6VU3 Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6VU3_004 | 1/B/13:22 | No text annotation | ||
| HL_6VU3_007 | 1/D/12:22 | No text annotation | homologous HL_4LFB_001 HL_31940.1 | |
| HL_6VU3_010 | 1/D/186:191 | GNRA | homologous HL_5J7L_004 NA | |
| HL_6VU3_012 | 1/D/259:267 | GNRA related | homologous HL_5J7L_006 NA | |
| HL_6VU3_013 | 1/D/296:301 | GNRA | homologous HL_4LFB_007 HL_34789.1 | |
| HL_6VU3_014 | 1/D/320:333 | No text annotation | homologous HL_5J7L_008 NA | |
| HL_6VU3_017 | 1/D/419:424 | UNCG | homologous HL_5J7L_011 NA | |
| HL_6VU3_020 | 1/D/617:623 | GNRA-like with tWH | homologous HL_5J7L_014 NA | |
| HL_6VU3_022 | 1/D/726:731 | GNRA | homologous HL_5J7L_016 NA | |
| HL_6VU3_023 | 1/D/786:796 | No text annotation | homologous HL_5J7L_017 NA | |
| HL_6VU3_025 | 1/D/862:867 | GNRA | homologous HL_5J7L_019 NA | |
| HL_6VU3_026 | 1/D/897:902 | GNRA | homologous HL_4LFB_020 HL_34789.1 | |
| HL_6VU3_029 | 1/D/1076:1081 | GNRA | homologous HL_5J7L_023 NA | |
| HL_6VU3_030 | 1/D/1089:1096 | T-loop related | homologous HL_4LFB_025 HL_63894.1 | |
| HL_6VU3_034 | 1/D/1314:1323 | T-loop with 3 stacked bulged bases | homologous HL_4LFB_029 HL_93658.1 | |
| HL_6VU3_035 | 1/D/1356:1366 | No text annotation | homologous HL_4LFB_030 HL_86432.1 | |
| HL_6VU3_038 | 1/a/59:68 | No text annotation | homologous HL_5J7L_134 NA | |
| HL_6VU3_039 | 1/a/87:95 | No text annotation | homologous HL_5J7L_135 NA | |
| HL_6VU3_040 | 1/a/123:128 | No text annotation | homologous HL_5J7L_136 NA | |
| HL_6VU3_041 | 1/a/137:142 | UNCG | geometric HL_5J7L_030 NA | |
| HL_6VU3_042 | 1/a/158:168 | No text annotation | homologous HL_5J7L_138 NA | |
| HL_6VU3_043 | 1/a/194:201 | No text annotation | geometric HL_5J7L_139 NA | |
| HL_6VU3_045 | 1/a/246:252 | No text annotation | homologous HL_5J7L_141 NA | |
| HL_6VU3_046 | 1/a/305:312 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_142 NA | |
| HL_6VU3_047 | 1/a/319:323 | No text annotation | homologous HL_5J7L_143 NA | |
| HL_6VU3_048 | 1/a/327:335 | T-loop with unstacked turn | homologous HL_5J7L_144 NA | |
| HL_6VU3_049 | 1/a/382:392 | No text annotation | homologous HL_5J7L_145 NA | |
| HL_6VU3_050 | 1/a/410:417 | Pseudoknot geometry | homologous HL_5J7L_146 NA | |
| HL_6VU3_051 | 1/a/462:467 | GNRA | homologous HL_5J7L_147 NA | |
| HL_6VU3_052 | 1/a/487:493 | GNRA | homologous HL_5J7L_148 NA | |
| HL_6VU3_054 | 1/a/566:575 | T-loop with 2 stacked bulged bases | geometric HL_5J7L_150 NA | |
| HL_6VU3_055 | 1/a/611:617 | No text annotation | homologous HL_5J7L_151 NA | |
| HL_6VU3_056 | 1/a/629:634 | GNRA | homologous HL_5J7L_152 NA | |
| HL_6VU3_057 | 1/a/641:647 | No text annotation | homologous HL_5J7L_153 NA | |
| HL_6VU3_060 | 1/a/779:785 | No text annotation | homologous HL_5J7L_156 NA | |
| HL_6VU3_061 | 1/a/826:831 | No text annotation | homologous HL_5J7L_157 NA | |
| HL_6VU3_064 | 1/a/978:985 | No text annotation | homologous HL_5J7L_160 NA | |
| HL_6VU3_068 | 1/a/1222:1227 | GNRA | homologous HL_5J7L_164 NA | |
| HL_6VU3_069 | 1/a/1281:1289 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_165 NA | |
| HL_6VU3_070 | 1/a/1324:1330 | Pseudoknot geometry with 3' bulge | homologous HL_5J7L_166 NA | |
| HL_6VU3_071 | 1/a/1363:1368 | GNRA | homologous HL_5J7L_167 NA | |
| HL_6VU3_072 | 1/a/1389:1398 | No text annotation | homologous HL_5J7L_168 NA | |
| HL_6VU3_073 | 1/a/1451:1459 | Mini UNCG with extended bulge | geometric HL_7A0S_017 HL_90436.1 | |
| HL_6VU3_076 | 1/a/1565:1568 | Mini UNCG | homologous HL_5J7L_172 NA | |
| HL_6VU3_078 | 1/a/1630:1636 | GNRA | homologous HL_5J7L_174 NA | |
| HL_6VU3_079 | 1/a/1691:1696 | UNCG | homologous HL_5J7L_175 NA | |
