RNA 3D Hub //

9S7D Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_9S7D_0011/A/1722:1729No text annotation
geometric
HL_9E6Q_006
HL_02262.1
HL_9S7D_0021/A/1746:1752No text annotation
geometric
HL_9E6Q_008
HL_76371.4
HL_9S7D_0031/A/1786:1791No text annotation
homologous
HL_8B0X_046
HL_34789.6
HL_9S7D_0041/A/1831:1839No text annotation
HL_9S7D_0051/A/1847:1856T-loop with 2 stacked bulged bases
homologous
HL_8B0X_048
HL_33597.7
HL_9S7D_0061/A/1884:1889No text annotation
HL_9S7D_0071/A/1934:1940No text annotation
HL_9S7D_0081/A/1954:1963No text annotation
homologous
HL_7A0S_022
HL_50204.3
HL_9S7D_0091/A/1988:1996No text annotation
geometric
HL_9E6Q_025
HL_28253.1
HL_9S7D_0101/A/2035:2040No text annotation
homologous
HL_8B0X_055
HL_27530.3
HL_9S7D_0111/A/2064:2075No text annotation
HL_9S7D_0121/A/2107:2114GNRA
homologous
HL_7A0S_026
HL_34789.6
HL_9S7D_0131/A/2129:2136No text annotation
homologous
HL_8B0X_058
HL_47171.3
HL_9S7D_0161/A/2279:2286No text annotation
geometric
HL_5E6M_002
HL_55735.1
HL_9S7D_0171/A/2319:2324UNCG variation
geometric
HL_6DME_002
HL_13571.1
HL_9S7D_0181/A/2400:2403Mini UNCG
geometric
HL_7A0S_039
HL_90436.5
HL_9S7D_0191/A/2428:2435No text annotation
homologous
HL_8B0X_068
HL_28592.4
HL_9S7D_0201/A/2497:2507No text annotation
homologous
HL_8B0X_073
HL_87681.3
HL_9S7D_0211/A/2518:2532No text annotation
HL_9S7D_0221/A/2555:2560No text annotation
HL_9S7D_0241/A/2612:2620No text annotation
homologous
HL_7A0S_048
HL_33350.1
HL_9S7D_0251/A/2690:2699No text annotation
homologous
HL_8B0X_078
HL_78372.3
HL_9S7D_0271/A/2812:2820LSU P loop
homologous
HL_8B0X_080
HL_11974.4
HL_9S7D_0281/A/2828:2840No text annotation
HL_9S7D_0291/A/2862:2870No text annotation
HL_9S7D_0321/A/3015:3022GNRA variation
homologous
HL_7A0S_060
HL_02262.1
HL_9S7D_0331/A/3038:3044LSU A loop
homologous
HL_8B0X_089
HL_02262.1
HL_9S7D_0341/A/3081:3086No text annotation
homologous
HL_8B0X_090
HL_34789.6
HL_9S7D_0361/A/3154:3159No text annotation
geometric
HL_5FMZ_001
HL_21043.1
HL_9S7D_0371/A/3176:3193No text annotation
HL_9S7D_0381/A/3216:3224No text annotation
geometric
HL_7A0S_067
HL_37889.3
HL_9S7D_0391/AA/7:17No text annotation
homologous
HL_8B0X_001
HL_73535.3
HL_9S7D_0471/AA/342:351No text annotation
geometric
HL_8B0X_014
HL_38491.4
HL_9S7D_0481/AA/376:381GNRA
geometric
HL_6M0X_001
HL_34789.6
HL_9S7D_0491/AA/427:437No text annotation
homologous
HL_8B0X_016
HL_38491.4
HL_9S7D_0501/AA/468:479No text annotation
HL_9S7D_0511/AA/503:508No text annotation
geometric
HL_5E08_001
HL_89167.4
HL_9S7D_0531/AA/634:640No text annotation
geometric
HL_9AXU_017
HL_37569.4
HL_9S7D_0591/AA/933:938No text annotation
homologous
HL_8B0X_029
HL_34789.6
HL_9S7D_0641/Ax/31:39No text annotation
homologous
HL_7U2J_104
HL_81376.4
HL_9S7D_0671/B/31:39tRNA anticodon loop
homologous
HL_7VNV_002
HL_81376.4

Problematic loops

#loop idProblemSequence
HL_9S7D_014No text annotation
HL_9S7D_015No text annotation
HL_9S7D_023No text annotation
HL_9S7D_026GNRA
HL_9S7D_030No text annotation
HL_9S7D_031No text annotation
HL_9S7D_035No text annotation
HL_9S7D_040No text annotation
HL_9S7D_041No text annotation
HL_9S7D_042GNRA
HL_9S7D_043No text annotation
HL_9S7D_044No text annotation
HL_9S7D_045No text annotation
HL_9S7D_046No text annotation
HL_9S7D_052No text annotation
HL_9S7D_054No text annotation
HL_9S7D_055No text annotation
HL_9S7D_056T-loop with 2 stacked bulged bases
HL_9S7D_057No text annotation
HL_9S7D_058No text annotation
HL_9S7D_060No text annotation
HL_9S7D_061tRNA anticodon loop
HL_9S7D_062No text annotation
HL_9S7D_063tRNA D-loop
HL_9S7D_065No text annotation
HL_9S7D_066tRNA D-loop
HL_9S7D_068No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_9S7D_0011/A/1672:1678,
1/A/1797:1816		No text annotation
IL_9S7D_0021/A/1682:1683,
1/A/1768:1770		No text annotation
homologous
IL_8B0X_066
IL_14190.4
IL_9S7D_0031/A/1845:1847,
1/A/1856:1858		No text annotation
homologous
IL_8B0X_077
IL_01334.1
IL_9S7D_0041/A/1877:1879,
1/A/1895:1897		Isolated non-canonical cWW pair
geometric
IL_3GM7_004
IL_01003.6
IL_9S7D_0051/A/1880:1883,
1/A/1890:1894		No text annotation
IL_9S7D_0061/A/1904:1906,
1/A/2016:2018		Isolated non-canonical cWW pair
homologous
IL_7A0S_014
IL_01003.6
IL_9S7D_0071/A/1906:1910,
1/A/2009:2016		No text annotation
homologous
IL_8B0X_080
IL_73855.3
IL_9S7D_0081/A/1913:1915,
1/A/2004:2006		Isolated non-canonical cWW pair
geometric
IL_9AXU_076
IL_01003.6
IL_9S7D_0091/A/1925:1927,
1/A/1977:1979		Isolated non-canonical cWW pair
geometric
IL_3CUL_008
IL_01003.6
IL_9S7D_0101/A/1929:1930,
1/A/1973:1975		No text annotation
homologous
IL_8B0X_081
IL_14190.4
IL_9S7D_0111/A/1948:1951,
1/A/1966:1968		Major groove platform with extra cWW
homologous
IL_7A0S_019
IL_36931.4
IL_9S7D_0121/A/1985:1987,
1/A/1997:2001		Multiple bulged bases
geometric
IL_7A0S_021
IL_89509.3
IL_9S7D_0131/A/2046:2048,
1/A/2091:2094		No text annotation
geometric
IL_4N0T_004
IL_32983.3
IL_9S7D_0141/A/2057:2063,
1/A/2076:2082		No text annotation
geometric
IL_5XWG_002
IL_74768.1
IL_9S7D_0151/A/2145:2147,
1/A/2254:2255		No text annotation
homologous
IL_8B0X_096
IL_05642.5
IL_9S7D_0161/A/2149:2153,
1/A/2248:2252		UAA/GAN
homologous
IL_7A0S_033
IL_08938.3
IL_9S7D_0201/A/2306:2313,
1/A/2674:2680		8x7 Sarcin-Ricin; G-bulge
homologous
IL_8B0X_108
IL_62167.5
IL_9S7D_0211/A/2330:2333,
1/A/2441:2447		No text annotation
IL_9S7D_0241/A/2384:2400,
1/A/2403:2408		No text annotation
IL_9S7D_0251/A/2456:2461,
1/A/2666:2668		No text annotation
IL_9S7D_0261/A/2467:2469,
1/A/2658:2660		No text annotation
homologous
IL_8B0X_124
IL_10432.3
IL_9S7D_0271/A/2470:2473,
1/A/2656:2657		No text annotation
geometric
IL_9E6Q_063
IL_74641.4
IL_9S7D_0281/A/2470:2478,
1/A/2653:2657		No text annotation
geometric
IL_9PN5_075
IL_80252.3
IL_9S7D_0291/A/2473:2478,
1/A/2653:2656		No text annotation
homologous
IL_8B0X_126
IL_28217.3
IL_9S7D_0301/A/2478:2487,
1/A/2648:2653		No text annotation
IL_9S7D_0311/A/2490:2491,
1/A/2643:2645		Single bulged A
homologous
IL_7A0S_064
IL_14190.4
IL_9S7D_0321/A/2548:2551,
1/A/2566:2567		No text annotation
homologous
IL_8B0X_133
IL_55206.3
IL_9S7D_0331/A/2552:2553,
1/A/2562:2565		No text annotation
homologous
IL_8B0X_134
IL_71421.5
IL_9S7D_0341/A/2596:2597,
1/A/2627:2630		No text annotation
geometric
IL_8ZAU_001
IL_09092.1
IL_9S7D_0351/A/2597:2608,
1/A/2624:2627		No text annotation
IL_9S7D_0361/A/2712:2715,
1/A/3104:3106		No text annotation
geometric
IL_8OI5_093
IL_75527.4
IL_9S7D_0371/A/2717:2719,
1/A/3099:3102		No text annotation
homologous
IL_8B0X_140
IL_80025.3
IL_9S7D_0381/A/2730:2732,
1/A/2929:2930		No text annotation
homologous
IL_8B0X_182
IL_97561.7
IL_9S7D_0391/A/2733:2734,
1/A/2925:2928		No text annotation
homologous
IL_8B0X_143
IL_98469.1
IL_9S7D_0401/A/2744:2746,
1/A/2802:2803		No text annotation
geometric
IL_9E6Q_003
IL_98469.1
IL_9S7D_0411/A/2753:2769,
1/A/2778:2795		No text annotation
IL_9S7D_0421/A/2849:2855,
1/A/2877:2889		No text annotation
IL_9S7D_0431/A/2857:2860,
1/A/2872:2875		Double sheared
geometric
IL_4LFB_060
IL_58355.4
IL_9S7D_0441/A/2940:2941,
1/A/2985:2987		Single stack bend
homologous
IL_7A0S_083
IL_15011.5
IL_9S7D_0451/A/2941:2942,
1/A/2983:2985		No text annotation
homologous
IL_8B0X_184
IL_48076.10
IL_9S7D_0461/A/2943:2946,
1/A/2980:2982		No text annotation
homologous
IL_8B0X_151
NA
IL_9S7D_0471/A/2946:2948,
1/A/2976:2980		Major groove minor groove platform with extra cWW
homologous
IL_7A0S_086
IL_36931.4
IL_9S7D_0481/A/2953:2955,
1/A/2968:2971		No text annotation
geometric
IL_4V9F_053
IL_49140.2
IL_9S7D_0501/A/2994:2995,
1/A/3067:3069		Major groove platform
homologous
IL_7A0S_088
IL_46637.4
IL_9S7D_0511/A/2997:2999,
1/A/3061:3065		No text annotation
homologous
IL_8B0X_155
IL_30722.1
IL_9S7D_0521/A/2999:3000,
1/A/3058:3061		No text annotation
homologous
IL_8B0X_156
IL_44609.4
IL_9S7D_0531/A/3008:3010,
1/A/3027:3031		No text annotation
IL_9S7D_0541/A/3078:3079,
1/A/3088:3090		No text annotation
geometric
IL_8GLP_097
IL_14190.4
IL_9S7D_0551/A/3115:3117,
1/A/3139:3141		Isolated non-canonical cWW pair
geometric
IL_9E6Q_036
IL_01003.6
IL_9S7D_0571/A/3148:3152,
1/A/3161:3163		No text annotation
geometric
IL_8B0X_162
IL_63596.14
IL_9S7D_0581/A/3212:3213,
1/A/3227:3230		Major groove intercalation
geometric
IL_4V9F_021
IL_71421.5
IL_9S7D_0591/AA/2:4,
1/AA/20:21		No text annotation
IL_9S7D_0651/AA/109:114,
1/AA/132:139		Kink-turn with non-sequential stacking
geometric
IL_4LFB_011
IL_46174.6
IL_9S7D_0741/AA/288:294,
1/AA/486:487		No text annotation
homologous
IL_8B0X_025
IL_20847.3
IL_9S7D_0761/AA/305:321,
1/AA/389:395		No text annotation
IL_9S7D_0771/AA/327:333,
1/AA/361:367		No text annotation
IL_9S7D_0811/AA/415:419,
1/AA/445:446		No text annotation
homologous
IL_8B0X_035
IL_29346.3
IL_9S7D_0821/AA/420:424,
1/AA/440:444		No text annotation
geometric
IL_9H3G_204
IL_05821.3
IL_9S7D_0841/AA/492:500,
1/AA/511:517		No text annotation
IL_9S7D_0851/AA/528:529,
1/AA/830:832		No text annotation
homologous
IL_8B0X_038
IL_14190.4
IL_9S7D_0961/AA/631:632,
1/AA/642:650		No text annotation
IL_9S7D_0981/AA/836:838,
1/AA/919:922		No text annotation
homologous
IL_8B0X_057
IL_18228.3
IL_9S7D_0991/AA/838:841,
1/AA/915:919		No text annotation
homologous
IL_8B0X_058
IL_25873.4
IL_9S7D_1011/AA/844:848,
1/AA/907:912		No text annotation
IL_9S7D_1021/AA/853:857,
1/AA/899:902		UAA/GAN related
geometric
IL_2R8S_002
IL_77691.7
IL_9S7D_1041/AA/863:864,
1/AA/891:893		No text annotation
IL_9S7D_1081/B/28:30,
1/B/40:42		No text annotation
homologous
IL_5E81_376
NA

Problematic loops

#loop idProblemSequence
IL_9S7D_017Isolated non-canonical cWW pair
IL_9S7D_018No text annotation
IL_9S7D_019No text annotation
IL_9S7D_022No text annotation
IL_9S7D_023No text annotation
IL_9S7D_049Minor groove platform
IL_9S7D_0568x7 Sarcin-Ricin; G-bulge
IL_9S7D_060No text annotation
IL_9S7D_061No text annotation
IL_9S7D_062No text annotation
IL_9S7D_063No text annotation
IL_9S7D_064No text annotation
IL_9S7D_066Major groove platform; stack outside cWW
IL_9S7D_067No text annotation
IL_9S7D_068No text annotation
IL_9S7D_069No text annotation
IL_9S7D_070No text annotation
IL_9S7D_071No text annotation
IL_9S7D_072No text annotation
IL_9S7D_073Kink-turn related
IL_9S7D_075No text annotation
IL_9S7D_078Isolated non-canonical cWW pair
IL_9S7D_079No text annotation
IL_9S7D_080Other IL
IL_9S7D_083Isolated non-canonical cWW pair
IL_9S7D_086No text annotation
IL_9S7D_087No text annotation
IL_9S7D_088Minor groove platform
IL_9S7D_089No text annotation
IL_9S7D_090No text annotation
IL_9S7D_091No text annotation
IL_9S7D_092No text annotation
IL_9S7D_093No text annotation
IL_9S7D_094No text annotation
IL_9S7D_095Double sheared
IL_9S7D_097No text annotation
IL_9S7D_100Isolated non-canonical cWW pair
IL_9S7D_103Tandem non-canonical cWW pairs
IL_9S7D_105No text annotation
IL_9S7D_106No text annotation
IL_9S7D_107No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_9S7D_0011/A/1678:1681,
1/A/1771:1785,
1/A/1792:1797		No text annotation
J3_9S7D_0021/A/1684:1722,
1/A/1729:1745,
1/A/1753:1767		No text annotation
J3_9S7D_0031/A/1915:1921,
1/A/1983:1985,
1/A/2001:2004		No text annotation
homologous
J3_7A0S_004
J3_46658.3
J3_9S7D_0041/A/1930:1932,
1/A/1942:1946,
1/A/1970:1973		No text annotation
homologous
J3_8B0X_017
J3_69816.3
J3_9S7D_0051/A/2153:2168,
1/A/2192:2197,
1/A/2212:2248		No text annotation
J3_9S7D_0061/A/2336:2343,
1/A/2423:2427,
1/A/2436:2438		No text annotation
J3_9S7D_0071/A/2343:2345,
1/A/2368:2375,
1/A/2421:2423		No text annotation
J3_9S7D_0081/A/2846:2848,
1/A/2890:2900,
1/A/2909:2915		No text annotation
J3_9S7D_0091/A/3004:3007,
1/A/3032:3034,
1/A/3048:3054		No text annotation
homologous
J3_7A0S_011
J3_32601.6
J3_9S7D_0121/AA/326:327,
1/AA/367:373,
1/AA/383:384		No text annotation
J4_9S7D_0011/A/2314:2317,
1/A/2326:2327,
1/A/2450:2453,
1/A/2671:2673		No text annotation
J4_9S7D_0021/A/2336:2345,
1/A/2368:2375,
1/A/2421:2427,
1/A/2436:2438		No text annotation
J4_9S7D_0031/A/2492:2496,
1/A/2508:2513,
1/A/2537:2542,
1/A/2637:2642		No text annotation
J4_9S7D_0041/A/2544:2546,
1/A/2569:2570,
1/A/2587:2596,
1/A/2630:2635		No text annotation
homologous
J4_8B0X_012
J4_42306.3
J4_9S7D_0051/A/3111:3113,
1/A/3143:3144,
1/A/3167:3174,
1/A/3195:3202		No text annotation
J4_9S7D_0081/AA/294:296,
1/AA/405:410,
1/AA/451:462,
1/AA/485:486		No text annotation
homologous
J4_8B0X_003
J4_14595.3
J5_9S7D_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_9S7D_0021/A/1865:1875,
1/A/1899:1903,
1/A/2019:2022,
1/A/2271:2275,
1/A/2290:2300		No text annotation
J5_9S7D_0031/A/2720:2727,
1/A/2933:2940,
1/A/2987:2994,
1/A/3069:3075,
1/A/3093:3098		No text annotation
J5_9S7D_0041/A/2737:2740,
1/A/2807:2810,
1/A/2822:2823,
1/A/2845:2846,
1/A/2915:2922		No text annotation
homologous
J5_8B0X_009
J5_39529.2
J6_9S7D_0011/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_9S7D_0021/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_9S7D_010No text annotation
J3_9S7D_011No text annotation
J3_9S7D_013No text annotation
J3_9S7D_014No text annotation
J3_9S7D_015No text annotation
J3_9S7D_016No text annotation
J3_9S7D_017No text annotation
J4_9S7D_006No text annotation
J4_9S7D_007No text annotation
J4_9S7D_009tRNA junction
J4_9S7D_010No text annotation
J4_9S7D_011No text annotation

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