RNA 3D Hub //

7ODE Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_7ODE_0011/I/59:68No text annotation
geometric
HL_5J7L_134
NA
HL_7ODE_0021/I/87:95No text annotation
geometric
HL_5J7L_135
NA
HL_7ODE_0031/I/123:128No text annotation
geometric
HL_4WF9_003
HL_75660.7
HL_7ODE_0041/I/137:142UNCG
geometric
HL_4AY2_001
HL_61337.3
HL_7ODE_0051/I/158:168No text annotation
geometric
HL_5J7L_138
NA
HL_7ODE_0061/I/225:230UNCG variation
geometric
HL_1P6V_001
NA
HL_7ODE_0081/I/305:312T-loop with 2 stacked bulged bases
geometric
HL_5J7L_142
NA
HL_7ODE_0091/I/319:323No text annotation
geometric
HL_5J7L_143
NA
HL_7ODE_0101/I/327:335T-loop with unstacked turn
geometric
HL_5J7L_144
NA
HL_7ODE_0131/I/462:467GNRA
geometric
HL_4WF9_015
HL_34789.3
HL_7ODE_0141/I/487:493GNRA
geometric
HL_5J7L_148
NA
HL_7ODE_0491/I/567:574GNRA
geometric
HL_8C3A_042
NA
HL_7ODE_0171/I/611:617No text annotation
geometric
HL_5J7L_151
NA
HL_7ODE_0181/I/712:719GNRA wlth tandem sheared
geometric
HL_5J7L_154
NA
HL_7ODE_0191/I/744:753No text annotation
geometric
HL_5TBW_020
NA
HL_7ODE_0201/I/779:785No text annotation
geometric
HL_5J7L_156
NA
HL_7ODE_0231/I/978:985No text annotation
geometric
HL_5TBW_006
NA
HL_7ODE_0251/I/1222:1227GNRA
geometric
HL_5J7L_164
NA
HL_7ODE_0261/I/1281:1289T-loop with 2 stacked bulged bases
geometric
HL_5J7L_165
NA
HL_7ODE_0271/I/1324:1330Pseudoknot geometry with 3' bulge
geometric
HL_5J7L_166
NA
HL_7ODE_0281/I/1363:1368GNRA
geometric
HL_3NVI_002
NA
HL_7ODE_0291/I/1389:1398No text annotation
geometric
HL_5J7L_168
NA
HL_7ODE_0301/I/1451:1459Mini UNCG with extended bulge
geometric
HL_7A0S_017
HL_90436.3
HL_7ODE_0311/I/1492:1498Pseudoknot geometry with 3' bulge
geometric
HL_5J7L_170
NA
HL_7ODE_0331/I/1565:1568No text annotation
geometric
HL_7RQB_039
NA
HL_7ODE_0341/I/1612:1619No text annotation
geometric
HL_7RQB_040
NA
HL_7ODE_0351/I/1630:1636GNRA
geometric
HL_5J7L_174
NA
HL_7ODE_0361/I/1691:1696UNCG
geometric
HL_5D5L_003
HL_61337.3
HL_7ODE_0381/I/1752:1756No text annotation
geometric
HL_4WF9_042
HL_80709.5
HL_7ODE_0391/I/1777:1787No text annotation
geometric
HL_4WF9_043
HL_87681.1
HL_7ODE_0401/I/1806:1811GNRA
geometric
HL_4FRG_002
HL_34789.3
HL_7ODE_0441/I/2658:2663GNRA
geometric
HL_3P22_001
HL_34789.3
HL_7ODE_0451/I/2701:2706Ribsomal LSU H95
geometric
HL_5J7L_198
NA
HL_7ODE_0461/I/2795:2801No text annotation
geometric
HL_5J7L_018
NA
HL_7ODE_0471/I/2819:2827No text annotation
geometric
HL_5J7L_201
NA
HL_7ODE_0481/I/2856:2861GNRA
geometric
HL_5J7L_202
NA

Problematic loops

#loop idProblemSequence
HL_7ODE_007GNRA related
HL_7ODE_011No text annotation
HL_7ODE_012No text annotation
HL_7ODE_015No text annotation
HL_7ODE_016GNRA wlth extra near cWW
HL_7ODE_021No text annotation
HL_7ODE_022No text annotation
HL_7ODE_024No text annotation
HL_7ODE_032No text annotation
HL_7ODE_037No text annotation
HL_7ODE_041No text annotation
HL_7ODE_042No text annotation
HL_7ODE_043No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_7ODE_0011/I/24:30,
1/I/510:516		Triple sheared with non-canonical cWW
geometric
IL_4WF9_001
IL_22311.1
IL_7ODE_0021/I/36:37,
1/I/442:444		Single bulged A
geometric
IL_7RQB_002
NA
IL_7ODE_0031/I/43:44,
1/I/434:436		Minor groove platform
geometric
IL_7RQB_003
NA
IL_7ODE_0041/I/81:85,
1/I/97:105		No text annotation
geometric
IL_5J7L_248
NA
IL_7ODE_0051/I/183:184,
1/I/212:214		Single stack bend
geometric
IL_4WF9_007
IL_15011.2
IL_7ODE_0061/I/188:194,
1/I/201:208		8x7 Sarcin-Ricin; G-bulge
geometric
IL_7RQB_006
NA
IL_7ODE_0071/I/239:245,
1/I/253:258		7x6 Sarcin-Ricin; G-bulge
geometric
IL_7RQB_007
NA
IL_7ODE_0081/I/269:271,
1/I/366:370		No text annotation
geometric
IL_5J7L_252
NA
IL_7ODE_0091/I/274:281,
1/I/359:363		No text annotation
geometric
IL_5J7L_253
NA
IL_7ODE_0101/I/293:295,
1/I/343:347		No text annotation
geometric
IL_5J7L_254
NA
IL_7ODE_0111/I/481:484,
1/I/496:509		No text annotation
geometric
IL_5J7L_255
NA
IL_7ODE_0121/I/536:539,
1/I/554:557		Double sheared
geometric
IL_5J7L_256
NA
IL_7ODE_0131/I/564:566,
1/I/575:577		Isolated non-canonical cWW pair
geometric
IL_4WF9_017
IL_71625.2
IL_7ODE_0151/I/606:610,
1/I/618:622		AAA cross-strand stack
geometric
IL_5J7L_258
NA
IL_7ODE_0171/I/697:698,
1/I/763:765		Single bulged A
geometric
IL_5J7L_261
NA
IL_7ODE_0181/I/702:703,
1/I/728:730		Single bulged G
geometric
IL_4V9F_026
IL_28408.2
IL_7ODE_0191/I/703:707,
1/I/724:728		Triple sheared
geometric
IL_4V9F_027
IL_15190.2
IL_7ODE_0201/I/738:740,
1/I/757:758		Major groove platform
geometric
IL_4LFB_024
IL_48076.8
IL_7ODE_0211/I/775:777,
1/I/787:791		Multiple bulged bases
geometric
IL_5J7L_265
NA
IL_7ODE_0221/I/844:847,
1/I/933:934		90 degree turn
geometric
IL_5J7L_267
NA
IL_7ODE_0691/I/844:852,
1/I/925:934		No text annotation
IL_7ODE_0231/I/847:848,
1/I/930:933		Stack outside cWW
geometric
IL_5J7L_268
NA
IL_7ODE_0701/I/847:852,
1/I/925:933		No text annotation
IL_7ODE_0241/I/848:853,
1/I/924:930		No text annotation
IL_7ODE_0251/I/994:996,
1/I/1159:1160		Single bulged C
geometric
IL_5J7L_276
NA
IL_7ODE_0261/I/998:1002,
1/I/1153:1157		UAA/GAN
geometric
IL_4WF9_036
IL_08938.1
IL_7ODE_0271/I/1004:1011,
1/I/1150:1151		SSU/LSU pseudoknot
geometric
IL_5J7L_278
NA
IL_7ODE_0281/I/1011:1013,
1/I/1149:1150		Single bulged U
geometric
IL_5J7L_279
NA
IL_7ODE_0291/I/1018:1024,
1/I/1140:1144		Kink-turn related
geometric
IL_5J7L_280
NA
IL_7ODE_0301/I/1196:1198,
1/I/1247:1250		Isolated cWS basepair
geometric
IL_5J7L_286
NA
IL_7ODE_0311/I/1202:1206,
1/I/1240:1243		No text annotation
geometric
IL_5J7L_287
NA
IL_7ODE_0321/I/1208:1215,
1/I/1234:1238		Kink-turn
geometric
IL_5J7L_288
NA
IL_7ODE_0331/I/1262:1269,
1/I/2011:2017		8x7 Sarcin-Ricin; G-bulge
geometric
IL_5J7L_289
NA
IL_7ODE_0341/I/1310:1313,
1/I/1603:1604		Major groove platform; stack outside cWW
geometric
IL_7RQB_050
NA
IL_7ODE_0351/I/1319:1323,
1/I/1331:1333		C-loop
geometric
IL_5J7L_291
NA
IL_7ODE_0361/I/1351:1355,
1/I/1376:1380		UAA/GAN
geometric
IL_5J7L_292
NA
IL_7ODE_0371/I/1357:1361,
1/I/1370:1374		tSH-tHW-tHS
geometric
IL_5J7L_293
NA
IL_7ODE_0391/I/1417:1421,
1/I/1577:1581		UAA/GAN
geometric
IL_5J7L_295
NA
IL_7ODE_0401/I/1432:1435,
1/I/1557:1561		Tandem non-canonical cWW pairs
geometric
IL_5J7L_296
NA
IL_7ODE_0411/I/1437:1440,
1/I/1551:1555		tSH-tHW
geometric
IL_5J7L_297
NA
IL_7ODE_0421/I/1450:1451,
1/I/1459:1461		Single bulged U
geometric
IL_5J7L_298
NA
IL_7ODE_0431/I/1468:1471,
1/I/1520:1524		No text annotation
geometric
IL_5J7L_299
NA
IL_7ODE_0441/I/1474:1478,
1/I/1513:1517		tSH-tHW-tHS
geometric
IL_5J7L_300
NA
IL_7ODE_0451/I/1481:1482,
1/I/1507:1510		180 degree turn
homologous
IL_5J7L_301
NA
IL_7ODE_0461/I/1489:1491,
1/I/1499:1500		Single bulged A
geometric
IL_5J7L_302
NA
IL_7ODE_0471/I/1526:1529,
1/I/1542:1546		UAA/GAN variation
geometric
IL_5J7L_303
NA
IL_7ODE_0481/I/1651:1656,
1/I/2004:2006		No text annotation
geometric
IL_7RQB_064
NA
IL_7ODE_0491/I/1663:1665,
1/I/1995:1997		Isolated tWW turn
geometric
IL_5J7L_305
NA
IL_7ODE_0501/I/1666:1669,
1/I/1993:1994		Major groove platform; stack outside cWW
geometric
IL_7RQB_066
NA
IL_7ODE_0711/I/1666:1674,
1/I/1990:1994		No text annotation
homologous
IL_4WF9_117
IL_80252.1
IL_7ODE_0511/I/1669:1674,
1/I/1990:1993		Intercalated tWH
geometric
IL_4WF9_065
IL_28217.1
IL_7ODE_0521/I/1686:1691,
1/I/1696:1702		tSH-tSH-tHH-tHS
geometric
IL_5J7L_308
NA
IL_7ODE_0531/I/1712:1718,
1/I/1742:1746		6x5 Sarcin-Ricin; G-bulge
geometric
IL_5J7L_309
NA
IL_7ODE_0541/I/1720:1724,
1/I/1736:1740		Triple sheared
geometric
IL_5J7L_310
NA
IL_7ODE_0551/I/1770:1771,
1/I/1980:1982		Single bulged A
geometric
IL_4WF9_068
IL_14190.2
IL_7ODE_0561/I/1798:1804,
1/I/1813:1821		Kink-turn related
geometric
IL_5J7L_313
NA
IL_7ODE_0571/I/2050:2052,
1/I/2617:2618		Major groove platform
geometric
IL_7RQB_078
NA
IL_7ODE_0581/I/2202:2204,
1/I/2220:2221		Single bulged U
geometric
IL_5J7L_331
NA
IL_7ODE_0591/I/2636:2640,
1/I/2774:2782		tSH-tHS-tHW
geometric
IL_4WF9_099
IL_04638.4
IL_7ODE_0601/I/2652:2658,
1/I/2663:2668		Sarcin-Ricin target in LSU H95; G-bulge
geometric
IL_7RQB_103
NA
IL_7ODE_0611/I/2680:2684,
1/I/2725:2727		C-loop
geometric
IL_5J7L_347
NA
IL_7ODE_0621/I/2687:2691,
1/I/2718:2722		UAA/GAN related, with intercalation
geometric
IL_5J7L_348
NA
IL_7ODE_0631/I/2695:2696,
1/I/2711:2714		Multiple bulged bases
geometric
IL_5J7L_349
NA
IL_7ODE_0651/I/2806:2811,
1/I/2889:2892		No text annotation
geometric
IL_5J7L_351
NA
IL_7ODE_0661/I/2838:2839,
1/I/2878:2880		Major groove intercalation
geometric
IL_4WF9_112
IL_14190.2
IL_7ODE_0671/I/2843:2846,
1/I/2870:2874		Multiple bulged bases with non-canonical cWW
geometric
IL_5J7L_353
NA
IL_7ODE_0681/I/2847:2852,
1/I/2865:2869		tHS double platform
geometric
IL_7RQB_110
NA

Problematic loops

#loop idProblemSequence
IL_7ODE_014No text annotation
IL_7ODE_016No text annotation
IL_7ODE_038No text annotation
IL_7ODE_064No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_7ODE_0011/I/30:31,
1/I/474:481,
1/I/509:510		No text annotation
geometric
J3_8VTW_036
NA
J3_7ODE_0101/I/30:31,
1/I/474:484,
1/I/496:510		No text annotation
homologous
J3_9DFE_002
J3_17917.1
J3_7ODE_0111/I/32:35,
1/I/445:461,
1/I/468:473		No text annotation
homologous
J3_5J7L_067
NA
J3_7ODE_0021/I/56:57,
1/I/70:76,
1/I/110:114		No text annotation
homologous
J3_5J7L_037
NA
J3_7ODE_0121/I/297:301,
1/I/316:325,
1/I/337:341		No text annotation
homologous
J3_5J7L_068
NA
J3_7ODE_0031/I/683:689,
1/I/773:775,
1/I/791:794		No text annotation
homologous
J3_8VTW_001
NA
J3_7ODE_0041/I/698:700,
1/I/732:736,
1/I/760:763		No text annotation
homologous
J3_8VTW_002
NA
J3_7ODE_0051/I/1298:1303,
1/I/1625:1627,
1/I/1639:1642		No text annotation
homologous
J3_8VTW_004
NA
J3_7ODE_0061/I/1306:1309,
1/I/1605:1611,
1/I/1620:1622		No text annotation
homologous
J3_8VTW_005
NA
J3_7ODE_0071/I/1344:1349,
1/I/1382:1385,
1/I/1402:1403		No text annotation
homologous
J3_5J7L_043
NA
J3_7ODE_0131/I/1424:1429,
1/I/1564:1565,
1/I/1568:1574		No text annotation
homologous
J3_5J7L_069
NA
J3_7ODE_0081/I/2789:2791,
1/I/2805:2806,
1/I/2892:2894		No text annotation
homologous
J3_5J7L_047
NA
J3_7ODE_0091/I/2812:2815,
1/I/2831:2836,
1/I/2882:2888		No text annotation
homologous
J3_5J7L_048
NA
J4_7ODE_0011/I/297:301,
1/I/316:319,
1/I/323:325,
1/I/337:341		No text annotation
homologous
J4_5J7L_019
NA
J4_7ODE_0021/I/1270:1276,
1/I/1294:1295,
1/I/1645:1648,
1/I/2009:2010		No text annotation
homologous
J4_5J7L_021
NA
J4_7ODE_0031/I/1310:1314,
1/I/1338:1343,
1/I/1404:1405,
1/I/1597:1604		No text annotation
homologous
J4_5J7L_022
NA
J4_7ODE_0041/I/1313:1314,
1/I/1338:1343,
1/I/1404:1405,
1/I/1597:1603		No text annotation
homologous
J4_5J7L_023
NA
J4_7ODE_0051/I/1444:1445,
1/I/1466:1467,
1/I/1525:1526,
1/I/1546:1547		No text annotation
homologous
J4_5J7L_024
NA
J4_7ODE_0061/I/1772:1776,
1/I/1788:1792,
1/I/1827:1830,
1/I/1975:1979		No text annotation
homologous
J4_5J7L_025
NA
J4_7ODE_0071/I/2643:2646,
1/I/2674:2676,
1/I/2731:2735,
1/I/2769:2771		No text annotation
homologous
J4_5J7L_028
NA
J5_7ODE_0011/I/47:54,
1/I/116:121,
1/I/130:131,
1/I/148:150,
1/I/176:178		No text annotation
homologous
J5_5J7L_013
NA
J5_7ODE_0021/I/531:533,
1/I/560:564,
1/I/577:579,
1/I/1261:1262,
1/I/2017:2018		No text annotation
homologous
J5_9DFE_003
J5_43153.6
J5_7ODE_0031/I/584:589,
1/I/668:671,
1/I/809:812,
1/I/1195:1196,
1/I/1250:1256		No text annotation
homologous
J5_7A0S_004
J5_74302.6
J5_7ODE_0041/I/1674:1682,
1/I/1706:1707,
1/I/1751:1752,
1/I/1756:1764,
1/I/1988:1990		No text annotation
homologous
J5_5J7L_016
NA
J6_7ODE_0011/I/45:46,
1/I/179:183,
1/I/214:224,
1/I/231:235,
1/I/262:266,
1/I/426:433		No text annotation
J7_7ODE_0011/I/8:15,
1/I/525:531,
1/I/2018:2023,
1/I/2040:2043,
1/I/2625:2630,
1/I/2788:2789,
1/I/2894:2895		No text annotation
J7_7ODE_0021/I/817:822,
1/I/835:838,
1/I/940:946,
1/I/971:976,
1/I/987:991,
1/I/1163:1164,
1/I/1185:1190		No text annotation

Problematic loops

No problematic loops


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