IL_5NGM_0141/AA/527:530,
1/AA/541:554		No text annotation
homologous
IL_4WF9_015
IL_81516.2
IL_5NGM_0151/AA/581:584,
1/AA/597:600		Double sheared
homologous
IL_4WF9_016
IL_09705.15
IL_5NGM_0161/AA/607:609,
1/AA/618:620		Isolated non-canonical cWW pair
geometric
IL_5J7L_257
IL_07785.1
IL_5NGM_0171/AA/638:640,
1/AA/705:707		Isolated non-canonical cWW pair
homologous
IL_4WF9_018
IL_07785.1
IL_5NGM_0181/AA/649:653,
1/AA/663:667		AAA cross-strand stack
homologous
IL_4WF9_019
IL_66798.2
IL_5NGM_0191/AA/717:719,
1/AA/851:853		Isolated non-canonical cWW pair
geometric
IL_4WF9_020
IL_87907.2
IL_5NGM_0201/AA/719:723,
1/AA/844:851		tHW-tHW cross-strand stack
homologous
IL_4WF9_021
IL_54041.2
IL_5NGM_0211/AA/742:743,
1/AA/808:810		Single bulged A
homologous
IL_4WF9_022
IL_31462.7
IL_5NGM_0221/AA/747:748,
1/AA/773:775		Single bulged G
geometric
IL_5J7L_262
IL_00225.14
IL_5NGM_0231/AA/748:752,
1/AA/769:773		Triple sheared
homologous
IL_7RQB_021
NA
IL_5NGM_0241/AA/783:785,
1/AA/802:803		Major groove platform
homologous
IL_4WF9_026
IL_48076.6
IL_5NGM_0251/AA/820:822,
1/AA/832:836		Multiple bulged bases
homologous
IL_5J7L_265
IL_06549.2
IL_5NGM_0261/AA/881:883,
1/AA/984:987		No text annotation
geometric
IL_8P9A_292
IL_15698.3
IL_5NGM_0271/AA/889:893,
1/AA/975:978		No text annotation
homologous
IL_4WF9_029
IL_06300.1
IL_5NGM_0281/AA/897:898,
1/AA/969:971		No text annotation
IL_5NGM_0291/AA/901:907,
1/AA/960:966		7x7 Sarcin-Ricin with intercalated A; G-bulge
geometric
IL_4WF9_031
IL_29198.2
IL_5NGM_0301/AA/907:908,
1/AA/958:960		Minor groove platform
homologous
IL_4WF9_032
IL_51454.3
IL_5NGM_0311/AA/909:913,
1/AA/954:957		C-loop with bulged stacked A's
homologous
IL_7RQB_029
NA
IL_5NGM_0321/AA/920:924,
1/AA/943:947		Triple sheared
homologous
IL_5J7L_274
IL_17948.2
IL_5NGM_0331/AA/1038:1040,
1/AA/1203:1204		Single bulged C
homologous
IL_4WF9_035
IL_61258.15
IL_5NGM_0341/AA/1042:1046,
1/AA/1197:1201		UAA/GAN
homologous
IL_4WF9_036
IL_38507.2
IL_5NGM_0351/AA/1048:1055,
1/AA/1194:1195		SSU/LSU pseudoknot
homologous
IL_5J7L_278
IL_41203.4
IL_5NGM_0361/AA/1055:1057,
1/AA/1193:1194		Single bulged U
geometric
IL_5J7L_279
IL_89505.4
IL_5NGM_0371/AA/1062:1068,
1/AA/1184:1188		Kink-turn related
geometric
IL_4WF9_039
IL_57188.5
IL_5NGM_0381/AA/1068:1074,
1/AA/1168:1184		No text annotation
geometric
IL_4WF9_040
IL_50715.3
IL_5NGM_1841/AA/1075:1077,
1/AA/1166:1167		Single stack bend
geometric
IL_7A0S_005
IL_90729.1
IL_5NGM_0401/AA/1081:1083,
1/AA/1160:1162		Isolated non-canonical cWW pair
homologous
IL_4WF9_042
IL_87907.2
IL_5NGM_1851/AA/1087:1102,
1/AA/1124:1156		No text annotation
IL_5NGM_0411/AA/1235:1237,
1/AA/1285:1288		Isolated cWS basepair
homologous
IL_4WF9_044
IL_42997.3
IL_5NGM_0421/AA/1243:1245,
1/AA/1277:1279		Isolated cWH basepair
homologous
IL_4WF9_045
IL_10167.6
IL_5NGM_0431/AA/1246:1253,
1/AA/1272:1276		Kink-turn
homologous
IL_7RQB_047
NA
IL_5NGM_0441/AA/1257:1259,
1/AA/1266:1268		Intercalated cWW
homologous
IL_4WF9_047
IL_31737.3
IL_5NGM_0451/AA/1300:1307,
1/AA/2038:2044		8x7 Sarcin-Ricin; G-bulge
homologous
IL_4WF9_048
IL_04346.10
IL_5NGM_0461/AA/1356:1360,
1/AA/1368:1370		Major groove minor groove platform with tHH
homologous
IL_4WF9_050
IL_83150.2
IL_5NGM_0471/AA/1388:1392,
1/AA/1413:1417		UAA/GAN
homologous
IL_5J7L_292
IL_89021.2
IL_5NGM_0481/AA/1394:1398,
1/AA/1407:1411		tSH-tHW-tHS
homologous
IL_5J7L_293
IL_17136.7
IL_5NGM_1861/AA/1447:1460,
1/AA/1628:1636		No text annotation
IL_5NGM_0501/AA/1461:1465,
1/AA/1624:1627		Other IL
homologous
IL_4WF9_054
IL_99646.2
IL_5NGM_0511/AA/1476:1480,
1/AA/1604:1608		No text annotation
homologous
IL_4WF9_122
IL_67780.1
IL_5NGM_0521/AA/1481:1485,
1/AA/1598:1603		No text annotation
IL_5NGM_1711/AA/1481:1510,
1/AA/1571:1603		No text annotation
IL_5NGM_0531/AA/1485:1511,
1/AA/1570:1598		No text annotation
IL_5NGM_1721/AA/1511:1515,
1/AA/1565:1570		No text annotation
homologous
IL_4WF9_116
IL_25186.4
IL_5NGM_0551/AA/1518:1522,
1/AA/1558:1562		tSH-tHW-tHS
homologous
IL_5J7L_300
IL_38862.4
IL_5NGM_1731/AA/1524:1526,
1/AA/1549:1556		No text annotation
IL_5NGM_0571/AA/1532:1534,
1/AA/1542:1543		No text annotation
IL_5NGM_0581/AA/1695:1700,
1/AA/2031:2033		No text annotation
homologous
IL_4WF9_062
IL_12566.4
IL_5NGM_0591/AA/1707:1709,
1/AA/2022:2024		Isolated tWW turn
homologous
IL_4WF9_063
IL_67095.2
IL_5NGM_0601/AA/1710:1713,
1/AA/2020:2021		Major groove platform; stack outside cWW
homologous
IL_7RQB_066
NA
IL_5NGM_1741/AA/1710:1718,
1/AA/2017:2021		No text annotation
homologous
IL_4WF9_117
IL_22854.4
IL_5NGM_0611/AA/1713:1718,
1/AA/2017:2020		Intercalated tWH
geometric
IL_4WF9_065
IL_76758.2
IL_5NGM_0621/AA/1730:1735,
1/AA/1740:1746		tSH-tSH-tHH-tHS
homologous
IL_7RQB_068
NA
IL_5NGM_0631/AA/1756:1759,
1/AA/1770:1773		No text annotation
IL_5NGM_0641/AA/1797:1798,
1/AA/2007:2009		Single bulged A
homologous
IL_7A0S_064
IL_31462.7
IL_5NGM_0651/AA/1825:1831,
1/AA/1840:1848		Kink-turn related
homologous
IL_7RQB_070
NA
IL_5NGM_0661/AA/1864:1867,
1/AA/1929:1930		Minor groove platform, major groove intercalation
homologous
IL_5J7L_314
IL_95583.2
IL_5NGM_0671/AA/1868:1869,
1/AA/1925:1928		Major groove intercalation
homologous
IL_5J7L_315
IL_82107.5
IL_5NGM_0681/AA/1873:1876,
1/AA/1920:1921		No text annotation
IL_5NGM_0691/AA/1878:1882,
1/AA/1914:1918		UAA/GAN with extra pair
homologous
IL_4WF9_073
IL_89021.2
IL_5NGM_0701/AA/1883:1887,
1/AA/1909:1913		Triple sheared
homologous
IL_7RQB_075
NA
IL_5NGM_0711/AA/1961:1972,
1/AA/1988:1991		No text annotation
homologous
IL_7A0S_072
IL_04332.3
IL_5NGM_0721/AA/2077:2079,
1/AA/2644:2645		Major groove platform
homologous
IL_5J7L_320
IL_48076.6
IL_5NGM_0731/AA/2081:2083,
1/AA/2639:2642		No text annotation
homologous
IL_4WF9_079
IL_83389.2
IL_5NGM_0741/AA/2094:2096,
1/AA/2469:2470		Single bulged U
homologous
IL_7RQB_080
NA
IL_5NGM_0751/AA/2097:2098,
1/AA/2465:2468		Minor groove platform
homologous
IL_7RQB_081
NA
IL_5NGM_0761/AA/2108:2110,
1/AA/2263:2266		Isolated tHS basepair with bulges
homologous
IL_7A0S_077
IL_85599.2
IL_5NGM_0771/AA/2123:2125,
1/AA/2218:2220		Isolated non-canonical cWW pair
geometric
IL_4P3T_006
NA
IL_5NGM_1751/AA/2133:2156,
1/AA/2186:2210		No text annotation
IL_5NGM_0781/AA/2156:2169,
1/AA/2176:2186		No text annotation
IL_5NGM_0791/AA/2229:2231,
1/AA/2247:2248		Single bulged U
homologous
IL_5J7L_331
IL_89505.4
IL_5NGM_0801/AA/2324:2326,
1/AA/2344:2348		Isolated tHS basepair with bulges
homologous
IL_7RQB_088
NA
IL_5NGM_0811/AA/2377:2380,
1/AA/2391:2394		Double sheared
homologous
IL_5J7L_333
IL_09705.15
IL_5NGM_0821/AA/2428:2430,
1/AA/2441:2442		Single bulged U
homologous
IL_5J7L_334
IL_89505.4
IL_5NGM_0831/AA/2480:2481,
1/AA/2525:2527		Single stack bend
geometric
IL_4WF9_089
IL_26793.1
IL_5NGM_0841/AA/2481:2482,
1/AA/2523:2525		Major groove platform
homologous
IL_4WF9_090
IL_48076.6
IL_5NGM_0851/AA/2484:2486,
1/AA/2520:2521		Major groove platform
geometric
IL_4WF9_091
IL_48076.6
IL_5NGM_0861/AA/2486:2488,
1/AA/2516:2520		Major groove minor groove platform with extra cWW
homologous
IL_7RQB_094
NA
IL_5NGM_0871/AA/2493:2497,
1/AA/2507:2511		Triple sheared
homologous
IL_4WF9_093
IL_17948.2
IL_5NGM_0881/AA/2534:2535,
1/AA/2607:2609		Major groove platform
homologous
IL_7RQB_096
NA
IL_5NGM_0891/AA/2537:2539,
1/AA/2601:2605		Isolated non-canonical cWW with bulges
homologous
IL_4WF9_095
IL_07785.1
IL_5NGM_0901/AA/2539:2540,
1/AA/2598:2601		No text annotation
geometric
IL_5J7L_341
IL_42626.2
IL_5NGM_0911/AA/2549:2550,
1/AA/2567:2570		Major groove platform with intercalation
homologous
IL_5J7L_342
IL_02555.1
IL_5NGM_0921/AA/2618:2619,
1/AA/2628:2630		Single bulged A
geometric
IL_4V9F_090
IL_42771.1
IL_5NGM_0931/AA/2663:2667,
1/AA/2801:2809		tSH-tHS-tHW
homologous
IL_4WF9_099
IL_04638.3
IL_5NGM_0941/AA/2679:2685,
1/AA/2690:2695		Sarcin-Ricin target in LSU H95; G-bulge
geometric
IL_7RQB_103
NA
IL_5NGM_0951/AA/2707:2711,
1/AA/2752:2754		C-loop
homologous
IL_5J7L_347
IL_63596.11
IL_5NGM_0961/AA/2714:2718,
1/AA/2745:2749		No text annotation
homologous
IL_7RQB_105
NA
IL_5NGM_0971/AA/2722:2723,
1/AA/2738:2741		Multiple bulged bases
homologous
IL_5J7L_349
IL_42626.2
IL_5NGM_0981/AA/2764:2769,
1/AA/2789:2794		UAA/GAN with extra cWW
homologous
IL_5J7L_350
IL_49767.8
IL_5NGM_0991/AA/2858:2859,
1/AA/2898:2900		Major groove intercalation
homologous
IL_4WF9_106
IL_66635.5
IL_5NGM_1001/AA/2863:2865,
1/AA/2891:2894		No text annotation
homologous
IL_4WF9_107
IL_31531.3
IL_5NGM_1011/AA/2867:2872,
1/AA/2885:2889		tHS double platform
homologous
IL_4WF9_108
IL_70411.2
IL_5NGM_1021/AB/15:16,
1/AB/63:65		Major groove intercalation
homologous
IL_4WF9_112
IL_31462.7
IL_5NGM_1031/AB/21:27,
1/AB/53:58		No text annotation
IL_5NGM_1041/AB/28:29,
1/AB/49:52		Major groove minor groove platform; mini C-loop
homologous
IL_7RQB_113
NA
IL_5NGM_1051/AB/32:36,
1/AB/42:46		Symmetric double minor groove platform
geometric
IL_7RQB_114
NA
IL_5NGM_1061/AB/69:77,
1/AB/94:102		Bacterial 5S Loop E
homologous
IL_7A0S_106
IL_56455.6
IL_5NGM_1071/AB/78:80,
1/AB/91:93		Isolated non-canonical cWW pair
homologous
IL_7A0S_107
IL_07785.1
IL_5NGM_1081/Aa/31:33,
1/Aa/560:561		Single bulged G
homologous
IL_6CZR_113
NA
IL_5NGM_1091/Aa/45:46,
1/Aa/404:406		Single bulged A
homologous
IL_5J7L_002
IL_31462.7
IL_5NGM_1101/Aa/48:53,
1/Aa/367:369		No text annotation
homologous
IL_5J7L_003
IL_14177.2
IL_5NGM_1111/Aa/54:57,
1/Aa/364:366		No text annotation
IL_5NGM_1121/Aa/64:67,
1/Aa/102:103		Multiple bulged bases
homologous
IL_4LFB_005
IL_82107.5
IL_5NGM_1131/Aa/68:71,
1/Aa/98:101		Tandem non-canonical cWW pairs
geometric
IL_5LQO_002
IL_85033.2
IL_5NGM_1141/Aa/128:131,
1/Aa/239:240		Minor groove platform
homologous
IL_4LFB_007
IL_33761.2
IL_5NGM_1151/Aa/132:136,
1/Aa/235:238		Minor groove platform related
homologous
IL_5J7L_010
IL_64231.5
IL_5NGM_1161/Aa/147:153,
1/Aa/168:175		tWH-tWH-tHW-tHW
homologous
IL_5J7L_012
IL_80604.6
IL_5NGM_1761/Aa/185:186,
1/Aa/204:206		Single stack bend
geometric
IL_7A0S_054
IL_26793.1
IL_5NGM_1171/Aa/187:190,
1/Aa/201:203		No text annotation
geometric
IL_4WSM_372
IL_09990.4
IL_5NGM_1181/Aa/250:255,
1/Aa/285:292		Kink-turn with non-sequential stacking
homologous
IL_4LFB_011
IL_46174.3
IL_5NGM_1781/Aa/257:260,
1/Aa/282:283		No text annotation
homologous
IL_4LFB_012
IL_47074.2
IL_5NGM_1201/Aa/300:301,
1/Aa/312:316		C-loop
homologous
IL_4LFB_013
IL_03109.3
IL_5NGM_1211/Aa/375:377,
1/Aa/400:401		Single bulged U
homologous
IL_4LFB_014
IL_89505.4
IL_5NGM_1221/Aa/379:383,
1/Aa/397:398		C-loop
geometric
IL_5J7L_018
IL_03109.3
IL_5NGM_1231/Aa/383:384,
1/Aa/395:397		Single bulged G
homologous
IL_5J7L_019
IL_00225.14
IL_5NGM_1241/Aa/417:427,
1/Aa/432:441		No text annotation
IL_5NGM_1251/Aa/454:458,
1/Aa/491:496		6x5 Sarcin-Ricin; G-bulge
homologous
IL_4LFB_018
IL_88269.4
IL_5NGM_1791/Aa/458:466,
1/Aa/483:491		No text annotation
homologous
IL_6CZR_360
NA
IL_5NGM_1261/Aa/512:519,
1/Aa/548:549		SSU/LSU pseudoknot
homologous
IL_6CZR_132
NA
IL_5NGM_1271/Aa/523:529,
1/Aa/536:544		Kink-turn related
geometric
IL_4V88_415
NA
IL_5NGM_1281/Aa/577:583,
1/Aa/889:890		No text annotation
homologous
IL_5J7L_026
IL_38186.6
IL_5NGM_1291/Aa/588:592,
1/Aa/765:769		tSH-tHW-tHS
homologous
IL_4LFB_023
IL_17136.7
IL_5NGM_1301/Aa/598:600,
1/Aa/655:657		Isolated non-canonical cWW pair
geometric
IL_4WF9_042
IL_87907.2
IL_5NGM_1311/Aa/602:604,
1/Aa/652:653		Major groove platform
homologous
IL_5J7L_028
IL_48076.6
IL_5NGM_1321/Aa/605:606,
1/Aa/648:651		Major groove minor groove platform; mini C-loop
homologous
IL_5J7L_029
IL_68140.4
IL_5NGM_1331/Aa/612:620,
1/Aa/636:642		No text annotation
IL_5NGM_1341/Aa/662:663,
1/Aa/759:762		Major groove platform; stack outside cWW
homologous
IL_4LFB_027
IL_50694.7
IL_5NGM_1351/Aa/665:666,
1/Aa/755:757		Major groove platform
homologous
IL_4LFB_028
IL_48076.6
IL_5NGM_1801/Aa/670:674,
1/Aa/748:751		Tandem non-canonical cWW pairs
homologous
IL_5J7L_033
IL_85033.2
IL_5NGM_1811/Aa/681:685,
1/Aa/721:725		Triple non-canonical cWW pairs
homologous
IL_4LFB_065
IL_49751.4
IL_5NGM_1381/Aa/692:696,
1/Aa/707:714		Kink-turn
homologous
IL_5J7L_035
IL_01488.3
IL_5NGM_1391/Aa/782:787,
1/Aa/811:813		Other IL
geometric
IL_4V88_435
NA
IL_5NGM_1401/Aa/787:791,
1/Aa/807:811		tSH-tHW-tHS
geometric
IL_4LFB_033
IL_17136.7
IL_5NGM_1411/Aa/896:903,
1/Aa/914:919		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_4LFB_034
IL_41756.4
IL_5NGM_1421/Aa/931:932,
1/Aa/1403:1405		Single bulged A
homologous
IL_4LFB_035
IL_31462.7
IL_5NGM_1431/Aa/934:936,
1/Aa/1400:1401		Single bulged G
homologous
IL_4LFB_036
IL_00225.14
IL_5NGM_1441/Aa/942:944,
1/Aa/1390:1394		Minor groove platform
homologous
IL_5J7L_041
IL_47078.3
IL_5NGM_1451/Aa/962:963,
1/Aa/1236:1238		No text annotation
homologous
IL_6CZR_150
NA
IL_5NGM_1461/Aa/1002:1006,
1/Aa/1055:1056		Minor groove platform
geometric
IL_4LFB_039
IL_47078.3
IL_5NGM_1871/Aa/1006:1008,
1/Aa/1052:1055		No text annotation
IL_5NGM_1481/Aa/1059:1061,
1/Aa/1218:1219		Single bulged U
homologous
IL_5J7L_046
IL_89505.4
IL_5NGM_1491/Aa/1062:1067,
1/Aa/1214:1217		Tandem non-canonical cWW pairs
geometric
IL_4V88_473
NA
IL_5NGM_1501/Aa/1068:1069,
1/Aa/1209:1213		Minor groove platform
homologous
IL_5J7L_048
IL_95583.2
IL_5NGM_1511/Aa/1071:1072,
1/Aa/1205:1207		Single bulged U
homologous
IL_4LFB_046
IL_89505.4
IL_5NGM_1521/Aa/1072:1074,
1/Aa/1203:1205		Isolated non-canonical cWW pair
geometric
IL_4LFB_047
IL_28037.2
IL_5NGM_1881/Aa/1127:1171,
1/Aa/1185:1194		No text annotation
IL_5NGM_1531/Aa/1257:1263,
1/Aa/1294:1300		No text annotation
homologous
IL_5J7L_054
IL_09129.2
IL_5NGM_1541/Aa/1265:1268,
1/Aa/1287:1292		No text annotation
IL_5NGM_1551/Aa/1269:1274,
1/Aa/1281:1286		tSH-tHW-tHS-cWW
geometric
IL_1L9A_008
IL_71294.3
IL_5NGM_1561/Aa/1313:1318,
1/Aa/1339:1344		No text annotation
geometric
IL_4LFB_055
IL_85536.2
IL_5NGM_1571/Aa/1409:1411,
1/Aa/1512:1515		No text annotation
homologous
IL_4LFB_056
IL_61438.4
IL_5NGM_1581/Aa/1411:1414,
1/Aa/1508:1512		No text annotation
geometric
IL_4V88_464
NA
IL_5NGM_1591/Aa/1415:1417,
1/Aa/1505:1507		Isolated non-canonical cWW pair
geometric
IL_5TBW_110
NA
IL_5NGM_1601/Aa/1417:1419,
1/Aa/1502:1505		No text annotation
geometric
IL_4V9F_072
IL_55516.2
IL_5NGM_1611/Aa/1422:1424,
1/Aa/1497:1499		Isolated non-canonical cWW pair
homologous
IL_5J7L_061
IL_87907.2
IL_5NGM_1621/Aa/1426:1429,
1/Aa/1492:1495		Double sheared
homologous
IL_5J7L_062
IL_09705.15
IL_5NGM_1631/Aa/1434:1437,
1/Aa/1484:1487		Tandem non-canonical cWW pairs
geometric
IL_5LQO_002
IL_85033.2
IL_5NGM_1641/Aa/1440:1445,
1/Aa/1477:1481		Triple sheared related
geometric
IL_5J7L_063
IL_80231.1
IL_5NGM_1651/Aa/1445:1447,
1/Aa/1475:1477		Isolated non-canonical cWW pair
homologous
IL_4LFB_063
IL_87907.2
IL_5NGM_1661/Aa/1450:1453,
1/Aa/1470:1472		No text annotation
IL_5NGM_1671/Aa/1455:1458,
1/Aa/1466:1468		No text annotation
homologous
IL_5J7L_065
IL_31531.3

Problematic loops

#loop idProblemSequence
IL_5NGM_004Kink-turn
IL_5NGM_006Isolated cWH basepair
IL_5NGM_011No text annotation
IL_5NGM_168Isolated cWH basepair
IL_5NGM_169Isolated cWS basepair
IL_5NGM_039Other IL
IL_5NGM_170No text annotation
IL_5NGM_049No text annotation
IL_5NGM_054No text annotation
IL_5NGM_056No text annotation
IL_5NGM_177No text annotation
IL_5NGM_119No text annotation
IL_5NGM_136Partly complementary
IL_5NGM_137No text annotation
IL_5NGM_147No text annotation
IL_5NGM_182No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_5NGM_0011/AA/30:31,
1/AA/520:527,
1/AA/554:555		No text annotation
homologous
J3_5J7L_036
J3_60031.2
J3_5NGM_0251/AA/30:31,
1/AA/520:530,
1/AA/541:555		No text annotation
homologous
J3_4WF9_011
J3_92134.2
J3_5NGM_0261/AA/32:35,
1/AA/491:507,
1/AA/514:519		No text annotation
homologous
J3_4WF9_012
J3_30040.2
J3_5NGM_0021/AA/56:57,
1/AA/70:76,
1/AA/109:113		No text annotation
homologous
J3_5J7L_037
J3_35667.2
J3_5NGM_0031/AA/272:276,
1/AA/295:302,
1/AA/415:416		No text annotation
homologous
J3_7RQB_003
NA
J3_5NGM_0041/AA/728:734,
1/AA/818:820,
1/AA/836:839		No text annotation
homologous
J3_4WF9_002
J3_64189.2
J3_5NGM_0051/AA/743:745,
1/AA/777:781,
1/AA/805:808		No text annotation
homologous
J3_4WF9_003
J3_44724.7
J3_5NGM_0061/AA/1335:1340,
1/AA/1669:1671,
1/AA/1683:1686		No text annotation
homologous
J3_4WF9_004
J3_32852.6
J3_5NGM_0071/AA/1342:1346,
1/AA/1649:1655,
1/AA/1664:1667		No text annotation
homologous
J3_4WF9_005
J3_68164.1
J3_5NGM_0271/AA/1381:1388,
1/AA/1417:1422,
1/AA/1439:1440		No text annotation
homologous
J3_4WF9_016
J3_31965.2
J3_5NGM_0281/AA/1468:1473,
1/AA/1611:1612,
1/AA/1615:1621		No text annotation
homologous
J3_5J7L_069
J3_34864.2
J3_5NGM_0081/AA/2118:2120,
1/AA/2223:2229,
1/AA/2248:2255		No text annotation
J3_5NGM_0291/AA/2309:2312,
1/AA/2410:2422,
1/AA/2448:2454		No text annotation
homologous
J3_4WF9_019
J3_39320.1
J3_5NGM_0091/AA/2322:2324,
1/AA/2348:2350,
1/AA/2359:2364		No text annotation
homologous
J3_4WF9_008
J3_61124.2
J3_5NGM_0101/AA/2544:2547,
1/AA/2572:2574,
1/AA/2588:2594		No text annotation
homologous
J3_4WF9_009
J3_32601.5
J3_5NGM_0111/AA/2816:2817,
1/AA/2826:2831,
1/AA/2909:2913		No text annotation
homologous
J3_7RQB_013
NA
J3_5NGM_0121/AA/2834:2835,
1/AA/2851:2856,
1/AA/2902:2906		No text annotation
homologous
J3_7RQB_014
NA
J3_5NGM_0131/AB/9:14,
1/AB/66:68,
1/AB/103:106		No text annotation
J3_5NGM_0141/Aa/47:48,
1/Aa/369:375,
1/Aa/401:403		No text annotation
homologous
J3_5J7L_001
J3_67856.4
J3_5NGM_0301/Aa/47:53,
1/Aa/367:375,
1/Aa/401:403		No text annotation
homologous
J3_5J7L_050
J3_46317.4
J3_5NGM_0311/Aa/142:144,
1/Aa/178:185,
1/Aa/206:229		No text annotation
J3_5NGM_0151/Aa/594:596,
1/Aa/659:662,
1/Aa/762:763		No text annotation
homologous
J3_5J7L_002
J3_56052.5
J3_5NGM_0321/Aa/594:596,
1/Aa/659:663,
1/Aa/759:763		No text annotation
homologous
J3_5J7L_051
J3_17385.4
J3_5NGM_0161/Aa/680:681,
1/Aa/725:733,
1/Aa/740:742		No text annotation
homologous
J3_5J7L_003
J3_11934.4
J3_5NGM_0171/Aa/834:837,
1/Aa/866:870,
1/Aa/877:883		No text annotation
homologous
J3_5J7L_004
J3_85054.4
J3_5NGM_0181/Aa/945:948,
1/Aa/1354:1360,
1/Aa/1382:1389		No text annotation
J3_5NGM_0191/Aa/952:955,
1/Aa/1245:1247,
1/Aa/1347:1350		No text annotation
homologous
J3_4LFB_003
J3_52655.4
J3_5NGM_0201/Aa/964:971,
1/Aa/982:993,
1/Aa/1231:1235		No text annotation
homologous
J3_4LFB_004
J3_83516.4
J3_5NGM_0211/Aa/999:1002,
1/Aa/1056:1058,
1/Aa/1220:1225		No text annotation
homologous
J3_4LFB_005
J3_82572.1
J3_5NGM_0331/Aa/999:1006,
1/Aa/1055:1058,
1/Aa/1220:1225		No text annotation
homologous
J3_4LFB_016
J3_76475.2
J3_5NGM_0371/Aa/1010:1017,
1/Aa/1030:1036,
1/Aa/1045:1050		No text annotation
J3_5NGM_0221/Aa/1074:1079,
1/Aa/1118:1124,
1/Aa/1197:1203		No text annotation
homologous
J3_5J7L_008
J3_08394.3
J3_5NGM_0351/Aa/1084:1085,
1/Aa/1094:1097,
1/Aa/1110:1113		No text annotation
homologous
J3_4LFB_017
J3_79369.1
J3_5NGM_0241/Aa/1247:1251,
1/Aa/1306:1313,
1/Aa/1344:1347		No text annotation
homologous
J3_5J7L_011
J3_37047.6
J3_5NGM_0361/Aa/1247:1251,
1/Aa/1306:1318,
1/Aa/1339:1347		No text annotation
J4_5NGM_0011/AA/271:272,
1/AA/416:421,
1/AA/445:452,
1/AA/467:470		No text annotation
homologous
J4_4WF9_001
J4_45801.6
J4_5NGM_0021/AA/340:344,
1/AA/359:362,
1/AA/366:368,
1/AA/380:384		No text annotation
homologous
J4_9DFE_002
J4_71729.5
J4_5NGM_0031/AA/644:647,
1/AA/669:673,
1/AA/680:683,
1/AA/695:701		No text annotation
homologous
J4_5J7L_020
J4_60168.1
J4_5NGM_0041/AA/1308:1313,
1/AA/1331:1332,
1/AA/1689:1693,
1/AA/2035:2037		No text annotation
J4_5NGM_0051/AA/1347:1351,
1/AA/1375:1380,
1/AA/1441:1442,
1/AA/1641:1648		No text annotation
homologous
J4_4WF9_005
J4_69051.6
J4_5NGM_0061/AA/1799:1803,
1/AA/1815:1819,
1/AA/1854:1857,
1/AA/2002:2006		No text annotation
homologous
J4_5J7L_025
J4_61477.5
J4_5NGM_0071/AA/1860:1863,
1/AA/1931:1933,
1/AA/1951:1961,
1/AA/1991:1999		No text annotation
J4_5NGM_0081/AA/2312:2317,
1/AA/2369:2374,
1/AA/2397:2399,
1/AA/2408:2410		No text annotation
J4_5NGM_0091/AA/2670:2673,
1/AA/2701:2703,
1/AA/2758:2762,
1/AA/2796:2798		No text annotation
homologous
J4_9DFE_010
J4_77044.4
J4_5NGM_0101/Aa/114:122,
1/Aa/246:248,
1/Aa/294:297,
1/Aa/319:320		No text annotation
J4_5NGM_0111/Aa/583:585,
1/Aa/772:777,
1/Aa/818:829,
1/Aa/888:889		No text annotation
homologous
J4_5J7L_003
J4_61885.6
J5_5NGM_0011/AA/47:54,
1/AA/115:120,
1/AA/129:130,
1/AA/149:151,
1/AA/178:180		No text annotation
homologous
J5_4WF9_001
J5_01737.2
J5_5NGM_0021/AA/627:632,
1/AA/713:716,
1/AA/854:857,
1/AA/1234:1235,
1/AA/1288:1294		No text annotation
homologous
J5_4WF9_004
J5_74302.5
J5_5NGM_0031/AA/1718:1726,
1/AA/1750:1751,
1/AA/1778:1779,
1/AA/1783:1791,
1/AA/2015:2017		No text annotation
homologous
J5_4WF9_005
J5_62523.6
J5_5NGM_0041/AA/2084:2091,
1/AA/2473:2480,
1/AA/2527:2534,
1/AA/2609:2615,
1/AA/2633:2638		No text annotation
J5_5NGM_0051/AA/2101:2104,
1/AA/2270:2273,
1/AA/2285:2286,
1/AA/2308:2309,
1/AA/2454:2462		No text annotation
homologous
J5_4WF9_007
J5_39529.1
J5_5NGM_0061/Aa/37:41,
1/Aa/410:416,
1/Aa/442:449,
1/Aa/501:512,
1/Aa/549:556		No text annotation
J5_5NGM_0081/Aa/54:62,
1/Aa/105:112,
1/Aa/322:324,
1/Aa/345:347,
1/Aa/358:366		No text annotation
J6_5NGM_0011/AA/45:47,
1/AA/180:186,
1/AA/217:227,
1/AA/234:238,
1/AA/265:269,
1/AA/472:479		No text annotation
J6_5NGM_0021/AA/2101:2104,
1/AA/2270:2273,
1/AA/2285:2286,
1/AA/2308:2312,
1/AA/2410:2422,
1/AA/2448:2462		No text annotation
J7_5NGM_0011/AA/862:867,
1/AA/880:881,
1/AA/987:990,
1/AA/1015:1020,
1/AA/1031:1035,
1/AA/1207:1209,
1/AA/1223:1229		No text annotation
J10_5NGM_0011/AA/8:15,
1/AA/570:578,
1/AA/603:607,
1/AA/620:622,
1/AA/1299:1300,
1/AA/2044:2050,
1/AA/2067:2070,
1/AA/2652:2657,
1/AA/2815:2816,
1/AA/2913:2914		No text annotation

Problematic loops

#loop idProblemSequence
J3_5NGM_034No text annotation
J3_5NGM_023No text annotation
J5_5NGM_007No text annotation

Coloring options:
Copyright 2025 BGSU RNA group. Page generated in 0.0844 s