RNA 3D Hub //

4WF9 Internal, Hairpin and 3-way Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_4WF9_0011/X/67:74No text annotation
HL_86769.3
HL_4WF9_0021/X/87:95No text annotation
HL_96598.1
HL_4WF9_0031/X/122:127No text annotation
HL_75407.1
HL_4WF9_0041/X/136:143No text annotation
HL_84085.2
HL_4WF9_0061/X/197:204No text annotation
HL_06192.2
HL_4WF9_0071/X/228:233No text annotation
HL_02862.2
HL_4WF9_0081/X/249:255No text annotation
HL_67216.7
HL_4WF9_0091/X/283:288No text annotation
HL_09829.1
HL_4WF9_0101/X/348:355T-loop with 1 bulged base
HL_89380.2
HL_4WF9_0111/X/362:366No text annotation
HL_75407.1
HL_4WF9_0121/X/370:378No text annotation
HL_08002.8
HL_4WF9_0131/X/427:439No text annotation
HL_91503.4
HL_4WF9_0141/X/456:463No text annotation
HL_96598.1
HL_4WF9_0151/X/508:513GNRA
HL_42097.1
HL_4WF9_0161/X/533:538GNRA
HL_42097.1
HL_4WF9_0171/X/587:594No text annotation
HL_50318.1
HL_4WF9_0181/X/609:618T-loop with 2 stacked bulged bases
HL_89380.2
HL_4WF9_0191/X/654:662No text annotation
HL_22280.1
HL_4WF9_0201/X/674:679GNRA
HL_42097.1
HL_4WF9_0211/X/686:692GNRA with one bulged base
HL_42097.1
HL_4WF9_0231/X/789:798No text annotation
HL_39334.6
HL_4WF9_0241/X/824:830No text annotation
HL_74322.1
HL_4WF9_0251/X/871:876No text annotation
HL_64365.1
HL_4WF9_0271/X/999:1006GNRA
HL_42097.1
HL_4WF9_0281/X/1022:1029No text annotation
HL_64430.2
HL_4WF9_0311/X/1260:1265No text annotation
HL_87030.2
HL_4WF9_0321/X/1318:1326T-loop with 2 stacked bulged bases
HL_89380.2
HL_4WF9_0331/X/1361:1367No text annotation
HL_46680.1
HL_4WF9_0341/X/1400:1405Other HL
HL_87030.2
HL_4WF9_0351/X/1426:1435No text annotation
HL_69023.2
HL_4WF9_0371/X/1612:1615No text annotation
HL_94803.1
HL_4WF9_0381/X/1656:1663No text annotation
HL_64430.2
HL_4WF9_0391/X/1673:1681No text annotation
HL_92229.2
HL_4WF9_0401/X/1735:1740UNCG
HL_03562.2
HL_4WF9_0411/X/1761:1768No text annotation
HL_49288.1
HL_4WF9_0421/X/1779:1783No text annotation
HL_76539.2
HL_4WF9_0431/X/1804:1814No text annotation
HL_43613.5
HL_4WF9_0461/X/1976:1984No text annotation
HL_51824.1
HL_4WF9_0471/X/2054:2063No text annotation
HL_90642.6
HL_4WF9_0481/X/2236:2242No text annotation
HL_16845.6
HL_4WF9_0491/X/2275:2283No text annotation
HL_53171.2
HL_4WF9_0501/X/2291:2303No text annotation
HL_19870.6
HL_4WF9_0521/X/2351:2358No text annotation
HL_12078.2
HL_4WF9_0531/X/2382:2389No text annotation
HL_09136.1
HL_4WF9_0541/X/2401:2406GNRA
HL_42097.1
HL_4WF9_0551/X/2431:2440No text annotation
HL_30784.2
HL_4WF9_0561/X/2498:2506No text annotation
HL_06192.2
HL_4WF9_0571/X/2555:2562No text annotation
HL_88526.2
HL_4WF9_0581/X/2578:2584No text annotation
HL_43656.2
HL_4WF9_0591/X/2621:2626GNRA
HL_42097.1
HL_4WF9_0601/X/2685:2690GNRA
HL_42097.1
HL_4WF9_0611/X/2728:2733Ribsomal LSU H95
HL_46680.1
HL_4WF9_0621/X/2772:2786No text annotation
HL_56677.7
HL_4WF9_0641/X/2839:2847No text annotation
HL_27930.1
HL_4WF9_0651/X/2876:2881Other HL
HL_42097.1
HL_4WF9_0661/Y/36:42No text annotation
HL_87939.1

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_044No text annotation
HL_4WF9_045No 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_66414.6
IL_4WF9_0021/X/36:37,
1/X/488:490		Single bulged A
IL_37497.2
IL_4WF9_0031/X/42:44,
1/X/480:483		Minor groove platform with extra cWW
IL_65006.1
IL_4WF9_0041/X/81:85,
1/X/97:104		Kink-turn
IL_45067.2
IL_4WF9_0061/X/152:153,
1/X/175:177		Single bulged A
IL_37497.2
IL_4WF9_0071/X/186:187,
1/X/215:217		Single stack bend
IL_76488.2
IL_4WF9_0081/X/190:197,
1/X/204:212		9x8 Sarcin-Ricin; G-bulge
IL_35728.2
IL_4WF9_0091/X/241:248,
1/X/256:262		8x7 Sarcin-Ricin; G-bulge
IL_04346.7
IL_4WF9_0121/X/304:306,
1/X/409:413		Major groove minor groove platform with extra cWW
IL_92788.2
IL_4WF9_0141/X/336:338,
1/X/386:390		No text annotation
IL_69440.1
IL_4WF9_0151/X/527:530,
1/X/541:554		No text annotation
IL_60992.6
IL_4WF9_0161/X/581:584,
1/X/597:600		Double sheared
IL_09705.9
IL_4WF9_0171/X/607:609,
1/X/618:620		No text annotation
IL_95997.1
IL_4WF9_0181/X/638:640,
1/X/705:707		No text annotation
IL_51629.2
IL_4WF9_0191/X/649:653,
1/X/663:667		AAA cross-strand stack
IL_17136.1
IL_4WF9_0201/X/717:719,
1/X/851:853		No text annotation
IL_95997.1
IL_4WF9_0211/X/719:723,
1/X/844:851		tHW-tHW cross-strand stack
IL_17470.6
IL_4WF9_0221/X/742:743,
1/X/808:810		Single bulged A
IL_37497.2
IL_4WF9_0231/X/747:748,
1/X/773:775		Single bulged G
IL_00225.2
IL_4WF9_0241/X/748:752,
1/X/769:773		Triple sheared
IL_56467.8
IL_4WF9_0261/X/783:785,
1/X/802:803		Major groove platform
IL_27635.1
IL_4WF9_0271/X/820:822,
1/X/832:836		Multiple bulged bases
IL_90991.6
IL_4WF9_0281/X/882:883,
1/X/984:986		Single stack bend
IL_92001.1
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_83039.13
IL_4WF9_0311/X/901:907,
1/X/960:966		7x7 Sarcin-Ricin with intercalated A; G-bulge
IL_93830.3
IL_4WF9_0321/X/907:908,
1/X/958:960		Minor groove platform
IL_42622.2
IL_4WF9_0331/X/909:913,
1/X/954:957		C-loop
IL_02509.1
IL_4WF9_0341/X/915:917,
1/X/950:952		Isolated cWS basepair
IL_52767.2
IL_4WF9_0351/X/1038:1040,
1/X/1203:1204		Single bulged C
IL_61258.12
IL_4WF9_0361/X/1042:1046,
1/X/1197:1201		UAA/GAN
IL_89002.2
IL_4WF9_0371/X/1048:1055,
1/X/1194:1195		SSU/LSU pseudoknot
IL_15861.7
IL_4WF9_0381/X/1055:1057,
1/X/1193:1194		Single bulged U
IL_83039.13
IL_4WF9_0391/X/1062:1068,
1/X/1184:1188		No text annotation
IL_57188.3
IL_4WF9_0401/X/1068:1074,
1/X/1168:1184		No text annotation
IL_50715.1
IL_4WF9_0411/X/1075:1078,
1/X/1165:1167		Isolated non-canonical cWW with bulges
IL_82068.2
IL_4WF9_0421/X/1081:1083,
1/X/1160:1162		No text annotation
IL_95997.1
IL_4WF9_0441/X/1235:1237,
1/X/1285:1288		Isolated cWS basepair
IL_52767.2
IL_4WF9_0451/X/1243:1245,
1/X/1277:1279		Isolated cWH basepair
IL_51629.2
IL_4WF9_0461/X/1246:1253,
1/X/1272:1276		Kink-turn
IL_70923.2
IL_4WF9_0471/X/1257:1259,
1/X/1266:1268		Intercalated cWW
IL_82842.2
IL_4WF9_0481/X/1300:1307,
1/X/2038:2044		8x7 Sarcin-Ricin; G-bulge
IL_04346.7
IL_4WF9_0491/X/1347:1350,
1/X/1647:1648		Major groove platform; stack outside cWW
IL_50694.2
IL_4WF9_0501/X/1356:1360,
1/X/1368:1370		Major groove minor groove platform with tHH
IL_37712.2
IL_4WF9_0511/X/1388:1392,
1/X/1413:1417		UAA/GAN
IL_89002.2
IL_4WF9_0521/X/1394:1398,
1/X/1407:1411		tSH-tHW-tHS
IL_17136.1
IL_4WF9_0541/X/1461:1465,
1/X/1624:1627		Other IL
IL_04059.1
IL_4WF9_0551/X/1465:1467,
1/X/1622:1624		No text annotation
IL_95997.1
IL_4WF9_0561/X/1475:1480,
1/X/1604:1609		No text annotation
IL_81631.1
IL_4WF9_0581/X/1511:1516,
1/X/1564:1570		No text annotation
IL_88190.1
IL_4WF9_0621/X/1695:1700,
1/X/2031:2033		No text annotation
IL_12566.2
IL_4WF9_0631/X/1707:1709,
1/X/2022:2024		Isolated tWW turn
IL_54997.7
IL_4WF9_0641/X/1710:1713,
1/X/2020:2021		Major groove platform; stack outside cWW
IL_50694.2
IL_4WF9_0651/X/1713:1718,
1/X/2017:2020		Intercalated tWH
IL_82842.2
IL_4WF9_0661/X/1730:1735,
1/X/1740:1746		No text annotation
IL_65969.2
IL_4WF9_0671/X/1756:1761,
1/X/1768:1773		No text annotation
IL_65969.2
IL_4WF9_0681/X/1797:1798,
1/X/2007:2009		Single bulged A
IL_37497.2
IL_4WF9_0691/X/1825:1831,
1/X/1840:1848		Kink-turn related
IL_17069.3
IL_4WF9_0711/X/1868:1869,
1/X/1925:1928		Major groove outside cWW, minor groove, intercalation pocket
IL_69996.1
IL_4WF9_0731/X/1878:1882,
1/X/1914:1918		UAA/GAN with extra pair
IL_90318.1
IL_4WF9_0741/X/1883:1887,
1/X/1909:1913		Triple sheared
IL_96141.1
IL_4WF9_0751/X/1891:1894,
1/X/1901:1905		UAA/GAN
IL_77691.1
IL_4WF9_0761/X/1960:1961,
1/X/1991:1994		No text annotation
IL_59677.2
IL_4WF9_0771/X/1961:1972,
1/X/1988:1991		No text annotation
IL_81589.2
IL_4WF9_0781/X/2077:2079,
1/X/2644:2645		Major groove platform
IL_27635.1
IL_4WF9_0791/X/2081:2083,
1/X/2639:2642		No text annotation
IL_54678.5
IL_4WF9_0801/X/2094:2096,
1/X/2469:2470		Single bulged U
IL_83039.13
IL_4WF9_0811/X/2097:2098,
1/X/2465:2468		Minor groove platform
IL_42622.2
IL_4WF9_0821/X/2108:2110,
1/X/2263:2266		Isolated tHS basepair with bulges
IL_38958.7
IL_4WF9_0831/X/2111:2113,
1/X/2260:2262		No text annotation
IL_95997.1
IL_4WF9_0841/X/2122:2126,
1/X/2217:2221		Other IL
IL_05145.2
IL_4WF9_0851/X/2229:2233,
1/X/2245:2248		Tandem non-canonical cWW pairs
IL_67743.1
IL_4WF9_0861/X/2324:2326,
1/X/2344:2348		Isolated tHS basepair with bulges
IL_38958.7
IL_4WF9_0871/X/2377:2380,
1/X/2391:2394		Double sheared
IL_09705.9
IL_4WF9_0881/X/2428:2430,
1/X/2441:2442		Single bulged U
IL_83039.13
IL_4WF9_0891/X/2480:2481,
1/X/2525:2527		Single stack bend
IL_76488.2
IL_4WF9_0901/X/2481:2482,
1/X/2523:2525		Major groove platform
IL_27635.1
IL_4WF9_0911/X/2484:2486,
1/X/2520:2521		Major groove platform
IL_27635.1
IL_4WF9_0921/X/2486:2488,
1/X/2516:2520		Major groove minor groove platform with extra cWW
IL_92788.2
IL_4WF9_0931/X/2493:2497,
1/X/2507:2511		Triple sheared
IL_56467.8
IL_4WF9_0941/X/2534:2535,
1/X/2607:2609		Major groove platform
IL_76223.2
IL_4WF9_0951/X/2537:2539,
1/X/2601:2605		Isolated non-canonical cWW with bulges
IL_90933.2
IL_4WF9_0961/X/2539:2540,
1/X/2598:2601		No text annotation
IL_71530.2
IL_4WF9_0971/X/2549:2550,
1/X/2567:2570		Minor groove platform with intercalation
IL_95601.3
IL_4WF9_0981/X/2618:2619,
1/X/2628:2630		Single bulged A
IL_69996.1
IL_4WF9_0991/X/2663:2667,
1/X/2801:2809		tSH-tHS-tHW
IL_04638.1
IL_4WF9_1001/X/2679:2685,
1/X/2690:2695		Sarcin-Ricin target in LSU H95; G-bulge
IL_16458.1
IL_4WF9_1011/X/2707:2711,
1/X/2752:2754		C-loop
IL_63596.6
IL_4WF9_1021/X/2714:2718,
1/X/2745:2749		No text annotation
IL_08296.3
IL_4WF9_1031/X/2722:2723,
1/X/2738:2741		Multiple bulged bases
IL_71530.2
IL_4WF9_1041/X/2764:2769,
1/X/2789:2794		UAA/GAN with extra cWW
IL_49767.5
IL_4WF9_1061/X/2858:2859,
1/X/2898:2900		Major groove intercalation
IL_16396.2
IL_4WF9_1071/X/2863:2865,
1/X/2891:2894		No text annotation
IL_02284.5
IL_4WF9_1081/X/2867:2872,
1/X/2885:2889		No text annotation
IL_83162.5
IL_4WF9_1091/Y/2:5,
1/Y/110:113		Tandem non-canonical cWW pairs
IL_30621.2
IL_4WF9_1101/Y/5:8,
1/Y/107:110		Tandem non-canonical cWW pairs
IL_67743.1
IL_4WF9_1111/Y/8:14,
1/Y/66:107		No text annotation
IL_77827.1
IL_4WF9_1121/Y/15:16,
1/Y/63:65		Major groove intercalation
IL_37497.2
IL_4WF9_1131/Y/20:27,
1/Y/53:59		No text annotation
IL_19048.1
IL_4WF9_1141/Y/28:30,
1/Y/48:52		No text annotation
IL_10810.1
IL_4WF9_1151/Y/32:36,
1/Y/42:46		Symmetric double minor groove platform
IL_58103.6

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_043No text annotation
IL_4WF9_053No text annotation
IL_4WF9_057No text annotation
IL_4WF9_059No text annotation
IL_4WF9_060No text annotation
IL_4WF9_061No text annotation
IL_4WF9_070No text annotation
IL_4WF9_072No text annotation
IL_4WF9_105No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_4WF9_0011/X/56:67,
1/X/74:76,
1/X/109:113		No text annotation
Not in a motif group
J3_4WF9_0021/X/728:734,
1/X/818:820,
1/X/836:839		No text annotation
Not in a motif group
J3_4WF9_0031/X/743:745,
1/X/777:781,
1/X/805:808		No text annotation
Not in a motif group
J3_4WF9_0041/X/1335:1340,
1/X/1669:1671,
1/X/1683:1686		No text annotation
Not in a motif group
J3_4WF9_0051/X/1342:1346,
1/X/1649:1655,
1/X/1664:1667		No text annotation
Not in a motif group
J3_4WF9_0061/X/1860:1863,
1/X/1931:1960,
1/X/1994:1999		No text annotation
Not in a motif group
J3_4WF9_0071/X/2118:2120,
1/X/2223:2228,
1/X/2249:2255		No text annotation
Not in a motif group
J3_4WF9_0081/X/2322:2324,
1/X/2348:2350,
1/X/2359:2364		No text annotation
Not in a motif group
J3_4WF9_0091/X/2544:2547,
1/X/2572:2574,
1/X/2588:2594		No text annotation
Not in a motif group

Problematic loops

No problematic loops


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