RNA 3D Hub //

7O9K Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_7O9K_0011/A/1722:1729No text annotation
geometric
HL_4WF9_006
HL_48677.1
HL_7O9K_0021/A/1746:1752No text annotation
geometric
HL_7A0S_008
HL_76371.1
HL_7O9K_0031/A/1786:1791GNRA
homologous
HL_4WF9_015
HL_34789.1
HL_7O9K_0041/A/1831:1839No text annotation
homologous
HL_7RQB_017
NA
HL_7O9K_0421/A/1847:1856No text annotation
geometric
HL_7VTI_001
NA
HL_7O9K_0051/A/1848:1855No text annotation
HL_7O9K_0061/A/1884:1889No text annotation
geometric
HL_7RQB_011
NA
HL_7O9K_0071/A/1934:1940No text annotation
geometric
HL_4V9F_025
HL_92935.1
HL_7O9K_0081/A/1954:1963No text annotation
homologous
HL_7RQB_023
NA
HL_7O9K_0091/A/1988:1996No text annotation
geometric
HL_5TBW_021
NA
HL_7O9K_0101/A/2035:2040No text annotation
homologous
HL_4WF9_025
HL_27530.1
HL_7O9K_0111/A/2064:2075No text annotation
HL_7O9K_0121/A/2107:2114No text annotation
HL_7O9K_0131/A/2129:2136No text annotation
homologous
HL_5J7L_160
NA
HL_7O9K_0141/A/2175:2185No text annotation
homologous
HL_6PRV_001
HL_20174.1
HL_7O9K_0151/A/2202:2209GNRA wlth tandem sheared
homologous
HL_6PRV_002
HL_98423.1
HL_7O9K_0161/A/2279:2286No text annotation
geometric
HL_5E6M_002
HL_37734.1
HL_7O9K_0171/A/2319:2324UNCG
geometric
HL_4U7U_001
HL_61337.1
HL_7O9K_0191/A/2400:2403Mini UNCG
geometric
HL_7A0S_039
HL_90436.1
HL_7O9K_0201/A/2428:2435No text annotation
homologous
HL_7RQB_040
NA
HL_7O9K_0211/A/2497:2507No text annotation
homologous
HL_4WF9_043
HL_87681.1
HL_7O9K_0221/A/2518:2532No text annotation
HL_7O9K_0241/A/2612:2620No text annotation
geometric
HL_1WZ2_007
HL_75660.6
HL_7O9K_0251/A/2690:2699No text annotation
homologous
HL_4WF9_047
HL_78372.1
HL_7O9K_0271/A/2813:2819No text annotation
geometric
HL_5TBW_006
NA
HL_7O9K_0281/A/2826:2842No text annotation
HL_7O9K_0291/A/2862:2870No text annotation
geometric
HL_2ZZM_002
NA
HL_7O9K_0301/A/2902:2907GNRA
geometric
HL_5X2G_001
HL_34789.1
HL_7O9K_0311/A/2958:2966No text annotation
homologous
HL_5J7L_193
NA
HL_7O9K_0321/A/3015:3022GNRA variation
homologous
HL_7A0S_060
HL_46665.1
HL_7O9K_0331/A/3038:3044No text annotation
homologous
HL_4WF9_058
HL_48677.1
HL_7O9K_0341/A/3081:3086GNRA
homologous
HL_7RQB_063
NA
HL_7O9K_0351/A/3126:3131GNRA
geometric
HL_4JF2_001
NA
HL_7O9K_0361/A/3154:3159No text annotation
geometric
HL_4WSB_001
NA
HL_7O9K_0371/A/3176:3193No text annotation
geometric
HL_7A0S_074
NA
HL_7O9K_0381/A/3216:3224No text annotation
geometric
HL_7A0S_067
HL_37889.1
HL_7O9K_0391/B/1613:1622tRNA D-loop
geometric
HL_5B63_003
HL_65478.1
HL_7O9K_0401/B/1630:1638Anticodon loop related
geometric
HL_5T83_002
NA

Problematic loops

#loop idProblemSequence
HL_7O9K_018No text annotation
HL_7O9K_023No text annotation
HL_7O9K_026No text annotation
HL_7O9K_043No text annotation
HL_7O9K_041No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_7O9K_0021/A/1682:1683,
1/A/1768:1770		Single bulged A
homologous
IL_7A0S_002
IL_14190.1
IL_7O9K_0031/A/1739:1745,
1/A/1753:1758		7x6 Sarcin-Ricin; G-bulge
geometric
IL_4V9F_106
IL_02666.1
IL_7O9K_0481/A/1845:1847,
1/A/1856:1858		Isolated non-canonical cWW pair
homologous
IL_5J7L_257
NA
IL_7O9K_0051/A/1877:1879,
1/A/1895:1897		Isolated non-canonical cWW pair
geometric
IL_3SZX_002
IL_01003.1
IL_7O9K_0061/A/1880:1883,
1/A/1890:1894		No text annotation
IL_7O9K_0071/A/1904:1906,
1/A/2016:2018		Isolated non-canonical cWW pair
homologous
IL_4WF9_020
IL_01003.1
IL_7O9K_0081/A/1906:1910,
1/A/2009:2016		tHW-tHW cross-strand stack
geometric
IL_7RQB_018
NA
IL_7O9K_0091/A/1913:1915,
1/A/2004:2006		Isolated non-canonical cWW pair
geometric
IL_5TBW_079
NA
IL_7O9K_0101/A/1925:1927,
1/A/1977:1979		Isolated non-canonical cWW contact
geometric
IL_5UNE_001
NA
IL_7O9K_0111/A/1929:1930,
1/A/1973:1975		Single bulged A
geometric
IL_4V9F_025
IL_14190.1
IL_7O9K_0121/A/1948:1951,
1/A/1966:1968		Major groove platform with extra cWW
homologous
IL_7RQB_022
NA
IL_7O9K_0131/A/1985:1987,
1/A/1997:2001		Multiple bulged bases
geometric
IL_5J7L_265
NA
IL_7O9K_0141/A/2046:2048,
1/A/2091:2094		No text annotation
geometric
IL_4N0T_004
IL_32983.1
IL_7O9K_0151/A/2057:2063,
1/A/2076:2082		No text annotation
geometric
IL_5XWG_002
NA
IL_7O9K_0161/A/2145:2147,
1/A/2254:2255		Single bulged C
homologous
IL_5J7L_276
NA
IL_7O9K_0171/A/2149:2153,
1/A/2248:2252		UAA/GAN
homologous
IL_7RQB_036
NA
IL_7O9K_0181/A/2168:2170,
1/A/2190:2192		Isolated near basepair
geometric
IL_4V88_406
NA
IL_7O9K_0491/A/2168:2173,
1/A/2187:2192		No text annotation
IL_7O9K_0191/A/2170:2173,
1/A/2187:2190		No text annotation
geometric
IL_5D8H_002
IL_28482.1
IL_7O9K_0201/A/2197:2200,
1/A/2211:2212		No text annotation
homologous
IL_6PRV_002
NA
IL_7O9K_0211/A/2306:2313,
1/A/2674:2680		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
NA
IL_7O9K_0501/A/2330:2333,
1/A/2441:2447		No text annotation
IL_7O9K_0511/A/2377:2381,
1/A/2411:2419		No text annotation
IL_7O9K_0521/A/2384:2400,
1/A/2403:2408		No text annotation
IL_7O9K_0231/A/2456:2461,
1/A/2666:2668		No text annotation
IL_7O9K_0241/A/2467:2469,
1/A/2658:2660		Isolated tWW turn
homologous
IL_4WF9_063
IL_10432.1
IL_7O9K_0251/A/2470:2473,
1/A/2656:2657		Major groove platform; stack outside cWW
geometric
IL_7RQB_066
NA
IL_7O9K_0531/A/2470:2478,
1/A/2653:2657		No text annotation
homologous
IL_4WF9_117
IL_80252.1
IL_7O9K_0261/A/2473:2478,
1/A/2653:2656		Intercalated tWH
geometric
IL_4WF9_065
IL_28217.1
IL_7O9K_0271/A/2478:2487,
1/A/2648:2653		No text annotation
IL_7O9K_0281/A/2490:2491,
1/A/2643:2645		Single bulged A
homologous
IL_7RQB_069
NA
IL_7O9K_0291/A/2712:2715,
1/A/3104:3106		Major groove platform with extra pair
geometric
IL_5TBW_091
NA
IL_7O9K_0301/A/2717:2719,
1/A/3099:3102		No text annotation
homologous
IL_4WF9_079
IL_80025.1
IL_7O9K_0311/A/2730:2732,
1/A/2929:2930		Single bulged U
homologous
IL_7RQB_080
NA
IL_7O9K_0321/A/2733:2734,
1/A/2925:2928		Minor groove platform
homologous
IL_7RQB_081
NA
IL_7O9K_0331/A/2744:2746,
1/A/2802:2803		Minor groove platform
geometric
IL_7A0S_003
IL_34520.1
IL_7O9K_0351/A/2856:2860,
1/A/2872:2876		Double sheared with non-canonical cWW
geometric
IL_5J7L_274
NA
IL_7O9K_0361/A/2943:2946,
1/A/2980:2982		Major groove platform with extra pair
homologous
IL_7RQB_093
NA
IL_7O9K_0541/A/2946:2948,
1/A/2976:2980		Major groove minor groove platform with extra cWW
homologous
IL_4WF9_092
IL_36931.1
IL_7O9K_0381/A/2953:2957,
1/A/2967:2971		Double sheared with non-canonical cWW
homologous
IL_5J7L_338
NA
IL_7O9K_0391/A/2994:2995,
1/A/3067:3069		Major groove platform
homologous
IL_4WF9_094
IL_46637.1
IL_7O9K_0401/A/2997:2999,
1/A/3061:3065		Isolated non-canonical cWW with bulges
geometric
IL_7RQB_097
NA
IL_7O9K_0411/A/2999:3000,
1/A/3058:3061		No text annotation
homologous
IL_5J7L_341
NA
IL_7O9K_0421/A/3008:3010,
1/A/3027:3031		No text annotation
IL_7O9K_0431/A/3078:3079,
1/A/3088:3090		Single bulged A
homologous
IL_7RQB_101
NA
IL_7O9K_0441/A/3115:3117,
1/A/3139:3141		Isolated non-canonical cWW pair
geometric
IL_4LFB_061
NA
IL_7O9K_0451/A/3119:3126,
1/A/3131:3137		8x7 Sarcin-Ricin; G-bulge
geometric
IL_5TBW_116
NA
IL_7O9K_0461/A/3148:3152,
1/A/3161:3163		C-loop
geometric
IL_7RQB_051
NA
IL_7O9K_0471/B/1627:1629,
1/B/1639:1641		Isolated non-canonical cWW contact
geometric
IL_5UNE_009
NA

Problematic loops

#loop idProblemSequence
IL_7O9K_001No text annotation
IL_7O9K_004Tandem non-canonical cWW pairs
IL_7O9K_022No text annotation
IL_7O9K_034No text annotation
IL_7O9K_037No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_7O9K_0061/A/1678:1681,
1/A/1771:1785,
1/A/1792:1797		No text annotation
J3_7O9K_0011/A/1915:1921,
1/A/1983:1985,
1/A/2001:2004		No text annotation
homologous
J3_5J7L_038
NA
J3_7O9K_0021/A/1930:1932,
1/A/1942:1946,
1/A/1970:1973		No text annotation
homologous
J3_7RQB_005
NA
J3_7O9K_0031/A/2336:2343,
1/A/2423:2427,
1/A/2436:2438		No text annotation
J3_7O9K_0041/A/2343:2345,
1/A/2368:2375,
1/A/2421:2423		No text annotation
J3_7O9K_0071/A/2544:2550,
1/A/2606:2608,
1/A/2624:2635		No text annotation
J3_7O9K_0081/A/2846:2848,
1/A/2890:2900,
1/A/2909:2915		No text annotation
J3_7O9K_0051/A/3004:3007,
1/A/3032:3034,
1/A/3048:3054		No text annotation
homologous
J3_7RQB_012
NA
J4_7O9K_0011/A/2314:2317,
1/A/2326:2327,
1/A/2450:2453,
1/A/2671:2673		No text annotation
J4_7O9K_0021/A/2336:2345,
1/A/2368:2375,
1/A/2421:2427,
1/A/2436:2438		No text annotation
J4_7O9K_0031/A/2492:2496,
1/A/2508:2513,
1/A/2537:2542,
1/A/2637:2642		No text annotation
J5_7O9K_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_7O9K_0021/A/1865:1875,
1/A/1899:1903,
1/A/2019:2022,
1/A/2271:2275,
1/A/2290:2300		No text annotation
J5_7O9K_0051/A/2720:2726,
1/A/2934:2942,
1/A/2983:2992,
1/A/3071:3075,
1/A/3093:3098		No text annotation
J5_7O9K_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_7A0S_007
J5_39529.2
J6_7O9K_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_7O9K_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
J5_7O9K_003No text annotation
J6_7O9K_001No text annotation

Coloring options:
Copyright 2025 BGSU RNA group. Page generated in 0.0595 s