RNA 3D Hub //

4WF9 Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_4WF9_0671/X/59:68Pseudoknot with intercalation
HL_93438.2
HL_4WF9_0011/X/67:74No text annotation
HL_86769.4
HL_4WF9_0021/X/87:95Pseudoknot geometry
HL_77600.2
HL_4WF9_0031/X/122:127No text annotation
HL_75660.5
HL_4WF9_0041/X/136:143GNRA wlth tandem sheared
HL_81538.2
HL_4WF9_0061/X/197:204No text annotation
HL_30068.2
HL_4WF9_0071/X/228:233No text annotation
HL_53890.2
HL_4WF9_0081/X/249:255No text annotation
HL_37369.2
HL_4WF9_0681/X/280:291No text annotation
HL_99769.3
HL_4WF9_0091/X/283:288No text annotation
HL_81100.2
HL_4WF9_0101/X/348:355T-loop with 2 stacked bulged bases
HL_01609.3
HL_4WF9_0111/X/362:366No text annotation
HL_75660.5
HL_4WF9_0121/X/370:378T-loop with unstacked turn
HL_27670.2
HL_4WF9_0131/X/427:439No text annotation
HL_69139.1
HL_4WF9_0141/X/456:463Pseudoknot geometry
HL_30680.3
HL_4WF9_0151/X/508:513GNRA
HL_37824.7
HL_4WF9_0161/X/533:538GNRA
HL_37824.7
HL_4WF9_0171/X/587:594No text annotation
HL_50318.1
HL_4WF9_0181/X/609:618T-loop with 2 stacked bulged bases
HL_28252.8
HL_4WF9_0191/X/654:662Other HL
HL_77436.5
HL_4WF9_0201/X/674:679GNRA
HL_37824.7
HL_4WF9_0211/X/686:692GNRA
HL_37824.7
HL_4WF9_0231/X/789:798No text annotation
HL_88205.2
HL_4WF9_0241/X/824:830No text annotation
HL_87954.2
HL_4WF9_0251/X/871:876No text annotation
HL_55195.3
HL_4WF9_0271/X/999:1006GNRA
HL_37824.7
HL_4WF9_0281/X/1022:1029No text annotation
HL_42998.2
HL_4WF9_0311/X/1260:1265GNRA
HL_37824.7
HL_4WF9_0321/X/1318:1326T-loop with 2 stacked bulged bases
HL_28252.8
HL_4WF9_0331/X/1361:1367Pseudoknot geometry with 3' bulge
HL_57176.2
HL_4WF9_0341/X/1400:1405GNRA
HL_37824.7
HL_4WF9_0351/X/1426:1435No text annotation
HL_81545.2
HL_4WF9_0371/X/1612:1615Mini UNCG
HL_48778.2
HL_4WF9_0381/X/1656:1663No text annotation
HL_89567.2
HL_4WF9_0391/X/1673:1681GNRA with extra cWW
HL_20167.2
HL_4WF9_0401/X/1735:1740UNCG
HL_34617.5
HL_4WF9_0711/X/1762:1767GNRA
HL_37824.7
HL_4WF9_0421/X/1779:1783No text annotation
HL_80709.3
HL_4WF9_0431/X/1804:1814No text annotation
HL_01962.2
HL_4WF9_0461/X/1976:1984No text annotation
HL_20167.2
HL_4WF9_0471/X/2054:2063No text annotation
HL_61996.2
HL_4WF9_0481/X/2236:2242No text annotation
HL_49922.4
HL_4WF9_0491/X/2275:2283No text annotation
HL_85367.2
HL_4WF9_0501/X/2291:2303No text annotation
HL_91939.2
HL_4WF9_0521/X/2351:2358Pseudoknot geometry
HL_93324.4
HL_4WF9_0531/X/2382:2389GNRA with extra cWW
HL_04259.3
HL_4WF9_0541/X/2401:2406GNRA
HL_37824.7
HL_4WF9_0551/X/2431:2440No text annotation
HL_53454.2
HL_4WF9_0561/X/2498:2506No text annotation
HL_32735.2
HL_4WF9_0571/X/2555:2562No text annotation
HL_31585.4
HL_4WF9_0581/X/2578:2584No text annotation
HL_30068.2
HL_4WF9_0591/X/2621:2626GNRA
HL_37824.7
HL_4WF9_0601/X/2685:2690GNRA
HL_37824.7
HL_4WF9_0611/X/2728:2733Ribsomal LSU H95
HL_65794.5
HL_4WF9_0621/X/2772:2786No text annotation
HL_74055.2
HL_4WF9_0641/X/2839:2847No text annotation
HL_64690.6
HL_4WF9_0651/X/2876:2881GNRA
HL_37824.7
HL_4WF9_0701/Y/32:46No text annotation
HL_97756.2
HL_4WF9_0661/Y/36:42No text annotation
HL_47787.2

Problematic loops

#loop idProblemSequence
HL_4WF9_005No text annotation
HL_4WF9_022No text annotation
HL_4WF9_026No text annotation
HL_4WF9_029No text annotation
HL_4WF9_030No text annotation
HL_4WF9_036No text annotation
HL_4WF9_041No text annotation
HL_4WF9_044No text annotation
HL_4WF9_045No text annotation
HL_4WF9_069No text annotation
HL_4WF9_051No text annotation
HL_4WF9_063No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_4WF9_0011/X/24:30,
1/X/555:561		Triple sheared with non-canonical cWW
IL_04021.2
IL_4WF9_0021/X/36:37,
1/X/488:490		Single bulged A
IL_31462.6
IL_4WF9_0031/X/42:44,
1/X/480:483		Minor groove platform with extra cWW
IL_90351.1
IL_4WF9_0041/X/81:85,
1/X/97:104		Kink-turn
IL_01488.3
IL_4WF9_0061/X/152:153,
1/X/175:177		Single bulged A
IL_31462.6
IL_4WF9_0071/X/186:187,
1/X/215:217		Single stack bend
IL_90729.1
IL_4WF9_0081/X/190:197,
1/X/204:212		9x8 Sarcin-Ricin; G-bulge
IL_84694.2
IL_4WF9_0091/X/241:248,
1/X/256:262		8x7 Sarcin-Ricin; G-bulge
IL_04346.10
IL_4WF9_0121/X/304:306,
1/X/409:413		Major groove minor groove platform with extra cWW
IL_49061.1
IL_4WF9_0141/X/336:338,
1/X/386:390		No text annotation
IL_69440.3
IL_4WF9_0151/X/527:530,
1/X/541:554		No text annotation
IL_81516.2
IL_4WF9_0161/X/581:584,
1/X/597:600		Double sheared
IL_09705.15
IL_4WF9_0171/X/607:609,
1/X/618:620		Isolated non-canonical cWW pair
IL_07785.1
IL_4WF9_0181/X/638:640,
1/X/705:707		Isolated non-canonical cWW pair
IL_07785.1
IL_4WF9_0191/X/649:653,
1/X/663:667		AAA cross-strand stack
IL_66798.2
IL_4WF9_0201/X/717:719,
1/X/851:853		Isolated non-canonical cWW pair
IL_87907.2
IL_4WF9_0211/X/719:723,
1/X/844:851		tHW-tHW cross-strand stack
IL_54041.2
IL_4WF9_0221/X/742:743,
1/X/808:810		Single bulged A
IL_31462.6
IL_4WF9_0231/X/747:748,
1/X/773:775		Single bulged G
IL_00225.13
IL_4WF9_0241/X/748:752,
1/X/769:773		Triple sheared
IL_50730.2
IL_4WF9_0261/X/783:785,
1/X/802:803		Major groove platform
IL_48076.6
IL_4WF9_0271/X/820:822,
1/X/832:836		Multiple bulged bases
IL_06549.2
IL_4WF9_0281/X/882:883,
1/X/984:986		Single stack bend
IL_90729.1
IL_4WF9_0291/X/889:893,
1/X/975:978		No text annotation
IL_06300.1
IL_4WF9_0301/X/897:898,
