5KPS Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_5KPS_001 | 1/27/12:22 | No text annotation | homologous HL_5J7L_001 NA | |
| HL_5KPS_006 | 1/27/259:267 | GNRA related | homologous HL_5J7L_006 NA | |
| HL_5KPS_007 | 1/27/296:301 | GNRA | homologous HL_5J7L_007 NA | |
| HL_5KPS_008 | 1/27/320:333 | No text annotation | homologous HL_5J7L_008 NA | |
| HL_5KPS_009 | 1/27/342:347 | UNCG | homologous HL_6CZR_080 NA | |
| HL_5KPS_013 | 1/27/522:527 | No text annotation | geometric HL_4WF9_003 HL_75660.7 | |
| HL_5KPS_014 | 1/27/617:623 | GNRA-like with tWH | homologous HL_5J7L_014 NA | |
| HL_5KPS_015 | 1/27/689:698 | No text annotation | homologous HL_5J7L_015 NA | |
| HL_5KPS_016 | 1/27/726:731 | GNRA | homologous HL_5J7L_016 NA | |
| HL_5KPS_017 | 1/27/786:796 | No text annotation | homologous HL_4LFB_017 HL_38491.2 | |
| HL_5KPS_019 | 1/27/862:867 | GNRA | homologous HL_4LFB_019 HL_34789.2 | |
| HL_5KPS_020 | 1/27/897:902 | GNRA | homologous HL_5J7L_020 NA | |
| HL_5KPS_021 | 1/27/963:972 | No text annotation | homologous HL_5J7L_021 NA | |
| HL_5KPS_024 | 1/27/1076:1081 | GNRA | homologous HL_5J7L_023 NA | |
| HL_5KPS_026 | 1/27/1134:1140 | No text annotation | homologous HL_4LFB_026 HL_92935.1 | |
| HL_5KPS_029 | 1/27/1314:1323 | T-loop with 3 stacked bulged bases | homologous HL_4LFB_029 HL_93658.1 | |
| HL_5KPS_030 | 1/27/1356:1366 | No text annotation | homologous HL_4LFB_030 HL_86432.1 | |
| HL_5KPS_032 | 1/27/1515:1520 | GNRA | homologous HL_6CZR_103 NA | |
| HL_5KPS_033 | 1/28/59:68 | No text annotation | homologous HL_5J7L_134 NA | |
| HL_5KPS_034 | 1/28/87:95 | No text annotation | homologous HL_5J7L_135 NA | |
| HL_5KPS_035 | 1/28/123:128 | No text annotation | homologous HL_7A0S_003 HL_82710.3 | |
| HL_5KPS_037 | 1/28/158:168 | No text annotation | homologous HL_5J7L_138 NA | |
| HL_5KPS_038 | 1/28/194:201 | No text annotation | homologous HL_5J7L_139 NA | |
| HL_5KPS_039 | 1/28/225:230 | No text annotation | homologous HL_5J7L_140 NA | |
| HL_5KPS_040 | 1/28/246:252 | No text annotation | homologous HL_5J7L_141 NA | |
| HL_5KPS_042 | 1/28/327:335 | T-loop with unstacked turn | homologous HL_5J7L_144 NA | |
| HL_5KPS_043 | 1/28/382:392 | No text annotation | homologous HL_5J7L_145 NA | |
| HL_5KPS_044 | 1/28/410:417 | Pseudoknot geometry | homologous HL_5J7L_146 NA | |
| HL_5KPS_045 | 1/28/462:467 | GNRA | homologous HL_4WF9_015 HL_34789.2 | |
| HL_5KPS_046 | 1/28/487:493 | GNRA | homologous HL_5J7L_148 NA | |
| HL_5KPS_048 | 1/28/566:575 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_150 NA | |
| HL_5KPS_050 | 1/28/629:634 | GNRA | homologous HL_5J7L_152 NA | |
| HL_5KPS_051 | 1/28/641:647 | No text annotation | homologous HL_5J7L_153 NA | |
| HL_5KPS_053 | 1/28/744:753 | No text annotation | homologous HL_4WF9_023 HL_50204.1 | |
| HL_5KPS_054 | 1/28/779:785 | UNCG variation | geometric HL_2NUE_001 HL_51020.2 | |
| HL_5KPS_055 | 1/28/826:831 | No text annotation | homologous HL_5J7L_157 NA | |
| HL_5KPS_057 | 1/28/954:963 | tRNA anticodon loop | geometric HL_3RG5_006 HL_87268.1 | |
| HL_5KPS_058 | 1/28/978:985 | No text annotation | homologous HL_5J7L_160 NA | |
| HL_5KPS_062 | 1/28/1222:1227 | GNRA | homologous HL_5J7L_164 NA | |
| HL_5KPS_063 | 1/28/1281:1289 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_165 NA | |
| HL_5KPS_064 | 1/28/1324:1330 | Pseudoknot geometry with 3' bulge | homologous HL_5J7L_166 NA | |
| HL_5KPS_065 | 1/28/1363:1368 | GNRA | homologous HL_5J7L_167 NA | |
| HL_5KPS_066 | 1/28/1389:1398 | No text annotation | homologous HL_5J7L_168 NA | |
| HL_5KPS_109 | 1/28/1450:1461 | UNCG variation | geometric HL_5J7L_200 NA | |
| HL_5KPS_067 | 1/28/1451:1459 | Mini UNCG with extended bulge | homologous HL_5J7L_169 NA | |
| HL_5KPS_068 | 1/28/1492:1498 | Pseudoknot geometry with 3' bulge | homologous HL_5J7L_170 NA | |
| HL_5KPS_070 | 1/28/1565:1568 | No text annotation | homologous HL_7RQB_039 NA | |
| HL_5KPS_071 | 1/28/1612:1619 | No text annotation | homologous HL_7A0S_040 HL_28592.1 | |
| HL_5KPS_072 | 1/28/1630:1636 | GNRA | homologous HL_5J7L_174 NA | |
| HL_5KPS_073 | 1/28/1691:1696 | No text annotation | homologous HL_7RQB_042 NA | |
| HL_5KPS_075 | 1/28/1752:1756 | No text annotation | homologous HL_5J7L_177 NA | |
| HL_5KPS_076 | 1/28/1777:1787 | No text annotation | homologous HL_5J7L_178 NA | |
| HL_5KPS_077 | 1/28/1806:1811 | GNRA related | homologous HL_5J7L_179 NA | |
| HL_5KPS_079 | 1/28/1910:1920 | No text annotation | geometric HL_5TBW_049 NA | |
| HL_5KPS_080 | 1/28/1949:1957 | No text annotation | homologous HL_7RQB_049 NA | |
| HL_5KPS_081 | 1/28/2027:2036 | No text annotation | homologous HL_4WF9_047 HL_78372.1 | |
| HL_5KPS_083 | 1/28/2209:2215 | No text annotation | homologous HL_5J7L_185 NA | |
| HL_5KPS_084 | 1/28/2248:2256 | No text annotation | homologous HL_7RQB_053 NA | |
| HL_5KPS_085 | 1/28/2264:2276 | No text annotation | homologous HL_7RQB_054 NA | |
| HL_5KPS_112 | 1/28/2304:2312 | No text annotation | homologous HL_9DFE_198 HL_02452.1 | |
| HL_5KPS_087 | 1/28/2324:2331 | Pseudoknot geometry | homologous HL_5J7L_189 NA | |
| HL_5KPS_088 | 1/28/2356:2361 | GNRA | homologous HL_5J7L_190 NA | |
| HL_5KPS_089 | 1/28/2374:2379 | GNRA | homologous HL_5J7L_191 NA | |
| HL_5KPS_090 | 1/28/2404:2413 | No text annotation | homologous HL_5J7L_192 NA | |
| HL_5KPS_091 | 1/28/2471:2479 | No text annotation | homologous HL_4WF9_056 HL_52011.1 | |
| HL_5KPS_092 | 1/28/2528:2535 | GNRA variation | homologous HL_5J7L_194 NA | |
| HL_5KPS_093 | 1/28/2551:2557 | No text annotation | homologous HL_5J7L_195 NA | |
| HL_5KPS_094 | 1/28/2594:2599 | GNRA | homologous HL_7RQB_063 NA | |
| HL_5KPS_096 | 1/28/2701:2706 | Ribsomal LSU H95 | homologous HL_5J7L_198 NA | |
| HL_5KPS_097 | 1/28/2745:2759 | No text annotation | homologous HL_4WF9_062 HL_53269.2 | |
| HL_5KPS_099 | 1/28/2819:2827 | No text annotation | homologous HL_5J7L_201 NA | |
| HL_5KPS_100 | 1/28/2856:2861 | GNRA | homologous HL_7A0S_068 HL_34789.2 | |
| HL_5KPS_110 | 1/29/34:48 | No text annotation | homologous HL_4V9F_074 HL_97756.3 | |
| HL_5KPS_101 | 1/29/38:44 | No text annotation | geometric HL_7RQB_070 NA | |
| HL_5KPS_102 | 1/29/86:90 | Mini UNCG | homologous HL_5J7L_204 NA | |
| HL_5KPS_103 | 1/31/13:22 | tRNA D-loop | homologous HL_5B63_003 HL_20490.1 | |
| HL_5KPS_104 | 1/31/31:39 | tRNA anticodon loop | homologous HL_6CFJ_107 HL_81376.2 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_5KPS_002 | No text annotation | ||
| HL_5KPS_111 | No text annotation | ||
| HL_5KPS_003 | GNRA | ||
| HL_5KPS_004 | GNRA | ||
| HL_5KPS_005 | No text annotation | ||
| HL_5KPS_010 | GNRA | ||
| HL_5KPS_011 | UNCG | ||
| HL_5KPS_012 | GNRA wlth extra near cWW | ||
| HL_5KPS_018 | Externally structured | ||
| HL_5KPS_022 | GNRA | ||
| HL_5KPS_023 | No text annotation | ||
| HL_5KPS_025 | T-loop related | ||
| HL_5KPS_027 | GNRA | ||
| HL_5KPS_028 | GNRA | ||
| HL_5KPS_031 | UNCG | ||
| HL_5KPS_036 | No text annotation | ||
| HL_5KPS_041 | T-loop with 2 stacked bulged bases | ||
| HL_5KPS_047 | Mini UNCG with extended bulge | ||
| HL_5KPS_049 | No text annotation | ||
| HL_5KPS_052 | GNRA wlth tandem sheared | ||
| HL_5KPS_056 | No text annotation | ||
| HL_5KPS_059 | No text annotation | ||
| HL_5KPS_060 | GNRA wlth tandem sheared | ||
| HL_5KPS_061 | No text annotation | ||
| HL_5KPS_069 | UNCG | ||
| HL_5KPS_074 | No text annotation | ||
| HL_5KPS_078 | GNRA variation | ||
| HL_5KPS_082 | No text annotation | ||
| HL_5KPS_086 | No text annotation | ||
| HL_5KPS_095 | GNRA | ||
| HL_5KPS_098 | UNCG variation | ||
| HL_5KPS_105 | T-loop with 2 stacked bulged bases | ||
| HL_5KPS_106 | tRNA D-loop | ||
| HL_5KPS_107 | tRNA anticodon loop | ||
| HL_5KPS_108 | T-loop with 2 stacked bulged bases |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_5KPS_001 | 1/27/30:32, 1/27/552:553 | Single bulged G | homologous IL_4LFB_001 IL_28408.2 | |
| IL_5KPS_002 | 1/27/44:45, 1/27/396:398 | Single bulged A | homologous IL_5J7L_002 NA | |
| IL_5KPS_003 | 1/27/47:52, 1/27/359:361 | No text annotation | geometric IL_5J7L_003 NA | |
| IL_5KPS_005 | 1/27/63:66, 1/27/103:104 | Multiple bulged bases | homologous IL_5J7L_005 NA | |
| IL_5KPS_009 | 1/27/128:131, 1/27/231:233 | Isolated non-canonical cWW pair | homologous IL_5J7L_009 NA | |
| IL_5KPS_010 | 1/27/132:136, 1/27/227:230 | Minor groove platform related | homologous IL_5J7L_010 NA | |
| IL_5KPS_011 | 1/27/144:146, 1/27/176:178 | Isolated cWH basepair | homologous IL_5J7L_011 NA | |
| IL_5KPS_012 | 1/27/147:153, 1/27/168:175 | tWH-tWH-tHW-tHW | homologous IL_5J7L_012 NA | |
| IL_5KPS_014 | 1/27/242:247, 1/27/277:284 | Kink-turn with non-sequential stacking | homologous IL_5J7L_014 NA | |
| IL_5KPS_015 | 1/27/249:252, 1/27/274:275 | No text annotation | homologous IL_4LFB_012 IL_22002.1 | |
| IL_5KPS_016 | 1/27/292:293, 1/27/304:308 | C-loop | homologous IL_4LFB_013 IL_06671.1 | |
| IL_5KPS_017 | 1/27/367:369, 1/27/392:393 | Single bulged U | homologous IL_5J7L_017 NA | |
| IL_5KPS_018 | 1/27/371:375, 1/27/389:390 | C-loop | geometric IL_5J7L_018 NA | |
| IL_5KPS_019 | 1/27/375:376, 1/27/387:389 | Single bulged G | homologous IL_4LFB_016 IL_28408.2 | |
| IL_5KPS_021 | 1/27/440:442, 1/27/492:497 | No text annotation | homologous IL_5J7L_021 NA | |
| IL_5KPS_024 | 1/27/504:511, 1/27/540:541 | SSU/LSU pseudoknot | homologous IL_5J7L_024 NA | |
| IL_5KPS_025 | 1/27/515:521, 1/27/528:536 | Kink-turn related | geometric IL_4V88_415 NA | |
| IL_5KPS_026 | 1/27/569:575, 1/27/880:881 | No text annotation | homologous IL_4LFB_022 IL_20847.1 | |
| IL_5KPS_027 | 1/27/580:584, 1/27/757:761 | tSH-tHW-tHS | homologous IL_5J7L_027 NA | |
| IL_5KPS_029 | 1/27/597:598, 1/27/640:643 | Major groove minor groove platform; mini C-loop | homologous IL_5J7L_029 NA | |
| IL_5KPS_030 | 1/27/605:612, 1/27/628:633 | No text annotation | homologous IL_5J7L_030 NA | |
| IL_5KPS_033 | 1/27/662:666, 1/27/740:743 | Tandem non-canonical cWW pairs | homologous IL_5J7L_033 NA | |
| IL_5KPS_178 | 1/27/673:677, 1/27/713:717 | Triple non-canonical cWW pairs | homologous IL_5J7L_361 NA | |
| IL_5KPS_035 | 1/27/684:688, 1/27/699:706 | Kink-turn | homologous IL_5J7L_035 NA | |
| IL_5KPS_036 | 1/27/774:778, 1/27/804:805 | Left turn | homologous IL_5J7L_036 NA | |
| IL_5KPS_037 | 1/27/779:783, 1/27/799:803 | tSH-tHW-tHS | homologous IL_5J7L_037 NA | |
| IL_5KPS_038 | 1/27/887:894, 1/27/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_5J7L_038 NA | |
| IL_5KPS_039 | 1/27/922:923, 1/27/1393:1395 | Single bulged A | homologous IL_6CZR_147 NA | |
| IL_5KPS_040 | 1/27/925:927, 1/27/1390:1391 | Single bulged G | homologous IL_4LFB_036 IL_28408.2 | |
| IL_5KPS_041 | 1/27/933:935, 1/27/1380:1384 | Minor groove platform | homologous IL_4LFB_037 IL_61370.1 | |
| IL_5KPS_042 | 1/27/953:954, 1/27/1226:1228 | No text annotation | homologous IL_6CZR_150 NA | |
| IL_5KPS_043 | 1/27/993:997, 1/27/1044:1045 | Minor groove platform | homologous IL_5J7L_043 NA | |
| IL_5KPS_044 | 1/27/998:999, 1/27/1041:1043 | Single stack bend | homologous IL_5J7L_044 NA | |
| IL_5KPS_045 | 1/27/1048:1050, 1/27/1208:1209 | Single bulged U | homologous IL_4LFB_042 IL_97561.2 | |
| IL_5KPS_179 | 1/27/1052:1056, 1/27/1204:1206 | No text annotation | homologous IL_6CZR_154 NA | |
| IL_5KPS_047 | 1/27/1057:1058, 1/27/1199:1203 | Minor groove platform | homologous IL_5J7L_048 NA | |
| IL_5KPS_048 | 1/27/1060:1061, 1/27/1195:1197 | Single bulged A | homologous IL_5J7L_049 NA | |
| IL_5KPS_049 | 1/27/1061:1063, 1/27/1193:1195 | Isolated non-canonical cWW pair | geometric IL_4LFB_047 IL_68118.2 | |
| IL_5KPS_050 | 1/27/1124:1128, 1/27/1144:1149 | No text annotation | homologous IL_5J7L_051 NA | |
| IL_5KPS_053 | 1/27/1247:1253, 1/27/1284:1290 | No text annotation | homologous IL_5J7L_054 NA | |
| IL_5KPS_054 | 1/27/1255:1258, 1/27/1277:1282 | 180 degree turn | homologous IL_5J7L_055 NA | |
| IL_5KPS_055 | 1/27/1259:1263, 1/27/1272:1276 | Double sheared with non-canonical cWW | homologous IL_5J7L_056 NA | |
| IL_5KPS_057 | 1/27/1399:1401, 1/27/1501:1504 | No text annotation | homologous IL_5J7L_058 NA | |
| IL_5KPS_058 | 1/27/1401:1404, 1/27/1497:1501 | No text annotation | geometric IL_4V88_464 NA | |
| IL_5KPS_059 | 1/27/1405:1407, 1/27/1494:1496 | Isolated non-canonical cWW pair | geometric IL_5MWI_007 NA | |
| IL_5KPS_060 | 1/27/1407:1409, 1/27/1491:1494 | Decoding loop related | geometric IL_3C3Z_002 IL_53541.1 | |
| IL_5KPS_062 | 1/27/1416:1419, 1/27/1481:1484 | Double sheared | homologous IL_5J7L_062 NA | |
| IL_5KPS_063 | 1/27/1430:1435, 1/27/1466:1470 | Triple sheared related | homologous IL_5J7L_063 NA | |
| IL_5KPS_066 | 1/28/24:30, 1/28/510:516 | Triple sheared with non-canonical cWW | homologous IL_5J7L_245 NA | |
| IL_5KPS_067 | 1/28/36:37, 1/28/442:444 | Single bulged A | homologous IL_4WF9_002 IL_14190.2 | |
| IL_5KPS_068 | 1/28/43:44, 1/28/434:436 | Minor groove platform | homologous IL_5J7L_247 NA | |
| IL_5KPS_069 | 1/28/81:85, 1/28/97:105 | No text annotation | homologous IL_5J7L_248 NA | |
| IL_5KPS_070 | 1/28/183:184, 1/28/212:214 | Single stack bend | homologous IL_5J7L_249 NA | |
| IL_5KPS_071 | 1/28/188:194, 1/28/201:208 | 8x7 Sarcin-Ricin; G-bulge | geometric IL_5J7L_250 NA | |
| IL_5KPS_072 | 1/28/239:245, 1/28/253:258 | 7x6 Sarcin-Ricin; G-bulge | homologous IL_5J7L_251 NA | |
| IL_5KPS_073 | 1/28/269:271, 1/28/366:370 | No text annotation | homologous IL_5J7L_252 NA | |
| IL_5KPS_075 | 1/28/293:295, 1/28/343:347 | No text annotation | homologous IL_5J7L_254 NA | |
| IL_5KPS_076 | 1/28/481:484, 1/28/496:509 | No text annotation | geometric IL_5J7L_255 NA | |
| IL_5KPS_077 | 1/28/536:539, 1/28/554:557 | Double sheared | homologous IL_5J7L_256 NA | |
| IL_5KPS_078 | 1/28/564:566, 1/28/575:577 | Isolated non-canonical cWW pair | geometric IL_5J7L_257 NA | |
| IL_5KPS_079 | 1/28/606:610, 1/28/618:622 | AAA cross-strand stack | homologous IL_5J7L_258 NA | |
| IL_5KPS_080 | 1/28/672:674, 1/28/806:808 | Isolated non-canonical cWW pair | homologous IL_4WF9_020 IL_01003.2 | |
| IL_5KPS_081 | 1/28/674:678, 1/28/799:806 | tHW-tHW cross-strand stack | geometric IL_7RQB_018 NA | |
| IL_5KPS_082 | 1/28/697:698, 1/28/763:765 | Single bulged A | homologous IL_5J7L_261 NA | |
| IL_5KPS_083 | 1/28/702:703, 1/28/728:730 | Single bulged G | homologous IL_4WF9_023 IL_28408.2 | |
| IL_5KPS_084 | 1/28/703:707, 1/28/724:728 | Triple sheared | geometric IL_7RQB_021 NA | |
| IL_5KPS_085 | 1/28/738:740, 1/28/757:758 | Major groove platform | homologous IL_4WF9_026 IL_48076.8 | |
| IL_5KPS_086 | 1/28/775:777, 1/28/787:791 | Multiple bulged bases | homologous IL_7A0S_021 IL_89509.1 | |
| IL_5KPS_087 | 1/28/837:838, 1/28/940:942 | Single stack bend | homologous IL_4WF9_028 IL_15011.2 | |
| IL_5KPS_088 | 1/28/844:847, 1/28/933:934 | 90 degree turn | homologous IL_5J7L_267 NA | |
| IL_5KPS_180 | 1/28/844:848, 1/28/930:934 | No text annotation | homologous IL_5J7L_399 NA | |
| IL_5KPS_089 | 1/28/847:848, 1/28/930:933 | Stack outside cWW | geometric IL_5J7L_268 NA | |
| IL_5KPS_090 | 1/28/850:851, 1/28/926:928 | Single stack bend | homologous IL_5J7L_269 NA | |
| IL_5KPS_092 | 1/28/862:863, 1/28/913:915 | Single bulged G | homologous IL_5J7L_271 NA | |
| IL_5KPS_093 | 1/28/864:868, 1/28/909:912 | C-loop with bulged stacked A's | homologous IL_5J7L_272 NA | |
| IL_5KPS_094 | 1/28/870:872, 1/28/905:907 | Isolated non-canonical cWW pair | homologous IL_5J7L_273 NA | |
| IL_5KPS_097 | 1/28/994:996, 1/28/1159:1160 | Single bulged C | homologous IL_5J7L_276 NA | |
| IL_5KPS_098 | 1/28/998:1002, 1/28/1153:1157 | UAA/GAN | homologous IL_4WF9_036 IL_08938.1 | |
| IL_5KPS_099 | 1/28/1004:1011, 1/28/1150:1151 | SSU/LSU pseudoknot | geometric IL_5J7L_278 NA | |
| IL_5KPS_100 | 1/28/1011:1013, 1/28/1149:1150 | Single bulged U | homologous IL_5J7L_279 NA | |
| IL_5KPS_101 | 1/28/1018:1024, 1/28/1140:1144 | Kink-turn related | homologous IL_4WF9_039 IL_57188.6 | |
| IL_5KPS_102 | 1/28/1024:1030, 1/28/1124:1140 | No text annotation | geometric IL_5J7L_281 NA | |
| IL_5KPS_103 | 1/28/1031:1034, 1/28/1121:1123 | Isolated non-canonical cWW pair | homologous IL_7RQB_041 NA | |
| IL_5KPS_108 | 1/28/1196:1198, 1/28/1247:1250 | Isolated cWS basepair | homologous IL_4WF9_044 IL_42997.5 | |
| IL_5KPS_109 | 1/28/1202:1206, 1/28/1240:1243 | No text annotation | homologous IL_5J7L_287 NA | |
| IL_5KPS_110 | 1/28/1208:1215, 1/28/1234:1238 | Kink-turn | homologous IL_5J7L_288 NA | |
| IL_5KPS_111 | 1/28/1262:1269, 1/28/2011:2017 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_5J7L_289 NA | |
| IL_5KPS_112 | 1/28/1310:1313, 1/28/1603:1604 | Major groove platform; stack outside cWW | homologous IL_4WF9_049 IL_74641.2 | |
| IL_5KPS_113 | 1/28/1319:1323, 1/28/1331:1333 | C-loop | homologous IL_5J7L_291 NA | |
| IL_5KPS_114 | 1/28/1351:1355, 1/28/1376:1380 | UAA/GAN | homologous IL_5J7L_292 NA | |
| IL_5KPS_115 | 1/28/1357:1361, 1/28/1370:1374 | tSH-tHW-tHS | homologous IL_5J7L_293 NA | |
| IL_5KPS_118 | 1/28/1432:1435, 1/28/1557:1561 | Tandem non-canonical cWW pairs | homologous IL_5J7L_296 NA | |
| IL_5KPS_119 | 1/28/1437:1440, 1/28/1551:1555 | tSH-tHW | homologous IL_5J7L_297 NA | |
| IL_5KPS_121 | 1/28/1468:1471, 1/28/1520:1524 | No text annotation | homologous IL_5J7L_299 NA | |
| IL_5KPS_122 | 1/28/1474:1478, 1/28/1513:1517 | tSH-tHW-tHS | homologous IL_5J7L_300 NA | |
| IL_5KPS_123 | 1/28/1481:1482, 1/28/1507:1510 | 180 degree turn | homologous IL_5J7L_301 NA | |
| IL_5KPS_124 | 1/28/1489:1491, 1/28/1499:1500 | Single bulged A | homologous IL_5J7L_302 NA | |
| IL_5KPS_125 | 1/28/1526:1529, 1/28/1542:1546 | UAA/GAN variation | homologous IL_5J7L_303 NA | |
| IL_5KPS_126 | 1/28/1651:1656, 1/28/2004:2006 | No text annotation | homologous IL_5J7L_304 NA | |
| IL_5KPS_127 | 1/28/1663:1665, 1/28/1995:1997 | Isolated tWW turn | homologous IL_5J7L_305 NA | |
| IL_5KPS_128 | 1/28/1666:1669, 1/28/1993:1994 | Major groove platform; stack outside cWW | geometric IL_4V9F_061 IL_74641.2 | |
| IL_5KPS_181 | 1/28/1666:1674, 1/28/1990:1994 | No text annotation | homologous IL_5J7L_386 NA | |
| IL_5KPS_129 | 1/28/1669:1674, 1/28/1990:1993 | Intercalated tWH | homologous IL_5J7L_307 NA | |
| IL_5KPS_130 | 1/28/1686:1691, 1/28/1696:1702 | tSH-tSH-tHH-tHS | geometric IL_5J7L_308 NA | |
| IL_5KPS_131 | 1/28/1712:1718, 1/28/1742:1746 | 6x5 Sarcin-Ricin; G-bulge | homologous IL_5J7L_309 NA | |
| IL_5KPS_134 | 1/28/1770:1771, 1/28/1980:1982 | Single bulged A | homologous IL_7A0S_064 IL_14190.2 | |
| IL_5KPS_135 | 1/28/1798:1804, 1/28/1813:1821 | Kink-turn related | homologous IL_5J7L_313 NA | |
| IL_5KPS_136 | 1/28/1837:1840, 1/28/1902:1903 | Minor groove platform, major groove intercalation | homologous IL_5J7L_314 NA | |
| IL_5KPS_137 | 1/28/1841:1842, 1/28/1898:1901 | Major groove intercalation | homologous IL_5J7L_315 NA | |
| IL_5KPS_138 | 1/28/1846:1849, 1/28/1893:1894 | Major groove minor groove platform; mini C-loop | homologous IL_5J7L_316 NA | |
| IL_5KPS_182 | 1/28/1851:1860, 1/28/1882:1891 | No text annotation | homologous IL_5J7L_387 NA | |
| IL_5KPS_139 | 1/28/1864:1867, 1/28/1874:1878 | UAA/GAN related | homologous IL_5J7L_317 NA | |
| IL_5KPS_140 | 1/28/1933:1934, 1/28/1964:1967 | Bulged stacked bases | geometric IL_5J7L_318 NA | |
| IL_5KPS_141 | 1/28/1934:1945, 1/28/1961:1964 | No text annotation | homologous IL_4WF9_077 IL_84014.1 | |
| IL_5KPS_142 | 1/28/2050:2052, 1/28/2617:2618 | Major groove platform | homologous IL_5J7L_320 NA | |
| IL_5KPS_143 | 1/28/2054:2056, 1/28/2612:2615 | No text annotation | homologous IL_5J7L_321 NA | |
| IL_5KPS_144 | 1/28/2067:2069, 1/28/2442:2443 | Single bulged U | homologous IL_7A0S_075 IL_97561.2 | |
| IL_5KPS_145 | 1/28/2070:2071, 1/28/2438:2441 | Minor groove platform | homologous IL_7RQB_081 NA | |
| IL_5KPS_146 | 1/28/2081:2083, 1/28/2236:2239 | Isolated tHS basepair with bulges | homologous IL_5J7L_325 NA | |
| IL_5KPS_147 | 1/28/2085:2087, 1/28/2232:2234 | Isolated non-canonical cWW pair | homologous IL_5J7L_326 NA | |
| IL_5KPS_150 | 1/28/2202:2204, 1/28/2220:2221 | Single bulged U | homologous IL_5J7L_331 NA | |
| IL_5KPS_152 | 1/28/2401:2403, 1/28/2414:2415 | No text annotation | geometric IL_9AXU_122 IL_97561.2 | |
| IL_5KPS_153 | 1/28/2453:2454, 1/28/2498:2500 | Single stack bend | homologous IL_4WF9_089 IL_15011.2 | |
| IL_5KPS_154 | 1/28/2454:2455, 1/28/2496:2498 | Major groove platform | geometric IL_4V9F_082 IL_48076.8 | |
| IL_5KPS_156 | 1/28/2459:2461, 1/28/2489:2493 | Major groove minor groove platform with extra cWW | homologous IL_5J7L_337 NA | |
| IL_5KPS_157 | 1/28/2466:2470, 1/28/2480:2484 | Double sheared with non-canonical cWW | homologous IL_5J7L_338 NA | |
| IL_5KPS_158 | 1/28/2507:2509, 1/28/2579:2582 | Major groove platform with extra pair | geometric IL_7RQB_093 NA | |
| IL_5KPS_159 | 1/28/2510:2512, 1/28/2574:2578 | Isolated non-canonical cWW with bulges | homologous IL_5J7L_340 NA | |
| IL_5KPS_160 | 1/28/2512:2513, 1/28/2571:2574 | No text annotation | geometric IL_5J7L_341 NA | |
| IL_5KPS_161 | 1/28/2522:2523, 1/28/2540:2543 | Major groove platform with intercalation | homologous IL_7RQB_099 NA | |
| IL_5KPS_162 | 1/28/2591:2592, 1/28/2601:2603 | Single bulged A | homologous IL_7RQB_101 NA | |
| IL_5KPS_163 | 1/28/2636:2640, 1/28/2774:2782 | tSH-tHS-tHW | homologous IL_5J7L_345 NA | |
| IL_5KPS_164 | 1/28/2652:2658, 1/28/2663:2668 | Sarcin-Ricin target in LSU H95; G-bulge | homologous IL_7RQB_103 NA | |
| IL_5KPS_165 | 1/28/2680:2684, 1/28/2725:2727 | C-loop | homologous IL_5J7L_347 NA | |
| IL_5KPS_166 | 1/28/2687:2691, 1/28/2718:2722 | UAA/GAN related, with intercalation | homologous IL_5J7L_348 NA | |
| IL_5KPS_167 | 1/28/2695:2696, 1/28/2711:2714 | Multiple bulged bases | homologous IL_4WF9_103 IL_44609.2 | |
| IL_5KPS_168 | 1/28/2737:2742, 1/28/2762:2767 | UAA/GAN with extra cWW | homologous IL_5J7L_350 NA | |
| IL_5KPS_169 | 1/28/2806:2811, 1/28/2889:2892 | No text annotation | geometric IL_5J7L_351 NA | |
| IL_5KPS_170 | 1/28/2838:2839, 1/28/2878:2880 | Major groove intercalation | homologous IL_5J7L_352 NA | |
| IL_5KPS_171 | 1/28/2843:2846, 1/28/2870:2874 | Multiple bulged bases with non-canonical cWW | homologous IL_5J7L_353 NA | |
| IL_5KPS_172 | 1/28/2847:2852, 1/28/2865:2869 | tHS double platform | homologous IL_5J7L_354 NA | |
| IL_5KPS_176 | 1/29/34:38, 1/29/44:48 | Symmetric double minor groove platform | homologous IL_5J7L_358 NA | |
| IL_5KPS_177 | 1/29/71:79, 1/29/97:105 | Bacterial 5S Loop E | homologous IL_5J7L_359 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_5KPS_004 | Minor groove platform | ||
| IL_5KPS_006 | Minor groove platform with extra cWW | ||
| IL_5KPS_007 | Minor groove platform | ||
| IL_5KPS_008 | Single bulged G | ||
| IL_5KPS_013 | Minor groove platform | ||
| IL_5KPS_020 | No text annotation | ||
| IL_5KPS_022 | tSH-tHW-tWW | ||
| IL_5KPS_023 | No text annotation | ||
| IL_5KPS_028 | Major groove platform | ||
| IL_5KPS_031 | Major groove platform; stack outside cWW | ||
| IL_5KPS_032 | Single stack bend | ||
| IL_5KPS_034 | No text annotation | ||
| IL_5KPS_046 | Tandem non-canonical cWW pairs | ||
| IL_5KPS_051 | Minor groove platform | ||
| IL_5KPS_052 | No text annotation | ||
| IL_5KPS_056 | No text annotation | ||
| IL_5KPS_061 | Isolated non-canonical cWW pair | ||
| IL_5KPS_064 | Single bulged A | ||
| IL_5KPS_065 | No text annotation | ||
| IL_5KPS_187 | No text annotation | ||
| IL_5KPS_074 | No text annotation | ||
| IL_5KPS_091 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | ||
| IL_5KPS_095 | Double sheared with non-canonical cWW | ||
| IL_5KPS_096 | Single bulged A | ||
| IL_5KPS_104 | Tandem non-canonical cWW pairs | ||
| IL_5KPS_105 | Kink-turn | ||
| IL_5KPS_106 | No text annotation | ||
| IL_5KPS_107 | No text annotation | ||
| IL_5KPS_116 | No text annotation | ||
| IL_5KPS_117 | UAA/GAN | ||
| IL_5KPS_120 | Single bulged U | ||
| IL_5KPS_132 | Triple sheared | ||
| IL_5KPS_133 | Single bulged C | ||
| IL_5KPS_148 | Isolated non-canonical cWW pair | ||
| IL_5KPS_149 | No text annotation | ||
| IL_5KPS_183 | No text annotation | ||
| IL_5KPS_184 | No text annotation | ||
| IL_5KPS_185 | No text annotation | ||
| IL_5KPS_186 | Tandem non-canonical cWW pairs | ||
| IL_5KPS_151 | Double sheared | ||
| IL_5KPS_155 | Major groove platform with extra pair | ||
| IL_5KPS_173 | Major groove intercalation | ||
| IL_5KPS_174 | No text annotation | ||
| IL_5KPS_175 | Major groove minor groove platform; mini C-loop |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_5KPS_001 | 1/27/46:47, 1/27/361:367, 1/27/393:395 | No text annotation | homologous J3_5J7L_001 NA | |
| J3_5KPS_028 | 1/27/46:52, 1/27/359:367, 1/27/393:395 | No text annotation | homologous J3_5J7L_050 NA | |
| J3_5KPS_002 | 1/27/586:588, 1/27/651:654, 1/27/754:755 | No text annotation | homologous J3_5J7L_002 NA | |
| J3_5KPS_029 | 1/27/586:588, 1/27/651:655, 1/27/751:755 | No text annotation | homologous J3_5J7L_051 NA | |
| J3_5KPS_003 | 1/27/672:673, 1/27/717:725, 1/27/732:734 | No text annotation | homologous J3_5J7L_003 NA | |
| J3_5KPS_004 | 1/27/826:829, 1/27/857:861, 1/27/868:874 | No text annotation | homologous J3_5J7L_004 NA | |
| J3_5KPS_005 | 1/27/936:939, 1/27/1344:1350, 1/27/1372:1379 | No text annotation | homologous J3_4LFB_002 J3_85722.1 | |
| J3_5KPS_006 | 1/27/943:946, 1/27/1235:1237, 1/27/1337:1340 | No text annotation | homologous J3_5J7L_005 NA | |
| J3_5KPS_007 | 1/27/955:962, 1/27/973:984, 1/27/1221:1225 | No text annotation | homologous J3_5J7L_006 NA | |
| J3_5KPS_008 | 1/27/990:993, 1/27/1045:1047, 1/27/1210:1215 | No text annotation | homologous J3_5J7L_007 NA | |
| J3_5KPS_030 | 1/27/990:997, 1/27/1044:1047, 1/27/1210:1215 | No text annotation | homologous J3_5J7L_053 NA | |
| J3_5KPS_010 | 1/27/1063:1068, 1/27/1107:1113, 1/27/1187:1193 | No text annotation | homologous J3_5J7L_008 NA | |
| J3_5KPS_032 | 1/27/1073:1074, 1/27/1083:1086, 1/27/1099:1102 | No text annotation | homologous J3_4LFB_017 J3_11018.1 | |
| J3_5KPS_012 | 1/27/1116:1118, 1/27/1155:1158, 1/27/1181:1184 | No text annotation | homologous J3_5J7L_010 NA | |
| J3_5KPS_033 | 1/27/1116:1118, 1/27/1155:1161, 1/27/1175:1184 | No text annotation | homologous J3_5J7L_054 NA | |
| J3_5KPS_013 | 1/27/1237:1241, 1/27/1296:1303, 1/27/1334:1337 | No text annotation | homologous J3_4LFB_009 J3_03192.1 | |
| J3_5KPS_014 | 1/28/30:31, 1/28/474:481, 1/28/509:510 | No text annotation | homologous J3_5J7L_036 NA | |
| J3_5KPS_034 | 1/28/30:31, 1/28/474:484, 1/28/496:510 | No text annotation | homologous J3_5J7L_066 NA | |
| J3_5KPS_035 | 1/28/32:35, 1/28/445:461, 1/28/468:473 | No text annotation | homologous J3_5J7L_067 NA | |
| J3_5KPS_015 | 1/28/56:57, 1/28/70:76, 1/28/110:114 | No text annotation | homologous J3_5J7L_037 NA | |
| J3_5KPS_036 | 1/28/297:301, 1/28/316:325, 1/28/337:341 | No text annotation | homologous J3_5J7L_068 NA | |
| J3_5KPS_016 | 1/28/683:689, 1/28/773:775, 1/28/791:794 | No text annotation | homologous J3_5J7L_038 NA | |
| J3_5KPS_017 | 1/28/698:700, 1/28/732:736, 1/28/760:763 | No text annotation | homologous J3_7RQB_005 NA | |
| J3_5KPS_019 | 1/28/1298:1303, 1/28/1625:1627, 1/28/1639:1642 | No text annotation | homologous J3_5J7L_041 NA | |
| J3_5KPS_020 | 1/28/1306:1309, 1/28/1605:1611, 1/28/1620:1622 | No text annotation | homologous J3_7A0S_007 J3_47341.1 | |
| J3_5KPS_021 | 1/28/1344:1349, 1/28/1382:1385, 1/28/1402:1403 | No text annotation | homologous J3_5J7L_043 NA | |
| J3_5KPS_037 | 1/28/1424:1429, 1/28/1564:1565, 1/28/1568:1574 | No text annotation | homologous J3_5J7L_069 NA | |
| J3_5KPS_022 | 1/28/2091:2093, 1/28/2196:2200, 1/28/2223:2228 | Kink-turn 3-way junction | homologous J3_5J7L_044 NA | |
| J3_5KPS_038 | 1/28/2282:2284, 1/28/2384:2395, 1/28/2421:2427 | No text annotation | homologous J3_5J7L_070 NA | |
| J3_5KPS_023 | 1/28/2295:2299, 1/28/2317:2323, 1/28/2332:2337 | No text annotation | ||
| J3_5KPS_024 | 1/28/2517:2520, 1/28/2545:2547, 1/28/2561:2567 | No text annotation | homologous J3_5J7L_046 NA | |
| J3_5KPS_026 | 1/28/2812:2815, 1/28/2831:2836, 1/28/2882:2888 | No text annotation | homologous J3_5J7L_048 NA | |
| J3_5KPS_027 | 1/29/10:16, 1/29/68:70, 1/29/106:110 | No text annotation | homologous J3_5J7L_049 NA | |
| J4_5KPS_001 | 1/27/115:122, 1/27/239:240, 1/27/286:289, 1/27/311:312 | No text annotation | homologous J4_5J7L_001 NA | |
| J4_5KPS_002 | 1/27/142:144, 1/27/178:184, 1/27/193:198, 1/27/219:221 | No text annotation | homologous J4_5J7L_002 NA | |
| J4_5KPS_003 | 1/27/575:577, 1/27/764:769, 1/27/810:821, 1/27/879:880 | No text annotation | homologous J4_5J7L_003 NA | |
| J4_5KPS_004 | 1/28/268:269, 1/28/370:375, 1/28/399:406, 1/28/421:424 | No text annotation | homologous J4_5J7L_018 NA | |
| J4_5KPS_006 | 1/28/1270:1276, 1/28/1294:1295, 1/28/1645:1648, 1/28/2009:2010 | No text annotation | homologous J4_5J7L_021 NA | |
| J4_5KPS_007 | 1/28/1310:1314, 1/28/1338:1343, 1/28/1404:1405, 1/28/1597:1604 | No text annotation | homologous J4_5J7L_022 NA | |
| J4_5KPS_008 | 1/28/1313:1314, 1/28/1338:1343, 1/28/1404:1405, 1/28/1597:1603 | No text annotation | homologous J4_5J7L_023 NA | |
| J4_5KPS_009 | 1/28/1444:1445, 1/28/1466:1467, 1/28/1525:1526, 1/28/1546:1547 | No text annotation | homologous J4_5J7L_024 NA | |
| J4_5KPS_010 | 1/28/1772:1776, 1/28/1788:1792, 1/28/1827:1830, 1/28/1975:1979 | No text annotation | homologous J4_9DFE_007 J4_61477.6 | |
| J4_5KPS_011 | 1/28/1833:1835, 1/28/1905:1906, 1/28/1924:1933, 1/28/1967:1972 | No text annotation | homologous J4_9DFE_008 J4_42306.1 | |
| J4_5KPS_012 | 1/28/2285:2289, 1/28/2343:2347, 1/28/2370:2372, 1/28/2381:2383 | No text annotation | homologous J4_5J7L_027 NA | |
| J4_5KPS_013 | 1/28/2643:2646, 1/28/2674:2676, 1/28/2731:2735, 1/28/2769:2771 | No text annotation | homologous J4_5J7L_028 NA | |
| J4_5KPS_014 | 1/31/7:10, 1/31/25:27, 1/31/43:49, 1/31/65:66 | tRNA junction | homologous J4_6UFM_001 J4_95067.1 | |
| J5_5KPS_001 | 1/27/36:39, 1/27/403:406, 1/27/436:440, 1/27/497:500, 1/27/545:548 | No text annotation | homologous J5_5J7L_001 NA | |
| J5_5KPS_002 | 1/27/36:39, 1/27/403:406, 1/27/436:442, 1/27/492:500, 1/27/545:548 | No text annotation | homologous J5_5J7L_002 NA | |
| J5_5KPS_003 | 1/27/58:61, 1/27/106:113, 1/27/314:316, 1/27/337:339, 1/27/350:354 | No text annotation | homologous J5_5J7L_003 NA | |
| J5_5KPS_004 | 1/28/47:54, 1/28/116:121, 1/28/130:131, 1/28/148:150, 1/28/176:178 | No text annotation | homologous J5_5J7L_013 NA | |
| J5_5KPS_005 | 1/28/531:533, 1/28/560:564, 1/28/577:579, 1/28/1261:1262, 1/28/2017:2018 | No text annotation | homologous J5_5J7L_014 NA | |
| J5_5KPS_006 | 1/28/584:589, 1/28/668:671, 1/28/809:812, 1/28/1195:1196, 1/28/1250:1256 | No text annotation | homologous J5_5J7L_015 NA | |
| J5_5KPS_007 | 1/28/1674:1682, 1/28/1706:1707, 1/28/1751:1752, 1/28/1756:1764, 1/28/1988:1990 | No text annotation | homologous J5_5J7L_016 NA | |
| J5_5KPS_008 | 1/28/2057:2064, 1/28/2446:2453, 1/28/2500:2507, 1/28/2582:2588, 1/28/2606:2611 | No text annotation | ||
| J5_5KPS_009 | 1/28/2074:2077, 1/28/2243:2246, 1/28/2258:2259, 1/28/2281:2282, 1/28/2427:2435 | No text annotation | homologous J5_4WF9_007 J5_39529.2 | |
| J6_5KPS_001 | 1/28/45:46, 1/28/179:183, 1/28/214:224, 1/28/231:235, 1/28/262:266, 1/28/426:433 | No text annotation | ||
| J6_5KPS_002 | 1/28/2074:2077, 1/28/2243:2246, 1/28/2258:2259, 1/28/2281:2284, 1/28/2384:2395, 1/28/2421:2435 | No text annotation | ||
| J7_5KPS_001 | 1/28/8:15, 1/28/525:531, 1/28/2018:2023, 1/28/2040:2043, 1/28/2625:2630, 1/28/2788:2789, 1/28/2894:2895 | No text annotation | ||
| J7_5KPS_002 | 1/28/817:822, 1/28/835:837, 1/28/942:946, 1/28/971:976, 1/28/987:991, 1/28/1163:1164, 1/28/1185:1190 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_5KPS_031 | No text annotation | ||
| J3_5KPS_009 | No text annotation | ||
| J3_5KPS_011 | No text annotation | ||
| J3_5KPS_018 | No text annotation | ||
| J3_5KPS_025 | No text annotation | ||
| J4_5KPS_005 | No text annotation | ||
| J4_5KPS_015 | tRNA junction |
Coloring options: