3J9Y Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_3J9Y_001 | 1/A/59:68 | No text annotation | homologous HL_5J7L_134 NA | |
| HL_3J9Y_002 | 1/A/87:95 | No text annotation | homologous HL_5J7L_135 NA | |
| HL_3J9Y_003 | 1/A/123:128 | No text annotation | homologous HL_5J7L_136 NA | |
| HL_3J9Y_006 | 1/A/194:201 | No text annotation | homologous HL_5J7L_139 NA | |
| HL_3J9Y_008 | 1/A/246:252 | No text annotation | homologous HL_5J7L_141 NA | |
| HL_3J9Y_009 | 1/A/305:312 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_142 NA | |
| HL_3J9Y_010 | 1/A/327:335 | T-loop with unstacked turn | homologous HL_5J7L_144 NA | |
| HL_3J9Y_011 | 1/A/382:392 | No text annotation | homologous HL_5J7L_145 NA | |
| HL_3J9Y_012 | 1/A/410:417 | Pseudoknot geometry | homologous HL_5J7L_146 NA | |
| HL_3J9Y_013 | 1/A/462:467 | GNRA | homologous HL_4WF9_015 HL_34789.3 | |
| HL_3J9Y_014 | 1/A/487:493 | GNRA | homologous HL_5J7L_148 NA | |
| HL_3J9Y_016 | 1/A/566:575 | T-loop with 2 stacked bulged bases | geometric HL_5J7L_150 NA | |
| HL_3J9Y_017 | 1/A/611:617 | No text annotation | homologous HL_5J7L_151 NA | |
| HL_3J9Y_021 | 1/A/744:753 | No text annotation | homologous HL_5J7L_155 NA | |
| HL_3J9Y_022 | 1/A/779:785 | UNCG variation | homologous HL_7A0S_023 HL_51020.2 | |
| HL_3J9Y_023 | 1/A/826:831 | No text annotation | homologous HL_7RQB_025 NA | |
| HL_3J9Y_104 | 1/A/955:962 | GNRA | homologous HL_5J7L_211 NA | |
| HL_3J9Y_026 | 1/A/978:985 | No text annotation | homologous HL_7A0S_027 HL_47171.1 | |
| HL_3J9Y_029 | 1/A/1222:1227 | GNRA | homologous HL_5J7L_164 NA | |
| HL_3J9Y_030 | 1/A/1281:1289 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_165 NA | |
| HL_3J9Y_031 | 1/A/1324:1330 | Pseudoknot geometry with 3' bulge | homologous HL_5J7L_166 NA | |
| HL_3J9Y_032 | 1/A/1363:1368 | GNRA | homologous HL_5J7L_167 NA | |
| HL_3J9Y_033 | 1/A/1389:1398 | No text annotation | homologous HL_7RQB_036 NA | |
| HL_3J9Y_034 | 1/A/1450:1461 | No text annotation | geometric HL_5J7L_018 NA | |
| HL_3J9Y_035 | 1/A/1492:1498 | Pseudoknot geometry with 3' bulge | homologous HL_5J7L_170 NA | |
| HL_3J9Y_037 | 1/A/1565:1568 | Mini UNCG | homologous HL_7A0S_039 HL_90436.3 | |
| HL_3J9Y_038 | 1/A/1612:1619 | No text annotation | homologous HL_9DFE_038 HL_28592.2 | |
| HL_3J9Y_106 | 1/A/1630:1636 | GNRA | homologous HL_5J7L_174 NA | |
| HL_3J9Y_040 | 1/A/1691:1696 | No text annotation | homologous HL_7RQB_042 NA | |
| HL_3J9Y_042 | 1/A/1752:1756 | No text annotation | homologous HL_5J7L_177 NA | |
| HL_3J9Y_043 | 1/A/1777:1787 | No text annotation | homologous HL_4WF9_043 HL_87681.1 | |
| HL_3J9Y_044 | 1/A/1806:1811 | GNRA related | homologous HL_5J7L_179 NA | |
| HL_3J9Y_046 | 1/A/1910:1920 | No text annotation | homologous HL_5J7L_181 NA | |
| HL_3J9Y_047 | 1/A/1949:1957 | No text annotation | homologous HL_5J7L_182 NA | |
| HL_3J9Y_048 | 1/A/2027:2036 | No text annotation | homologous HL_5J7L_183 NA | |
| HL_3J9Y_050 | 1/A/2209:2215 | No text annotation | homologous HL_5J7L_185 NA | |
| HL_3J9Y_051 | 1/A/2248:2256 | No text annotation | homologous HL_7RQB_053 NA | |
| HL_3J9Y_052 | 1/A/2264:2276 | No text annotation | homologous HL_7RQB_054 NA | |
| HL_3J9Y_054 | 1/A/2324:2331 | Pseudoknot geometry | homologous HL_5J7L_189 NA | |
| HL_3J9Y_055 | 1/A/2356:2361 | GNRA | homologous HL_5J7L_190 NA | |
| HL_3J9Y_056 | 1/A/2374:2379 | GNRA | homologous HL_4WF9_054 HL_34789.3 | |
| HL_3J9Y_057 | 1/A/2404:2413 | No text annotation | homologous HL_5J7L_192 NA | |
| HL_3J9Y_058 | 1/A/2471:2479 | No text annotation | homologous HL_4WF9_056 HL_52011.1 | |
| HL_3J9Y_059 | 1/A/2528:2535 | GNRA variation | homologous HL_5J7L_194 NA | |
| HL_3J9Y_060 | 1/A/2551:2557 | No text annotation | homologous HL_5J7L_195 NA | |
| HL_3J9Y_061 | 1/A/2594:2599 | GNRA | homologous HL_5J7L_196 NA | |
| HL_3J9Y_062 | 1/A/2658:2663 | GNRA | geometric HL_5J7L_197 NA | |
| HL_3J9Y_063 | 1/A/2701:2706 | Ribsomal LSU H95 | homologous HL_5J7L_198 NA | |
| HL_3J9Y_064 | 1/A/2745:2759 | No text annotation | homologous HL_5J7L_199 NA | |
| HL_3J9Y_066 | 1/A/2819:2827 | No text annotation | homologous HL_5J7L_201 NA | |
| HL_3J9Y_067 | 1/A/2856:2861 | GNRA | homologous HL_5J7L_202 NA | |
| HL_3J9Y_069 | 1/B/86:90 | Mini UNCG | homologous HL_5J7L_204 NA | |
| HL_3J9Y_070 | 1/a/12:22 | No text annotation | homologous HL_5J7L_001 NA | |
| HL_3J9Y_076 | 1/a/296:301 | GNRA | homologous HL_5J7L_007 NA | |
| HL_3J9Y_077 | 1/a/320:333 | No text annotation | homologous HL_5J7L_008 NA | |
| HL_3J9Y_108 | 1/a/522:527 | GNRA variation | homologous HL_5J7L_205 NA | |
| HL_3J9Y_083 | 1/a/617:623 | GNRA-like with tWH | homologous HL_4LFB_014 HL_86621.1 | |
| HL_3J9Y_085 | 1/a/726:731 | GNRA | homologous HL_5J7L_016 NA | |
| HL_3J9Y_089 | 1/a/897:902 | GNRA | homologous HL_4LFB_020 HL_34789.3 | |
| HL_3J9Y_090 | 1/a/963:972 | No text annotation | homologous HL_5J7L_021 NA | |
| HL_3J9Y_092 | 1/a/1076:1081 | GNRA | homologous HL_5J7L_023 NA | |
| HL_3J9Y_093 | 1/a/1089:1096 | T-loop related | homologous HL_4LFB_025 HL_63894.2 | |
| HL_3J9Y_096 | 1/a/1265:1270 | GNRA | homologous HL_5J7L_027 NA | |
| HL_3J9Y_097 | 1/a/1314:1323 | T-loop with 3 stacked bulged bases | homologous HL_5J7L_028 NA | |
| HL_3J9Y_098 | 1/a/1356:1366 | No text annotation | homologous HL_4LFB_030 HL_86432.1 | |
| HL_3J9Y_100 | 1/a/1515:1520 | GNRA | homologous HL_6CZR_103 NA | |
| HL_3J9Y_102 | 1/v/31:39 | tRNA anticodon loop | homologous HL_6CFJ_107 HL_81376.3 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_3J9Y_004 | No text annotation | ||
| HL_3J9Y_005 | No text annotation | ||
| HL_3J9Y_007 | No text annotation | ||
| HL_3J9Y_015 | Mini UNCG with extended bulge | ||
| HL_3J9Y_018 | GNRA | ||
| HL_3J9Y_019 | No text annotation | ||
| HL_3J9Y_020 | GNRA wlth tandem sheared | ||
| HL_3J9Y_024 | No text annotation | ||
| HL_3J9Y_025 | No text annotation | ||
| HL_3J9Y_027 | GNRA wlth tandem sheared | ||
| HL_3J9Y_028 | No text annotation | ||
| HL_3J9Y_105 | No text annotation | ||
| HL_3J9Y_109 | No text annotation | ||
| HL_3J9Y_036 | No text annotation | ||
| HL_3J9Y_039 | GNRA with extra cWW | ||
| HL_3J9Y_107 | No text annotation | ||
| HL_3J9Y_041 | No text annotation | ||
| HL_3J9Y_045 | GNRA variation | ||
| HL_3J9Y_049 | No text annotation | ||
| HL_3J9Y_053 | No text annotation | ||
| HL_3J9Y_110 | No text annotation | ||
| HL_3J9Y_065 | UNCG variation | ||
| HL_3J9Y_068 | No text annotation | ||
| HL_3J9Y_071 | No text annotation | ||
| HL_3J9Y_072 | GNRA with extra near cWW | ||
| HL_3J9Y_073 | GNRA | ||
| HL_3J9Y_074 | No text annotation | ||
| HL_3J9Y_075 | GNRA related | ||
| HL_3J9Y_078 | UNCG | ||
| HL_3J9Y_079 | GNRA | ||
| HL_3J9Y_080 | UNCG | ||
| HL_3J9Y_081 | GNRA wlth extra near cWW | ||
| HL_3J9Y_082 | No text annotation | ||
| HL_3J9Y_084 | No text annotation | ||
| HL_3J9Y_086 | No text annotation | ||
| HL_3J9Y_087 | No text annotation | ||
| HL_3J9Y_088 | GNRA | ||
| HL_3J9Y_091 | GNRA | ||
| HL_3J9Y_094 | No text annotation | ||
| HL_3J9Y_095 | GNRA | ||
| HL_3J9Y_099 | UNCG | ||
| HL_3J9Y_101 | tRNA D-loop | ||
| HL_3J9Y_103 | T-loop with 2 stacked bulged bases |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_3J9Y_001 | 1/A/24:30, 1/A/510:516 | Triple sheared with non-canonical cWW | homologous IL_5J7L_245 NA | |
| IL_3J9Y_002 | 1/A/36:37, 1/A/442:444 | Single bulged A | homologous IL_7RQB_002 NA | |
| IL_3J9Y_003 | 1/A/43:44, 1/A/434:436 | Minor groove platform | homologous IL_5J7L_247 NA | |
| IL_3J9Y_004 | 1/A/81:85, 1/A/97:105 | No text annotation | homologous IL_5J7L_248 NA | |
| IL_3J9Y_005 | 1/A/183:184, 1/A/212:214 | Single stack bend | homologous IL_4WF9_007 IL_15011.2 | |
| IL_3J9Y_006 | 1/A/188:194, 1/A/201:208 | 8x7 Sarcin-Ricin; G-bulge | geometric IL_7RQB_006 NA | |
| IL_3J9Y_007 | 1/A/239:245, 1/A/253:258 | 7x6 Sarcin-Ricin; G-bulge | homologous IL_5J7L_251 NA | |
| IL_3J9Y_010 | 1/A/293:295, 1/A/343:347 | No text annotation | homologous IL_5J7L_254 NA | |
| IL_3J9Y_011 | 1/A/481:484, 1/A/496:509 | No text annotation | homologous IL_5J7L_255 NA | |
| IL_3J9Y_012 | 1/A/536:539, 1/A/554:557 | Double sheared | homologous IL_5J7L_256 NA | |
| IL_3J9Y_013 | 1/A/564:566, 1/A/575:577 | Isolated non-canonical cWW pair | homologous IL_5J7L_257 NA | |
| IL_3J9Y_014 | 1/A/606:610, 1/A/618:622 | AAA cross-strand stack | homologous IL_5J7L_258 NA | |
| IL_3J9Y_015 | 1/A/672:674, 1/A/806:808 | No text annotation | homologous IL_7RQB_017 NA | |
| IL_3J9Y_016 | 1/A/674:678, 1/A/799:806 | tHW-tHW cross-strand stack | geometric IL_7RQB_018 NA | |
| IL_3J9Y_017 | 1/A/697:698, 1/A/763:765 | Single bulged A | homologous IL_5J7L_261 NA | |
| IL_3J9Y_018 | 1/A/702:703, 1/A/728:730 | Single bulged G | geometric IL_5J7L_262 NA | |
| IL_3J9Y_019 | 1/A/703:707, 1/A/724:728 | Triple sheared | homologous IL_5J7L_263 NA | |
| IL_3J9Y_020 | 1/A/738:740, 1/A/757:758 | Major groove platform | homologous IL_4WF9_026 IL_48076.8 | |
| IL_3J9Y_021 | 1/A/775:777, 1/A/787:791 | Multiple bulged bases | homologous IL_5J7L_265 NA | |
| IL_3J9Y_022 | 1/A/837:838, 1/A/940:942 | Single stack bend | homologous IL_7RQB_024 NA | |
| IL_3J9Y_179 | 1/A/844:848, 1/A/930:934 | No text annotation | geometric IL_5J7L_399 NA | |
| IL_3J9Y_024 | 1/A/847:848, 1/A/930:933 | Stack outside cWW | geometric IL_5J7L_268 NA | |
| IL_3J9Y_026 | 1/A/856:862, 1/A/915:921 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | homologous IL_5J7L_270 NA | |
| IL_3J9Y_027 | 1/A/862:863, 1/A/913:915 | Single bulged G | geometric IL_5J7L_271 NA | |
| IL_3J9Y_028 | 1/A/864:868, 1/A/909:912 | C-loop with bulged stacked A's | homologous IL_5J7L_272 NA | |
| IL_3J9Y_029 | 1/A/870:872, 1/A/905:907 | Isolated non-canonical cWW pair | homologous IL_5J7L_273 NA | |
| IL_3J9Y_032 | 1/A/994:996, 1/A/1159:1160 | Single bulged C | homologous IL_7RQB_035 NA | |
| IL_3J9Y_033 | 1/A/998:1002, 1/A/1153:1157 | UAA/GAN | homologous IL_5J7L_277 NA | |
| IL_3J9Y_034 | 1/A/1004:1011, 1/A/1150:1151 | SSU/LSU pseudoknot | geometric IL_5J7L_278 NA | |
| IL_3J9Y_035 | 1/A/1011:1013, 1/A/1149:1150 | Single bulged U | homologous IL_5J7L_279 NA | |
| IL_3J9Y_036 | 1/A/1018:1024, 1/A/1140:1144 | Kink-turn related | geometric IL_4WF9_039 IL_57188.6 | |
| IL_3J9Y_037 | 1/A/1024:1030, 1/A/1124:1140 | No text annotation | geometric IL_5J7L_281 NA | |
| IL_3J9Y_043 | 1/A/1196:1198, 1/A/1247:1250 | Isolated cWS basepair | homologous IL_5J7L_286 NA | |
| IL_3J9Y_044 | 1/A/1202:1206, 1/A/1240:1243 | No text annotation | homologous IL_5J7L_287 NA | |
| IL_3J9Y_045 | 1/A/1208:1215, 1/A/1234:1238 | Kink-turn | homologous IL_5J7L_288 NA | |
| IL_3J9Y_046 | 1/A/1262:1269, 1/A/2011:2017 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_5J7L_289 NA | |
| IL_3J9Y_047 | 1/A/1310:1313, 1/A/1603:1604 | Major groove platform; stack outside cWW | homologous IL_4WF9_049 IL_74641.2 | |
| IL_3J9Y_048 | 1/A/1319:1323, 1/A/1331:1333 | C-loop | homologous IL_5J7L_291 NA | |
| IL_3J9Y_049 | 1/A/1351:1355, 1/A/1376:1380 | UAA/GAN | homologous IL_5J7L_292 NA | |
| IL_3J9Y_050 | 1/A/1357:1361, 1/A/1370:1374 | tSH-tHW-tHS | homologous IL_5J7L_293 NA | |
| IL_3J9Y_183 | 1/A/1415:1421, 1/A/1577:1587 | No text annotation | ||
| IL_3J9Y_052 | 1/A/1416:1421, 1/A/1577:1582 | No text annotation | geometric IL_9AXU_113 IL_74322.2 | |
| IL_3J9Y_053 | 1/A/1432:1435, 1/A/1557:1561 | Tandem non-canonical cWW pairs | homologous IL_5J7L_296 NA | |
| IL_3J9Y_054 | 1/A/1437:1440, 1/A/1551:1555 | tSH-tHW | homologous IL_5J7L_297 NA | |
| IL_3J9Y_055 | 1/A/1468:1471, 1/A/1520:1524 | No text annotation | homologous IL_5J7L_299 NA | |
| IL_3J9Y_057 | 1/A/1481:1482, 1/A/1507:1510 | 180 degree turn | homologous IL_5J7L_301 NA | |
| IL_3J9Y_060 | 1/A/1651:1656, 1/A/2004:2006 | No text annotation | homologous IL_7RQB_064 NA | |
| IL_3J9Y_061 | 1/A/1663:1665, 1/A/1995:1997 | Isolated tWW turn | homologous IL_4WF9_063 IL_10432.1 | |
| IL_3J9Y_062 | 1/A/1666:1669, 1/A/1993:1994 | Major groove platform; stack outside cWW | homologous IL_7RQB_066 NA | |
| IL_3J9Y_185 | 1/A/1666:1674, 1/A/1990:1994 | No text annotation | homologous IL_5J7L_386 NA | |
| IL_3J9Y_063 | 1/A/1669:1674, 1/A/1990:1993 | Intercalated tWH | geometric IL_5J7L_307 NA | |
| IL_3J9Y_064 | 1/A/1686:1691, 1/A/1696:1702 | tSH-tSH-tHH-tHS | geometric IL_5J7L_308 NA | |
| IL_3J9Y_065 | 1/A/1712:1718, 1/A/1742:1746 | 6x5 Sarcin-Ricin; G-bulge | homologous IL_5J7L_309 NA | |
| IL_3J9Y_068 | 1/A/1770:1771, 1/A/1980:1982 | Single bulged A | homologous IL_7A0S_064 IL_14190.2 | |
| IL_3J9Y_069 | 1/A/1798:1804, 1/A/1813:1821 | Kink-turn related | homologous IL_5J7L_313 NA | |
| IL_3J9Y_070 | 1/A/1837:1840, 1/A/1902:1903 | Minor groove platform, major groove intercalation | homologous IL_5J7L_314 NA | |
| IL_3J9Y_071 | 1/A/1841:1842, 1/A/1898:1901 | Major groove intercalation | homologous IL_5J7L_315 NA | |
| IL_3J9Y_186 | 1/A/1851:1860, 1/A/1882:1891 | No text annotation | homologous IL_5J7L_387 NA | |
| IL_3J9Y_073 | 1/A/1864:1867, 1/A/1874:1878 | UAA/GAN related | homologous IL_5J7L_317 NA | |
| IL_3J9Y_074 | 1/A/1933:1934, 1/A/1964:1967 | Bulged stacked bases | geometric IL_5J7L_318 NA | |
| IL_3J9Y_075 | 1/A/1934:1945, 1/A/1961:1964 | No text annotation | homologous IL_7A0S_072 IL_04332.3 | |
| IL_3J9Y_076 | 1/A/2050:2052, 1/A/2617:2618 | Major groove platform | homologous IL_5J7L_320 NA | |
| IL_3J9Y_077 | 1/A/2054:2056, 1/A/2612:2615 | No text annotation | homologous IL_5J7L_321 NA | |
| IL_3J9Y_187 | 1/A/2067:2069, 1/A/2442:2443 | Single bulged U | homologous IL_4WF9_080 IL_97561.3 | |
| IL_3J9Y_080 | 1/A/2070:2071, 1/A/2438:2441 | Minor groove platform | geometric IL_5J7L_324 NA | |
| IL_3J9Y_081 | 1/A/2081:2083, 1/A/2236:2239 | Isolated tHS basepair with bulges | homologous IL_5J7L_325 NA | |
| IL_3J9Y_082 | 1/A/2085:2087, 1/A/2232:2234 | Isolated non-canonical cWW pair | homologous IL_5J7L_326 NA | |
| IL_3J9Y_085 | 1/A/2202:2204, 1/A/2220:2221 | Single bulged U | homologous IL_5J7L_331 NA | |
| IL_3J9Y_086 | 1/A/2350:2353, 1/A/2364:2367 | Double sheared | homologous IL_5J7L_333 NA | |
| IL_3J9Y_087 | 1/A/2401:2403, 1/A/2414:2415 | No text annotation | ||
| IL_3J9Y_191 | 1/A/2453:2454, 1/A/2498:2500 | Single stack bend | homologous IL_5J7L_391 NA | |
| IL_3J9Y_192 | 1/A/2454:2455, 1/A/2496:2498 | Major groove platform | homologous IL_9DFE_092 IL_48076.8 | |
| IL_3J9Y_193 | 1/A/2457:2459, 1/A/2493:2494 | Major groove platform | homologous IL_5J7L_393 NA | |
| IL_3J9Y_090 | 1/A/2459:2461, 1/A/2489:2493 | Major groove minor groove platform with extra cWW | homologous IL_7RQB_094 NA | |
| IL_3J9Y_091 | 1/A/2466:2470, 1/A/2480:2484 | Double sheared with non-canonical cWW | homologous IL_5J7L_338 NA | |
| IL_3J9Y_194 | 1/A/2507:2508, 1/A/2580:2582 | Major groove platform | homologous IL_5J7L_394 NA | |
| IL_3J9Y_093 | 1/A/2510:2512, 1/A/2574:2578 | Isolated non-canonical cWW with bulges | geometric IL_5J7L_340 NA | |
| IL_3J9Y_094 | 1/A/2512:2513, 1/A/2571:2574 | No text annotation | homologous IL_5J7L_341 NA | |
| IL_3J9Y_095 | 1/A/2522:2523, 1/A/2540:2543 | Major groove platform with intercalation | homologous IL_5J7L_342 NA | |
| IL_3J9Y_097 | 1/A/2591:2592, 1/A/2601:2603 | Single bulged A | homologous IL_7RQB_101 NA | |
| IL_3J9Y_098 | 1/A/2636:2640, 1/A/2774:2782 | tSH-tHS-tHW | homologous IL_5J7L_345 NA | |
| IL_3J9Y_099 | 1/A/2652:2658, 1/A/2663:2668 | Sarcin-Ricin target in LSU H95; G-bulge | homologous IL_7RQB_103 NA | |
| IL_3J9Y_100 | 1/A/2680:2684, 1/A/2725:2727 | C-loop | homologous IL_5J7L_347 NA | |
| IL_3J9Y_101 | 1/A/2687:2691, 1/A/2718:2722 | UAA/GAN related, with intercalation | homologous IL_5J7L_348 NA | |
| IL_3J9Y_102 | 1/A/2695:2696, 1/A/2711:2714 | Multiple bulged bases | homologous IL_5J7L_349 NA | |
| IL_3J9Y_103 | 1/A/2737:2742, 1/A/2762:2767 | UAA/GAN with extra cWW | homologous IL_5J7L_350 NA | |
| IL_3J9Y_104 | 1/A/2806:2811, 1/A/2889:2892 | No text annotation | homologous IL_5J7L_351 NA | |
| IL_3J9Y_106 | 1/A/2843:2846, 1/A/2870:2874 | Multiple bulged bases with non-canonical cWW | homologous IL_5J7L_353 NA | |
| IL_3J9Y_107 | 1/A/2847:2852, 1/A/2865:2869 | tHS double platform | homologous IL_5J7L_354 NA | |
| IL_3J9Y_109 | 1/B/23:28, 1/B/56:60 | No text annotation | homologous IL_5J7L_356 NA | |
| IL_3J9Y_112 | 1/B/71:79, 1/B/97:105 | Bacterial 5S Loop E | homologous IL_5J7L_359 NA | |
| IL_3J9Y_113 | 1/a/30:32, 1/a/552:553 | Single bulged G | homologous IL_4LFB_001 IL_28408.2 | |
| IL_3J9Y_121 | 1/a/128:131, 1/a/231:233 | Isolated non-canonical cWW pair | homologous IL_5J7L_009 NA | |
| IL_3J9Y_128 | 1/a/292:293, 1/a/304:308 | C-loop | homologous IL_4LFB_013 IL_06671.1 | |
| IL_3J9Y_136 | 1/a/504:511, 1/a/540:541 | SSU/LSU pseudoknot | homologous IL_5J7L_024 NA | |
| IL_3J9Y_137 | 1/a/515:521, 1/a/528:536 | Kink-turn related | homologous IL_5J7L_025 NA | |
| IL_3J9Y_138 | 1/a/569:575, 1/a/880:881 | No text annotation | homologous IL_4LFB_022 IL_20847.1 | |
| IL_3J9Y_139 | 1/a/580:584, 1/a/757:761 | tSH-tHW-tHS | homologous IL_5J7L_027 NA | |
| IL_3J9Y_141 | 1/a/597:598, 1/a/640:643 | Major groove minor groove platform; mini C-loop | homologous IL_5J7L_029 NA | |
| IL_3J9Y_142 | 1/a/605:612, 1/a/628:633 | No text annotation | homologous IL_5J7L_030 NA | |
| IL_3J9Y_144 | 1/a/659:660, 1/a/745:747 | Single stack bend | homologous IL_5J7L_032 NA | |
| IL_3J9Y_145 | 1/a/662:666, 1/a/740:743 | Tandem non-canonical cWW pairs | homologous IL_5J7L_033 NA | |
| IL_3J9Y_196 | 1/a/673:677, 1/a/713:717 | Triple non-canonical cWW pairs | homologous IL_5J7L_361 NA | |
| IL_3J9Y_148 | 1/a/774:778, 1/a/804:805 | Left turn | homologous IL_4LFB_032 IL_29346.3 | |
| IL_3J9Y_149 | 1/a/779:783, 1/a/799:803 | tSH-tHW-tHS | homologous IL_5J7L_037 NA | |
| IL_3J9Y_150 | 1/a/887:894, 1/a/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_5J7L_038 NA | |
| IL_3J9Y_151 | 1/a/922:923, 1/a/1393:1395 | Single bulged A | homologous IL_4LFB_035 IL_14190.2 | |
| IL_3J9Y_152 | 1/a/925:927, 1/a/1390:1391 | Single bulged G | homologous IL_5J7L_040 NA | |
| IL_3J9Y_153 | 1/a/933:935, 1/a/1380:1384 | Minor groove platform | homologous IL_5J7L_041 NA | |
| IL_3J9Y_154 | 1/a/953:954, 1/a/1226:1228 | No text annotation | homologous IL_6CZR_150 NA | |
| IL_3J9Y_158 | 1/a/1048:1050, 1/a/1208:1209 | Single bulged U | homologous IL_5J7L_046 NA | |
| IL_3J9Y_197 | 1/a/1052:1056, 1/a/1204:1206 | No text annotation | homologous IL_6CZR_154 NA | |
| IL_3J9Y_160 | 1/a/1057:1058, 1/a/1199:1203 | Minor groove platform | homologous IL_5J7L_048 NA | |
| IL_3J9Y_161 | 1/a/1060:1061, 1/a/1195:1197 | Single bulged U | homologous IL_4LFB_046 IL_97561.3 | |
| IL_3J9Y_162 | 1/a/1061:1063, 1/a/1193:1195 | Isolated non-canonical cWW pair | geometric IL_5J7L_050 NA | |
| IL_3J9Y_165 | 1/a/1158:1161, 1/a/1175:1181 | No text annotation | homologous IL_5J7L_053 NA | |
| IL_3J9Y_198 | 1/a/1247:1253, 1/a/1284:1290 | No text annotation | homologous IL_5J7L_054 NA | |
| IL_3J9Y_168 | 1/a/1259:1263, 1/a/1272:1276 | Double sheared with non-canonical cWW | homologous IL_5J7L_056 NA | |
| IL_3J9Y_169 | 1/a/1303:1308, 1/a/1329:1334 | No text annotation | homologous IL_4LFB_055 IL_57885.2 | |
| IL_3J9Y_170 | 1/a/1399:1401, 1/a/1501:1504 | No text annotation | homologous IL_6CZR_165 NA | |
| IL_3J9Y_171 | 1/a/1401:1404, 1/a/1497:1501 | No text annotation | geometric IL_4V88_464 NA | |
| IL_3J9Y_199 | 1/a/1405:1407, 1/a/1494:1496 | Isolated non-canonical cWW pair | homologous IL_5J7L_363 NA | |
| IL_3J9Y_173 | 1/a/1412:1414, 1/a/1486:1488 | Isolated non-canonical cWW pair | homologous IL_5J7L_061 NA | |
| IL_3J9Y_174 | 1/a/1416:1419, 1/a/1481:1484 | Double sheared | homologous IL_5J7L_062 NA | |
| IL_3J9Y_175 | 1/a/1430:1435, 1/a/1466:1470 | Triple sheared related | homologous IL_5J7L_063 NA | |
| IL_3J9Y_176 | 1/a/1440:1442, 1/a/1460:1461 | Single bulged A | homologous IL_5J7L_064 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_3J9Y_008 | No text annotation | ||
| IL_3J9Y_178 | No text annotation | ||
| IL_3J9Y_009 | No text annotation | ||
| IL_3J9Y_023 | 90 degree turn | ||
| IL_3J9Y_025 | Single stack bend | ||
| IL_3J9Y_030 | Double sheared with non-canonical cWW | ||
| IL_3J9Y_180 | No text annotation | ||
| IL_3J9Y_031 | No text annotation | ||
| IL_3J9Y_038 | Isolated non-canonical cWW pair | ||
| IL_3J9Y_039 | Tandem non-canonical cWW pairs | ||
| IL_3J9Y_181 | Partly complementary | ||
| IL_3J9Y_040 | Kink-turn | ||
| IL_3J9Y_041 | No text annotation | ||
| IL_3J9Y_182 | No text annotation | ||
| IL_3J9Y_042 | No text annotation | ||
| IL_3J9Y_051 | No text annotation | ||
| IL_3J9Y_184 | tSH-tHW-tHS | ||
| IL_3J9Y_056 | No text annotation | ||
| IL_3J9Y_058 | Single bulged A | ||
| IL_3J9Y_059 | UAA/GAN variation | ||
| IL_3J9Y_066 | Triple sheared | ||
| IL_3J9Y_067 | Single bulged C | ||
| IL_3J9Y_072 | Major groove minor groove platform; mini C-loop | ||
| IL_3J9Y_078 | No text annotation | ||
| IL_3J9Y_079 | No text annotation | ||
| IL_3J9Y_188 | Other IL | ||
| IL_3J9Y_083 | No text annotation | ||
| IL_3J9Y_084 | No text annotation | ||
| IL_3J9Y_201 | No text annotation | ||
| IL_3J9Y_189 | No text annotation | ||
| IL_3J9Y_190 | Tandem non-canonical cWW pairs | ||
| IL_3J9Y_088 | No text annotation | ||
| IL_3J9Y_089 | Major groove platform with extra pair | ||
| IL_3J9Y_092 | No text annotation | ||
| IL_3J9Y_096 | Tandem non-canonical cWW pairs | ||
| IL_3J9Y_105 | Major groove intercalation | ||
| IL_3J9Y_108 | Major groove intercalation | ||
| IL_3J9Y_110 | Major groove minor groove platform; mini C-loop | ||
| IL_3J9Y_111 | Symmetric double minor groove platform | ||
| IL_3J9Y_114 | Single bulged A | ||
| IL_3J9Y_115 | No text annotation | ||
| IL_3J9Y_116 | Minor groove platform | ||
| IL_3J9Y_117 | Multiple bulged bases | ||
| IL_3J9Y_118 | Minor groove platform with extra cWW | ||
| IL_3J9Y_119 | Minor groove platform | ||
| IL_3J9Y_195 | Single bulged G, near cWW | ||
| IL_3J9Y_120 | Tandem non-canonical cWW pairs | ||
| IL_3J9Y_122 | Minor groove platform related | ||
| IL_3J9Y_123 | Isolated cWH basepair | ||
| IL_3J9Y_124 | tWH-tWH-tHW-tHW | ||
| IL_3J9Y_125 | Minor groove platform | ||
| IL_3J9Y_126 | Kink-turn with non-sequential stacking | ||
| IL_3J9Y_127 | No text annotation | ||
| IL_3J9Y_129 | Single bulged U | ||
| IL_3J9Y_130 | C-loop | ||
| IL_3J9Y_131 | Single bulged G | ||
| IL_3J9Y_132 | No text annotation | ||
| IL_3J9Y_133 | No text annotation | ||
| IL_3J9Y_134 | tSH-tHW-tWW | ||
| IL_3J9Y_135 | No text annotation | ||
| IL_3J9Y_140 | Major groove platform | ||
| IL_3J9Y_143 | Major groove platform; stack outside cWW | ||
| IL_3J9Y_146 | No text annotation | ||
| IL_3J9Y_147 | Kink-turn | ||
| IL_3J9Y_155 | Minor groove platform | ||
| IL_3J9Y_156 | Single stack bend | ||
| IL_3J9Y_157 | No text annotation | ||
| IL_3J9Y_159 | No text annotation | ||
| IL_3J9Y_163 | No text annotation | ||
| IL_3J9Y_202 | No text annotation | ||
| IL_3J9Y_203 | Minor groove platform | ||
| IL_3J9Y_164 | No text annotation | ||
| IL_3J9Y_166 | No text annotation | ||
| IL_3J9Y_167 | 180 degree turn | ||
| IL_3J9Y_172 | No text annotation | ||
| IL_3J9Y_200 | Decoding loop related | ||
| IL_3J9Y_177 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_3J9Y_001 | 1/A/30:31, 1/A/474:481, 1/A/509:510 | No text annotation | homologous J3_7RQB_001 NA | |
| J3_3J9Y_026 | 1/A/30:31, 1/A/474:484, 1/A/496:510 | No text annotation | homologous J3_5J7L_066 NA | |
| J3_3J9Y_027 | 1/A/32:35, 1/A/445:461, 1/A/468:473 | No text annotation | homologous J3_5J7L_067 NA | |
| J3_3J9Y_002 | 1/A/56:57, 1/A/70:76, 1/A/110:114 | No text annotation | homologous J3_5J7L_037 NA | |
| J3_3J9Y_037 | 1/A/297:301, 1/A/316:325, 1/A/337:341 | No text annotation | homologous J3_5J7L_068 NA | |
| J3_3J9Y_003 | 1/A/683:689, 1/A/773:775, 1/A/791:794 | No text annotation | homologous J3_5J7L_038 NA | |
| J3_3J9Y_004 | 1/A/698:700, 1/A/732:736, 1/A/760:763 | No text annotation | homologous J3_7RQB_005 NA | |
| J3_3J9Y_005 | 1/A/1298:1303, 1/A/1625:1627, 1/A/1639:1642 | No text annotation | homologous J3_5J7L_041 NA | |
| J3_3J9Y_006 | 1/A/1306:1309, 1/A/1605:1611, 1/A/1620:1622 | No text annotation | homologous J3_5J7L_042 NA | |
| J3_3J9Y_029 | 1/A/1344:1349, 1/A/1382:1385, 1/A/1402:1403 | No text annotation | homologous J3_5J7L_043 NA | |
| J3_3J9Y_030 | 1/A/1424:1429, 1/A/1564:1565, 1/A/1568:1574 | No text annotation | homologous J3_5J7L_069 NA | |
| J3_3J9Y_008 | 1/A/2091:2093, 1/A/2196:2200, 1/A/2223:2228 | Kink-turn 3-way junction | homologous J3_5J7L_044 NA | |
| J3_3J9Y_031 | 1/A/2282:2284, 1/A/2384:2395, 1/A/2421:2427 | No text annotation | homologous J3_5J7L_070 NA | |
| J3_3J9Y_009 | 1/A/2295:2299, 1/A/2317:2323, 1/A/2332:2337 | No text annotation | ||
| J3_3J9Y_010 | 1/A/2517:2520, 1/A/2545:2547, 1/A/2561:2567 | No text annotation | homologous J3_5J7L_046 NA | |
| J3_3J9Y_012 | 1/A/2812:2815, 1/A/2831:2836, 1/A/2882:2888 | No text annotation | homologous J3_5J7L_048 NA | |
| J3_3J9Y_015 | 1/a/586:588, 1/a/651:654, 1/a/754:755 | No text annotation | geometric J3_5J7L_002 NA | |
| J3_3J9Y_034 | 1/a/586:588, 1/a/651:655, 1/a/751:755 | No text annotation | homologous J3_5J7L_051 NA | |
| J3_3J9Y_016 | 1/a/672:673, 1/a/717:725, 1/a/732:734 | No text annotation | homologous J3_5J7L_003 NA | |
| J3_3J9Y_017 | 1/a/826:829, 1/a/857:861, 1/a/868:874 | No text annotation | homologous J3_5J7L_004 NA | |
| J3_3J9Y_018 | 1/a/936:939, 1/a/1344:1350, 1/a/1372:1379 | No text annotation | homologous J3_4LFB_002 J3_85722.1 | |
| J3_3J9Y_019 | 1/a/943:946, 1/a/1235:1237, 1/a/1337:1340 | No text annotation | homologous J3_5J7L_005 NA | |
| J3_3J9Y_020 | 1/a/955:962, 1/a/973:984, 1/a/1221:1225 | No text annotation | homologous J3_5J7L_006 NA | |
| J3_3J9Y_021 | 1/a/990:993, 1/a/1045:1047, 1/a/1210:1215 | No text annotation | homologous J3_4LFB_005 J3_84394.1 | |
| J3_3J9Y_035 | 1/a/990:997, 1/a/1044:1047, 1/a/1210:1215 | No text annotation | homologous J3_4LFB_016 J3_28881.1 | |
| J3_3J9Y_022 | 1/a/1063:1068, 1/a/1107:1113, 1/a/1187:1193 | No text annotation | homologous J3_5J7L_008 NA | |
| J3_3J9Y_038 | 1/a/1073:1074, 1/a/1083:1086, 1/a/1099:1102 | No text annotation | homologous J3_4LFB_017 J3_11018.1 | |
| J3_3J9Y_024 | 1/a/1116:1118, 1/a/1155:1158, 1/a/1181:1184 | No text annotation | homologous J3_5J7L_010 NA | |
| J3_3J9Y_036 | 1/a/1116:1118, 1/a/1155:1161, 1/a/1175:1184 | No text annotation | homologous J3_5J7L_054 NA | |
| J3_3J9Y_025 | 1/a/1237:1241, 1/a/1296:1303, 1/a/1334:1337 | No text annotation | homologous J3_4LFB_009 J3_03192.1 | |
| J4_3J9Y_001 | 1/A/268:269, 1/A/370:375, 1/A/399:406, 1/A/421:424 | No text annotation | homologous J4_5J7L_018 NA | |
| J4_3J9Y_002 | 1/A/601:604, 1/A/624:628, 1/A/635:638, 1/A/650:656 | No text annotation | homologous J4_5J7L_020 NA | |
| J4_3J9Y_003 | 1/A/1270:1276, 1/A/1294:1295, 1/A/1645:1648, 1/A/2009:2010 | No text annotation | homologous J4_5J7L_021 NA | |
| J4_3J9Y_004 | 1/A/1310:1314, 1/A/1338:1343, 1/A/1404:1405, 1/A/1597:1604 | No text annotation | homologous J4_5J7L_022 NA | |
| J4_3J9Y_005 | 1/A/1313:1314, 1/A/1338:1343, 1/A/1404:1405, 1/A/1597:1603 | No text annotation | homologous J4_5J7L_023 NA | |
| J4_3J9Y_006 | 1/A/1444:1445, 1/A/1466:1467, 1/A/1525:1526, 1/A/1546:1547 | No text annotation | homologous J4_5J7L_024 NA | |
| J4_3J9Y_007 | 1/A/1772:1776, 1/A/1788:1792, 1/A/1827:1830, 1/A/1975:1979 | No text annotation | homologous J4_5J7L_025 NA | |
| J4_3J9Y_008 | 1/A/1833:1835, 1/A/1905:1906, 1/A/1924:1933, 1/A/1967:1972 | No text annotation | homologous J4_9DFE_008 J4_42306.1 | |
| J4_3J9Y_009 | 1/A/2285:2289, 1/A/2343:2347, 1/A/2370:2372, 1/A/2381:2383 | No text annotation | homologous J4_5J7L_027 NA | |
| J4_3J9Y_010 | 1/A/2643:2646, 1/A/2674:2676, 1/A/2731:2735, 1/A/2769:2771 | No text annotation | homologous J4_5J7L_028 NA | |
| J4_3J9Y_011 | 1/a/115:122, 1/a/239:240, 1/a/286:289, 1/a/311:312 | No text annotation | homologous J4_5J7L_001 NA | |
| J4_3J9Y_013 | 1/a/575:577, 1/a/764:769, 1/a/810:821, 1/a/879:880 | No text annotation | homologous J4_5J7L_003 NA | |
| J4_3J9Y_014 | 1/v/7:10, 1/v/25:27, 1/v/43:49, 1/v/65:66 | tRNA junction | homologous J4_9DFC_015 NA | |
| J5_3J9Y_001 | 1/A/47:54, 1/A/116:121, 1/A/130:131, 1/A/148:150, 1/A/176:178 | No text annotation | homologous J5_5J7L_013 NA | |
| J5_3J9Y_002 | 1/A/531:533, 1/A/560:564, 1/A/577:579, 1/A/1261:1262, 1/A/2017:2018 | No text annotation | homologous J5_5J7L_014 NA | |
| J5_3J9Y_003 | 1/A/584:589, 1/A/668:671, 1/A/809:812, 1/A/1195:1196, 1/A/1250:1256 | No text annotation | homologous J5_5J7L_015 NA | |
| J5_3J9Y_004 | 1/A/1674:1682, 1/A/1706:1707, 1/A/1751:1752, 1/A/1756:1764, 1/A/1988:1990 | No text annotation | homologous J5_5J7L_016 NA | |
| J5_3J9Y_005 | 1/A/2057:2064, 1/A/2446:2453, 1/A/2500:2507, 1/A/2582:2588, 1/A/2606:2611 | No text annotation | ||
| J5_3J9Y_006 | 1/A/2074:2077, 1/A/2243:2246, 1/A/2258:2259, 1/A/2281:2282, 1/A/2427:2435 | No text annotation | homologous J5_4WF9_007 J5_39529.2 | |
| J5_3J9Y_009 | 1/a/58:61, 1/a/106:113, 1/a/314:316, 1/a/337:339, 1/a/350:354 | No text annotation | homologous J5_5J7L_003 NA | |
| J6_3J9Y_001 | 1/A/45:46, 1/A/179:183, 1/A/214:224, 1/A/231:235, 1/A/262:266, 1/A/426:433 | No text annotation | ||
| J6_3J9Y_002 | 1/A/2074:2077, 1/A/2243:2246, 1/A/2258:2259, 1/A/2281:2284, 1/A/2384:2395, 1/A/2421:2435 | No text annotation | ||
| J7_3J9Y_001 | 1/A/8:15, 1/A/525:531, 1/A/2018:2023, 1/A/2040:2043, 1/A/2625:2630, 1/A/2788:2789, 1/A/2894:2895 | No text annotation | ||
| J7_3J9Y_002 | 1/A/817:822, 1/A/835:837, 1/A/942:946, 1/A/971:976, 1/A/987:991, 1/A/1163:1164, 1/A/1185:1190 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_3J9Y_028 | No text annotation | ||
| J3_3J9Y_007 | No text annotation | ||
| J3_3J9Y_032 | No text annotation | ||
| J3_3J9Y_011 | No text annotation | ||
| J3_3J9Y_013 | No text annotation | ||
| J3_3J9Y_014 | No text annotation | ||
| J3_3J9Y_033 | No text annotation | ||
| J3_3J9Y_023 | No text annotation | ||
| J4_3J9Y_012 | No text annotation | ||
| J5_3J9Y_007 | No text annotation | ||
| J5_3J9Y_008 | No text annotation |
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