1/X/969:971		Single bulged U
IL_89505.4
IL_4WF9_0311/X/901:907,
1/X/960:966		7x7 Sarcin-Ricin with intercalated A; G-bulge
IL_29198.2
IL_4WF9_0321/X/907:908,
1/X/958:960		Minor groove platform
IL_51454.3
IL_4WF9_0331/X/909:913,
1/X/954:957		C-loop
IL_26222.2
IL_4WF9_0351/X/1038:1040,
1/X/1203:1204		Single bulged C
IL_61258.15
IL_4WF9_0361/X/1042:1046,
1/X/1197:1201		UAA/GAN
IL_38507.2
IL_4WF9_0371/X/1048:1055,
1/X/1194:1195		SSU/LSU pseudoknot
IL_41203.4
IL_4WF9_0381/X/1055:1057,
1/X/1193:1194		Single bulged U
IL_89505.4
IL_4WF9_0391/X/1062:1068,
1/X/1184:1188		Kink-turn related
IL_57188.5
IL_4WF9_0401/X/1068:1074,
1/X/1168:1184		No text annotation
IL_50715.3
IL_4WF9_0411/X/1075:1078,
1/X/1165:1167		Isolated non-canonical cWW pair
IL_57744.1
IL_4WF9_0421/X/1081:1083,
1/X/1160:1162		Isolated non-canonical cWW pair
IL_87907.2
IL_4WF9_0441/X/1235:1237,
1/X/1285:1288		Isolated cWS basepair
IL_42997.3
IL_4WF9_0451/X/1243:1245,
1/X/1277:1279		Isolated cWH basepair
IL_10167.6
IL_4WF9_0461/X/1246:1253,
1/X/1272:1276		Kink-turn
IL_70923.9
IL_4WF9_0471/X/1257:1259,
1/X/1266:1268		Intercalated cWW
IL_31737.3
IL_4WF9_0481/X/1300:1307,
1/X/2038:2044		8x7 Sarcin-Ricin; G-bulge
IL_04346.10
IL_4WF9_0491/X/1347:1350,
1/X/1647:1648		Major groove platform; stack outside cWW
IL_50694.7
IL_4WF9_0501/X/1356:1360,
1/X/1368:1370		Major groove minor groove platform with tHH
IL_83150.2
IL_4WF9_0511/X/1388:1392,
1/X/1413:1417		UAA/GAN
IL_89021.2
IL_4WF9_0521/X/1394:1398,
1/X/1407:1411		tSH-tHW-tHS
IL_17136.7
IL_4WF9_0541/X/1461:1465,
1/X/1624:1627		Other IL
IL_99646.2
IL_4WF9_1221/X/1476:1480,
1/X/1604:1608		No text annotation
IL_67780.1
IL_4WF9_1161/X/1511:1515,
1/X/1565:1570		No text annotation
IL_25186.4
IL_4WF9_0621/X/1695:1700,
1/X/2031:2033		No text annotation
IL_12566.4
IL_4WF9_0631/X/1707:1709,
1/X/2022:2024		Isolated tWW turn
IL_67095.2
IL_4WF9_0641/X/1710:1713,
1/X/2020:2021		Major groove platform; stack outside cWW
IL_50694.7
IL_4WF9_1171/X/1710:1718,
1/X/2017:2021		No text annotation
IL_22854.4
IL_4WF9_0651/X/1713:1718,
1/X/2017:2020		Intercalated tWH
IL_76758.2
IL_4WF9_0661/X/1730:1735,
1/X/1740:1746		tSH-tSH-tHH-tHS
IL_47346.2
IL_4WF9_1231/X/1757:1761,
1/X/1768:1772		Partly complementary
IL_49751.4
IL_4WF9_0681/X/1797:1798,
1/X/2007:2009		Single bulged A
IL_31462.6
IL_4WF9_0691/X/1825:1831,
1/X/1840:1848		Kink-turn related
IL_17069.5
IL_4WF9_0711/X/1868:1869,
1/X/1925:1928		Major groove intercalation
IL_82107.4
IL_4WF9_0721/X/1873:1876,
1/X/1920:1921		Major groove minor groove platform; mini C-loop
IL_68140.4
IL_4WF9_0731/X/1878:1882,
1/X/1914:1918		UAA/GAN with extra pair
IL_89021.2
IL_4WF9_0741/X/1883:1887,
1/X/1909:1913		Triple sheared
IL_66798.2
IL_4WF9_0751/X/1891:1894,
1/X/1901:1905		UAA/GAN
IL_77691.5
IL_4WF9_0761/X/1960:1961,
1/X/1991:1994		Bulged stacked bases
IL_22551.4
IL_4WF9_0771/X/1961:1972,
1/X/1988:1991		No text annotation
IL_42218.2
IL_4WF9_0781/X/2077:2079,
1/X/2644:2645		Major groove platform
IL_48076.6
IL_4WF9_0791/X/2081:2083,
1/X/2639:2642		No text annotation
IL_83389.2
IL_4WF9_0801/X/2094:2096,
1/X/2469:2470		Single bulged U
IL_89505.4
IL_4WF9_0811/X/2097:2098,
1/X/2465:2468		Minor groove platform
IL_51454.3
IL_4WF9_0821/X/2108:2110,
1/X/2263:2266		Isolated tHS basepair with bulges
IL_85599.2
IL_4WF9_0831/X/2111:2113,
1/X/2260:2262		Isolated non-canonical cWW pair
IL_87907.2
IL_4WF9_1241/X/2123:2126,
1/X/2217:2220		No text annotation
IL_13404.2
IL_4WF9_1251/X/2229:2231,
1/X/2247:2248		Single bulged G
IL_00225.13
IL_4WF9_0861/X/2324:2326,
1/X/2344:2348		Isolated tHS basepair with bulges
IL_61476.2
IL_4WF9_0871/X/2377:2380,
1/X/2391:2394		Double sheared
IL_09705.15
IL_4WF9_0881/X/2428:2430,
1/X/2441:2442		Single bulged U
IL_89505.4
IL_4WF9_0891/X/2480:2481,
1/X/2525:2527		Single stack bend
IL_26793.1
IL_4WF9_0901/X/2481:2482,
1/X/2523:2525		Major groove platform
IL_48076.6
IL_4WF9_0911/X/2484:2486,
1/X/2520:2521		Major groove platform
IL_48076.6
IL_4WF9_0921/X/2486:2488,
1/X/2516:2520		Major groove minor groove platform with extra cWW
IL_51387.2
IL_4WF9_0931/X/2493:2497,
1/X/2507:2511		Triple sheared
IL_17948.2
IL_4WF9_0941/X/2534:2535,
1/X/2607:2609		Major groove platform
IL_07039.3
IL_4WF9_0951/X/2537:2539,
1/X/2601:2605		Isolated non-canonical cWW with bulges
IL_07785.1
IL_4WF9_0961/X/2539:2540,
1/X/2598:2601		No text annotation
IL_42626.2
IL_4WF9_0971/X/2549:2550,
1/X/2567:2570		Major groove platform with intercalation
IL_02555.1
IL_4WF9_0981/X/2618:2619,
1/X/2628:2630		Single bulged A
IL_31462.6
IL_4WF9_0991/X/2663:2667,
1/X/2801:2809		tSH-tHS-tHW
IL_04638.3
IL_4WF9_1001/X/2679:2685,
1/X/2690:2695		Sarcin-Ricin target in LSU H95; G-bulge
IL_16458.4
IL_4WF9_1011/X/2707:2711,
1/X/2752:2754		C-loop
IL_63596.11
IL_4WF9_1021/X/2714:2718,
1/X/2745:2749		No text annotation
IL_23774.1
IL_4WF9_1031/X/2722:2723,
1/X/2738:2741		Multiple bulged bases
IL_42626.2
IL_4WF9_1041/X/2764:2769,
1/X/2789:2794		UAA/GAN with extra cWW
IL_49767.8
IL_4WF9_1061/X/2858:2859,
1/X/2898:2900		Major groove intercalation
IL_66635.5
IL_4WF9_1071/X/2863:2865,
1/X/2891:2894		No text annotation
IL_31531.3
IL_4WF9_1081/X/2867:2872,
1/X/2885:2889		tHS double platform
IL_70411.2
IL_4WF9_1211/Y/3:5,
1/Y/110:112		Isolated cWH basepair
IL_10167.6
IL_4WF9_1101/Y/5:8,
1/Y/107:110		Tandem non-canonical cWW pairs
IL_51479.1
IL_4WF9_1111/Y/8:14,
1/Y/66:107		No text annotation
IL_4WF9_1121/Y/15:16,
1/Y/63:65		Major groove intercalation
IL_31462.6
IL_4WF9_1131/Y/20:27,
1/Y/53:59		No text annotation
IL_19048.1
IL_4WF9_1261/Y/28:29,
1/Y/49:52		Major groove minor groove platform; mini C-loop
IL_68140.4
IL_4WF9_1151/Y/32:36,
1/Y/42:46		Symmetric double minor groove platform
IL_58103.11

Problematic loops

#loop idProblemSequence
IL_4WF9_005No text annotation
IL_4WF9_010No text annotation
IL_4WF9_011No text annotation
IL_4WF9_013No text annotation
IL_4WF9_025No text annotation
IL_4WF9_034Isolated cWS basepair
IL_4WF9_043No text annotation
IL_4WF9_053No text annotation
IL_4WF9_055No text annotation
IL_4WF9_056No text annotation
IL_4WF9_057No text annotation
IL_4WF9_058No text annotation
IL_4WF9_059No text annotation
IL_4WF9_060No text annotation
IL_4WF9_061No text annotation
IL_4WF9_118No text annotation
IL_4WF9_067No text annotation
IL_4WF9_070No text annotation
IL_4WF9_119No text annotation
IL_4WF9_084Other IL
IL_4WF9_120No text annotation
IL_4WF9_085Tandem non-canonical cWW pairs
IL_4WF9_105No text annotation
IL_4WF9_109Tandem non-canonical cWW pairs
IL_4WF9_114No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_4WF9_0101/X/30:31,
1/X/520:527,
1/X/554:555		No text annotation
J3_60031.2
J3_4WF9_0111/X/30:31,
1/X/520:530,
1/X/541:555		No text annotation
J3_92134.2
J3_4WF9_0121/X/32:35,
1/X/491:507,
1/X/514:519		No text annotation
J3_30040.2
J3_4WF9_0131/X/56:57,
1/X/70:76,
1/X/109:113		No text annotation
J3_35667.2
J3_4WF9_0011/X/56:67,
1/X/74:76,
1/X/109:113		No text annotation
J3_47707.1
J3_4WF9_0221/X/272:276,
1/X/295:302,
1/X/415:416		No text annotation
J3_97971.2
J3_4WF9_0151/X/340:344,
1/X/359:368,
1/X/380:384		No text annotation
J3_46299.2
J3_4WF9_0021/X/728:734,
1/X/818:820,
1/X/836:839		No text annotation
J3_64189.2
J3_4WF9_0031/X/743:745,
1/X/777:781,
1/X/805:808		No text annotation
J3_44724.7
J3_4WF9_0041/X/1335:1340,
1/X/1669:1671,
1/X/1683:1686		No text annotation
J3_32852.6
J3_4WF9_0051/X/1342:1346,
1/X/1649:1655,
1/X/1664:1667		No text annotation
J3_68164.1
J3_4WF9_0161/X/1381:1387,
1/X/1418:1422,
1/X/1439:1440		No text annotation
J3_31965.2
J3_4WF9_0171/X/1468:1473,
1/X/1611:1612,
1/X/1615:1621		No text annotation
J3_34864.2
J3_4WF9_0071/X/2118:2120,
1/X/2223:2228,
1/X/2249:2255		No text annotation
J3_07703.1
J3_4WF9_0191/X/2309:2312,
1/X/2410:2422,
1/X/2448:2454		No text annotation
J3_39320.1
J3_4WF9_0081/X/2322:2324,
1/X/2348:2350,
1/X/2359:2364		No text annotation
J3_61124.2
J3_4WF9_0091/X/2544:2547,
1/X/2572:2574,
1/X/2588:2594		No text annotation
J3_32601.5
J3_4WF9_0201/X/2816:2817,
1/X/2826:2831,
1/X/2909:2913		No text annotation
J3_24127.1
J3_4WF9_0211/X/2834:2835,
1/X/2851:2856,
1/X/2902:2906		No text annotation
J3_76911.2
J4_4WF9_0011/X/271:272,
1/X/416:421,
1/X/445:452,
1/X/467:470		No text annotation
J4_45801.6
J4_4WF9_0021/X/340:344,
1/X/359:362,
1/X/366:368,
1/X/380:384		No text annotation
J4_71729.5
J4_4WF9_0031/X/644:647,
1/X/669:673,
1/X/680:684,
1/X/694:701		No text annotation
J4_60168.1
J4_4WF9_0041/X/1308:1313,
1/X/1331:1332,
1/X/1689:1692,
1/X/2036:2037		No text annotation
J4_64571.5
J4_4WF9_0051/X/1347:1351,
1/X/1375:1380,
1/X/1441:1442,
1/X/1641:1648		No text annotation
J4_69051.6
J4_4WF9_0061/X/1350:1351,
1/X/1375:1380,
1/X/1441:1442,
1/X/1641:1647		No text annotation
J4_10313.5
J4_4WF9_0071/X/1799:1803,
1/X/1815:1819,
1/X/1854:1857,
1/X/2002:2006		No text annotation
J4_61477.5
J4_4WF9_0081/X/2312:2316,
1/X/2370:2374,
1/X/2397:2399,
1/X/2408:2410		No text annotation
J4_04930.6
J4_4WF9_0091/X/2670:2673,
1/X/2701:2703,
1/X/2758:2762,
1/X/2796:2798		No text annotation
J4_77044.4
J5_4WF9_0011/X/47:54,
1/X/115:120,
1/X/129:130,
1/X/149:151,
1/X/178:180		No text annotation
J5_01737.2
J5_4WF9_0081/X/271:276,
1/X/295:302,
1/X/415:421,
1/X/445:452,
1/X/467:470		No text annotation
J5_31814.5
J5_4WF9_0021/X/271:276,
1/X/295:303,
1/X/414:421,
1/X/445:452,
1/X/467:470		No text annotation
J5_53867.1
J5_4WF9_0031/X/576:578,
1/X/603:607,
1/X/620:622,
1/X/1299:1300,
1/X/2044:2045		No text annotation
J5_43153.5
J5_4WF9_0041/X/627:632,
1/X/713:716,
1/X/854:857,
1/X/1234:1235,
1/X/1288:1294		No text annotation
J5_74302.5
J5_4WF9_0051/X/1718:1726,
1/X/1750:1751,
1/X/1778:1779,
1/X/1783:1791,
1/X/2015:2017		No text annotation
J5_62523.6
J5_4WF9_0061/X/2084:2091,
1/X/2473:2480,
1/X/2527:2534,
1/X/2609:2615,
1/X/2633:2638		No text annotation
J5_4WF9_0071/X/2101:2104,
1/X/2270:2273,
1/X/2285:2286,
1/X/2308:2309,
1/X/2454:2462		No text annotation
J5_39529.1
J6_4WF9_0011/X/45:46,
1/X/181:186,
1/X/217:227,
1/X/234:238,
1/X/265:269,
1/X/472:479		No text annotation
J6_45299.4
J6_4WF9_0021/X/2101:2104,
1/X/2270:2273,
1/X/2285:2286,
1/X/2308:2312,
1/X/2410:2422,
1/X/2448:2462		No text annotation
J6_93066.1
J7_4WF9_0011/X/8:15,
1/X/570:576,
1/X/2045:2050,
1/X/2067:2070,
1/X/2652:2657,
1/X/2815:2816,
1/X/2913:2914		No text annotation
J7_30280.5
J7_4WF9_0021/X/862:867,
1/X/880:881,
1/X/987:990,
1/X/1015:1020,
1/X/1031:1035,
1/X/1207:1208,
1/X/1224:1229		No text annotation
J7_21233.5

Problematic loops

#loop idProblemSequence
J3_4WF9_014No text annotation
J3_4WF9_006No text annotation
J3_4WF9_018No text annotation

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