6WD1 Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6WD1_001 | 1/1/59:68 | No text annotation | homologous HL_5J7L_134 NA | |
| HL_6WD1_002 | 1/1/87:95 | No text annotation | homologous HL_5J7L_135 NA | |
| HL_6WD1_003 | 1/1/123:128 | No text annotation | homologous HL_5J7L_136 NA | |
| HL_6WD1_005 | 1/1/158:168 | No text annotation | homologous HL_5J7L_138 NA | |
| HL_6WD1_006 | 1/1/194:201 | No text annotation | homologous HL_4WF9_006 HL_48677.1 | |
| HL_6WD1_007 | 1/1/225:230 | No text annotation | homologous HL_5J7L_140 NA | |
| HL_6WD1_008 | 1/1/246:252 | No text annotation | homologous HL_5J7L_141 NA | |
| HL_6WD1_009 | 1/1/305:312 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_142 NA | |
| HL_6WD1_010 | 1/1/327:335 | T-loop with unstacked turn | homologous HL_5J7L_144 NA | |
| HL_6WD1_011 | 1/1/382:392 | No text annotation | homologous HL_5J7L_145 NA | |
| HL_6WD1_012 | 1/1/410:417 | Pseudoknot geometry | homologous HL_5J7L_146 NA | |
| HL_6WD1_013 | 1/1/462:467 | GNRA | homologous HL_4WF9_015 HL_34789.1 | |
| HL_6WD1_014 | 1/1/487:493 | GNRA | homologous HL_5J7L_148 NA | |
| HL_6WD1_016 | 1/1/566:575 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_150 NA | |
| HL_6WD1_017 | 1/1/611:617 | No text annotation | homologous HL_5J7L_151 NA | |
| HL_6WD1_018 | 1/1/629:634 | GNRA | homologous HL_5J7L_152 NA | |
| HL_6WD1_019 | 1/1/641:647 | No text annotation | homologous HL_5J7L_153 NA | |
| HL_6WD1_021 | 1/1/744:753 | No text annotation | homologous HL_4WF9_023 HL_50204.1 | |
| HL_6WD1_105 | 1/1/779:785 | UNCG variation | homologous HL_7A0S_023 HL_51020.1 | |
| HL_6WD1_023 | 1/1/826:831 | No text annotation | homologous HL_4WF9_025 HL_27530.1 | |
| HL_6WD1_025 | 1/1/955:962 | GNRA | homologous HL_7RQB_027 NA | |
| HL_6WD1_026 | 1/1/978:985 | No text annotation | homologous HL_7A0S_027 HL_47171.1 | |
| HL_6WD1_030 | 1/1/1222:1227 | GNRA | homologous HL_5J7L_164 NA | |
| HL_6WD1_031 | 1/1/1281:1289 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_165 NA | |
| HL_6WD1_032 | 1/1/1324:1330 | Pseudoknot geometry with 3' bulge | homologous HL_5J7L_166 NA | |
| HL_6WD1_033 | 1/1/1363:1368 | GNRA | homologous HL_5J7L_167 NA | |
| HL_6WD1_034 | 1/1/1389:1398 | No text annotation | homologous HL_5J7L_168 NA | |
| HL_6WD1_035 | 1/1/1450:1461 | UNCG variation | geometric HL_5J7L_200 NA | |
| HL_6WD1_036 | 1/1/1492:1498 | Pseudoknot geometry with 3' bulge | homologous HL_5J7L_170 NA | |
| HL_6WD1_038 | 1/1/1565:1568 | No text annotation | homologous HL_7RQB_039 NA | |
| HL_6WD1_039 | 1/1/1612:1619 | No text annotation | homologous HL_4WF9_038 HL_28592.1 | |
| HL_6WD1_040 | 1/1/1630:1636 | GNRA | homologous HL_5J7L_174 NA | |
| HL_6WD1_041 | 1/1/1691:1696 | No text annotation | homologous HL_7RQB_042 NA | |
| HL_6WD1_106 | 1/1/1727:1733 | No text annotation | homologous HL_5J7L_214 NA | |
| HL_6WD1_043 | 1/1/1752:1756 | No text annotation | homologous HL_5J7L_177 NA | |
| HL_6WD1_044 | 1/1/1777:1787 | No text annotation | homologous HL_5J7L_178 NA | |
| HL_6WD1_045 | 1/1/1806:1811 | GNRA related | homologous HL_5J7L_179 NA | |
| HL_6WD1_048 | 1/1/1949:1957 | No text annotation | homologous HL_4WF9_046 HL_61418.1 | |
| HL_6WD1_049 | 1/1/2027:2036 | No text annotation | homologous HL_4WF9_047 HL_78372.1 | |
| HL_6WD1_051 | 1/1/2209:2215 | No text annotation | homologous HL_5J7L_185 NA | |
| HL_6WD1_052 | 1/1/2248:2256 | No text annotation | homologous HL_7RQB_053 NA | |
| HL_6WD1_053 | 1/1/2264:2276 | No text annotation | homologous HL_5J7L_187 NA | |
| HL_6WD1_055 | 1/1/2324:2331 | Pseudoknot geometry | homologous HL_5J7L_189 NA | |
| HL_6WD1_056 | 1/1/2356:2361 | GNRA | homologous HL_5J7L_190 NA | |
| HL_6WD1_057 | 1/1/2374:2379 | GNRA | homologous HL_4WF9_054 HL_34789.1 | |
| HL_6WD1_058 | 1/1/2404:2413 | No text annotation | homologous HL_5J7L_192 NA | |
| HL_6WD1_059 | 1/1/2471:2479 | No text annotation | homologous HL_4WF9_056 HL_52011.1 | |
| HL_6WD1_060 | 1/1/2528:2535 | GNRA variation | homologous HL_5J7L_194 NA | |
| HL_6WD1_061 | 1/1/2551:2557 | No text annotation | homologous HL_5J7L_195 NA | |
| HL_6WD1_062 | 1/1/2594:2599 | GNRA | homologous HL_5J7L_196 NA | |
| HL_6WD1_063 | 1/1/2658:2663 | GNRA | geometric HL_5Y7M_002 HL_34789.1 | |
| HL_6WD1_064 | 1/1/2701:2706 | Ribsomal LSU H95 | homologous HL_5J7L_198 NA | |
| HL_6WD1_065 | 1/1/2745:2759 | No text annotation | homologous HL_4WF9_062 HL_53269.1 | |
| HL_6WD1_067 | 1/1/2819:2827 | No text annotation | homologous HL_5J7L_201 NA | |
| HL_6WD1_068 | 1/1/2856:2861 | GNRA | homologous HL_7A0S_068 HL_34789.1 | |
| HL_6WD1_069 | 1/2/34:48 | No text annotation | homologous HL_5J7L_215 NA | |
| HL_6WD1_070 | 1/2/86:90 | Mini UNCG | homologous HL_5J7L_204 NA | |
| HL_6WD1_071 | 1/3/12:22 | No text annotation | homologous HL_5J7L_001 NA | |
| HL_6WD1_078 | 1/3/320:333 | No text annotation | homologous HL_4LFB_008 HL_39665.1 | |
| HL_6WD1_085 | 1/3/689:698 | No text annotation | homologous HL_4LFB_015 HL_38491.1 | |
| HL_6WD1_086 | 1/3/726:731 | GNRA | homologous HL_4LFB_016 HL_34789.1 | |
| HL_6WD1_087 | 1/3/786:796 | No text annotation | homologous HL_4LFB_017 HL_38491.1 | |
| HL_6WD1_089 | 1/3/862:867 | GNRA | homologous HL_5J7L_019 NA | |
| HL_6WD1_090 | 1/3/897:902 | GNRA | homologous HL_4LFB_020 HL_34789.1 | |
| HL_6WD1_093 | 1/3/1076:1081 | GNRA | homologous HL_5J7L_023 NA | |
| HL_6WD1_101 | 1/3/1515:1520 | GNRA | homologous HL_6CZR_103 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6WD1_004 | No text annotation | ||
| HL_6WD1_015 | Mini UNCG with extended bulge | ||
| HL_6WD1_020 | GNRA wlth tandem sheared | ||
| HL_6WD1_022 | No text annotation | ||
| HL_6WD1_024 | No text annotation | ||
| HL_6WD1_027 | No text annotation | ||
| HL_6WD1_028 | No text annotation | ||
| HL_6WD1_029 | No text annotation | ||
| HL_6WD1_037 | UNCG | ||
| HL_6WD1_042 | No text annotation | ||
| HL_6WD1_046 | GNRA variation | ||
| HL_6WD1_047 | No text annotation | ||
| HL_6WD1_050 | No text annotation | ||
| HL_6WD1_054 | No text annotation | ||
| HL_6WD1_066 | UNCG variation | ||
| HL_6WD1_072 | No text annotation | ||
| HL_6WD1_073 | GNRA | ||
| HL_6WD1_074 | GNRA | ||
| HL_6WD1_075 | No text annotation | ||
| HL_6WD1_076 | GNRA related | ||
| HL_6WD1_077 | GNRA | ||
| HL_6WD1_079 | UNCG | ||
| HL_6WD1_080 | GNRA | ||
| HL_6WD1_081 | UNCG | ||
| HL_6WD1_082 | GNRA wlth extra near cWW | ||
| HL_6WD1_083 | No text annotation | ||
| HL_6WD1_084 | GNRA-like with tWH | ||
| HL_6WD1_088 | No text annotation | ||
| HL_6WD1_091 | No text annotation | ||
| HL_6WD1_092 | GNRA | ||
| HL_6WD1_094 | T-loop related | ||
| HL_6WD1_095 | No text annotation | ||
| HL_6WD1_096 | GNRA | ||
| HL_6WD1_097 | GNRA | ||
| HL_6WD1_098 | T-loop with 3 stacked bulged bases | ||
| HL_6WD1_099 | No text annotation | ||
| HL_6WD1_100 | UNCG | ||
| HL_6WD1_102 | tRNA D-loop | ||
| HL_6WD1_103 | tRNA anticodon loop | ||
| HL_6WD1_104 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6WD1_001 | 1/1/24:30, 1/1/510:516 | Triple sheared with non-canonical cWW | geometric IL_4WF9_001 IL_22311.1 | |
| IL_6WD1_002 | 1/1/36:37, 1/1/442:444 | Single bulged A | homologous IL_7RQB_002 NA | |
| IL_6WD1_003 | 1/1/43:44, 1/1/434:436 | Minor groove platform | homologous IL_5J7L_247 NA | |
| IL_6WD1_004 | 1/1/81:85, 1/1/97:105 | No text annotation | homologous IL_5J7L_248 NA | |
| IL_6WD1_005 | 1/1/183:184, 1/1/212:214 | Single stack bend | homologous IL_5J7L_249 NA | |
| IL_6WD1_006 | 1/1/188:194, 1/1/201:208 | 8x7 Sarcin-Ricin; G-bulge | geometric IL_5J7L_250 NA | |
| IL_6WD1_007 | 1/1/239:245, 1/1/253:258 | 7x6 Sarcin-Ricin; G-bulge | homologous IL_5J7L_251 NA | |
| IL_6WD1_008 | 1/1/269:271, 1/1/366:370 | No text annotation | homologous IL_5J7L_252 NA | |
| IL_6WD1_010 | 1/1/293:295, 1/1/343:347 | No text annotation | homologous IL_5J7L_254 NA | |
| IL_6WD1_011 | 1/1/481:484, 1/1/496:509 | No text annotation | geometric IL_5J7L_255 NA | |
| IL_6WD1_012 | 1/1/536:539, 1/1/554:557 | Double sheared | homologous IL_5J7L_256 NA | |
| IL_6WD1_013 | 1/1/564:566, 1/1/575:577 | Isolated non-canonical cWW pair | geometric IL_5J7L_257 NA | |
| IL_6WD1_014 | 1/1/606:610, 1/1/618:622 | AAA cross-strand stack | homologous IL_5J7L_258 NA | |
| IL_6WD1_015 | 1/1/672:674, 1/1/806:808 | Isolated non-canonical cWW pair | homologous IL_5J7L_259 NA | |
| IL_6WD1_016 | 1/1/674:678, 1/1/799:806 | tHW-tHW cross-strand stack | geometric IL_5J7L_260 NA | |
| IL_6WD1_017 | 1/1/697:698, 1/1/763:765 | Single bulged A | geometric IL_5J7L_261 NA | |
| IL_6WD1_018 | 1/1/702:703, 1/1/728:730 | Single bulged G | homologous IL_5J7L_262 NA | |
| IL_6WD1_019 | 1/1/703:707, 1/1/724:728 | Triple sheared | geometric IL_4WF9_024 IL_15190.1 | |
| IL_6WD1_020 | 1/1/738:740, 1/1/757:758 | Major groove platform | homologous IL_5J7L_264 NA | |
| IL_6WD1_021 | 1/1/775:777, 1/1/787:791 | Multiple bulged bases | geometric IL_4V9F_030 IL_57881.1 | |
| IL_6WD1_022 | 1/1/844:847, 1/1/933:934 | 90 degree turn | geometric IL_5J7L_267 NA | |
| IL_6WD1_176 | 1/1/844:848, 1/1/930:934 | No text annotation | homologous IL_5J7L_399 NA | |
| IL_6WD1_023 | 1/1/847:848, 1/1/930:933 | Stack outside cWW | homologous IL_5J7L_268 NA | |
| IL_6WD1_024 | 1/1/850:851, 1/1/926:928 | Single stack bend | homologous IL_5J7L_269 NA | |
| IL_6WD1_025 | 1/1/856:862, 1/1/915:921 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | homologous IL_5J7L_270 NA | |
| IL_6WD1_026 | 1/1/862:863, 1/1/913:915 | Single bulged G | geometric IL_5J7L_271 NA | |
| IL_6WD1_027 | 1/1/864:868, 1/1/909:912 | C-loop with bulged stacked A's | homologous IL_5J7L_272 NA | |
| IL_6WD1_028 | 1/1/870:872, 1/1/905:907 | Isolated non-canonical cWW pair | homologous IL_5J7L_273 NA | |
| IL_6WD1_031 | 1/1/994:996, 1/1/1159:1160 | Single bulged C | homologous IL_7RQB_035 NA | |
| IL_6WD1_032 | 1/1/998:1002, 1/1/1153:1157 | UAA/GAN | homologous IL_4WF9_036 IL_08938.1 | |
| IL_6WD1_033 | 1/1/1004:1011, 1/1/1150:1151 | SSU/LSU pseudoknot | homologous IL_5J7L_278 NA | |
| IL_6WD1_034 | 1/1/1011:1013, 1/1/1149:1150 | Single bulged U | geometric IL_5J7L_279 NA | |
| IL_6WD1_035 | 1/1/1018:1024, 1/1/1140:1144 | Kink-turn related | geometric IL_5J7L_280 NA | |
| IL_6WD1_036 | 1/1/1024:1030, 1/1/1124:1140 | No text annotation | geometric IL_5J7L_281 NA | |
| IL_6WD1_037 | 1/1/1031:1034, 1/1/1121:1123 | Isolated non-canonical cWW pair | homologous IL_7RQB_041 NA | |
| IL_6WD1_042 | 1/1/1196:1198, 1/1/1247:1250 | Isolated cWS basepair | homologous IL_4WF9_044 IL_42997.4 | |
| IL_6WD1_043 | 1/1/1202:1206, 1/1/1240:1243 | No text annotation | homologous IL_5J7L_287 NA | |
| IL_6WD1_044 | 1/1/1208:1215, 1/1/1234:1238 | Kink-turn | homologous IL_7RQB_047 NA | |
| IL_6WD1_045 | 1/1/1262:1269, 1/1/2011:2017 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_5J7L_289 NA | |
| IL_6WD1_046 | 1/1/1310:1313, 1/1/1603:1604 | Major groove platform; stack outside cWW | homologous IL_7RQB_050 NA | |
| IL_6WD1_047 | 1/1/1319:1323, 1/1/1331:1333 | C-loop | homologous IL_5J7L_291 NA | |
| IL_6WD1_048 | 1/1/1351:1355, 1/1/1376:1380 | UAA/GAN | homologous IL_5J7L_292 NA | |
| IL_6WD1_049 | 1/1/1357:1361, 1/1/1370:1374 | tSH-tHW-tHS | homologous IL_5J7L_293 NA | |
| IL_6WD1_051 | 1/1/1417:1421, 1/1/1577:1581 | UAA/GAN | homologous IL_5J7L_295 NA | |
| IL_6WD1_052 | 1/1/1432:1435, 1/1/1557:1561 | Tandem non-canonical cWW pairs | homologous IL_5J7L_296 NA | |
| IL_6WD1_053 | 1/1/1437:1440, 1/1/1551:1555 | tSH-tHW | homologous IL_5J7L_297 NA | |
| IL_6WD1_054 | 1/1/1468:1471, 1/1/1520:1524 | No text annotation | homologous IL_5J7L_299 NA | |
| IL_6WD1_055 | 1/1/1474:1478, 1/1/1513:1517 | tSH-tHW-tHS | homologous IL_5J7L_300 NA | |
| IL_6WD1_056 | 1/1/1481:1482, 1/1/1507:1510 | 180 degree turn | homologous IL_5J7L_301 NA | |
| IL_6WD1_057 | 1/1/1489:1491, 1/1/1499:1500 | Single bulged A | homologous IL_7RQB_062 NA | |
| IL_6WD1_058 | 1/1/1526:1529, 1/1/1542:1546 | UAA/GAN variation | homologous IL_5J7L_303 NA | |
| IL_6WD1_059 | 1/1/1651:1656, 1/1/2004:2006 | No text annotation | homologous IL_5J7L_304 NA | |
| IL_6WD1_060 | 1/1/1663:1665, 1/1/1995:1997 | Isolated tWW turn | homologous IL_4WF9_063 IL_10432.1 | |
| IL_6WD1_061 | 1/1/1666:1669, 1/1/1993:1994 | Major groove platform; stack outside cWW | homologous IL_7RQB_066 NA | |
| IL_6WD1_178 | 1/1/1666:1674, 1/1/1990:1994 | No text annotation | homologous IL_5J7L_386 NA | |
| IL_6WD1_062 | 1/1/1669:1674, 1/1/1990:1993 | Intercalated tWH | geometric IL_5J7L_307 NA | |
| IL_6WD1_063 | 1/1/1686:1691, 1/1/1696:1702 | tSH-tSH-tHH-tHS | geometric IL_7RQB_068 NA | |
| IL_6WD1_064 | 1/1/1712:1718, 1/1/1742:1746 | 6x5 Sarcin-Ricin; G-bulge | homologous IL_5J7L_309 NA | |
| IL_6WD1_065 | 1/1/1720:1724, 1/1/1736:1740 | Triple sheared | homologous IL_5J7L_310 NA | |
| IL_6WD1_066 | 1/1/1727:1728, 1/1/1731:1733 | Single bulged C | geometric IL_5J7L_311 NA | |
| IL_6WD1_067 | 1/1/1770:1771, 1/1/1980:1982 | Single bulged A | homologous IL_5J7L_312 NA | |
| IL_6WD1_068 | 1/1/1798:1804, 1/1/1813:1821 | Kink-turn related | homologous IL_5J7L_313 NA | |
| IL_6WD1_069 | 1/1/1837:1840, 1/1/1902:1903 | Minor groove platform, major groove intercalation | homologous IL_5J7L_314 NA | |
| IL_6WD1_070 | 1/1/1841:1842, 1/1/1898:1901 | Major groove intercalation | homologous IL_5J7L_315 NA | |
| IL_6WD1_071 | 1/1/1846:1849, 1/1/1893:1894 | Major groove minor groove platform; mini C-loop | homologous IL_5J7L_316 NA | |
| IL_6WD1_179 | 1/1/1851:1860, 1/1/1882:1891 | No text annotation | homologous IL_5J7L_387 NA | |
| IL_6WD1_072 | 1/1/1864:1867, 1/1/1874:1878 | UAA/GAN related | homologous IL_5J7L_317 NA | |
| IL_6WD1_073 | 1/1/1933:1934, 1/1/1964:1967 | Bulged stacked bases | geometric IL_4WF9_076 IL_24886.1 | |
| IL_6WD1_074 | 1/1/1934:1945, 1/1/1961:1964 | No text annotation | homologous IL_7A0S_072 IL_04332.3 | |
| IL_6WD1_075 | 1/1/2050:2052, 1/1/2617:2618 | Major groove platform | homologous IL_5J7L_320 NA | |
| IL_6WD1_076 | 1/1/2054:2056, 1/1/2612:2615 | No text annotation | homologous IL_5J7L_321 NA | |
| IL_6WD1_077 | 1/1/2067:2069, 1/1/2442:2443 | Single bulged U | homologous IL_4WF9_080 IL_97561.1 | |
| IL_6WD1_078 | 1/1/2070:2071, 1/1/2438:2441 | Minor groove platform | homologous IL_5J7L_324 NA | |
| IL_6WD1_079 | 1/1/2081:2083, 1/1/2236:2239 | Isolated tHS basepair with bulges | homologous IL_5J7L_325 NA | |
| IL_6WD1_080 | 1/1/2085:2087, 1/1/2232:2234 | Isolated non-canonical cWW pair | homologous IL_5J7L_326 NA | |
| IL_6WD1_083 | 1/1/2202:2204, 1/1/2220:2221 | Single bulged U | homologous IL_5J7L_331 NA | |
| IL_6WD1_084 | 1/1/2350:2353, 1/1/2364:2367 | Double sheared | homologous IL_5J7L_333 NA | |
| IL_6WD1_085 | 1/1/2401:2403, 1/1/2414:2415 | No text annotation | ||
| IL_6WD1_086 | 1/1/2453:2454, 1/1/2498:2500 | Single stack bend | geometric IL_4WF9_089 IL_15011.1 | |
| IL_6WD1_087 | 1/1/2454:2455, 1/1/2496:2498 | Major groove platform | homologous IL_7RQB_092 NA | |
| IL_6WD1_088 | 1/1/2457:2459, 1/1/2493:2494 | Major groove platform | geometric IL_7A0S_085 IL_48076.7 | |
| IL_6WD1_090 | 1/1/2466:2470, 1/1/2480:2484 | Double sheared with non-canonical cWW | homologous IL_5J7L_338 NA | |
| IL_6WD1_091 | 1/1/2507:2508, 1/1/2580:2582 | Major groove platform | homologous IL_4WF9_094 IL_46637.1 | |
| IL_6WD1_092 | 1/1/2510:2512, 1/1/2574:2578 | Isolated non-canonical cWW with bulges | homologous IL_7RQB_097 NA | |
| IL_6WD1_093 | 1/1/2512:2513, 1/1/2571:2574 | No text annotation | geometric IL_5J7L_341 NA | |
| IL_6WD1_094 | 1/1/2522:2523, 1/1/2540:2543 | Major groove platform with intercalation | homologous IL_5J7L_342 NA | |
| IL_6WD1_095 | 1/1/2591:2592, 1/1/2601:2603 | Single bulged A | homologous IL_7RQB_101 NA | |
| IL_6WD1_096 | 1/1/2636:2640, 1/1/2774:2782 | tSH-tHS-tHW | homologous IL_5J7L_345 NA | |
| IL_6WD1_097 | 1/1/2652:2658, 1/1/2663:2668 | Sarcin-Ricin target in LSU H95; G-bulge | homologous IL_7RQB_103 NA | |
| IL_6WD1_098 | 1/1/2680:2684, 1/1/2725:2727 | C-loop | homologous IL_5J7L_347 NA | |
| IL_6WD1_099 | 1/1/2687:2691, 1/1/2718:2722 | UAA/GAN related, with intercalation | homologous IL_5J7L_348 NA | |
| IL_6WD1_100 | 1/1/2695:2696, 1/1/2711:2714 | Multiple bulged bases | homologous IL_4WF9_103 IL_44609.1 | |
| IL_6WD1_101 | 1/1/2737:2742, 1/1/2762:2767 | UAA/GAN with extra cWW | homologous IL_5J7L_350 NA | |
| IL_6WD1_102 | 1/1/2806:2811, 1/1/2889:2892 | No text annotation | geometric IL_5J7L_351 NA | |
| IL_6WD1_103 | 1/1/2838:2839, 1/1/2878:2880 | Major groove intercalation | homologous IL_5J7L_352 NA | |
| IL_6WD1_104 | 1/1/2843:2846, 1/1/2870:2874 | Multiple bulged bases with non-canonical cWW | homologous IL_5J7L_353 NA | |
| IL_6WD1_105 | 1/1/2847:2852, 1/1/2865:2869 | tHS double platform | homologous IL_7RQB_110 NA | |
| IL_6WD1_107 | 1/2/23:28, 1/2/56:60 | No text annotation | homologous IL_5J7L_356 NA | |
| IL_6WD1_109 | 1/2/71:79, 1/2/97:105 | Bacterial 5S Loop E | homologous IL_5J7L_359 NA | |
| IL_6WD1_110 | 1/3/30:32, 1/3/552:553 | Single bulged G | homologous IL_6CZR_113 NA | |
| IL_6WD1_112 | 1/3/47:52, 1/3/359:361 | No text annotation | homologous IL_5J7L_003 NA | |
| IL_6WD1_118 | 1/3/128:131, 1/3/231:233 | Isolated non-canonical cWW pair | homologous IL_5J7L_009 NA | |
| IL_6WD1_123 | 1/3/242:247, 1/3/277:284 | Kink-turn with non-sequential stacking | homologous IL_5J7L_014 NA | |
| IL_6WD1_135 | 1/3/569:575, 1/3/880:881 | No text annotation | homologous IL_4LFB_022 IL_20847.1 | |
| IL_6WD1_136 | 1/3/580:584, 1/3/757:761 | tSH-tHW-tHS | homologous IL_5J7L_027 NA | |
| IL_6WD1_139 | 1/3/605:612, 1/3/628:633 | No text annotation | homologous IL_5J7L_030 NA | |
| IL_6WD1_142 | 1/3/662:666, 1/3/740:743 | Tandem non-canonical cWW pairs | homologous IL_5J7L_033 NA | |
| IL_6WD1_183 | 1/3/673:677, 1/3/713:717 | Triple non-canonical cWW pairs | homologous IL_5J7L_361 NA | |
| IL_6WD1_145 | 1/3/774:778, 1/3/804:805 | Left turn | homologous IL_4LFB_032 IL_29346.3 | |
| IL_6WD1_146 | 1/3/779:783, 1/3/799:803 | tSH-tHW-tHS | homologous IL_4LFB_033 IL_05821.1 | |
| IL_6WD1_147 | 1/3/887:894, 1/3/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_5J7L_038 NA | |
| IL_6WD1_167 | 1/3/1399:1401, 1/3/1501:1504 | No text annotation | homologous IL_6CZR_165 NA | |
| IL_6WD1_168 | 1/3/1401:1404, 1/3/1497:1501 | No text annotation | geometric IL_4V88_464 NA | |
| IL_6WD1_172 | 1/3/1416:1419, 1/3/1481:1484 | Double sheared | homologous IL_6CZR_169 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6WD1_187 | No text annotation | ||
| IL_6WD1_009 | No text annotation | ||
| IL_6WD1_029 | Double sheared with non-canonical cWW | ||
| IL_6WD1_030 | No text annotation | ||
| IL_6WD1_038 | Tandem non-canonical cWW pairs | ||
| IL_6WD1_039 | Kink-turn | ||
| IL_6WD1_040 | No text annotation | ||
| IL_6WD1_041 | No text annotation | ||
| IL_6WD1_050 | No text annotation | ||
| IL_6WD1_177 | Isolated non-canonical cWW pair | ||
| IL_6WD1_180 | Other IL | ||
| IL_6WD1_081 | Isolated non-canonical cWW pair | ||
| IL_6WD1_082 | No text annotation | ||
| IL_6WD1_181 | No text annotation | ||
| IL_6WD1_182 | No text annotation | ||
| IL_6WD1_089 | Major groove minor groove platform with extra cWW | ||
| IL_6WD1_106 | Major groove intercalation | ||
| IL_6WD1_108 | Major groove minor groove platform; mini C-loop | ||
| IL_6WD1_111 | Single bulged A | ||
| IL_6WD1_113 | Minor groove platform | ||
| IL_6WD1_114 | Multiple bulged bases | ||
| IL_6WD1_115 | Minor groove platform with extra cWW | ||
| IL_6WD1_116 | Minor groove platform | ||
| IL_6WD1_188 | Single bulged G | ||
| IL_6WD1_117 | No text annotation | ||
| IL_6WD1_119 | Minor groove platform related | ||
| IL_6WD1_120 | Isolated cWH basepair | ||
| IL_6WD1_121 | tWH-tWH-tHW-tHW | ||
| IL_6WD1_122 | Minor groove platform | ||
| IL_6WD1_124 | No text annotation | ||
| IL_6WD1_125 | C-loop | ||
| IL_6WD1_126 | Single bulged U | ||
| IL_6WD1_127 | C-loop | ||
| IL_6WD1_128 | Single bulged G | ||
| IL_6WD1_129 | No text annotation | ||
| IL_6WD1_130 | No text annotation | ||
| IL_6WD1_131 | tSH-tHW-tWW | ||
| IL_6WD1_132 | No text annotation | ||
| IL_6WD1_133 | SSU/LSU pseudoknot | ||
| IL_6WD1_134 | Kink-turn related | ||
| IL_6WD1_137 | Major groove platform | ||
| IL_6WD1_138 | Major groove minor groove platform; mini C-loop | ||
| IL_6WD1_140 | Major groove platform; stack outside cWW | ||
| IL_6WD1_141 | Single stack bend | ||
| IL_6WD1_143 | No text annotation | ||
| IL_6WD1_144 | Kink-turn | ||
| IL_6WD1_148 | Single bulged A | ||
| IL_6WD1_149 | Single bulged G | ||
| IL_6WD1_150 | Minor groove platform | ||
| IL_6WD1_151 | No text annotation | ||
| IL_6WD1_152 | Minor groove platform | ||
| IL_6WD1_153 | Single stack bend | ||
| IL_6WD1_154 | No text annotation | ||
| IL_6WD1_155 | Single bulged U | ||
| IL_6WD1_156 | Tandem non-canonical cWW pairs | ||
| IL_6WD1_184 | No text annotation | ||
| IL_6WD1_157 | Minor groove platform | ||
| IL_6WD1_158 | Single bulged A | ||
| IL_6WD1_159 | Isolated non-canonical cWW pair | ||
| IL_6WD1_160 | No text annotation | ||
| IL_6WD1_161 | Minor groove platform | ||
| IL_6WD1_162 | No text annotation | ||
| IL_6WD1_163 | No text annotation | ||
| IL_6WD1_185 | No text annotation | ||
| IL_6WD1_164 | 180 degree turn | ||
| IL_6WD1_165 | Double sheared with non-canonical cWW | ||
| IL_6WD1_166 | No text annotation | ||
| IL_6WD1_169 | Isolated non-canonical cWW pair | ||
| IL_6WD1_170 | Decoding loop related | ||
| IL_6WD1_186 | Isolated non-canonical cWW pair | ||
| IL_6WD1_171 | Tandem non-canonical cWW pairs | ||
| IL_6WD1_173 | Triple sheared related | ||
| IL_6WD1_174 | Single bulged A | ||
| IL_6WD1_175 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6WD1_001 | 1/1/30:31, 1/1/474:481, 1/1/509:510 | No text annotation | homologous J3_7RQB_001 NA | |
| J3_6WD1_027 | 1/1/30:31, 1/1/474:484, 1/1/496:510 | No text annotation | homologous J3_5J7L_066 NA | |
| J3_6WD1_028 | 1/1/32:35, 1/1/445:461, 1/1/468:473 | No text annotation | homologous J3_5J7L_067 NA | |
| J3_6WD1_002 | 1/1/56:57, 1/1/70:76, 1/1/110:114 | No text annotation | homologous J3_5J7L_037 NA | |
| J3_6WD1_036 | 1/1/297:301, 1/1/316:325, 1/1/337:341 | No text annotation | homologous J3_5J7L_068 NA | |
| J3_6WD1_003 | 1/1/683:689, 1/1/773:775, 1/1/791:794 | No text annotation | homologous J3_5J7L_038 NA | |
| J3_6WD1_004 | 1/1/698:700, 1/1/732:736, 1/1/760:763 | No text annotation | homologous J3_7RQB_005 NA | |
| J3_6WD1_006 | 1/1/1298:1303, 1/1/1625:1627, 1/1/1639:1642 | No text annotation | homologous J3_5J7L_041 NA | |
| J3_6WD1_007 | 1/1/1306:1309, 1/1/1605:1611, 1/1/1620:1622 | No text annotation | homologous J3_7A0S_007 J3_47341.1 | |
| J3_6WD1_008 | 1/1/1344:1349, 1/1/1382:1385, 1/1/1402:1403 | No text annotation | homologous J3_5J7L_043 NA | |
| J3_6WD1_030 | 1/1/1424:1429, 1/1/1564:1565, 1/1/1568:1574 | No text annotation | homologous J3_5J7L_069 NA | |
| J3_6WD1_009 | 1/1/2091:2093, 1/1/2196:2200, 1/1/2223:2228 | Kink-turn 3-way junction | homologous J3_5J7L_044 NA | |
| J3_6WD1_031 | 1/1/2282:2284, 1/1/2384:2395, 1/1/2421:2427 | No text annotation | homologous J3_5J7L_070 NA | |
| J3_6WD1_010 | 1/1/2295:2299, 1/1/2317:2323, 1/1/2332:2337 | No text annotation | ||
| J3_6WD1_011 | 1/1/2517:2520, 1/1/2545:2547, 1/1/2561:2567 | No text annotation | homologous J3_5J7L_046 NA | |
| J3_6WD1_013 | 1/1/2812:2815, 1/1/2831:2836, 1/1/2882:2888 | No text annotation | homologous J3_5J7L_048 NA | |
| J3_6WD1_014 | 1/2/10:16, 1/2/68:70, 1/2/106:110 | No text annotation | homologous J3_5J7L_049 NA | |
| J3_6WD1_032 | 1/3/46:52, 1/3/359:367, 1/3/393:395 | No text annotation | homologous J3_5J7L_050 NA | |
| J3_6WD1_017 | 1/3/672:673, 1/3/717:725, 1/3/732:734 | No text annotation | homologous J3_5J7L_003 NA | |
| J3_6WD1_018 | 1/3/826:829, 1/3/857:861, 1/3/868:874 | No text annotation | homologous J3_5J7L_004 NA | |
| J3_6WD1_037 | 1/3/1073:1074, 1/3/1083:1086, 1/3/1099:1102 | No text annotation | homologous J3_4LFB_017 J3_11018.1 | |
| J4_6WD1_001 | 1/1/268:269, 1/1/370:375, 1/1/399:406, 1/1/421:424 | No text annotation | homologous J4_5J7L_018 NA | |
| J4_6WD1_002 | 1/1/601:604, 1/1/624:628, 1/1/635:638, 1/1/650:656 | No text annotation | homologous J4_5J7L_020 NA | |
| J4_6WD1_003 | 1/1/1270:1276, 1/1/1294:1295, 1/1/1645:1648, 1/1/2009:2010 | No text annotation | homologous J4_5J7L_021 NA | |
| J4_6WD1_004 | 1/1/1310:1314, 1/1/1338:1343, 1/1/1404:1405, 1/1/1597:1604 | No text annotation | homologous J4_5J7L_022 NA | |
| J4_6WD1_005 | 1/1/1313:1314, 1/1/1338:1343, 1/1/1404:1405, 1/1/1597:1603 | No text annotation | homologous J4_5J7L_023 NA | |
| J4_6WD1_006 | 1/1/1444:1445, 1/1/1466:1467, 1/1/1525:1526, 1/1/1546:1547 | No text annotation | homologous J4_5J7L_024 NA | |
| J4_6WD1_007 | 1/1/1772:1776, 1/1/1788:1792, 1/1/1827:1830, 1/1/1975:1979 | No text annotation | homologous J4_5J7L_025 NA | |
| J4_6WD1_008 | 1/1/1833:1835, 1/1/1905:1906, 1/1/1924:1933, 1/1/1967:1972 | No text annotation | homologous J4_5J7L_026 NA | |
| J4_6WD1_009 | 1/1/2285:2289, 1/1/2343:2347, 1/1/2370:2372, 1/1/2381:2383 | No text annotation | homologous J4_9DFE_009 J4_98139.1 | |
| J4_6WD1_010 | 1/1/2643:2646, 1/1/2674:2676, 1/1/2731:2735, 1/1/2769:2771 | No text annotation | homologous J4_5J7L_028 NA | |
| J4_6WD1_011 | 1/3/115:122, 1/3/239:240, 1/3/286:289, 1/3/311:312 | No text annotation | homologous J4_5J7L_001 NA | |
| J4_6WD1_013 | 1/3/575:577, 1/3/764:769, 1/3/810:821, 1/3/879:880 | No text annotation | homologous J4_5J7L_003 NA | |
| J5_6WD1_001 | 1/1/47:54, 1/1/116:121, 1/1/130:131, 1/1/148:150, 1/1/176:178 | No text annotation | homologous J5_5J7L_013 NA | |
| J5_6WD1_002 | 1/1/531:533, 1/1/560:564, 1/1/577:579, 1/1/1261:1262, 1/1/2017:2018 | No text annotation | homologous J5_5J7L_014 NA | |
| J5_6WD1_003 | 1/1/584:589, 1/1/668:671, 1/1/809:812, 1/1/1195:1196, 1/1/1250:1256 | No text annotation | homologous J5_5J7L_015 NA | |
| J5_6WD1_004 | 1/1/1674:1682, 1/1/1706:1707, 1/1/1751:1752, 1/1/1756:1764, 1/1/1988:1990 | No text annotation | homologous J5_5J7L_016 NA | |
| J5_6WD1_005 | 1/1/2057:2064, 1/1/2446:2453, 1/1/2500:2507, 1/1/2582:2588, 1/1/2606:2611 | No text annotation | ||
| J5_6WD1_006 | 1/1/2074:2077, 1/1/2243:2246, 1/1/2258:2259, 1/1/2281:2282, 1/1/2427:2435 | No text annotation | homologous J5_9DFE_007 J5_39529.2 | |
| J5_6WD1_009 | 1/3/58:61, 1/3/106:113, 1/3/314:316, 1/3/337:339, 1/3/350:354 | No text annotation | homologous J5_5J7L_003 NA | |
| J6_6WD1_001 | 1/1/45:46, 1/1/179:183, 1/1/214:224, 1/1/231:235, 1/1/262:266, 1/1/426:433 | No text annotation | ||
| J6_6WD1_002 | 1/1/2074:2077, 1/1/2243:2246, 1/1/2258:2259, 1/1/2281:2284, 1/1/2384:2395, 1/1/2421:2435 | No text annotation | ||
| J7_6WD1_001 | 1/1/8:15, 1/1/525:531, 1/1/2018:2023, 1/1/2040:2043, 1/1/2625:2630, 1/1/2788:2789, 1/1/2894:2895 | No text annotation | ||
| J7_6WD1_002 | 1/1/817:822, 1/1/835:838, 1/1/940:946, 1/1/971:976, 1/1/987:991, 1/1/1163:1164, 1/1/1185:1190 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6WD1_029 | No text annotation | ||
| J3_6WD1_005 | No text annotation | ||
| J3_6WD1_012 | No text annotation | ||
| J3_6WD1_015 | No text annotation | ||
| J3_6WD1_016 | No text annotation | ||
| J3_6WD1_033 | No text annotation | ||
| J3_6WD1_019 | No text annotation | ||
| J3_6WD1_020 | No text annotation | ||
| J3_6WD1_021 | No text annotation | ||
| J3_6WD1_022 | No text annotation | ||
| J3_6WD1_034 | No text annotation | ||
| J3_6WD1_023 | No text annotation | ||
| J3_6WD1_024 | No text annotation | ||
| J3_6WD1_025 | No text annotation | ||
| J3_6WD1_035 | No text annotation | ||
| J3_6WD1_026 | No text annotation | ||
| J4_6WD1_012 | No text annotation | ||
| J5_6WD1_007 | No text annotation | ||
| J5_6WD1_008 | No text annotation |
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