| HL_6VU3_082 | 1/a/1777:1787 | No text annotation | homologous HL_5J7L_178 NA | |
| HL_6VU3_083 | 1/a/1806:1811 | GNRA related | homologous HL_5J7L_179 NA | |
| HL_6VU3_089 | 1/a/2209:2215 | No text annotation | homologous HL_5J7L_185 NA | |
| HL_6VU3_091 | 1/a/2264:2276 | No text annotation | homologous HL_5J7L_187 NA | |
| HL_6VU3_114 | 1/a/2304:2312 | No text annotation | homologous HL_5J7L_219 NA | |
| HL_6VU3_096 | 1/a/2404:2413 | No text annotation | homologous HL_5J7L_192 NA | |
| HL_6VU3_100 | 1/a/2594:2599 | GNRA | homologous HL_5J7L_196 NA | |
| HL_6VU3_102 | 1/a/2701:2706 | Ribsomal LSU H95 | homologous HL_5J7L_198 NA | |
| HL_6VU3_103 | 1/a/2745:2759 | No text annotation | homologous HL_4WF9_062 HL_53269.1 | |
| HL_6VU3_105 | 1/a/2819:2827 | No text annotation | homologous HL_5J7L_201 NA | |
| HL_6VU3_106 | 1/a/2856:2861 | GNRA | homologous HL_5J7L_202 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6VU3_001 | No text annotation | ||
| HL_6VU3_002 | tRNA anticodon loop | ||
| HL_6VU3_003 | T-loop with 2 stacked bulged bases | ||
| HL_6VU3_005 | No text annotation | ||
| HL_6VU3_006 | T-loop with 2 stacked bulged bases | ||
| HL_6VU3_008 | No text annotation | ||
| HL_6VU3_009 | GNRA | ||
| HL_6VU3_109 | No text annotation | ||
| HL_6VU3_011 | UNCG | ||
| HL_6VU3_015 | UNCG | ||
| HL_6VU3_016 | GNRA | ||
| HL_6VU3_018 | GNRA wlth extra near cWW | ||
| HL_6VU3_019 | No text annotation | ||
| HL_6VU3_021 | No text annotation | ||
| HL_6VU3_024 | No text annotation | ||
| HL_6VU3_027 | No text annotation | ||
| HL_6VU3_028 | GNRA | ||
| HL_6VU3_110 | No text annotation | ||
| HL_6VU3_031 | No text annotation | ||
| HL_6VU3_032 | GNRA | ||
| HL_6VU3_033 | GNRA | ||
| HL_6VU3_036 | UNCG | ||
| HL_6VU3_037 | GNRA | ||
| HL_6VU3_044 | No text annotation | ||
| HL_6VU3_053 | No text annotation | ||
| HL_6VU3_058 | GNRA wlth tandem sheared | ||
| HL_6VU3_059 | No text annotation | ||
| HL_6VU3_111 | No text annotation | ||
| HL_6VU3_062 | No text annotation | ||
| HL_6VU3_063 | No text annotation | ||
| HL_6VU3_065 | No text annotation | ||
| HL_6VU3_066 | GNRA wlth tandem sheared | ||
| HL_6VU3_067 | No text annotation | ||
| HL_6VU3_074 | Pseudoknot geometry with 3' bulge | ||
| HL_6VU3_075 | UNCG | ||
| HL_6VU3_077 | No text annotation | ||
| HL_6VU3_112 | No text annotation | ||
| HL_6VU3_080 | No text annotation | ||
| HL_6VU3_081 | No text annotation | ||
| HL_6VU3_084 | GNRA variation | ||
| HL_6VU3_085 | No text annotation | ||
| HL_6VU3_086 | No text annotation | ||
| HL_6VU3_087 | No text annotation | ||
| HL_6VU3_088 | No text annotation | ||
| HL_6VU3_090 | No text annotation | ||
| HL_6VU3_092 | No text annotation | ||
| HL_6VU3_093 | Pseudoknot geometry | ||
| HL_6VU3_094 | GNRA | ||
| HL_6VU3_095 | GNRA | ||
| HL_6VU3_097 | No text annotation | ||
| HL_6VU3_098 | GNRA variation | ||
| HL_6VU3_099 | No text annotation | ||
| HL_6VU3_101 | GNRA | ||
| HL_6VU3_104 | No text annotation | ||
| HL_6VU3_115 | UNCG variation | ||
| HL_6VU3_113 | No text annotation | ||
| HL_6VU3_107 | No text annotation | ||
| HL_6VU3_108 | Mini UNCG |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6VU3_001 | 1/D/30:32, 1/D/552:553 | Single bulged G | homologous IL_4LFB_001 IL_28408.1 | |
| IL_6VU3_002 | 1/D/44:45, 1/D/396:398 | Single bulged A | homologous IL_5J7L_002 NA | |
| IL_6VU3_003 | 1/D/47:52, 1/D/359:361 | No text annotation | homologous IL_5J7L_003 NA | |
| IL_6VU3_004 | 1/D/54:56, 1/D/356:357 | Minor groove platform | homologous IL_4LFB_004 IL_34520.1 | |
| IL_6VU3_006 | 1/D/67:69, 1/D/99:102 | Minor groove platform with extra cWW | homologous IL_5J7L_006 NA | |
| IL_6VU3_009 | 1/D/128:131, 1/D/231:233 | Isolated non-canonical cWW pair | homologous IL_5J7L_009 NA | |
| IL_6VU3_010 | 1/D/132:136, 1/D/227:230 | Minor groove platform related | homologous IL_5J7L_010 NA | |
| IL_6VU3_014 | 1/D/242:247, 1/D/277:284 | Kink-turn with non-sequential stacking | homologous IL_5J7L_014 NA | |
| IL_6VU3_015 | 1/D/249:252, 1/D/274:275 | No text annotation | homologous IL_4LFB_012 IL_22002.1 | |
| IL_6VU3_016 | 1/D/292:293, 1/D/304:308 | C-loop | homologous IL_4LFB_013 IL_06671.1 | |
| IL_6VU3_017 | 1/D/367:369, 1/D/392:393 | Single bulged U | geometric IL_4LFB_014 IL_97561.1 | |
| IL_6VU3_018 | 1/D/371:375, 1/D/389:390 | C-loop | homologous IL_5J7L_018 NA | |
| IL_6VU3_019 | 1/D/375:376, 1/D/387:389 | Single bulged G | geometric IL_5J7L_019 NA | |
| IL_6VU3_020 | 1/D/409:416, 1/D/427:433 | No text annotation | geometric IL_6CZR_359 NA | |
| IL_6VU3_021 | 1/D/440:442, 1/D/492:497 | No text annotation | homologous IL_5J7L_021 NA | |
| IL_6VU3_022 | 1/D/446:450, 1/D/483:488 | tSH-tHW-tWW | geometric IL_5J7L_022 NA | |
| IL_6VU3_023 | 1/D/450:455, 1/D/477:483 | No text annotation | homologous IL_5J7L_023 NA | |
| IL_6VU3_024 | 1/D/504:511, 1/D/540:541 | SSU/LSU pseudoknot | homologous IL_5J7L_024 NA | |
| IL_6VU3_026 | 1/D/569:575, 1/D/880:881 | No text annotation | homologous IL_5J7L_026 NA | |
| IL_6VU3_027 | 1/D/580:584, 1/D/757:761 | tSH-tHW-tHS | homologous IL_5J7L_027 NA | |
| IL_6VU3_028 | 1/D/594:596, 1/D/644:645 | Major groove platform | homologous IL_5J7L_028 NA | |
| IL_6VU3_029 | 1/D/597:598, 1/D/640:643 | Major groove minor groove platform; mini C-loop | homologous IL_5J7L_029 NA | |
| IL_6VU3_030 | 1/D/605:612, 1/D/628:633 | No text annotation | homologous IL_5J7L_030 NA | |
| IL_6VU3_031 | 1/D/654:655, 1/D/751:754 | Major groove platform; stack outside cWW | homologous IL_5J7L_031 NA | |
| IL_6VU3_034 | 1/D/673:678, 1/D/712:717 | No text annotation | homologous IL_5J7L_034 NA | |
| IL_6VU3_036 | 1/D/774:778, 1/D/804:805 | Left turn | homologous IL_4LFB_032 IL_29346.3 | |
| IL_6VU3_037 | 1/D/779:783, 1/D/799:803 | tSH-tHW-tHS | homologous IL_5J7L_037 NA | |
| IL_6VU3_038 | 1/D/887:894, 1/D/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_5J7L_038 NA | |
| IL_6VU3_039 | 1/D/922:923, 1/D/1393:1395 | Single bulged A | homologous IL_5J7L_039 NA | |
| IL_6VU3_040 | 1/D/925:927, 1/D/1390:1391 | Single bulged G | homologous IL_5J7L_040 NA | |
| IL_6VU3_041 | 1/D/933:935, 1/D/1380:1384 | Minor groove platform | homologous IL_5J7L_041 NA | |
| IL_6VU3_043 | 1/D/993:997, 1/D/1044:1045 | Minor groove platform | homologous IL_5J7L_043 NA | |
| IL_6VU3_200 | 1/D/998:999, 1/D/1041:1043 | Single stack bend | homologous IL_5J7L_044 NA | |
| IL_6VU3_046 | 1/D/1048:1050, 1/D/1208:1209 | Single bulged U | geometric IL_5J7L_046 NA | |
| IL_6VU3_048 | 1/D/1052:1056, 1/D/1204:1206 | Isolated cWS basepair | homologous IL_4LFB_044 IL_82453.1 | |
| IL_6VU3_049 | 1/D/1057:1058, 1/D/1199:1203 | Minor groove platform | homologous IL_5J7L_048 NA | |
| IL_6VU3_050 | 1/D/1060:1061, 1/D/1195:1197 | Single bulged U | homologous IL_4LFB_046 IL_97561.1 | |
| IL_6VU3_051 | 1/D/1061:1063, 1/D/1193:1195 | Isolated non-canonical cWW pair | geometric IL_4LFB_047 IL_68118.1 | |
| IL_6VU3_052 | 1/D/1124:1128, 1/D/1144:1149 | No text annotation | homologous IL_5J7L_051 NA | |
| IL_6VU3_054 | 1/D/1158:1161, 1/D/1175:1181 | No text annotation | homologous IL_5J7L_053 NA | |
| IL_6VU3_055 | 1/D/1247:1253, 1/D/1284:1290 | No text annotation | homologous IL_5J7L_054 NA | |
| IL_6VU3_059 | 1/D/1399:1401, 1/D/1501:1504 | No text annotation | homologous IL_5J7L_058 NA | |
| IL_6VU3_062 | 1/D/1412:1414, 1/D/1486:1488 | Isolated non-canonical cWW pair | homologous IL_5J7L_061 NA | |
| IL_6VU3_063 | 1/D/1416:1419, 1/D/1481:1484 | Double sheared | homologous IL_5J7L_062 NA | |
| IL_6VU3_064 | 1/D/1430:1435, 1/D/1466:1470 | Triple sheared related | homologous IL_5J7L_063 NA | |
| IL_6VU3_067 | 1/a/24:30, 1/a/510:516 | Triple sheared with non-canonical cWW | geometric IL_5J7L_245 NA | |
| IL_6VU3_068 | 1/a/36:37, 1/a/442:444 | Single bulged A | homologous IL_7RQB_002 NA | |
| IL_6VU3_069 | 1/a/43:44, 1/a/434:436 | Minor groove platform | homologous IL_5J7L_247 NA | |
| IL_6VU3_070 | 1/a/81:85, 1/a/97:105 | No text annotation | homologous IL_5J7L_248 NA | |
| IL_6VU3_071 | 1/a/183:184, 1/a/212:214 | Single stack bend | homologous IL_4WF9_007 IL_15011.1 | |
| IL_6VU3_072 | 1/a/188:194, 1/a/201:208 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_5J7L_250 NA | |
| IL_6VU3_073 | 1/a/239:245, 1/a/253:258 | 7x6 Sarcin-Ricin; G-bulge | homologous IL_5J7L_251 NA | |
| IL_6VU3_074 | 1/a/269:271, 1/a/366:370 | No text annotation | homologous IL_5J7L_252 NA | |
| IL_6VU3_076 | 1/a/293:295, 1/a/343:347 | No text annotation | homologous IL_5J7L_254 NA | |
| IL_6VU3_077 | 1/a/481:484, 1/a/496:509 | No text annotation | homologous IL_5J7L_255 NA | |
| IL_6VU3_078 | 1/a/536:539, 1/a/554:557 | Double sheared | homologous IL_5J7L_256 NA | |
| IL_6VU3_079 | 1/a/564:566, 1/a/575:577 | Isolated non-canonical cWW pair | homologous IL_5J7L_257 NA | |
| IL_6VU3_080 | 1/a/606:610, 1/a/618:622 | AAA cross-strand stack | homologous IL_5J7L_258 NA | |
| IL_6VU3_081 | 1/a/672:674, 1/a/806:808 | No text annotation | geometric IL_7RQB_017 NA | |
| IL_6VU3_082 | 1/a/674:678, 1/a/799:806 | tHW-tHW cross-strand stack | homologous IL_7RQB_018 NA | |
| IL_6VU3_083 | 1/a/697:698, 1/a/763:765 | Single bulged A | geometric IL_5J7L_261 NA | |
| IL_6VU3_086 | 1/a/738:740, 1/a/757:758 | Major groove platform | homologous IL_5J7L_264 NA | |
| IL_6VU3_087 | 1/a/741:742, 1/a/754:756 | Single stack bend | geometric IL_4LFB_041 IL_15011.1 | |
| IL_6VU3_088 | 1/a/742:744, 1/a/753:754 | Single stack bend | geometric IL_4V83_236 IL_15011.1 | |
| IL_6VU3_089 | 1/a/775:777, 1/a/787:791 | Multiple bulged bases | homologous IL_5J7L_265 NA | |
| IL_6VU3_090 | 1/a/844:847, 1/a/933:934 | 90 degree turn | homologous IL_5J7L_267 NA | |
| IL_6VU3_192 | 1/a/844:848, 1/a/930:934 | No text annotation | homologous IL_5J7L_399 NA | |
| IL_6VU3_091 | 1/a/847:848, 1/a/930:933 | Stack outside cWW | geometric IL_5J7L_268 NA | |
| IL_6VU3_092 | 1/a/849:850, 1/a/927:929 | Single stack bend | homologous IL_5J7L_269 NA | |
| IL_6VU3_093 | 1/a/856:862, 1/a/915:921 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | homologous IL_5J7L_270 NA | |
| IL_6VU3_094 | 1/a/862:863, 1/a/913:915 | Single bulged G | geometric IL_5J7L_271 NA | |
| IL_6VU3_095 | 1/a/864:868, 1/a/909:912 | C-loop with bulged stacked A's | homologous IL_5J7L_272 NA | |
| IL_6VU3_096 | 1/a/870:872, 1/a/905:907 | Isolated non-canonical cWW pair | homologous IL_5J7L_273 NA | |
| IL_6VU3_099 | 1/a/994:996, 1/a/1159:1160 | Single bulged C | homologous IL_5J7L_276 NA | |
| IL_6VU3_100 | 1/a/998:1002, 1/a/1153:1157 | UAA/GAN | homologous IL_5J7L_277 NA | |
| IL_6VU3_101 | 1/a/1004:1011, 1/a/1150:1151 | SSU/LSU pseudoknot | geometric IL_5J7L_278 NA | |
| IL_6VU3_102 | 1/a/1011:1013, 1/a/1149:1150 | Single bulged U | homologous IL_5J7L_279 NA | |
| IL_6VU3_103 | 1/a/1018:1024, 1/a/1140:1144 | Kink-turn related | homologous IL_5J7L_280 NA | |
| IL_6VU3_104 | 1/a/1024:1030, 1/a/1124:1140 | No text annotation | geometric IL_5J7L_281 NA | |
| IL_6VU3_105 | 1/a/1031:1034, 1/a/1121:1123 | Isolated non-canonical cWW pair | homologous IL_7RQB_041 NA | |
| IL_6VU3_110 | 1/a/1196:1198, 1/a/1247:1250 | Isolated cWS basepair | homologous IL_5J7L_286 NA | |
| IL_6VU3_111 | 1/a/1202:1206, 1/a/1240:1243 | No text annotation | homologous IL_5J7L_287 NA | |
| IL_6VU3_112 | 1/a/1208:1215, 1/a/1234:1238 | Kink-turn | homologous IL_5J7L_288 NA | |
| IL_6VU3_113 | 1/a/1262:1269, 1/a/2011:2017 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_5J7L_289 NA | |
| IL_6VU3_114 | 1/a/1310:1313, 1/a/1603:1604 | Major groove platform; stack outside cWW | homologous IL_7RQB_050 NA | |
| IL_6VU3_115 | 1/a/1319:1323, 1/a/1331:1333 | C-loop | homologous IL_5J7L_291 NA | |
| IL_6VU3_116 | 1/a/1351:1355, 1/a/1376:1380 | UAA/GAN | homologous IL_5J7L_292 NA | |
| IL_6VU3_117 | 1/a/1357:1361, 1/a/1370:1374 | tSH-tHW-tHS | homologous IL_5J7L_293 NA | |
| IL_6VU3_122 | 1/a/1432:1435, 1/a/1557:1561 | Tandem non-canonical cWW pairs | homologous IL_5J7L_296 NA | |
| IL_6VU3_124 | 1/a/1450:1451, 1/a/1459:1461 | Single bulged U | homologous IL_5J7L_298 NA | |
| IL_6VU3_126 | 1/a/1474:1478, 1/a/1513:1517 | tSH-tHW-tHS | homologous IL_5J7L_300 NA | |
| IL_6VU3_130 | 1/a/1651:1656, 1/a/2004:2006 | No text annotation | homologous IL_5J7L_304 NA | |
| IL_6VU3_131 | 1/a/1663:1665, 1/a/1995:1997 | Isolated tWW turn | homologous IL_5J7L_305 NA | |
| IL_6VU3_132 | 1/a/1666:1669, 1/a/1993:1994 | Major groove platform; stack outside cWW | geometric IL_7RQB_066 NA | |
| IL_6VU3_197 | 1/a/1666:1674, 1/a/1990:1994 | No text annotation | homologous IL_5J7L_386 NA | |
| IL_6VU3_133 | 1/a/1669:1674, 1/a/1990:1993 | Intercalated tWH | homologous IL_5J7L_307 NA | |
| IL_6VU3_134 | 1/a/1686:1691, 1/a/1696:1702 | tSH-tSH-tHH-tHS | geometric IL_5J7L_308 NA | |
| IL_6VU3_139 | 1/a/1798:1804, 1/a/1813:1821 | Kink-turn related | homologous IL_5J7L_313 NA | |
| IL_6VU3_140 | 1/a/1837:1840, 1/a/1902:1903 | Minor groove platform, major groove intercalation | homologous IL_5J7L_314 NA | |
| IL_6VU3_141 | 1/a/1841:1842, 1/a/1898:1901 | Major groove intercalation | homologous IL_5J7L_315 NA | |
| IL_6VU3_142 | 1/a/1846:1849, 1/a/1893:1894 | Major groove minor groove platform; mini C-loop | homologous IL_5J7L_316 NA | |
| IL_6VU3_198 | 1/a/1851:1860, 1/a/1882:1891 | No text annotation | homologous IL_5J7L_387 NA | |
| IL_6VU3_144 | 1/a/1933:1934, 1/a/1964:1967 | Bulged stacked bases | homologous IL_7RQB_076 NA | |
| IL_6VU3_146 | 1/a/2050:2052, 1/a/2617:2618 | Major groove platform | homologous IL_5J7L_320 NA | |
| IL_6VU3_147 | 1/a/2054:2056, 1/a/2612:2615 | No text annotation | homologous IL_5J7L_321 NA | |
| IL_6VU3_150 | 1/a/2070:2071, 1/a/2438:2441 | Minor groove platform | homologous IL_5J7L_324 NA | |
| IL_6VU3_151 | 1/a/2081:2083, 1/a/2236:2239 | Isolated tHS basepair with bulges | homologous IL_5J7L_325 NA | |
| IL_6VU3_152 | 1/a/2085:2087, 1/a/2232:2234 | Isolated non-canonical cWW pair | homologous IL_5J7L_326 NA | |
| IL_6VU3_158 | 1/a/2202:2204, 1/a/2220:2221 | Single bulged U | homologous IL_5J7L_331 NA | |
| IL_6VU3_159 | 1/a/2350:2353, 1/a/2364:2367 | Double sheared | homologous IL_5J7L_333 NA | |
| IL_6VU3_163 | 1/a/2459:2461, 1/a/2489:2493 | Major groove minor groove platform with extra cWW | geometric IL_5J7L_337 NA | |
| IL_6VU3_164 | 1/a/2466:2470, 1/a/2480:2484 | Double sheared with non-canonical cWW | homologous IL_5J7L_338 NA | |
| IL_6VU3_166 | 1/a/2510:2512, 1/a/2574:2578 | Isolated non-canonical cWW with bulges | homologous IL_5J7L_340 NA | |
| IL_6VU3_167 | 1/a/2512:2513, 1/a/2571:2574 | No text annotation | geometric IL_5J7L_341 NA | |
| IL_6VU3_168 | 1/a/2522:2523, 1/a/2540:2543 | Major groove platform with intercalation | homologous IL_5J7L_342 NA | |
