6VWM Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6VWM_001 | 1/1/12:22 | No text annotation | homologous HL_4LFB_001 HL_31940.1 | |
| HL_6VWM_005 | 1/1/259:267 | GNRA related | homologous HL_5J7L_006 NA | |
| HL_6VWM_006 | 1/1/296:301 | GNRA | homologous HL_5J7L_007 NA | |
| HL_6VWM_007 | 1/1/320:333 | No text annotation | homologous HL_5J7L_008 NA | |
| HL_6VWM_008 | 1/1/342:347 | UNCG | homologous HL_6CZR_080 NA | |
| HL_6VWM_012 | 1/1/522:527 | No text annotation | geometric HL_4WF9_003 HL_75660.6 | |
| HL_6VWM_013 | 1/1/617:623 | GNRA-like with tWH | homologous HL_4LFB_014 HL_92337.1 | |
| HL_6VWM_014 | 1/1/689:698 | No text annotation | homologous HL_6CZR_086 NA | |
| HL_6VWM_015 | 1/1/726:731 | GNRA | homologous HL_5J7L_016 NA | |
| HL_6VWM_016 | 1/1/786:796 | No text annotation | homologous HL_4LFB_017 HL_38491.1 | |
| HL_6VWM_017 | 1/1/862:867 | GNRA | homologous HL_5J7L_019 NA | |
| HL_6VWM_018 | 1/1/897:902 | GNRA | homologous HL_4LFB_020 HL_34789.1 | |
| HL_6VWM_019 | 1/1/963:972 | No text annotation | homologous HL_5J7L_021 NA | |
| HL_6VWM_022 | 1/1/1076:1081 | GNRA | homologous HL_5J7L_023 NA | |
| HL_6VWM_030 | 1/1/1515:1520 | GNRA | homologous HL_6CZR_103 NA | |
| HL_6VWM_031 | 1/2/59:68 | Pseudoknot with intercalation | homologous HL_7A0S_001 HL_17803.1 | |
| HL_6VWM_032 | 1/2/87:95 | No text annotation | homologous HL_5J7L_135 NA | |
| HL_6VWM_033 | 1/2/123:128 | No text annotation | homologous HL_4WF9_003 HL_75660.6 | |
| HL_6VWM_034 | 1/2/137:142 | No text annotation | geometric HL_2Y9H_003 HL_75660.6 | |
| HL_6VWM_035 | 1/2/158:168 | No text annotation | homologous HL_5J7L_138 NA | |
| HL_6VWM_036 | 1/2/194:201 | No text annotation | geometric HL_4WF9_006 HL_48677.1 | |
| HL_6VWM_037 | 1/2/225:230 | No text annotation | homologous HL_5J7L_140 NA | |
| HL_6VWM_038 | 1/2/246:252 | No text annotation | homologous HL_5J7L_141 NA | |
| HL_6VWM_039 | 1/2/305:312 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_142 NA | |
| HL_6VWM_040 | 1/2/327:335 | T-loop with unstacked turn | homologous HL_5J7L_144 NA | |
| HL_6VWM_041 | 1/2/382:392 | No text annotation | homologous HL_5J7L_145 NA | |
| HL_6VWM_042 | 1/2/410:417 | Pseudoknot geometry | homologous HL_7A0S_014 HL_30680.4 | |
| HL_6VWM_043 | 1/2/462:467 | GNRA | homologous HL_4WF9_015 HL_34789.1 | |
| HL_6VWM_044 | 1/2/487:493 | GNRA | homologous HL_5J7L_148 NA | |
| HL_6VWM_046 | 1/2/566:575 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_150 NA | |
| HL_6VWM_047 | 1/2/611:617 | No text annotation | geometric HL_361D_002 NA | |
| HL_6VWM_048 | 1/2/629:634 | GNRA | homologous HL_5J7L_152 NA | |
| HL_6VWM_049 | 1/2/641:647 | GNRA | homologous HL_4WF9_021 HL_34789.1 | |
| HL_6VWM_050 | 1/2/712:719 | GNRA wlth tandem sheared | homologous HL_5J7L_154 NA | |
| HL_6VWM_051 | 1/2/744:753 | No text annotation | homologous HL_4WF9_023 HL_50204.1 | |
| HL_6VWM_052 | 1/2/779:785 | UNCG variation | geometric HL_1P6V_001 NA | |
| HL_6VWM_053 | 1/2/826:831 | No text annotation | homologous HL_5J7L_157 NA | |
| HL_6VWM_055 | 1/2/955:962 | GNRA | homologous HL_7A0S_026 HL_34789.1 | |
| HL_6VWM_056 | 1/2/978:985 | No text annotation | homologous HL_4WF9_028 HL_47171.1 | |
| HL_6VWM_058 | 1/2/1222:1227 | GNRA | homologous HL_5J7L_164 NA | |
| HL_6VWM_105 | 1/2/1281:1289 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_165 NA | |
| HL_6VWM_060 | 1/2/1324:1330 | Pseudoknot geometry with 3' bulge | homologous HL_5J7L_166 NA | |
| HL_6VWM_061 | 1/2/1363:1368 | GNRA | homologous HL_5J7L_167 NA | |
| HL_6VWM_062 | 1/2/1389:1398 | No text annotation | homologous HL_5J7L_168 NA | |
| HL_6VWM_063 | 1/2/1451:1459 | No text annotation | ||
| HL_6VWM_066 | 1/2/1565:1568 | Mini UNCG | homologous HL_7A0S_039 HL_90436.1 | |
| HL_6VWM_067 | 1/2/1612:1619 | No text annotation | homologous HL_7RQB_040 NA | |
| HL_6VWM_068 | 1/2/1630:1636 | GNRA | homologous HL_5J7L_174 NA | |
| HL_6VWM_069 | 1/2/1691:1696 | UNCG | geometric HL_4PMI_004 NA | |
| HL_6VWM_071 | 1/2/1752:1756 | No text annotation | homologous HL_5J7L_177 NA | |
| HL_6VWM_072 | 1/2/1777:1787 | No text annotation | homologous HL_4WF9_043 HL_87681.1 | |
| HL_6VWM_073 | 1/2/1806:1811 | GNRA related | homologous HL_5J7L_179 NA | |
| HL_6VWM_075 | 1/2/1910:1920 | No text annotation | geometric HL_5TBW_049 NA | |
| HL_6VWM_076 | 1/2/1949:1957 | No text annotation | homologous HL_5J7L_182 NA | |
| HL_6VWM_077 | 1/2/2027:2036 | No text annotation | homologous HL_4WF9_047 HL_78372.1 | |
| HL_6VWM_079 | 1/2/2209:2215 | No text annotation | homologous HL_5J7L_185 NA | |
| HL_6VWM_080 | 1/2/2248:2256 | No text annotation | homologous HL_4WF9_049 HL_11974.1 | |
| HL_6VWM_081 | 1/2/2264:2276 | No text annotation | homologous HL_5J7L_187 NA | |
| HL_6VWM_082 | 1/2/2303:2313 | No text annotation | homologous HL_7RQB_055 NA | |
| HL_6VWM_083 | 1/2/2324:2331 | Pseudoknot geometry | homologous HL_5J7L_189 NA | |
| HL_6VWM_084 | 1/2/2356:2361 | GNRA | homologous HL_5J7L_190 NA | |
| HL_6VWM_085 | 1/2/2374:2379 | GNRA | homologous HL_4WF9_054 HL_34789.1 | |
| HL_6VWM_086 | 1/2/2404:2413 | No text annotation | homologous HL_7A0S_058 HL_51853.1 | |
| HL_6VWM_087 | 1/2/2471:2479 | No text annotation | homologous HL_5J7L_193 NA | |
| HL_6VWM_088 | 1/2/2528:2535 | GNRA variation | homologous HL_5J7L_194 NA | |
| HL_6VWM_089 | 1/2/2551:2557 | No text annotation | homologous HL_4WF9_058 HL_48677.1 | |
| HL_6VWM_090 | 1/2/2594:2599 | GNRA | homologous HL_7RQB_063 NA | |
| HL_6VWM_092 | 1/2/2701:2706 | Ribsomal LSU H95 | homologous HL_5J7L_198 NA | |
| HL_6VWM_093 | 1/2/2745:2759 | No text annotation | homologous HL_7RQB_066 NA | |
| HL_6VWM_095 | 1/2/2819:2827 | No text annotation | homologous HL_5J7L_201 NA | |
| HL_6VWM_096 | 1/2/2856:2861 | GNRA | homologous HL_7A0S_068 HL_34789.1 | |
| HL_6VWM_097 | 1/3/38:44 | No text annotation | homologous HL_7RQB_070 NA | |
| HL_6VWM_098 | 1/3/86:90 | Mini UNCG | homologous HL_5J7L_204 NA | |
| HL_6VWM_101 | 1/5/31:39 | tRNA anticodon loop | homologous HL_4V90_033 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6VWM_002 | No text annotation | ||
| HL_6VWM_003 | GNRA | ||
| HL_6VWM_004 | UNCG | ||
| HL_6VWM_009 | GNRA | ||
| HL_6VWM_010 | UNCG | ||
| HL_6VWM_011 | GNRA wlth extra near cWW | ||
| HL_6VWM_020 | GNRA | ||
| HL_6VWM_021 | No text annotation | ||
| HL_6VWM_023 | T-loop related | ||
| HL_6VWM_024 | No text annotation | ||
| HL_6VWM_103 | No text annotation | ||
| HL_6VWM_025 | GNRA | ||
| HL_6VWM_026 | No text annotation | ||
| HL_6VWM_027 | T-loop with 3 stacked bulged bases | ||
| HL_6VWM_028 | No text annotation | ||
| HL_6VWM_029 | UNCG | ||
| HL_6VWM_045 | No text annotation | ||
| HL_6VWM_104 | No text annotation | ||
| HL_6VWM_054 | No text annotation | ||
| HL_6VWM_057 | No text annotation | ||
| HL_6VWM_059 | No text annotation | ||
| HL_6VWM_064 | Pseudoknot geometry with 3' bulge | ||
| HL_6VWM_065 | UNCG | ||
| HL_6VWM_070 | No text annotation | ||
| HL_6VWM_074 | No text annotation | ||
| HL_6VWM_078 | No text annotation | ||
| HL_6VWM_091 | GNRA | ||
| HL_6VWM_094 | No text annotation | ||
| HL_6VWM_106 | No text annotation | ||
| HL_6VWM_099 | No text annotation | ||
| HL_6VWM_100 | No text annotation | ||
| HL_6VWM_102 | T-loop with 2 stacked bulged bases |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6VWM_001 | 1/1/30:32, 1/1/552:553 | Single bulged G | homologous IL_5J7L_001 NA | |
| IL_6VWM_002 | 1/1/44:45, 1/1/396:398 | Single bulged A | homologous IL_5J7L_002 NA | |
| IL_6VWM_003 | 1/1/47:52, 1/1/359:361 | No text annotation | homologous IL_5J7L_003 NA | |
| IL_6VWM_004 | 1/1/54:56, 1/1/356:357 | Minor groove platform | homologous IL_5J7L_004 NA | |
| IL_6VWM_005 | 1/1/63:66, 1/1/103:104 | Multiple bulged bases | homologous IL_6CZR_117 NA | |
| IL_6VWM_006 | 1/1/67:69, 1/1/99:102 | Minor groove platform with extra cWW | homologous IL_5J7L_006 NA | |
| IL_6VWM_009 | 1/1/128:131, 1/1/231:233 | Isolated non-canonical cWW pair | homologous IL_5J7L_009 NA | |
| IL_6VWM_010 | 1/1/132:136, 1/1/227:230 | No text annotation | homologous IL_4LFB_008 IL_60988.1 | |
| IL_6VWM_011 | 1/1/144:146, 1/1/176:178 | Isolated cWH basepair | homologous IL_5J7L_011 NA | |
| IL_6VWM_014 | 1/1/242:247, 1/1/277:284 | Kink-turn with non-sequential stacking | homologous IL_4LFB_011 IL_46174.4 | |
| IL_6VWM_015 | 1/1/249:252, 1/1/274:275 | No text annotation | homologous IL_4LFB_012 IL_22002.1 | |
| IL_6VWM_016 | 1/1/292:293, 1/1/304:308 | C-loop | homologous IL_6CZR_125 NA | |
| IL_6VWM_017 | 1/1/367:369, 1/1/392:393 | Single bulged U | geometric IL_4V9F_074 IL_97561.1 | |
| IL_6VWM_018 | 1/1/371:375, 1/1/389:390 | C-loop | homologous IL_4LFB_015 IL_26900.1 | |
| IL_6VWM_019 | 1/1/375:376, 1/1/387:389 | Single bulged G | geometric IL_5J7L_019 NA | |
| IL_6VWM_023 | 1/1/450:454, 1/1/479:483 | No text annotation | ||
| IL_6VWM_175 | 1/1/450:455, 1/1/477:483 | No text annotation | homologous IL_5J7L_023 NA | |
| IL_6VWM_024 | 1/1/454:455, 1/1/477:479 | Single stack bend | geometric IL_5J7L_032 NA | |
| IL_6VWM_027 | 1/1/569:575, 1/1/880:881 | No text annotation | homologous IL_4LFB_022 IL_20847.1 | |
| IL_6VWM_028 | 1/1/580:584, 1/1/757:761 | tSH-tHW-tHS | homologous IL_5J7L_027 NA | |
| IL_6VWM_029 | 1/1/594:596, 1/1/644:645 | Major groove platform | homologous IL_4LFB_024 IL_48076.7 | |
| IL_6VWM_030 | 1/1/597:598, 1/1/640:643 | Major groove minor groove platform; mini C-loop | homologous IL_4LFB_025 IL_73108.1 | |
| IL_6VWM_031 | 1/1/605:612, 1/1/628:633 | No text annotation | homologous IL_5J7L_030 NA | |
| IL_6VWM_032 | 1/1/654:655, 1/1/751:754 | Major groove platform; stack outside cWW | homologous IL_5J7L_031 NA | |
| IL_6VWM_034 | 1/1/662:666, 1/1/740:743 | Tandem non-canonical cWW pairs | homologous IL_5J7L_033 NA | |
| IL_6VWM_176 | 1/1/673:677, 1/1/713:717 | Triple non-canonical cWW pairs | homologous IL_4LFB_065 IL_71154.1 | |
| IL_6VWM_036 | 1/1/684:688, 1/1/699:706 | Kink-turn | homologous IL_5J7L_035 NA | |
| IL_6VWM_037 | 1/1/774:778, 1/1/804:805 | Left turn | homologous IL_4LFB_032 IL_29346.3 | |
| IL_6VWM_038 | 1/1/779:783, 1/1/799:803 | tSH-tHW-tHS | homologous IL_5J7L_037 NA | |
| IL_6VWM_039 | 1/1/887:894, 1/1/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_5J7L_038 NA | |
| IL_6VWM_177 | 1/1/922:923, 1/1/1393:1395 | Single bulged A | homologous IL_6CZR_147 NA | |
| IL_6VWM_041 | 1/1/925:927, 1/1/1390:1391 | Single bulged G | homologous IL_4LFB_036 IL_28408.1 | |
| IL_6VWM_042 | 1/1/953:954, 1/1/1226:1228 | No text annotation | homologous IL_6CZR_150 NA | |
| IL_6VWM_045 | 1/1/1048:1050, 1/1/1208:1209 | Single bulged U | homologous IL_4LFB_042 IL_97561.1 | |
| IL_6VWM_048 | 1/1/1060:1061, 1/1/1195:1197 | Single bulged A | geometric IL_5J7L_049 NA | |
| IL_6VWM_049 | 1/1/1061:1063, 1/1/1193:1195 | Isolated non-canonical cWW pair | geometric IL_5J7L_050 NA | |
| IL_6VWM_057 | 1/1/1399:1401, 1/1/1501:1504 | No text annotation | homologous IL_6CZR_165 NA | |
| IL_6VWM_058 | 1/1/1401:1404, 1/1/1497:1501 | No text annotation | geometric IL_4V88_464 NA | |
| IL_6VWM_059 | 1/1/1405:1409, 1/1/1491:1496 | Partly complementary | homologous IL_6CZR_167 NA | |
| IL_6VWM_060 | 1/1/1412:1414, 1/1/1486:1488 | Isolated non-canonical cWW pair | homologous IL_4LFB_059 IL_01003.1 | |
| IL_6VWM_061 | 1/1/1416:1419, 1/1/1481:1484 | Double sheared | homologous IL_6CZR_169 NA | |
| IL_6VWM_062 | 1/1/1430:1435, 1/1/1466:1470 | Triple sheared related | geometric IL_4V9F_018 IL_67427.1 | |
| IL_6VWM_063 | 1/1/1440:1442, 1/1/1460:1461 | Major groove platform | geometric IL_7RQB_092 NA | |
| IL_6VWM_064 | 1/1/1445:1448, 1/1/1455:1457 | Decoding loop related | geometric IL_2O3X_003 IL_61702.1 | |
| IL_6VWM_065 | 1/2/24:30, 1/2/510:516 | Triple sheared with non-canonical cWW | homologous IL_5J7L_245 NA | |
| IL_6VWM_066 | 1/2/36:37, 1/2/442:444 | Single bulged A | homologous IL_7A0S_002 IL_14190.1 | |
| IL_6VWM_067 | 1/2/43:44, 1/2/434:436 | Minor groove platform | homologous IL_5J7L_247 NA | |
| IL_6VWM_179 | 1/2/82:85, 1/2/97:104 | No text annotation | ||
| IL_6VWM_069 | 1/2/183:184, 1/2/212:214 | Single stack bend | homologous IL_7A0S_005 IL_15011.1 | |
| IL_6VWM_070 | 1/2/188:194, 1/2/201:208 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_7A0S_006 IL_62167.1 | |
| IL_6VWM_071 | 1/2/239:245, 1/2/253:258 | 7x6 Sarcin-Ricin; G-bulge | homologous IL_5J7L_251 NA | |
| IL_6VWM_072 | 1/2/269:271, 1/2/366:370 | No text annotation | ||
| IL_6VWM_074 | 1/2/293:295, 1/2/343:347 | No text annotation | homologous IL_5J7L_254 NA | |
| IL_6VWM_075 | 1/2/481:484, 1/2/496:509 | No text annotation | geometric IL_5J7L_255 NA | |
| IL_6VWM_076 | 1/2/536:539, 1/2/554:557 | Double sheared | homologous IL_5J7L_256 NA | |
| IL_6VWM_077 | 1/2/564:566, 1/2/575:577 | Isolated non-canonical cWW pair | geometric IL_4WF9_017 IL_71625.1 | |
| IL_6VWM_078 | 1/2/606:610, 1/2/618:622 | AAA cross-strand stack | homologous IL_5J7L_258 NA | |
| IL_6VWM_079 | 1/2/672:674, 1/2/806:808 | Isolated non-canonical cWW pair | geometric IL_4E48_006 IL_01003.1 | |
| IL_6VWM_080 | 1/2/674:678, 1/2/799:806 | tHW-tHW cross-strand stack | homologous IL_5J7L_260 NA | |
| IL_6VWM_081 | 1/2/697:698, 1/2/763:765 | Single bulged A | homologous IL_5J7L_261 NA | |
| IL_6VWM_082 | 1/2/702:703, 1/2/728:730 | Single bulged G | geometric IL_7RQB_020 NA | |
| IL_6VWM_083 | 1/2/703:707, 1/2/724:728 | Triple sheared | homologous IL_7RQB_021 NA | |
| IL_6VWM_084 | 1/2/738:740, 1/2/757:758 | Major groove platform | homologous IL_5J7L_264 NA | |
| IL_6VWM_085 | 1/2/775:777, 1/2/787:791 | Multiple bulged bases | homologous IL_5J7L_265 NA | |
| IL_6VWM_086 | 1/2/844:847, 1/2/933:934 | 90 degree turn | geometric IL_5J7L_267 NA | |
| IL_6VWM_087 | 1/2/847:848, 1/2/930:933 | Stack outside cWW | homologous IL_5J7L_268 NA | |
| IL_6VWM_088 | 1/2/850:851, 1/2/926:928 | Single stack bend | homologous IL_5J7L_269 NA | |
| IL_6VWM_089 | 1/2/856:862, 1/2/915:921 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | homologous IL_5J7L_270 NA | |
| IL_6VWM_090 | 1/2/862:863, 1/2/913:915 | Single bulged G | geometric IL_5J7L_271 NA | |
| IL_6VWM_091 | 1/2/864:868, 1/2/909:912 | C-loop with bulged stacked A's | homologous IL_5J7L_272 NA | |
| IL_6VWM_092 | 1/2/870:872, 1/2/905:907 | Isolated cWS basepair | homologous IL_4WF9_034 NA | |
| IL_6VWM_093 | 1/2/874:879, 1/2/898:903 | No text annotation | ||
| IL_6VWM_095 | 1/2/994:996, 1/2/1159:1160 | Single bulged C | homologous IL_7RQB_035 NA | |
| IL_6VWM_096 | 1/2/998:1002, 1/2/1153:1157 | UAA/GAN | homologous IL_4WF9_036 IL_08938.1 | |
| IL_6VWM_097 | 1/2/1004:1011, 1/2/1150:1151 | SSU/LSU pseudoknot | homologous IL_4WF9_037 IL_11411.1 | |
| IL_6VWM_098 | 1/2/1011:1013, 1/2/1149:1150 | Single bulged U | geometric IL_4WF9_038 IL_97561.1 | |
| IL_6VWM_099 | 1/2/1018:1024, 1/2/1140:1144 | Kink-turn related | homologous IL_4WF9_039 IL_57188.6 | |
| IL_6VWM_100 | 1/2/1024:1030, 1/2/1124:1140 | No text annotation | geometric IL_5J7L_281 NA | |
| IL_6VWM_101 | 1/2/1031:1034, 1/2/1121:1123 | Isolated non-canonical cWW pair | homologous IL_7A0S_038 IL_30229.1 | |
| IL_6VWM_180 | 1/2/1197:1198, 1/2/1247:1249 | No text annotation | ||
| IL_6VWM_104 | 1/2/1202:1206, 1/2/1240:1243 | No text annotation | homologous IL_5J7L_287 NA | |
| IL_6VWM_105 | 1/2/1208:1215, 1/2/1234:1238 | Kink-turn | homologous IL_7RQB_047 NA | |
| IL_6VWM_106 | 1/2/1262:1269, 1/2/2011:2017 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_5J7L_289 NA | |
| IL_6VWM_107 | 1/2/1310:1313, 1/2/1603:1604 | Major groove platform; stack outside cWW | homologous IL_5J7L_290 NA | |
| IL_6VWM_108 | 1/2/1319:1323, 1/2/1331:1333 | Major groove minor groove platform with tHH | homologous IL_4WF9_050 IL_06671.1 | |
| IL_6VWM_109 | 1/2/1351:1355, 1/2/1376:1380 | UAA/GAN | homologous IL_5J7L_292 NA | |
| IL_6VWM_110 | 1/2/1357:1361, 1/2/1370:1374 | tSH-tHW-tHS | homologous IL_5J7L_293 NA | |
| IL_6VWM_112 | 1/2/1417:1421, 1/2/1577:1581 | UAA/GAN | homologous IL_5J7L_295 NA | |
| IL_6VWM_113 | 1/2/1432:1435, 1/2/1557:1561 | Tandem non-canonical cWW pairs | homologous IL_5J7L_296 NA | |
| IL_6VWM_114 | 1/2/1437:1440, 1/2/1551:1555 | tSH-tHW | homologous IL_5J7L_297 NA | |
| IL_6VWM_115 | 1/2/1450:1451, 1/2/1459:1461 | Single bulged U | geometric IL_5J7L_298 NA | |
| IL_6VWM_116 | 1/2/1468:1471, 1/2/1520:1524 | No text annotation | homologous IL_5J7L_299 NA | |
| IL_6VWM_117 | 1/2/1474:1478, 1/2/1513:1517 | tSH-tHW-tHS | homologous IL_5J7L_300 NA | |
| IL_6VWM_182 | 1/2/1526:1529, 1/2/1542:1546 | UAA/GAN variation | homologous IL_5J7L_303 NA | |
| IL_6VWM_121 | 1/2/1651:1656, 1/2/2004:2006 | No text annotation | homologous IL_5J7L_304 NA | |
| IL_6VWM_122 | 1/2/1663:1665, 1/2/1995:1997 | Isolated tWW turn | homologous IL_4WF9_063 IL_10432.1 | |
| IL_6VWM_123 | 1/2/1666:1669, 1/2/1993:1994 | Major groove platform; stack outside cWW | homologous IL_7RQB_066 NA | |
| IL_6VWM_184 | 1/2/1666:1674, 1/2/1990:1994 | No text annotation | homologous IL_4WF9_117 IL_80252.1 | |
| IL_6VWM_124 | 1/2/1669:1674, 1/2/1990:1993 | Intercalated tWH | geometric IL_5TBW_077 NA | |
| IL_6VWM_125 | 1/2/1686:1691, 1/2/1696:1702 | tSH-tSH-tHH-tHS | homologous IL_5J7L_308 NA | |
| IL_6VWM_126 | 1/2/1712:1718, 1/2/1742:1746 | 6x5 Sarcin-Ricin; G-bulge | homologous IL_5J7L_309 NA | |
| IL_6VWM_127 | 1/2/1720:1725, 1/2/1735:1740 | No text annotation | ||
| IL_6VWM_129 | 1/2/1770:1771, 1/2/1980:1982 | Single bulged A | homologous IL_5J7L_312 NA | |
| IL_6VWM_130 | 1/2/1798:1804, 1/2/1813:1821 | Kink-turn related | homologous IL_7A0S_065 IL_17069.6 | |
| IL_6VWM_131 | 1/2/1837:1840, 1/2/1902:1903 | Minor groove platform, major groove intercalation | homologous IL_5J7L_314 NA | |
| IL_6VWM_132 | 1/2/1841:1842, 1/2/1898:1901 | Major groove intercalation | homologous IL_5J7L_315 NA | |
| IL_6VWM_133 | 1/2/1846:1850, 1/2/1892:1894 | No text annotation | ||
| IL_6VWM_185 | 1/2/1851:1860, 1/2/1882:1891 | No text annotation | homologous IL_5J7L_387 NA | |
| IL_6VWM_134 | 1/2/1865:1867, 1/2/1874:1877 | No text annotation | ||
| IL_6VWM_135 | 1/2/1933:1934, 1/2/1964:1967 | Bulged stacked bases | geometric IL_7A0S_071 IL_24886.1 | |
| IL_6VWM_136 | 1/2/1934:1945, 1/2/1961:1964 | No text annotation | homologous IL_7A0S_072 IL_04332.3 | |
| IL_6VWM_137 | 1/2/2050:2052, 1/2/2617:2618 | Major groove platform | homologous IL_5J7L_320 NA | |
| IL_6VWM_138 | 1/2/2054:2056, 1/2/2612:2615 | No text annotation | homologous IL_5J7L_321 NA | |
| IL_6VWM_139 | 1/2/2067:2069, 1/2/2442:2443 | Single bulged U | homologous IL_7A0S_075 IL_97561.1 | |
| IL_6VWM_140 | 1/2/2070:2071, 1/2/2438:2441 | Minor groove platform | homologous IL_7RQB_081 NA | |
| IL_6VWM_141 | 1/2/2081:2083, 1/2/2236:2239 | Isolated tHS basepair with bulges | homologous IL_5J7L_325 NA | |
| IL_6VWM_142 | 1/2/2085:2087, 1/2/2232:2234 | Isolated non-canonical cWW pair | homologous IL_5J7L_326 NA | |
| IL_6VWM_146 | 1/2/2129:2138, 1/2/2153:2159 | No text annotation | ||
| IL_6VWM_147 | 1/2/2202:2204, 1/2/2220:2221 | Single bulged U | homologous IL_5J7L_331 NA | |
| IL_6VWM_148 | 1/2/2297:2299, 1/2/2317:2321 | No text annotation | homologous IL_5J7L_332 NA | |
| IL_6VWM_149 | 1/2/2350:2353, 1/2/2364:2367 | Double sheared | homologous IL_7RQB_089 NA | |
| IL_6VWM_150 | 1/2/2401:2403, 1/2/2414:2415 | Single bulged U | homologous IL_4WF9_088 IL_97561.1 | |
| IL_6VWM_151 | 1/2/2454:2455, 1/2/2496:2498 | Major groove platform | homologous IL_7RQB_092 NA | |
| IL_6VWM_152 | 1/2/2457:2459, 1/2/2493:2494 | Major groove platform | geometric IL_7A0S_085 IL_48076.7 | |
| IL_6VWM_153 | 1/2/2459:2461, 1/2/2489:2493 | Major groove minor groove platform with extra cWW | homologous IL_7RQB_094 NA | |
| IL_6VWM_154 | 1/2/2466:2470, 1/2/2480:2484 | Double sheared with non-canonical cWW | homologous IL_5J7L_338 NA | |
| IL_6VWM_155 | 1/2/2507:2508, 1/2/2580:2582 | Major groove platform | homologous IL_7A0S_088 IL_46637.1 | |
| IL_6VWM_156 | 1/2/2510:2512, 1/2/2574:2578 | Isolated non-canonical cWW with bulges | geometric IL_4WF9_095 IL_68118.1 | |
| IL_6VWM_157 | 1/2/2512:2513, 1/2/2571:2574 | No text annotation | homologous IL_5J7L_341 NA | |
| IL_6VWM_158 | 1/2/2522:2523, 1/2/2540:2543 | Major groove platform with intercalation | homologous IL_5J7L_342 NA | |
| IL_6VWM_159 | 1/2/2591:2592, 1/2/2601:2603 | No text annotation | geometric IL_9AXU_106 IL_14190.1 | |
| IL_6VWM_160 | 1/2/2636:2640, 1/2/2774:2782 | tSH-tHS-tHW | homologous IL_5J7L_345 NA | |
| IL_6VWM_161 | 1/2/2652:2658, 1/2/2663:2668 | Sarcin-Ricin target in LSU H95; G-bulge | geometric IL_7A0S_094 IL_16458.5 | |
| IL_6VWM_162 | 1/2/2680:2684, 1/2/2725:2727 | C-loop | homologous IL_5J7L_347 NA | |
| IL_6VWM_163 | 1/2/2687:2691, 1/2/2718:2722 | UAA/GAN related, with intercalation | homologous IL_5J7L_348 NA | |
| IL_6VWM_164 | 1/2/2695:2696, 1/2/2711:2714 | Multiple bulged bases | homologous IL_5J7L_349 NA | |
| IL_6VWM_165 | 1/2/2737:2742, 1/2/2762:2767 | UAA/GAN with extra cWW | homologous IL_7A0S_098 IL_91079.1 | |
| IL_6VWM_166 | 1/2/2806:2811, 1/2/2889:2892 | No text annotation | geometric IL_5J7L_351 NA | |
| IL_6VWM_167 | 1/2/2838:2839, 1/2/2878:2880 | Major groove intercalation | homologous IL_4WF9_106 IL_78536.1 | |
| IL_6VWM_168 | 1/2/2843:2846, 1/2/2870:2874 | Multiple bulged bases with non-canonical cWW | homologous IL_5J7L_353 NA | |
| IL_6VWM_169 | 1/2/2847:2852, 1/2/2865:2869 | tHS double platform | homologous IL_5J7L_354 NA | |
| IL_6VWM_171 | 1/3/23:28, 1/3/56:60 | No text annotation | ||
| IL_6VWM_173 | 1/3/34:38, 1/3/44:48 | Symmetric double minor groove platform | geometric IL_5J7L_358 NA | |
| IL_6VWM_174 | 1/3/71:79, 1/3/97:105 | Bacterial 5S Loop E | homologous IL_5J7L_359 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6VWM_007 | Minor groove platform | ||
| IL_6VWM_008 | Major groove intercalation | ||
| IL_6VWM_012 | No text annotation | ||
| IL_6VWM_013 | Minor groove platform | ||
| IL_6VWM_020 | No text annotation | ||
| IL_6VWM_021 | No text annotation | ||
| IL_6VWM_022 | tSH-tHW-tWW | ||
| IL_6VWM_025 | SSU/LSU pseudoknot | ||
| IL_6VWM_026 | Kink-turn related | ||
| IL_6VWM_033 | Single stack bend | ||
| IL_6VWM_035 | No text annotation | ||
| IL_6VWM_040 | Isolated non-canonical cWW with bulges | ||
| IL_6VWM_043 | Minor groove platform | ||
| IL_6VWM_044 | Single stack bend | ||
| IL_6VWM_046 | Tandem non-canonical cWW pairs | ||
| IL_6VWM_178 | No text annotation | ||
| IL_6VWM_047 | Minor groove platform | ||
| IL_6VWM_050 | No text annotation | ||
| IL_6VWM_051 | Minor groove platform | ||
| IL_6VWM_052 | No text annotation | ||
| IL_6VWM_053 | No text annotation | ||
| IL_6VWM_054 | 180 degree turn | ||
| IL_6VWM_055 | Double sheared with non-canonical cWW | ||
| IL_6VWM_056 | No text annotation | ||
| IL_6VWM_068 | No text annotation | ||
| IL_6VWM_073 | No text annotation | ||
| IL_6VWM_094 | No text annotation | ||
| IL_6VWM_102 | Tandem non-canonical cWW pairs | ||
| IL_6VWM_103 | Isolated cWS basepair | ||
| IL_6VWM_111 | No text annotation | ||
| IL_6VWM_118 | 180 degree turn | ||
| IL_6VWM_181 | No text annotation | ||
| IL_6VWM_119 | Single bulged A | ||
| IL_6VWM_120 | Triple sheared related | ||
| IL_6VWM_183 | No text annotation | ||
| IL_6VWM_128 | Single bulged C | ||
| IL_6VWM_143 | No text annotation | ||
| IL_6VWM_188 | No text annotation | ||
| IL_6VWM_144 | No text annotation | ||
| IL_6VWM_145 | No text annotation | ||
| IL_6VWM_186 | No text annotation | ||
| IL_6VWM_189 | Single bulged A | ||
| IL_6VWM_187 | Major groove intercalation | ||
| IL_6VWM_170 | Major groove platform with extra pair | ||
| IL_6VWM_172 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6VWM_001 | 1/1/46:47, 1/1/361:367, 1/1/393:395 | No text annotation | homologous J3_5J7L_001 NA | |
| J3_6VWM_026 | 1/1/580:588, 1/1/651:654, 1/1/754:761 | No text annotation | ||
| J3_6VWM_027 | 1/1/580:588, 1/1/651:655, 1/1/751:761 | No text annotation | ||
| J3_6VWM_002 | 1/1/586:588, 1/1/651:654, 1/1/754:755 | No text annotation | homologous J3_5J7L_002 NA | |
| J3_6VWM_003 | 1/1/672:673, 1/1/717:725, 1/1/732:734 | No text annotation | homologous J3_5J7L_003 NA | |
| J3_6VWM_004 | 1/1/826:829, 1/1/857:861, 1/1/868:874 | No text annotation | homologous J3_5J7L_004 NA | |
| J3_6VWM_005 | 1/1/943:946, 1/1/1235:1237, 1/1/1337:1340 | No text annotation | homologous J3_4LFB_003 J3_44359.1 | |
| J3_6VWM_006 | 1/1/955:962, 1/1/973:984, 1/1/1221:1225 | No text annotation | homologous J3_5J7L_006 NA | |
| J3_6VWM_009 | 1/1/1063:1068, 1/1/1107:1113, 1/1/1187:1193 | No text annotation | homologous J3_4LFB_007 J3_01343.1 | |
| J3_6VWM_030 | 1/1/1073:1074, 1/1/1083:1086, 1/1/1099:1102 | No text annotation | homologous J3_4LFB_017 J3_11018.1 | |
| J3_6VWM_013 | 1/2/30:31, 1/2/474:481, 1/2/509:510 | No text annotation | homologous J3_5J7L_036 NA | |
| J3_6VWM_032 | 1/2/30:31, 1/2/474:484, 1/2/496:510 | No text annotation | homologous J3_5J7L_066 NA | |
| J3_6VWM_033 | 1/2/32:35, 1/2/445:461, 1/2/468:473 | No text annotation | homologous J3_5J7L_067 NA | |
| J3_6VWM_014 | 1/2/56:57, 1/2/70:76, 1/2/110:114 | No text annotation | homologous J3_5J7L_037 NA | |
| J3_6VWM_034 | 1/2/297:301, 1/2/316:325, 1/2/337:341 | No text annotation | homologous J3_5J7L_068 NA | |
| J3_6VWM_015 | 1/2/683:689, 1/2/773:775, 1/2/791:794 | No text annotation | homologous J3_5J7L_038 NA | |
| J3_6VWM_016 | 1/2/698:700, 1/2/732:736, 1/2/760:763 | No text annotation | homologous J3_7RQB_005 NA | |
| J3_6VWM_017 | 1/2/1298:1303, 1/2/1625:1627, 1/2/1639:1642 | No text annotation | homologous J3_7RQB_007 NA | |
| J3_6VWM_018 | 1/2/1306:1309, 1/2/1605:1611, 1/2/1620:1622 | No text annotation | homologous J3_5J7L_042 NA | |
| J3_6VWM_019 | 1/2/1344:1349, 1/2/1382:1385, 1/2/1402:1403 | No text annotation | homologous J3_5J7L_043 NA | |
| J3_6VWM_035 | 1/2/1424:1429, 1/2/1564:1565, 1/2/1568:1574 | No text annotation | homologous J3_5J7L_069 NA | |
| J3_6VWM_020 | 1/2/2091:2093, 1/2/2196:2200, 1/2/2223:2228 | Kink-turn 3-way junction | homologous J3_5J7L_044 NA | |
| J3_6VWM_036 | 1/2/2282:2284, 1/2/2384:2395, 1/2/2421:2427 | No text annotation | homologous J3_5J7L_070 NA | |
| J3_6VWM_021 | 1/2/2295:2297, 1/2/2321:2323, 1/2/2332:2337 | No text annotation | homologous J3_5J7L_045 NA | |
| J3_6VWM_037 | 1/2/2295:2299, 1/2/2317:2323, 1/2/2332:2337 | No text annotation | homologous J3_5J7L_071 NA | |
| J3_6VWM_022 | 1/2/2517:2520, 1/2/2545:2547, 1/2/2561:2567 | No text annotation | homologous J3_5J7L_046 NA | |
| J3_6VWM_023 | 1/2/2789:2791, 1/2/2805:2806, 1/2/2892:2894 | No text annotation | homologous J3_5J7L_047 NA | |
| J3_6VWM_024 | 1/2/2812:2815, 1/2/2831:2836, 1/2/2882:2888 | No text annotation | homologous J3_5J7L_048 NA | |
| J3_6VWM_025 | 1/3/10:16, 1/3/68:70, 1/3/106:110 | No text annotation | homologous J3_5J7L_049 NA | |
| J4_6VWM_001 | 1/1/115:122, 1/1/239:240, 1/1/286:289, 1/1/311:312 | No text annotation | homologous J4_5J7L_001 NA | |
| J4_6VWM_002 | 1/1/142:144, 1/1/178:184, 1/1/193:198, 1/1/219:221 | No text annotation | homologous J4_5J7L_002 NA | |
| J4_6VWM_003 | 1/1/569:577, 1/1/764:769, 1/1/810:821, 1/1/879:881 | No text annotation | ||
| J4_6VWM_004 | 1/2/268:269, 1/2/370:375, 1/2/399:406, 1/2/421:424 | No text annotation | homologous J4_5J7L_018 NA | |
| J4_6VWM_005 | 1/2/601:604, 1/2/624:628, 1/2/635:638, 1/2/650:656 | No text annotation | homologous J4_5J7L_020 NA | |
| J4_6VWM_006 | 1/2/1270:1276, 1/2/1294:1295, 1/2/1645:1648, 1/2/2009:2010 | No text annotation | homologous J4_5J7L_021 NA | |
| J4_6VWM_007 | 1/2/1310:1314, 1/2/1338:1343, 1/2/1404:1405, 1/2/1597:1604 | No text annotation | homologous J4_5J7L_022 NA | |
| J4_6VWM_008 | 1/2/1313:1314, 1/2/1338:1343, 1/2/1404:1405, 1/2/1597:1603 | No text annotation | homologous J4_5J7L_023 NA | |
| J4_6VWM_009 | 1/2/1444:1445, 1/2/1466:1467, 1/2/1525:1526, 1/2/1546:1547 | No text annotation | homologous J4_5J7L_024 NA | |
| J4_6VWM_010 | 1/2/1772:1776, 1/2/1788:1792, 1/2/1827:1830, 1/2/1975:1979 | No text annotation | homologous J4_5J7L_025 NA | |
| J4_6VWM_015 | 1/2/1833:1835, 1/2/1905:1906, 1/2/1924:1933, 1/2/1967:1972 | No text annotation | homologous J4_9DFE_008 J4_42306.1 | |
| J4_6VWM_012 | 1/2/2285:2289, 1/2/2343:2347, 1/2/2370:2372, 1/2/2381:2383 | No text annotation | homologous J4_5J7L_027 NA | |
| J4_6VWM_013 | 1/2/2643:2646, 1/2/2674:2676, 1/2/2731:2735, 1/2/2769:2771 | No text annotation | homologous J4_5J7L_028 NA | |
| J5_6VWM_001 | 1/1/36:39, 1/1/403:406, 1/1/436:439, 1/1/498:500, 1/1/545:548 | No text annotation | ||
| J5_6VWM_002 | 1/1/58:61, 1/1/106:113, 1/1/314:316, 1/1/337:339, 1/1/350:354 | No text annotation | homologous J5_5J7L_003 NA | |
| J5_6VWM_003 | 1/2/47:54, 1/2/116:121, 1/2/130:131, 1/2/148:150, 1/2/176:178 | No text annotation | homologous J5_5J7L_013 NA | |
| J5_6VWM_004 | 1/2/531:533, 1/2/560:564, 1/2/577:579, 1/2/1261:1262, 1/2/2017:2018 | No text annotation | homologous J5_5J7L_014 NA | |
| J5_6VWM_005 | 1/2/584:589, 1/2/668:671, 1/2/809:812, 1/2/1195:1196, 1/2/1250:1256 | No text annotation | homologous J5_7A0S_004 J5_74302.6 | |
| J5_6VWM_006 | 1/2/1674:1682, 1/2/1706:1707, 1/2/1751:1752, 1/2/1756:1764, 1/2/1988:1990 | No text annotation | homologous J5_5J7L_016 NA | |
| J5_6VWM_007 | 1/2/2057:2064, 1/2/2446:2454, 1/2/2498:2507, 1/2/2582:2588, 1/2/2606:2611 | No text annotation | ||
| J5_6VWM_008 | 1/2/2074:2077, 1/2/2243:2246, 1/2/2258:2259, 1/2/2281:2282, 1/2/2427:2435 | No text annotation | homologous J5_4WF9_007 J5_39529.2 | |
| J6_6VWM_001 | 1/2/45:46, 1/2/179:183, 1/2/214:224, 1/2/231:235, 1/2/262:266, 1/2/426:433 | No text annotation | ||
| J6_6VWM_002 | 1/2/2074:2077, 1/2/2243:2246, 1/2/2258:2259, 1/2/2281:2284, 1/2/2384:2395, 1/2/2421:2435 | No text annotation | ||
| J7_6VWM_001 | 1/2/8:15, 1/2/525:531, 1/2/2018:2023, 1/2/2040:2043, 1/2/2625:2630, 1/2/2788:2789, 1/2/2894:2895 | No text annotation | ||
| J7_6VWM_002 | 1/2/817:822, 1/2/835:838, 1/2/940:946, 1/2/971:976, 1/2/987:991, 1/2/1163:1164, 1/2/1185:1190 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6VWM_028 | No text annotation | ||
| J3_6VWM_007 | No text annotation | ||
| J3_6VWM_029 | No text annotation | ||
| J3_6VWM_008 | No text annotation | ||
| J3_6VWM_010 | No text annotation | ||
| J3_6VWM_011 | No text annotation | ||
| J3_6VWM_031 | No text annotation | ||
| J3_6VWM_012 | No text annotation | ||
| J4_6VWM_011 | No text annotation | ||
| J4_6VWM_014 | tRNA junction |
Coloring options: