6QT0 Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
# | loop id | location | annotation (mapped to, source) | motif group (similar to) |
---|---|---|---|---|
1/A/38:45 | geometric HL_5TBW_001 | NA HL_23481.5* | ||
1/A/69:74 | homologous HL_5TBW_114 | NA | ||
1/A/90:96 | homologous HL_5TBW_115 | NA | ||
1/A/132:136 | homologous HL_5TBW_116 | NA | ||
1/A/194:201 | homologous HL_5TBW_117 | NA | ||
1/A/208:212 | homologous HL_5TBW_118 | NA | ||
1/A/216:224 | homologous HL_5TBW_119 | NA | ||
1/A/278:287 | homologous HL_5TBW_120 | NA | ||
1/A/357:362 | homologous HL_5TBW_122 | NA | ||
1/A/382:387 | homologous HL_5TBW_123 | NA | ||
1/A/541:550 | NA | NA | ||
1/A/599:604 | homologous HL_5TBW_125 | NA | ||
1/A/640:649 | homologous HL_5TBW_126 | NA | ||
1/A/686:694 | homologous HL_5TBW_127 | NA | ||
1/A/732:737 | homologous HL_5TBW_129 | NA | ||
1/A/958:963 | homologous HL_5TBW_134 | NA | ||
1/A/1148:1155 | homologous HL_5TBW_138 | NA | ||
1/A/1347:1357 | NA | NA | ||
1/A/1403:1408 | homologous HL_5TBW_142 | NA | ||
1/A/3025:3030 | homologous HL_5TBW_178 | NA | ||
1/A/3068:3073 | homologous HL_5TBW_179 | NA | ||
1/A/3110:3124 | homologous HL_5TBW_180 | NA | ||
1/A/3194:3197 | homologous HL_5TBW_181 | NA | ||
1/A/3303:3311 | homologous HL_5TBW_183 | NA | ||
1/x/36:41 | NA | NA | ||
1/x/88:93 | NA | NA | ||
1/y/47:56 | geometric HL_7A0S_001 | NA HL_29414.1* | ||
1/y/69:89 | NA | NA | ||
1/y/108:114 | homologous HL_5TBW_075 | NA HL_06569.2* | ||
1/y/124:129 | homologous HL_5TBW_076 | NA HL_60357.1* |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
HL_6QT0_009 | homologous HL_5TBW_121 | ||
HL_6QT0_016 | homologous HL_5TBW_128 | ||
HL_6QT0_018 | homologous HL_5TBW_130 | ||
HL_6QT0_019 | geometric HL_6SVS_001 | ||
HL_6QT0_020 | homologous HL_5TBW_132 | ||
HL_6QT0_021 | homologous HL_5TBW_133 | ||
HL_6QT0_023 | geometric HL_4V9F_032 | ||
HL_6QT0_024 | geometric HL_5TBW_024 | ||
HL_6QT0_025 | homologous HL_5TBW_137 | ||
HL_6QT0_027 | geometric HL_5TBW_027 | ||
HL_6QT0_028 | geometric HL_5TBW_028 | ||
HL_6QT0_031 | geometric HL_4WSM_226 | ||
HL_6QT0_032 | homologous HL_5TBW_144 | ||
HL_6QT0_033 | homologous HL_5TBW_145 | ||
HL_6QT0_034 | NA | ||
HL_6QT0_035 | homologous HL_5TBW_147 | ||
HL_6QT0_036 | homologous HL_5TBW_148 | ||
HL_6QT0_037 | homologous HL_5TBW_149 | ||
HL_6QT0_038 | homologous HL_5TBW_150 | ||
HL_6QT0_039 | NA | ||
HL_6QT0_040 | homologous HL_5TBW_152 | ||
HL_6QT0_041 | homologous HL_5TBW_153 | ||
HL_6QT0_042 | homologous HL_5TBW_154 | ||
HL_6QT0_043 | UNCG geometric HL_4LFB_009 | ||
HL_6QT0_044 | geometric HL_2Y9H_005 | ||
HL_6QT0_045 | homologous HL_5TBW_157 | ||
HL_6QT0_046 | homologous HL_5TBW_158 | ||
HL_6QT0_047 | homologous HL_5TBW_159 | ||
HL_6QT0_048 | homologous HL_5TBW_160 | ||
HL_6QT0_049 | NA | ||
HL_6QT0_050 | homologous HL_5TBW_162 | ||
HL_6QT0_051 | NA | ||
HL_6QT0_052 | NA | ||
HL_6QT0_053 | NA | ||
HL_6QT0_054 | homologous HL_5TBW_167 | ||
HL_6QT0_055 | homologous HL_5TBW_168 | ||
HL_6QT0_056 | homologous HL_5TBW_169 | ||
HL_6QT0_057 | homologous HL_5TBW_170 | ||
HL_6QT0_058 | homologous HL_5TBW_171 | ||
HL_6QT0_059 | homologous HL_5TBW_172 | ||
HL_6QT0_060 | homologous HL_5TBW_173 | ||
HL_6QT0_061 | homologous HL_5TBW_174 | ||
HL_6QT0_062 | homologous HL_5TBW_175 | ||
HL_6QT0_063 | homologous HL_5TBW_176 | ||
HL_6QT0_064 | homologous HL_5TBW_177 | ||
HL_6QT0_069 | NA | ||
HL_6QT0_071 | homologous HL_5TBW_184 |
Valid loops
# | loop id | location | annotation (mapped to, source) | motif group (similar to) |
---|---|---|---|---|
1/A/7:8, 1/y/150:152 | Single bulged C homologous IL_5TBW_002 | NA IL_61258.10* | ||
1/A/13:15, 1/y/144:145 | Single bulged U homologous IL_5TBW_003 | NA IL_83039.11* | ||
1/A/27:28, 1/A/56:58 | homologous IL_5TBW_240 | NA | ||
1/A/31:38, 1/A/45:53 | homologous IL_5TBW_241 | NA | ||
1/A/82:89, 1/A/97:103 | homologous IL_5TBW_242 | NA | ||
1/A/123:124, 1/A/144:149 | homologous IL_5TBW_243 | NA | ||
1/A/125:127, 1/A/141:143 | homologous IL_5TBW_244 | NA | ||
1/A/177:178, 1/A/238:241 | NA | NA | ||
1/A/189:191, 1/A/204:205 | homologous IL_5TBW_248 | NA | ||
1/A/337:339, 1/y/25:26 | Single bulged A homologous IL_5TBW_013 | NA IL_80007.16* | ||
1/A/376:379, 1/A/390:403 | homologous IL_5TBW_250 | NA | ||
1/A/404:410, 1/y/13:19 | Triple sheared with non-canonical cWW geometric IL_5TBW_015 | NA IL_66414.5* | ||
1/A/429:431, 1/A/628:630 | homologous IL_5TBW_252 | NA | ||
1/A/512:513, 1/A/577:579 | homologous IL_5TBW_254 | NA | ||
1/A/517:525, 1/A/567:573 | homologous IL_5TBW_255 | NA | ||
1/A/531:539, 1/A/552:561 | NA | NA | ||
1/A/668:670, 1/A/792:794 | homologous IL_5TBW_257 | NA | ||
1/A/680:684, 1/A/696:700 | homologous IL_5TBW_258 | NA | ||
1/A/725:728, 1/A/741:745 | homologous IL_5TBW_259 | NA | ||
1/A/752:753, 1/A/779:781 | homologous IL_5TBW_260 | NA | ||
1/A/755:757, 1/A/774:777 | geometric IL_5E81_376 | NA IL_01312.13* | ||
1/A/803:805, 1/A/938:940 | geometric IL_5TBW_027 | NA IL_01312.13* | ||
1/A/805:809, 1/A/931:938 | homologous IL_5TBW_264 | NA | ||
1/A/954:956, 1/A/965:967 | homologous IL_5TBW_270 | NA | ||
1/A/969:970, 1/A/1111:1113 | homologous IL_5TBW_271 | NA | ||
1/A/977:982, 1/A/1101:1104 | NA | NA | ||
1/A/983:985, 1/A/1099:1100 | homologous IL_5TBW_273 | NA | ||
1/A/1120:1122, 1/A/1136:1138 | homologous IL_5TBW_282 | NA | ||
1/A/1167:1171, 1/A/1328:1332 | homologous IL_5TBW_284 | NA | ||
1/A/1173:1180, 1/A/1325:1326 | homologous IL_5TBW_285 | NA | ||
1/A/1180:1182, 1/A/1324:1325 | Single bulged U geometric IL_5TBW_050 | NA IL_83039.11* | ||
1/A/1207:1209, 1/A/1296:1297 | homologous IL_5TBW_289 | NA | ||
1/A/1376:1378, 1/A/1428:1431 | homologous IL_5TBW_293 | NA | ||
1/A/1388:1395, 1/A/1415:1419 | homologous IL_5TBW_295 | NA | ||
1/A/1444:1450, 1/A/2354:2359 | homologous IL_5TBW_297 | NA | ||
1/A/3004:3007, 1/A/3139:3144 | homologous IL_5TBW_349 | NA | ||
1/A/3012:3014, 1/A/3040:3042 | homologous IL_5TBW_350 | NA | ||
1/A/3018:3025, 1/A/3030:3036 | 8x7 Sarcin-Ricin; G-bulge geometric IL_5TBW_116 | NA IL_04346.5* | ||
1/A/3047:3051, 1/A/3091:3094 | homologous IL_5TBW_352 | NA | ||
1/A/3054:3059, 1/A/3084:3088 | homologous IL_5TBW_353 | NA | ||
1/A/3103:3107, 1/A/3127:3131 | homologous IL_5TBW_355 | NA | ||
1/A/3164:3166, 1/A/3284:3286 | geometric IL_4M4O_001 | NA IL_01312.13* | ||
1/A/3177:3179, 1/A/3210:3211 | homologous IL_5TBW_358 | NA | ||
1/A/3179:3188, 1/A/3204:3210 | geometric IL_5TBW_124 | NA IL_56867.1* | ||
1/A/3192:3194, 1/A/3197:3200 | geometric IL_5UNE_007 | NA IL_01312.13* | ||
1/A/3300:3303, 1/A/3311:3314 | Tandem non-canonical cWW pairs geometric IL_5TBW_129 | NA IL_85877.10* | ||
1/A/3318:3320, 1/A/3387:3388 | Single bulged U geometric IL_3D2V_001 | NA IL_83039.11* | ||
1/A/3324:3325, 1/A/3381:3383 | NA | NA | ||
1/A/3332:3337, 1/A/3367:3371 | homologous IL_5TBW_368 | NA | ||
1/x/15:16, 1/x/63:65 | NA | NA | ||
1/x/21:27, 1/x/53:58 | NA | NA | ||
1/x/28:29, 1/x/49:52 | NA | NA | ||
1/x/29:30, 1/x/47:49 | NA | NA | ||
1/x/32:36, 1/x/41:45 | NA | NA | ||
1/x/72:80, 1/x/100:106 | NA | NA | ||
1/x/84:87, 1/x/94:96 | NA | NA | ||
1/y/64:67, 1/y/92:96 | NA | NA | ||
1/y/68:69, 1/y/89:91 | Single bulged U homologous IL_5TBW_146 | NA IL_83039.11* |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
IL_6QT0_008 | NA | ||
IL_6QT0_015 | NA | ||
IL_6QT0_024 | geometric IL_5TBW_026 | ||
IL_6QT0_027 | Single bulged G geometric IL_4V9F_026 | ||
IL_6QT0_028 | homologous IL_5TBW_266 | ||
IL_6QT0_029 | homologous IL_5TBW_267 | ||
IL_6QT0_030 | homologous IL_5TBW_268 | ||
IL_6QT0_031 | Multiple bulged bases geometric IL_5TBW_033 | ||
IL_6QT0_036 | 7x7 Sarcin-Ricin with intercalated A; G-bulge geometric IL_5TBW_038 | ||
IL_6QT0_037 | Major groove platform with extra cWW geometric IL_3PDR_004 | ||
IL_6QT0_038 | homologous IL_5TBW_276 | ||
IL_6QT0_039 | homologous IL_5TBW_277 | ||
IL_6QT0_040 | geometric IL_5TBW_127 | ||
IL_6QT0_041 | NA | ||
IL_6QT0_042 | homologous IL_5TBW_280 | ||
IL_6QT0_043 | homologous IL_5TBW_281 | ||
IL_6QT0_048 | homologous IL_5TBW_287 | ||
IL_6QT0_049 | geometric IL_5TBW_052 | ||
IL_6QT0_051 | NA | ||
IL_6QT0_053 | homologous IL_5TBW_294 | ||
IL_6QT0_055 | homologous IL_5TBW_296 | ||
IL_6QT0_057 | C-loop geometric IL_7RQB_051 | ||
IL_6QT0_058 | homologous IL_5TBW_299 | ||
IL_6QT0_059 | homologous IL_5TBW_300 | ||
IL_6QT0_060 | Isolated non-canonical cWW with bulges geometric IL_4PKD_001 | ||
IL_6QT0_061 | geometric IL_5TBW_066 | ||
IL_6QT0_062 | Triple sheared geometric IL_5TBW_067 | ||
IL_6QT0_063 | homologous IL_5TBW_304 | ||
IL_6QT0_064 | homologous IL_5TBW_305 | ||
IL_6QT0_065 | Single stack bend geometric IL_5TBW_070 | ||
IL_6QT0_066 | homologous IL_5TBW_307 | ||
IL_6QT0_067 | homologous IL_5TBW_308 | ||
IL_6QT0_068 | homologous IL_5TBW_309 | ||
IL_6QT0_069 | NA | ||
IL_6QT0_070 | homologous IL_5TBW_311 | ||
IL_6QT0_071 | homologous IL_5TBW_312 | ||
IL_6QT0_072 | Intercalated tWH geometric IL_5J7L_307 | ||
IL_6QT0_073 | homologous IL_5TBW_314 | ||
IL_6QT0_074 | homologous IL_5TBW_315 | ||
IL_6QT0_075 | homologous IL_5TBW_316 | ||
IL_6QT0_076 | geometric IL_4V9K_064 | ||
IL_6QT0_077 | homologous IL_5TBW_319 | ||
IL_6QT0_078 | homologous IL_5TBW_320 | ||
IL_6QT0_079 | homologous IL_5TBW_321 | ||
IL_6QT0_080 | homologous IL_5TBW_322 | ||
IL_6QT0_081 | Major groove platform with extra pair geometric IL_5TBW_087 | ||
IL_6QT0_082 | homologous IL_5TBW_324 | ||
IL_6QT0_083 | Multiple bulged bases geometric IL_5TBW_089 | ||
IL_6QT0_084 | homologous IL_5TBW_326 | ||
IL_6QT0_085 | homologous IL_5TBW_327 | ||
IL_6QT0_086 | homologous IL_5TBW_328 | ||
IL_6QT0_087 | homologous IL_5TBW_329 | ||
IL_6QT0_088 | homologous IL_5TBW_330 | ||
IL_6QT0_089 | homologous IL_5TBW_331 | ||
IL_6QT0_090 | NA | ||
IL_6QT0_091 | homologous IL_5TBW_332 | ||
IL_6QT0_092 | NA | ||
IL_6QT0_093 | homologous IL_5TBW_333 | ||
IL_6QT0_094 | homologous IL_5TBW_334 | ||
IL_6QT0_095 | Single bulged A geometric IL_5WWT_001 | ||
IL_6QT0_096 | homologous IL_5TBW_335 | ||
IL_6QT0_097 | homologous IL_5TBW_336 | ||
IL_6QT0_098 | Major groove platform geometric IL_5TBW_102 | ||
IL_6QT0_099 | homologous IL_5TBW_338 | ||
IL_6QT0_100 | Major groove platform geometric IL_5TBW_104 | ||
IL_6QT0_101 | homologous IL_5TBW_340 | ||
IL_6QT0_102 | homologous IL_5TBW_341 | ||
IL_6QT0_103 | homologous IL_5TBW_342 | ||
IL_6QT0_104 | Isolated non-canonical cWW with bulges geometric IL_5TBW_108 | ||
IL_6QT0_105 | homologous IL_5TBW_344 | ||
IL_6QT0_106 | geometric IL_5TBW_110 | ||
IL_6QT0_107 | homologous IL_5TBW_346 | ||
IL_6QT0_108 | geometric IL_5TBW_112 | ||
IL_6QT0_109 | homologous IL_5TBW_348 | ||
IL_6QT0_115 | homologous IL_5TBW_354 | ||
IL_6QT0_124 | homologous IL_5TBW_367 | ||
IL_6QT0_126 | Single bulged U geometric IL_3WBM_001 | ||
IL_6QT0_127 | homologous IL_5TBW_370 | ||
IL_6QT0_128 | Multiple bulged bases geometric IL_7V9E_001 |
Valid loops
# | loop id | location | annotation (mapped to, source) | motif group (similar to) |
---|---|---|---|---|
1/A/369:376, 1/A/403:404, 1/y/19:20 | homologous J3_5TBW_002 | NA | ||
1/A/502:503, 1/A/588:597, 1/A/606:611 | homologous J3_5TBW_032 | NA | ||
1/A/3298:3300, 1/A/3314:3318, 1/A/3388:3390 | homologous J3_5TBW_044 | NA | ||
1/x/9:14, 1/x/66:67, 1/x/111:112 | NA | NA | ||
1/y/43:45, 1/y/58:64, 1/y/96:101 | NA | NA |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
J3_6QT0_001 | NA | ||
J3_6QT0_004 | NA | ||
J3_6QT0_005 | homologous J3_5TBW_034 | ||
J3_6QT0_006 | NA | ||
J3_6QT0_007 | homologous J3_5TBW_037 | ||
J3_6QT0_008 | homologous J3_5TBW_038 | ||
J3_6QT0_009 | homologous J3_5TBW_039 | ||
J3_6QT0_010 | homologous J3_5TBW_040 | ||
J3_6QT0_011 | NA | ||
J3_6QT0_012 | NA | ||
J3_6QT0_013 | homologous J3_5TBW_043 |
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