5KPX Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_5KPX_001 | 1/26/12:22 | No text annotation | homologous HL_5J7L_001 NA | |
| HL_5KPX_006 | 1/26/259:267 | GNRA related | homologous HL_5J7L_006 NA | |
| HL_5KPX_007 | 1/26/296:301 | GNRA | homologous HL_5J7L_007 NA | |
| HL_5KPX_008 | 1/26/320:333 | No text annotation | homologous HL_6CZR_079 NA | |
| HL_5KPX_009 | 1/26/342:347 | UNCG | homologous HL_6CZR_080 NA | |
| HL_5KPX_013 | 1/26/522:527 | No text annotation | geometric HL_4WF9_003 HL_75660.6 | |
| HL_5KPX_014 | 1/26/617:623 | GNRA-like with tWH | homologous HL_4LFB_014 HL_92337.1 | |
| HL_5KPX_016 | 1/26/726:731 | GNRA | homologous HL_5J7L_016 NA | |
| HL_5KPX_017 | 1/26/786:796 | No text annotation | homologous HL_4LFB_017 HL_38491.1 | |
| HL_5KPX_019 | 1/26/862:867 | GNRA | homologous HL_4LFB_019 HL_34789.1 | |
| HL_5KPX_020 | 1/26/897:902 | GNRA | homologous HL_4LFB_020 HL_34789.1 | |
| HL_5KPX_021 | 1/26/963:972 | No text annotation | homologous HL_5J7L_021 NA | |
| HL_5KPX_022 | 1/26/1012:1017 | GNRA | homologous HL_4LFB_022 HL_34789.1 | |
| HL_5KPX_023 | 1/26/1076:1081 | GNRA | homologous HL_5J7L_023 NA | |
| HL_5KPX_025 | 1/26/1134:1140 | No text annotation | homologous HL_5J7L_025 NA | |
| HL_5KPX_026 | 1/26/1165:1171 | GNRA | homologous HL_4LFB_027 HL_34789.1 | |
| HL_5KPX_028 | 1/26/1314:1323 | T-loop with 3 stacked bulged bases | homologous HL_4LFB_029 HL_93658.1 | |
| HL_5KPX_029 | 1/26/1356:1366 | No text annotation | homologous HL_4LFB_030 HL_86432.1 | |
| HL_5KPX_031 | 1/26/1515:1520 | GNRA | geometric HL_4WF9_031 HL_34789.1 | |
| HL_5KPX_032 | 1/27/59:68 | No text annotation | homologous HL_5J7L_134 NA | |
| HL_5KPX_033 | 1/27/87:95 | No text annotation | homologous HL_5J7L_135 NA | |
| HL_5KPX_034 | 1/27/123:128 | No text annotation | homologous HL_5J7L_136 NA | |
| HL_5KPX_037 | 1/27/194:201 | No text annotation | geometric HL_5J7L_139 NA | |
| HL_5KPX_038 | 1/27/225:230 | No text annotation | homologous HL_5J7L_140 NA | |
| HL_5KPX_039 | 1/27/246:252 | No text annotation | homologous HL_5J7L_141 NA | |
| HL_5KPX_040 | 1/27/305:312 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_142 NA | |
| HL_5KPX_041 | 1/27/327:335 | T-loop with unstacked turn | homologous HL_4WF9_012 HL_27670.3 | |
| HL_5KPX_042 | 1/27/382:392 | No text annotation | homologous HL_5J7L_145 NA | |
| HL_5KPX_043 | 1/27/410:417 | Pseudoknot geometry | homologous HL_5J7L_146 NA | |
| HL_5KPX_044 | 1/27/462:467 | GNRA | homologous HL_7RQB_015 NA | |
| HL_5KPX_045 | 1/27/487:493 | GNRA | homologous HL_5J7L_148 NA | |
| HL_5KPX_047 | 1/27/566:575 | T-loop with 2 stacked bulged bases | geometric HL_5J7L_150 NA | |
| HL_5KPX_049 | 1/27/629:634 | GNRA | homologous HL_5J7L_152 NA | |
| HL_5KPX_050 | 1/27/641:647 | No text annotation | homologous HL_5J7L_153 NA | |
| HL_5KPX_052 | 1/27/744:753 | No text annotation | homologous HL_7A0S_022 HL_50204.1 | |
| HL_5KPX_053 | 1/27/779:785 | UNCG variation | geometric HL_1P6V_001 NA | |
| HL_5KPX_054 | 1/27/826:831 | No text annotation | homologous HL_5J7L_157 NA | |
| HL_5KPX_056 | 1/27/954:963 | tRNA anticodon loop | geometric HL_3RG5_006 HL_45359.1 | |
| HL_5KPX_057 | 1/27/978:985 | No text annotation | homologous HL_4WF9_028 HL_47171.1 | |
| HL_5KPX_061 | 1/27/1222:1227 | GNRA | homologous HL_5J7L_164 NA | |
| HL_5KPX_062 | 1/27/1281:1289 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_165 NA | |
| HL_5KPX_063 | 1/27/1324:1330 | Pseudoknot geometry with 3' bulge | homologous HL_5J7L_166 NA | |
| HL_5KPX_064 | 1/27/1363:1368 | GNRA | homologous HL_5J7L_167 NA | |
| HL_5KPX_065 | 1/27/1389:1398 | No text annotation | homologous HL_7RQB_036 NA | |
| HL_5KPX_066 | 1/27/1450:1461 | No text annotation | geometric HL_4V88_197 NA | |
| HL_5KPX_069 | 1/27/1565:1568 | Mini UNCG | homologous HL_7A0S_039 HL_90436.1 | |
| HL_5KPX_070 | 1/27/1612:1619 | No text annotation | homologous HL_7A0S_040 HL_28592.1 | |
| HL_5KPX_071 | 1/27/1630:1636 | GNRA | homologous HL_5J7L_174 NA | |
| HL_5KPX_072 | 1/27/1691:1696 | No text annotation | homologous HL_7RQB_042 NA | |
| HL_5KPX_113 | 1/27/1727:1733 | No text annotation | homologous HL_5J7L_214 NA | |
| HL_5KPX_073 | 1/27/1728:1731 | No text annotation | homologous HL_5J7L_176 NA | |
| HL_5KPX_074 | 1/27/1752:1756 | No text annotation | homologous HL_5J7L_177 NA | |
| HL_5KPX_075 | 1/27/1777:1787 | No text annotation | homologous HL_7RQB_045 NA | |
| HL_5KPX_076 | 1/27/1806:1811 | GNRA related | homologous HL_5J7L_179 NA | |
| HL_5KPX_078 | 1/27/1910:1920 | No text annotation | geometric HL_5TBW_049 NA | |
| HL_5KPX_079 | 1/27/1949:1957 | No text annotation | homologous HL_4WF9_046 HL_61418.1 | |
| HL_5KPX_080 | 1/27/2027:2036 | No text annotation | homologous HL_4WF9_047 HL_78372.1 | |
| HL_5KPX_082 | 1/27/2209:2215 | No text annotation | homologous HL_5J7L_185 NA | |
| HL_5KPX_083 | 1/27/2248:2256 | No text annotation | homologous HL_7RQB_053 NA | |
| HL_5KPX_084 | 1/27/2264:2276 | No text annotation | homologous HL_7RQB_054 NA | |
| HL_5KPX_116 | 1/27/2304:2312 | No text annotation | homologous HL_9DFE_198 HL_02452.1 | |
| HL_5KPX_086 | 1/27/2324:2331 | Pseudoknot geometry | homologous HL_5J7L_189 NA | |
| HL_5KPX_087 | 1/27/2356:2361 | GNRA | homologous HL_5J7L_190 NA | |
| HL_5KPX_089 | 1/27/2404:2413 | No text annotation | homologous HL_5J7L_192 NA | |
| HL_5KPX_090 | 1/27/2471:2479 | No text annotation | homologous HL_7A0S_059 HL_52011.1 | |
| HL_5KPX_091 | 1/27/2528:2535 | GNRA variation | homologous HL_5J7L_194 NA | |
| HL_5KPX_092 | 1/27/2551:2557 | No text annotation | homologous HL_5J7L_195 NA | |
| HL_5KPX_093 | 1/27/2594:2599 | GNRA | homologous HL_7RQB_063 NA | |
| HL_5KPX_096 | 1/27/2745:2759 | No text annotation | homologous HL_5J7L_199 NA | |
| HL_5KPX_098 | 1/27/2819:2827 | No text annotation | homologous HL_5J7L_201 NA | |
| HL_5KPX_099 | 1/27/2856:2861 | GNRA | homologous HL_5J7L_202 NA | |
| HL_5KPX_114 | 1/28/34:48 | No text annotation | homologous HL_5J7L_215 NA | |
| HL_5KPX_100 | 1/28/38:44 | No text annotation | geometric HL_5J7L_203 NA | |
| HL_5KPX_101 | 1/28/86:90 | Mini UNCG | homologous HL_5J7L_204 NA | |
| HL_5KPX_103 | 1/30/31:39 | tRNA anticodon loop | homologous HL_3TUP_002 HL_81376.1 | |
| HL_5KPX_105 | 1/31/13:22 | tRNA D-loop | homologous HL_4TUE_033 NA | |
| HL_5KPX_106 | 1/31/31:39 | tRNA anticodon loop | homologous HL_4TUE_034 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_5KPX_002 | No text annotation | ||
| HL_5KPX_003 | GNRA | ||
| HL_5KPX_004 | GNRA | ||
| HL_5KPX_005 | No text annotation | ||
| HL_5KPX_010 | GNRA | ||
| HL_5KPX_011 | UNCG | ||
| HL_5KPX_012 | GNRA wlth extra near cWW | ||
| HL_5KPX_015 | No text annotation | ||
| HL_5KPX_018 | No text annotation | ||
| HL_5KPX_024 | T-loop related | ||
| HL_5KPX_027 | GNRA | ||
| HL_5KPX_030 | UNCG | ||
| HL_5KPX_035 | No text annotation | ||
| HL_5KPX_111 | No text annotation | ||
| HL_5KPX_036 | No text annotation | ||
| HL_5KPX_046 | No text annotation | ||
| HL_5KPX_112 | No text annotation | ||
| HL_5KPX_048 | No text annotation | ||
| HL_5KPX_051 | GNRA wlth tandem sheared | ||
| HL_5KPX_055 | No text annotation | ||
| HL_5KPX_058 | No text annotation | ||
| HL_5KPX_059 | GNRA wlth tandem sheared | ||
| HL_5KPX_060 | No text annotation | ||
| HL_5KPX_067 | Pseudoknot geometry with 3' bulge | ||
| HL_5KPX_068 | UNCG | ||
| HL_5KPX_077 | GNRA | ||
| HL_5KPX_081 | No text annotation | ||
| HL_5KPX_085 | No text annotation | ||
| HL_5KPX_088 | GNRA | ||
| HL_5KPX_094 | GNRA | ||
| HL_5KPX_095 | Ribsomal LSU H95 | ||
| HL_5KPX_097 | UNCG variation | ||
| HL_5KPX_102 | tRNA D-loop | ||
| HL_5KPX_104 | No text annotation | ||
| HL_5KPX_107 | T-loop with 2 stacked bulged bases | ||
| HL_5KPX_115 | No text annotation | ||
| HL_5KPX_108 | tRNA D-loop | ||
| HL_5KPX_109 | tRNA anticodon loop | ||
| HL_5KPX_110 | T-loop with 2 stacked bulged bases |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_5KPX_001 | 1/26/30:32, 1/26/552:553 | Single bulged G | homologous IL_6CZR_113 NA | |
| IL_5KPX_002 | 1/26/44:45, 1/26/396:398 | Single bulged A | homologous IL_5J7L_002 NA | |
| IL_5KPX_003 | 1/26/47:52, 1/26/359:361 | No text annotation | geometric IL_5J7L_003 NA | |
| IL_5KPX_005 | 1/26/63:66, 1/26/103:104 | Multiple bulged bases | homologous IL_6CZR_117 NA | |
| IL_5KPX_009 | 1/26/128:131, 1/26/231:233 | Isolated non-canonical cWW pair | homologous IL_5J7L_009 NA | |
| IL_5KPX_012 | 1/26/147:153, 1/26/168:175 | tWH-tWH-tHW-tHW | homologous IL_5J7L_012 NA | |
| IL_5KPX_014 | 1/26/242:247, 1/26/277:284 | Kink-turn with non-sequential stacking | homologous IL_5J7L_014 NA | |
| IL_5KPX_015 | 1/26/249:252, 1/26/274:275 | No text annotation | homologous IL_4LFB_012 IL_22002.1 | |
| IL_5KPX_016 | 1/26/292:293, 1/26/304:308 | C-loop | homologous IL_4LFB_013 IL_06671.1 | |
| IL_5KPX_017 | 1/26/367:369, 1/26/392:393 | Single bulged U | geometric IL_5J7L_017 NA | |
| IL_5KPX_019 | 1/26/375:376, 1/26/387:389 | Single bulged G | geometric IL_5J7L_019 NA | |
| IL_5KPX_020 | 1/26/409:416, 1/26/427:433 | No text annotation | homologous IL_5J7L_020 NA | |
| IL_5KPX_022 | 1/26/446:450, 1/26/483:488 | tSH-tHW-tWW | geometric IL_5J7L_022 NA | |
| IL_5KPX_024 | 1/26/504:511, 1/26/540:541 | SSU/LSU pseudoknot | homologous IL_5J7L_024 NA | |
| IL_5KPX_025 | 1/26/515:521, 1/26/528:536 | Kink-turn related | geometric IL_4V88_415 NA | |
| IL_5KPX_026 | 1/26/569:575, 1/26/880:881 | No text annotation | homologous IL_4LFB_022 IL_20847.1 | |
| IL_5KPX_027 | 1/26/580:584, 1/26/757:761 | tSH-tHW-tHS | homologous IL_5J7L_027 NA | |
| IL_5KPX_029 | 1/26/597:598, 1/26/640:643 | Major groove minor groove platform; mini C-loop | homologous IL_5J7L_029 NA | |
| IL_5KPX_030 | 1/26/605:612, 1/26/628:633 | No text annotation | homologous IL_5J7L_030 NA | |
| IL_5KPX_031 | 1/26/654:655, 1/26/751:754 | Major groove platform; stack outside cWW | geometric IL_5J7L_031 NA | |
| IL_5KPX_033 | 1/26/662:666, 1/26/740:743 | Tandem non-canonical cWW pairs | homologous IL_5J7L_033 NA | |
| IL_5KPX_177 | 1/26/673:677, 1/26/713:717 | Triple non-canonical cWW pairs | homologous IL_5J7L_361 NA | |
| IL_5KPX_035 | 1/26/684:688, 1/26/699:706 | Kink-turn | homologous IL_5J7L_035 NA | |
| IL_5KPX_036 | 1/26/774:778, 1/26/804:805 | Left turn | homologous IL_4LFB_032 IL_29346.3 | |
| IL_5KPX_037 | 1/26/779:783, 1/26/799:803 | tSH-tHW-tHS | homologous IL_4LFB_033 IL_05821.1 | |
| IL_5KPX_038 | 1/26/887:894, 1/26/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_5J7L_038 NA | |
| IL_5KPX_039 | 1/26/922:923, 1/26/1393:1395 | Single bulged A | homologous IL_4LFB_035 IL_14190.1 | |
| IL_5KPX_040 | 1/26/925:927, 1/26/1390:1391 | Single bulged G | homologous IL_5J7L_040 NA | |
| IL_5KPX_041 | 1/26/933:935, 1/26/1380:1384 | Minor groove platform | homologous IL_5J7L_041 NA | |
| IL_5KPX_042 | 1/26/953:954, 1/26/1226:1228 | No text annotation | homologous IL_6CZR_150 NA | |
| IL_5KPX_043 | 1/26/993:997, 1/26/1044:1045 | Minor groove platform | geometric IL_5J7L_043 NA | |
| IL_5KPX_045 | 1/26/1003:1006, 1/26/1023:1037 | No text annotation | ||
| IL_5KPX_046 | 1/26/1048:1050, 1/26/1208:1209 | Single bulged U | homologous IL_4LFB_042 IL_97561.1 | |
| IL_5KPX_047 | 1/26/1052:1056, 1/26/1204:1206 | Isolated cWS basepair | homologous IL_4LFB_044 IL_82453.1 | |
| IL_5KPX_049 | 1/26/1060:1061, 1/26/1195:1197 | Single bulged A | homologous IL_5J7L_049 NA | |
| IL_5KPX_050 | 1/26/1061:1063, 1/26/1193:1195 | Isolated non-canonical cWW pair | geometric IL_5J7L_050 NA | |
| IL_5KPX_051 | 1/26/1124:1128, 1/26/1144:1149 | No text annotation | homologous IL_5J7L_051 NA | |
| IL_5KPX_054 | 1/26/1247:1253, 1/26/1284:1290 | No text annotation | homologous IL_5J7L_054 NA | |
| IL_5KPX_055 | 1/26/1255:1258, 1/26/1277:1282 | 180 degree turn | homologous IL_5J7L_055 NA | |
| IL_5KPX_056 | 1/26/1259:1263, 1/26/1272:1276 | Double sheared with non-canonical cWW | homologous IL_5J7L_056 NA | |
| IL_5KPX_058 | 1/26/1399:1401, 1/26/1501:1504 | No text annotation | homologous IL_5J7L_058 NA | |
| IL_5KPX_059 | 1/26/1401:1404, 1/26/1497:1501 | No text annotation | geometric IL_4V88_464 NA | |
| IL_5KPX_060 | 1/26/1405:1407, 1/26/1494:1496 | Isolated non-canonical cWW pair | geometric IL_4P3T_006 NA | |
| IL_5KPX_061 | 1/26/1407:1409, 1/26/1491:1494 | Decoding loop related | geometric IL_3C3Z_002 IL_29925.1 | |
| IL_5KPX_062 | 1/26/1412:1414, 1/26/1486:1488 | Isolated non-canonical cWW pair | homologous IL_4LFB_059 IL_01003.1 | |
| IL_5KPX_063 | 1/26/1416:1419, 1/26/1481:1484 | Double sheared | homologous IL_5J7L_062 NA | |
| IL_5KPX_064 | 1/26/1430:1435, 1/26/1466:1470 | Triple sheared related | homologous IL_5J7L_063 NA | |
| IL_5KPX_065 | 1/26/1440:1442, 1/26/1460:1461 | Single bulged A | homologous IL_5J7L_064 NA | |
| IL_5KPX_067 | 1/27/24:30, 1/27/510:516 | Triple sheared with non-canonical cWW | geometric IL_7RQB_001 NA | |
| IL_5KPX_068 | 1/27/36:37, 1/27/442:444 | Single bulged A | homologous IL_5J7L_246 NA | |
| IL_5KPX_069 | 1/27/43:44, 1/27/434:436 | Minor groove platform | homologous IL_5J7L_247 NA | |
| IL_5KPX_070 | 1/27/81:85, 1/27/97:105 | No text annotation | homologous IL_5J7L_248 NA | |
| IL_5KPX_071 | 1/27/183:184, 1/27/212:214 | Single stack bend | homologous IL_4WF9_007 IL_15011.1 | |
| IL_5KPX_072 | 1/27/188:194, 1/27/201:208 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_5J7L_250 NA | |
| IL_5KPX_073 | 1/27/239:245, 1/27/253:258 | 7x6 Sarcin-Ricin; G-bulge | homologous IL_5J7L_251 NA | |
| IL_5KPX_074 | 1/27/269:271, 1/27/366:370 | No text annotation | homologous IL_5J7L_252 NA | |
| IL_5KPX_077 | 1/27/481:484, 1/27/496:509 | No text annotation | homologous IL_5J7L_255 NA | |
| IL_5KPX_079 | 1/27/564:566, 1/27/575:577 | Isolated non-canonical cWW pair | homologous IL_5J7L_257 NA | |
| IL_5KPX_080 | 1/27/606:610, 1/27/618:622 | AAA cross-strand stack | homologous IL_5J7L_258 NA | |
| IL_5KPX_081 | 1/27/672:674, 1/27/806:808 | Isolated non-canonical cWW pair | geometric IL_4LFB_010 IL_01003.1 | |
| IL_5KPX_082 | 1/27/674:678, 1/27/799:806 | tHW-tHW cross-strand stack | homologous IL_5J7L_260 NA | |
| IL_5KPX_083 | 1/27/697:698, 1/27/763:765 | Single bulged A | geometric IL_4V9F_025 IL_14190.1 | |
| IL_5KPX_084 | 1/27/702:703, 1/27/728:730 | Single bulged G | geometric IL_4WF9_023 IL_28408.1 | |
| IL_5KPX_086 | 1/27/738:740, 1/27/757:758 | Major groove platform | homologous IL_5J7L_264 NA | |
| IL_5KPX_087 | 1/27/775:777, 1/27/787:791 | Multiple bulged bases | geometric IL_5J7L_265 NA | |
| IL_5KPX_088 | 1/27/844:847, 1/27/933:934 | 90 degree turn | homologous IL_5J7L_267 NA | |
| IL_5KPX_178 | 1/27/844:848, 1/27/930:934 | No text annotation | homologous IL_5J7L_399 NA | |
| IL_5KPX_089 | 1/27/847:848, 1/27/930:933 | Stack outside cWW | geometric IL_5J7L_268 NA | |
| IL_5KPX_091 | 1/27/856:862, 1/27/915:921 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | homologous IL_5J7L_270 NA | |
| IL_5KPX_092 | 1/27/862:863, 1/27/913:915 | Single bulged G | geometric IL_5J7L_271 NA | |
| IL_5KPX_093 | 1/27/864:868, 1/27/909:912 | C-loop with bulged stacked A's | homologous IL_5J7L_272 NA | |
| IL_5KPX_094 | 1/27/870:872, 1/27/905:907 | Isolated non-canonical cWW pair | homologous IL_5J7L_273 NA | |
| IL_5KPX_095 | 1/27/875:879, 1/27/898:902 | Double sheared with non-canonical cWW | homologous IL_5J7L_274 NA | |
| IL_5KPX_097 | 1/27/994:996, 1/27/1159:1160 | Single bulged C | homologous IL_5J7L_276 NA | |
| IL_5KPX_098 | 1/27/998:1002, 1/27/1153:1157 | UAA/GAN | homologous IL_5J7L_277 NA | |
| IL_5KPX_099 | 1/27/1004:1011, 1/27/1150:1151 | SSU/LSU pseudoknot | geometric IL_5J7L_278 NA | |
| IL_5KPX_100 | 1/27/1011:1013, 1/27/1149:1150 | Single bulged U | homologous IL_5J7L_279 NA | |
| IL_5KPX_101 | 1/27/1018:1024, 1/27/1140:1144 | Kink-turn related | geometric IL_4WF9_039 IL_57188.6 | |
| IL_5KPX_102 | 1/27/1024:1030, 1/27/1124:1140 | No text annotation | geometric IL_5J7L_281 NA | |
| IL_5KPX_103 | 1/27/1031:1034, 1/27/1121:1123 | Isolated non-canonical cWW pair | homologous IL_7RQB_041 NA | |
| IL_5KPX_108 | 1/27/1196:1198, 1/27/1247:1250 | Isolated cWS basepair | homologous IL_5J7L_286 NA | |
| IL_5KPX_109 | 1/27/1202:1206, 1/27/1240:1243 | No text annotation | homologous IL_5J7L_287 NA | |
| IL_5KPX_110 | 1/27/1208:1215, 1/27/1234:1238 | Kink-turn | homologous IL_5J7L_288 NA | |
| IL_5KPX_111 | 1/27/1262:1269, 1/27/2011:2017 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_5J7L_289 NA | |
| IL_5KPX_112 | 1/27/1310:1313, 1/27/1603:1604 | Major groove platform; stack outside cWW | homologous IL_7RQB_050 NA | |
| IL_5KPX_113 | 1/27/1319:1323, 1/27/1331:1333 | C-loop | homologous IL_5J7L_291 NA | |
| IL_5KPX_114 | 1/27/1351:1355, 1/27/1376:1380 | UAA/GAN | homologous IL_5J7L_292 NA | |
| IL_5KPX_115 | 1/27/1357:1361, 1/27/1370:1374 | tSH-tHW-tHS | homologous IL_5J7L_293 NA | |
| IL_5KPX_118 | 1/27/1432:1435, 1/27/1557:1561 | Tandem non-canonical cWW pairs | homologous IL_5J7L_296 NA | |
| IL_5KPX_119 | 1/27/1437:1440, 1/27/1551:1555 | tSH-tHW | homologous IL_5J7L_297 NA | |
| IL_5KPX_120 | 1/27/1468:1471, 1/27/1520:1524 | No text annotation | homologous IL_5J7L_299 NA | |
| IL_5KPX_121 | 1/27/1474:1478, 1/27/1513:1517 | tSH-tHW-tHS | homologous IL_5J7L_300 NA | |
| IL_5KPX_123 | 1/27/1489:1491, 1/27/1499:1500 | Single bulged A | homologous IL_5J7L_302 NA | |
| IL_5KPX_125 | 1/27/1651:1656, 1/27/2004:2006 | No text annotation | homologous IL_5J7L_304 NA | |
| IL_5KPX_126 | 1/27/1663:1665, 1/27/1995:1997 | Isolated tWW turn | homologous IL_4WF9_063 IL_10432.1 | |
| IL_5KPX_127 | 1/27/1666:1669, 1/27/1993:1994 | Major groove platform; stack outside cWW | homologous IL_7A0S_061 IL_74641.1 | |
| IL_5KPX_181 | 1/27/1666:1674, 1/27/1990:1994 | No text annotation | homologous IL_4WF9_117 IL_80252.1 | |
| IL_5KPX_128 | 1/27/1669:1674, 1/27/1990:1993 | Intercalated tWH | geometric IL_4WF9_065 IL_28217.1 | |
| IL_5KPX_129 | 1/27/1686:1691, 1/27/1696:1702 | tSH-tSH-tHH-tHS | geometric IL_7RQB_068 NA | |
| IL_5KPX_130 | 1/27/1712:1718, 1/27/1742:1746 | 6x5 Sarcin-Ricin; G-bulge | homologous IL_5J7L_309 NA | |
| IL_5KPX_133 | 1/27/1770:1771, 1/27/1980:1982 | Single bulged A | homologous IL_7A0S_064 IL_14190.1 | |
| IL_5KPX_134 | 1/27/1798:1804, 1/27/1813:1821 | Kink-turn related | homologous IL_4WF9_069 IL_17069.6 | |
| IL_5KPX_135 | 1/27/1837:1840, 1/27/1902:1903 | Minor groove platform, major groove intercalation | homologous IL_5J7L_314 NA | |
| IL_5KPX_136 | 1/27/1841:1842, 1/27/1898:1901 | Major groove intercalation | homologous IL_5J7L_315 NA | |
| IL_5KPX_182 | 1/27/1851:1860, 1/27/1882:1891 | No text annotation | homologous IL_5J7L_387 NA | |
| IL_5KPX_139 | 1/27/1933:1934, 1/27/1964:1967 | Bulged stacked bases | homologous IL_5J7L_318 NA | |
| IL_5KPX_140 | 1/27/1934:1945, 1/27/1961:1964 | No text annotation | geometric IL_4WF9_077 IL_84014.1 | |
| IL_5KPX_141 | 1/27/2050:2052, 1/27/2617:2618 | Major groove platform | homologous IL_7RQB_078 NA | |
| IL_5KPX_142 | 1/27/2054:2056, 1/27/2612:2615 | No text annotation | homologous IL_5J7L_321 NA | |
| IL_5KPX_143 | 1/27/2067:2069, 1/27/2442:2443 | Single bulged U | homologous IL_7A0S_075 IL_97561.1 | |
| IL_5KPX_144 | 1/27/2070:2071, 1/27/2438:2441 | Minor groove platform | homologous IL_5J7L_324 NA | |
| IL_5KPX_145 | 1/27/2081:2083, 1/27/2236:2239 | Isolated tHS basepair with bulges | homologous IL_5J7L_325 NA | |
| IL_5KPX_146 | 1/27/2085:2087, 1/27/2232:2234 | No text annotation | homologous IL_7RQB_083 NA | |
| IL_5KPX_150 | 1/27/2350:2353, 1/27/2364:2367 | Double sheared | homologous IL_5J7L_333 NA | |
| IL_5KPX_151 | 1/27/2401:2403, 1/27/2414:2415 | No text annotation | ||
| IL_5KPX_152 | 1/27/2453:2454, 1/27/2498:2500 | Single stack bend | geometric IL_4WF9_089 IL_15011.1 | |
| IL_5KPX_153 | 1/27/2454:2455, 1/27/2496:2498 | Major groove platform | homologous IL_7RQB_092 NA | |
| IL_5KPX_155 | 1/27/2459:2461, 1/27/2489:2493 | Major groove minor groove platform with extra cWW | homologous IL_5J7L_337 NA | |
| IL_5KPX_156 | 1/27/2466:2470, 1/27/2480:2484 | Double sheared with non-canonical cWW | homologous IL_5J7L_338 NA | |
| IL_5KPX_157 | 1/27/2507:2508, 1/27/2580:2582 | Major groove platform | homologous IL_4WF9_094 IL_46637.1 | |
| IL_5KPX_158 | 1/27/2510:2512, 1/27/2574:2578 | Isolated non-canonical cWW with bulges | geometric IL_5J7L_340 NA | |
| IL_5KPX_159 | 1/27/2512:2513, 1/27/2571:2574 | No text annotation | homologous IL_5J7L_341 NA | |
| IL_5KPX_160 | 1/27/2522:2523, 1/27/2540:2543 | Major groove platform with intercalation | homologous IL_5J7L_342 NA | |
| IL_5KPX_161 | 1/27/2591:2592, 1/27/2601:2603 | Single bulged A | homologous IL_7RQB_101 NA | |
| IL_5KPX_162 | 1/27/2636:2640, 1/27/2774:2782 | tSH-tHS-tHW | homologous IL_7RQB_102 NA | |
| IL_5KPX_163 | 1/27/2652:2658, 1/27/2663:2668 | Sarcin-Ricin target in LSU H95; G-bulge | homologous IL_7RQB_103 NA | |
| IL_5KPX_164 | 1/27/2680:2684, 1/27/2725:2727 | C-loop | homologous IL_5J7L_347 NA | |
| IL_5KPX_165 | 1/27/2687:2691, 1/27/2718:2722 | UAA/GAN related, with intercalation | homologous IL_5J7L_348 NA | |
| IL_5KPX_166 | 1/27/2695:2696, 1/27/2711:2714 | Multiple bulged bases | homologous IL_5J7L_349 NA | |
| IL_5KPX_167 | 1/27/2737:2742, 1/27/2762:2767 | UAA/GAN with extra cWW | homologous IL_5J7L_350 NA | |
| IL_5KPX_168 | 1/27/2806:2811, 1/27/2889:2892 | No text annotation | homologous IL_5J7L_351 NA | |
| IL_5KPX_169 | 1/27/2838:2839, 1/27/2878:2880 | Major groove intercalation | homologous IL_5J7L_352 NA | |
| IL_5KPX_170 | 1/27/2843:2846, 1/27/2870:2874 | Multiple bulged bases with non-canonical cWW | homologous IL_5J7L_353 NA | |
| IL_5KPX_171 | 1/27/2847:2852, 1/27/2865:2869 | tHS double platform | homologous IL_5J7L_354 NA | |
| IL_5KPX_173 | 1/28/23:28, 1/28/56:60 | No text annotation | homologous IL_5J7L_356 NA | |
| IL_5KPX_175 | 1/28/34:38, 1/28/44:48 | Symmetric double minor groove platform | homologous IL_5J7L_358 NA | |
| IL_5KPX_176 | 1/28/71:79, 1/28/97:105 | Bacterial 5S Loop E | homologous IL_5J7L_359 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_5KPX_004 | Minor groove platform | ||
| IL_5KPX_006 | Minor groove platform with extra cWW | ||
| IL_5KPX_007 | Minor groove platform | ||
| IL_5KPX_008 | No text annotation | ||
| IL_5KPX_010 | Minor groove platform related | ||
| IL_5KPX_011 | Isolated cWH basepair | ||
| IL_5KPX_013 | Minor groove platform | ||
| IL_5KPX_018 | C-loop | ||
| IL_5KPX_021 | No text annotation | ||
| IL_5KPX_023 | No text annotation | ||
| IL_5KPX_028 | Major groove platform | ||
| IL_5KPX_032 | Single stack bend | ||
| IL_5KPX_034 | No text annotation | ||
| IL_5KPX_044 | Single stack bend | ||
| IL_5KPX_048 | Minor groove platform | ||
| IL_5KPX_052 | Minor groove platform | ||
| IL_5KPX_053 | No text annotation | ||
| IL_5KPX_057 | No text annotation | ||
| IL_5KPX_066 | No text annotation | ||
| IL_5KPX_075 | No text annotation | ||
| IL_5KPX_076 | No text annotation | ||
| IL_5KPX_078 | Double sheared | ||
| IL_5KPX_085 | Triple sheared | ||
| IL_5KPX_090 | No text annotation | ||
| IL_5KPX_179 | Single stack bend | ||
| IL_5KPX_096 | No text annotation | ||
| IL_5KPX_104 | Tandem non-canonical cWW pairs | ||
| IL_5KPX_105 | Kink-turn | ||
| IL_5KPX_106 | No text annotation | ||
| IL_5KPX_107 | Major groove platform | ||
| IL_5KPX_180 | No text annotation | ||
| IL_5KPX_116 | No text annotation | ||
| IL_5KPX_117 | UAA/GAN | ||
| IL_5KPX_122 | 180 degree turn | ||
| IL_5KPX_124 | UAA/GAN variation | ||
| IL_5KPX_131 | Triple sheared | ||
| IL_5KPX_132 | Single bulged C | ||
| IL_5KPX_137 | Major groove minor groove platform; mini C-loop | ||
| IL_5KPX_138 | UAA/GAN related | ||
| IL_5KPX_147 | Isolated non-canonical cWW pair | ||
| IL_5KPX_148 | No text annotation | ||
| IL_5KPX_183 | No text annotation | ||
| IL_5KPX_184 | No text annotation | ||
| IL_5KPX_149 | Single bulged U | ||
| IL_5KPX_154 | Major groove platform with extra pair | ||
| IL_5KPX_172 | Major groove intercalation | ||
| IL_5KPX_174 | Major groove minor groove platform; mini C-loop |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_5KPX_001 | 1/26/46:47, 1/26/361:367, 1/26/393:395 | No text annotation | homologous J3_6CZR_015 NA | |
| J3_5KPX_027 | 1/26/46:52, 1/26/359:367, 1/26/393:395 | No text annotation | homologous J3_4LFB_014 J3_63856.1 | |
| J3_5KPX_002 | 1/26/586:588, 1/26/651:654, 1/26/754:755 | No text annotation | geometric J3_5J7L_002 NA | |
| J3_5KPX_028 | 1/26/586:588, 1/26/651:655, 1/26/751:755 | No text annotation | homologous J3_5J7L_051 NA | |
| J3_5KPX_003 | 1/26/672:673, 1/26/717:725, 1/26/732:734 | No text annotation | homologous J3_5J7L_003 NA | |
| J3_5KPX_004 | 1/26/826:829, 1/26/857:861, 1/26/868:874 | No text annotation | homologous J3_5J7L_004 NA | |
| J3_5KPX_005 | 1/26/936:939, 1/26/1344:1350, 1/26/1372:1379 | No text annotation | homologous J3_4LFB_002 J3_85722.1 | |
| J3_5KPX_006 | 1/26/943:946, 1/26/1235:1237, 1/26/1337:1340 | No text annotation | homologous J3_5J7L_005 NA | |
| J3_5KPX_007 | 1/26/955:962, 1/26/973:984, 1/26/1221:1225 | No text annotation | homologous J3_5J7L_006 NA | |
| J3_5KPX_008 | 1/26/990:993, 1/26/1045:1047, 1/26/1210:1215 | No text annotation | homologous J3_4LFB_005 J3_84394.1 | |
| J3_5KPX_029 | 1/26/990:997, 1/26/1044:1047, 1/26/1210:1215 | No text annotation | homologous J3_5J7L_053 NA | |
| J3_5KPX_009 | 1/26/1063:1068, 1/26/1107:1113, 1/26/1187:1193 | No text annotation | homologous J3_5J7L_008 NA | |
| J3_5KPX_037 | 1/26/1073:1074, 1/26/1083:1086, 1/26/1099:1102 | No text annotation | homologous J3_4LFB_017 J3_11018.1 | |
| J3_5KPX_011 | 1/26/1116:1118, 1/26/1155:1158, 1/26/1181:1184 | No text annotation | homologous J3_5J7L_010 NA | |
| J3_5KPX_031 | 1/26/1116:1118, 1/26/1155:1161, 1/26/1175:1184 | No text annotation | homologous J3_5J7L_054 NA | |
| J3_5KPX_012 | 1/26/1237:1241, 1/26/1296:1303, 1/26/1334:1337 | No text annotation | homologous J3_4LFB_009 J3_03192.1 | |
| J3_5KPX_013 | 1/27/30:31, 1/27/474:481, 1/27/509:510 | No text annotation | homologous J3_5J7L_036 NA | |
| J3_5KPX_032 | 1/27/30:31, 1/27/474:484, 1/27/496:510 | No text annotation | homologous J3_5J7L_066 NA | |
| J3_5KPX_033 | 1/27/32:35, 1/27/445:461, 1/27/468:473 | No text annotation | homologous J3_5J7L_067 NA | |
| J3_5KPX_014 | 1/27/56:57, 1/27/70:76, 1/27/110:114 | No text annotation | homologous J3_5J7L_037 NA | |
| J3_5KPX_034 | 1/27/297:301, 1/27/316:325, 1/27/337:341 | No text annotation | homologous J3_5J7L_068 NA | |
| J3_5KPX_015 | 1/27/683:689, 1/27/773:775, 1/27/791:794 | No text annotation | homologous J3_5J7L_038 NA | |
| J3_5KPX_016 | 1/27/698:700, 1/27/732:736, 1/27/760:763 | No text annotation | homologous J3_7RQB_005 NA | |
| J3_5KPX_018 | 1/27/1298:1303, 1/27/1625:1627, 1/27/1639:1642 | No text annotation | homologous J3_5J7L_041 NA | |
| J3_5KPX_019 | 1/27/1306:1309, 1/27/1605:1611, 1/27/1620:1622 | No text annotation | homologous J3_7A0S_007 J3_47341.1 | |
| J3_5KPX_020 | 1/27/1344:1349, 1/27/1382:1385, 1/27/1402:1403 | No text annotation | homologous J3_5J7L_043 NA | |
| J3_5KPX_035 | 1/27/1424:1429, 1/27/1564:1565, 1/27/1568:1574 | No text annotation | homologous J3_5J7L_069 NA | |
| J3_5KPX_036 | 1/27/2282:2284, 1/27/2384:2395, 1/27/2421:2427 | No text annotation | homologous J3_5J7L_070 NA | |
| J3_5KPX_022 | 1/27/2295:2299, 1/27/2317:2323, 1/27/2332:2337 | No text annotation | ||
| J3_5KPX_023 | 1/27/2517:2520, 1/27/2545:2547, 1/27/2561:2567 | No text annotation | homologous J3_5J7L_046 NA | |
| J3_5KPX_024 | 1/27/2789:2791, 1/27/2805:2806, 1/27/2892:2894 | No text annotation | homologous J3_5J7L_047 NA | |
| J3_5KPX_025 | 1/27/2812:2815, 1/27/2831:2836, 1/27/2882:2888 | No text annotation | homologous J3_5J7L_048 NA | |
| J3_5KPX_026 | 1/28/10:16, 1/28/68:70, 1/28/106:110 | No text annotation | homologous J3_5J7L_049 NA | |
| J4_5KPX_001 | 1/26/115:122, 1/26/239:240, 1/26/286:289, 1/26/311:312 | No text annotation | homologous J4_5J7L_001 NA | |
| J4_5KPX_002 | 1/26/142:144, 1/26/178:184, 1/26/193:198, 1/26/219:221 | No text annotation | homologous J4_5J7L_002 NA | |
| J4_5KPX_003 | 1/26/575:577, 1/26/764:769, 1/26/810:821, 1/26/879:880 | No text annotation | homologous J4_5J7L_003 NA | |
| J4_5KPX_004 | 1/27/268:269, 1/27/370:375, 1/27/399:406, 1/27/421:424 | No text annotation | homologous J4_5J7L_018 NA | |
| J4_5KPX_005 | 1/27/601:604, 1/27/624:628, 1/27/635:638, 1/27/650:656 | No text annotation | homologous J4_5J7L_020 NA | |
| J4_5KPX_006 | 1/27/1270:1276, 1/27/1294:1295, 1/27/1645:1648, 1/27/2009:2010 | No text annotation | homologous J4_5J7L_021 NA | |
| J4_5KPX_007 | 1/27/1313:1314, 1/27/1338:1343, 1/27/1404:1405, 1/27/1597:1603 | No text annotation | homologous J4_5J7L_023 NA | |
| J4_5KPX_009 | 1/27/1772:1776, 1/27/1788:1792, 1/27/1827:1830, 1/27/1975:1979 | No text annotation | homologous J4_5J7L_025 NA | |
| J4_5KPX_010 | 1/27/1833:1835, 1/27/1905:1906, 1/27/1924:1933, 1/27/1967:1972 | No text annotation | homologous J4_9DFE_008 J4_42306.1 | |
| J4_5KPX_011 | 1/27/2285:2289, 1/27/2343:2347, 1/27/2370:2372, 1/27/2381:2383 | No text annotation | homologous J4_9DFE_009 J4_98139.1 | |
| J4_5KPX_012 | 1/27/2643:2646, 1/27/2674:2676, 1/27/2731:2735, 1/27/2769:2771 | No text annotation | homologous J4_5J7L_028 NA | |
| J4_5KPX_014 | 1/31/7:10, 1/31/25:27, 1/31/43:49, 1/31/65:66 | tRNA junction | homologous J4_4TUE_004 NA | |
| J5_5KPX_001 | 1/26/36:39, 1/26/403:406, 1/26/436:440, 1/26/497:500, 1/26/545:548 | No text annotation | homologous J5_5J7L_001 NA | |
| J5_5KPX_002 | 1/26/36:39, 1/26/403:406, 1/26/436:442, 1/26/492:500, 1/26/545:548 | No text annotation | homologous J5_5J7L_002 NA | |
| J5_5KPX_003 | 1/26/58:61, 1/26/106:113, 1/26/314:316, 1/26/337:339, 1/26/350:354 | No text annotation | homologous J5_5J7L_003 NA | |
| J5_5KPX_004 | 1/27/47:54, 1/27/116:121, 1/27/130:131, 1/27/148:150, 1/27/176:178 | No text annotation | homologous J5_5J7L_013 NA | |
| J5_5KPX_005 | 1/27/531:533, 1/27/560:564, 1/27/577:579, 1/27/1261:1262, 1/27/2017:2018 | No text annotation | homologous J5_5J7L_014 NA | |
| J5_5KPX_006 | 1/27/584:589, 1/27/668:671, 1/27/809:812, 1/27/1195:1196, 1/27/1250:1256 | No text annotation | homologous J5_5J7L_015 NA | |
| J5_5KPX_007 | 1/27/1674:1682, 1/27/1706:1707, 1/27/1751:1752, 1/27/1756:1764, 1/27/1988:1990 | No text annotation | homologous J5_5J7L_016 NA | |
| J5_5KPX_008 | 1/27/2057:2064, 1/27/2446:2453, 1/27/2500:2507, 1/27/2582:2588, 1/27/2606:2611 | No text annotation | ||
| J5_5KPX_009 | 1/27/2074:2077, 1/27/2243:2246, 1/27/2258:2259, 1/27/2281:2282, 1/27/2427:2435 | No text annotation | homologous J5_7A0S_007 J5_39529.2 | |
| J6_5KPX_001 | 1/27/45:46, 1/27/179:183, 1/27/214:224, 1/27/231:235, 1/27/262:266, 1/27/426:433 | No text annotation | ||
| J6_5KPX_002 | 1/27/2074:2077, 1/27/2243:2246, 1/27/2258:2259, 1/27/2281:2284, 1/27/2384:2395, 1/27/2421:2435 | No text annotation | ||
| J7_5KPX_001 | 1/27/8:15, 1/27/525:531, 1/27/2018:2023, 1/27/2040:2043, 1/27/2625:2630, 1/27/2788:2789, 1/27/2894:2895 | No text annotation | ||
| J7_5KPX_002 | 1/27/817:822, 1/27/835:838, 1/27/940:946, 1/27/971:976, 1/27/987:991, 1/27/1163:1164, 1/27/1185:1190 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_5KPX_010 | No text annotation | ||
| J3_5KPX_030 | No text annotation | ||
| J3_5KPX_017 | No text annotation | ||
| J3_5KPX_021 | Kink-turn 3-way junction | ||
| J4_5KPX_008 | No text annotation | ||
| J4_5KPX_013 | tRNA junction | ||
| J4_5KPX_015 | tRNA junction |
Coloring options: