RNA 3D Hub //

6GZQ Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_6GZQ_0011/A1/58:67No text annotation
homologous
HL_7RQB_001
NA
HL_6GZQ_0021/A1/86:94No text annotation
homologous
HL_7RQB_002
NA
HL_6GZQ_0031/A1/121:126No text annotation
homologous
HL_5J7L_136
HL_82710.2
HL_6GZQ_0041/A1/136:141No text annotation
HL_6GZQ_0051/A1/155:161No text annotation
HL_6GZQ_0061/A1/178:198No text annotation
HL_6GZQ_1151/A1/215:220No text annotation
HL_6GZQ_0081/A1/236:242No text annotation
homologous
HL_7RQB_008
NA
HL_6GZQ_0091/A1/270:276No text annotation
geometric
HL_5J7L_151
HL_80922.2
HL_6GZQ_1161/A1/330:337T-loop with 2 stacked bulged bases
homologous
HL_4WF9_010
HL_01609.3
HL_6GZQ_0111/A1/344:348No text annotation
homologous
HL_5J7L_143
HL_75660.5
HL_6GZQ_0121/A1/352:360T-loop with unstacked turn
homologous
HL_5J7L_144
HL_27670.2
HL_6GZQ_0131/A1/409:421No text annotation
homologous
HL_4WF9_013
HL_69139.1
HL_6GZQ_0141/A1/438:445Pseudoknot geometry
homologous
HL_5J7L_146
HL_30680.3
HL_6GZQ_0151/A1/490:495GNRA
homologous
HL_7RQB_015
NA
HL_6GZQ_0161/A1/515:520GNRA
homologous
HL_7RQB_016
NA
HL_6GZQ_0171/A1/570:575GNRA
geometric
HL_4ZT0_004
NA
HL_6GZQ_0181/A1/589:602No text annotation
HL_6GZQ_0191/A1/637:643No text annotation
homologous
HL_7A0S_019
HL_47787.2
HL_6GZQ_0201/A1/656:661GNRA
homologous
HL_5J7L_152
HL_37824.7
HL_6GZQ_0211/A1/668:674GNRA
homologous
HL_4WF9_021
HL_37824.7
HL_6GZQ_0221/A1/761:768No text annotation
homologous
HL_7RQB_022
NA
HL_6GZQ_0231/A1/793:802No text annotation
homologous
HL_7RQB_023
NA
HL_6GZQ_0241/A1/828:834No text annotation
homologous
HL_7A0S_023
HL_53890.2
HL_6GZQ_0251/A1/875:880No text annotation
homologous
HL_7RQB_025
NA
HL_6GZQ_0261/A1/929:945No text annotation
HL_6GZQ_0271/A1/1002:1009GNRA
geometric
HL_7RQB_027
NA
HL_6GZQ_1171/A1/1026:1033No text annotation
homologous
HL_9DFE_026
HL_42998.2
HL_6GZQ_0291/A1/1102:1153No text annotation
HL_6GZQ_0301/A1/1219:1225No text annotation
HL_6GZQ_0311/A1/1270:1275GNRA
homologous
HL_7RQB_032
NA
HL_6GZQ_0321/A1/1329:1337T-loop with 2 stacked bulged bases
homologous
HL_4WF9_032
HL_28252.6
HL_6GZQ_1041/A1/1366:1382No text annotation
HL_6GZQ_0331/A1/1372:1378Pseudoknot geometry with 3' bulge
homologous
HL_4WF9_033
HL_57176.2
HL_6GZQ_0341/A1/1411:1416GNRA
homologous
HL_7RQB_035
NA
HL_6GZQ_0351/A1/1437:1446No text annotation
homologous
HL_5J7L_168
HL_81545.2
HL_6GZQ_0361/A1/1501:1508No text annotation
homologous
HL_7RQB_037
NA
HL_6GZQ_0371/A1/1537:1548No text annotation
HL_6GZQ_0381/A1/1581:1586No text annotation
geometric
HL_5TBW_044
NA
HL_6GZQ_0391/A1/1614:1617Mini UNCG
homologous
HL_7A0S_039
HL_48778.2
HL_6GZQ_0401/A1/1660:1667No text annotation
homologous
HL_4WF9_038
HL_89567.2
HL_6GZQ_0411/A1/1679:1684No text annotation
homologous
HL_7RQB_041
NA
HL_6GZQ_0421/A1/1740:1745UNCG
homologous
HL_4WF9_040
HL_34617.5
HL_6GZQ_0431/A1/1767:1773No text annotation
homologous
HL_7RQB_043
NA
HL_6GZQ_0441/A1/1785:1789No text annotation
homologous
HL_7RQB_044
NA
HL_6GZQ_0451/A1/1810:1820No text annotation
homologous
HL_4WF9_043
HL_01962.2
HL_6GZQ_0461/A1/1839:1844GNRA related
homologous
HL_5J7L_179
HL_04783.2
HL_6GZQ_0471/A1/1897:1902GNRA
homologous
HL_7RQB_047
NA
HL_6GZQ_0481/A1/1934:1944No text annotation
geometric
HL_5TBW_049
NA
HL_6GZQ_0491/A1/1973:1981No text annotation
homologous
HL_4WF9_046
HL_20167.2
HL_6GZQ_0501/A1/2051:2060No text annotation
homologous
HL_7RQB_050
NA
HL_6GZQ_1061/A1/2131:2206No text annotation
HL_6GZQ_0511/A1/2145:2201No text annotation
HL_6GZQ_0521/A1/2228:2233No text annotation
homologous
HL_7RQB_052
NA
HL_6GZQ_1071/A1/2262:2270No text annotation
homologous
HL_7A0S_052
HL_85367.2
HL_6GZQ_0541/A1/2278:2290No text annotation
homologous
HL_4WF9_050
HL_91939.2
HL_6GZQ_0551/A1/2316:2328No text annotation
HL_6GZQ_0561/A1/2338:2345Pseudoknot geometry
homologous
HL_7RQB_056
NA
HL_6GZQ_0571/A1/2369:2376No text annotation
homologous
HL_7RQB_057
NA
HL_6GZQ_0581/A1/2388:2393GNRA
homologous
HL_4WF9_054
HL_37824.7
HL_6GZQ_0591/A1/2418:2427No text annotation
homologous
HL_7RQB_059
NA
HL_6GZQ_0601/A1/2485:2493No text annotation
homologous
HL_7RQB_060
NA
HL_6GZQ_0611/A1/2542:2549No text annotation
homologous
HL_7RQB_061
NA
HL_6GZQ_0621/A1/2565:2571No text annotation
homologous
HL_4WF9_058
HL_30068.2
HL_6GZQ_0631/A1/2608:2613GNRA
homologous
HL_7RQB_063
NA
HL_6GZQ_0641/A1/2672:2677GNRA
homologous
HL_5J7L_197
HL_37824.7
HL_6GZQ_0651/A1/2715:2720No text annotation
homologous
HL_7RQB_065
NA
HL_6GZQ_1181/A1/2760:2774No text annotation
homologous
HL_9DFE_064
HL_74055.2
HL_6GZQ_0671/A1/2806:2818No text annotation
HL_6GZQ_0681/A1/2831:2839No text annotation
homologous
HL_7RQB_068
NA
HL_6GZQ_0691/A1/2868:2873GNRA
homologous
HL_5J7L_202
HL_37824.7
HL_6GZQ_0701/A2/12:22No text annotation
homologous
HL_4LFB_001
HL_89881.5
HL_6GZQ_0711/A2/67:95No text annotation
HL_6GZQ_0721/A2/152:157GNRA
homologous
HL_5J7L_003
HL_37824.7
HL_6GZQ_0731/A2/186:191No text annotation
homologous
HL_6CZR_075
NA
HL_6GZQ_0741/A2/205:213Mini UNCG
homologous
HL_4LFB_005
HL_48778.2
HL_6GZQ_0751/A2/254:262GNRA related
homologous
HL_5J7L_006
HL_84299.4
HL_6GZQ_0761/A2/291:296GNRA
homologous
HL_4LFB_007
HL_37824.7
HL_6GZQ_0771/A2/315:328No text annotation
homologous
HL_4LFB_008
HL_81205.3
HL_6GZQ_0781/A2/337:342UNCG
homologous
HL_6CZR_080
NA
HL_6GZQ_0791/A2/374:379GNRA
homologous
HL_4LFB_010
HL_37824.7
HL_6GZQ_0801/A2/414:419UNCG
homologous
HL_5J7L_011
HL_34617.5
HL_6GZQ_0811/A2/452:458GNRA
homologous
HL_4LFB_012
HL_37824.7
HL_6GZQ_0821/A2/505:510No text annotation
geometric
HL_4WF9_003
HL_75660.5
HL_6GZQ_0831/A2/600:606No text annotation
homologous
HL_5J7L_014
HL_10453.3
HL_6GZQ_0841/A2/672:681No text annotation
homologous
HL_4LFB_015
HL_75293.5
HL_6GZQ_0851/A2/709:714GNRA
homologous
HL_4LFB_016
HL_37824.7
HL_6GZQ_0861/A2/769:779No text annotation
homologous
HL_6CZR_088
NA
HL_6GZQ_0871/A2/821:825Mini UNCG
homologous
HL_4LFB_018
HL_48778.2
HL_6GZQ_0881/A2/839:844GNRA
homologous
HL_4LFB_019
HL_37824.7
HL_6GZQ_0891/A2/874:879GNRA
homologous
HL_4LFB_020
HL_37824.7
HL_6GZQ_0901/A2/940:949No text annotation
homologous
HL_4LFB_021
HL_50779.4
HL_6GZQ_1111/A2/990:995GNRA
homologous
HL_4LFB_022
HL_37824.7
HL_6GZQ_0921/A2/1058:1063GNRA
homologous
HL_5J7L_023
HL_37824.7
HL_6GZQ_0931/A2/1071:1078T-loop related
homologous
HL_4LFB_025
HL_77436.5
HL_6GZQ_1121/A2/1100:1137No text annotation
HL_6GZQ_0941/A2/1116:1122No text annotation
homologous
HL_5J7L_025
HL_87954.2
HL_6GZQ_0951/A2/1147:1152GNRA
homologous
HL_4LFB_027
HL_37824.7
HL_6GZQ_0961/A2/1246:1251GNRA
homologous
HL_4LFB_028
HL_37824.7
HL_6GZQ_1191/A2/1295:1304T-loop with 3 stacked bulged bases
homologous
HL_4LFB_029
HL_02887.3
HL_6GZQ_0981/A2/1336:1349No text annotation
HL_6GZQ_0991/A2/1429:1434No text annotation
geometric
HL_4V88_198
NA
HL_6GZQ_1001/A2/1492:1497GNRA
homologous
HL_6CZR_103
NA
HL_6GZQ_1141/B1/36:50No text annotation
homologous
HL_8C3A_228
NA
HL_6GZQ_1011/B1/40:46No text annotation
geometric
HL_5J7L_203
HL_47787.2
HL_6GZQ_1021/B1/88:93GNRA
homologous
HL_5TBW_186
NA

Problematic loops

#loop idProblemSequence
HL_6GZQ_103No text annotation
HL_6GZQ_007No text annotation
HL_6GZQ_010No text annotation
HL_6GZQ_028tRNA D-loop
HL_6GZQ_105No text annotation
HL_6GZQ_053No text annotation
HL_6GZQ_066No text annotation
HL_6GZQ_108No text annotation
HL_6GZQ_109No text annotation
HL_6GZQ_110tRNA anticodon loop
HL_6GZQ_091No text annotation
HL_6GZQ_097No text annotation
HL_6GZQ_113No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_6GZQ_0011/A1/24:30,
1/A1/537:543		Triple sheared with non-canonical cWW
homologous
IL_7A0S_001
IL_04021.2
IL_6GZQ_0021/A1/36:37,
1/A1/470:472		Single bulged A
homologous
IL_7A0S_002
IL_31462.5
IL_6GZQ_0031/A1/42:43,
1/A1/463:465		Minor groove platform
homologous
IL_5J7L_247
IL_51454.2
IL_6GZQ_0041/A1/80:84,
1/A1/96:103		Kink-turn
homologous
IL_4WF9_004
IL_01488.3
IL_6GZQ_0051/A1/173:174,
1/A1/202:204		Single stack bend
homologous
IL_7RQB_005
NA
IL_6GZQ_0061/A1/228:235,
1/A1/243:249		8x7 Sarcin-Ricin; G-bulge
homologous
IL_4WF9_009
IL_04346.10
IL_6GZQ_0071/A1/292:294,
1/A1/392:395		No text annotation
geometric
IL_6DME_003
IL_55516.2
IL_6GZQ_1481/A1/297:315,
1/A1/375:389		No text annotation
IL_6GZQ_0081/A1/318:320,
1/A1/368:372		No text annotation
homologous
IL_7RQB_013
NA
IL_6GZQ_0091/A1/509:512,
1/A1/523:536		No text annotation
homologous
IL_7RQB_014
NA
IL_6GZQ_0101/A1/631:635,
1/A1/645:649		AAA cross-strand stack
homologous
IL_4WF9_019
IL_66798.2
IL_6GZQ_0111/A1/721:723,
1/A1/855:857		Isolated non-canonical cWW pair
geometric
IL_5J7L_259
IL_87907.2
IL_6GZQ_0121/A1/723:727,
1/A1/848:855		tHW-tHW cross-strand stack
homologous
IL_4WF9_021
IL_54041.2
IL_6GZQ_0131/A1/746:747,
1/A1/812:814		Single bulged A
homologous
IL_4WF9_022
IL_31462.5
IL_6GZQ_0141/A1/751:752,
1/A1/777:779		Single bulged G
homologous
IL_7RQB_020
NA
IL_6GZQ_0151/A1/752:756,
1/A1/773:777		Triple sheared
geometric
IL_4WF9_024
IL_50730.2
IL_6GZQ_0161/A1/787:790,
1/A1/805:807		Major groove platform with extra cWW
homologous
IL_7RQB_022
NA
IL_6GZQ_0171/A1/824:826,
1/A1/836:840		Multiple bulged bases
homologous
IL_4WF9_027
IL_06549.2
IL_6GZQ_0181/A1/886:887,
1/A1/987:989		Single stack bend
homologous
IL_5J7L_266
IL_90729.1
IL_6GZQ_0191/A1/893:895,
1/A1/978:981		Intercalated cWW
homologous
IL_7RQB_025
NA
IL_6GZQ_0201/A1/895:899,
1/A1/975:978		No text annotation
geometric
IL_7RQB_026
NA
IL_6GZQ_0211/A1/906:911,
1/A1/963:968		5x5 Sarcin-Ricin with intercalated A; G-bulge
geometric
IL_7A0S_027
NA
IL_6GZQ_1841/A1/907:917,
1/A1/957:967		No text annotation
IL_6GZQ_0221/A1/911:912,
1/A1/961:963		Minor groove platform
geometric
IL_4V9F_034
IL_51454.2
IL_6GZQ_0231/A1/912:917,
1/A1/957:961		No text annotation
IL_6GZQ_0241/A1/924:929,
1/A1/945:950		Triple sheared
homologous
IL_5J7L_274
IL_17948.2
IL_6GZQ_1851/A1/999:1001,
1/A1/1010:1012		Isolated non-canonical cWW pair
homologous
IL_7A0S_031
IL_87907.2
IL_6GZQ_0261/A1/1042:1044,
1/A1/1207:1208		Single bulged C
homologous
IL_5J7L_276
IL_61258.15
IL_6GZQ_0271/A1/1046:1050,
1/A1/1201:1205		UAA/GAN
homologous
IL_7A0S_033
IL_38507.2
IL_6GZQ_0281/A1/1052:1059,
1/A1/1198:1199		SSU/LSU pseudoknot
homologous
IL_4WF9_037
IL_41203.4
IL_6GZQ_1521/A1/1052:1061,
1/A1/1197:1199		Isolated non-canonical cWW pair
geometric
IL_7A0S_020
IL_87907.2
IL_6GZQ_0291/A1/1059:1061,
1/A1/1197:1198		Single bulged U
geometric
IL_5J7L_279
IL_89505.4
IL_6GZQ_0301/A1/1066:1072,
1/A1/1187:1192		Kink-turn related
homologous
IL_4WF9_039
IL_57188.5
IL_6GZQ_1861/A1/1066:1078,
1/A1/1172:1192		No text annotation
IL_6GZQ_0311/A1/1072:1078,
1/A1/1172:1187		No text annotation
homologous
IL_7A0S_037
IL_50715.3
IL_6GZQ_0321/A1/1079:1082,
1/A1/1169:1171		Isolated non-canonical cWW pair
homologous
IL_4WF9_041
IL_57744.1
IL_6GZQ_1871/A1/1091:1099,
1/A1/1156:1160		No text annotation
homologous
IL_9DFE_041
IL_99692.2
IL_6GZQ_1881/A1/1243:1245,
1/A1/1295:1298		Isolated cWS basepair
homologous
IL_5J7L_286
IL_42997.3
IL_6GZQ_0351/A1/1249:1253,
1/A1/1288:1291		No text annotation
homologous
IL_7RQB_046
NA
IL_6GZQ_0361/A1/1255:1262,
1/A1/1282:1286		Kink-turn
homologous
IL_7RQB_047
NA
IL_6GZQ_1891/A1/1266:1268,
1/A1/1277:1278		Single bulged A
homologous
IL_9DFE_047
IL_31462.5
IL_6GZQ_0381/A1/1310:1317,
1/A1/2035:2041		8x7 Sarcin-Ricin; G-bulge
homologous
IL_7RQB_049
NA
IL_6GZQ_0391/A1/1358:1361,
1/A1/1651:1652		Major groove platform; stack outside cWW
homologous
IL_7RQB_050
NA
IL_6GZQ_0401/A1/1366:1372,
1/A1/1378:1382		No text annotation
IL_6GZQ_0411/A1/1399:1403,
1/A1/1424:1428		UAA/GAN
homologous
IL_7RQB_052
NA
IL_6GZQ_0421/A1/1405:1409,
1/A1/1418:1422		tSH-tHW-tHS
homologous
IL_7RQB_053
NA
IL_6GZQ_0431/A1/1463:1469,
1/A1/1626:1635		No text annotation
IL_6GZQ_1551/A1/1472:1477,
1/A1/1613:1623		No text annotation
IL_6GZQ_0441/A1/1481:1483,
1/A1/1606:1609		Isolated tWW turn
homologous
IL_7RQB_056
NA
IL_6GZQ_1561/A1/1485:1488,
1/A1/1600:1604		No text annotation
homologous
IL_9DFE_056
IL_99646.2
IL_6GZQ_0461/A1/1497:1499,
1/A1/1511:1512		Single stack bend
homologous
IL_7RQB_058
NA
IL_6GZQ_0471/A1/1500:1501,
1/A1/1508:1510		Single bulged A
geometric
IL_7RQB_059
NA
IL_6GZQ_0481/A1/1518:1522,
1/A1/1568:1571		UAA/GAN
homologous
IL_7RQB_060
NA
IL_6GZQ_0491/A1/1530:1531,
1/A1/1554:1560		No text annotation
homologous
IL_7RQB_061
NA
IL_6GZQ_1901/A1/1574:1578,
1/A1/1589:1595		No text annotation
homologous
IL_9DFE_062
IL_09044.1
IL_6GZQ_0511/A1/1700:1705,
1/A1/2028:2030		No text annotation
homologous
IL_7RQB_064
NA
IL_6GZQ_0521/A1/1712:1714,
1/A1/2019:2021		Isolated tWW turn
homologous
IL_7A0S_060
IL_67095.2
IL_6GZQ_1591/A1/1715:1718,
1/A1/2017:2018		Major groove platform; stack outside cWW
homologous
IL_4WF9_064
IL_50694.7
IL_6GZQ_1601/A1/1718:1723,
1/A1/2014:2017		Intercalated tWH
homologous
IL_7A0S_062
IL_76758.2
IL_6GZQ_0541/A1/1735:1740,
1/A1/1745:1751		tSH-tSH-tHH-tHS
geometric
IL_7RQB_068
NA
IL_6GZQ_0551/A1/1803:1804,
1/A1/2004:2006		Single bulged A
homologous
IL_4WF9_068
IL_31462.5
IL_6GZQ_0561/A1/1831:1837,
1/A1/1846:1854		Kink-turn related
homologous
IL_7RQB_070
NA
IL_6GZQ_0571/A1/1870:1873,
1/A1/1926:1927		Minor groove platform, major groove intercalation
geometric
IL_7RQB_071
NA
IL_6GZQ_1911/A1/1874:1875,
1/A1/1922:1925		Major groove intercalation
homologous
IL_7A0S_067
IL_66635.5
IL_6GZQ_0591/A1/1879:1882,
1/A1/1917:1918		Major groove minor groove platform; mini C-loop
homologous
IL_5J7L_316
IL_68140.4
IL_6GZQ_0601/A1/1884:1888,
1/A1/1911:1915		UAA/GAN with extra pair
homologous
IL_7RQB_074
NA
IL_6GZQ_0611/A1/1889:1893,
1/A1/1906:1910		Triple sheared
homologous
IL_7RQB_075
NA
IL_6GZQ_0621/A1/1957:1958,
1/A1/1988:1991		Bulged stacked bases
geometric
IL_5J7L_318
IL_22551.3
IL_6GZQ_0631/A1/1958:1969,
1/A1/1985:1988		No text annotation
homologous
IL_4WF9_077
IL_42218.2
IL_6GZQ_0641/A1/2074:2076,
1/A1/2631:2632		Major groove platform
homologous
IL_7RQB_078
NA
IL_6GZQ_0651/A1/2091:2093,
1/A1/2456:2457		Single bulged U
homologous
IL_7RQB_080
NA
IL_6GZQ_0661/A1/2094:2095,
1/A1/2452:2455		Minor groove platform
homologous
IL_7RQB_081
NA
IL_6GZQ_0671/A1/2105:2107,
1/A1/2250:2253		Isolated tHS basepair with bulges
homologous
IL_7RQB_082
NA
IL_6GZQ_0681/A1/2109:2111,
1/A1/2246:2248		Isolated non-canonical cWW pair
homologous
IL_7A0S_078
IL_28037.2
IL_6GZQ_0691/A1/2131:2145,
1/A1/2201:2206		No text annotation
IL_6GZQ_0701/A1/2311:2313,
1/A1/2331:2335		Isolated tHS basepair with bulges
geometric
IL_4WF9_086
IL_61476.2
IL_6GZQ_0711/A1/2364:2367,
1/A1/2378:2381		Double sheared
homologous
IL_7RQB_089
NA
IL_6GZQ_0721/A1/2415:2417,
1/A1/2428:2429		Single bulged U
homologous
IL_5J7L_334
IL_89505.4
IL_6GZQ_0731/A1/2467:2468,
1/A1/2512:2514		Single stack bend
homologous
IL_7RQB_091
NA
IL_6GZQ_0741/A1/2468:2469,
1/A1/2510:2512		Major groove platform
geometric
IL_7RQB_092
NA
IL_6GZQ_1921/A1/2471:2475,
1/A1/2503:2508		No text annotation
IL_6GZQ_0761/A1/2480:2484,
1/A1/2494:2498		Triple sheared
homologous
IL_7A0S_087
IL_17948.2
IL_6GZQ_0771/A1/2521:2522,
1/A1/2594:2596		Major groove platform
homologous
IL_4WF9_094
IL_07039.3
IL_6GZQ_0781/A1/2524:2526,
1/A1/2588:2592		Isolated non-canonical cWW with bulges
homologous
IL_5J7L_340
IL_07785.1
IL_6GZQ_0791/A1/2526:2527,
1/A1/2585:2588		Multiple bulged bases
geometric
IL_7RQB_098
NA
IL_6GZQ_0801/A1/2536:2537,
1/A1/2554:2557		Major groove platform with intercalation
homologous
IL_7A0S_091
IL_02555.1
IL_6GZQ_1651/A1/2536:2540,
1/A1/2551:2557		No text annotation
IL_6GZQ_1931/A1/2605:2606,
1/A1/2615:2617		No text annotation
IL_6GZQ_0821/A1/2650:2654,
1/A1/2789:2797		tSH-tHS-tHW
homologous
IL_4WF9_099
IL_04638.3
IL_6GZQ_0831/A1/2666:2672,
1/A1/2677:2682		Sarcin-Ricin target in LSU H95; G-bulge
geometric
IL_7RQB_103
NA
IL_6GZQ_1941/A1/2694:2698,
1/A1/2740:2742		C-loop
homologous
IL_5J7L_347
IL_63596.11
IL_6GZQ_0851/A1/2701:2705,
1/A1/2733:2737		No text annotation
homologous
IL_7RQB_105
NA
IL_6GZQ_0861/A1/2709:2710,
1/A1/2725:2729		Multiple bulged bases
homologous
IL_7A0S_097
IL_42626.2
IL_6GZQ_0871/A1/2752:2757,
1/A1/2777:2782		UAA/GAN with extra cWW
homologous
IL_7RQB_107
NA
IL_6GZQ_0881/A1/2850:2851,
1/A1/2890:2892		Single bulged C
homologous
IL_7RQB_108
NA
IL_6GZQ_1951/A1/2855:2857,
1/A1/2883:2886		No text annotation
homologous
IL_4WF9_107
IL_31531.3
IL_6GZQ_0901/A1/2859:2864,
1/A1/2877:2881		tHS double platform
geometric
IL_7RQB_110
NA
IL_6GZQ_0911/A2/30:32,
1/A2/535:536		Single bulged G
homologous
IL_4LFB_001
IL_00225.13
IL_6GZQ_0921/A2/44:45,
1/A2/391:393		Single bulged A
homologous
IL_6CZR_114
NA
IL_6GZQ_0931/A2/47:52,
1/A2/354:356		No text annotation
homologous
IL_4LFB_003
IL_14177.2
IL_6GZQ_0941/A2/54:56,
1/A2/351:352		Minor groove platform
homologous
IL_4LFB_004
IL_51454.2
IL_6GZQ_0951/A2/63:66,
1/A2/96:97		Multiple bulged bases
homologous
IL_6CZR_117
NA
IL_6GZQ_0961/A2/122:125,
1/A2/226:227		Multiple bulged bases
homologous
IL_6CZR_119
NA
IL_6GZQ_0971/A2/126:133,
1/A2/219:225		No text annotation
IL_6GZQ_0981/A2/142:147,
1/A2/162:168		tWH-tWH-tHW-tHW
homologous
IL_4LFB_009
IL_12745.1
IL_6GZQ_1681/A2/142:149,
1/A2/160:168		No text annotation
IL_6GZQ_0991/A2/180:182,
1/A2/195:197		Isolated non-canonical cWW pair
homologous
IL_4LFB_010
IL_87907.2
IL_6GZQ_1001/A2/237:242,
1/A2/272:279		Kink-turn with non-sequential stacking
homologous
IL_4LFB_011
IL_46174.3
IL_6GZQ_1011/A2/242:248,
1/A2/268:272		No text annotation
IL_6GZQ_1961/A2/287:288,
1/A2/299:303		C-loop
homologous
IL_4LFB_013
IL_03109.3
IL_6GZQ_1031/A2/362:364,
1/A2/387:388		Single bulged U
geometric
IL_3D2V_001
IL_89505.4
IL_6GZQ_1041/A2/366:370,
1/A2/384:385		C-loop
homologous
IL_4LFB_015
IL_03109.3
IL_6GZQ_1971/A2/366:372,
1/A2/381:385		No text annotation
IL_6GZQ_1051/A2/370:372,
1/A2/381:384		Isolated non-canonical cWW with bulges
geometric
IL_4V9F_097
IL_07785.1
IL_6GZQ_1061/A2/404:411,
1/A2/422:428		No text annotation
homologous
IL_4LFB_017
IL_28026.3
IL_6GZQ_1711/A2/440:444,
1/A2/467:472		6x5 Sarcin-Ricin; G-bulge
homologous
IL_6CZR_130
NA
IL_6GZQ_1981/A2/444:449,
1/A2/461:467		No text annotation
homologous
IL_4LFB_019
IL_31561.1
IL_6GZQ_1091/A2/487:494,
1/A2/523:524		SSU/LSU pseudoknot
homologous
IL_4LFB_020
IL_41203.4
IL_6GZQ_1101/A2/498:504,
1/A2/511:519		Kink-turn related
homologous
IL_4LFB_021
IL_54177.4
IL_6GZQ_1111/A2/552:558,
1/A2/857:858		No text annotation
homologous
IL_4LFB_022
IL_38186.6
IL_6GZQ_1121/A2/560:568,
1/A2/739:747		No text annotation
IL_6GZQ_1131/A2/573:580,
1/A2/626:632		No text annotation
IL_6GZQ_1991/A2/580:581,
1/A2/623:626		Major groove minor groove platform; mini C-loop
homologous
IL_4LFB_025
IL_68140.4
IL_6GZQ_1151/A2/588:595,
1/A2/611:616		No text annotation
homologous
IL_4LFB_026
IL_78349.3
IL_6GZQ_1161/A2/637:638,
1/A2/734:737		Major groove platform; stack outside cWW
homologous
IL_4LFB_027
IL_50694.7
IL_6GZQ_2001/A2/637:651,
1/A2/721:737		No text annotation
IL_6GZQ_1171/A2/666:671,
1/A2/682:690		No text annotation
homologous
IL_6CZR_143
NA
IL_6GZQ_1181/A2/757:761,
1/A2/787:788		Left turn
homologous
IL_4LFB_032
IL_29346.2
IL_6GZQ_2011/A2/762:766,
1/A2/782:786		tSH-tHW-tHS
homologous
IL_4LFB_033
IL_17136.7
IL_6GZQ_1201/A2/864:871,
1/A2/882:887		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_4LFB_034
IL_41756.4
IL_6GZQ_1211/A2/899:904,
1/A2/1372:1377		No text annotation
IL_6GZQ_1221/A2/910:912,
1/A2/1362:1366		Minor groove platform
homologous
IL_5J7L_041
IL_47078.3
IL_6GZQ_1231/A2/922:924,
1/A2/1215:1218		No text annotation
geometric
IL_4V9F_053
IL_09990.4
IL_6GZQ_2021/A2/1034:1039,
1/A2/1184:1187		No text annotation
homologous
IL_6CZR_365
NA
IL_6GZQ_1251/A2/1039:1040,
1/A2/1180:1184		Minor groove platform
geometric
IL_4LFB_045
IL_95583.2
IL_6GZQ_1261/A2/1042:1043,
1/A2/1176:1178		Single bulged U
homologous
IL_6CZR_156
NA
IL_6GZQ_1271/A2/1043:1045,
1/A2/1174:1176		Isolated non-canonical cWW pair
geometric
IL_4LFB_047
IL_28037.2
IL_6GZQ_1771/A2/1100:1116,
1/A2/1122:1137		No text annotation
IL_6GZQ_1781/A2/1226:1236,
1/A2/1263:1273		No text annotation
IL_6GZQ_1281/A2/1236:1239,
1/A2/1258:1263		180 degree turn
homologous
IL_5J7L_055
IL_11344.2
IL_6GZQ_1291/A2/1240:1243,
1/A2/1254:1257		Double sheared
geometric
IL_5J7L_256
IL_09705.15
IL_6GZQ_1301/A2/1284:1289,
1/A2/1310:1315		No text annotation
homologous
IL_4LFB_055
IL_85536.2
IL_6GZQ_1311/A2/1381:1383,
1/A2/1478:1481		No text annotation
homologous
IL_4LFB_056
IL_61438.4
IL_6GZQ_1321/A2/1383:1386,
1/A2/1474:1478		No text annotation
geometric
IL_4V88_464
NA
IL_6GZQ_1331/A2/1387:1389,
1/A2/1471:1473		Isolated non-canonical cWW pair
geometric
IL_4V88_465
NA
IL_6GZQ_2031/A2/1389:1391,
1/A2/1468:1471		Decoding loop related
geometric
IL_2O3X_003
IL_31737.3
IL_6GZQ_1351/A2/1394:1398,
1/A2/1461:1465		No text annotation
geometric
IL_5TBW_121
NA
IL_6GZQ_1361/A2/1398:1405,
1/A2/1454:1461		No text annotation
IL_6GZQ_1371/A2/1413:1417,
1/A2/1443:1446		UAA/GAN variation
homologous
IL_4LFB_062
IL_77691.5
IL_6GZQ_2041/A2/1413:1419,
1/A2/1441:1446		No text annotation
IL_6GZQ_1381/A2/1417:1419,
1/A2/1441:1443		Isolated non-canonical cWW pair
geometric
IL_4LFB_063
IL_87907.2
IL_6GZQ_2051/A2/1422:1427,
1/A2/1436:1438		No text annotation
IL_6GZQ_1401/B1/19:20,
1/B1/67:69		Major groove intercalation
homologous
IL_5J7L_355
IL_31462.5
IL_6GZQ_1411/B1/25:30,
1/B1/58:62		No text annotation
homologous
IL_5J7L_356
IL_18472.4
IL_6GZQ_2061/B1/32:33,
1/B1/53:56		Major groove minor groove platform; mini C-loop
homologous
IL_4WF9_126
IL_68140.4
IL_6GZQ_1431/B1/36:40,
1/B1/46:50		Symmetric double minor groove platform
homologous
IL_7RQB_114
NA
IL_6GZQ_1441/B1/73:81,
1/B1/100:108		Bacterial 5S Loop E
homologous
IL_7RQB_115
NA
IL_6GZQ_1831/B1/73:85,
1/B1/96:108		No text annotation

Problematic loops

#loop idProblemSequence
IL_6GZQ_145Isolated non-canonical cWW contact
IL_6GZQ_146Kink-turn
IL_6GZQ_147No text annotation
IL_6GZQ_149No text annotation
IL_6GZQ_150No text annotation
IL_6GZQ_151Isolated cWS basepair
IL_6GZQ_025Tandem non-canonical cWW pairs
IL_6GZQ_153No text annotation
IL_6GZQ_033No text annotation
IL_6GZQ_034Tandem non-canonical cWW pairs
IL_6GZQ_154No text annotation
IL_6GZQ_037No text annotation
IL_6GZQ_045tSH-tHW-tHS
IL_6GZQ_157No text annotation
IL_6GZQ_050No text annotation
IL_6GZQ_158No text annotation
IL_6GZQ_053No text annotation
IL_6GZQ_161Tandem non-canonical cWW pairs
IL_6GZQ_058Isolated non-canonical cWW pair
IL_6GZQ_162Triple non-canonical cWW pairs
IL_6GZQ_163No text annotation
IL_6GZQ_075No text annotation
IL_6GZQ_164Tandem non-canonical cWW pairs
IL_6GZQ_081Other IL
IL_6GZQ_084No text annotation
IL_6GZQ_166No text annotation
IL_6GZQ_089No text annotation
IL_6GZQ_167Isolated non-canonical cWW pair
IL_6GZQ_169Partly complementary
IL_6GZQ_102No text annotation
IL_6GZQ_170No text annotation
IL_6GZQ_107No text annotation
IL_6GZQ_108No text annotation
IL_6GZQ_172No text annotation
IL_6GZQ_1148-nt loop receptor
IL_6GZQ_173No text annotation
IL_6GZQ_174No text annotation
IL_6GZQ_119tSH-tHW-tHS-cWW
IL_6GZQ_175No text annotation
IL_6GZQ_176No text annotation
IL_6GZQ_124No text annotation
IL_6GZQ_179No text annotation
IL_6GZQ_180No text annotation
IL_6GZQ_134No text annotation
IL_6GZQ_181No text annotation
IL_6GZQ_182No text annotation
IL_6GZQ_139No text annotation
IL_6GZQ_142No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_6GZQ_0201/A1/24:31,
1/A1/502:512,
1/A1/523:543		No text annotation
J3_6GZQ_0011/A1/30:31,
1/A1/502:509,
1/A1/536:537		No text annotation
homologous
J3_7RQB_001
NA
J3_6GZQ_0211/A1/32:35,
1/A1/473:489,
1/A1/496:501		No text annotation
homologous
J3_5J7L_067
J3_30040.2
J3_6GZQ_0331/A1/55:56,
1/A1/69:75,
1/A1/108:112		No text annotation
homologous
J3_4WF9_013
J3_35667.2
J3_6GZQ_0031/A1/259:263,
1/A1/283:290,
1/A1/397:398		No text annotation
homologous
J3_7RQB_003
NA
J3_6GZQ_0041/A1/732:738,
1/A1/822:824,
1/A1/840:843		No text annotation
homologous
J3_7A0S_004
J3_64189.2
J3_6GZQ_0341/A1/732:738,
1/A1/822:826,
1/A1/836:843		No text annotation
J3_6GZQ_0051/A1/747:749,
1/A1/781:785,
1/A1/809:812		No text annotation
homologous
J3_7RQB_005
NA
J3_6GZQ_0061/A1/1346:1351,
1/A1/1673:1675,
1/A1/1688:1691		No text annotation
homologous
J3_7A0S_006
J3_32852.6
J3_6GZQ_0071/A1/1354:1357,
1/A1/1653:1659,
1/A1/1668:1670		No text annotation
homologous
J3_7RQB_008
NA
J3_6GZQ_0351/A1/1392:1398,
1/A1/1429:1433,
1/A1/1450:1451		No text annotation
homologous
J3_9DFE_012
J3_31965.2
J3_6GZQ_0081/A1/2115:2117,
1/A1/2220:2224,
1/A1/2237:2242		No text annotation
homologous
J3_7RQB_010
NA
J3_6GZQ_0261/A1/2296:2298,
1/A1/2398:2409,
1/A1/2435:2441		No text annotation
homologous
J3_5J7L_070
J3_20992.1
J3_6GZQ_0091/A1/2309:2311,
1/A1/2335:2337,
1/A1/2346:2351		No text annotation
homologous
J3_7RQB_011
NA
J3_6GZQ_0271/A1/2309:2313,
1/A1/2331:2337,
1/A1/2346:2351		No text annotation
homologous
J3_5J7L_071
J3_44961.1
J3_6GZQ_0101/A1/2531:2534,
1/A1/2559:2561,
1/A1/2575:2581		No text annotation
J3_6GZQ_0111/A1/2804:2806,
1/A1/2818:2823,
1/A1/2901:2905		No text annotation
homologous
J3_4WF9_020
J3_24127.1
J3_6GZQ_0121/A1/2826:2827,
1/A1/2843:2848,
1/A1/2894:2898		No text annotation
homologous
J3_7RQB_014
NA
J3_6GZQ_0361/A2/46:47,
1/A2/356:362,
1/A2/388:390		No text annotation
geometric
J3_4LFB_010
J3_67856.4
J3_6GZQ_0371/A2/46:52,
1/A2/354:362,
1/A2/388:390		No text annotation
homologous
J3_4LFB_014
J3_46317.4
J3_6GZQ_0141/A2/569:571,
1/A2/634:637,
1/A2/737:738		No text annotation
homologous
J3_4LFB_011
J3_56052.5
J3_6GZQ_0381/A2/569:571,
1/A2/634:651,
1/A2/721:738		No text annotation
J3_6GZQ_0391/A2/653:660,
1/A2/696:708,
1/A2/715:719		No text annotation
J3_6GZQ_0151/A2/809:812,
1/A2/834:838,
1/A2/845:851		No text annotation
homologous
J3_4LFB_001
J3_85054.4
J3_6GZQ_0401/A2/912:916,
1/A2/1325:1331,
1/A2/1354:1362		No text annotation
J3_6GZQ_0161/A2/1045:1050,
1/A2/1089:1095,
1/A2/1168:1174		No text annotation
homologous
J3_4LFB_007
J3_08394.3
J3_6GZQ_0171/A2/1055:1056,
1/A2/1065:1069,
1/A2/1080:1084		No text annotation
homologous
J3_5J7L_009
J3_76043.3
J3_6GZQ_0181/A2/1098:1100,
1/A2/1137:1143,
1/A2/1156:1165		No text annotation
homologous
J3_4LFB_018
J3_17791.2
J3_6GZQ_0191/B1/13:18,
1/B1/70:71,
1/B1/110:112		No text annotation
homologous
J3_7RQB_015
NA
J4_6GZQ_0011/A1/258:259,
1/A1/398:403,
1/A1/427:434,
1/A1/450:453		No text annotation
homologous
J4_9DFE_001
J4_45801.6
J4_6GZQ_0021/A1/322:326,
1/A1/341:344,
1/A1/348:350,
1/A1/362:366		No text annotation
homologous
J4_7A0S_002
J4_71729.5
J4_6GZQ_0031/A1/626:629,
1/A1/651:655,
1/A1/662:666,
1/A1/676:705		No text annotation
J4_6GZQ_0171/A1/1318:1324,
1/A1/1342:1343,
1/A1/1694:1697,
1/A1/2033:2034		No text annotation
homologous
J4_7A0S_004
J4_64571.5
J4_6GZQ_0181/A1/1358:1362,
1/A1/1386:1391,
1/A1/1452:1454,
1/A1/1644:1652		No text annotation
J4_6GZQ_0191/A1/1361:1362,
1/A1/1386:1391,
1/A1/1452:1454,
1/A1/1644:1651		No text annotation
J4_6GZQ_0071/A1/1492:1494,
1/A1/1515:1516,
1/A1/1573:1574,
1/A1/1595:1596		No text annotation
homologous
J4_9DFE_006
J4_24280.2
J4_6GZQ_0081/A1/1805:1809,
1/A1/1821:1825,
1/A1/1860:1863,
1/A1/1999:2003		No text annotation
homologous
J4_5J7L_025
J4_61477.5
J4_6GZQ_0201/A1/1866:1868,
1/A1/1929:1930,
1/A1/1948:1957,
1/A1/1991:1996		No text annotation
homologous
J4_9DFE_008
J4_93343.1
J4_6GZQ_0211/A1/2299:2303,
1/A1/2357:2361,
1/A1/2384:2386,
1/A1/2395:2397		No text annotation
homologous
J4_9DFE_009
J4_04930.6
J4_6GZQ_0221/A1/2657:2660,
1/A1/2688:2690,
1/A1/2746:2750,
1/A1/2784:2786		No text annotation
homologous
J4_4WF9_009
J4_77044.4
J4_6GZQ_0121/A2/108:117,
1/A2/232:235,
1/A2/281:284,
1/A2/306:307		No text annotation
J4_6GZQ_0231/A2/134:139,
1/A2/171:177,
1/A2/200:205,
1/A2/213:218		No text annotation
J4_6GZQ_0141/A2/552:560,
1/A2/747:752,
1/A2/793:804,
1/A2/856:858		No text annotation
J4_6GZQ_0241/A2/920:923,
1/A2/1216:1222,
1/A2/1277:1284,
1/A2/1315:1321		No text annotation
J4_6GZQ_0251/A2/930:939,
1/A2/950:987,
1/A2/998:1032,
1/A2/1189:1209		No text annotation
J5_6GZQ_0011/A1/46:53,
1/A1/114:119,
1/A1/128:129,
1/A1/148:150,
1/A1/166:168		No text annotation
homologous
J5_4WF9_001
J5_01737.2
J5_6GZQ_0021/A1/609:614,
1/A1/717:720,
1/A1/858:861,
1/A1/1242:1243,
1/A1/1298:1304		No text annotation
homologous
J5_7A0S_004
J5_74302.5
J5_6GZQ_0031/A1/1358:1362,
1/A1/1386:1398,
1/A1/1429:1435,
1/A1/1448:1455,
1/A1/1643:1652		No text annotation
J5_6GZQ_0041/A1/1723:1731,
1/A1/1755:1757,
1/A1/1783:1785,
1/A1/1789:1797,
1/A1/2012:2014		No text annotation
J5_6GZQ_0091/A1/2078:2088,
1/A1/2460:2467,
1/A1/2514:2521,
1/A1/2596:2602,
1/A1/2620:2629		No text annotation
J5_6GZQ_0101/A1/2098:2101,
1/A1/2257:2260,
1/A1/2272:2273,
1/A1/2295:2296,
1/A1/2441:2449		No text annotation
homologous
J5_7A0S_007
J5_39529.1
J5_6GZQ_0111/A2/36:39,
1/A2/398:401,
1/A2/431:436,
1/A2/476:483,
1/A2/528:531		No text annotation
homologous
J5_4LFB_001
J5_70703.1
J5_6GZQ_0121/A2/58:61,
1/A2/99:106,
1/A2/309:311,
1/A2/332:334,
1/A2/345:349		No text annotation
homologous
J5_4LFB_002
J5_59910.6
J6_6GZQ_0021/A1/44:45,
1/A1/169:173,
1/A1/204:214,
1/A1/221:225,
1/A1/252:256,
1/A1/455:462		No text annotation
J7_6GZQ_0011/A1/866:871,
1/A1/884:885,
1/A1/990:993,
1/A1/1018:1024,
1/A1/1035:1039,
1/A1/1211:1212,
1/A1/1232:1237		No text annotation

Problematic loops

#loop idProblemSequence
J3_6GZQ_002No text annotation
J3_6GZQ_022No text annotation
J3_6GZQ_023No text annotation
J3_6GZQ_024No text annotation
J3_6GZQ_025No text annotation
J3_6GZQ_028No text annotation
J3_6GZQ_013No text annotation
J3_6GZQ_029No text annotation
J3_6GZQ_030No text annotation
J3_6GZQ_031No text annotation
J3_6GZQ_032No text annotation
J4_6GZQ_004No text annotation
J4_6GZQ_005No text annotation
J4_6GZQ_006No text annotation
J4_6GZQ_009No text annotation
J4_6GZQ_010No text annotation
J4_6GZQ_011No text annotation
J4_6GZQ_013No text annotation
J4_6GZQ_015No text annotation
J4_6GZQ_016No text annotation
J5_6GZQ_005No text annotation
J5_6GZQ_006No text annotation
J5_6GZQ_007No text annotation
J5_6GZQ_008No text annotation
J6_6GZQ_001No text annotation

Coloring options:
Copyright 2025 BGSU RNA group. Page generated in 0.0954 s