RNA 3D Hub //

3J6B Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_3J6B_0031/A/153:158No text annotation
geometric
HL_5NFV_001
HL_69752.3
HL_3J6B_0041/A/234:241No text annotation
homologous
HL_4WF9_006
HL_48677.1
HL_3J6B_0051/A/265:270No text annotation
homologous
HL_5J7L_140
NA
HL_3J6B_0061/A/286:292No text annotation
homologous
HL_7A0S_008
HL_76371.1
HL_3J6B_0071/A/324:332No text annotation
geometric
HL_5U3G_001
NA
HL_3J6B_0081/A/347:355No text annotation
homologous
HL_7RQB_014
NA
HL_3J6B_0091/A/393:398GNRA
homologous
HL_4WF9_015
HL_34789.1
HL_3J6B_0101/A/440:449UNCG variation
geometric
HL_5J7L_200
NA
HL_3J6B_0111/A/465:474T-loop with 2 stacked bulged bases
geometric
HL_5J7L_150
NA
HL_3J6B_0121/A/505:511No text annotation
HL_3J6B_0131/A/542:551No text annotation
geometric
HL_4TUE_219
NA
HL_3J6B_0141/A/612:619No text annotation
geometric
HL_5TBW_006
NA
HL_3J6B_0151/A/635:644No text annotation
homologous
HL_7RQB_023
NA
HL_3J6B_0161/A/670:676No text annotation
homologous
HL_7RQB_024
NA
HL_3J6B_0171/A/717:722No text annotation
homologous
HL_5J7L_157
NA
HL_3J6B_0181/A/881:888GNRA
homologous
HL_7RQB_027
NA
HL_3J6B_0191/A/904:911No text annotation
homologous
HL_4WF9_028
HL_47171.1
HL_3J6B_0241/A/1254:1258Mini UNCG
geometric
HL_5J7L_204
NA
HL_3J6B_0251/A/1313:1320No text annotation
HL_3J6B_0261/A/1343:1351No text annotation
HL_3J6B_0271/A/1384:1389No text annotation
geometric
HL_5TBW_006
NA
HL_3J6B_0291/A/1564:1571No text annotation
homologous
HL_7RQB_040
NA
HL_3J6B_0301/A/1581:1589GNRA with extra cWW
homologous
HL_4WF9_039
HL_45359.1
HL_3J6B_0311/A/1643:1649UNCG
geometric
HL_6DLR_002
HL_61337.1
HL_3J6B_0321/A/1684:1694No text annotation
homologous
HL_4WF9_043
HL_87681.1
HL_3J6B_0331/A/1713:1719GNRA related
homologous
HL_5J7L_179
NA
HL_3J6B_0341/A/1773:1778GNRA
homologous
HL_7RQB_047
NA
HL_3J6B_0361/A/1849:1857No text annotation
homologous
HL_5J7L_182
NA
HL_3J6B_0371/A/1927:1936No text annotation
homologous
HL_4WF9_047
HL_78372.1
HL_3J6B_0391/A/2196:2201No text annotation
geometric
HL_1KH6_003
HL_05426.1
HL_3J6B_0411/A/2290:2302No text annotation
homologous
HL_5J7L_187
NA
HL_3J6B_0421/A/2327:2332No text annotation
geometric
HL_1WZ2_007
HL_75660.6
HL_3J6B_0431/A/2357:2363No text annotation
geometric
HL_5NFV_001
HL_69752.3
HL_3J6B_0451/A/2454:2462No text annotation
geometric
HL_4V9F_057
HL_02452.1
HL_3J6B_0611/A/2590:2597Pseudoknot geometry
homologous
HL_5J7L_189
NA
HL_3J6B_0481/A/2622:2629GNRA with extra cWW
homologous
HL_4WF9_053
HL_45359.1
HL_3J6B_0491/A/2641:2646GNRA
homologous
HL_7RQB_058
NA
HL_3J6B_0501/A/2671:2680No text annotation
homologous
HL_5J7L_192
NA
HL_3J6B_0511/A/2737:2745No text annotation
homologous
HL_4WF9_056
HL_52011.1
HL_3J6B_0521/A/2794:2802No text annotation
homologous
HL_7RQB_061
NA
HL_3J6B_0531/A/2818:2824No text annotation
homologous
HL_4WF9_058
HL_48677.1
HL_3J6B_0541/A/2861:2866GNRA
homologous
HL_5J7L_196
NA
HL_3J6B_0551/A/2925:2930GNRA
geometric
HL_5B2P_001
HL_34789.1
HL_3J6B_0621/A/3022:3029Pseudoknot geometry
geometric
HL_3HHN_009
HL_30680.4
HL_3J6B_0581/A/3081:3096No text annotation
homologous
HL_5J7L_199
NA
HL_3J6B_0591/A/3135:3143No text annotation
geometric
HL_7RQB_068
NA

Problematic loops

#loop idProblemSequence
HL_3J6B_001No text annotation
HL_3J6B_002No text annotation
HL_3J6B_020No text annotation
HL_3J6B_021Mini UNCG
HL_3J6B_022No text annotation
HL_3J6B_023Mini UNCG
HL_3J6B_028No text annotation
HL_3J6B_035No text annotation
HL_3J6B_038No text annotation
HL_3J6B_040No text annotation
HL_3J6B_044No text annotation
HL_3J6B_046No text annotation
HL_3J6B_047No text annotation
HL_3J6B_056No text annotation
HL_3J6B_057No text annotation
HL_3J6B_060Purine riboswitch

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_3J6B_0011/A/22:24,
1/A/3275:3277		Isolated non-canonical cWW pair
geometric
IL_2OE5_001
NA
IL_3J6B_0021/A/25:32,
1/A/3273:3274		No text annotation
IL_3J6B_0031/A/58:63,
1/A/407:413		Triple sheared with non-canonical cWW
geometric
IL_7A0S_018
IL_57885.1
IL_3J6B_0041/A/96:97,
1/A/378:380		Single bulged A
homologous
IL_7RQB_002
NA
IL_3J6B_0051/A/113:121,
1/A/140:145		No text annotation
IL_3J6B_0081/A/223:224,
1/A/252:254		Single stack bend
homologous
IL_5J7L_249
NA
IL_3J6B_0091/A/228:234,
1/A/241:248		8x7 Sarcin-Ricin; G-bulge
geometric
IL_5J7L_250
NA
IL_3J6B_0101/A/279:285,
1/A/293:298		7x6 Sarcin-Ricin; G-bulge
homologous
IL_7RQB_007
NA
IL_3J6B_0111/A/433:436,
1/A/453:456		No text annotation
IL_3J6B_0121/A/463:465,
1/A/474:476		No text annotation
homologous
IL_7RQB_015
NA
IL_3J6B_0131/A/581:583,
1/A/697:699		Isolated non-canonical cWW pair
homologous
IL_4WF9_020
IL_01003.1
IL_3J6B_0141/A/583:587,
1/A/690:697		tHW-tHW cross-strand stack
geometric
IL_7RQB_018
NA
IL_3J6B_0151/A/606:607,
1/A/654:656		Single bulged A
homologous
IL_5J7L_261
NA
IL_3J6B_0161/A/611:612,
1/A/619:621		Single bulged G
homologous
IL_4WF9_023
IL_28408.1
IL_3J6B_0171/A/629:632,
1/A/647:649		Major groove platform with extra cWW
homologous
IL_7RQB_022
NA
IL_3J6B_0181/A/666:669,
1/A/677:682		No text annotation
IL_3J6B_0961/A/728:729,
1/A/866:868		Single stack bend
homologous
IL_9DFE_022
IL_15011.1
IL_3J6B_0201/A/734:738,
1/A/858:861		Tandem non-canonical cWW pairs
geometric
IL_5J7L_033
NA
IL_3J6B_0911/A/734:740,
1/A/855:861		No text annotation
IL_3J6B_0211/A/738:740,
1/A/855:858		No text annotation
IL_3J6B_0221/A/780:785,
1/A/841:846		5x5 Sarcin-Ricin with intercalated A; G-bulge
homologous
IL_7A0S_027
NA
IL_3J6B_0231/A/785:786,
1/A/839:841		Minor groove platform related
geometric
IL_7TZS_003
IL_34520.1
IL_3J6B_0241/A/787:791,
1/A/835:838		C-loop with bulged stacked A's
homologous
IL_5J7L_272
NA
IL_3J6B_0251/A/797:799,
1/A/828:829		Single bulged A
geometric
IL_5TBW_060
NA
IL_3J6B_0281/A/877:879,
1/A/890:892		Isolated non-canonical cWW pair
homologous
IL_7A0S_031
IL_01003.1
IL_3J6B_0291/A/919:922,
1/A/1179:1181		Major groove platform with extra pair
geometric
IL_5TBW_091
NA
IL_3J6B_0301/A/924:928,
1/A/1173:1177		UAA/GAN
geometric
IL_4WF9_036
IL_08938.1
IL_3J6B_0311/A/943:949,
1/A/1106:1120		Kink-turn related
geometric
IL_4WF9_039
IL_57188.6
IL_3J6B_0921/A/950:957,
1/A/1091:1105		No text annotation
IL_3J6B_0321/A/1230:1232,
1/A/1280:1283		Isolated cWS basepair
homologous
IL_5J7L_286
NA
IL_3J6B_0331/A/1237:1244,
1/A/1268:1275		No text annotation
IL_3J6B_0341/A/1295:1302,
1/A/1911:1917		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
NA
IL_3J6B_0351/A/1355:1362,
1/A/1403:1409		No text annotation
IL_3J6B_0361/A/1364:1368,
1/A/1397:1401		UAA/GAN
homologous
IL_5J7L_292
NA
IL_3J6B_0371/A/1370:1372,
1/A/1394:1395		Single bulged A
geometric
IL_4WF9_006
IL_14190.1
IL_3J6B_0411/A/1492:1493,
1/A/1515:1521		No text annotation
IL_3J6B_0421/A/1603:1608,
1/A/1904:1906		No text annotation
homologous
IL_5J7L_304
NA
IL_3J6B_0431/A/1615:1617,
1/A/1895:1897		Isolated tWW turn
homologous
IL_5J7L_305
NA
IL_3J6B_0441/A/1618:1621,
1/A/1893:1894		Major groove platform; stack outside cWW
homologous
IL_7RQB_066
NA
IL_3J6B_0931/A/1618:1626,
1/A/1890:1894		No text annotation
homologous
IL_5J7L_386
NA
IL_3J6B_0451/A/1621:1626,
1/A/1890:1893		Intercalated tWH
geometric
IL_5J7L_307
NA
IL_3J6B_0461/A/1635:1636,
1/A/1658:1668		No text annotation
IL_3J6B_0471/A/1638:1643,
1/A/1649:1656		No text annotation
IL_3J6B_0481/A/1677:1678,
1/A/1880:1882		Single bulged A
homologous
IL_7RQB_069
NA
IL_3J6B_0491/A/1705:1711,
1/A/1721:1729		Kink-turn related
homologous
IL_7RQB_070
NA
IL_3J6B_0501/A/1745:1748,
1/A/1803:1804		Major groove minor groove platform; mini C-loop
geometric
IL_5J7L_029
NA
IL_3J6B_0511/A/1749:1750,
1/A/1799:1802		Major groove intercalation
homologous
IL_5J7L_315
NA
IL_3J6B_0521/A/1754:1757,
1/A/1793:1795		No text annotation
geometric
IL_4V84_070
NA
IL_3J6B_0531/A/1757:1764,
1/A/1786:1793		No text annotation
IL_3J6B_0541/A/1764:1766,
1/A/1785:1786		Single stack bend
geometric
IL_5TBW_375
NA
IL_3J6B_0551/A/1833:1834,
1/A/1864:1867		Bulged stacked bases
geometric
IL_4V9F_070
IL_24886.1
IL_3J6B_0561/A/1834:1845,
1/A/1861:1864		No text annotation
homologous
IL_4WF9_077
IL_84014.1
IL_3J6B_0571/A/1950:1952,
1/A/2884:2885		Major groove platform
homologous
IL_5J7L_320
NA
IL_3J6B_0581/A/1954:1956,
1/A/2879:2882		No text annotation
homologous
IL_5J7L_321
NA
IL_3J6B_0591/A/1967:1969,
1/A/2708:2709		Single bulged U
homologous
IL_4WF9_080
IL_97561.1
IL_3J6B_0601/A/1970:1971,
1/A/2704:2707		Minor groove platform
homologous
IL_7RQB_081
NA
IL_3J6B_0611/A/1981:1983,
1/A/2262:2265		Isolated tHS basepair with bulges
homologous
IL_5J7L_325
NA
IL_3J6B_0621/A/1988:1991,
1/A/2256:2257		Multiple bulged bases
geometric
IL_6JXM_001
NA
IL_3J6B_0641/A/2287:2288,
1/A/2304:2306		No text annotation
IL_3J6B_0651/A/2437:2440,
1/A/2608:2610		No text annotation
IL_3J6B_0661/A/2468:2472,
1/A/2578:2581		No text annotation
IL_3J6B_0671/A/2617:2620,
1/A/2631:2634		Double sheared
homologous
IL_7RQB_089
NA
IL_3J6B_0681/A/2668:2670,
1/A/2681:2682		Major groove platform
homologous
IL_7RQB_090
NA
IL_3J6B_0691/A/2720:2721,
1/A/2762:2764		Major groove platform
geometric
IL_7A0S_084
IL_48076.7
IL_3J6B_0701/A/2723:2725,
1/A/2759:2760		Major groove platform
geometric
IL_4WF9_091
IL_48076.7
IL_3J6B_0711/A/2725:2727,
1/A/2755:2759		Major groove minor groove platform with extra cWW
homologous
IL_5J7L_337
NA
IL_3J6B_0721/A/2731:2736,
1/A/2746:2751		tSH-tHW-tHS-cWW
geometric
IL_6DVK_004
NA
IL_3J6B_0731/A/2773:2774,
1/A/2847:2849		Major groove platform
homologous
IL_7A0S_088
IL_46637.1
IL_3J6B_0741/A/2776:2778,
1/A/2841:2845		Isolated non-canonical cWW with bulges
geometric
IL_5J7L_340
NA
IL_3J6B_0751/A/2778:2779,
1/A/2838:2841		No text annotation
homologous
IL_5J7L_341
NA
IL_3J6B_0761/A/2788:2789,
1/A/2807:2810		Major groove platform with intercalation
homologous
IL_7RQB_099
NA
IL_3J6B_0771/A/2858:2859,
1/A/2868:2870		Single bulged A
homologous
IL_5J7L_344
NA
IL_3J6B_0781/A/2902:2906,
1/A/3112:3116		Triple sheared
geometric
IL_7RQB_075
NA
IL_3J6B_0791/A/2919:2925,
1/A/2930:2935		Sarcin-Ricin target in LSU H95; G-bulge
homologous
IL_5J7L_346
NA
IL_3J6B_0801/A/2947:2951,
1/A/3061:3063		C-loop
homologous
IL_7RQB_104
NA
IL_3J6B_0811/A/2954:2959,
1/A/3053:3058		No text annotation
IL_3J6B_0821/A/2962:2963,
1/A/3047:3050		Multiple bulged bases
homologous
IL_5J7L_349
NA
IL_3J6B_0831/A/2970:2971,
1/A/3038:3040		Single bulged A
geometric
IL_7RQB_101
NA
IL_3J6B_0851/A/3073:3078,
1/A/3099:3104		UAA/GAN with extra cWW
homologous
IL_7RQB_107
NA
IL_3J6B_0861/A/3123:3126,
1/A/3259:3260		Multiple bulged bases
geometric
IL_7V9E_001
NA
IL_3J6B_0951/A/3158:3159,
1/A/3246:3248		Major groove intercalation
geometric
IL_7JNH_003
NA
IL_3J6B_0881/A/3161:3162,
1/A/3242:3244		Single stack bend
geometric
IL_4V83_236
IL_15011.1

Problematic loops

#loop idProblemSequence
IL_3J6B_006Tandem non-canonical cWW pairs
IL_3J6B_007Isolated non-canonical cWW contact
IL_3J6B_019No text annotation
IL_3J6B_026No text annotation
IL_3J6B_097Single stack bend
IL_3J6B_027Single stack bend
IL_3J6B_038Tandem non-canonical cWW pairs
IL_3J6B_039Isolated non-canonical cWW pair
IL_3J6B_040Tandem non-canonical cWW pairs
IL_3J6B_094No text annotation
IL_3J6B_063Isolated non-canonical cWW pair
IL_3J6B_084No text annotation
IL_3J6B_087Isolated non-canonical cWW with bulges
IL_3J6B_089No text annotation
IL_3J6B_090No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_3J6B_0131/A/309:319,
1/A/337:344,
1/A/358:361		No text annotation
J3_3J6B_0011/A/592:598,
1/A/664:666,
1/A/682:685		No text annotation
homologous
J3_7RQB_004
NA
J3_3J6B_0141/A/592:598,
1/A/664:669,
1/A/677:685		No text annotation
J3_3J6B_0021/A/607:609,
1/A/623:627,
1/A/651:654		No text annotation
homologous
J3_7RQB_005
NA
J3_3J6B_0031/A/746:747,
1/A/775:780,
1/A/846:849		No text annotation
J3_3J6B_0041/A/961:962,
1/A/1062:1068,
1/A/1085:1087		No text annotation
J3_3J6B_0051/A/1329:1334,
1/A/1577:1580,
1/A/1590:1594		No text annotation
J3_3J6B_0061/A/1337:1340,
1/A/1557:1563,
1/A/1572:1574		No text annotation
homologous
J3_7A0S_007
J3_47341.1
J3_3J6B_0071/A/1426:1432,
1/A/1489:1491,
1/A/1522:1527		No text annotation
J3_3J6B_0081/A/1626:1635,
1/A/1668:1672,
1/A/1887:1890		No text annotation
J3_3J6B_0101/A/1993:1995,
1/A/2091:2095,
1/A/2249:2254		No text annotation
J3_3J6B_0151/A/2309:2311,
1/A/2651:2663,
1/A/2687:2693		No text annotation
J3_3J6B_0111/A/2783:2786,
1/A/2812:2814,
1/A/2828:2834		No text annotation
homologous
J3_5J7L_046
NA
J3_3J6B_0161/A/2972:2976,
1/A/3013:3021,
1/A/3030:3037		No text annotation
J3_3J6B_0121/A/3130:3131,
1/A/3147:3156,
1/A/3250:3255		No text annotation
J4_3J6B_0011/A/66:71,
1/A/91:95,
1/A/381:392,
1/A/399:404		No text annotation
J4_3J6B_0021/A/930:937,
1/A/1126:1127,
1/A/1142:1144,
1/A/1168:1171		No text annotation
J4_3J6B_0031/A/1303:1308,
1/A/1325:1326,
1/A/1597:1600,
1/A/1909:1910		No text annotation
homologous
J4_4WF9_004
J4_64571.6
J4_3J6B_0041/A/1340:1343,
1/A/1351:1354,
1/A/1410:1413,
1/A/1545:1557		No text annotation
J4_3J6B_0051/A/1679:1683,
1/A/1695:1699,
1/A/1735:1740,
1/A/1873:1879		No text annotation
J4_3J6B_0061/A/1741:1743,
1/A/1806:1807,
1/A/1824:1833,
1/A/1867:1872		No text annotation
homologous
J4_9DFE_008
J4_42306.1
J4_3J6B_0071/A/2445:2450,
1/A/2466:2467,
1/A/2582:2589,
1/A/2598:2603		No text annotation
J4_3J6B_0081/A/2910:2913,
1/A/2941:2942,
1/A/3068:3072,
1/A/3105:3108		No text annotation
J5_3J6B_0011/A/428:430,
1/A/459:463,
1/A/476:478,
1/A/1294:1295,
1/A/1917:1918		No text annotation
homologous
J5_9DFE_003
J5_43153.6
J5_3J6B_0021/A/483:488,
1/A/577:580,
1/A/700:703,
1/A/1229:1230,
1/A/1283:1289		No text annotation
homologous
J5_4WF9_004
J5_74302.6
J5_3J6B_0031/A/1974:1977,
1/A/2269:2272,
1/A/2284:2285,
1/A/2308:2309,
1/A/2693:2701		No text annotation
homologous
J5_4WF9_007
J5_39529.2
J6_3J6B_0011/A/2312:2317,
1/A/2375:2381,
1/A/2421:2440,
1/A/2608:2614,
1/A/2637:2639,
1/A/2648:2650		No text annotation
J7_3J6B_0011/A/43:49,
1/A/422:428,
1/A/1918:1923,
1/A/1940:1943,
1/A/2892:2898,
1/A/3120:3123,
1/A/3260:3262		No text annotation
J7_3J6B_0021/A/708:713,
1/A/726:727,
1/A/869:872,
1/A/897:902,
1/A/913:917,
1/A/1183:1184,
1/A/1219:1224		No text annotation

Problematic loops

#loop idProblemSequence
J3_3J6B_009No text annotation

Coloring options:
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