5ND9 Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_5ND9_001 | 1/A/59:68 | Pseudoknot with intercalation | homologous HL_7A0S_001 HL_17803.1 | |
| HL_5ND9_002 | 1/A/87:95 | Pseudoknot geometry | homologous HL_4WF9_002 HL_00911.1 | |
| HL_5ND9_003 | 1/A/122:127 | No text annotation | homologous HL_4WF9_003 HL_75660.6 | |
| HL_5ND9_004 | 1/A/136:143 | GNRA wlth tandem sheared | homologous HL_4WF9_004 HL_98423.1 | |
| HL_5ND9_005 | 1/A/159:169 | No text annotation | homologous HL_5J7L_138 NA | |
| HL_5ND9_006 | 1/A/197:204 | No text annotation | geometric HL_4WF9_006 HL_48677.1 | |
| HL_5ND9_007 | 1/A/228:233 | No text annotation | homologous HL_4WF9_007 HL_51020.1 | |
| HL_5ND9_008 | 1/A/249:255 | No text annotation | homologous HL_4WF9_008 HL_76371.1 | |
| HL_5ND9_010 | 1/A/348:355 | T-loop with 1 bulged base | homologous HL_7A0S_010 HL_13999.1 | |
| HL_5ND9_011 | 1/A/362:366 | No text annotation | homologous HL_7RQB_011 NA | |
| HL_5ND9_012 | 1/A/370:378 | T-loop with unstacked turn | homologous HL_5J7L_144 NA | |
| HL_5ND9_013 | 1/A/427:439 | No text annotation | ||
| HL_5ND9_014 | 1/A/456:463 | Pseudoknot geometry | homologous HL_7A0S_014 HL_30680.4 | |
| HL_5ND9_015 | 1/A/508:513 | GNRA | homologous HL_7RQB_015 NA | |
| HL_5ND9_016 | 1/A/533:538 | GNRA | homologous HL_7RQB_016 NA | |
| HL_5ND9_017 | 1/A/587:594 | No text annotation | homologous HL_4WF9_017 HL_50318.1 | |
| HL_5ND9_018 | 1/A/609:618 | T-loop with 2 stacked bulged bases | homologous HL_4WF9_018 HL_33597.1 | |
| HL_5ND9_019 | 1/A/655:661 | Mini UNCG | geometric HL_4YAZ_004 HL_90436.1 | |
| HL_5ND9_020 | 1/A/674:679 | GNRA | homologous HL_4WF9_020 HL_34789.1 | |
| HL_5ND9_103 | 1/A/686:692 | GNRA | homologous HL_9DFE_019 HL_34789.1 | |
| HL_5ND9_023 | 1/A/789:798 | No text annotation | homologous HL_4WF9_023 HL_50204.1 | |
| HL_5ND9_024 | 1/A/824:830 | No text annotation | homologous HL_5J7L_156 NA | |
| HL_5ND9_025 | 1/A/871:876 | No text annotation | homologous HL_7RQB_025 NA | |
| HL_5ND9_027 | 1/A/999:1006 | GNRA | homologous HL_4WF9_027 HL_34789.1 | |
| HL_5ND9_028 | 1/A/1022:1029 | No text annotation | homologous HL_5J7L_160 NA | |
| HL_5ND9_031 | 1/A/1260:1265 | GNRA | homologous HL_7A0S_031 HL_34789.1 | |
| HL_5ND9_032 | 1/A/1318:1326 | No text annotation | homologous HL_7RQB_033 NA | |
| HL_5ND9_033 | 1/A/1361:1367 | Pseudoknot geometry with 3' bulge | homologous HL_7A0S_033 HL_49081.1 | |
| HL_5ND9_034 | 1/A/1400:1405 | GNRA | homologous HL_5J7L_167 NA | |
| HL_5ND9_035 | 1/A/1426:1435 | No text annotation | homologous HL_4WF9_035 HL_77449.1 | |
| HL_5ND9_036 | 1/A/1535:1541 | Pseudoknot geometry with 3' bulge | homologous HL_5J7L_170 NA | |
| HL_5ND9_037 | 1/A/1612:1615 | Mini UNCG | homologous HL_5J7L_172 NA | |
| HL_5ND9_038 | 1/A/1656:1663 | No text annotation | homologous HL_4WF9_038 HL_28592.1 | |
| HL_5ND9_039 | 1/A/1673:1681 | GNRA with extra cWW | homologous HL_4WF9_039 HL_45359.1 | |
| HL_5ND9_040 | 1/A/1735:1740 | No text annotation | homologous HL_7RQB_042 NA | |
| HL_5ND9_042 | 1/A/1779:1783 | No text annotation | homologous HL_7RQB_044 NA | |
| HL_5ND9_043 | 1/A/1804:1814 | No text annotation | homologous HL_4WF9_043 HL_87681.1 | |
| HL_5ND9_044 | 1/A/1833:1838 | GNRA | homologous HL_7RQB_046 NA | |
| HL_5ND9_047 | 1/A/1976:1984 | No text annotation | homologous HL_4WF9_046 HL_61418.1 | |
| HL_5ND9_048 | 1/A/2054:2063 | No text annotation | homologous HL_4WF9_047 HL_78372.1 | |
| HL_5ND9_050 | 1/A/2236:2242 | No text annotation | homologous HL_5J7L_185 NA | |
| HL_5ND9_051 | 1/A/2275:2283 | No text annotation | homologous HL_7A0S_052 HL_11974.1 | |
| HL_5ND9_052 | 1/A/2291:2303 | No text annotation | homologous HL_4WF9_050 HL_02042.1 | |
| HL_5ND9_054 | 1/A/2351:2358 | Pseudoknot geometry | homologous HL_5J7L_189 NA | |
| HL_5ND9_055 | 1/A/2382:2389 | GNRA with extra cWW | homologous HL_4WF9_053 HL_45359.1 | |
| HL_5ND9_056 | 1/A/2401:2406 | GNRA | homologous HL_7A0S_057 HL_34789.1 | |
| HL_5ND9_057 | 1/A/2431:2440 | No text annotation | homologous HL_7A0S_058 HL_51853.1 | |
| HL_5ND9_058 | 1/A/2498:2506 | No text annotation | homologous HL_4WF9_056 HL_52011.1 | |
| HL_5ND9_059 | 1/A/2555:2562 | GNRA variation | homologous HL_5J7L_194 NA | |
| HL_5ND9_060 | 1/A/2578:2584 | No text annotation | homologous HL_4WF9_058 HL_48677.1 | |
| HL_5ND9_061 | 1/A/2621:2626 | GNRA | homologous HL_7A0S_062 HL_34789.1 | |
| HL_5ND9_062 | 1/A/2685:2690 | GNRA | homologous HL_4WF9_060 HL_34789.1 | |
| HL_5ND9_063 | 1/A/2728:2733 | Ribsomal LSU H95 | homologous HL_4WF9_061 HL_12125.1 | |
| HL_5ND9_064 | 1/A/2772:2786 | No text annotation | homologous HL_5J7L_199 NA | |
| HL_5ND9_066 | 1/A/2839:2847 | No text annotation | homologous HL_4WF9_064 HL_37889.1 | |
| HL_5ND9_067 | 1/A/2876:2881 | GNRA | homologous HL_7RQB_069 NA | |
| HL_5ND9_104 | 1/B/32:46 | No text annotation | homologous HL_4V9F_074 HL_97756.3 | |
| HL_5ND9_068 | 1/B/36:42 | No text annotation | geometric HL_5J7L_203 NA | |
| HL_5ND9_069 | 1/B/79:92 | No text annotation | ||
| HL_5ND9_070 | 1/a/13:23 | No text annotation | homologous HL_4LFB_001 HL_31940.1 | |
| HL_5ND9_073 | 1/a/193:198 | GNRA | homologous HL_5J7L_004 NA | |
| HL_5ND9_075 | 1/a/267:275 | GNRA related | homologous HL_4LFB_006 HL_36455.1 | |
| HL_5ND9_076 | 1/a/304:309 | GNRA | homologous HL_5J7L_007 NA | |
| HL_5ND9_077 | 1/a/328:341 | No text annotation | homologous HL_5J7L_008 NA | |
| HL_5ND9_078 | 1/a/350:355 | UNCG | homologous HL_6CZR_080 NA | |
| HL_5ND9_079 | 1/a/387:392 | GNRA | homologous HL_5J7L_010 NA | |
| HL_5ND9_082 | 1/a/530:535 | No text annotation | geometric HL_5J7L_143 NA | |
| HL_5ND9_083 | 1/a/625:631 | GNRA-like with tWH | homologous HL_5J7L_014 NA | |
| HL_5ND9_084 | 1/a/697:706 | No text annotation | homologous HL_4LFB_015 HL_38491.1 | |
| HL_5ND9_085 | 1/a/734:739 | GNRA | homologous HL_4LFB_016 HL_34789.1 | |
| HL_5ND9_086 | 1/a/794:804 | No text annotation | homologous HL_5J7L_017 NA | |
| HL_5ND9_088 | 1/a/872:877 | GNRA | homologous HL_6CZR_090 NA | |
| HL_5ND9_089 | 1/a/907:912 | GNRA | homologous HL_6CZR_091 NA | |
| HL_5ND9_090 | 1/a/973:982 | No text annotation | homologous HL_4LFB_021 HL_97521.1 | |
| HL_5ND9_093 | 1/a/1088:1093 | GNRA | homologous HL_4LFB_024 HL_34789.1 | |
| HL_5ND9_094 | 1/a/1101:1108 | T-loop related | homologous HL_5J7L_024 NA | |
| HL_5ND9_096 | 1/a/1176:1182 | GNRA | homologous HL_5J7L_026 NA | |
| HL_5ND9_099 | 1/a/1367:1377 | No text annotation | homologous HL_5J7L_029 NA | |
| HL_5ND9_101 | 1/a/1527:1532 | GNRA | homologous HL_6CZR_103 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_5ND9_009 | No text annotation | ||
| HL_5ND9_102 | No text annotation | ||
| HL_5ND9_021 | Anticodon loop related | ||
| HL_5ND9_022 | GNRA wlth tandem sheared | ||
| HL_5ND9_026 | No text annotation | ||
| HL_5ND9_029 | No text annotation | ||
| HL_5ND9_030 | Mini UNCG | ||
| HL_5ND9_041 | No text annotation | ||
| HL_5ND9_105 | GNRA | ||
| HL_5ND9_045 | No text annotation | ||
| HL_5ND9_046 | No text annotation | ||
| HL_5ND9_049 | UNCG | ||
| HL_5ND9_053 | No text annotation | ||
| HL_5ND9_106 | No text annotation | ||
| HL_5ND9_065 | No text annotation | ||
| HL_5ND9_071 | Mini UNCG | ||
| HL_5ND9_072 | GNRA | ||
| HL_5ND9_074 | No text annotation | ||
| HL_5ND9_080 | UNCG | ||
| HL_5ND9_081 | GNRA wlth extra near cWW | ||
| HL_5ND9_087 | tRNA D-loop | ||
| HL_5ND9_091 | GNRA | ||
| HL_5ND9_092 | No text annotation | ||
| HL_5ND9_095 | No text annotation | ||
| HL_5ND9_097 | GNRA | ||
| HL_5ND9_098 | T-loop with 3 stacked bulged bases | ||
| HL_5ND9_100 | Mini UNCG |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_5ND9_001 | 1/A/24:30, 1/A/555:561 | Triple sheared with non-canonical cWW | geometric IL_7A0S_001 IL_22311.1 | |
| IL_5ND9_002 | 1/A/36:37, 1/A/488:490 | Single bulged A | homologous IL_7RQB_002 NA | |
| IL_5ND9_003 | 1/A/43:44, 1/A/480:482 | Minor groove platform | homologous IL_5J7L_247 NA | |
| IL_5ND9_004 | 1/A/81:85, 1/A/97:104 | Kink-turn | homologous IL_4WF9_004 IL_54465.1 | |
| IL_5ND9_197 | 1/A/152:155, 1/A/173:177 | No text annotation | ||
| IL_5ND9_006 | 1/A/186:187, 1/A/215:217 | Single stack bend | homologous IL_7A0S_005 IL_15011.1 | |
| IL_5ND9_007 | 1/A/190:197, 1/A/204:212 | 9x8 Sarcin-Ricin; G-bulge | homologous IL_4WF9_008 IL_93502.1 | |
| IL_5ND9_008 | 1/A/241:248, 1/A/256:262 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_4WF9_009 IL_62167.1 | |
| IL_5ND9_176 | 1/A/310:330, 1/A/396:405 | No text annotation | ||
| IL_5ND9_010 | 1/A/336:338, 1/A/386:390 | No text annotation | homologous IL_7RQB_013 NA | |
| IL_5ND9_011 | 1/A/527:530, 1/A/541:554 | No text annotation | geometric IL_4WF9_015 IL_44923.1 | |
| IL_5ND9_012 | 1/A/581:584, 1/A/597:600 | Double sheared | homologous IL_5J7L_256 NA | |
| IL_5ND9_013 | 1/A/607:609, 1/A/618:620 | Isolated non-canonical cWW pair | geometric IL_4V88_465 NA | |
| IL_5ND9_014 | 1/A/638:640, 1/A/705:707 | Isolated non-canonical cWW pair | homologous IL_4WF9_018 IL_71625.1 | |
| IL_5ND9_015 | 1/A/649:653, 1/A/663:667 | AAA cross-strand stack | homologous IL_7RQB_016 NA | |
| IL_5ND9_016 | 1/A/717:719, 1/A/851:853 | No text annotation | homologous IL_7RQB_017 NA | |
| IL_5ND9_017 | 1/A/719:723, 1/A/844:851 | tHW-tHW cross-strand stack | geometric IL_7RQB_018 NA | |
| IL_5ND9_018 | 1/A/742:743, 1/A/808:810 | Single bulged A | geometric IL_4V9F_025 IL_14190.1 | |
| IL_5ND9_019 | 1/A/747:752, 1/A/769:775 | No text annotation | geometric IL_4LFB_055 IL_57885.1 | |
| IL_5ND9_020 | 1/A/783:785, 1/A/802:803 | Major groove platform | homologous IL_4WF9_026 IL_48076.7 | |
| IL_5ND9_021 | 1/A/820:822, 1/A/832:836 | Multiple bulged bases | homologous IL_5J7L_265 NA | |
| IL_5ND9_022 | 1/A/882:883, 1/A/984:986 | Single stack bend | homologous IL_7A0S_022 IL_15011.1 | |
| IL_5ND9_023 | 1/A/889:893, 1/A/975:978 | No text annotation | homologous IL_4WF9_029 IL_01742.1 | |
| IL_5ND9_024 | 1/A/897:898, 1/A/969:971 | Single bulged U | geometric IL_6MWN_006 IL_97561.1 | |
| IL_5ND9_025 | 1/A/901:907, 1/A/960:966 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | homologous IL_4WF9_031 IL_94128.1 | |
| IL_5ND9_026 | 1/A/907:908, 1/A/958:960 | Minor groove platform | geometric IL_4WF9_032 IL_34520.1 | |
| IL_5ND9_027 | 1/A/909:913, 1/A/954:957 | C-loop | homologous IL_7RQB_029 NA | |
| IL_5ND9_029 | 1/A/1038:1040, 1/A/1203:1204 | Single bulged C | homologous IL_4WF9_035 IL_05642.1 | |
| IL_5ND9_030 | 1/A/1042:1046, 1/A/1197:1201 | UAA/GAN | homologous IL_7A0S_033 IL_08938.1 | |
| IL_5ND9_031 | 1/A/1048:1055, 1/A/1194:1195 | SSU/LSU pseudoknot | geometric IL_4WF9_037 IL_11411.1 | |
| IL_5ND9_178 | 1/A/1048:1057, 1/A/1193:1195 | Isolated non-canonical cWW pair | geometric IL_4KNQ_004 NA | |
| IL_5ND9_032 | 1/A/1055:1057, 1/A/1193:1194 | Single bulged U | homologous IL_5J7L_279 NA | |
| IL_5ND9_033 | 1/A/1062:1068, 1/A/1184:1188 | Kink-turn related | homologous IL_5J7L_280 NA | |
| IL_5ND9_034 | 1/A/1068:1074, 1/A/1168:1184 | No text annotation | geometric IL_5J7L_281 NA | |
| IL_5ND9_035 | 1/A/1075:1078, 1/A/1165:1167 | Isolated non-canonical cWW pair | homologous IL_7RQB_041 NA | |
| IL_5ND9_036 | 1/A/1081:1083, 1/A/1160:1162 | Isolated non-canonical cWW pair | homologous IL_4WF9_042 IL_01003.1 | |
| IL_5ND9_040 | 1/A/1243:1245, 1/A/1277:1279 | Isolated cWH basepair | homologous IL_4WF9_045 IL_10892.1 | |
| IL_5ND9_041 | 1/A/1246:1253, 1/A/1272:1276 | Kink-turn | homologous IL_7A0S_043 IL_90775.1 | |
| IL_5ND9_042 | 1/A/1257:1259, 1/A/1266:1268 | Intercalated cWW | homologous IL_4WF9_047 IL_61702.1 | |
| IL_5ND9_179 | 1/A/1300:1307, 1/A/2038:2044 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_9DFE_048 IL_62167.1 | |
| IL_5ND9_044 | 1/A/1347:1350, 1/A/1647:1648 | Major groove platform; stack outside cWW | homologous IL_4WF9_049 IL_74641.1 | |
| IL_5ND9_045 | 1/A/1356:1360, 1/A/1368:1370 | Major groove minor groove platform with tHH | homologous IL_4WF9_050 IL_06671.1 | |
| IL_5ND9_046 | 1/A/1388:1392, 1/A/1413:1417 | UAA/GAN | homologous IL_4WF9_051 IL_89021.3 | |
| IL_5ND9_047 | 1/A/1394:1398, 1/A/1407:1411 | tSH-tHW-tHS | homologous IL_4WF9_052 IL_05821.1 | |
| IL_5ND9_049 | 1/A/1461:1465, 1/A/1624:1627 | Other IL | homologous IL_4WF9_054 IL_74317.1 | |
| IL_5ND9_050 | 1/A/1476:1480, 1/A/1604:1608 | No text annotation | geometric IL_4WF9_122 IL_67780.1 | |
| IL_5ND9_181 | 1/A/1481:1515, 1/A/1565:1603 | No text annotation | ||
| IL_5ND9_051 | 1/A/1511:1515, 1/A/1565:1570 | No text annotation | geometric IL_3BNN_006 IL_25186.4 | |
| IL_5ND9_052 | 1/A/1518:1522, 1/A/1558:1562 | Double sheared with near cWW | homologous IL_7A0S_056 IL_87767.1 | |
| IL_5ND9_053 | 1/A/1524:1526, 1/A/1549:1556 | No text annotation | ||
| IL_5ND9_054 | 1/A/1530:1534, 1/A/1542:1545 | No text annotation | ||
| IL_5ND9_055 | 1/A/1695:1700, 1/A/2031:2033 | No text annotation | homologous IL_4WF9_062 IL_12566.5 | |
| IL_5ND9_056 | 1/A/1707:1709, 1/A/2022:2024 | Isolated tWW turn | homologous IL_4WF9_063 IL_10432.1 | |
| IL_5ND9_057 | 1/A/1710:1713, 1/A/2020:2021 | Major groove platform; stack outside cWW | geometric IL_5J7L_306 NA | |
| IL_5ND9_183 | 1/A/1710:1718, 1/A/2017:2021 | No text annotation | homologous IL_4WF9_117 IL_80252.1 | |
| IL_5ND9_058 | 1/A/1713:1718, 1/A/2017:2020 | Intercalated tWH | homologous IL_4WF9_065 IL_28217.1 | |
| IL_5ND9_059 | 1/A/1730:1735, 1/A/1740:1746 | tSH-tSH-tHH-tHS | geometric IL_5TBW_078 NA | |
| IL_5ND9_061 | 1/A/1797:1798, 1/A/2007:2009 | Single bulged A | homologous IL_7A0S_064 IL_14190.1 | |
| IL_5ND9_062 | 1/A/1825:1831, 1/A/1840:1848 | Kink-turn related | homologous IL_7A0S_065 IL_17069.6 | |
| IL_5ND9_063 | 1/A/1864:1867, 1/A/1929:1930 | Minor groove platform, major groove intercalation | homologous IL_5J7L_314 NA | |
| IL_5ND9_064 | 1/A/1868:1869, 1/A/1925:1928 | Major groove intercalation | homologous IL_4WF9_071 IL_78536.1 | |
| IL_5ND9_065 | 1/A/1873:1876, 1/A/1920:1921 | Major groove minor groove platform; mini C-loop | homologous IL_5J7L_316 NA | |
| IL_5ND9_066 | 1/A/1878:1882, 1/A/1914:1918 | UAA/GAN with extra stack | homologous IL_4WF9_073 IL_89021.3 | |
| IL_5ND9_067 | 1/A/1883:1887, 1/A/1909:1913 | Triple sheared | homologous IL_7RQB_075 NA | |
| IL_5ND9_068 | 1/A/1891:1894, 1/A/1901:1905 | UAA/GAN related | homologous IL_5J7L_317 NA | |
| IL_5ND9_069 | 1/A/1960:1961, 1/A/1991:1994 | Bulged stacked bases | geometric IL_7RQB_076 NA | |
| IL_5ND9_070 | 1/A/1961:1972, 1/A/1988:1991 | No text annotation | homologous IL_4WF9_077 IL_84014.1 | |
| IL_5ND9_071 | 1/A/2077:2079, 1/A/2644:2645 | Major groove platform | homologous IL_7RQB_078 NA | |
| IL_5ND9_072 | 1/A/2081:2083, 1/A/2639:2642 | Major groove platform with intercalation | geometric IL_5TBW_092 NA | |
| IL_5ND9_073 | 1/A/2094:2096, 1/A/2469:2470 | Single bulged U | geometric IL_7RQB_080 NA | |
| IL_5ND9_185 | 1/A/2097:2098, 1/A/2465:2468 | Minor groove platform | homologous IL_4WF9_081 IL_34520.1 | |
| IL_5ND9_075 | 1/A/2108:2110, 1/A/2263:2266 | Isolated tHS basepair with bulges | homologous IL_4WF9_082 IL_87316.1 | |
| IL_5ND9_078 | 1/A/2137:2147, 1/A/2205:2206 | No text annotation | ||
| IL_5ND9_081 | 1/A/2229:2231, 1/A/2247:2248 | Single bulged U | homologous IL_5J7L_331 NA | |
| IL_5ND9_082 | 1/A/2324:2326, 1/A/2344:2348 | Isolated tHS basepair with bulges | geometric IL_7RQB_082 NA | |
| IL_5ND9_083 | 1/A/2377:2380, 1/A/2391:2394 | Double sheared | homologous IL_7A0S_081 IL_58355.1 | |
| IL_5ND9_084 | 1/A/2428:2430, 1/A/2441:2442 | Single bulged U | homologous IL_5J7L_334 NA | |
| IL_5ND9_085 | 1/A/2480:2481, 1/A/2525:2527 | Single stack bend | geometric IL_7A0S_083 IL_15011.1 | |
| IL_5ND9_086 | 1/A/2481:2482, 1/A/2523:2525 | Major groove platform | homologous IL_4WF9_090 IL_48076.7 | |
| IL_5ND9_087 | 1/A/2484:2486, 1/A/2520:2521 | Major groove platform | geometric IL_4WF9_091 IL_48076.7 | |
| IL_5ND9_088 | 1/A/2486:2488, 1/A/2516:2520 | Major groove minor groove platform with extra cWW | homologous IL_4WF9_092 IL_36931.1 | |
| IL_5ND9_089 | 1/A/2493:2497, 1/A/2507:2511 | Double sheared with non-canonical cWW | homologous IL_4WF9_093 IL_87767.1 | |
| IL_5ND9_090 | 1/A/2534:2535, 1/A/2607:2609 | Major groove platform | homologous IL_4WF9_094 IL_46637.1 | |
| IL_5ND9_091 | 1/A/2537:2539, 1/A/2601:2605 | Isolated non-canonical cWW with bulges | homologous IL_7RQB_097 NA | |
| IL_5ND9_092 | 1/A/2539:2540, 1/A/2598:2601 | Multiple bulged bases | geometric IL_7RQB_098 NA | |
| IL_5ND9_093 | 1/A/2549:2550, 1/A/2567:2570 | Major groove platform with intercalation | homologous IL_5J7L_342 NA | |
| IL_5ND9_094 | 1/A/2618:2619, 1/A/2628:2630 | No text annotation | ||
| IL_5ND9_095 | 1/A/2663:2667, 1/A/2801:2809 | tSH-tHS-tHW | homologous IL_4WF9_099 IL_04638.4 | |
| IL_5ND9_096 | 1/A/2679:2685, 1/A/2690:2695 | Sarcin-Ricin target in LSU H95; G-bulge | geometric IL_5J7L_346 NA | |
| IL_5ND9_097 | 1/A/2707:2711, 1/A/2752:2754 | C-loop | homologous IL_4WF9_101 IL_63596.12 | |
| IL_5ND9_098 | 1/A/2714:2718, 1/A/2745:2749 | UAA/GAN related, with intercalation | homologous IL_5J7L_348 NA | |
| IL_5ND9_099 | 1/A/2722:2723, 1/A/2738:2741 | Multiple bulged bases | homologous IL_4WF9_103 IL_44609.1 | |
| IL_5ND9_100 | 1/A/2764:2769, 1/A/2789:2794 | UAA/GAN with extra cWW | homologous IL_5J7L_350 NA | |
| IL_5ND9_101 | 1/A/2858:2861, 1/A/2896:2900 | No text annotation | ||
| IL_5ND9_102 | 1/A/2863:2865, 1/A/2891:2894 | No text annotation | homologous IL_4WF9_107 IL_05502.1 | |
| IL_5ND9_103 | 1/A/2867:2872, 1/A/2885:2889 | tHS double platform | homologous IL_4WF9_108 IL_48489.1 | |
| IL_5ND9_104 | 1/B/2:5, 1/B/110:113 | Tandem non-canonical cWW pairs | homologous IL_4WF9_109 NA | |
| IL_5ND9_105 | 1/B/5:8, 1/B/107:110 | Tandem non-canonical cWW pairs | geometric IL_4V88_391 NA | |
| IL_5ND9_106 | 1/B/15:16, 1/B/63:65 | Major groove intercalation | homologous IL_4WF9_112 IL_14190.1 | |
| IL_5ND9_107 | 1/B/20:27, 1/B/53:59 | No text annotation | homologous IL_4WF9_113 IL_19048.1 | |
| IL_5ND9_109 | 1/B/32:36, 1/B/42:46 | Symmetric double minor groove platform | homologous IL_4V9F_104 IL_58103.12 | |
| IL_5ND9_110 | 1/B/77:79, 1/B/92:94 | Isolated non-canonical cWW pair | homologous IL_7A0S_107 IL_71625.1 | |
| IL_5ND9_111 | 1/a/31:33, 1/a/560:561 | Single bulged G | homologous IL_4LFB_001 IL_28408.1 | |
| IL_5ND9_112 | 1/a/45:46, 1/a/404:406 | Single bulged A | homologous IL_5J7L_002 NA | |
| IL_5ND9_113 | 1/a/48:53, 1/a/367:369 | No text annotation | homologous IL_5J7L_003 NA | |
| IL_5ND9_114 | 1/a/55:57, 1/a/364:365 | Minor groove platform | homologous IL_4LFB_004 IL_34520.1 | |
| IL_5ND9_115 | 1/a/64:67, 1/a/102:103 | Multiple bulged bases | homologous IL_6CZR_117 NA | |
| IL_5ND9_116 | 1/a/68:71, 1/a/98:101 | Tandem non-canonical cWW pairs | geometric IL_6JDV_002 IL_15225.1 | |
| IL_5ND9_118 | 1/a/128:131, 1/a/239:240 | Multiple bulged bases | homologous IL_4LFB_007 IL_75289.1 | |
| IL_5ND9_119 | 1/a/132:136, 1/a/235:238 | Minor groove platform related | homologous IL_5J7L_010 NA | |
| IL_5ND9_120 | 1/a/147:153, 1/a/168:175 | tWH-tWH-tHW-tHW | homologous IL_5J7L_012 NA | |
| IL_5ND9_122 | 1/a/250:255, 1/a/285:292 | Kink-turn with non-sequential stacking | homologous IL_5J7L_014 NA | |
| IL_5ND9_190 | 1/a/257:260, 1/a/282:283 | No text annotation | homologous IL_4LFB_012 IL_22002.1 | |
| IL_5ND9_124 | 1/a/300:301, 1/a/312:316 | C-loop | homologous IL_4LFB_013 IL_06671.1 | |
| IL_5ND9_125 | 1/a/375:377, 1/a/400:401 | Single bulged U | homologous IL_5J7L_017 NA | |
| IL_5ND9_126 | 1/a/379:383, 1/a/397:398 | C-loop | homologous IL_5J7L_018 NA | |
| IL_5ND9_127 | 1/a/383:384, 1/a/395:397 | Single bulged G | geometric IL_5J7L_019 NA | |
| IL_5ND9_128 | 1/a/417:424, 1/a/435:441 | No text annotation | homologous IL_4LFB_017 IL_62329.1 | |
| IL_5ND9_191 | 1/a/454:468, 1/a/481:496 | No text annotation | ||
| IL_5ND9_130 | 1/a/512:519, 1/a/548:549 | SSU/LSU pseudoknot | homologous IL_4LFB_020 IL_11411.1 | |
| IL_5ND9_131 | 1/a/523:529, 1/a/536:544 | Kink-turn related | homologous IL_4LFB_021 IL_52042.1 | |
| IL_5ND9_132 | 1/a/577:583, 1/a/890:891 | No text annotation | homologous IL_6CZR_134 NA | |
| IL_5ND9_133 | 1/a/588:592, 1/a/765:769 | tSH-tHW-tHS | homologous IL_5J7L_027 NA | |
| IL_5ND9_134 | 1/a/602:604, 1/a/652:653 | Major groove platform | homologous IL_5J7L_028 NA | |
| IL_5ND9_135 | 1/a/605:606, 1/a/648:651 | Major groove minor groove platform; mini C-loop | homologous IL_4LFB_025 IL_73108.1 | |
| IL_5ND9_136 | 1/a/612:613, 1/a/640:642 | Single bulged U | geometric IL_8VMA_002 IL_97561.1 | |
| IL_5ND9_192 | 1/a/612:623, 1/a/633:642 | No text annotation | ||
| IL_5ND9_137 | 1/a/613:620, 1/a/636:640 | No text annotation | geometric IL_5J7L_030 NA | |
| IL_5ND9_138 | 1/a/662:663, 1/a/759:762 | Major groove platform; stack outside cWW | homologous IL_4LFB_027 IL_74641.1 | |
| IL_5ND9_139 | 1/a/664:667, 1/a/754:758 | No text annotation | ||
| IL_5ND9_140 | 1/a/670:674, 1/a/748:751 | Tandem non-canonical cWW pairs | homologous IL_5J7L_033 NA | |
| IL_5ND9_193 | 1/a/681:685, 1/a/721:725 | Triple non-canonical cWW pairs | homologous IL_6CZR_409 NA | |
| IL_5ND9_142 | 1/a/692:696, 1/a/707:714 | Kink-turn | homologous IL_5J7L_035 NA | |
| IL_5ND9_143 | 1/a/782:787, 1/a/811:813 | Other IL | geometric IL_4V88_435 NA | |
| IL_5ND9_144 | 1/a/787:791, 1/a/807:811 | tSH-tHW-tHS | homologous IL_4LFB_033 IL_05821.1 | |
| IL_5ND9_145 | 1/a/897:905, 1/a/914:920 | 9x7 Sarcin-Ricin with inserted C; G-bulge | homologous IL_6CZR_146 NA | |
| IL_5ND9_198 | 1/a/932:933, 1/a/1404:1406 | Single bulged A | homologous IL_6CZR_147 NA | |
| IL_5ND9_147 | 1/a/935:937, 1/a/1401:1402 | Single bulged G | homologous IL_6CZR_148 NA | |
| IL_5ND9_153 | 1/a/1060:1062, 1/a/1219:1220 | Single bulged U | homologous IL_4LFB_042 IL_97561.1 | |
| IL_5ND9_157 | 1/a/1073:1075, 1/a/1204:1206 | Isolated non-canonical cWW pair | homologous IL_4LFB_047 IL_68118.1 | |
| IL_5ND9_160 | 1/a/1169:1172, 1/a/1186:1192 | No text annotation | homologous IL_5J7L_053 NA | |
| IL_5ND9_161 | 1/a/1258:1264, 1/a/1295:1301 | No text annotation | homologous IL_5J7L_054 NA | |
| IL_5ND9_165 | 1/a/1410:1412, 1/a/1513:1516 | No text annotation | homologous IL_5J7L_058 NA | |
| IL_5ND9_166 | 1/a/1412:1415, 1/a/1509:1513 | No text annotation | geometric IL_4V88_464 NA | |
| IL_5ND9_167 | 1/a/1416:1418, 1/a/1506:1508 | Isolated non-canonical cWW pair | geometric IL_3SZX_003 IL_01003.1 | |
| IL_5ND9_168 | 1/a/1418:1420, 1/a/1503:1506 | Isolated non-canonical cWW pair | geometric IL_4RUM_001 NA | |
| IL_5ND9_169 | 1/a/1423:1425, 1/a/1498:1500 | Isolated non-canonical cWW pair | homologous IL_5J7L_061 NA | |
| IL_5ND9_170 | 1/a/1427:1430, 1/a/1493:1496 | Double sheared | homologous IL_5J7L_062 NA | |
| IL_5ND9_171 | 1/a/1435:1438, 1/a/1485:1488 | Tandem non-canonical cWW pairs | geometric IL_5J7L_283 NA | |
| IL_5ND9_172 | 1/a/1441:1446, 1/a/1478:1482 | Triple sheared related | geometric IL_5J7L_063 NA | |
| IL_5ND9_173 | 1/a/1446:1448, 1/a/1476:1478 | Isolated non-canonical cWW pair | homologous IL_4LFB_063 IL_01003.1 | |
| IL_5ND9_175 | 1/a/1456:1459, 1/a/1467:1469 | No text annotation | homologous IL_5J7L_065 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_5ND9_005 | Partly complementary | ||
| IL_5ND9_009 | Major groove minor groove platform; mini C-loop | ||
| IL_5ND9_177 | No text annotation | ||
| IL_5ND9_028 | No text annotation | ||
| IL_5ND9_037 | Kink-turn | ||
| IL_5ND9_038 | No text annotation | ||
| IL_5ND9_039 | No text annotation | ||
| IL_5ND9_043 | 9x8 Sarcin-Ricin; G-bulge | ||
| IL_5ND9_048 | No text annotation | ||
| IL_5ND9_180 | No text annotation | ||
| IL_5ND9_182 | No text annotation | ||
| IL_5ND9_060 | Isolated cWH basepair | ||
| IL_5ND9_184 | No text annotation | ||
| IL_5ND9_074 | Tandem non-canonical cWW pairs | ||
| IL_5ND9_076 | Isolated non-canonical cWW pair | ||
| IL_5ND9_186 | Tandem non-canonical cWW pairs | ||
| IL_5ND9_077 | Isolated non-canonical cWW pair | ||
| IL_5ND9_079 | No text annotation | ||
| IL_5ND9_080 | Kink-turn | ||
| IL_5ND9_187 | No text annotation | ||
| IL_5ND9_108 | Major groove minor groove platform; mini C-loop | ||
| IL_5ND9_188 | No text annotation | ||
| IL_5ND9_117 | No text annotation | ||
| IL_5ND9_189 | No text annotation | ||
| IL_5ND9_121 | Isolated non-canonical cWW pair | ||
| IL_5ND9_123 | No text annotation | ||
| IL_5ND9_129 | No text annotation | ||
| IL_5ND9_141 | No text annotation | ||
| IL_5ND9_146 | Tandem non-canonical cWW pairs | ||
| IL_5ND9_194 | Isolated non-canonical cWW with bulges | ||
| IL_5ND9_148 | Minor groove platform | ||
| IL_5ND9_149 | Minor groove platform | ||
| IL_5ND9_150 | Minor groove platform | ||
| IL_5ND9_151 | Single stack bend | ||
| IL_5ND9_152 | Single stack bend | ||
| IL_5ND9_154 | Isolated cWS basepair | ||
| IL_5ND9_155 | Minor groove platform | ||
| IL_5ND9_156 | Single bulged A | ||
| IL_5ND9_158 | Minor groove platform | ||
| IL_5ND9_159 | Minor groove platform | ||
| IL_5ND9_162 | 180 degree turn | ||
| IL_5ND9_163 | Double sheared with non-canonical cWW | ||
| IL_5ND9_195 | No text annotation | ||
| IL_5ND9_164 | No text annotation | ||
| IL_5ND9_196 | No text annotation | ||
| IL_5ND9_174 | Isolated tHS basepair with bulges |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_5ND9_001 | 1/A/30:31, 1/A/520:527, 1/A/554:555 | No text annotation | homologous J3_7RQB_001 NA | |
| J3_5ND9_025 | 1/A/32:35, 1/A/491:507, 1/A/514:519 | No text annotation | homologous J3_9DFE_003 J3_07616.1 | |
| J3_5ND9_002 | 1/A/56:57, 1/A/70:76, 1/A/109:113 | No text annotation | homologous J3_5J7L_037 NA | |
| J3_5ND9_003 | 1/A/272:276, 1/A/295:302, 1/A/415:416 | No text annotation | homologous J3_7RQB_003 NA | |
| J3_5ND9_004 | 1/A/728:734, 1/A/818:820, 1/A/836:839 | No text annotation | homologous J3_5J7L_038 NA | |
| J3_5ND9_005 | 1/A/743:745, 1/A/777:781, 1/A/805:808 | No text annotation | homologous J3_4WF9_003 J3_69816.1 | |
| J3_5ND9_006 | 1/A/1335:1340, 1/A/1669:1671, 1/A/1683:1686 | No text annotation | homologous J3_4WF9_004 J3_32852.7 | |
| J3_5ND9_007 | 1/A/1343:1346, 1/A/1649:1655, 1/A/1664:1666 | No text annotation | homologous J3_7RQB_008 NA | |
| J3_5ND9_008 | 1/A/1381:1387, 1/A/1418:1422, 1/A/1439:1440 | No text annotation | homologous J3_7RQB_009 NA | |
| J3_5ND9_026 | 1/A/1468:1473, 1/A/1611:1612, 1/A/1615:1621 | No text annotation | homologous J3_7A0S_019 J3_34864.3 | |
| J3_5ND9_009 | 1/A/2118:2120, 1/A/2223:2228, 1/A/2249:2255 | No text annotation | homologous J3_4WF9_007 J3_07703.1 | |
| J3_5ND9_010 | 1/A/2322:2324, 1/A/2348:2350, 1/A/2359:2364 | No text annotation | homologous J3_4WF9_008 J3_05327.1 | |
| J3_5ND9_011 | 1/A/2544:2547, 1/A/2572:2574, 1/A/2588:2594 | No text annotation | homologous J3_7RQB_012 NA | |
| J3_5ND9_012 | 1/A/2816:2817, 1/A/2826:2831, 1/A/2909:2913 | No text annotation | homologous J3_7RQB_013 NA | |
| J3_5ND9_013 | 1/A/2834:2835, 1/A/2851:2856, 1/A/2902:2906 | No text annotation | homologous J3_7A0S_013 J3_76911.2 | |
| J3_5ND9_027 | 1/B/8:14, 1/B/66:77, 1/B/94:107 | No text annotation | ||
| J3_5ND9_014 | 1/a/47:48, 1/a/369:375, 1/a/401:403 | No text annotation | homologous J3_6CZR_015 NA | |
| J3_5ND9_028 | 1/a/47:53, 1/a/367:375, 1/a/401:403 | No text annotation | homologous J3_4LFB_014 J3_63856.1 | |
| J3_5ND9_015 | 1/a/594:596, 1/a/659:662, 1/a/762:763 | No text annotation | homologous J3_5J7L_002 NA | |
| J3_5ND9_029 | 1/a/594:596, 1/a/659:663, 1/a/759:763 | No text annotation | homologous J3_5J7L_051 NA | |
| J3_5ND9_016 | 1/a/680:681, 1/a/725:733, 1/a/740:742 | No text annotation | homologous J3_5J7L_003 NA | |
| J3_5ND9_017 | 1/a/834:837, 1/a/867:871, 1/a/878:884 | No text annotation | homologous J3_5J7L_004 NA | |
| J3_5ND9_030 | 1/a/946:949, 1/a/1355:1361, 1/a/1383:1390 | No text annotation | homologous J3_5J7L_052 NA | |
| J3_5ND9_021 | 1/a/1075:1080, 1/a/1119:1125, 1/a/1198:1204 | No text annotation | homologous J3_5J7L_008 NA | |
| J3_5ND9_035 | 1/a/1085:1086, 1/a/1095:1098, 1/a/1111:1114 | No text annotation | homologous J3_4LFB_017 J3_11018.1 | |
| J3_5ND9_023 | 1/a/1128:1130, 1/a/1166:1169, 1/a/1192:1195 | No text annotation | homologous J3_5J7L_010 NA | |
| J3_5ND9_034 | 1/a/1128:1130, 1/a/1166:1172, 1/a/1186:1195 | No text annotation | homologous J3_5J7L_054 NA | |
| J4_5ND9_001 | 1/A/271:272, 1/A/416:421, 1/A/445:452, 1/A/467:470 | No text annotation | homologous J4_4WF9_001 J4_94698.1 | |
| J4_5ND9_002 | 1/A/340:344, 1/A/359:362, 1/A/366:368, 1/A/380:384 | No text annotation | homologous J4_4WF9_002 J4_16174.1 | |
| J4_5ND9_003 | 1/A/644:647, 1/A/669:673, 1/A/680:684, 1/A/694:701 | No text annotation | homologous J4_4WF9_003 J4_69347.1 | |
| J4_5ND9_004 | 1/A/1308:1313, 1/A/1331:1332, 1/A/1689:1692, 1/A/2036:2037 | No text annotation | homologous J4_4WF9_004 J4_64571.6 | |
| J4_5ND9_005 | 1/A/1347:1351, 1/A/1375:1380, 1/A/1441:1442, 1/A/1641:1648 | No text annotation | homologous J4_4WF9_005 J4_77353.1 | |
| J4_5ND9_006 | 1/A/1350:1351, 1/A/1375:1380, 1/A/1441:1442, 1/A/1641:1647 | No text annotation | homologous J4_4WF9_006 J4_48150.1 | |
| J4_5ND9_007 | 1/A/1799:1803, 1/A/1815:1819, 1/A/1854:1857, 1/A/2002:2006 | No text annotation | homologous J4_7A0S_008 J4_61477.6 | |
| J4_5ND9_008 | 1/A/1860:1862, 1/A/1932:1933, 1/A/1951:1960, 1/A/1994:1999 | No text annotation | homologous J4_9DFE_008 J4_42306.1 | |
| J4_5ND9_009 | 1/A/2312:2316, 1/A/2370:2374, 1/A/2397:2399, 1/A/2408:2410 | No text annotation | homologous J4_9DFE_009 J4_98139.1 | |
| J4_5ND9_010 | 1/A/2670:2673, 1/A/2701:2703, 1/A/2758:2762, 1/A/2796:2798 | No text annotation | homologous J4_5J7L_028 NA | |
| J4_5ND9_011 | 1/a/114:122, 1/a/246:248, 1/a/294:297, 1/a/319:320 | No text annotation | homologous J4_4LFB_001 J4_90044.1 | |
| J4_5ND9_012 | 1/a/142:144, 1/a/178:185, 1/a/206:213, 1/a/227:229 | No text annotation | ||
| J4_5ND9_013 | 1/a/583:585, 1/a/772:777, 1/a/818:829, 1/a/889:890 | No text annotation | homologous J4_6CZR_013 NA | |
| J5_5ND9_001 | 1/A/47:54, 1/A/115:120, 1/A/129:130, 1/A/149:151, 1/A/178:180 | No text annotation | homologous J5_4WF9_001 J5_27223.1 | |
| J5_5ND9_002 | 1/A/271:276, 1/A/295:302, 1/A/415:421, 1/A/445:452, 1/A/467:470 | No text annotation | ||
| J5_5ND9_003 | 1/A/576:578, 1/A/603:607, 1/A/620:622, 1/A/1299:1300, 1/A/2044:2045 | No text annotation | homologous J5_5J7L_014 NA | |
| J5_5ND9_009 | 1/A/627:632, 1/A/713:716, 1/A/854:858, 1/A/1233:1237, 1/A/1285:1294 | No text annotation | ||
| J5_5ND9_005 | 1/A/1718:1727, 1/A/1749:1751, 1/A/1778:1779, 1/A/1783:1791, 1/A/2015:2017 | No text annotation | ||
| J5_5ND9_006 | 1/A/2084:2091, 1/A/2473:2480, 1/A/2527:2533, 1/A/2610:2615, 1/A/2633:2638 | No text annotation | ||
| J5_5ND9_007 | 1/a/37:40, 1/a/411:414, 1/a/444:450, 1/a/500:508, 1/a/553:556 | No text annotation | homologous J5_5J7L_002 NA | |
| J5_5ND9_008 | 1/a/59:62, 1/a/105:112, 1/a/322:324, 1/a/345:347, 1/a/358:362 | No text annotation | homologous J5_4LFB_002 J5_58574.1 | |
| J6_5ND9_001 | 1/A/45:46, 1/A/181:186, 1/A/217:227, 1/A/234:238, 1/A/265:269, 1/A/472:479 | No text annotation | ||
| J6_5ND9_002 | 1/A/2101:2104, 1/A/2270:2273, 1/A/2285:2286, 1/A/2308:2311, 1/A/2411:2422, 1/A/2448:2462 | No text annotation | ||
| J7_5ND9_001 | 1/A/8:15, 1/A/570:576, 1/A/2045:2050, 1/A/2067:2070, 1/A/2652:2657, 1/A/2815:2816, 1/A/2913:2914 | No text annotation | ||
| J7_5ND9_002 | 1/A/862:867, 1/A/880:881, 1/A/987:990, 1/A/1015:1020, 1/A/1031:1035, 1/A/1207:1208, 1/A/1224:1229 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_5ND9_018 | No text annotation | ||
| J3_5ND9_019 | No text annotation | ||
| J3_5ND9_020 | No text annotation | ||
| J3_5ND9_031 | No text annotation | ||
| J3_5ND9_032 | No text annotation | ||
| J3_5ND9_022 | No text annotation | ||
| J3_5ND9_033 | No text annotation | ||
| J3_5ND9_024 | No text annotation | ||
| J5_5ND9_004 | No text annotation |
Coloring options: