RNA 3D Hub //

1NKW Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_1NKW_0781/0/58:67Pseudoknot with intercalation
homologous
HL_4WF9_067
HL_93438.2
HL_1NKW_0021/0/85:95No text annotation
homologous
HL_7A0S_002
HL_50418.1
HL_1NKW_0031/0/121:126No text annotation
homologous
HL_4WF9_003
HL_75660.5
HL_1NKW_0041/0/133:138No text annotation
geometric
HL_5U3G_001
HL_75660.5
HL_1NKW_0051/0/146:151No text annotation
geometric
HL_5U3G_001
HL_75660.5
HL_1NKW_0691/0/165:185No text annotation
HL_1NKW_0061/0/172:177No text annotation
HL_1NKW_0791/0/202:207No text annotation
homologous
HL_7A0S_007
HL_53890.2
HL_1NKW_0081/0/223:229No text annotation
homologous
HL_7A0S_008
HL_37369.2
HL_1NKW_0091/0/316:323No text annotation
homologous
HL_7RQB_010
NA
HL_1NKW_0101/0/330:334No text annotation
homologous
HL_5J7L_143
HL_75660.5
HL_1NKW_0701/0/338:346T-loop with unstacked turn
homologous
HL_5J7L_144
HL_27670.2
HL_1NKW_0121/0/395:405No text annotation
homologous
HL_7A0S_013
HL_91503.7
HL_1NKW_0131/0/423:430Pseudoknot geometry
homologous
HL_5J7L_146
HL_30680.3
HL_1NKW_0141/0/473:478GNRA
homologous
HL_7RQB_015
NA
HL_1NKW_0151/0/498:503GNRA
homologous
HL_7RQB_016
NA
HL_1NKW_0161/0/552:560No text annotation
geometric
HL_2Y8W_001
HL_81100.2
HL_1NKW_0171/0/575:584T-loop with 2 stacked bulged bases
homologous
HL_7A0S_018
HL_28252.8
HL_1NKW_0721/0/622:627No text annotation
HL_1NKW_0191/0/640:645GNRA
homologous
HL_7A0S_020
HL_37824.7
HL_1NKW_0201/0/725:732No text annotation
HL_1NKW_0801/0/758:765No text annotation
HL_1NKW_0221/0/791:799No text annotation
geometric
HL_6CF2_001
HL_87553.1
HL_1NKW_0231/0/839:844No text annotation
geometric
HL_7A0S_024
HL_55195.3
HL_1NKW_0251/0/966:973GNRA
homologous
HL_7A0S_026
HL_37824.7
HL_1NKW_0261/0/989:996No text annotation
homologous
HL_7A0S_027
HL_42998.2
HL_1NKW_0271/0/1075:1085No text annotation
homologous
HL_6PRV_001
HL_19210.3
HL_1NKW_0281/0/1103:1110No text annotation
homologous
HL_7RQB_030
NA
HL_1NKW_0291/0/1185:1189No text annotation
geometric
HL_4WF9_009
HL_81100.2
HL_1NKW_0301/0/1235:1240GNRA
homologous
HL_7A0S_031
HL_37824.7
HL_1NKW_0311/0/1294:1302T-loop with 2 stacked bulged bases
homologous
HL_4WF9_032
HL_28252.8
HL_1NKW_0321/0/1337:1343Pseudoknot geometry with 3' bulge
homologous
HL_4WF9_033
HL_57176.2
HL_1NKW_0331/0/1376:1381GNRA
homologous
HL_7RQB_035
NA
HL_1NKW_0811/0/1402:1411No text annotation
homologous
HL_5J7L_168
HL_81545.2
HL_1NKW_0351/0/1466:1476Pseudoknot
homologous
HL_7A0S_036
HL_93135.1
HL_1NKW_0361/0/1508:1514No text annotation
homologous
HL_7A0S_037
HL_39243.1
HL_1NKW_0371/0/1549:1554No text annotation
geometric
HL_7RQB_011
NA
HL_1NKW_0381/0/1628:1635No text annotation
homologous
HL_7A0S_040
HL_89567.2
HL_1NKW_0391/0/1647:1652No text annotation
homologous
HL_7RQB_041
NA
HL_1NKW_0401/0/1708:1713UNCG
homologous
HL_7A0S_042
HL_34617.5
HL_1NKW_0411/0/1731:1735No text annotation
geometric
HL_4V88_198
NA
HL_1NKW_0421/0/1743:1747No text annotation
homologous
HL_7A0S_044
HL_80709.3
HL_1NKW_0431/0/1767:1779No text annotation
homologous
HL_7A0S_045
HL_60266.1
HL_1NKW_0441/0/1797:1803GNRA related
homologous
HL_5J7L_179
HL_04783.2
HL_1NKW_0451/0/1856:1861GNRA
homologous
HL_7A0S_047
HL_37824.7
HL_1NKW_0741/0/1894:1901No text annotation
HL_1NKW_0471/0/1932:1940No text annotation
homologous
HL_7A0S_048
HL_20167.2
HL_1NKW_0481/0/2010:2019No text annotation
homologous
HL_7A0S_049
HL_61996.2
HL_1NKW_0491/0/2188:2197No text annotation
HL_1NKW_0501/0/2227:2235No text annotation
homologous
HL_7A0S_052
HL_85367.2
HL_1NKW_0511/0/2243:2255No text annotation
homologous
HL_4WF9_050
HL_91939.2
HL_1NKW_0521/0/2282:2292No text annotation
HL_1NKW_0531/0/2303:2310Pseudoknot geometry
homologous
HL_7A0S_055
HL_93324.4
HL_1NKW_0541/0/2334:2341No text annotation
geometric
HL_7VTI_001
HL_48417.5
HL_1NKW_0551/0/2353:2358GNRA
homologous
HL_4WF9_054
HL_37824.7
HL_1NKW_0561/0/2383:2392No text annotation
homologous
HL_4WF9_055
HL_53454.2
HL_1NKW_0571/0/2450:2458No text annotation
homologous
HL_4WF9_056
HL_32735.2
HL_1NKW_0761/0/2507:2514No text annotation
homologous
HL_7A0S_060
HL_31585.4
HL_1NKW_0591/0/2530:2536No text annotation
homologous
HL_7A0S_061
HL_30068.2
HL_1NKW_0601/0/2573:2578GNRA
homologous
HL_7A0S_062
HL_37824.7
HL_1NKW_0611/0/2637:2642GNRA
homologous
HL_7RQB_064
NA
HL_1NKW_0771/0/2680:2685Ribsomal LSU H95
homologous
HL_7A0S_064
HL_65794.5
HL_1NKW_0631/0/2725:2739No text annotation
homologous
HL_7A0S_065
HL_74055.2
HL_1NKW_0651/0/2794:2802No text annotation
geometric
HL_7RQB_068
NA
HL_1NKW_0661/0/2831:2836GNRA
geometric
HL_5J7L_004
HL_37824.7
HL_1NKW_0671/9/35:51No text annotation
HL_1NKW_0681/9/88:93GNRA
homologous
HL_7A0S_070
HL_37824.7

Problematic loops

#loop idProblemSequence
HL_1NKW_001No text annotation
HL_1NKW_007No text annotation
HL_1NKW_011No text annotation
HL_1NKW_071No text annotation
HL_1NKW_018No text annotation
HL_1NKW_021No text annotation
HL_1NKW_024No text annotation
HL_1NKW_073No text annotation
HL_1NKW_034No text annotation
HL_1NKW_046No text annotation
HL_1NKW_075No text annotation
HL_1NKW_058tRNA anticodon loop
HL_1NKW_062No text annotation
HL_1NKW_064No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_1NKW_0011/0/24:30,
1/0/520:526		Triple sheared with non-canonical cWW
homologous
IL_7A0S_001
IL_04021.2
IL_1NKW_0021/0/36:37,
1/0/454:456		Single bulged A
homologous
IL_7A0S_002
IL_31462.6
IL_1NKW_0041/0/42:43,
1/0/447:449		Minor groove platform
homologous
IL_7RQB_003
NA
IL_1NKW_0051/0/80:84,
1/0/96:103		Kink-turn
homologous
IL_7A0S_004
IL_94910.1
IL_1NKW_0061/0/160:161,
1/0/189:191		Single stack bend
homologous
IL_7A0S_005
IL_90729.1
IL_1NKW_0071/0/165:172,
1/0/177:185		9x8 Sarcin-Ricin with GA cWW pair; G-bulge
geometric
IL_3DIL_003
IL_34470.3
IL_1NKW_0091/0/215:222,
1/0/230:236		8x7 Sarcin-Ricin; G-bulge
homologous
IL_7A0S_007
IL_04346.10
IL_1NKW_0101/0/299:301,
1/0/361:363		No text annotation
IL_1NKW_0111/0/303:306,
1/0/354:359		No text annotation
homologous
IL_7A0S_008
IL_05192.4
IL_1NKW_0151/0/573:575,
1/0/584:586		Isolated non-canonical cWW pair
geometric
IL_7A0S_011
IL_07785.1
IL_1NKW_0161/0/600:602,
1/0/678:679		Single bulged A
homologous
IL_7A0S_012
IL_31462.6
IL_1NKW_1391/0/614:620,
1/0/629:635		No text annotation
IL_1NKW_0181/0/615:620,
1/0/629:634		No text annotation
IL_1NKW_0191/0/685:687,
1/0/819:821		Isolated non-canonical cWW pair
geometric
IL_4KNQ_002
IL_87907.2
IL_1NKW_0201/0/687:691,
1/0/812:819		tHW-tHW cross-strand stack
homologous
IL_7A0S_015
IL_54041.2
IL_1NKW_0221/0/715:716,
1/0/741:743		Single bulged G
homologous
IL_5J7L_262
IL_00225.13
IL_1NKW_0231/0/716:721,
1/0/736:741		Triple sheared with non-canonical cWW
geometric
IL_7A0S_018
IL_06136.2
IL_1NKW_0241/0/751:754,
1/0/769:771		Major groove platform with extra cWW
homologous
IL_7RQB_022
NA
IL_1NKW_0251/0/754:756,
1/0/767:769		Isolated non-canonical cWW pair
geometric
IL_4LFB_010
IL_87907.2
IL_1NKW_0271/0/850:851,
1/0/951:953		Single stack bend
geometric
IL_7A0S_022
IL_90729.1
IL_1NKW_0291/0/857:860,
1/0/944:945		Multiple bulged bases
geometric
IL_4V9F_021
IL_82107.4
IL_1NKW_1581/0/860:861,
1/0/942:944		No text annotation
IL_1NKW_0311/0/863:864,
1/0/938:940		Single stack bend
homologous
IL_5J7L_269
IL_26793.1
IL_1NKW_0321/0/864:866,
1/0/936:938		Isolated non-canonical cWW pair
geometric
IL_3MEI_002
IL_87907.2
IL_1NKW_1591/0/871:875,
1/0/927:931		No text annotation
IL_1NKW_0341/0/875:877,
1/0/924:927		Isolated non-canonical cWW with bulges
geometric
IL_4PKD_001
IL_07785.1
IL_1NKW_1601/0/877:881,
1/0/921:924		C-loop with bulged stacked A's
homologous
IL_7A0S_029
IL_26222.2
IL_1NKW_1611/0/883:885,
1/0/917:919		Isolated near basepair
homologous
IL_7A0S_030
IL_42997.3
IL_1NKW_0381/0/963:965,
1/0/974:976		Isolated non-canonical cWW pair
homologous
IL_7A0S_031
IL_87907.2
IL_1NKW_1621/0/1005:1007,
1/0/1170:1171		Single bulged C
homologous
IL_7A0S_032
IL_61258.15
IL_1NKW_0401/0/1009:1013,
1/0/1164:1168		UAA/GAN
homologous
IL_7A0S_033
IL_38507.2
IL_1NKW_0411/0/1015:1022,
1/0/1161:1162		SSU/LSU pseudoknot
homologous
IL_7A0S_034
IL_41203.4
IL_1NKW_0421/0/1022:1024,
1/0/1160:1161		Single bulged U
geometric
IL_5J7L_279
IL_89505.4
IL_1NKW_0431/0/1029:1035,
1/0/1150:1155		Kink-turn related
homologous
IL_4WF9_039
IL_57188.5
IL_1NKW_1371/0/1035:1041,
1/0/1135:1150		No text annotation
homologous
IL_9DFE_039
IL_50715.3
IL_1NKW_0441/0/1042:1045,
1/0/1132:1134		Isolated non-canonical cWW pair
homologous
IL_7RQB_041
NA
IL_1NKW_0461/0/1054:1062,
1/0/1120:1123		No text annotation
IL_1NKW_0471/0/1062:1063,
1/0/1118:1120		Single stack bend
geometric
IL_5J7L_044
IL_26793.1
IL_1NKW_0491/0/1070:1073,
1/0/1087:1090		No text annotation
IL_1NKW_1631/0/1210:1212,
1/0/1260:1263		Isolated cWS basepair
homologous
IL_4WF9_044
IL_42997.3
IL_1NKW_0521/0/1218:1220,
1/0/1252:1254		Isolated cWH basepair
homologous
IL_4WF9_045
IL_10167.6
IL_1NKW_0531/0/1221:1228,
1/0/1247:1251		Kink-turn
homologous
IL_7A0S_043
IL_70923.9
IL_1NKW_1641/0/1232:1234,
1/0/1241:1243		Intercalated cWW
homologous
IL_7A0S_044
IL_31737.3
IL_1NKW_0551/0/1275:1282,
1/0/1994:2000		8x7 Sarcin-Ricin; G-bulge
homologous
IL_7RQB_049
NA
IL_1NKW_0561/0/1332:1336,
1/0/1344:1346		C-loop
homologous
IL_7A0S_047
IL_83150.2
IL_1NKW_0571/0/1364:1368,
1/0/1389:1393		UAA/GAN
homologous
IL_7RQB_052
NA
IL_1NKW_0581/0/1370:1374,
1/0/1383:1387		tSH-tHW-tHS
homologous
IL_7A0S_049
IL_17136.7
IL_1NKW_0601/0/1426:1430,
1/0/1598:1605		Kink-turn
homologous
IL_7A0S_050
IL_69229.3
IL_1NKW_0611/0/1431:1437,
1/0/1591:1597		No text annotation
IL_1NKW_1651/0/1438:1443,
1/0/1580:1590		No text annotation
IL_1NKW_0621/0/1447:1449,
1/0/1573:1576		No text annotation
homologous
IL_7A0S_052
IL_14688.1
IL_1NKW_0631/0/1451:1454,
1/0/1567:1571		tSH-tHW
homologous
IL_7A0S_053
IL_99646.2
IL_1NKW_0641/0/1463:1465,
1/0/1477:1478		Single stack bend
homologous
IL_7RQB_058
NA
IL_1NKW_0651/0/1483:1485,
1/0/1538:1539		Single stack bend
geometric
IL_4V9F_005
IL_90729.1
IL_1NKW_0661/0/1488:1490,
1/0/1534:1535		Single bulged C
homologous
IL_7A0S_055
IL_61258.15
IL_1NKW_0671/0/1490:1492,
1/0/1530:1534		No text annotation
IL_1NKW_1441/0/1490:1498,
1/0/1522:1534		No text annotation
IL_1NKW_0691/0/1503:1508,
1/0/1514:1517		No text annotation
IL_1NKW_0701/0/1668:1673,
1/0/1987:1989		No text annotation
homologous
IL_5J7L_304
IL_12566.4
IL_1NKW_0711/0/1680:1683,
1/0/1977:1980		No text annotation
IL_1NKW_1451/0/1680:1686,
1/0/1976:1980		No text annotation
IL_1NKW_1461/0/1680:1691,
1/0/1973:1980		No text annotation
IL_1NKW_0721/0/1683:1686,
1/0/1976:1977		Major groove platform; stack outside cWW
geometric
IL_4V9F_008
IL_50694.7
IL_1NKW_0731/0/1686:1691,
1/0/1973:1976		Intercalated tWH
homologous
IL_7RQB_067
NA
IL_1NKW_0741/0/1703:1708,
1/0/1713:1719		tSH-tSH-tHH-tHS
geometric
IL_4WF9_066
IL_47346.2
IL_1NKW_0751/0/1760:1762,
1/0/1963:1966		Isolated non-canonical cWW pair
geometric
IL_4V9F_105
IL_87907.2
IL_1NKW_1661/0/1789:1795,
1/0/1805:1813		Kink-turn related
homologous
IL_4WF9_069
IL_17069.5
IL_1NKW_0781/0/1829:1832,
1/0/1885:1886		Minor groove platform, major groove intercalation
homologous
IL_5J7L_314
IL_95583.2
IL_1NKW_0791/0/1833:1835,
1/0/1880:1884		Isolated non-canonical cWW with bulges
geometric
IL_5ML7_010
IL_07785.1
IL_1NKW_0801/0/1838:1841,
1/0/1876:1877		Major groove minor groove platform; mini C-loop
homologous
IL_7A0S_068
IL_68140.4
IL_1NKW_0811/0/1842:1848,
1/0/1869:1875		No text annotation
IL_1NKW_0821/0/1848:1852,
1/0/1865:1869		Triple sheared
geometric
IL_5J7L_274
IL_17948.2
IL_1NKW_1481/0/1893:1894,
1/0/1901:1903		No text annotation
geometric
IL_8VTW_057
NA
IL_1NKW_1671/0/1916:1928,
1/0/1944:1950		No text annotation
IL_1NKW_0871/0/2033:2035,
1/0/2596:2597		Major groove platform
homologous
IL_7A0S_073
IL_48076.6
IL_1NKW_1681/0/2037:2040,
1/0/2590:2594		No text annotation
homologous
IL_7A0S_074
IL_70335.1
IL_1NKW_0881/0/2050:2052,
1/0/2421:2422		Single bulged U
homologous
IL_4WF9_080
IL_89505.4
IL_1NKW_0891/0/2053:2054,
1/0/2417:2420		Minor groove platform
homologous
IL_7A0S_076
IL_51454.3
IL_1NKW_1691/0/2064:2066,
1/0/2215:2218		Isolated tHS basepair with bulges
homologous
IL_7A0S_077
IL_85599.2
IL_1NKW_1501/0/2068:2070,
1/0/2211:2213		Isolated non-canonical cWW pair
homologous
IL_7A0S_078
IL_28037.2
IL_1NKW_0961/0/2091:2093,
1/0/2162:2164		Not an internal loop
geometric
IL_5VCI_005
NA
IL_1NKW_1031/0/2276:2278,
1/0/2296:2300		Isolated tHS basepair with bulges
homologous
IL_7A0S_080
IL_61476.2
IL_1NKW_1041/0/2329:2332,
1/0/2343:2346		Double sheared
homologous
IL_7A0S_081
IL_09705.15
IL_1NKW_1051/0/2380:2382,
1/0/2393:2394		Major groove platform
homologous
IL_7A0S_082
IL_48076.6
IL_1NKW_1061/0/2432:2433,
1/0/2477:2479		Single stack bend
homologous
IL_9DFE_091
IL_26793.1
IL_1NKW_1511/0/2432:2434,
1/0/2475:2479		No text annotation
homologous
IL_5J7L_335
NA
IL_1NKW_1071/0/2433:2434,
1/0/2475:2477		Major groove platform
homologous
IL_5J7L_392
IL_48076.6
IL_1NKW_1081/0/2436:2438,
1/0/2472:2473		No text annotation
IL_1NKW_1521/0/2436:2440,
1/0/2468:2473		No text annotation
IL_1NKW_1091/0/2438:2440,
1/0/2468:2472		No text annotation
IL_1NKW_1101/0/2445:2449,
1/0/2459:2463		Triple sheared
homologous
IL_7A0S_087
IL_17948.2
IL_1NKW_1111/0/2486:2487,
1/0/2559:2561		Major groove platform
homologous
IL_7A0S_088
IL_07039.3
IL_1NKW_1121/0/2489:2491,
1/0/2553:2557		Isolated non-canonical cWW with bulges
homologous
IL_7A0S_089
IL_07785.1
IL_1NKW_1131/0/2491:2492,
1/0/2550:2553		No text annotation
geometric
IL_4WF9_096
IL_42626.2
IL_1NKW_1151/0/2501:2502,
1/0/2519:2522		Major groove platform with intercalation
homologous
IL_7RQB_099
NA
IL_1NKW_1161/0/2570:2571,
1/0/2580:2582		Single bulged A
homologous
IL_7RQB_101
NA
IL_1NKW_1541/0/2615:2619,
1/0/2754:2762		tSH-tHS-tHW
homologous
IL_7A0S_093
IL_04638.3
IL_1NKW_1191/0/2631:2637,
1/0/2642:2647		7x6 Sarcin-Ricin; G-bulge
geometric
IL_4V9F_019
IL_16458.4
IL_1NKW_1201/0/2659:2663,
1/0/2705:2707		C-loop
geometric
IL_4WF9_101
IL_63596.11
IL_1NKW_1221/0/2666:2670,
1/0/2698:2702		No text annotation
homologous
IL_7A0S_096
IL_23774.1
IL_1NKW_1231/0/2674:2675,
1/0/2690:2694		Multiple bulged bases
homologous
IL_7RQB_106
NA
IL_1NKW_1241/0/2717:2722,
1/0/2742:2747		UAA/GAN with extra cWW
homologous
IL_7RQB_107
NA
IL_1NKW_1561/0/2813:2814,
1/0/2853:2855		Major groove intercalation
homologous
IL_7A0S_099
IL_00225.13
IL_1NKW_1271/0/2818:2820,
1/0/2846:2849		Decoding loop related
homologous
IL_7A0S_100
IL_31531.3
IL_1NKW_1701/0/2822:2827,
1/0/2840:2844		No text annotation
homologous
IL_7A0S_101
IL_70411.2
IL_1NKW_1311/9/19:21,
1/9/66:69		Isolated non-canonical cWW pair
geometric
IL_1U6B_001
IL_57744.1
IL_1NKW_1331/9/25:30,
1/9/58:62		No text annotation
IL_1NKW_1571/9/25:31,
1/9/57:62		No text annotation
IL_1NKW_1341/9/32:33,
1/9/53:56		Minor groove platform
homologous
IL_5TBW_374
NA
IL_1NKW_1351/9/73:81,
1/9/100:108		Bacterial 5S Loop E
geometric
IL_364D_003
IL_56455.6
IL_1NKW_1361/9/82:84,
1/9/97:99		Isolated non-canonical cWW pair
homologous
IL_7A0S_107
IL_07785.1

Problematic loops

#loop idProblemSequence
IL_1NKW_138Isolated non-canonical cWW pair
IL_1NKW_003No text annotation
IL_1NKW_008Isolated non-canonical cWW pair
IL_1NKW_012Isolated non-canonical cWW pair
IL_1NKW_013Isolated non-canonical cWW pair
IL_1NKW_014Isolated non-canonical cWW pair
IL_1NKW_017Isolated non-canonical cWW pair
IL_1NKW_021Tandem non-canonical cWW pairs
IL_1NKW_140No text annotation
IL_1NKW_026No text annotation
IL_1NKW_141No text annotation
IL_1NKW_028Isolated non-canonical cWW pair
IL_1NKW_030No text annotation
IL_1NKW_033No text annotation
IL_1NKW_035No text annotation
IL_1NKW_036No text annotation
IL_1NKW_037Isolated non-canonical cWW pair
IL_1NKW_039Isolated cWS basepair
IL_1NKW_045No text annotation
IL_1NKW_048No text annotation
IL_1NKW_050Tandem non-canonical cWW pairs
IL_1NKW_051Isolated non-canonical cWW pair
IL_1NKW_054No text annotation
IL_1NKW_142UAA/GAN with extra cWW
IL_1NKW_059No text annotation
IL_1NKW_143No text annotation
IL_1NKW_068Isolated non-canonical cWW pair
IL_1NKW_076Isolated cWH basepair
IL_1NKW_077No text annotation
IL_1NKW_147No text annotation
IL_1NKW_083Isolated non-canonical cWW pair
IL_1NKW_084Isolated non-canonical cWW pair
IL_1NKW_149No text annotation
IL_1NKW_085No text annotation
IL_1NKW_086Isolated cWH basepair
IL_1NKW_090Double sheared
IL_1NKW_091Isolated cWH basepair
IL_1NKW_092Tandem non-canonical cWW pairs
IL_1NKW_093Isolated cWH basepair
IL_1NKW_094Isolated non-canonical cWW pair
IL_1NKW_095No text annotation
IL_1NKW_097No text annotation
IL_1NKW_098Isolated non-canonical cWW pair
IL_1NKW_099Isolated non-canonical cWW pair
IL_1NKW_100No text annotation
IL_1NKW_101Isolated non-canonical cWW pair
IL_1NKW_102Isolated cWH basepair
IL_1NKW_153No text annotation
IL_1NKW_114No text annotation
IL_1NKW_117No text annotation
IL_1NKW_118Tandem non-canonical cWW pairs
IL_1NKW_155C-loop with extra cWW pair
IL_1NKW_121Isolated non-canonical cWW pair
IL_1NKW_125Isolated cWH basepair
IL_1NKW_126Isolated non-canonical cWW with bulges
IL_1NKW_128No text annotation
IL_1NKW_129Isolated non-canonical cWW pair
IL_1NKW_130Isolated cWH basepair
IL_1NKW_132No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_1NKW_0131/0/30:31,
1/0/485:495,
1/0/506:520		No text annotation
homologous
J3_4WF9_011
J3_92134.2
J3_1NKW_0141/0/32:35,
1/0/457:472,
1/0/479:484		No text annotation
homologous
J3_7A0S_016
J3_30040.2
J3_1NKW_0101/0/55:56,
1/0/69:75,
1/0/108:112		No text annotation
homologous
J3_5J7L_037
J3_35667.2
J3_1NKW_0151/0/611:614,
1/0/635:639,
1/0/646:669		No text annotation
J3_1NKW_0011/0/696:702,
1/0/786:790,
1/0/800:807		No text annotation
J3_1NKW_0021/0/710:713,
1/0/745:749,
1/0/773:778		No text annotation
geometric
J3_5TBW_005
NA
J3_1NKW_0031/0/1066:1068,
1/0/1092:1102,
1/0/1111:1115		No text annotation
J3_1NKW_0041/0/1311:1316,
1/0/1641:1643,
1/0/1656:1659		No text annotation
homologous
J3_7A0S_006
J3_32852.6
J3_1NKW_0051/0/1319:1322,
1/0/1621:1627,
1/0/1636:1638		No text annotation
homologous
J3_7A0S_007
J3_71677.1
J3_1NKW_0171/0/1323:1327,
1/0/1351:1358,
1/0/1617:1620		No text annotation
J3_1NKW_0111/0/1357:1363,
1/0/1394:1398,
1/0/1415:1416		No text annotation
homologous
J3_7RQB_009
NA
J3_1NKW_0201/0/2074:2076,
1/0/2179:2183,
1/0/2202:2207		Kink-turn in J3
homologous
J3_5J7L_044
J3_89368.5
J3_1NKW_0071/0/2274:2276,
1/0/2300:2303,
1/0/2310:2316		No text annotation
J3_1NKW_0181/0/2274:2278,
1/0/2296:2303,
1/0/2310:2316		No text annotation
J3_1NKW_0081/0/2496:2499,
1/0/2524:2526,
1/0/2540:2546		No text annotation
homologous
J3_7RQB_012
NA
J3_1NKW_0121/0/2789:2790,
1/0/2806:2811,
1/0/2857:2861		No text annotation
homologous
J3_7A0S_013
J3_76911.2
J3_1NKW_0211/9/12:18,
1/9/70:71,
1/9/110:113		No text annotation
homologous
J3_7A0S_021
J3_47324.1
J4_1NKW_0011/0/308:312,
1/0/327:330,
1/0/334:336,
1/0/348:352		No text annotation
homologous
J4_7A0S_002
J4_71729.5
J4_1NKW_0021/0/1283:1289,
1/0/1307:1308,
1/0/1662:1665,
1/0/1992:1993		No text annotation
homologous
J4_7A0S_004
J4_64571.5
J4_1NKW_0031/0/1361:1363,
1/0/1394:1398,
1/0/1415:1418,
1/0/1613:1614		No text annotation
J4_1NKW_0041/0/1458:1460,
1/0/1481:1485,
1/0/1538:1545,
1/0/1558:1563		No text annotation
J4_1NKW_0051/0/1763:1767,
1/0/1779:1783,
1/0/1819:1822,
1/0/1958:1962		No text annotation
homologous
J4_7A0S_008
J4_61477.5
J4_1NKW_0061/0/1825:1827,
1/0/1888:1889,
1/0/1907:1916,
1/0/1950:1955		No text annotation
homologous
J4_5J7L_026
J4_93343.1
J4_1NKW_0071/0/2264:2269,
1/0/2321:2326,
1/0/2349:2351,
1/0/2360:2362		No text annotation
J4_1NKW_0081/0/2622:2625,
1/0/2653:2655,
1/0/2711:2716,
1/0/2748:2751		No text annotation
homologous
J4_7A0S_010
J4_54165.1
J5_1NKW_0011/0/46:53,
1/0/114:119,
1/0/128:129,
1/0/142:144,
1/0/153:155		No text annotation
homologous
J5_4WF9_001
J5_01737.2
J5_1NKW_0051/0/593:598,
1/0/681:684,
1/0/822:825,
1/0/1209:1210,
1/0/1263:1269		No text annotation
homologous
J5_7A0S_004
J5_74302.5
J5_1NKW_0061/0/1691:1700,
1/0/1722:1724,
1/0/1742:1743,
1/0/1747:1755,
1/0/1971:1973		No text annotation
J5_1NKW_0071/0/2040:2047,
1/0/2425:2432,
1/0/2479:2486,
1/0/2561:2567,
1/0/2585:2590		No text annotation
J6_1NKW_0011/0/44:45,
1/0/156:160,
1/0/191:201,
1/0/208:212,
1/0/239:243,
1/0/439:446		No text annotation
J6_1NKW_0021/0/2057:2061,
1/0/2221:2225,
1/0/2237:2238,
1/0/2260:2263,
1/0/2363:2374,
1/0/2400:2414		No text annotation
J7_1NKW_0021/0/829:835,
1/0/848:849,
1/0/954:957,
1/0/982:987,
1/0/998:1002,
1/0/1174:1178,
1/0/1196:1205		No text annotation
J11_1NKW_0021/0/8:16,
1/0/534:543,
1/0/569:573,
1/0/586:588,
1/0/1274:1275,
1/0/2000:2006,
1/0/2023:2026,
1/0/2604:2609,
1/0/2768:2771,
1/0/2781:2786,
1/0/2864:2869		No text annotation

Problematic loops

#loop idProblemSequence
J3_1NKW_016No text annotation
J3_1NKW_006No text annotation
J3_1NKW_019No text annotation
J3_1NKW_009No text annotation
J5_1NKW_002No text annotation
J5_1NKW_003No text annotation
J5_1NKW_004No text annotation
J7_1NKW_001No text annotation
J11_1NKW_001No text annotation

Coloring options:
Copyright 2025 BGSU RNA group. Page generated in 0.1059 s
Application loaded.