9PS0 Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_9PS0_001 | 1/A/1722:1729 | No text annotation | geometric HL_9E6Q_006 HL_48677.1 | |
| HL_9PS0_002 | 1/A/1746:1752 | No text annotation | geometric HL_9E6Q_008 HL_76371.2 | |
| HL_9PS0_003 | 1/A/1786:1791 | GNRA | homologous HL_7A0S_015 HL_34789.4 | |
| HL_9PS0_005 | 1/A/1847:1856 | T-loop with 2 stacked bulged bases | homologous HL_7A0S_018 HL_33597.3 | |
| HL_9PS0_006 | 1/A/1884:1889 | No text annotation | ||
| HL_9PS0_007 | 1/A/1934:1940 | No text annotation | ||
| HL_9PS0_008 | 1/A/1954:1963 | No text annotation | homologous HL_7A0S_022 HL_50204.1 | |
| HL_9PS0_009 | 1/A/1988:1996 | No text annotation | geometric HL_9E6Q_025 HL_92598.1 | |
| HL_9PS0_010 | 1/A/2035:2040 | No text annotation | homologous HL_7A0S_024 HL_27530.1 | |
| HL_9PS0_012 | 1/A/2107:2114 | GNRA | homologous HL_7A0S_026 HL_34789.4 | |
| HL_9PS0_013 | 1/A/2129:2136 | No text annotation | homologous HL_7A0S_027 HL_47171.1 | |
| HL_9PS0_016 | 1/A/2279:2286 | No text annotation | geometric HL_5E6M_002 HL_10874.1 | |
| HL_9PS0_020 | 1/A/2428:2435 | No text annotation | homologous HL_7A0S_040 HL_28592.2 | |
| HL_9PS0_021 | 1/A/2497:2507 | No text annotation | geometric HL_9E6Q_045 HL_87681.1 | |
| HL_9PS0_022 | 1/A/2518:2532 | No text annotation | ||
| HL_9PS0_025 | 1/A/2612:2620 | No text annotation | homologous HL_7A0S_048 HL_61418.2 | |
| HL_9PS0_026 | 1/A/2690:2699 | No text annotation | homologous HL_7A0S_049 HL_78372.1 | |
| HL_9PS0_028 | 1/A/2812:2820 | No text annotation | homologous HL_7A0S_052 HL_11974.2 | |
| HL_9PS0_029 | 1/A/2828:2840 | No text annotation | ||
| HL_9PS0_030 | 1/A/2862:2870 | No text annotation | ||
| HL_9PS0_033 | 1/A/3015:3022 | GNRA variation | homologous HL_7A0S_060 HL_46665.2 | |
| HL_9PS0_034 | 1/A/3038:3044 | No text annotation | homologous HL_7A0S_061 HL_48677.1 | |
| HL_9PS0_035 | 1/A/3081:3086 | GNRA | homologous HL_7A0S_062 HL_34789.4 | |
| HL_9PS0_037 | 1/A/3154:3159 | No text annotation | geometric HL_4WRT_001 HL_19413.2 | |
| HL_9PS0_040 | 1/AA/654:664 | No text annotation | homologous HL_6CZR_072 NA | |
| HL_9PS0_047 | 1/AA/894:899 | GNRA variation | homologous HL_6CZR_216 NA | |
| HL_9PS0_050 | 1/AA/1074:1084 | No text annotation | homologous HL_6CZR_088 NA | |
| HL_9PS0_052 | 1/AA/1150:1155 | No text annotation | ||
| HL_9PS0_060 | 1/AA/1580:1585 | GNRA | homologous HL_6CZR_103 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_9PS0_004 | No text annotation | ||
| HL_9PS0_011 | No text annotation | ||
| HL_9PS0_014 | No text annotation | ||
| HL_9PS0_015 | GNRA wlth tandem sheared | ||
| HL_9PS0_017 | UNCG variation | ||
| HL_9PS0_018 | No text annotation | ||
| HL_9PS0_019 | Mini UNCG | ||
| HL_9PS0_023 | No text annotation | ||
| HL_9PS0_024 | No text annotation | ||
| HL_9PS0_027 | GNRA | ||
| HL_9PS0_031 | GNRA | ||
| HL_9PS0_032 | No text annotation | ||
| HL_9PS0_036 | GNRA | ||
| HL_9PS0_038 | No text annotation | ||
| HL_9PS0_039 | No text annotation | ||
| HL_9PS0_041 | No text annotation | ||
| HL_9PS0_042 | No text annotation | ||
| HL_9PS0_043 | GNRA | ||
| HL_9PS0_044 | No text annotation | ||
| HL_9PS0_045 | No text annotation | ||
| HL_9PS0_046 | GNRA | ||
| HL_9PS0_048 | GNRA wlth tandem sheared | ||
| HL_9PS0_049 | GNRA | ||
| HL_9PS0_051 | No text annotation | ||
| HL_9PS0_053 | No text annotation | ||
| HL_9PS0_054 | No text annotation | ||
| HL_9PS0_055 | No text annotation | ||
| HL_9PS0_056 | No text annotation | ||
| HL_9PS0_057 | T-loop with 2 stacked bulged bases | ||
| HL_9PS0_058 | No text annotation | ||
| HL_9PS0_059 | UNCG | ||
| HL_9PS0_061 | tRNA anticodon loop | ||
| HL_9PS0_062 | No text annotation | ||
| HL_9PS0_063 | T-loop with 2 stacked bulged bases | ||
| HL_9PS0_064 | tRNA D-loop | ||
| HL_9PS0_065 | tRNA anticodon loop | ||
| HL_9PS0_066 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_9PS0_001 | 1/A/1672:1678, 1/A/1797:1816 | No text annotation | ||
| IL_9PS0_002 | 1/A/1682:1683, 1/A/1768:1770 | Single bulged A | homologous IL_7A0S_002 IL_14190.2 | |
| IL_9PS0_003 | 1/A/1845:1847, 1/A/1856:1858 | Isolated non-canonical cWW pair | homologous IL_7A0S_011 IL_71625.3 | |
| IL_9PS0_004 | 1/A/1877:1879, 1/A/1895:1897 | Isolated non-canonical cWW pair | geometric IL_4E48_003 IL_01003.4 | |
| IL_9PS0_005 | 1/A/1880:1883, 1/A/1890:1894 | No text annotation | ||
| IL_9PS0_006 | 1/A/1904:1906, 1/A/2016:2018 | Isolated non-canonical cWW pair | homologous IL_7A0S_014 IL_01003.4 | |
| IL_9PS0_007 | 1/A/1906:1910, 1/A/2009:2016 | tHW-tHW cross-strand stack | homologous IL_7A0S_015 IL_73855.1 | |
| IL_9PS0_008 | 1/A/1913:1915, 1/A/2004:2006 | Isolated non-canonical cWW pair | geometric IL_7ZLQ_002 IL_01003.4 | |
| IL_9PS0_010 | 1/A/1929:1930, 1/A/1973:1975 | Single bulged A | homologous IL_7A0S_016 IL_14190.2 | |
| IL_9PS0_011 | 1/A/1948:1951, 1/A/1966:1968 | Major groove platform with extra cWW | homologous IL_7A0S_019 IL_36931.2 | |
| IL_9PS0_012 | 1/A/1985:1987, 1/A/1997:2001 | No text annotation | geometric IL_9E6Q_032 IL_89509.1 | |
| IL_9PS0_013 | 1/A/2046:2048, 1/A/2091:2094 | No text annotation | geometric IL_4N0T_004 IL_32983.2 | |
| IL_9PS0_014 | 1/A/2057:2063, 1/A/2076:2082 | No text annotation | geometric IL_5XWG_002 IL_74768.1 | |
| IL_9PS0_015 | 1/A/2145:2147, 1/A/2254:2255 | Single bulged C | homologous IL_7A0S_032 IL_05642.3 | |
| IL_9PS0_016 | 1/A/2149:2153, 1/A/2248:2252 | UAA/GAN | homologous IL_7A0S_033 IL_08938.1 | |
| IL_9PS0_020 | 1/A/2306:2313, 1/A/2674:2680 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_7A0S_045 IL_62167.3 | |
| IL_9PS0_024 | 1/A/2384:2400, 1/A/2403:2408 | No text annotation | ||
| IL_9PS0_025 | 1/A/2456:2461, 1/A/2666:2668 | No text annotation | ||
| IL_9PS0_026 | 1/A/2467:2469, 1/A/2658:2660 | Isolated tWW turn | homologous IL_7A0S_060 IL_10432.1 | |
| IL_9PS0_027 | 1/A/2470:2473, 1/A/2656:2657 | No text annotation | geometric IL_8GLP_304 IL_74641.2 | |
| IL_9PS0_028 | 1/A/2470:2478, 1/A/2653:2657 | No text annotation | geometric IL_8GLP_305 IL_80252.1 | |
| IL_9PS0_029 | 1/A/2473:2478, 1/A/2653:2656 | Intercalated tWH | homologous IL_7A0S_062 IL_28217.1 | |
| IL_9PS0_030 | 1/A/2478:2487, 1/A/2648:2653 | No text annotation | ||
| IL_9PS0_031 | 1/A/2490:2491, 1/A/2643:2645 | Single bulged A | homologous IL_7A0S_064 IL_14190.2 | |
| IL_9PS0_032 | 1/A/2548:2551, 1/A/2566:2567 | Minor groove platform, major groove intercalation | homologous IL_7A0S_066 IL_55206.1 | |
| IL_9PS0_033 | 1/A/2552:2553, 1/A/2562:2565 | Major groove intercalation | homologous IL_7A0S_067 IL_77710.1 | |
| IL_9PS0_034 | 1/A/2596:2597, 1/A/2627:2630 | No text annotation | geometric IL_8ZAU_001 IL_05670.1 | |
| IL_9PS0_035 | 1/A/2597:2608, 1/A/2624:2627 | No text annotation | ||
| IL_9PS0_036 | 1/A/2712:2715, 1/A/3104:3106 | No text annotation | geometric IL_8OI5_093 IL_75527.2 | |
| IL_9PS0_037 | 1/A/2717:2719, 1/A/3099:3102 | No text annotation | geometric IL_8B0X_140 IL_80025.1 | |
| IL_9PS0_038 | 1/A/2730:2732, 1/A/2929:2930 | Single bulged U | homologous IL_7A0S_075 IL_97561.5 | |
| IL_9PS0_039 | 1/A/2733:2734, 1/A/2925:2928 | Minor groove platform | homologous IL_7A0S_076 IL_34520.3 | |
| IL_9PS0_045 | 1/A/2940:2941, 1/A/2985:2987 | Single stack bend | homologous IL_7A0S_083 IL_15011.3 | |
| IL_9PS0_046 | 1/A/2941:2942, 1/A/2983:2985 | Major groove platform | homologous IL_7A0S_084 IL_48076.8 | |
| IL_9PS0_047 | 1/A/2943:2946, 1/A/2980:2982 | No text annotation | geometric IL_6DME_003 IL_75527.2 | |
| IL_9PS0_048 | 1/A/2946:2948, 1/A/2976:2980 | Major groove minor groove platform with extra cWW | homologous IL_7A0S_086 IL_36931.2 | |
| IL_9PS0_049 | 1/A/2953:2957, 1/A/2967:2971 | Double sheared with non-canonical cWW | homologous IL_7A0S_087 IL_87767.2 | |
| IL_9PS0_050 | 1/A/2994:2995, 1/A/3067:3069 | Major groove platform | homologous IL_7A0S_088 IL_46637.2 | |
| IL_9PS0_051 | 1/A/2997:2999, 1/A/3061:3065 | Isolated non-canonical cWW with bulges | homologous IL_7A0S_089 IL_68118.4 | |
| IL_9PS0_052 | 1/A/2999:3000, 1/A/3058:3061 | Multiple bulged bases | homologous IL_7A0S_090 IL_44609.2 | |
| IL_9PS0_053 | 1/A/3008:3010, 1/A/3027:3031 | No text annotation | ||
| IL_9PS0_054 | 1/A/3078:3079, 1/A/3088:3090 | No text annotation | geometric IL_8GLP_097 IL_14190.2 | |
| IL_9PS0_057 | 1/A/3148:3152, 1/A/3161:3163 | No text annotation | geometric IL_8B0X_162 IL_63596.12 | |
| IL_9PS0_066 | 1/AA/756:761, 1/AA/779:786 | Kink-turn with non-sequential stacking | geometric IL_4LFB_011 IL_46174.4 | |
| IL_9PS0_078 | 1/AA/974:980, 1/AA/1008:1014 | No text annotation | ||
| IL_9PS0_080 | 1/AA/986:988, 1/AA/999:1002 | No text annotation | ||
| IL_9PS0_082 | 1/AA/1062:1066, 1/AA/1092:1093 | Left turn | homologous IL_6CZR_144 NA | |
| IL_9PS0_083 | 1/AA/1067:1071, 1/AA/1087:1091 | tSH-tHW-tHS | geometric IL_4WF9_052 IL_05821.1 | |
| IL_9PS0_085 | 1/AA/1139:1148, 1/AA/1157:1164 | No text annotation | ||
| IL_9PS0_086 | 1/AA/1175:1176, 1/AA/1477:1479 | Single bulged A | homologous IL_6CZR_147 NA | |
| IL_9PS0_099 | 1/AA/1483:1485, 1/AA/1566:1569 | No text annotation | homologous IL_6CZR_165 NA | |
| IL_9PS0_100 | 1/AA/1485:1488, 1/AA/1562:1566 | No text annotation | homologous IL_6CZR_368 NA | |
| IL_9PS0_101 | 1/AA/1489:1491, 1/AA/1559:1561 | No text annotation | geometric IL_8GLP_276 IL_01003.4 | |
| IL_9PS0_102 | 1/AA/1491:1495, 1/AA/1554:1559 | No text annotation | ||
| IL_9PS0_103 | 1/AA/1500:1504, 1/AA/1546:1549 | UAA/GAN related | geometric IL_2R8S_002 IL_77691.7 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_9PS0_009 | Isolated non-canonical cWW pair | ||
| IL_9PS0_017 | Isolated near basepair | ||
| IL_9PS0_018 | No text annotation | ||
| IL_9PS0_019 | No text annotation | ||
| IL_9PS0_021 | No text annotation | ||
| IL_9PS0_022 | No text annotation | ||
| IL_9PS0_023 | No text annotation | ||
| IL_9PS0_040 | No text annotation | ||
| IL_9PS0_041 | No text annotation | ||
| IL_9PS0_042 | No text annotation | ||
| IL_9PS0_043 | No text annotation | ||
| IL_9PS0_044 | No text annotation | ||
| IL_9PS0_055 | No text annotation | ||
| IL_9PS0_056 | No text annotation | ||
| IL_9PS0_058 | Major groove intercalation | ||
| IL_9PS0_059 | No text annotation | ||
| IL_9PS0_060 | No text annotation | ||
| IL_9PS0_061 | Single bulged A | ||
| IL_9PS0_062 | Single bulged A | ||
| IL_9PS0_063 | Minor groove platform | ||
| IL_9PS0_064 | No text annotation | ||
| IL_9PS0_065 | No text annotation | ||
| IL_9PS0_067 | Major groove platform; stack outside cWW | ||
| IL_9PS0_068 | No text annotation | ||
| IL_9PS0_069 | No text annotation | ||
| IL_9PS0_070 | Single bulged U | ||
| IL_9PS0_071 | C-loop | ||
| IL_9PS0_072 | Single bulged G | ||
| IL_9PS0_073 | No text annotation | ||
| IL_9PS0_074 | Kink-turn related | ||
| IL_9PS0_075 | No text annotation | ||
| IL_9PS0_076 | No text annotation | ||
| IL_9PS0_077 | No text annotation | ||
| IL_9PS0_079 | No text annotation | ||
| IL_9PS0_081 | Other IL | ||
| IL_9PS0_084 | Isolated non-canonical cWW pair | ||
| IL_9PS0_087 | Single bulged G | ||
| IL_9PS0_088 | No text annotation | ||
| IL_9PS0_089 | Minor groove platform | ||
| IL_9PS0_090 | No text annotation | ||
| IL_9PS0_091 | No text annotation | ||
| IL_9PS0_092 | No text annotation | ||
| IL_9PS0_093 | Minor groove platform | ||
| IL_9PS0_094 | Single bulged U | ||
| IL_9PS0_095 | Isolated non-canonical cWW pair | ||
| IL_9PS0_096 | Double sheared | ||
| IL_9PS0_097 | No text annotation | ||
| IL_9PS0_098 | No text annotation | ||
| IL_9PS0_104 | Tandem non-canonical cWW pairs | ||
| IL_9PS0_105 | Single bulged C | ||
| IL_9PS0_106 | No text annotation | ||
| IL_9PS0_107 | No text annotation | ||
| IL_9PS0_108 | No text annotation | ||
| IL_9PS0_109 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_9PS0_001 | 1/A/1678:1681, 1/A/1771:1785, 1/A/1792:1797 | No text annotation | ||
| J3_9PS0_002 | 1/A/1684:1722, 1/A/1729:1745, 1/A/1753:1767 | No text annotation | ||
| J3_9PS0_003 | 1/A/1915:1921, 1/A/1983:1985, 1/A/2001:2004 | No text annotation | homologous J3_7A0S_004 J3_46658.1 | |
| J3_9PS0_004 | 1/A/1930:1932, 1/A/1942:1946, 1/A/1970:1973 | No text annotation | homologous J3_7A0S_005 J3_69816.1 | |
| J3_9PS0_005 | 1/A/2153:2168, 1/A/2192:2197, 1/A/2212:2248 | No text annotation | ||
| J3_9PS0_008 | 1/A/2846:2848, 1/A/2890:2900, 1/A/2909:2915 | No text annotation | ||
| J3_9PS0_009 | 1/A/3004:3007, 1/A/3032:3034, 1/A/3048:3054 | No text annotation | homologous J3_7A0S_011 J3_32601.6 | |
| J3_9PS0_012 | 1/AA/973:974, 1/AA/1014:1020, 1/AA/1030:1031 | No text annotation | ||
| J3_9PS0_016 | 1/AA/1268:1273, 1/AA/1302:1308, 1/AA/1317:1323 | No text annotation | homologous J3_6CZR_023 NA | |
| J4_9PS0_001 | 1/A/2314:2317, 1/A/2326:2327, 1/A/2450:2453, 1/A/2671:2673 | No text annotation | ||
| J4_9PS0_003 | 1/A/2492:2496, 1/A/2508:2513, 1/A/2537:2542, 1/A/2637:2642 | No text annotation | ||
| J4_9PS0_004 | 1/A/2544:2546, 1/A/2569:2570, 1/A/2587:2596, 1/A/2630:2635 | No text annotation | ||
| J4_9PS0_005 | 1/A/3111:3113, 1/A/3143:3144, 1/A/3167:3174, 1/A/3195:3202 | No text annotation | ||
| J4_9PS0_006 | 1/AA/698:701, 1/AA/708:715, 1/AA/800:802, 1/AA/811:817 | No text annotation | ||
| J4_9PS0_008 | 1/AA/941:943, 1/AA/1052:1057, 1/AA/1098:1109, 1/AA/1132:1133 | No text annotation | homologous J4_6CZR_013 NA | |
| J5_9PS0_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_7A0S_003 J5_43153.6 | |
| J5_9PS0_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_9PS0_003 | 1/A/2720:2727, 1/A/2933:2940, 1/A/2987:2994, 1/A/3069:3075, 1/A/3093:3098 | No text annotation | ||
| J5_9PS0_004 | 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_9PS0_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_9PS0_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 |
|---|---|---|---|
| J3_9PS0_006 | No text annotation | ||
| J3_9PS0_007 | No text annotation | ||
| J3_9PS0_010 | No text annotation | ||
| J3_9PS0_011 | No text annotation | ||
| J3_9PS0_013 | No text annotation | ||
| J3_9PS0_014 | No text annotation | ||
| J3_9PS0_015 | No text annotation | ||
| J3_9PS0_017 | No text annotation | ||
| J4_9PS0_002 | No text annotation | ||
| J4_9PS0_007 | No text annotation | ||
| J4_9PS0_009 | No text annotation |
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