7ODR Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_7ODR_001 | 1/A/1722:1729 | No text annotation | geometric HL_4WF9_006 HL_48677.1 | |
| HL_7ODR_002 | 1/A/1746:1752 | No text annotation | geometric HL_7A0S_008 HL_76371.2 | |
| HL_7ODR_003 | 1/A/1786:1791 | GNRA | homologous HL_4WF9_015 HL_34789.4 | |
| HL_7ODR_004 | 1/A/1831:1839 | No text annotation | homologous HL_7RQB_017 NA | |
| HL_7ODR_005 | 1/A/1847:1856 | T-loop with 2 stacked bulged bases | geometric HL_5HR6_003 HL_33597.3 | |
| HL_7ODR_006 | 1/A/1884:1889 | No text annotation | geometric HL_5TBW_006 NA | |
| HL_7ODR_007 | 1/A/1934:1940 | No text annotation | geometric HL_5M3H_001 NA | |
| HL_7ODR_008 | 1/A/1954:1963 | No text annotation | homologous HL_7RQB_023 NA | |
| HL_7ODR_009 | 1/A/1988:1996 | No text annotation | geometric HL_5TBW_021 NA | |
| HL_7ODR_010 | 1/A/2035:2040 | No text annotation | homologous HL_4WF9_025 HL_27530.1 | |
| HL_7ODR_011 | 1/A/2064:2075 | No text annotation | ||
| HL_7ODR_012 | 1/A/2107:2114 | No text annotation | ||
| HL_7ODR_013 | 1/A/2129:2136 | No text annotation | homologous HL_5J7L_160 NA | |
| HL_7ODR_016 | 1/A/2279:2286 | No text annotation | geometric HL_5E6M_002 HL_10874.1 | |
| HL_7ODR_017 | 1/A/2319:2324 | UNCG | geometric HL_4U7U_001 HL_61337.4 | |
| HL_7ODR_018 | 1/A/2349:2364 | No text annotation | ||
| HL_7ODR_019 | 1/A/2400:2403 | Mini UNCG | geometric HL_7A0S_039 HL_90436.3 | |
| HL_7ODR_020 | 1/A/2428:2435 | No text annotation | homologous HL_7RQB_040 NA | |
| HL_7ODR_021 | 1/A/2497:2507 | No text annotation | homologous HL_7RQB_045 NA | |
| HL_7ODR_022 | 1/A/2518:2532 | No text annotation | ||
| HL_7ODR_024 | 1/A/2690:2699 | No text annotation | homologous HL_4WF9_047 HL_78372.1 | |
| HL_7ODR_026 | 1/A/2813:2819 | Pseudoknot geometry | geometric HL_4KQY_001 HL_30680.5 | |
| HL_7ODR_027 | 1/A/2828:2840 | No text annotation | ||
| HL_7ODR_028 | 1/A/2862:2870 | No text annotation | geometric HL_2ZZM_002 HL_33487.1 | |
| HL_7ODR_029 | 1/A/2902:2907 | GNRA | geometric HL_5TBW_017 NA | |
| HL_7ODR_030 | 1/A/2958:2966 | No text annotation | homologous HL_4WF9_056 HL_52011.1 | |
| HL_7ODR_031 | 1/A/3015:3022 | No text annotation | homologous HL_7RQB_061 NA | |
| HL_7ODR_032 | 1/A/3038:3044 | No text annotation | geometric HL_5M3H_001 NA | |
| HL_7ODR_033 | 1/A/3081:3086 | GNRA | homologous HL_7RQB_063 NA | |
| HL_7ODR_034 | 1/A/3126:3131 | GNRA | geometric HL_4FRG_002 HL_34789.4 | |
| HL_7ODR_035 | 1/A/3154:3159 | No text annotation | geometric HL_4WRT_001 HL_19413.2 | |
| HL_7ODR_036 | 1/A/3176:3193 | No text annotation | geometric HL_7A0S_074 NA | |
| HL_7ODR_037 | 1/A/3216:3224 | No text annotation | geometric HL_7RQB_068 NA | |
| HL_7ODR_038 | 1/B/1613:1622 | tRNA D-loop | geometric HL_5B63_003 HL_20490.1 | |
| HL_7ODR_039 | 1/B/1630:1638 | Anticodon loop related | geometric HL_5T83_002 HL_81376.3 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_7ODR_014 | No text annotation | ||
| HL_7ODR_041 | No text annotation | ||
| HL_7ODR_043 | No text annotation | ||
| HL_7ODR_015 | GNRA wlth tandem sheared | ||
| HL_7ODR_023 | No text annotation | ||
| HL_7ODR_025 | No text annotation | ||
| HL_7ODR_042 | No text annotation | ||
| HL_7ODR_040 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_7ODR_001 | 1/A/1672:1678, 1/A/1797:1816 | No text annotation | ||
| IL_7ODR_002 | 1/A/1682:1683, 1/A/1768:1770 | Single bulged A | homologous IL_7RQB_002 NA | |
| IL_7ODR_003 | 1/A/1845:1847, 1/A/1856:1858 | Isolated non-canonical cWW pair | homologous IL_5J7L_257 NA | |
| IL_7ODR_004 | 1/A/1877:1879, 1/A/1895:1897 | Isolated non-canonical cWW pair | geometric IL_4E59_001 IL_01003.4 | |
| IL_7ODR_005 | 1/A/1880:1883, 1/A/1890:1894 | No text annotation | ||
| IL_7ODR_006 | 1/A/1904:1906, 1/A/2016:2018 | Isolated non-canonical cWW pair | geometric IL_4WF9_020 IL_01003.4 | |
| IL_7ODR_007 | 1/A/1906:1910, 1/A/2009:2016 | tHW-tHW cross-strand stack | homologous IL_7RQB_018 NA | |
| IL_7ODR_008 | 1/A/1913:1915, 1/A/2004:2006 | Isolated non-canonical cWW pair | geometric IL_5TBW_079 NA | |
| IL_7ODR_009 | 1/A/1925:1927, 1/A/1977:1979 | Isolated non-canonical cWW contact | geometric IL_5UNE_001 IL_87720.1 | |
| IL_7ODR_010 | 1/A/1929:1930, 1/A/1973:1975 | Single bulged A | homologous IL_5J7L_261 NA | |
| IL_7ODR_011 | 1/A/1948:1951, 1/A/1966:1968 | Major groove platform with extra cWW | homologous IL_7RQB_022 NA | |
| IL_7ODR_012 | 1/A/1985:1987, 1/A/1997:2001 | Multiple bulged bases | homologous IL_7A0S_021 IL_89509.1 | |
| IL_7ODR_013 | 1/A/2046:2048, 1/A/2091:2094 | No text annotation | geometric IL_4N0T_004 IL_32983.2 | |
| IL_7ODR_014 | 1/A/2057:2063, 1/A/2076:2082 | No text annotation | geometric IL_5XWG_002 IL_74768.1 | |
| IL_7ODR_015 | 1/A/2145:2147, 1/A/2254:2255 | Single bulged C | homologous IL_5J7L_276 NA | |
| IL_7ODR_016 | 1/A/2149:2153, 1/A/2248:2252 | UAA/GAN | homologous IL_7RQB_036 NA | |
| IL_7ODR_019 | 1/A/2306:2313, 1/A/2674:2680 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_5J7L_289 NA | |
| IL_7ODR_045 | 1/A/2330:2333, 1/A/2441:2447 | No text annotation | ||
| IL_7ODR_046 | 1/A/2377:2381, 1/A/2411:2419 | No text annotation | ||
| IL_7ODR_047 | 1/A/2384:2400, 1/A/2403:2408 | No text annotation | ||
| IL_7ODR_021 | 1/A/2456:2461, 1/A/2666:2668 | No text annotation | ||
| IL_7ODR_022 | 1/A/2467:2469, 1/A/2658:2660 | Isolated tWW turn | homologous IL_4WF9_063 IL_10432.1 | |
| IL_7ODR_023 | 1/A/2470:2473, 1/A/2656:2657 | Major groove platform; stack outside cWW | geometric IL_7RQB_066 NA | |
| IL_7ODR_048 | 1/A/2470:2478, 1/A/2653:2657 | No text annotation | homologous IL_4WF9_117 IL_80252.1 | |
| IL_7ODR_024 | 1/A/2473:2478, 1/A/2653:2656 | Intercalated tWH | geometric IL_4WF9_065 IL_28217.1 | |
| IL_7ODR_049 | 1/A/2478:2487, 1/A/2648:2653 | No text annotation | ||
| IL_7ODR_026 | 1/A/2490:2491, 1/A/2643:2645 | Single bulged A | homologous IL_7RQB_069 NA | |
| IL_7ODR_027 | 1/A/2712:2715, 1/A/3104:3106 | Major groove platform with extra pair | geometric IL_5TBW_091 NA | |
| IL_7ODR_028 | 1/A/2717:2719, 1/A/3099:3102 | No text annotation | homologous IL_4WF9_079 IL_80025.1 | |
| IL_7ODR_029 | 1/A/2730:2732, 1/A/2929:2930 | Single bulged U | homologous IL_7RQB_080 NA | |
| IL_7ODR_030 | 1/A/2733:2734, 1/A/2925:2928 | Minor groove platform | homologous IL_7RQB_081 NA | |
| IL_7ODR_050 | 1/A/2744:2746, 1/A/2802:2803 | Minor groove platform | geometric IL_7A0S_003 IL_34520.3 | |
| IL_7ODR_033 | 1/A/2856:2860, 1/A/2872:2876 | Double sheared with non-canonical cWW | geometric IL_5J7L_274 NA | |
| IL_7ODR_034 | 1/A/2953:2955, 1/A/2968:2971 | No text annotation | geometric IL_4P3T_002 NA | |
| IL_7ODR_035 | 1/A/2955:2957, 1/A/2967:2968 | Minor groove platform | geometric IL_2QWY_009 IL_34520.3 | |
| IL_7ODR_036 | 1/A/2997:2999, 1/A/3061:3065 | Isolated non-canonical cWW with bulges | homologous IL_7RQB_097 NA | |
| IL_7ODR_037 | 1/A/2999:3000, 1/A/3058:3061 | No text annotation | geometric IL_5J7L_341 NA | |
| IL_7ODR_038 | 1/A/3008:3010, 1/A/3027:3031 | No text annotation | ||
| IL_7ODR_039 | 1/A/3078:3079, 1/A/3088:3090 | Single bulged A | geometric IL_7RQB_048 NA | |
| IL_7ODR_040 | 1/A/3115:3117, 1/A/3139:3141 | No text annotation | geometric IL_2ZNI_001 NA | |
| IL_7ODR_041 | 1/A/3119:3126, 1/A/3131:3137 | 8x7 Sarcin-Ricin; G-bulge | geometric IL_5TBW_116 NA | |
| IL_7ODR_042 | 1/A/3148:3152, 1/A/3161:3163 | C-loop | geometric IL_7RQB_051 NA | |
| IL_7ODR_043 | 1/A/3173:3174, 1/A/3195:3197 | No text annotation | ||
| IL_7ODR_044 | 1/B/1627:1629, 1/B/1639:1641 | Isolated non-canonical cWW pair | geometric IL_4WF9_042 IL_01003.4 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_7ODR_017 | No text annotation | ||
| IL_7ODR_018 | No text annotation | ||
| IL_7ODR_020 | No text annotation | ||
| IL_7ODR_025 | No text annotation | ||
| IL_7ODR_031 | No text annotation | ||
| IL_7ODR_032 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_7ODR_001 | 1/A/1678:1681, 1/A/1771:1785, 1/A/1792:1797 | No text annotation | ||
| J3_7ODR_007 | 1/A/1684:1722, 1/A/1729:1745, 1/A/1753:1767 | No text annotation | ||
| J3_7ODR_002 | 1/A/1915:1921, 1/A/1983:1985, 1/A/2001:2004 | No text annotation | homologous J3_4WF9_002 J3_46658.1 | |
| J3_7ODR_003 | 1/A/1930:1932, 1/A/1942:1946, 1/A/1970:1973 | No text annotation | homologous J3_7RQB_005 NA | |
| J3_7ODR_004 | 1/A/2336:2343, 1/A/2423:2427, 1/A/2436:2438 | No text annotation | ||
| J3_7ODR_005 | 1/A/2343:2345, 1/A/2368:2375, 1/A/2421:2423 | No text annotation | ||
| J3_7ODR_008 | 1/A/2846:2848, 1/A/2890:2900, 1/A/2909:2915 | No text annotation | ||
| J3_7ODR_006 | 1/A/3004:3007, 1/A/3032:3034, 1/A/3048:3054 | No text annotation | homologous J3_7RQB_012 NA | |
| J4_7ODR_001 | 1/A/2314:2317, 1/A/2326:2327, 1/A/2450:2453, 1/A/2671:2673 | No text annotation | ||
| J4_7ODR_002 | 1/A/2336:2345, 1/A/2368:2375, 1/A/2421:2427, 1/A/2436:2438 | No text annotation | ||
| J4_7ODR_003 | 1/A/2492:2496, 1/A/2508:2513, 1/A/2537:2542, 1/A/2637:2642 | No text annotation | ||
| J4_7ODR_005 | 1/B/1608:1611, 1/B/1624:1626, 1/B/1642:1648, 1/B/1661:1663 | No text annotation | ||
| J5_7ODR_001 | 1/A/1827:1829, 1/A/1841:1845, 1/A/1858:1860, 1/A/2305:2306, 1/A/2680:2681 | No text annotation | homologous J5_9DFE_003 J5_43153.6 | |
| J5_7ODR_002 | 1/A/1865:1875, 1/A/1899:1903, 1/A/2019:2022, 1/A/2271:2275, 1/A/2290:2300 | No text annotation | ||
| J5_7ODR_003 | 1/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_7ODR_001 | 1/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_7ODR_002 | 1/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 id | Problem | Sequence |
|---|---|---|---|
| J4_7ODR_004 | No text annotation |
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