| IL_6VU3_170 | 1/a/2591:2592, 1/a/2601:2603 | Single bulged A | homologous IL_7RQB_101 NA | |
| IL_6VU3_171 | 1/a/2636:2640, 1/a/2774:2782 | tSH-tHS-tHW | homologous IL_5J7L_345 NA | |
| IL_6VU3_173 | 1/a/2680:2684, 1/a/2725:2727 | C-loop | homologous IL_5J7L_347 NA | |
| IL_6VU3_174 | 1/a/2687:2691, 1/a/2718:2722 | UAA/GAN related, with intercalation | homologous IL_5J7L_348 NA | |
| IL_6VU3_175 | 1/a/2695:2696, 1/a/2711:2714 | Multiple bulged bases | homologous IL_5J7L_349 NA | |
| IL_6VU3_176 | 1/a/2737:2742, 1/a/2762:2767 | UAA/GAN with extra cWW | homologous IL_5J7L_350 NA | |
| IL_6VU3_177 | 1/a/2806:2811, 1/a/2889:2892 | No text annotation | homologous IL_5J7L_351 NA | |
| IL_6VU3_179 | 1/a/2843:2846, 1/a/2870:2874 | Multiple bulged bases with non-canonical cWW | homologous IL_5J7L_353 NA | |
| IL_6VU3_181 | 1/d/17:18, 1/d/65:67 | Major groove intercalation | homologous IL_5J7L_355 NA | |
| IL_6VU3_182 | 1/d/23:28, 1/d/56:60 | No text annotation | homologous IL_5J7L_356 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6VU3_186 | No text annotation | ||
| IL_6VU3_187 | No text annotation | ||
| IL_6VU3_188 | No text annotation | ||
| IL_6VU3_005 | Multiple bulged bases | ||
| IL_6VU3_007 | Minor groove platform | ||
| IL_6VU3_189 | Single bulged G | ||
| IL_6VU3_008 | Single bulged G, near cWW | ||
| IL_6VU3_011 | Isolated cWH basepair | ||
| IL_6VU3_190 | No text annotation | ||
| IL_6VU3_012 | tWH-tWH-tHW-tHW | ||
| IL_6VU3_013 | No text annotation | ||
| IL_6VU3_025 | Kink-turn related | ||
| IL_6VU3_032 | Single stack bend | ||
| IL_6VU3_033 | Tandem non-canonical cWW pairs | ||
| IL_6VU3_035 | Kink-turn | ||
| IL_6VU3_042 | No text annotation | ||
| IL_6VU3_044 | No text annotation | ||
| IL_6VU3_045 | No text annotation | ||
| IL_6VU3_047 | Not an internal loop | ||
| IL_6VU3_053 | Minor groove platform | ||
| IL_6VU3_056 | 180 degree turn | ||
| IL_6VU3_191 | No text annotation | ||
| IL_6VU3_057 | Double sheared with non-canonical cWW | ||
| IL_6VU3_058 | No text annotation | ||
| IL_6VU3_060 | No text annotation | ||
| IL_6VU3_061 | Partly complementary | ||
| IL_6VU3_065 | Single bulged A | ||
| IL_6VU3_066 | No text annotation | ||
| IL_6VU3_075 | No text annotation | ||
| IL_6VU3_084 | Single bulged G | ||
| IL_6VU3_085 | Triple sheared | ||
| IL_6VU3_193 | No text annotation | ||
| IL_6VU3_201 | Single stack bend | ||
| IL_6VU3_097 | Double sheared with non-canonical cWW | ||
| IL_6VU3_194 | No text annotation | ||
| IL_6VU3_098 | No text annotation | ||
| IL_6VU3_106 | Tandem non-canonical cWW pairs | ||
| IL_6VU3_107 | Kink-turn | ||
| IL_6VU3_195 | No text annotation | ||
| IL_6VU3_108 | No text annotation | ||
| IL_6VU3_109 | No text annotation | ||
| IL_6VU3_118 | Single stack bend | ||
| IL_6VU3_119 | Single stack bend | ||
| IL_6VU3_196 | No text annotation | ||
| IL_6VU3_120 | No text annotation | ||
| IL_6VU3_121 | UAA/GAN | ||
| IL_6VU3_123 | tSH-tHW | ||
| IL_6VU3_125 | No text annotation | ||
| IL_6VU3_127 | No text annotation | ||
| IL_6VU3_202 | 180 degree turn | ||
| IL_6VU3_128 | Single bulged A | ||
| IL_6VU3_129 | UAA/GAN variation | ||
| IL_6VU3_135 | 6x5 Sarcin-Ricin; G-bulge | ||
| IL_6VU3_136 | Triple sheared | ||
| IL_6VU3_137 | Single bulged C | ||
| IL_6VU3_138 | Single bulged A | ||
| IL_6VU3_143 | UAA/GAN related | ||
| IL_6VU3_145 | No text annotation | ||
| IL_6VU3_148 | No text annotation | ||
| IL_6VU3_149 | Not an internal loop | ||
| IL_6VU3_153 | Isolated non-canonical cWW pair | ||
| IL_6VU3_154 | Isolated non-canonical cWW pair | ||
| IL_6VU3_155 | Isolated non-canonical cWW pair | ||
| IL_6VU3_156 | No text annotation | ||
| IL_6VU3_199 | No text annotation | ||
| IL_6VU3_157 | Kink-turn | ||
| IL_6VU3_160 | No text annotation | ||
| IL_6VU3_161 | No text annotation | ||
| IL_6VU3_162 | No text annotation | ||
| IL_6VU3_165 | No text annotation | ||
| IL_6VU3_169 | No text annotation | ||
| IL_6VU3_172 | Sarcin-Ricin target in LSU H95; G-bulge | ||
| IL_6VU3_178 | Major groove intercalation | ||
| IL_6VU3_180 | tHS double platform | ||
| IL_6VU3_183 | Major groove minor groove platform; mini C-loop | ||
| IL_6VU3_184 | Symmetric double minor groove platform | ||
| IL_6VU3_185 | Bacterial 5S Loop E |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6VU3_001 | 1/D/46:47, 1/D/361:367, 1/D/393:395 | No text annotation | homologous J3_5J7L_001 NA | |
| J3_6VU3_027 | 1/D/46:52, 1/D/359:367, 1/D/393:395 | No text annotation | homologous J3_5J7L_050 NA | |
| J3_6VU3_002 | 1/D/586:588, 1/D/651:654, 1/D/754:755 | No text annotation | homologous J3_5J7L_002 NA | |
| J3_6VU3_028 | 1/D/586:588, 1/D/651:655, 1/D/751:755 | No text annotation | homologous J3_5J7L_051 NA | |
| J3_6VU3_003 | 1/D/672:673, 1/D/717:725, 1/D/732:734 | No text annotation | homologous J3_5J7L_003 NA | |
| J3_6VU3_004 | 1/D/826:829, 1/D/857:861, 1/D/868:874 | No text annotation | homologous J3_5J7L_004 NA | |
| J3_6VU3_005 | 1/D/936:939, 1/D/1344:1350, 1/D/1372:1379 | No text annotation | homologous J3_4LFB_002 J3_85722.1 | |
| J3_6VU3_029 | 1/D/943:946, 1/D/1235:1237, 1/D/1337:1340 | No text annotation | homologous J3_5J7L_005 NA | |
| J3_6VU3_007 | 1/D/955:962, 1/D/973:984, 1/D/1221:1225 | No text annotation | homologous J3_5J7L_006 NA | |
| J3_6VU3_008 | 1/D/990:993, 1/D/1045:1047, 1/D/1210:1215 | No text annotation | homologous J3_4LFB_005 J3_84394.1 | |
| J3_6VU3_030 | 1/D/990:997, 1/D/1044:1047, 1/D/1210:1215 | No text annotation | homologous J3_5J7L_053 NA | |
| J3_6VU3_009 | 1/D/1063:1068, 1/D/1107:1113, 1/D/1187:1193 | No text annotation | homologous J3_5J7L_008 NA | |
| J3_6VU3_010 | 1/D/1073:1074, 1/D/1083:1087, 1/D/1098:1102 | No text annotation | homologous J3_5J7L_009 NA | |
| J3_6VU3_011 | 1/D/1116:1118, 1/D/1155:1158, 1/D/1181:1184 | No text annotation | homologous J3_5J7L_010 NA | |
| J3_6VU3_031 | 1/D/1116:1118, 1/D/1155:1161, 1/D/1175:1184 | No text annotation | homologous J3_5J7L_054 NA | |
| J3_6VU3_012 | 1/D/1237:1241, 1/D/1296:1303, 1/D/1334:1337 | No text annotation | homologous J3_4LFB_009 J3_03192.1 | |
| J3_6VU3_013 | 1/a/30:31, 1/a/474:481, 1/a/509:510 | No text annotation | homologous J3_7RQB_001 NA | |
| J3_6VU3_032 | 1/a/30:31, 1/a/474:484, 1/a/496:510 | No text annotation | homologous J3_9DFE_002 J3_17917.1 | |
| J3_6VU3_033 | 1/a/32:35, 1/a/445:461, 1/a/468:473 | No text annotation | homologous J3_5J7L_067 NA | |
| J3_6VU3_014 | 1/a/56:57, 1/a/70:76, 1/a/110:114 | No text annotation | homologous J3_5J7L_037 NA | |
| J3_6VU3_034 | 1/a/297:301, 1/a/316:325, 1/a/337:341 | No text annotation | homologous J3_5J7L_068 NA | |
| J3_6VU3_015 | 1/a/683:689, 1/a/773:775, 1/a/791:794 | No text annotation | homologous J3_5J7L_038 NA | |
| J3_6VU3_016 | 1/a/698:700, 1/a/732:736, 1/a/760:763 | No text annotation | homologous J3_5J7L_039 NA | |
| J3_6VU3_018 | 1/a/1298:1303, 1/a/1625:1627, 1/a/1639:1642 | No text annotation | homologous J3_5J7L_041 NA | |
| J3_6VU3_019 | 1/a/1306:1309, 1/a/1605:1611, 1/a/1620:1622 | No text annotation | homologous J3_7A0S_007 J3_47341.1 | |
| J3_6VU3_020 | 1/a/1344:1349, 1/a/1382:1385, 1/a/1402:1403 | No text annotation | homologous J3_5J7L_043 NA | |
| J3_6VU3_035 | 1/a/1424:1429, 1/a/1564:1565, 1/a/1568:1574 | No text annotation | homologous J3_5J7L_069 NA | |
| J3_6VU3_021 | 1/a/2091:2093, 1/a/2196:2200, 1/a/2223:2228 | Kink-turn 3-way junction | homologous J3_5J7L_044 NA | |
| J3_6VU3_036 | 1/a/2282:2284, 1/a/2384:2395, 1/a/2421:2427 | No text annotation | homologous J3_5J7L_070 NA | |
| J3_6VU3_023 | 1/a/2517:2520, 1/a/2545:2547, 1/a/2561:2567 | No text annotation | homologous J3_5J7L_046 NA | |
| J3_6VU3_024 | 1/a/2789:2791, 1/a/2805:2806, 1/a/2892:2894 | No text annotation | homologous J3_5J7L_047 NA | |
| J3_6VU3_025 | 1/a/2812:2815, 1/a/2831:2836, 1/a/2882:2888 | No text annotation | homologous J3_5J7L_048 NA | |
| J3_6VU3_026 | 1/d/10:16, 1/d/68:70, 1/d/106:110 | No text annotation | homologous J3_5J7L_049 NA | |
| J4_6VU3_003 | 1/D/115:122, 1/D/239:240, 1/D/286:289, 1/D/311:312 | No text annotation | homologous J4_5J7L_001 NA | |
| J4_6VU3_005 | 1/D/575:577, 1/D/764:769, 1/D/810:821, 1/D/879:880 | No text annotation | homologous J4_5J7L_003 NA | |
| J4_6VU3_006 | 1/a/268:269, 1/a/370:375, 1/a/399:406, 1/a/421:424 | No text annotation | homologous J4_5J7L_018 NA | |
| J4_6VU3_007 | 1/a/297:301, 1/a/316:319, 1/a/323:325, 1/a/337:341 | No text annotation | homologous J4_5J7L_019 NA | |
| J4_6VU3_008 | 1/a/601:604, 1/a/624:628, 1/a/635:638, 1/a/650:656 | No text annotation | homologous J4_5J7L_020 NA | |
| J4_6VU3_009 | 1/a/1270:1276, 1/a/1294:1295, 1/a/1645:1648, 1/a/2009:2010 | No text annotation | homologous J4_5J7L_021 NA | |
| J4_6VU3_010 | 1/a/1310:1314, 1/a/1338:1343, 1/a/1404:1405, 1/a/1597:1604 | No text annotation | homologous J4_5J7L_022 NA | |
| J4_6VU3_011 | 1/a/1313:1314, 1/a/1338:1343, 1/a/1404:1405, 1/a/1597:1603 | No text annotation | homologous J4_5J7L_023 NA | |
| J4_6VU3_012 | 1/a/1444:1445, 1/a/1466:1467, 1/a/1525:1526, 1/a/1546:1547 | No text annotation | homologous J4_5J7L_024 NA | |
| J4_6VU3_013 | 1/a/1772:1776, 1/a/1788:1792, 1/a/1827:1830, 1/a/1975:1979 | No text annotation | homologous J4_5J7L_025 NA | |
| J4_6VU3_014 | 1/a/2285:2289, 1/a/2343:2347, 1/a/2370:2372, 1/a/2381:2383 | No text annotation | homologous J4_5J7L_027 NA | |
| J4_6VU3_015 | 1/a/2643:2646, 1/a/2674:2676, 1/a/2731:2735, 1/a/2769:2771 | No text annotation | homologous J4_5J7L_028 NA | |
| J5_6VU3_001 | 1/D/36:39, 1/D/403:406, 1/D/436:440, 1/D/497:500, 1/D/545:548 | No text annotation | homologous J5_5J7L_001 NA | |
| J5_6VU3_002 | 1/D/36:39, 1/D/403:406, 1/D/436:442, 1/D/492:500, 1/D/545:548 | No text annotation | homologous J5_5J7L_002 NA | |
| J5_6VU3_003 | 1/D/58:61, 1/D/106:113, 1/D/314:316, 1/D/337:339, 1/D/350:354 | No text annotation | homologous J5_5J7L_003 NA | |
| J5_6VU3_004 | 1/a/47:54, 1/a/116:121, 1/a/130:131, 1/a/148:150, 1/a/176:178 | No text annotation | homologous J5_5J7L_013 NA | |
| J5_6VU3_005 | 1/a/531:533, 1/a/560:564, 1/a/577:579, 1/a/1261:1262, 1/a/2017:2018 | No text annotation | homologous J5_5J7L_014 NA | |
| J5_6VU3_006 | 1/a/584:589, 1/a/668:671, 1/a/809:812, 1/a/1195:1196, 1/a/1250:1256 | No text annotation | homologous J5_5J7L_015 NA | |
| J5_6VU3_007 | 1/a/1674:1682, 1/a/1706:1707, 1/a/1751:1752, 1/a/1756:1764, 1/a/1988:1990 | No text annotation | homologous J5_5J7L_016 NA | |
| J6_6VU3_001 | 1/a/45:46, 1/a/179:183, 1/a/214:224, 1/a/231:235, 1/a/262:266, 1/a/426:433 | No text annotation | ||
| J7_6VU3_001 | 1/a/8:15, 1/a/525:531, 1/a/2018:2023, 1/a/2040:2043, 1/a/2625:2630, 1/a/2788:2789, 1/a/2894:2895 | No text annotation | ||
| J7_6VU3_002 | 1/a/817:822, 1/a/835:838, 1/a/940:946, 1/a/971:976, 1/a/987:991, 1/a/1163:1164, 1/a/1185:1190 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6VU3_006 | No text annotation | ||
| J3_6VU3_017 | No text annotation | ||
| J3_6VU3_022 | No text annotation | ||
| J4_6VU3_001 | tRNA junction | ||
| J4_6VU3_002 | tRNA junction | ||
| J4_6VU3_004 | No text annotation |
Coloring options: