5UYP Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_5UYP_001 | 1/01/59:68 | No text annotation | homologous HL_5J7L_134 NA | |
| HL_5UYP_002 | 1/01/87:95 | No text annotation | homologous HL_5J7L_135 NA | |
| HL_5UYP_003 | 1/01/123:128 | No text annotation | homologous HL_5J7L_136 NA | |
| HL_5UYP_005 | 1/01/158:168 | No text annotation | homologous HL_5J7L_138 NA | |
| HL_5UYP_006 | 1/01/194:201 | No text annotation | homologous HL_5J7L_139 NA | |
| HL_5UYP_007 | 1/01/225:230 | No text annotation | homologous HL_5J7L_140 NA | |
| HL_5UYP_008 | 1/01/246:252 | No text annotation | homologous HL_5J7L_141 NA | |
| HL_5UYP_010 | 1/01/327:335 | T-loop with unstacked turn | homologous HL_5J7L_144 NA | |
| HL_5UYP_011 | 1/01/382:392 | No text annotation | homologous HL_5J7L_145 NA | |
| HL_5UYP_012 | 1/01/410:417 | Pseudoknot geometry | homologous HL_5J7L_146 NA | |
| HL_5UYP_013 | 1/01/462:467 | GNRA | homologous HL_4WF9_015 HL_34789.1 | |
| HL_5UYP_016 | 1/01/566:575 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_150 NA | |
| HL_5UYP_017 | 1/01/611:617 | No text annotation | homologous HL_5J7L_151 NA | |
| HL_5UYP_018 | 1/01/629:634 | GNRA | homologous HL_5J7L_152 NA | |
| HL_5UYP_019 | 1/01/641:647 | No text annotation | homologous HL_5J7L_153 NA | |
| HL_5UYP_021 | 1/01/744:753 | No text annotation | homologous HL_7A0S_022 HL_50204.1 | |
| HL_5UYP_022 | 1/01/779:785 | No text annotation | geometric HL_7A0S_007 HL_51020.1 | |
| HL_5UYP_023 | 1/01/826:831 | No text annotation | homologous HL_7RQB_025 NA | |
| HL_5UYP_025 | 1/01/955:962 | GNRA | homologous HL_4WF9_027 HL_34789.1 | |
| HL_5UYP_026 | 1/01/978:985 | No text annotation | homologous HL_5J7L_160 NA | |
| HL_5UYP_030 | 1/01/1222:1227 | GNRA | homologous HL_5J7L_164 NA | |
| HL_5UYP_031 | 1/01/1281:1289 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_165 NA | |
| HL_5UYP_032 | 1/01/1324:1330 | Pseudoknot geometry with 3' bulge | homologous HL_5J7L_166 NA | |
| HL_5UYP_033 | 1/01/1363:1368 | GNRA | homologous HL_5J7L_167 NA | |
| HL_5UYP_034 | 1/01/1389:1398 | No text annotation | homologous HL_7RQB_036 NA | |
| HL_5UYP_035 | 1/01/1450:1461 | No text annotation | geometric HL_5J7L_018 NA | |
| HL_5UYP_036 | 1/01/1492:1498 | Pseudoknot geometry with 3' bulge | homologous HL_5J7L_170 NA | |
| HL_5UYP_038 | 1/01/1565:1568 | No text annotation | homologous HL_7RQB_039 NA | |
| HL_5UYP_039 | 1/01/1612:1619 | No text annotation | homologous HL_4WF9_038 HL_28592.1 | |
| HL_5UYP_040 | 1/01/1630:1636 | GNRA | homologous HL_5J7L_174 NA | |
| HL_5UYP_041 | 1/01/1691:1696 | UNCG | geometric HL_1I6U_001 HL_61337.1 | |
| HL_5UYP_043 | 1/01/1752:1756 | No text annotation | homologous HL_4WF9_042 HL_80709.4 | |
| HL_5UYP_044 | 1/01/1777:1787 | No text annotation | homologous HL_4WF9_043 HL_87681.1 | |
| HL_5UYP_045 | 1/01/1806:1811 | No text annotation | homologous HL_4WF9_044 NA | |
| HL_5UYP_047 | 1/01/1910:1920 | No text annotation | geometric HL_5TBW_049 NA | |
| HL_5UYP_048 | 1/01/1949:1957 | No text annotation | homologous HL_7RQB_049 NA | |
| HL_5UYP_049 | 1/01/2027:2036 | No text annotation | homologous HL_4WF9_047 HL_78372.1 | |
| HL_5UYP_051 | 1/01/2209:2215 | No text annotation | homologous HL_5J7L_185 NA | |
| HL_5UYP_052 | 1/01/2248:2256 | No text annotation | homologous HL_7RQB_053 NA | |
| HL_5UYP_053 | 1/01/2264:2276 | No text annotation | homologous HL_7RQB_054 NA | |
| HL_5UYP_054 | 1/01/2303:2313 | No text annotation | homologous HL_5J7L_188 NA | |
| HL_5UYP_055 | 1/01/2324:2331 | Pseudoknot geometry | homologous HL_5J7L_189 NA | |
| HL_5UYP_056 | 1/01/2356:2361 | GNRA | homologous HL_5J7L_190 NA | |
| HL_5UYP_057 | 1/01/2374:2379 | GNRA | homologous HL_4WF9_054 HL_34789.1 | |
| HL_5UYP_059 | 1/01/2471:2479 | No text annotation | homologous HL_4WF9_056 HL_52011.1 | |
| HL_5UYP_060 | 1/01/2528:2535 | GNRA variation | homologous HL_4WF9_057 HL_46665.1 | |
| HL_5UYP_061 | 1/01/2551:2557 | No text annotation | homologous HL_5J7L_195 NA | |
| HL_5UYP_062 | 1/01/2594:2599 | GNRA | homologous HL_5J7L_196 NA | |
| HL_5UYP_064 | 1/01/2701:2706 | Ribsomal LSU H95 | homologous HL_5J7L_198 NA | |
| HL_5UYP_065 | 1/01/2745:2759 | No text annotation | homologous HL_4WF9_062 HL_53269.1 | |
| HL_5UYP_067 | 1/01/2819:2827 | No text annotation | homologous HL_5J7L_201 NA | |
| HL_5UYP_068 | 1/01/2856:2861 | GNRA | homologous HL_5J7L_202 NA | |
| HL_5UYP_069 | 1/02/34:48 | No text annotation | homologous HL_5J7L_215 NA | |
| HL_5UYP_070 | 1/02/86:90 | Mini UNCG | homologous HL_5J7L_204 NA | |
| HL_5UYP_071 | 1/A/12:22 | No text annotation | homologous HL_5J7L_001 NA | |
| HL_5UYP_073 | 1/A/158:163 | GNRA | homologous HL_5J7L_003 NA | |
| HL_5UYP_076 | 1/A/259:267 | GNRA related | homologous HL_5J7L_006 NA | |
| HL_5UYP_112 | 1/A/296:301 | GNRA | homologous HL_5J7L_007 NA | |
| HL_5UYP_078 | 1/A/320:333 | No text annotation | homologous HL_5J7L_008 NA | |
| HL_5UYP_079 | 1/A/342:347 | UNCG | homologous HL_6CZR_080 NA | |
| HL_5UYP_080 | 1/A/379:384 | GNRA | homologous HL_5J7L_010 NA | |
| HL_5UYP_085 | 1/A/689:698 | No text annotation | homologous HL_6CZR_086 NA | |
| HL_5UYP_086 | 1/A/726:731 | GNRA | homologous HL_5J7L_016 NA | |
| HL_5UYP_087 | 1/A/786:796 | No text annotation | homologous HL_5J7L_017 NA | |
| HL_5UYP_089 | 1/A/862:867 | GNRA | homologous HL_5J7L_019 NA | |
| HL_5UYP_090 | 1/A/897:902 | GNRA | homologous HL_6CZR_091 NA | |
| HL_5UYP_091 | 1/A/963:972 | No text annotation | homologous HL_5J7L_021 NA | |
| HL_5UYP_094 | 1/A/1076:1081 | GNRA | homologous HL_5J7L_023 NA | |
| HL_5UYP_095 | 1/A/1089:1096 | T-loop related | homologous HL_4LFB_025 HL_63894.1 | |
| HL_5UYP_099 | 1/A/1314:1323 | T-loop with 3 stacked bulged bases | homologous HL_4LFB_029 HL_93658.1 | |
| HL_5UYP_100 | 1/A/1356:1366 | No text annotation | homologous HL_4LFB_030 HL_86432.1 | |
| HL_5UYP_102 | 1/A/1515:1520 | GNRA | homologous HL_6CZR_103 NA | |
| HL_5UYP_104 | 1/W/31:39 | tRNA anticodon loop | homologous HL_4TUE_034 NA | |
| HL_5UYP_105 | 1/W/53:61 | T-loop with 2 stacked bulged bases | homologous HL_5AH5_008 HL_33597.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_5UYP_004 | Externally structured | ||
| HL_5UYP_009 | T-loop with 2 stacked bulged bases | ||
| HL_5UYP_014 | GNRA | ||
| HL_5UYP_015 | Mini UNCG with extended bulge | ||
| HL_5UYP_020 | GNRA wlth tandem sheared | ||
| HL_5UYP_024 | No text annotation | ||
| HL_5UYP_027 | No text annotation | ||
| HL_5UYP_028 | No text annotation | ||
| HL_5UYP_029 | No text annotation | ||
| HL_5UYP_037 | UNCG | ||
| HL_5UYP_042 | No text annotation | ||
| HL_5UYP_046 | GNRA variation | ||
| HL_5UYP_050 | No text annotation | ||
| HL_5UYP_058 | No text annotation | ||
| HL_5UYP_063 | GNRA | ||
| HL_5UYP_066 | UNCG variation | ||
| HL_5UYP_072 | No text annotation | ||
| HL_5UYP_074 | GNRA | ||
| HL_5UYP_075 | No text annotation | ||
| HL_5UYP_077 | GNRA with extra cWW | ||
| HL_5UYP_081 | UNCG | ||
| HL_5UYP_082 | GNRA wlth extra near cWW | ||
| HL_5UYP_083 | No text annotation | ||
| HL_5UYP_084 | GNRA-like with tWH | ||
| HL_5UYP_088 | No text annotation | ||
| HL_5UYP_092 | GNRA | ||
| HL_5UYP_093 | No text annotation | ||
| HL_5UYP_096 | No text annotation | ||
| HL_5UYP_097 | GNRA | ||
| HL_5UYP_098 | GNRA | ||
| HL_5UYP_101 | UNCG | ||
| HL_5UYP_103 | tRNA D-loop | ||
| HL_5UYP_106 | tRNA D-loop | ||
| HL_5UYP_107 | tRNA anticodon loop | ||
| HL_5UYP_108 | T-loop with 2 stacked bulged bases | ||
| HL_5UYP_109 | tRNA D-loop | ||
| HL_5UYP_110 | tRNA anticodon loop | ||
| HL_5UYP_111 | T-loop with 2 stacked bulged bases |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_5UYP_001 | 1/01/24:30, 1/01/510:516 | Triple sheared with non-canonical cWW | geometric IL_4WF9_001 IL_22311.1 | |
| IL_5UYP_004 | 1/01/81:85, 1/01/97:105 | Kink-turn | homologous IL_7RQB_004 NA | |
| IL_5UYP_006 | 1/01/188:194, 1/01/201:208 | 8x7 Sarcin-Ricin; G-bulge | geometric IL_7RQB_006 NA | |
| IL_5UYP_007 | 1/01/239:245, 1/01/253:258 | 7x6 Sarcin-Ricin; G-bulge | homologous IL_5J7L_251 NA | |
| IL_5UYP_010 | 1/01/293:295, 1/01/343:347 | No text annotation | homologous IL_5J7L_254 NA | |
| IL_5UYP_011 | 1/01/481:484, 1/01/496:509 | No text annotation | geometric IL_5J7L_255 NA | |
| IL_5UYP_012 | 1/01/536:539, 1/01/554:557 | Double sheared | homologous IL_5J7L_256 NA | |
| IL_5UYP_013 | 1/01/564:566, 1/01/575:577 | Isolated non-canonical cWW pair | geometric IL_5J7L_257 NA | |
| IL_5UYP_014 | 1/01/606:610, 1/01/618:622 | AAA cross-strand stack | homologous IL_5J7L_258 NA | |
| IL_5UYP_015 | 1/01/672:674, 1/01/806:808 | Isolated non-canonical cWW pair | homologous IL_5J7L_259 NA | |
| IL_5UYP_016 | 1/01/674:678, 1/01/799:806 | tHW-tHW cross-strand stack | geometric IL_7RQB_018 NA | |
| IL_5UYP_017 | 1/01/697:698, 1/01/763:765 | Single bulged A | geometric IL_5J7L_261 NA | |
| IL_5UYP_018 | 1/01/702:703, 1/01/728:730 | Single bulged G | geometric IL_4V9F_026 IL_28408.1 | |
| IL_5UYP_019 | 1/01/703:707, 1/01/724:728 | Triple sheared | homologous IL_7RQB_021 NA | |
| IL_5UYP_020 | 1/01/738:740, 1/01/757:758 | Major groove platform | homologous IL_5J7L_264 NA | |
| IL_5UYP_021 | 1/01/775:777, 1/01/787:791 | Multiple bulged bases | homologous IL_7A0S_021 IL_89509.1 | |
| IL_5UYP_022 | 1/01/844:847, 1/01/933:934 | 90 degree turn | homologous IL_5J7L_267 NA | |
| IL_5UYP_176 | 1/01/844:848, 1/01/930:934 | No text annotation | homologous IL_5J7L_399 NA | |
| IL_5UYP_023 | 1/01/847:848, 1/01/930:933 | Stack outside cWW | geometric IL_5J7L_268 NA | |
| IL_5UYP_024 | 1/01/850:851, 1/01/926:928 | Single stack bend | homologous IL_5J7L_269 NA | |
| IL_5UYP_025 | 1/01/856:862, 1/01/915:921 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | homologous IL_5J7L_270 NA | |
| IL_5UYP_026 | 1/01/862:863, 1/01/913:915 | Single bulged G | geometric IL_5J7L_271 NA | |
| IL_5UYP_027 | 1/01/864:868, 1/01/909:912 | C-loop with bulged stacked A's | homologous IL_5J7L_272 NA | |
| IL_5UYP_028 | 1/01/870:872, 1/01/905:907 | Isolated non-canonical cWW pair | homologous IL_5J7L_273 NA | |
| IL_5UYP_031 | 1/01/994:996, 1/01/1159:1160 | Single bulged C | homologous IL_7RQB_035 NA | |
| IL_5UYP_032 | 1/01/998:1002, 1/01/1153:1157 | UAA/GAN | homologous IL_4WF9_036 IL_08938.1 | |
| IL_5UYP_033 | 1/01/1004:1011, 1/01/1150:1151 | Multiple bulged bases | geometric IL_1R3E_002 IL_44609.1 | |
| IL_5UYP_034 | 1/01/1011:1013, 1/01/1149:1150 | Single bulged U | homologous IL_5J7L_279 NA | |
| IL_5UYP_035 | 1/01/1018:1024, 1/01/1140:1144 | Kink-turn related | geometric IL_4WF9_039 IL_57188.6 | |
| IL_5UYP_036 | 1/01/1024:1030, 1/01/1124:1140 | No text annotation | geometric IL_5J7L_281 NA | |
| IL_5UYP_037 | 1/01/1031:1034, 1/01/1121:1123 | Isolated non-canonical cWW pair | homologous IL_5J7L_282 NA | |
| IL_5UYP_042 | 1/01/1196:1198, 1/01/1247:1250 | Isolated cWS basepair | homologous IL_5J7L_286 NA | |
| IL_5UYP_043 | 1/01/1202:1206, 1/01/1240:1243 | No text annotation | homologous IL_5J7L_287 NA | |
| IL_5UYP_044 | 1/01/1208:1215, 1/01/1234:1238 | Kink-turn | homologous IL_5J7L_288 NA | |
| IL_5UYP_045 | 1/01/1262:1269, 1/01/2011:2017 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_5J7L_289 NA | |
| IL_5UYP_046 | 1/01/1310:1313, 1/01/1603:1604 | Major groove platform; stack outside cWW | homologous IL_4WF9_049 IL_74641.1 | |
| IL_5UYP_047 | 1/01/1319:1323, 1/01/1331:1333 | C-loop | homologous IL_5J7L_291 NA | |
| IL_5UYP_048 | 1/01/1351:1355, 1/01/1376:1380 | UAA/GAN | homologous IL_5J7L_292 NA | |
| IL_5UYP_049 | 1/01/1357:1361, 1/01/1370:1374 | tSH-tHW-tHS | homologous IL_5J7L_293 NA | |
| IL_5UYP_051 | 1/01/1417:1421, 1/01/1577:1581 | UAA/GAN | homologous IL_5J7L_295 NA | |
| IL_5UYP_052 | 1/01/1432:1435, 1/01/1557:1561 | Tandem non-canonical cWW pairs | homologous IL_5J7L_296 NA | |
| IL_5UYP_053 | 1/01/1437:1440, 1/01/1551:1555 | tSH-tHW | homologous IL_5J7L_297 NA | |
| IL_5UYP_054 | 1/01/1468:1471, 1/01/1520:1524 | No text annotation | homologous IL_5J7L_299 NA | |
| IL_5UYP_057 | 1/01/1489:1491, 1/01/1499:1500 | Single bulged A | homologous IL_5J7L_302 NA | |
| IL_5UYP_058 | 1/01/1526:1529, 1/01/1542:1546 | UAA/GAN variation | homologous IL_5J7L_303 NA | |
| IL_5UYP_059 | 1/01/1651:1656, 1/01/2004:2006 | No text annotation | homologous IL_7RQB_064 NA | |
| IL_5UYP_060 | 1/01/1663:1665, 1/01/1995:1997 | Isolated tWW turn | homologous IL_5J7L_305 NA | |
| IL_5UYP_061 | 1/01/1666:1669, 1/01/1993:1994 | Major groove platform; stack outside cWW | homologous IL_7RQB_066 NA | |
| IL_5UYP_180 | 1/01/1666:1674, 1/01/1990:1994 | No text annotation | homologous IL_5J7L_386 NA | |
| IL_5UYP_062 | 1/01/1669:1674, 1/01/1990:1993 | Intercalated tWH | geometric IL_5J7L_307 NA | |
| IL_5UYP_063 | 1/01/1686:1691, 1/01/1696:1702 | tSH-tSH-tHH-tHS | homologous IL_7RQB_068 NA | |
| IL_5UYP_065 | 1/01/1720:1724, 1/01/1736:1740 | Triple sheared | homologous IL_5J7L_310 NA | |
| IL_5UYP_066 | 1/01/1770:1771, 1/01/1980:1982 | Single bulged A | homologous IL_5J7L_312 NA | |
| IL_5UYP_067 | 1/01/1798:1804, 1/01/1813:1821 | Kink-turn related | homologous IL_5J7L_313 NA | |
| IL_5UYP_068 | 1/01/1837:1840, 1/01/1902:1903 | Minor groove platform, major groove intercalation | homologous IL_5J7L_314 NA | |
| IL_5UYP_069 | 1/01/1841:1842, 1/01/1898:1901 | Major groove intercalation | homologous IL_5J7L_315 NA | |
| IL_5UYP_070 | 1/01/1846:1849, 1/01/1893:1894 | Major groove minor groove platform; mini C-loop | homologous IL_5J7L_316 NA | |
| IL_5UYP_181 | 1/01/1851:1860, 1/01/1882:1891 | No text annotation | homologous IL_5J7L_387 NA | |
| IL_5UYP_071 | 1/01/1864:1867, 1/01/1874:1878 | UAA/GAN related | homologous IL_5J7L_317 NA | |
| IL_5UYP_072 | 1/01/1933:1934, 1/01/1964:1967 | Bulged stacked bases | geometric IL_7RQB_076 NA | |
| IL_5UYP_073 | 1/01/1934:1945, 1/01/1961:1964 | No text annotation | homologous IL_4WF9_077 IL_84014.1 | |
| IL_5UYP_074 | 1/01/2050:2052, 1/01/2617:2618 | Major groove platform | homologous IL_5J7L_320 NA | |
| IL_5UYP_075 | 1/01/2054:2056, 1/01/2612:2615 | No text annotation | homologous IL_5J7L_321 NA | |
| IL_5UYP_076 | 1/01/2067:2069, 1/01/2442:2443 | Single bulged U | homologous IL_7RQB_080 NA | |
| IL_5UYP_077 | 1/01/2070:2071, 1/01/2438:2441 | Minor groove platform | homologous IL_7RQB_081 NA | |
| IL_5UYP_078 | 1/01/2081:2083, 1/01/2236:2239 | Isolated tHS basepair with bulges | homologous IL_5J7L_325 NA | |
| IL_5UYP_079 | 1/01/2085:2087, 1/01/2232:2234 | Isolated non-canonical cWW pair | homologous IL_5J7L_326 NA | |
| IL_5UYP_190 | 1/01/2106:2124, 1/01/2174:2183 | No text annotation | ||
| IL_5UYP_084 | 1/01/2202:2204, 1/01/2220:2221 | Single bulged U | homologous IL_5J7L_331 NA | |
| IL_5UYP_085 | 1/01/2350:2353, 1/01/2364:2367 | Double sheared | homologous IL_5J7L_333 NA | |
| IL_5UYP_087 | 1/01/2453:2454, 1/01/2498:2500 | Single stack bend | geometric IL_4WF9_089 IL_15011.1 | |
| IL_5UYP_088 | 1/01/2454:2455, 1/01/2496:2498 | Major groove platform | homologous IL_7RQB_092 NA | |
| IL_5UYP_184 | 1/01/2457:2459, 1/01/2493:2494 | Major groove platform | homologous IL_7A0S_085 IL_48076.7 | |
| IL_5UYP_090 | 1/01/2459:2461, 1/01/2489:2493 | Major groove minor groove platform with extra cWW | geometric IL_5J7L_337 NA | |
| IL_5UYP_091 | 1/01/2466:2470, 1/01/2480:2484 | Double sheared with non-canonical cWW | homologous IL_5J7L_338 NA | |
| IL_5UYP_092 | 1/01/2507:2508, 1/01/2580:2582 | Major groove platform | homologous IL_7RQB_096 NA | |
| IL_5UYP_093 | 1/01/2510:2512, 1/01/2574:2578 | Isolated non-canonical cWW with bulges | geometric IL_7RQB_097 NA | |
| IL_5UYP_094 | 1/01/2512:2513, 1/01/2571:2574 | Multiple bulged bases | homologous IL_7RQB_098 NA | |
| IL_5UYP_095 | 1/01/2522:2523, 1/01/2540:2543 | Major groove platform with intercalation | homologous IL_5J7L_342 NA | |
| IL_5UYP_096 | 1/01/2591:2592, 1/01/2601:2603 | Single bulged A | homologous IL_7RQB_101 NA | |
| IL_5UYP_097 | 1/01/2636:2640, 1/01/2774:2782 | tSH-tHS-tHW | homologous IL_7RQB_102 NA | |
| IL_5UYP_098 | 1/01/2652:2658, 1/01/2663:2668 | Sarcin-Ricin target in LSU H95; G-bulge | geometric IL_7RQB_103 NA | |
| IL_5UYP_099 | 1/01/2680:2684, 1/01/2725:2727 | C-loop | homologous IL_5J7L_347 NA | |
| IL_5UYP_100 | 1/01/2687:2691, 1/01/2718:2722 | UAA/GAN related, with intercalation | homologous IL_4WF9_102 IL_82016.1 | |
| IL_5UYP_101 | 1/01/2695:2696, 1/01/2711:2714 | Multiple bulged bases | homologous IL_4WF9_103 IL_44609.1 | |
| IL_5UYP_102 | 1/01/2737:2742, 1/01/2762:2767 | UAA/GAN with extra cWW | homologous IL_5J7L_350 NA | |
| IL_5UYP_105 | 1/01/2843:2846, 1/01/2870:2874 | Multiple bulged bases with non-canonical cWW | homologous IL_5J7L_353 NA | |
| IL_5UYP_106 | 1/01/2847:2852, 1/01/2865:2869 | tHS double platform | homologous IL_5J7L_354 NA | |
| IL_5UYP_107 | 1/02/17:18, 1/02/65:67 | Major groove intercalation | homologous IL_4WF9_112 IL_14190.1 | |
| IL_5UYP_108 | 1/02/23:28, 1/02/56:60 | No text annotation | homologous IL_5J7L_356 NA | |
| IL_5UYP_109 | 1/02/30:31, 1/02/51:54 | Major groove minor groove platform; mini C-loop | homologous IL_5J7L_357 NA | |
| IL_5UYP_110 | 1/02/71:79, 1/02/97:105 | Bacterial 5S Loop E | homologous IL_5J7L_359 NA | |
| IL_5UYP_111 | 1/A/30:32, 1/A/552:553 | Single bulged G | homologous IL_5J7L_001 NA | |
| IL_5UYP_112 | 1/A/44:45, 1/A/396:398 | Single bulged A | homologous IL_5J7L_002 NA | |
| IL_5UYP_113 | 1/A/47:52, 1/A/359:361 | No text annotation | geometric IL_5J7L_003 NA | |
| IL_5UYP_114 | 1/A/54:56, 1/A/356:357 | Minor groove platform | homologous IL_4LFB_004 IL_34520.1 | |
| IL_5UYP_115 | 1/A/63:66, 1/A/103:104 | Multiple bulged bases | homologous IL_4LFB_005 IL_71421.1 | |
| IL_5UYP_116 | 1/A/67:69, 1/A/99:102 | Minor groove platform with extra cWW | homologous IL_5J7L_006 NA | |
| IL_5UYP_119 | 1/A/128:131, 1/A/231:233 | Isolated non-canonical cWW pair | homologous IL_5J7L_009 NA | |
| IL_5UYP_121 | 1/A/144:146, 1/A/176:178 | Isolated cWH basepair | homologous IL_5J7L_011 NA | |
| IL_5UYP_124 | 1/A/242:247, 1/A/277:284 | Kink-turn with non-sequential stacking | homologous IL_4LFB_011 IL_46174.4 | |
| IL_5UYP_126 | 1/A/292:293, 1/A/304:308 | C-loop | homologous IL_6CZR_125 NA | |
| IL_5UYP_127 | 1/A/367:369, 1/A/392:393 | Single bulged U | geometric IL_5J7L_017 NA | |
| IL_5UYP_128 | 1/A/371:375, 1/A/389:390 | C-loop | geometric IL_5J7L_018 NA | |
| IL_5UYP_129 | 1/A/375:376, 1/A/387:389 | Single bulged G | homologous IL_5J7L_019 NA | |
| IL_5UYP_132 | 1/A/446:450, 1/A/483:488 | tSH-tHW-tWW | homologous IL_5J7L_022 NA | |
| IL_5UYP_133 | 1/A/450:455, 1/A/477:483 | No text annotation | geometric IL_5J7L_023 NA | |
| IL_5UYP_134 | 1/A/504:511, 1/A/540:541 | SSU/LSU pseudoknot | homologous IL_5J7L_024 NA | |
| IL_5UYP_135 | 1/A/515:521, 1/A/528:536 | Kink-turn related | geometric IL_4V88_415 NA | |
| IL_5UYP_136 | 1/A/569:575, 1/A/880:881 | No text annotation | homologous IL_5J7L_026 NA | |
| IL_5UYP_137 | 1/A/580:584, 1/A/757:761 | tSH-tHW-tHS | homologous IL_5J7L_027 NA | |
| IL_5UYP_138 | 1/A/594:596, 1/A/644:645 | Major groove platform | homologous IL_5J7L_028 NA | |
| IL_5UYP_140 | 1/A/605:612, 1/A/628:633 | No text annotation | homologous IL_5J7L_030 NA | |
| IL_5UYP_141 | 1/A/654:655, 1/A/751:754 | Major groove platform; stack outside cWW | geometric IL_7RQB_066 NA | |
| IL_5UYP_143 | 1/A/662:666, 1/A/740:743 | Tandem non-canonical cWW pairs | homologous IL_5J7L_033 NA | |
| IL_5UYP_186 | 1/A/673:677, 1/A/713:717 | Triple non-canonical cWW pairs | homologous IL_5J7L_361 NA | |
| IL_5UYP_145 | 1/A/684:688, 1/A/699:706 | Kink-turn | homologous IL_5J7L_035 NA | |
| IL_5UYP_146 | 1/A/774:778, 1/A/804:805 | Left turn | homologous IL_4LFB_032 IL_29346.3 | |
| IL_5UYP_147 | 1/A/779:783, 1/A/799:803 | tSH-tHW-tHS | homologous IL_5J7L_037 NA | |
| IL_5UYP_148 | 1/A/887:894, 1/A/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_5J7L_038 NA | |
| IL_5UYP_149 | 1/A/922:923, 1/A/1393:1395 | Single bulged A | homologous IL_5J7L_039 NA | |
| IL_5UYP_150 | 1/A/925:927, 1/A/1390:1391 | Single bulged G | homologous IL_5J7L_040 NA | |
| IL_5UYP_151 | 1/A/933:935, 1/A/1380:1384 | Minor groove platform | homologous IL_5J7L_041 NA | |
| IL_5UYP_152 | 1/A/953:954, 1/A/1226:1228 | No text annotation | homologous IL_6CZR_150 NA | |
| IL_5UYP_154 | 1/A/998:999, 1/A/1041:1043 | Single stack bend | homologous IL_5J7L_044 NA | |
| IL_5UYP_155 | 1/A/1048:1050, 1/A/1208:1209 | Single bulged U | homologous IL_5J7L_046 NA | |
| IL_5UYP_188 | 1/A/1052:1056, 1/A/1204:1206 | No text annotation | homologous IL_6CZR_154 NA | |
| IL_5UYP_157 | 1/A/1057:1058, 1/A/1199:1203 | Minor groove platform | homologous IL_5J7L_048 NA | |
| IL_5UYP_158 | 1/A/1060:1061, 1/A/1195:1197 | Single bulged U | homologous IL_6CZR_156 NA | |
| IL_5UYP_159 | 1/A/1061:1063, 1/A/1193:1195 | Isolated non-canonical cWW pair | geometric IL_4LFB_047 IL_68118.1 | |
| IL_5UYP_160 | 1/A/1124:1128, 1/A/1144:1149 | No text annotation | homologous IL_5J7L_051 NA | |
| IL_5UYP_162 | 1/A/1158:1161, 1/A/1175:1181 | No text annotation | geometric IL_5J7L_053 NA | |
| IL_5UYP_163 | 1/A/1247:1253, 1/A/1284:1290 | No text annotation | homologous IL_5J7L_054 NA | |
| IL_5UYP_164 | 1/A/1255:1258, 1/A/1277:1282 | 180 degree turn | homologous IL_5J7L_055 NA | |
| IL_5UYP_167 | 1/A/1399:1401, 1/A/1501:1504 | No text annotation | geometric IL_4V88_463 NA | |
| IL_5UYP_168 | 1/A/1401:1404, 1/A/1497:1501 | No text annotation | geometric IL_4V88_464 NA | |
| IL_5UYP_169 | 1/A/1405:1407, 1/A/1494:1496 | Isolated non-canonical cWW pair | geometric IL_5VCI_002 IL_01003.1 | |
| IL_5UYP_170 | 1/A/1407:1409, 1/A/1491:1494 | Isolated cWH basepair | geometric IL_2W2H_002 NA | |
| IL_5UYP_171 | 1/A/1412:1414, 1/A/1486:1488 | Isolated non-canonical cWW pair | homologous IL_5J7L_061 NA | |
| IL_5UYP_172 | 1/A/1416:1419, 1/A/1481:1484 | Double sheared | homologous IL_6CZR_169 NA | |
| IL_5UYP_173 | 1/A/1430:1435, 1/A/1466:1470 | Triple sheared related | homologous IL_5J7L_063 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_5UYP_002 | Single bulged A | ||
| IL_5UYP_003 | Minor groove platform | ||
| IL_5UYP_005 | Single stack bend | ||
| IL_5UYP_008 | No text annotation | ||
| IL_5UYP_189 | No text annotation | ||
| IL_5UYP_009 | No text annotation | ||
| IL_5UYP_029 | Double sheared with non-canonical cWW | ||
| IL_5UYP_177 | No text annotation | ||
| IL_5UYP_030 | Isolated non-canonical cWW pair | ||
| IL_5UYP_038 | Tandem non-canonical cWW pairs | ||
| IL_5UYP_178 | Kink-turn | ||
| IL_5UYP_039 | No text annotation | ||
| IL_5UYP_040 | No text annotation | ||
| IL_5UYP_179 | No text annotation | ||
| IL_5UYP_041 | Major groove platform | ||
| IL_5UYP_050 | No text annotation | ||
| IL_5UYP_055 | tSH-tHW-tHS | ||
| IL_5UYP_056 | 180 degree turn | ||
| IL_5UYP_064 | 6x5 Sarcin-Ricin; G-bulge | ||
| IL_5UYP_080 | Tandem non-canonical cWW pairs | ||
| IL_5UYP_182 | Isolated non-canonical cWW pair | ||
| IL_5UYP_081 | No text annotation | ||
| IL_5UYP_183 | No text annotation | ||
| IL_5UYP_082 | Kink-turn related | ||
| IL_5UYP_083 | No text annotation | ||
| IL_5UYP_086 | No text annotation | ||
| IL_5UYP_089 | Major groove platform with extra pair | ||
| IL_5UYP_103 | No text annotation | ||
| IL_5UYP_104 | Major groove intercalation | ||
| IL_5UYP_117 | Minor groove platform | ||
| IL_5UYP_118 | Major groove intercalation | ||
| IL_5UYP_120 | Minor groove platform related | ||
| IL_5UYP_122 | tWH-tWH-tHW-tHW | ||
| IL_5UYP_123 | Minor groove platform | ||
| IL_5UYP_125 | No text annotation | ||
| IL_5UYP_185 | No text annotation | ||
| IL_5UYP_130 | No text annotation | ||
| IL_5UYP_131 | No text annotation | ||
| IL_5UYP_139 | Major groove minor groove platform; mini C-loop | ||
| IL_5UYP_142 | Single stack bend | ||
| IL_5UYP_144 | No text annotation | ||
| IL_5UYP_153 | Minor groove platform | ||
| IL_5UYP_187 | No text annotation | ||
| IL_5UYP_156 | Tandem non-canonical cWW pairs | ||
| IL_5UYP_161 | Minor groove platform | ||
| IL_5UYP_165 | Double sheared with non-canonical cWW | ||
| IL_5UYP_166 | No text annotation | ||
| IL_5UYP_174 | Single bulged A | ||
| IL_5UYP_175 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_5UYP_001 | 1/01/30:31, 1/01/474:481, 1/01/509:510 | No text annotation | homologous J3_7RQB_001 NA | |
| J3_5UYP_028 | 1/01/30:31, 1/01/474:484, 1/01/496:510 | No text annotation | homologous J3_5J7L_066 NA | |
| J3_5UYP_029 | 1/01/32:35, 1/01/445:461, 1/01/468:473 | No text annotation | homologous J3_5J7L_067 NA | |
| J3_5UYP_002 | 1/01/56:57, 1/01/70:76, 1/01/110:114 | No text annotation | homologous J3_5J7L_037 NA | |
| J3_5UYP_030 | 1/01/297:301, 1/01/316:325, 1/01/337:341 | No text annotation | homologous J3_5J7L_068 NA | |
| J3_5UYP_003 | 1/01/683:689, 1/01/773:775, 1/01/791:794 | No text annotation | homologous J3_7RQB_004 NA | |
| J3_5UYP_004 | 1/01/698:700, 1/01/732:736, 1/01/760:763 | No text annotation | homologous J3_7RQB_005 NA | |
| J3_5UYP_006 | 1/01/1298:1303, 1/01/1625:1627, 1/01/1639:1642 | No text annotation | homologous J3_5J7L_041 NA | |
| J3_5UYP_007 | 1/01/1306:1309, 1/01/1605:1611, 1/01/1620:1622 | No text annotation | homologous J3_5J7L_042 NA | |
| J3_5UYP_008 | 1/01/1344:1349, 1/01/1382:1385, 1/01/1402:1403 | No text annotation | homologous J3_5J7L_043 NA | |
| J3_5UYP_031 | 1/01/1424:1429, 1/01/1564:1565, 1/01/1568:1574 | No text annotation | homologous J3_5J7L_069 NA | |
| J3_5UYP_009 | 1/01/2091:2093, 1/01/2196:2200, 1/01/2223:2228 | Kink-turn 3-way junction | homologous J3_5J7L_044 NA | |
| J3_5UYP_032 | 1/01/2282:2284, 1/01/2384:2395, 1/01/2421:2427 | No text annotation | homologous J3_5J7L_070 NA | |
| J3_5UYP_010 | 1/01/2295:2299, 1/01/2317:2323, 1/01/2332:2337 | No text annotation | ||
| J3_5UYP_011 | 1/01/2517:2520, 1/01/2545:2547, 1/01/2561:2567 | No text annotation | homologous J3_5J7L_046 NA | |
| J3_5UYP_013 | 1/01/2812:2815, 1/01/2831:2836, 1/01/2882:2888 | No text annotation | homologous J3_5J7L_048 NA | |
| J3_5UYP_015 | 1/A/46:47, 1/A/361:367, 1/A/393:395 | No text annotation | homologous J3_5J7L_001 NA | |
| J3_5UYP_034 | 1/A/46:52, 1/A/359:367, 1/A/393:395 | No text annotation | homologous J3_5J7L_050 NA | |
| J3_5UYP_016 | 1/A/586:588, 1/A/651:654, 1/A/754:755 | No text annotation | homologous J3_5J7L_002 NA | |
| J3_5UYP_035 | 1/A/586:588, 1/A/651:655, 1/A/751:755 | No text annotation | homologous J3_5J7L_051 NA | |
| J3_5UYP_017 | 1/A/672:673, 1/A/717:725, 1/A/732:734 | No text annotation | homologous J3_5J7L_003 NA | |
| J3_5UYP_018 | 1/A/826:829, 1/A/857:861, 1/A/868:874 | No text annotation | homologous J3_5J7L_004 NA | |
| J3_5UYP_019 | 1/A/936:939, 1/A/1344:1350, 1/A/1372:1379 | No text annotation | homologous J3_4LFB_002 J3_85722.1 | |
| J3_5UYP_020 | 1/A/943:946, 1/A/1235:1237, 1/A/1337:1340 | No text annotation | homologous J3_5J7L_005 NA | |
| J3_5UYP_021 | 1/A/955:962, 1/A/973:984, 1/A/1221:1225 | No text annotation | homologous J3_5J7L_006 NA | |
| J3_5UYP_024 | 1/A/1063:1068, 1/A/1107:1113, 1/A/1187:1193 | No text annotation | homologous J3_5J7L_008 NA | |
| J3_5UYP_025 | 1/A/1073:1074, 1/A/1083:1087, 1/A/1098:1102 | No text annotation | homologous J3_6CZR_024 NA | |
| J3_5UYP_026 | 1/A/1116:1118, 1/A/1155:1158, 1/A/1181:1184 | No text annotation | homologous J3_5J7L_010 NA | |
| J3_5UYP_037 | 1/A/1116:1118, 1/A/1155:1161, 1/A/1175:1184 | No text annotation | homologous J3_5J7L_054 NA | |
| J3_5UYP_027 | 1/A/1237:1241, 1/A/1296:1303, 1/A/1334:1337 | No text annotation | homologous J3_4LFB_009 J3_03192.1 | |
| J4_5UYP_001 | 1/01/268:269, 1/01/370:375, 1/01/399:406, 1/01/421:424 | No text annotation | homologous J4_5J7L_018 NA | |
| J4_5UYP_002 | 1/01/601:604, 1/01/624:628, 1/01/635:638, 1/01/650:656 | No text annotation | homologous J4_5J7L_020 NA | |
| J4_5UYP_003 | 1/01/1270:1276, 1/01/1294:1295, 1/01/1645:1648, 1/01/2009:2010 | No text annotation | homologous J4_5J7L_021 NA | |
| J4_5UYP_004 | 1/01/1310:1314, 1/01/1338:1343, 1/01/1404:1405, 1/01/1597:1604 | No text annotation | homologous J4_5J7L_022 NA | |
| J4_5UYP_005 | 1/01/1313:1314, 1/01/1338:1343, 1/01/1404:1405, 1/01/1597:1603 | No text annotation | homologous J4_5J7L_023 NA | |
| J4_5UYP_006 | 1/01/1444:1445, 1/01/1466:1467, 1/01/1525:1526, 1/01/1546:1547 | No text annotation | homologous J4_5J7L_024 NA | |
| J4_5UYP_007 | 1/01/1772:1776, 1/01/1788:1792, 1/01/1827:1830, 1/01/1975:1979 | No text annotation | homologous J4_4WF9_007 J4_61477.6 | |
| J4_5UYP_008 | 1/01/1833:1835, 1/01/1905:1906, 1/01/1924:1933, 1/01/1967:1972 | No text annotation | homologous J4_9DFE_008 J4_42306.1 | |
| J4_5UYP_009 | 1/01/2285:2289, 1/01/2343:2347, 1/01/2370:2372, 1/01/2381:2383 | No text annotation | homologous J4_5J7L_027 NA | |
| J4_5UYP_010 | 1/01/2643:2646, 1/01/2674:2676, 1/01/2731:2735, 1/01/2769:2771 | No text annotation | homologous J4_5J7L_028 NA | |
| J4_5UYP_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_5UYP_012 | 1/A/142:144, 1/A/178:184, 1/A/193:198, 1/A/219:221 | No text annotation | homologous J4_5J7L_002 NA | |
| J4_5UYP_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_5UYP_014 | 1/W/7:10, 1/W/25:27, 1/W/43:49, 1/W/65:66 | tRNA junction | homologous J4_4TUE_004 NA | |
| J5_5UYP_001 | 1/01/47:54, 1/01/116:121, 1/01/130:131, 1/01/148:150, 1/01/176:178 | No text annotation | homologous J5_5J7L_013 NA | |
| J5_5UYP_002 | 1/01/531:533, 1/01/560:564, 1/01/577:579, 1/01/1261:1262, 1/01/2017:2018 | No text annotation | homologous J5_5J7L_014 NA | |
| J5_5UYP_003 | 1/01/584:589, 1/01/668:671, 1/01/809:812, 1/01/1195:1196, 1/01/1250:1256 | No text annotation | homologous J5_5J7L_015 NA | |
| J5_5UYP_004 | 1/01/1674:1682, 1/01/1706:1707, 1/01/1751:1752, 1/01/1756:1764, 1/01/1988:1990 | No text annotation | homologous J5_5J7L_016 NA | |
| J5_5UYP_005 | 1/01/2057:2064, 1/01/2446:2453, 1/01/2500:2507, 1/01/2582:2588, 1/01/2606:2611 | No text annotation | ||
| J5_5UYP_006 | 1/01/2074:2077, 1/01/2243:2246, 1/01/2258:2259, 1/01/2281:2282, 1/01/2427:2435 | No text annotation | homologous J5_4WF9_007 J5_39529.2 | |
| J5_5UYP_007 | 1/A/36:39, 1/A/403:406, 1/A/436:440, 1/A/497:500, 1/A/545:548 | No text annotation | homologous J5_5J7L_001 NA | |
| J5_5UYP_008 | 1/A/36:39, 1/A/403:406, 1/A/436:442, 1/A/492:500, 1/A/545:548 | No text annotation | homologous J5_5J7L_002 NA | |
| J5_5UYP_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_4LFB_002 J5_58574.1 | |
| J6_5UYP_001 | 1/01/45:46, 1/01/179:183, 1/01/214:224, 1/01/231:235, 1/01/262:266, 1/01/426:433 | No text annotation | ||
| J6_5UYP_002 | 1/01/2074:2077, 1/01/2243:2246, 1/01/2258:2259, 1/01/2281:2284, 1/01/2384:2395, 1/01/2421:2435 | No text annotation | ||
| J7_5UYP_001 | 1/01/8:15, 1/01/525:531, 1/01/2018:2023, 1/01/2040:2043, 1/01/2625:2630, 1/01/2788:2789, 1/01/2894:2895 | No text annotation | ||
| J7_5UYP_003 | 1/01/817:822, 1/01/835:838, 1/01/940:946, 1/01/971:976, 1/01/987:991, 1/01/1163:1164, 1/01/1185:1190 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_5UYP_005 | No text annotation | ||
| J3_5UYP_038 | No text annotation | ||
| J3_5UYP_033 | No text annotation | ||
| J3_5UYP_012 | No text annotation | ||
| J3_5UYP_014 | No text annotation | ||
| J3_5UYP_022 | No text annotation | ||
| J3_5UYP_036 | No text annotation | ||
| J3_5UYP_023 | No text annotation | ||
| J4_5UYP_015 | tRNA junction | ||
| J4_5UYP_016 | tRNA junction | ||
| J7_5UYP_002 | No text annotation |
Coloring options: