RNA 3D Hub //

7ASO Internal, Hairpin and 3-way Junction Loop Motifs

Download loops

Valid loops

#loop idlocationannotation
(mapped to, source)		motif group
(similar to)
1/C/31:47NANA
1/C/79:92NANA
1/X/12:24NANA
1/X/64:103NANA
1/X/158:163NANA
1/X/267:275NANA
1/X/304:309NANA
1/X/330:340NANA
1/X/387:392NANA
1/X/529:536NANA
1/X/624:632NANA
1/X/690:718NANA
1/X/794:804NANA
1/X/871:878NANA
1/X/906:913NANA
1/X/973:982NANA
1/X/1008:1055NANA
1/X/1088:1093NANA
1/X/1100:1109NANA
1/X/1175:1183NANA
1/X/1320:1339NANA
1/X/1367:1377NANA
1/X/1455:1470NANA
1/X/1527:1532NANA
1/Y/67:74
geometric
HL_4WF9_001		NA

HL_86769.2*
1/Y/87:95
homologous
HL_7RQB_002		NA

HL_17926.5*
1/Y/122:127
homologous
HL_7RQB_003		NA

HL_62869.3*
1/Y/135:144NANA
1/Y/152:177NANA
1/Y/197:204
homologous
HL_7RQB_006		NA

HL_23481.5*
1/Y/228:233NANA
1/Y/249:255
homologous
HL_7RQB_008		NA

HL_67216.5*
1/Y/278:293NANA
1/Y/348:355
homologous
HL_7RQB_010		NA

HL_68493.6*
1/Y/370:378
homologous
HL_7RQB_012		NA

HL_08002.6*
1/Y/427:439NANA
1/Y/456:463
homologous
HL_7RQB_014		NA

HL_32512.8*
1/Y/508:513
homologous
HL_7RQB_015		NA

HL_43074.18*
1/Y/533:538
homologous
HL_7RQB_016		NA

HL_43074.18*
1/Y/587:594
geometric
HL_4WF9_017		NA

HL_23219.1*
1/Y/609:618
homologous
HL_7RQB_018		NA

HL_33239.17*
1/Y/654:662NANA
1/Y/674:679
homologous
HL_7RQB_020		NA

HL_43074.18*
1/Y/686:692NANA
1/Y/747:775NANA
1/Y/789:798
homologous
HL_7RQB_023		NA

HL_39334.5*
1/Y/823:831NANA
1/Y/871:876
homologous
HL_7RQB_025		NA

HL_15942.5*
1/Y/919:948NANA
1/Y/998:1007
geometric
HL_3RG5_006		NA

HL_83315.1*
1/Y/1022:1029
homologous
HL_7RQB_028		NA

HL_72451.5*
1/Y/1083:1160NANA
1/Y/1211:1221NANA
1/Y/1260:1265
homologous
HL_7RQB_032		NA

HL_43074.18*
1/Y/1318:1326
homologous
HL_7RQB_033		NA

HL_33239.17*
1/Y/1361:1367
homologous
HL_7RQB_034		NA

HL_86880.5*
1/Y/1400:1405
homologous
HL_7RQB_035		NA

HL_43074.18*
1/Y/1426:1435
homologous
HL_7RQB_036		NA

HL_78457.4*
1/Y/1511:1570NANA
1/Y/1612:1615
homologous
HL_7RQB_039		NA

HL_69353.7*
1/Y/1656:1663
homologous
HL_7RQB_040		NA

HL_66171.3*
1/Y/1673:1681
geometric
HL_4WF9_039		NA

HL_42733.4*
1/Y/1735:1740UNCG
geometric
HL_4LFB_009		NA

HL_79299.11*
1/Y/1756:1773NANA
1/Y/1779:1783
homologous
HL_7RQB_044		NA

HL_79272.3*
1/Y/1804:1814
homologous
HL_7RQB_045		NA

HL_43613.4*
1/Y/1833:1838
homologous
HL_7RQB_046		NA

HL_43074.18*
1/Y/1894:1901NANA
1/Y/1976:1984
homologous
HL_7RQB_049		NA

HL_53760.4*
1/Y/2054:2063
homologous
HL_7RQB_050		NA

HL_90642.5*
1/Y/2134:2209NANA
1/Y/2236:2242NANA
1/Y/2275:2283
homologous
HL_7RQB_053		NA
1/Y/2291:2303
homologous
HL_7RQB_054		NA

HL_19870.5*
1/Y/2350:2359NANA
1/Y/2382:2389
homologous
HL_7RQB_057		NA

HL_93727.5*
1/Y/2401:2406
homologous
HL_7RQB_058		NA

HL_43074.18*
1/Y/2431:2440
homologous
HL_7RQB_059		NA

HL_48376.4*
1/Y/2497:2507NANA
1/Y/2554:2563NANA
1/Y/2578:2584NANA
1/Y/2621:2626
homologous
HL_7RQB_063		NA

HL_43074.18*
1/Y/2679:2695NANA
1/Y/2727:2734
geometric
HL_5TBW_012		NA

HL_94386.1*
1/Y/2772:2786NANA
1/Y/2839:2847
homologous
HL_7RQB_068		NA

HL_05018.6*
1/Y/2876:2881
homologous
HL_7RQB_069		NA

HL_43074.18*

Problematic loops

#loop idProblemSequence
HL_7ASO_014NA
HL_7ASO_076NA

Valid loops

#loop idlocationannotation
(mapped to, source)		motif group
(similar to)
1/C/3:5,
1/C/110:112		NANA
1/X/29:34,
1/X/559:564		NANA
1/X/48:54,
1/X/366:369		NANA
1/X/125:127,
1/X/241:243		NANA
1/X/127:132,
1/X/239:241		NANA
1/X/132:137,
1/X/234:239		NANA
1/X/138:144,
1/X/178:233		NANA
1/X/297:303,
1/X/311:319		NANA
1/X/303:304,
1/X/309:311		NANA
1/X/327:330,
1/X/340:342		NANA
1/X/378:383,
1/X/397:399		NANA
1/X/383:384,
1/X/395:397		NANA
1/X/510:520,
1/X/547:552		NANA
1/X/522:529,
1/X/536:545		NANA
1/X/599:607,
1/X/647:656		NANA
1/X/607:610,
1/X/645:647		NANA
1/X/662:667,
1/X/754:762		NANA
1/X/669:674,
1/X/748:752		NANA
1/X/679:681,
1/X/725:743		NANA
1/X/681:690,
1/X/718:725		NANA
1/X/787:791,
1/X/807:811		NANA
1/X/897:906,
1/X/913:920		NANA
1/X/1314:1320,
1/X/1339:1345		NANA
1/X/1440:1442,
1/X/1482:1483		NANA
1/X/1442:1446,
1/X/1478:1482		NANA
1/X/1446:1448,
1/X/1476:1478		NANA
1/X/1449:1454,
1/X/1471:1475		NANA
1/X/1524:1527,
1/X/1532:1535		NANA
1/Y/4:7,
1/Y/2915:2918		Tandem non-canonical cWW pairs
geometric
IL_1L9A_005		NA

IL_85877.10*
1/Y/24:30,
1/Y/555:561		Triple sheared with non-canonical cWW
geometric
IL_4WF9_001		NA

IL_66414.5*
1/Y/36:37,
1/Y/488:490		Single bulged A
homologous
IL_7RQB_002		NA

IL_80007.16*
1/Y/42:44,
1/Y/480:483		Minor groove platform with extra cWW
geometric
IL_4WF9_003		NA

IL_87332.1*
1/Y/80:85,
1/Y/97:105
geometric
IL_6CZR_143		NA

IL_37722.1*
1/Y/186:187,
1/Y/215:217		NANA
1/Y/190:197,
1/Y/204:212		9x8 Sarcin-Ricin; G-bulge
geometric
IL_4WF9_008		NA

IL_61812.1*
1/Y/241:248,
1/Y/256:262		8x7 Sarcin-Ricin; G-bulge
geometric
IL_4WF9_009		NA

IL_04346.5*
1/Y/304:308,
1/Y/407:413		NANA
1/Y/336:338,
1/Y/386:390		NANA
1/Y/527:530,
1/Y/541:554
geometric
IL_4WF9_015		NA

IL_60992.5*
1/Y/581:584,
1/Y/597:600		Double sheared
geometric
IL_4WF9_016		NA

IL_09705.7*
1/Y/607:609,
1/Y/618:620
geometric
IL_4WF9_017		NA

IL_01312.13*
1/Y/638:640,
1/Y/705:707
geometric
IL_2O3V_004		NA

IL_01312.13*
1/Y/649:653,
1/Y/663:667		AAA cross-strand stack
homologous
IL_7RQB_016		NA

IL_56467.6*
1/Y/717:719,
1/Y/851:853
geometric
IL_7RQB_017		NA

IL_01312.13*
1/Y/719:723,
1/Y/844:851
homologous
IL_7RQB_018		NA

IL_17470.5*
1/Y/742:743,
1/Y/808:810		Single bulged A
homologous
IL_7RQB_019		NA

IL_80007.16*
1/Y/783:785,
1/Y/802:803		Major groove platform
geometric
IL_5J7L_264		NA

IL_80663.10*
1/Y/820:822,
1/Y/832:836		Multiple bulged bases
homologous
IL_7RQB_023		NA

IL_90991.5*
1/Y/882:883,
1/Y/984:986		Single stack bend
homologous
IL_7RQB_024		NA

IL_04038.4*
1/Y/889:893,
1/Y/975:978
geometric
IL_4WF9_029		NA

IL_06300.1*
1/Y/897:898,
1/Y/969:971		Single bulged U
geometric
IL_2A64_002		NA

IL_83039.11*
1/Y/901:907,
1/Y/960:966		7x7 Sarcin-Ricin with intercalated A; G-bulge
geometric
IL_4WF9_031		NA

IL_93830.2*
1/Y/907:908,
1/Y/958:960		Minor groove platform
geometric
IL_7RQB_028		NA

IL_06437.11*
1/Y/909:913,
1/Y/954:957		C-loop
homologous
IL_7RQB_029		NA

IL_63596.4*
1/Y/1038:1040,
1/Y/1203:1204		Single bulged C
homologous
IL_7RQB_035		NA

IL_61258.10*
1/Y/1042:1046,
1/Y/1197:1201		UAA/GAN
homologous
IL_7RQB_036		NA

IL_53523.5*
1/Y/1048:1055,
1/Y/1194:1195		SSU/LSU pseudoknot
geometric
IL_7A0S_034		NA

IL_15861.6*
1/Y/1055:1057,
1/Y/1193:1194		Single bulged U
homologous
IL_7RQB_038		NA

IL_83039.11*
1/Y/1062:1068,
1/Y/1184:1188
homologous
IL_7RQB_039		NA

IL_57188.3*
1/Y/1068:1074,
1/Y/1168:1184
geometric
IL_4WF9_040		NA

IL_22615.1*
1/Y/1075:1078,
1/Y/1165:1167		Isolated non-canonical cWW with bulges
homologous
IL_7RQB_041		NA

IL_55456.1*
1/Y/1081:1083,
1/Y/1160:1162
geometric
IL_4WF9_042		NA

IL_01312.13*
1/Y/1235:1237,
1/Y/1285:1288		Isolated cWS basepair
homologous
IL_7RQB_045		NA

IL_67621.5*
1/Y/1243:1245,
1/Y/1277:1279		Isolated cWH basepair
geometric
IL_4WF9_045		NA

IL_42589.6*
1/Y/1246:1253,
1/Y/1272:1276		Kink-turn
homologous
IL_7RQB_047		NA

IL_29549.9*
1/Y/1257:1259,
1/Y/1266:1268		Intercalated cWW
geometric
IL_4WF9_047		NA

IL_04038.4*
1/Y/1300:1307,
1/Y/2038:2044		8x7 Sarcin-Ricin; G-bulge
homologous
IL_7RQB_049		NA

IL_04346.5*
1/Y/1356:1360,
1/Y/1368:1370		NANA
1/Y/1388:1392,
1/Y/1413:1417		UAA/GAN
geometric
IL_4WF9_051		NA

IL_34907.2*
1/Y/1394:1398,
1/Y/1407:1411		tSH-tHW-tHS
homologous
IL_7RQB_053		NA

IL_39521.5*
1/Y/1695:1700,
1/Y/2031:2033
homologous
IL_7RQB_064		NA

IL_12566.2*
1/Y/1707:1709,
1/Y/2022:2024		Isolated tWW turn
homologous
IL_7RQB_065		NA

IL_54997.5*
1/Y/1710:1713,
1/Y/2020:2021		Major groove platform; stack outside cWW
geometric
IL_4WF9_064		NA

IL_70995.6*
1/Y/1713:1718,
1/Y/2017:2020		Intercalated tWH
homologous
IL_7RQB_067		NA

IL_01312.13*
1/Y/1730:1735,
1/Y/1740:1746		tSH-tSH-tHH-tHS
homologous
IL_7RQB_068		NA

IL_66584.5*
1/Y/1797:1798,
1/Y/2007:2009		Single bulged A
homologous
IL_7RQB_069		NA

IL_80007.16*
1/Y/1825:1831,
1/Y/1840:1848		Kink-turn related
homologous
IL_7RQB_070		NA

IL_17069.3*
1/Y/1864:1867,
1/Y/1929:1930		Major groove outside cWW, minor groove, intercalation pocket
homologous
IL_7RQB_071		NA

IL_31836.1*
1/Y/1868:1869,
1/Y/1925:1928		Major groove outside cWW, minor groove, intercalation pocket
geometric
IL_4WF9_071		NA

IL_13730.12*
1/Y/1873:1876,
1/Y/1920:1921		NANA
1/Y/1877:1883,
1/Y/1913:1919		NANA
1/Y/1960:1961,
1/Y/1991:1994
geometric
IL_4V9F_070		NA

IL_69632.1*
1/Y/1961:1972,
1/Y/1988:1991
geometric
IL_7A0S_072		NA

IL_07097.1*
1/Y/2077:2079,
1/Y/2644:2645		Major groove platform
homologous
IL_7RQB_078		NA

IL_80663.10*
1/Y/2081:2083,
1/Y/2639:2642
geometric
IL_5J7L_321		NA

IL_54678.3*
1/Y/2094:2096,
1/Y/2469:2470		Single bulged U
homologous
IL_7RQB_080		NA

IL_83039.11*
1/Y/2097:2098,
1/Y/2465:2468		Minor groove platform
homologous
IL_7RQB_081		NA

IL_06437.11*
1/Y/2108:2110,
1/Y/2263:2266		Isolated tHS basepair with bulges
homologous
IL_7RQB_082		NA

IL_38958.6*
1/Y/2111:2113,
1/Y/2260:2262
homologous
IL_7RQB_083		NA

IL_01312.13*
1/Y/2123:2126,
1/Y/2217:2220		Tandem non-canonical cWW pairs
geometric
IL_1D4R_001		NA

IL_85877.10*
1/Y/2126:2128,
1/Y/2215:2217		NANA
1/Y/2229:2236,
1/Y/2242:2248		NANA
1/Y/2324:2328,
1/Y/2342:2348		NANA
1/Y/2377:2380,
1/Y/2391:2394		Double sheared
homologous
IL_7RQB_089		NA

IL_09705.7*
1/Y/2426:2431,
1/Y/2440:2444		NANA
1/Y/2480:2481,
1/Y/2525:2527		Single stack bend
homologous
IL_7RQB_091		NA

IL_04038.4*
1/Y/2481:2482,
1/Y/2523:2525		Major groove platform
geometric
IL_4V9F_082		NA

IL_80663.10*
1/Y/2484:2486,
1/Y/2520:2521		Major groove platform
geometric
IL_7A0S_085		NA

IL_80663.10*
1/Y/2486:2488,
1/Y/2516:2520		Major groove minor groove platform with extra cWW
geometric
IL_7RQB_094		NA

IL_96042.4*
1/Y/2493:2497,
1/Y/2507:2511		Triple sheared
geometric
IL_4V9F_085		NA

IL_56467.6*
1/Y/2534:2536,
1/Y/2606:2609		Major groove platform with extra pair
geometric
IL_7RQB_093		NA

IL_87630.5*
1/Y/2537:2539,
1/Y/2601:2605		Isolated non-canonical cWW with bulges
homologous
IL_7RQB_097		NA

IL_01312.13*
1/Y/2539:2540,
1/Y/2598:2601
geometric
IL_4WF9_096		NA

IL_69632.1*
1/Y/2548:2552,
1/Y/2565:2571		NANA
1/Y/2618:2619,
1/Y/2628:2630		Major groove platform
geometric
IL_4LFB_028		NA

IL_80663.10*
1/Y/2663:2667,
1/Y/2801:2809		tSH-tHS-tHW
homologous
IL_7RQB_102		NA

IL_34907.2*
1/Y/2707:2711,
1/Y/2752:2754		C-loop
homologous
IL_7RQB_104		NA

IL_63596.4*
1/Y/2714:2718,
1/Y/2745:2749
homologous
IL_7RQB_105		NA

IL_08296.3*
1/Y/2722:2723,
1/Y/2738:2741		Multiple bulged bases
homologous
IL_7RQB_106		NA

IL_77034.1*
1/Y/2764:2770,
1/Y/2788:2794		NANA
1/Y/2858:2859,
1/Y/2898:2900		Single bulged C
homologous
IL_7RQB_108		NA

IL_61258.10*
1/Y/2863:2865,
1/Y/2891:2894
geometric
IL_4WF9_107		NA

IL_02284.3*
1/Y/2867:2872,
1/Y/2885:2889
homologous
IL_7RQB_110		NA

IL_83162.3*

Problematic loops

No problematic loops

Valid loops

#loop idlocationannotation
(mapped to, source)		motif group
(similar to)
1/X/45:48,
1/X/369:378,
1/X/399:406		NANA
1/X/833:838,
1/X/866:871,
1/X/878:885		NANA
1/X/1000:1008,
1/X/1055:1059,
1/X/1221:1226		NANA
1/X/1084:1087,
1/X/1094:1100,
1/X/1109:1115		NANA
1/Y/30:31,
1/Y/520:527,
1/Y/554:555
homologous
J3_7RQB_001		NA
1/Y/56:67,
1/Y/74:76,
1/Y/109:113		NANA
1/Y/272:276,
1/Y/295:302,
1/Y/415:416
homologous
J3_7RQB_003		NA
1/Y/728:734,
1/Y/818:820,
1/Y/836:839		NANA
1/Y/743:745,
1/Y/777:781,
1/Y/805:808		NANA
1/Y/1335:1340,
1/Y/1669:1671,
1/Y/1683:1686
homologous
J3_7RQB_007		NA
1/Y/1343:1346,
1/Y/1649:1655,
1/Y/1664:1666
homologous
J3_7RQB_008		NA
1/Y/1860:1863,
1/Y/1931:1960,
1/Y/1994:1999		NANA
1/Y/2118:2120,
1/Y/2223:2229,
1/Y/2248:2255		NANA
1/Y/2322:2324,
1/Y/2348:2350,
1/Y/2359:2364		NANA
1/Y/2544:2547,
1/Y/2572:2574,
1/Y/2588:2594
homologous
J3_7RQB_012		NA
1/Y/2834:2835,
1/Y/2851:2856,
1/Y/2902:2906		NANA

Problematic loops

#loop idProblemSequence
J3_7ASO_001NA

Coloring options:
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