RNA 3D Hub //

6VMI Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_6VMI_0011/A/1722:1729No text annotation
geometric
HL_4WF9_006
HL_48677.1
HL_6VMI_0021/A/1746:1752No text annotation
geometric
HL_4WF9_008
HL_76371.2
HL_6VMI_0031/A/1786:1791GNRA
homologous
HL_4WF9_015
HL_34789.4
HL_6VMI_0041/A/1831:1839No text annotation
homologous
HL_5J7L_149
NA
HL_6VMI_0051/A/1845:1858No text annotation
HL_6VMI_0061/A/1884:1889No text annotation
geometric
HL_5J7L_143
NA
HL_6VMI_0071/A/1934:1940No text annotation
HL_6VMI_0081/A/1954:1963No text annotation
homologous
HL_4WF9_023
HL_50204.1
HL_6VMI_0091/A/1988:1996No text annotation
geometric
HL_5TBW_021
NA
HL_6VMI_0101/A/2035:2040No text annotation
homologous
HL_4WF9_025
HL_27530.1
HL_6VMI_0111/A/2064:2075Externally structured
geometric
HL_8C3A_022
NA
HL_6VMI_0121/A/2107:2114GNRA
homologous
HL_7A0S_026
HL_34789.4
HL_6VMI_0131/A/2129:2136No text annotation
homologous
HL_5J7L_160
NA
HL_6VMI_0161/A/2279:2286No text annotation
geometric
HL_8H9D_001
NA
HL_6VMI_0171/A/2319:2324No text annotation
geometric
HL_7RQB_011
NA
HL_6VMI_0191/A/2400:2403Mini UNCG
geometric
HL_5U30_001
HL_90436.3
HL_6VMI_0201/A/2428:2435No text annotation
homologous
HL_4WF9_038
HL_28592.2
HL_6VMI_0211/A/2497:2507No text annotation
homologous
HL_5J7L_178
NA
HL_6VMI_0221/A/2518:2532No text annotation
HL_6VMI_0231/A/2555:2560No text annotation
geometric
HL_5TBW_006
NA
HL_6VMI_0641/A/2613:2619Mini UNCG
geometric
HL_5T16_002
HL_12626.2
HL_6VMI_0261/A/2690:2699No text annotation
homologous
HL_4WF9_047
HL_78372.1
HL_6VMI_0281/A/2812:2820No text annotation
homologous
HL_7A0S_052
HL_11974.2
HL_6VMI_0291/A/2828:2840No text annotation
HL_6VMI_0301/A/2862:2870No text annotation
geometric
HL_2ZZM_002
HL_33487.1
HL_6VMI_0311/A/2902:2907No text annotation
geometric
HL_5U3G_001
HL_75660.8
HL_6VMI_0321/A/2958:2966No text annotation
homologous
HL_4WF9_056
HL_52011.1
HL_6VMI_0331/A/3015:3022GNRA variation
homologous
HL_4WF9_057
HL_46665.2
HL_6VMI_0351/A/3081:3086GNRA
homologous
HL_5J7L_196
NA
HL_6VMI_0371/A/3154:3159Externally structured
geometric
HL_8C3A_022
NA
HL_6VMI_0381/A/3176:3193No text annotation
geometric
HL_7A0S_074
NA
HL_6VMI_0391/A/3216:3224No text annotation
geometric
HL_7A0S_067
HL_37889.1
HL_6VMI_0401/AA/654:664No text annotation
geometric
HL_5J7L_001
NA
HL_6VMI_0431/AA/768:773Mini UNCG
geometric
HL_4YAZ_004
HL_90436.3
HL_6VMI_0441/AA/792:796No text annotation
geometric
HL_5TBW_004
NA
HL_6VMI_0721/AA/990:997No text annotation
geometric
HL_5J7L_025
NA
HL_6VMI_0491/AA/1023:1028No text annotation
geometric
HL_5U3G_001
HL_75660.8
HL_6VMI_0501/AA/1074:1084No text annotation
geometric
HL_6CZR_088
NA
HL_6VMI_0511/AA/1115:1126No text annotation
geometric
HL_2Y8W_001
HL_40612.1
HL_6VMI_0521/AA/1150:1155No text annotation
geometric
HL_2Y8W_001
HL_40612.1
HL_6VMI_0541/AA/1281:1287No text annotation
geometric
HL_1WZ2_007
HL_75660.8
HL_6VMI_0581/AA/1440:1450tRNA D-loop
geometric
HL_4V90_032
NA
HL_6VMI_0601/AA/1580:1585No text annotation
geometric
HL_5NFV_001
HL_69752.4
HL_6VMI_0621/B/1630:1638Anticodon loop related
geometric
HL_4R4V_001
HL_81376.3

Problematic loops

#loop idProblemSequence
HL_6VMI_063No text annotation
HL_6VMI_014No text annotation
HL_6VMI_015No text annotation
HL_6VMI_018No text annotation
HL_6VMI_024No text annotation
HL_6VMI_025No text annotation
HL_6VMI_027No text annotation
HL_6VMI_065No text annotation
HL_6VMI_034No text annotation
HL_6VMI_036GNRA
HL_6VMI_066No text annotation
HL_6VMI_067No text annotation
HL_6VMI_068No text annotation
HL_6VMI_069No text annotation
HL_6VMI_070No text annotation
HL_6VMI_041No text annotation
HL_6VMI_071No text annotation
HL_6VMI_042No text annotation
HL_6VMI_045Mini UNCG
HL_6VMI_046GNRA
HL_6VMI_047GNRA with GA tSW pair
HL_6VMI_048No text annotation
HL_6VMI_053No text annotation
HL_6VMI_055No text annotation
HL_6VMI_056No text annotation
HL_6VMI_057No text annotation
HL_6VMI_059No text annotation
HL_6VMI_061tRNA D-loop

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_6VMI_0011/A/1672:1678,
1/A/1797:1816		No text annotation
IL_6VMI_0021/A/1682:1683,
1/A/1768:1770		Single bulged A
homologous
IL_7A0S_002
IL_14190.2
IL_6VMI_0031/A/1739:1745,
1/A/1753:1758		7x6 Sarcin-Ricin; G-bulge
geometric
IL_4V9F_106
IL_02666.1
IL_6VMI_0041/A/1877:1879,
1/A/1895:1897		Isolated non-canonical cWW pair
geometric
IL_5MWI_007
NA
IL_6VMI_0051/A/1880:1883,
1/A/1890:1894		No text annotation
IL_6VMI_0061/A/1904:1906,
1/A/2016:2018		Isolated non-canonical cWW pair
geometric
IL_5CCB_001
IL_01003.4
IL_6VMI_0071/A/1906:1910,
1/A/2009:2016		tHW-tHW cross-strand stack
homologous
IL_5J7L_260
NA
IL_6VMI_0081/A/1913:1915,
1/A/2004:2006		Isolated non-canonical cWW pair
geometric
IL_4YHW_001
NA
IL_6VMI_0091/A/1925:1927,
1/A/1977:1979		Isolated non-canonical cWW pair
geometric
IL_5TBW_027
NA
IL_6VMI_0101/A/1929:1930,
1/A/1973:1975		Single bulged A
homologous
IL_5J7L_261
NA
IL_6VMI_1161/A/1948:1951,
1/A/1966:1968		No text annotation
homologous
IL_9DFE_020
IL_36931.2
IL_6VMI_0121/A/1985:1987,
1/A/1997:2001		Multiple bulged bases
homologous
IL_7A0S_021
IL_89509.1
IL_6VMI_1171/A/2046:2049,
1/A/2090:2094		No text annotation
IL_6VMI_0141/A/2057:2063,
1/A/2076:2082		No text annotation
IL_6VMI_0151/A/2145:2147,
1/A/2254:2255		Single bulged C
homologous
IL_5J7L_276
NA
IL_6VMI_0161/A/2149:2153,
1/A/2248:2252		UAA/GAN
homologous
IL_7A0S_033
IL_08938.1
IL_6VMI_0171/A/2168:2170,
1/A/2190:2192		Isolated near basepair
geometric
IL_4V88_406
NA
IL_6VMI_0191/A/2197:2200,
1/A/2211:2212		No text annotation
homologous
IL_6PRV_002
NA
IL_6VMI_0201/A/2306:2313,
1/A/2674:2680		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
NA
IL_6VMI_0211/A/2329:2333,
1/A/2441:2448		No text annotation
IL_6VMI_1041/A/2377:2381,
1/A/2411:2419		No text annotation
IL_6VMI_1051/A/2384:2400,
1/A/2403:2408		No text annotation
IL_6VMI_1181/A/2457:2461,
1/A/2666:2667		No text annotation
IL_6VMI_1061/A/2470:2487,
1/A/2648:2657		No text annotation
IL_6VMI_0261/A/2473:2487,
1/A/2648:2656		No text annotation
IL_6VMI_0271/A/2490:2491,
1/A/2643:2645		Single bulged A
homologous
IL_5J7L_312
NA
IL_6VMI_0281/A/2548:2551,
1/A/2566:2567		Minor groove platform, major groove intercalation
homologous
IL_5J7L_314
NA
IL_6VMI_0291/A/2552:2553,
1/A/2562:2565		Major groove intercalation
homologous
IL_5J7L_315
NA
IL_6VMI_0301/A/2596:2597,
1/A/2627:2630		Multiple bulged bases
geometric
IL_6JXM_001
IL_05670.1
IL_6VMI_0311/A/2597:2608,
1/A/2624:2627		No text annotation
IL_6VMI_0321/A/2712:2715,
1/A/3104:3106		No text annotation
geometric
IL_6DME_003
IL_75527.2
IL_6VMI_0331/A/2717:2719,
1/A/3099:3102		No text annotation
homologous
IL_4WF9_079
IL_80025.1
IL_6VMI_0341/A/2730:2732,
1/A/2929:2930		Single bulged U
homologous
IL_7A0S_075
IL_97561.5
IL_6VMI_0351/A/2733:2734,
1/A/2925:2928		Minor groove platform
homologous
IL_4WF9_081
IL_34520.3
IL_6VMI_0371/A/2753:2758,
1/A/2789:2795		No text annotation
IL_6VMI_0391/A/2857:2860,
1/A/2872:2875		Double sheared
geometric
IL_5AOX_003
IL_58355.2
IL_6VMI_0401/A/2940:2941,
1/A/2985:2987		Single stack bend
geometric
IL_7KGA_006
IL_90176.1
IL_6VMI_0411/A/2941:2942,
1/A/2983:2985		Major groove platform
homologous
IL_4WF9_090
IL_48076.8
IL_6VMI_0421/A/2943:2946,
1/A/2980:2982		No text annotation
geometric
IL_6DME_003
IL_75527.2
IL_6VMI_1191/A/2946:2948,
1/A/2976:2980		No text annotation
IL_6VMI_0441/A/2953:2955,
1/A/2968:2971		No text annotation
geometric
IL_4P3T_002
NA
IL_6VMI_0451/A/2955:2957,
1/A/2967:2968		Single stack bend
geometric
IL_7RQB_058
NA
IL_6VMI_0461/A/2994:2996,
1/A/3066:3069		Isolated non-canonical cWW with bulges
geometric
IL_5ML7_010
IL_68118.4
IL_6VMI_0471/A/2997:2999,
1/A/3061:3065		Isolated non-canonical cWW with bulges
homologous
IL_4WF9_095
IL_68118.4
IL_6VMI_0481/A/2999:3000,
1/A/3058:3061		Multiple bulged bases
geometric
IL_7RQB_098
NA
IL_6VMI_0491/A/3008:3010,
1/A/3027:3031		No text annotation
IL_6VMI_0501/A/3078:3079,
1/A/3088:3090		Single bulged A
homologous
IL_5J7L_344
NA
IL_6VMI_0511/A/3115:3117,
1/A/3139:3141		Isolated non-canonical cWW pair
geometric
IL_4WF9_042
IL_01003.4
IL_6VMI_0521/A/3119:3126,
1/A/3131:3137		No text annotation
IL_6VMI_0531/A/3148:3152,
1/A/3161:3163		No text annotation
IL_6VMI_0541/AA/649:651,
1/AA/667:668		No text annotation
IL_6VMI_0551/AA/674:676,
1/AA/922:923		Single stack bend
geometric
IL_7KGA_003
IL_15011.3
IL_6VMI_0561/AA/676:677,
1/AA/920:922		No text annotation
IL_6VMI_0581/AA/690:692,
1/AA/822:823		Single bulged A
geometric
IL_6CYT_001
IL_14190.2
IL_6VMI_0591/AA/694:696,
1/AA/819:820		Minor groove platform
geometric
IL_4V88_388
NA
IL_6VMI_0601/AA/727:729,
1/AA/744:747		No text annotation
geometric
IL_4P3T_002
NA
IL_6VMI_0611/AA/729:732,
1/AA/742:744		No text annotation
IL_6VMI_0621/AA/756:761,
1/AA/779:786		Kink-turn with non-sequential stacking
geometric
IL_6CZR_123
NA
IL_6VMI_0631/AA/762:765,
1/AA/777:778		Major groove intercalation
geometric
IL_1U9S_003
IL_71421.3
IL_6VMI_1091/AA/762:766,
1/AA/775:778		No text annotation
IL_6VMI_0641/AA/765:766,
1/AA/775:777		No text annotation
IL_6VMI_0651/AA/830:832,
1/AA/855:856		Single bulged U
geometric
IL_2OIU_003
IL_97561.5
IL_6VMI_0681/AA/876:885,
1/AA/910:913		No text annotation
IL_6VMI_0691/AA/887:893,
1/AA/900:908		Kink-turn related
geometric
IL_4V88_415
NA
IL_6VMI_0701/AA/935:941,
1/AA/1133:1134		Multiple bulged bases
geometric
IL_6JXM_001
IL_05670.1
IL_6VMI_0711/AA/946:950,
1/AA/1044:1049		UAA/GAN
geometric
IL_5TBW_048
NA
IL_6VMI_0721/AA/974:980,
1/AA/1008:1014		No text annotation
IL_6VMI_0731/AA/982:984,
1/AA/1004:1006		Isolated non-canonical cWW pair
geometric
IL_5TBW_046
NA
IL_6VMI_0741/AA/986:988,
1/AA/999:1002		No text annotation
IL_6VMI_0751/AA/1020:1022,
1/AA/1029:1030		No text annotation
IL_6VMI_0771/AA/1067:1071,
1/AA/1087:1091		tSH-tHW-tHS
geometric
IL_4V88_436
NA
IL_6VMI_0781/AA/1109:1111,
1/AA/1130:1132		Isolated non-canonical cWW pair
geometric
IL_7A0S_026
IL_01003.4
IL_6VMI_1101/AA/1138:1140,
1/AA/1164:1165		Single stack bend
geometric
IL_7A0S_054
IL_15011.3
IL_6VMI_1111/AA/1140:1147,
1/AA/1158:1164		No text annotation
IL_6VMI_0801/AA/1175:1176,
1/AA/1477:1479		Single bulged A
geometric
IL_6CZR_147
NA
IL_6VMI_0811/AA/1178:1180,
1/AA/1474:1475		Single bulged G
homologous
IL_6CZR_148
NA
IL_6VMI_1201/AA/1186:1190,
1/AA/1464:1468		No text annotation
IL_6VMI_0911/AA/1278:1279,
1/AA/1289:1297		Major groove intercalation
geometric
IL_1U9S_003
IL_71421.3
IL_6VMI_0941/AA/1483:1485,
1/AA/1566:1569		No text annotation
geometric
IL_4V88_463
NA
IL_6VMI_0951/AA/1485:1488,
1/AA/1562:1566		No text annotation
geometric
IL_4V88_464
NA
IL_6VMI_0981/AA/1500:1503,
1/AA/1547:1549		No text annotation
IL_6VMI_0991/AA/1507:1510,
1/AA/1540:1543		Tandem non-canonical cWW pairs
geometric
IL_3R2D_002
IL_71194.2
IL_6VMI_1001/AA/1510:1511,
1/AA/1538:1540		No text annotation
IL_6VMI_1011/AA/1511:1516,
1/AA/1533:1538		No text annotation
IL_6VMI_1021/AA/1516:1521,
1/AA/1529:1533		No text annotation
IL_6VMI_1031/B/1627:1629,
1/B/1639:1641		Isolated cWH basepair
geometric
IL_4KQ0_004
IL_10892.2

Problematic loops

#loop idProblemSequence
IL_6VMI_011No text annotation
IL_6VMI_013No text annotation
IL_6VMI_018No text annotation
IL_6VMI_022No text annotation
IL_6VMI_023No text annotation
IL_6VMI_024Isolated tWW turn
IL_6VMI_025Major groove platform; stack outside cWW
IL_6VMI_036No text annotation
IL_6VMI_038No text annotation
IL_6VMI_043No text annotation
IL_6VMI_107No text annotation
IL_6VMI_108No text annotation
IL_6VMI_057Single bulged A
IL_6VMI_066C-loop
IL_6VMI_067Single bulged A
IL_6VMI_076Left turn
IL_6VMI_079No text annotation
IL_6VMI_082No text annotation
IL_6VMI_112No text annotation
IL_6VMI_083Minor groove platform
IL_6VMI_084No text annotation
IL_6VMI_085Single bulged C
IL_6VMI_113Isolated non-canonical cWW pair
IL_6VMI_086Tandem non-canonical cWW pairs
IL_6VMI_114No text annotation
IL_6VMI_115No text annotation
IL_6VMI_121No text annotation
IL_6VMI_087Minor groove platform
IL_6VMI_088Single bulged A
IL_6VMI_089Isolated non-canonical cWW pair
IL_6VMI_090No text annotation
IL_6VMI_092No text annotation
IL_6VMI_093Single stack bend
IL_6VMI_096Isolated non-canonical cWW pair
IL_6VMI_097No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_6VMI_0131/A/1678:1681,
1/A/1771:1785,
1/A/1792:1797		No text annotation
J3_6VMI_0141/A/1684:1722,
1/A/1729:1739,
1/A/1758:1767		No text annotation
J3_6VMI_0011/A/1915:1921,
1/A/1983:1985,
1/A/2001:2004		No text annotation
homologous
J3_7A0S_004
J3_46658.1
J3_6VMI_0021/A/1930:1932,
1/A/1942:1946,
1/A/1970:1973		No text annotation
homologous
J3_7A0S_005
J3_69816.1
J3_6VMI_0151/A/2153:2168,
1/A/2192:2197,
1/A/2212:2248		No text annotation
J3_6VMI_0031/A/2336:2343,
1/A/2423:2427,
1/A/2436:2438		No text annotation
J3_6VMI_0191/A/2343:2345,
1/A/2368:2375,
1/A/2421:2423		No text annotation
J3_6VMI_0171/A/2846:2848,
1/A/2890:2900,
1/A/2909:2915		No text annotation
J3_6VMI_0051/AA/677:680,
1/AA/866:872,
1/AA/917:920		No text annotation
J3_6VMI_0181/AA/687:692,
1/AA/822:832,
1/AA/855:858		No text annotation
J3_6VMI_0071/AA/973:974,
1/AA/1014:1020,
1/AA/1030:1031		No text annotation
J3_6VMI_0111/AA/1268:1273,
1/AA/1302:1308,
1/AA/1317:1323		No text annotation
homologous
J3_4LFB_007
J3_01343.1
J4_6VMI_0011/A/2314:2317,
1/A/2326:2327,
1/A/2450:2453,
1/A/2671:2673		No text annotation
J4_6VMI_0101/A/2336:2345,
1/A/2368:2375,
1/A/2421:2427,
1/A/2436:2438		No text annotation
J4_6VMI_0021/A/2336:2345,
1/A/2368:2376,
1/A/2420:2427,
1/A/2436:2438		No text annotation
J4_6VMI_0031/A/2492:2496,
1/A/2508:2513,
1/A/2537:2542,
1/A/2637:2642		No text annotation
J4_6VMI_0041/A/2544:2546,
1/A/2569:2570,
1/A/2587:2596,
1/A/2630:2635		No text annotation
homologous
J4_9DFE_008
J4_42306.1
J4_6VMI_0111/A/3111:3113,
1/A/3143:3144,
1/A/3167:3174,
1/A/3195:3202		No text annotation
J4_6VMI_0071/AA/698:701,
1/AA/708:715,
1/AA/800:802,
1/AA/811:817		No text annotation
J4_6VMI_0081/AA/717:725,
1/AA/749:753,
1/AA/789:791,
1/AA/797:798		No text annotation
J4_6VMI_0091/AA/941:943,
1/AA/1052:1057,
1/AA/1098:1109,
1/AA/1132:1133		No text annotation
homologous
J4_5J7L_003
NA
J5_6VMI_0011/A/1827:1829,
1/A/1841:1845,
1/A/1858:1860,
1/A/2305:2306,
1/A/2680:2681		No text annotation
homologous
J5_7A0S_003
J5_43153.6
J5_6VMI_0051/A/1865:1875,
1/A/1899:1903,
1/A/2019:2022,
1/A/2271:2275,
1/A/2290:2300		No text annotation
J5_6VMI_0061/A/2720:2727,
1/A/2933:2941,
1/A/2985:2995,
1/A/3067:3075,
1/A/3093:3098		No text annotation
J5_6VMI_0071/A/2737:2740,
1/A/2807:2810,
1/A/2822:2823,
1/A/2845:2846,
1/A/2915:2922		No text annotation
homologous
J5_4WF9_007
J5_39529.2
J6_6VMI_0031/A/2027:2032,
1/A/2043:2045,
1/A/2095:2098,
1/A/2123:2127,
1/A/2138:2143,
1/A/2257:2266		No text annotation
J6_6VMI_0021/A/2736:2740,
1/A/2807:2810,
1/A/2822:2823,
1/A/2845:2848,
1/A/2890:2900,
1/A/2909:2923		No text annotation
J6_6VMI_0041/A/2737:2740,
1/A/2807:2810,
1/A/2822:2823,
1/A/2845:2848,
1/A/2890:2900,
1/A/2909:2922		No text annotation

Problematic loops

#loop idProblemSequence
J3_6VMI_016No text annotation
J3_6VMI_004No text annotation
J3_6VMI_006No text annotation
J3_6VMI_008No text annotation
J3_6VMI_009No text annotation
J3_6VMI_010No text annotation
J3_6VMI_012No text annotation
J4_6VMI_005No text annotation
J4_6VMI_006No text annotation
J5_6VMI_002No text annotation
J5_6VMI_003No text annotation
J5_6VMI_004No text annotation
J6_6VMI_001No text annotation

Coloring options:
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