8VUP Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_8VUP_001 | 1/1/59:68 | No text annotation | geometric HL_5J7L_134 NA | |
| HL_8VUP_002 | 1/1/87:95 | No text annotation | geometric HL_5J7L_135 NA | |
| HL_8VUP_003 | 1/1/123:128 | No text annotation | geometric HL_5J7L_136 NA | |
| HL_8VUP_005 | 1/1/158:168 | No text annotation | geometric HL_5J7L_138 NA | |
| HL_8VUP_006 | 1/1/194:201 | No text annotation | geometric HL_8CRE_001 NA | |
| HL_8VUP_007 | 1/1/225:230 | No text annotation | geometric HL_5J7L_140 NA | |
| HL_8VUP_008 | 1/1/246:252 | No text annotation | geometric HL_5J7L_141 NA | |
| HL_8VUP_009 | 1/1/305:312 | T-loop with 1 bulged base | geometric HL_7A0S_010 HL_13999.1 | |
| HL_8VUP_010 | 1/1/327:335 | T-loop with unstacked turn | geometric HL_5J7L_144 NA | |
| HL_8VUP_011 | 1/1/381:393 | No text annotation | ||
| HL_8VUP_012 | 1/1/410:417 | Pseudoknot geometry | geometric HL_7A0S_014 HL_30680.4 | |
| HL_8VUP_013 | 1/1/462:467 | GNRA | geometric HL_8CRE_218 HL_34789.1 | |
| HL_8VUP_014 | 1/1/487:493 | GNRA | geometric HL_5J7L_148 NA | |
| HL_8VUP_016 | 1/1/564:577 | No text annotation | ||
| HL_8VUP_017 | 1/1/611:617 | No text annotation | geometric HL_5J7L_151 NA | |
| HL_8VUP_018 | 1/1/629:634 | GNRA | geometric HL_5J7L_152 NA | |
| HL_8VUP_019 | 1/1/641:647 | No text annotation | geometric HL_5J7L_153 NA | |
| HL_8VUP_021 | 1/1/744:753 | No text annotation | geometric HL_4WF9_023 HL_50204.1 | |
| HL_8VUP_022 | 1/1/779:785 | UNCG variation | geometric HL_7A0S_023 HL_51020.1 | |
| HL_8VUP_023 | 1/1/826:831 | No text annotation | geometric HL_9DFE_023 HL_27530.1 | |
| HL_8VUP_025 | 1/1/955:962 | GNRA | geometric HL_4WF9_027 HL_34789.1 | |
| HL_8VUP_026 | 1/1/978:985 | No text annotation | geometric HL_7A0S_027 HL_47171.1 | |
| HL_8VUP_030 | 1/1/1222:1227 | GNRA | geometric HL_7A0S_031 HL_34789.1 | |
| HL_8VUP_031 | 1/1/1281:1289 | T-loop with 2 stacked bulged bases | geometric HL_8CRE_030 NA | |
| HL_8VUP_032 | 1/1/1324:1330 | Pseudoknot geometry with 3' bulge | geometric HL_5J7L_166 NA | |
| HL_8VUP_033 | 1/1/1363:1368 | GNRA | geometric HL_9DFE_033 HL_34789.1 | |
| HL_8VUP_034 | 1/1/1389:1398 | No text annotation | geometric HL_5J7L_168 NA | |
| HL_8VUP_035 | 1/1/1451:1459 | No text annotation | ||
| HL_8VUP_036 | 1/1/1492:1498 | Pseudoknot geometry with 3' bulge | geometric HL_5J7L_170 NA | |
| HL_8VUP_038 | 1/1/1565:1568 | Mini UNCG | geometric HL_7QQP_002 HL_90436.1 | |
| HL_8VUP_039 | 1/1/1612:1619 | No text annotation | geometric HL_5J7L_173 NA | |
| HL_8VUP_040 | 1/1/1630:1636 | GNRA | geometric HL_5J7L_174 NA | |
| HL_8VUP_041 | 1/1/1691:1696 | UNCG | geometric HL_4PMI_004 NA | |
| HL_8VUP_042 | 1/1/1727:1733 | UNCG variation | geometric HL_7A0S_023 HL_51020.1 | |
| HL_8VUP_043 | 1/1/1752:1756 | No text annotation | geometric HL_9DFE_042 HL_80709.4 | |
| HL_8VUP_044 | 1/1/1777:1787 | No text annotation | geometric HL_5J7L_178 NA | |
| HL_8VUP_045 | 1/1/1806:1811 | GNRA related | geometric HL_3OXE_002 HL_37569.1 | |
| HL_8VUP_046 | 1/1/1868:1873 | GNRA | geometric HL_5D5L_001 HL_34789.1 | |
| HL_8VUP_047 | 1/1/1910:1920 | No text annotation | geometric HL_8CRE_047 NA | |
| HL_8VUP_048 | 1/1/1949:1957 | No text annotation | geometric HL_4WF9_046 HL_61418.1 | |
| HL_8VUP_049 | 1/1/2027:2036 | No text annotation | geometric HL_5J7L_183 NA | |
| HL_8VUP_051 | 1/1/2209:2215 | No text annotation | geometric HL_5J7L_185 NA | |
| HL_8VUP_052 | 1/1/2248:2256 | No text annotation | geometric HL_7A0S_052 HL_11974.1 | |
| HL_8VUP_053 | 1/1/2264:2276 | No text annotation | geometric HL_5J7L_187 NA | |
| HL_8VUP_054 | 1/1/2304:2312 | No text annotation | geometric HL_9DFE_198 HL_02452.1 | |
| HL_8VUP_055 | 1/1/2324:2331 | Pseudoknot geometry | geometric HL_5J7L_189 NA | |
| HL_8VUP_056 | 1/1/2356:2361 | GNRA | geometric HL_5J7L_190 NA | |
| HL_8VUP_057 | 1/1/2374:2379 | GNRA | geometric HL_5J7L_191 NA | |
| HL_8VUP_058 | 1/1/2404:2413 | No text annotation | geometric HL_5J7L_192 NA | |
| HL_8VUP_059 | 1/1/2471:2479 | No text annotation | geometric HL_4WF9_056 HL_52011.1 | |
| HL_8VUP_060 | 1/1/2528:2535 | GNRA variation | geometric HL_5J7L_194 NA | |
| HL_8VUP_061 | 1/1/2551:2557 | No text annotation | geometric HL_5J7L_195 NA | |
| HL_8VUP_062 | 1/1/2594:2599 | GNRA | geometric HL_7A0S_068 HL_34789.1 | |
| HL_8VUP_063 | 1/1/2658:2663 | GNRA | geometric HL_4Y1M_004 HL_34789.1 | |
| HL_8VUP_064 | 1/1/2701:2706 | Ribsomal LSU H95 | geometric HL_5J7L_198 NA | |
| HL_8VUP_065 | 1/1/2745:2759 | No text annotation | geometric HL_5J7L_199 NA | |
| HL_8VUP_066 | 1/1/2795:2801 | No text annotation | geometric HL_8CRE_038 NA | |
| HL_8VUP_067 | 1/1/2819:2827 | No text annotation | geometric HL_5J7L_201 NA | |
| HL_8VUP_068 | 1/1/2856:2861 | GNRA | geometric HL_5J7L_202 NA | |
| HL_8VUP_069 | 1/2/12:22 | No text annotation | geometric HL_5J7L_001 NA | |
| HL_8VUP_077 | 1/2/342:347 | UNCG | geometric HL_4WF9_040 HL_61337.1 | |
| HL_8VUP_082 | 1/2/617:623 | GNRA-like with tWH | geometric HL_5J7L_014 NA | |
| HL_8VUP_083 | 1/2/689:698 | No text annotation | geometric HL_5J7L_015 NA | |
| HL_8VUP_084 | 1/2/726:731 | GNRA | geometric HL_4LFB_016 HL_34789.1 | |
| HL_8VUP_085 | 1/2/786:796 | No text annotation | geometric HL_4LFB_017 HL_38491.1 | |
| HL_8VUP_087 | 1/2/862:867 | GNRA | geometric HL_4LFB_019 HL_34789.1 | |
| HL_8VUP_088 | 1/2/897:902 | GNRA | geometric HL_5U3G_002 NA | |
| HL_8VUP_089 | 1/2/963:972 | No text annotation | ||
| HL_8VUP_091 | 1/2/1076:1081 | GNRA | geometric HL_5J7L_027 NA | |
| HL_8VUP_092 | 1/2/1089:1096 | No text annotation | ||
| HL_8VUP_096 | 1/2/1314:1323 | T-loop with 3 stacked bulged bases | geometric HL_4LFB_029 HL_93658.1 | |
| HL_8VUP_097 | 1/2/1356:1366 | No text annotation | geometric HL_4LFB_030 HL_86432.1 | |
| HL_8VUP_099 | 1/2/1515:1520 | GNRA | geometric HL_6SVS_001 HL_34789.1 | |
| HL_8VUP_100 | 1/3/34:48 | No text annotation | geometric HL_5J7L_215 NA | |
| HL_8VUP_101 | 1/3/38:44 | No text annotation | geometric HL_5J7L_203 NA | |
| HL_8VUP_102 | 1/3/86:90 | Mini UNCG | geometric HL_5J7L_204 NA | |
| HL_8VUP_103 | 1/5/13:22 | No text annotation | ||
| HL_8VUP_104 | 1/5/31:39 | tRNA anticodon loop | geometric HL_5IBB_210 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_8VUP_004 | No text annotation | ||
| HL_8VUP_015 | No text annotation | ||
| HL_8VUP_020 | GNRA wlth tandem sheared | ||
| HL_8VUP_024 | No text annotation | ||
| HL_8VUP_027 | No text annotation | ||
| HL_8VUP_028 | No text annotation | ||
| HL_8VUP_029 | No text annotation | ||
| HL_8VUP_037 | No text annotation | ||
| HL_8VUP_050 | No text annotation | ||
| HL_8VUP_070 | No text annotation | ||
| HL_8VUP_071 | GNRA | ||
| HL_8VUP_072 | GNRA | ||
| HL_8VUP_073 | No text annotation | ||
| HL_8VUP_074 | GNRA related | ||
| HL_8VUP_075 | GNRA | ||
| HL_8VUP_076 | No text annotation | ||
| HL_8VUP_078 | GNRA | ||
| HL_8VUP_079 | UNCG | ||
| HL_8VUP_080 | No text annotation | ||
| HL_8VUP_081 | GNRA variation | ||
| HL_8VUP_086 | No text annotation | ||
| HL_8VUP_090 | GNRA | ||
| HL_8VUP_093 | No text annotation | ||
| HL_8VUP_094 | GNRA | ||
| HL_8VUP_095 | GNRA | ||
| HL_8VUP_098 | No text annotation | ||
| HL_8VUP_105 | T-loop with 2 stacked bulged bases |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_8VUP_001 | 1/1/24:30, 1/1/510:516 | Triple sheared with non-canonical cWW | geometric IL_4WF9_001 IL_22311.1 | |
| IL_8VUP_002 | 1/1/36:37, 1/1/442:444 | Single bulged A | geometric IL_7A0S_002 IL_14190.1 | |
| IL_8VUP_003 | 1/1/43:44, 1/1/434:436 | Minor groove platform | geometric IL_5J7L_247 NA | |
| IL_8VUP_004 | 1/1/81:85, 1/1/97:105 | No text annotation | geometric IL_5J7L_248 NA | |
| IL_8VUP_005 | 1/1/183:184, 1/1/212:214 | Single stack bend | geometric IL_7A0S_005 IL_15011.1 | |
| IL_8VUP_006 | 1/1/188:194, 1/1/201:208 | 8x7 Sarcin-Ricin; G-bulge | geometric IL_7A0S_006 IL_62167.1 | |
| IL_8VUP_007 | 1/1/239:245, 1/1/253:258 | 7x6 Sarcin-Ricin; G-bulge | geometric IL_5J7L_251 NA | |
| IL_8VUP_008 | 1/1/269:271, 1/1/366:370 | No text annotation | geometric IL_5J7L_252 NA | |
| IL_8VUP_010 | 1/1/293:295, 1/1/343:347 | No text annotation | geometric IL_5J7L_254 NA | |
| IL_8VUP_011 | 1/1/481:484, 1/1/496:509 | No text annotation | geometric IL_5J7L_255 NA | |
| IL_8VUP_012 | 1/1/536:539, 1/1/554:557 | Double sheared | geometric IL_5J7L_256 NA | |
| IL_8VUP_013 | 1/1/606:610, 1/1/618:622 | AAA cross-strand stack | geometric IL_5J7L_258 NA | |
| IL_8VUP_014 | 1/1/674:678, 1/1/799:806 | tHW-tHW cross-strand stack | geometric IL_5J7L_260 NA | |
| IL_8VUP_015 | 1/1/697:698, 1/1/763:765 | Single bulged A | geometric IL_9DFE_017 IL_14190.1 | |
| IL_8VUP_016 | 1/1/702:703, 1/1/728:730 | Single bulged G | geometric IL_4V9F_026 IL_28408.1 | |
| IL_8VUP_017 | 1/1/703:707, 1/1/724:728 | Triple sheared | geometric IL_5J7L_263 NA | |
| IL_8VUP_018 | 1/1/738:740, 1/1/757:758 | Major groove platform | geometric IL_5J7L_264 NA | |
| IL_8VUP_019 | 1/1/775:777, 1/1/787:791 | Multiple bulged bases | geometric IL_5J7L_265 NA | |
| IL_8VUP_020 | 1/1/844:848, 1/1/930:934 | No text annotation | geometric IL_5J7L_399 NA | |
| IL_8VUP_021 | 1/1/850:851, 1/1/926:928 | Single stack bend | geometric IL_5J7L_269 NA | |
| IL_8VUP_022 | 1/1/856:862, 1/1/915:921 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | geometric IL_5J7L_270 NA | |
| IL_8VUP_023 | 1/1/862:863, 1/1/913:915 | Single bulged G | geometric IL_5J7L_271 NA | |
| IL_8VUP_024 | 1/1/864:868, 1/1/909:912 | C-loop with bulged stacked A's | geometric IL_5J7L_272 NA | |
| IL_8VUP_025 | 1/1/870:872, 1/1/905:907 | Isolated non-canonical cWW pair | geometric IL_5J7L_273 NA | |
| IL_8VUP_026 | 1/1/875:879, 1/1/898:902 | Double sheared with non-canonical cWW | geometric IL_4WFL_001 IL_87767.1 | |
| IL_8VUP_028 | 1/1/994:996, 1/1/1159:1160 | Single bulged C | geometric IL_7A0S_032 IL_05642.1 | |
| IL_8VUP_029 | 1/1/998:1002, 1/1/1153:1157 | UAA/GAN | geometric IL_4WF9_036 IL_08938.1 | |
| IL_8VUP_030 | 1/1/1004:1011, 1/1/1150:1151 | SSU/LSU pseudoknot | geometric IL_4WF9_037 IL_11411.1 | |
| IL_8VUP_031 | 1/1/1011:1013, 1/1/1149:1150 | Single bulged U | geometric IL_5J7L_279 NA | |
| IL_8VUP_032 | 1/1/1018:1024, 1/1/1140:1144 | Kink-turn related | geometric IL_4WF9_039 IL_57188.6 | |
| IL_8VUP_033 | 1/1/1024:1030, 1/1/1124:1140 | No text annotation | geometric IL_5J7L_281 NA | |
| IL_8VUP_034 | 1/1/1031:1034, 1/1/1121:1123 | Isolated non-canonical cWW pair | geometric IL_4K31_002 IL_30229.1 | |
| IL_8VUP_035 | 1/1/1038:1041, 1/1/1114:1117 | Tandem non-canonical cWW pairs | geometric IL_5J7L_283 NA | |
| IL_8VUP_036 | 1/1/1043:1051, 1/1/1108:1112 | Kink-turn | geometric IL_4V9F_042 IL_99692.3 | |
| IL_8VUP_038 | 1/1/1196:1198, 1/1/1247:1250 | Isolated cWS basepair | geometric IL_7A0S_041 IL_42997.4 | |
| IL_8VUP_039 | 1/1/1202:1206, 1/1/1240:1243 | No text annotation | geometric IL_5J7L_287 NA | |
| IL_8VUP_040 | 1/1/1208:1215, 1/1/1234:1238 | Kink-turn | geometric IL_5J7L_288 NA | |
| IL_8VUP_041 | 1/1/1262:1269, 1/1/2011:2017 | 8x7 Sarcin-Ricin; G-bulge | geometric IL_5J7L_289 NA | |
| IL_8VUP_042 | 1/1/1319:1323, 1/1/1331:1333 | C-loop | geometric IL_5J7L_291 NA | |
| IL_8VUP_043 | 1/1/1351:1355, 1/1/1376:1380 | UAA/GAN | geometric IL_5J7L_292 NA | |
| IL_8VUP_044 | 1/1/1357:1361, 1/1/1370:1374 | tSH-tHW-tHS | geometric IL_5J7L_293 NA | |
| IL_8VUP_045 | 1/1/1415:1416, 1/1/1582:1587 | No text annotation | ||
| IL_8VUP_046 | 1/1/1417:1421, 1/1/1577:1581 | UAA/GAN | geometric IL_8CRE_129 NA | |
| IL_8VUP_047 | 1/1/1432:1435, 1/1/1557:1561 | Tandem non-canonical cWW pairs | geometric IL_5J7L_296 NA | |
| IL_8VUP_048 | 1/1/1437:1440, 1/1/1551:1555 | tSH-tHW | geometric IL_5J7L_297 NA | |
| IL_8VUP_049 | 1/1/1450:1451, 1/1/1459:1461 | Single bulged U | geometric IL_5J7L_298 NA | |
| IL_8VUP_050 | 1/1/1468:1473, 1/1/1518:1524 | No text annotation | ||
| IL_8VUP_051 | 1/1/1474:1478, 1/1/1513:1517 | tSH-tHW-tHS | geometric IL_5J7L_300 NA | |
| IL_8VUP_052 | 1/1/1481:1482, 1/1/1507:1510 | 180 degree turn | geometric IL_5J7L_301 NA | |
| IL_8VUP_053 | 1/1/1489:1491, 1/1/1499:1500 | Single bulged A | geometric IL_4V9F_098 IL_14190.1 | |
| IL_8VUP_054 | 1/1/1526:1529, 1/1/1542:1546 | UAA/GAN variation | geometric IL_5J7L_303 NA | |
| IL_8VUP_055 | 1/1/1651:1656, 1/1/2004:2006 | No text annotation | geometric IL_5J7L_304 NA | |
| IL_8VUP_056 | 1/1/1663:1665, 1/1/1995:1997 | Isolated tWW turn | geometric IL_7A0S_060 IL_10432.1 | |
| IL_8VUP_057 | 1/1/1666:1669, 1/1/1993:1994 | Major groove platform; stack outside cWW | geometric IL_8P9A_304 IL_74641.1 | |
| IL_8VUP_058 | 1/1/1666:1674, 1/1/1990:1994 | No text annotation | geometric IL_8P9A_305 IL_80252.1 | |
| IL_8VUP_059 | 1/1/1669:1674, 1/1/1990:1993 | No text annotation | geometric IL_8P9A_306 IL_28217.1 | |
| IL_8VUP_060 | 1/1/1686:1691, 1/1/1696:1702 | tSH-tSH-tHH-tHS | geometric IL_5J7L_308 NA | |
| IL_8VUP_061 | 1/1/1712:1718, 1/1/1742:1746 | 6x5 Sarcin-Ricin; G-bulge | geometric IL_5J7L_309 NA | |
| IL_8VUP_062 | 1/1/1720:1724, 1/1/1736:1740 | Triple sheared | geometric IL_5J7L_310 NA | |
| IL_8VUP_063 | 1/1/1770:1771, 1/1/1980:1982 | Single bulged A | geometric IL_7A0S_064 IL_14190.1 | |
| IL_8VUP_064 | 1/1/1798:1804, 1/1/1813:1821 | Kink-turn related | geometric IL_5J7L_313 NA | |
| IL_8VUP_065 | 1/1/1837:1840, 1/1/1902:1903 | Minor groove platform, major groove intercalation | geometric IL_1U9S_005 NA | |
| IL_8VUP_066 | 1/1/1841:1842, 1/1/1898:1901 | Major groove intercalation | geometric IL_4WF9_071 IL_78536.1 | |
| IL_8VUP_067 | 1/1/1846:1849, 1/1/1893:1894 | Major groove minor groove platform; mini C-loop | geometric IL_1S03_007 IL_73108.1 | |
| IL_8VUP_068 | 1/1/1851:1860, 1/1/1882:1891 | No text annotation | geometric IL_5J7L_387 NA | |
| IL_8VUP_069 | 1/1/1864:1867, 1/1/1874:1878 | UAA/GAN related | geometric IL_5J7L_317 NA | |
| IL_8VUP_070 | 1/1/1933:1945, 1/1/1961:1967 | No text annotation | ||
| IL_8VUP_071 | 1/1/2050:2052, 1/1/2617:2618 | Major groove platform | geometric IL_5J7L_320 NA | |
| IL_8VUP_072 | 1/1/2054:2056, 1/1/2612:2615 | No text annotation | geometric IL_4WF9_079 IL_80025.1 | |
| IL_8VUP_073 | 1/1/2067:2069, 1/1/2442:2443 | Single bulged U | geometric IL_8P9A_321 IL_97561.1 | |
| IL_8VUP_074 | 1/1/2070:2071, 1/1/2438:2441 | Minor groove platform | geometric IL_4V9F_075 IL_34520.1 | |
| IL_8VUP_075 | 1/1/2081:2083, 1/1/2236:2239 | No text annotation | geometric IL_8CRE_100 NA | |
| IL_8VUP_076 | 1/1/2085:2087, 1/1/2232:2234 | Isolated non-canonical cWW pair | geometric IL_5J7L_326 NA | |
| IL_8VUP_081 | 1/1/2202:2204, 1/1/2220:2221 | Single bulged U | geometric IL_5J7L_331 NA | |
| IL_8VUP_082 | 1/1/2350:2353, 1/1/2364:2367 | Double sheared | geometric IL_7A0S_081 IL_58355.1 | |
| IL_8VUP_083 | 1/1/2401:2403, 1/1/2414:2415 | No text annotation | ||
| IL_8VUP_084 | 1/1/2453:2455, 1/1/2496:2500 | No text annotation | ||
| IL_8VUP_085 | 1/1/2457:2459, 1/1/2493:2494 | Major groove platform | geometric IL_9DFE_093 IL_48076.7 | |
| IL_8VUP_086 | 1/1/2459:2461, 1/1/2489:2493 | No text annotation | ||
| IL_8VUP_087 | 1/1/2466:2470, 1/1/2480:2484 | Double sheared with non-canonical cWW | geometric IL_7A0S_087 IL_87767.1 | |
| IL_8VUP_088 | 1/1/2507:2508, 1/1/2580:2582 | Major groove platform | geometric IL_4WF9_094 IL_46637.1 | |
| IL_8VUP_089 | 1/1/2510:2512, 1/1/2574:2578 | Isolated non-canonical cWW with bulges | geometric IL_5J7L_340 NA | |
| IL_8VUP_090 | 1/1/2512:2515, 1/1/2569:2574 | No text annotation | ||
| IL_8VUP_091 | 1/1/2522:2523, 1/1/2540:2543 | Major groove platform with intercalation | geometric IL_5J7L_342 NA | |
| IL_8VUP_092 | 1/1/2591:2592, 1/1/2601:2603 | Single bulged A | geometric IL_8P9A_399 IL_14190.1 | |
| IL_8VUP_093 | 1/1/2636:2640, 1/1/2774:2782 | tSH-tHS-tHW | geometric IL_5J7L_345 NA | |
| IL_8VUP_094 | 1/1/2652:2658, 1/1/2663:2668 | Sarcin-Ricin target in LSU H95; G-bulge | geometric IL_5J7L_346 NA | |
| IL_8VUP_095 | 1/1/2676:2677, 1/1/2730:2732 | Single stack bend | geometric IL_7A0S_054 IL_15011.1 | |
| IL_8VUP_096 | 1/1/2680:2684, 1/1/2725:2727 | C-loop | geometric IL_7A0S_095 IL_63596.12 | |
| IL_8VUP_097 | 1/1/2687:2691, 1/1/2718:2722 | UAA/GAN related, with intercalation | geometric IL_4WF9_102 IL_82016.1 | |
| IL_8VUP_098 | 1/1/2695:2696, 1/1/2711:2714 | Multiple bulged bases | geometric IL_4WF9_103 IL_44609.1 | |
| IL_8VUP_099 | 1/1/2737:2742, 1/1/2762:2767 | UAA/GAN with extra cWW | geometric IL_5J7L_350 NA | |
| IL_8VUP_100 | 1/1/2806:2811, 1/1/2889:2892 | No text annotation | geometric IL_5J7L_351 NA | |
| IL_8VUP_101 | 1/1/2838:2839, 1/1/2878:2880 | Major groove intercalation | geometric IL_4WF9_106 IL_78536.1 | |
| IL_8VUP_102 | 1/1/2841:2846, 1/1/2870:2876 | No text annotation | ||
| IL_8VUP_103 | 1/1/2847:2852, 1/1/2865:2869 | tHS double platform | geometric IL_5J7L_354 NA | |
| IL_8VUP_106 | 1/2/54:56, 1/2/356:357 | Minor groove platform | geometric IL_8CRE_394 IL_34520.1 | |
| IL_8VUP_110 | 1/2/128:131, 1/2/231:233 | No text annotation | ||
| IL_8VUP_114 | 1/2/242:247, 1/2/277:284 | Kink-turn with non-sequential stacking | geometric IL_4LFB_011 IL_46174.4 | |
| IL_8VUP_116 | 1/2/292:293, 1/2/304:308 | C-loop | geometric IL_5J7L_016 NA | |
| IL_8VUP_124 | 1/2/580:584, 1/2/757:761 | tSH-tHW-tHS | geometric IL_5J7L_027 NA | |
| IL_8VUP_128 | 1/2/654:655, 1/2/751:754 | Major groove platform; stack outside cWW | geometric IL_5J7L_031 NA | |
| IL_8VUP_129 | 1/2/659:666, 1/2/740:747 | No text annotation | ||
| IL_8VUP_130 | 1/2/673:678, 1/2/712:717 | No text annotation | ||
| IL_8VUP_131 | 1/2/684:688, 1/2/699:706 | Kink-turn | geometric IL_5J7L_035 NA | |
| IL_8VUP_132 | 1/2/774:778, 1/2/804:805 | Left turn | geometric IL_5J7L_036 NA | |
| IL_8VUP_133 | 1/2/779:783, 1/2/799:803 | tSH-tHW-tHS | geometric IL_4LFB_033 IL_05821.1 | |
| IL_8VUP_134 | 1/2/887:895, 1/2/904:910 | No text annotation | ||
| IL_8VUP_135 | 1/2/922:923, 1/2/1393:1395 | Single bulged A | geometric IL_8CRE_443 IL_14190.1 | |
| IL_8VUP_136 | 1/2/925:927, 1/2/1390:1391 | Single bulged G | geometric IL_5J7L_040 NA | |
| IL_8VUP_143 | 1/2/1057:1058, 1/2/1199:1203 | Minor groove platform | geometric IL_5J7L_048 NA | |
| IL_8VUP_144 | 1/2/1060:1061, 1/2/1195:1197 | Single bulged A | geometric IL_5J7L_049 NA | |
| IL_8VUP_145 | 1/2/1061:1063, 1/2/1193:1195 | Isolated non-canonical cWW pair | geometric IL_5J7L_050 NA | |
| IL_8VUP_151 | 1/2/1259:1263, 1/2/1272:1276 | Double sheared with non-canonical cWW | geometric IL_5J7L_056 NA | |
| IL_8VUP_152 | 1/2/1399:1404, 1/2/1497:1504 | No text annotation | ||
| IL_8VUP_153 | 1/2/1405:1409, 1/2/1491:1496 | No text annotation | ||
| IL_8VUP_154 | 1/2/1412:1414, 1/2/1486:1488 | Isolated non-canonical cWW pair | geometric IL_8P9A_270 IL_01003.1 | |
| IL_8VUP_155 | 1/2/1416:1421, 1/2/1479:1484 | Double sheared; A in syn; two near cWW pairs | geometric IL_4N0T_001 IL_82292.2 | |
| IL_8VUP_156 | 1/2/1430:1437, 1/2/1464:1470 | No text annotation | ||
| IL_8VUP_159 | 1/3/17:18, 1/3/65:67 | Major groove intercalation | geometric IL_5J7L_355 NA | |
| IL_8VUP_160 | 1/3/23:28, 1/3/56:60 | No text annotation | geometric IL_5J7L_356 NA | |
| IL_8VUP_161 | 1/3/30:31, 1/3/51:54 | No text annotation | geometric IL_9DFE_112 IL_73108.1 | |
| IL_8VUP_162 | 1/3/34:38, 1/3/44:48 | Symmetric double minor groove platform | geometric IL_5J7L_358 NA | |
| IL_8VUP_163 | 1/3/71:79, 1/3/97:105 | Bacterial 5S Loop E | geometric IL_5J7L_359 NA | |
| IL_8VUP_164 | 1/5/29:31, 1/5/39:41 | Isolated non-canonical cWW pair | geometric IL_4E48_003 IL_01003.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_8VUP_009 | No text annotation | ||
| IL_8VUP_027 | No text annotation | ||
| IL_8VUP_037 | No text annotation | ||
| IL_8VUP_077 | Isolated non-canonical cWW pair | ||
| IL_8VUP_078 | No text annotation | ||
| IL_8VUP_079 | No text annotation | ||
| IL_8VUP_080 | No text annotation | ||
| IL_8VUP_104 | Tandem non-canonical cWW pairs | ||
| IL_8VUP_105 | Single bulged A | ||
| IL_8VUP_107 | Multiple bulged bases | ||
| IL_8VUP_108 | Minor groove platform with extra cWW | ||
| IL_8VUP_109 | Minor groove platform | ||
| IL_8VUP_111 | Minor groove platform related | ||
| IL_8VUP_112 | Isolated cWH basepair | ||
| IL_8VUP_113 | No text annotation | ||
| IL_8VUP_115 | No text annotation | ||
| IL_8VUP_117 | Single bulged U | ||
| IL_8VUP_118 | No text annotation | ||
| IL_8VUP_119 | No text annotation | ||
| IL_8VUP_120 | tSH-tHW-tWW | ||
| IL_8VUP_121 | No text annotation | ||
| IL_8VUP_122 | SSU/LSU pseudoknot | ||
| IL_8VUP_123 | Kink-turn related | ||
| IL_8VUP_125 | Major groove platform | ||
| IL_8VUP_126 | No text annotation | ||
| IL_8VUP_127 | No text annotation | ||
| IL_8VUP_137 | Minor groove platform | ||
| IL_8VUP_138 | Minor groove platform | ||
| IL_8VUP_139 | Single stack bend | ||
| IL_8VUP_140 | No text annotation | ||
| IL_8VUP_141 | Single bulged U | ||
| IL_8VUP_142 | No text annotation | ||
| IL_8VUP_146 | No text annotation | ||
| IL_8VUP_147 | Minor groove platform | ||
| IL_8VUP_148 | No text annotation | ||
| IL_8VUP_149 | No text annotation | ||
| IL_8VUP_150 | 180 degree turn | ||
| IL_8VUP_157 | Minor groove platform | ||
| IL_8VUP_158 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_8VUP_001 | 1/1/30:31, 1/1/474:481, 1/1/509:510 | No text annotation | geometric J3_5J7L_036 NA | |
| J3_8VUP_002 | 1/1/32:35, 1/1/445:461, 1/1/468:473 | No text annotation | geometric J3_5J7L_067 NA | |
| J3_8VUP_003 | 1/1/56:57, 1/1/70:76, 1/1/110:114 | No text annotation | geometric J3_4V9F_014 J3_01004.1 | |
| J3_8VUP_004 | 1/1/297:301, 1/1/316:325, 1/1/337:341 | No text annotation | geometric J3_5J7L_068 NA | |
| J3_8VUP_005 | 1/1/683:689, 1/1/773:775, 1/1/791:794 | No text annotation | geometric J3_5J7L_038 NA | |
| J3_8VUP_006 | 1/1/698:700, 1/1/732:736, 1/1/760:763 | No text annotation | geometric J3_4WF9_003 J3_69816.1 | |
| J3_8VUP_007 | 1/1/1055:1058, 1/1/1080:1087, 1/1/1102:1104 | No text annotation | ||
| J3_8VUP_008 | 1/1/1298:1303, 1/1/1625:1627, 1/1/1639:1642 | No text annotation | geometric J3_5J7L_041 NA | |
| J3_8VUP_009 | 1/1/1306:1309, 1/1/1605:1611, 1/1/1620:1622 | No text annotation | geometric J3_7A0S_007 J3_47341.1 | |
| J3_8VUP_010 | 1/1/1344:1349, 1/1/1382:1385, 1/1/1402:1403 | No text annotation | geometric J3_5J7L_043 NA | |
| J3_8VUP_011 | 1/1/1423:1429, 1/1/1564:1565, 1/1/1568:1575 | No text annotation | ||
| J3_8VUP_012 | 1/1/2091:2093, 1/1/2196:2200, 1/1/2223:2228 | Kink-turn 3-way junction | geometric J3_5J7L_044 NA | |
| J3_8VUP_013 | 1/1/2282:2284, 1/1/2384:2395, 1/1/2421:2427 | No text annotation | geometric J3_5J7L_070 NA | |
| J3_8VUP_014 | 1/1/2295:2299, 1/1/2317:2323, 1/1/2332:2337 | No text annotation | geometric J3_5J7L_071 NA | |
| J3_8VUP_015 | 1/1/2517:2520, 1/1/2545:2549, 1/1/2559:2567 | No text annotation | ||
| J3_8VUP_016 | 1/1/2789:2791, 1/1/2805:2806, 1/1/2892:2894 | No text annotation | geometric J3_5J7L_047 NA | |
| J3_8VUP_017 | 1/1/2812:2815, 1/1/2831:2836, 1/1/2882:2888 | No text annotation | ||
| J3_8VUP_018 | 1/2/46:52, 1/2/359:367, 1/2/393:395 | No text annotation | geometric J3_4LFB_014 J3_63856.1 | |
| J3_8VUP_020 | 1/2/586:590, 1/2/649:655, 1/2/751:755 | No text annotation | ||
| J3_8VUP_021 | 1/2/672:673, 1/2/717:725, 1/2/732:734 | No text annotation | geometric J3_5J7L_003 NA | |
| J3_8VUP_022 | 1/2/826:829, 1/2/857:861, 1/2/868:874 | No text annotation | ||
| J3_8VUP_023 | 1/2/933:939, 1/2/1344:1350, 1/2/1372:1384 | No text annotation | ||
| J3_8VUP_024 | 1/2/943:946, 1/2/1235:1237, 1/2/1337:1340 | No text annotation | geometric J3_8CRE_079 J3_44359.1 | |
| J3_8VUP_025 | 1/2/955:962, 1/2/973:984, 1/2/1221:1225 | No text annotation | geometric J3_5J7L_006 NA | |
| J3_8VUP_028 | 1/2/1063:1068, 1/2/1107:1113, 1/2/1187:1193 | No text annotation | geometric J3_5J7L_008 NA | |
| J3_8VUP_029 | 1/2/1073:1074, 1/2/1083:1087, 1/2/1098:1102 | No text annotation | ||
| J3_8VUP_033 | 1/3/10:16, 1/3/68:70, 1/3/106:110 | No text annotation | geometric J3_5J7L_049 NA | |
| J4_8VUP_001 | 1/1/268:269, 1/1/370:375, 1/1/399:406, 1/1/421:424 | No text annotation | ||
| J4_8VUP_002 | 1/1/601:604, 1/1/624:628, 1/1/635:638, 1/1/650:656 | No text annotation | ||
| J4_8VUP_003 | 1/1/1270:1276, 1/1/1294:1295, 1/1/1645:1648, 1/1/2009:2010 | No text annotation | ||
| J4_8VUP_004 | 1/1/1310:1314, 1/1/1338:1343, 1/1/1404:1405, 1/1/1597:1604 | No text annotation | ||
| J4_8VUP_005 | 1/1/1444:1445, 1/1/1466:1467, 1/1/1525:1526, 1/1/1546:1547 | No text annotation | ||
| J4_8VUP_006 | 1/1/1772:1776, 1/1/1788:1793, 1/1/1826:1830, 1/1/1975:1979 | No text annotation | ||
| J4_8VUP_007 | 1/1/1833:1835, 1/1/1905:1906, 1/1/1924:1933, 1/1/1967:1972 | No text annotation | ||
| J4_8VUP_008 | 1/1/2285:2289, 1/1/2343:2347, 1/1/2370:2372, 1/1/2381:2383 | No text annotation | ||
| J4_8VUP_009 | 1/1/2643:2646, 1/1/2674:2676, 1/1/2732:2735, 1/1/2769:2771 | No text annotation | ||
| J4_8VUP_010 | 1/2/115:122, 1/2/239:240, 1/2/286:289, 1/2/311:312 | No text annotation | ||
| J4_8VUP_012 | 1/2/569:577, 1/2/764:769, 1/2/810:821, 1/2/879:881 | No text annotation | ||
| J4_8VUP_013 | 1/5/7:10, 1/5/25:27, 1/5/43:49, 1/5/65:66 | No text annotation | ||
| J5_8VUP_001 | 1/1/47:54, 1/1/116:121, 1/1/130:131, 1/1/148:151, 1/1/175:178 | No text annotation | ||
| J5_8VUP_002 | 1/1/531:533, 1/1/560:564, 1/1/577:579, 1/1/1261:1262, 1/1/2017:2018 | No text annotation | ||
| J5_8VUP_003 | 1/1/584:589, 1/1/668:674, 1/1/806:812, 1/1/1195:1196, 1/1/1250:1256 | No text annotation | ||
| J5_8VUP_004 | 1/1/1674:1682, 1/1/1706:1707, 1/1/1751:1752, 1/1/1756:1764, 1/1/1988:1990 | No text annotation | ||
| J5_8VUP_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_8VUP_006 | 1/1/2074:2077, 1/1/2243:2246, 1/1/2258:2259, 1/1/2281:2282, 1/1/2427:2435 | No text annotation | ||
| J5_8VUP_007 | 1/2/36:39, 1/2/403:406, 1/2/436:443, 1/2/491:500, 1/2/545:548 | No text annotation | ||
| J5_8VUP_008 | 1/2/58:61, 1/2/106:113, 1/2/314:316, 1/2/337:340, 1/2/349:354 | No text annotation | ||
| J6_8VUP_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 | ||
| J7_8VUP_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_8VUP_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_8VUP_019 | No text annotation | ||
| J3_8VUP_026 | No text annotation | ||
| J3_8VUP_027 | No text annotation | ||
| J3_8VUP_030 | No text annotation | ||
| J3_8VUP_031 | No text annotation | ||
| J3_8VUP_032 | No text annotation | ||
| J4_8VUP_011 | No text annotation |
Coloring options: