3JCJ Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_3JCJ_001 | 1/0/38:44 | No text annotation Not in a motif group | homologous HL_5J7L_203 HL_87939.1 | |
| HL_3JCJ_002 | 1/0/86:90 | No text annotation Not in a motif group | homologous HL_5J7L_204 HL_38927.2 | |
| HL_3JCJ_003 | 1/A/59:68 | No text annotation Not in a motif group | homologous HL_5J7L_134 HL_18177.1 | |
| HL_3JCJ_004 | 1/A/87:95 | No text annotation Not in a motif group | homologous HL_5J7L_135 HL_84193.1 | |
| HL_3JCJ_005 | 1/A/123:128 | No text annotation Not in a motif group | homologous HL_5J7L_136 HL_75407.1 | |
| HL_3JCJ_006 | 1/A/136:143 | No text annotation Not in a motif group | ||
| HL_3JCJ_007 | 1/A/158:168 | No text annotation Not in a motif group | homologous HL_5J7L_138 HL_81820.1 | |
| HL_3JCJ_008 | 1/A/194:201 | No text annotation Not in a motif group | geometric HL_4WF9_006 HL_06192.2 | |
| HL_3JCJ_009 | 1/A/225:230 | No text annotation Not in a motif group | homologous HL_5J7L_140 HL_27930.1 | |
| HL_3JCJ_010 | 1/A/246:252 | No text annotation Not in a motif group | homologous HL_5J7L_141 HL_67216.7 | |
| HL_3JCJ_011 | 1/A/305:312 | T-loop with 1 bulged base Not in a motif group | homologous HL_5J7L_142 HL_89380.2 | |
| HL_3JCJ_012 | 1/A/319:323 | No text annotation Not in a motif group | homologous HL_5J7L_143 HL_75407.1 | |
| HL_3JCJ_013 | 1/A/327:335 | No text annotation Not in a motif group | homologous HL_5J7L_144 HL_08002.8 | |
| HL_3JCJ_014 | 1/A/381:393 | No text annotation Not in a motif group | ||
| HL_3JCJ_015 | 1/A/410:417 | No text annotation Not in a motif group | homologous HL_5J7L_146 HL_96598.1 | |
| HL_3JCJ_016 | 1/A/462:467 | GNRA Not in a motif group | homologous HL_4WF9_015 HL_42097.1 | |
| HL_3JCJ_017 | 1/A/487:493 | No text annotation Not in a motif group | homologous HL_5J7L_148 HL_42097.1 | |
| HL_3JCJ_018 | 1/A/543:550 | No text annotation Not in a motif group | homologous HL_7RQB_017 NA | |
| HL_3JCJ_019 | 1/A/566:575 | T-loop with 2 stacked bulged bases Not in a motif group | geometric HL_5J7L_150 HL_89380.2 | |
| HL_3JCJ_020 | 1/A/611:617 | No text annotation Not in a motif group | homologous HL_5J7L_151 HL_90617.2 | |
| HL_3JCJ_021 | 1/A/629:634 | GNRA Not in a motif group | homologous HL_5J7L_152 HL_42097.1 | |
| HL_3JCJ_022 | 1/A/641:647 | No text annotation Not in a motif group | homologous HL_5J7L_153 HL_77805.2 | |
| HL_3JCJ_025 | 1/A/779:785 | No text annotation Not in a motif group | geometric HL_5U3G_001 HL_87030.2 | |
| HL_3JCJ_026 | 1/A/826:831 | No text annotation Not in a motif group | homologous HL_4WF9_025 HL_64365.1 | |
| HL_3JCJ_028 | 1/A/954:963 | No text annotation Not in a motif group | geometric HL_3RG5_006 HL_49288.1 | |
| HL_3JCJ_029 | 1/A/978:985 | No text annotation Not in a motif group | homologous HL_7A0S_027 HL_64430.2 | |
| HL_3JCJ_032 | 1/A/1172:1177 | No text annotation Not in a motif group | geometric HL_4V88_198 HL_56691.2 | |
| HL_3JCJ_033 | 1/A/1222:1227 | Other HL Not in a motif group | homologous HL_5J7L_164 HL_87030.2 | |
| HL_3JCJ_034 | 1/A/1281:1289 | T-loop with 2 stacked bulged bases Not in a motif group | homologous HL_5J7L_165 HL_89380.2 | |
| HL_3JCJ_035 | 1/A/1324:1330 | No text annotation Not in a motif group | homologous HL_5J7L_166 HL_46680.1 | |
| HL_3JCJ_036 | 1/A/1363:1368 | Other HL Not in a motif group | homologous HL_5J7L_167 HL_87030.2 | |
| HL_3JCJ_037 | 1/A/1389:1398 | No text annotation Not in a motif group | homologous HL_7RQB_036 HL_69023.2 | |
| HL_3JCJ_038 | 1/A/1451:1459 | No text annotation Not in a motif group | homologous HL_5J7L_169 HL_53837.1 | |
| HL_3JCJ_039 | 1/A/1492:1498 | No text annotation Not in a motif group | homologous HL_5J7L_170 HL_46680.1 | |
| HL_3JCJ_040 | 1/A/1533:1538 | UNCG Not in a motif group | homologous HL_5J7L_171 HL_03562.2 | |
| HL_3JCJ_041 | 1/A/1565:1568 | No text annotation Not in a motif group | homologous HL_5J7L_172 HL_38927.2 | |
| HL_3JCJ_042 | 1/A/1612:1619 | No text annotation Not in a motif group | homologous HL_7RQB_040 HL_64430.2 | |
| HL_3JCJ_043 | 1/A/1630:1636 | GNRA with one bulged base Not in a motif group | homologous HL_5J7L_174 HL_42097.1 | |
| HL_3JCJ_045 | 1/A/1725:1735 | No text annotation Not in a motif group | geometric HL_4V90_032 HL_14843.1 | |
| HL_3JCJ_046 | 1/A/1752:1756 | No text annotation Not in a motif group | homologous HL_7A0S_044 HL_76539.2 | |
| HL_3JCJ_052 | 1/A/2027:2036 | No text annotation Not in a motif group | homologous HL_4WF9_047 HL_90642.6 | |
| HL_3JCJ_066 | 1/A/2658:2663 | GNRA Not in a motif group | homologous HL_5J7L_197 HL_42097.1 | |
| HL_3JCJ_067 | 1/A/2701:2706 | Ribsomal LSU H95 Not in a motif group | homologous HL_5J7L_198 HL_46680.1 | |
| HL_3JCJ_068 | 1/A/2745:2759 | No text annotation Not in a motif group | homologous HL_5J7L_199 HL_56677.7 | |
| HL_3JCJ_069 | 1/A/2795:2801 | Other HL Not in a motif group | homologous HL_5J7L_200 HL_34168.2 | |
| HL_3JCJ_070 | 1/A/2819:2827 | No text annotation Not in a motif group | homologous HL_5J7L_201 HL_27930.1 | |
| HL_3JCJ_071 | 1/A/2856:2861 | Other HL Not in a motif group | homologous HL_5J7L_202 HL_42097.1 | |
| HL_3JCJ_072 | 1/g/12:22 | No text annotation Not in a motif group | homologous HL_5J7L_001 HL_89881.2 | |
| HL_3JCJ_073 | 1/g/83:86 | No text annotation Not in a motif group | ||
| HL_3JCJ_074 | 1/g/158:163 | GNRA Not in a motif group | homologous HL_5J7L_003 HL_42097.1 | |
| HL_3JCJ_075 | 1/g/186:191 | GNRA Not in a motif group | homologous HL_5J7L_004 HL_42097.1 | |
| HL_3JCJ_076 | 1/g/203:214 | No text annotation Not in a motif group | ||
| HL_3JCJ_077 | 1/g/259:267 | No text annotation Not in a motif group | homologous HL_5J7L_006 HL_69023.2 | |
| HL_3JCJ_078 | 1/g/296:301 | GNRA Not in a motif group | homologous HL_5J7L_007 HL_42097.1 | |
| HL_3JCJ_079 | 1/g/320:333 | No text annotation Not in a motif group | homologous HL_5J7L_008 HL_81205.2 | |
| HL_3JCJ_080 | 1/g/342:347 | UNCG Not in a motif group | homologous HL_4LFB_009 HL_03562.2 | |
| HL_3JCJ_081 | 1/g/379:384 | GNRA Not in a motif group | homologous HL_5J7L_010 HL_42097.1 | |
| HL_3JCJ_082 | 1/g/419:424 | UNCG Not in a motif group | homologous HL_5J7L_011 HL_03562.2 | |
| HL_3JCJ_083 | 1/g/462:470 | No text annotation Not in a motif group | homologous HL_5J7L_012 HL_84085.2 | |
| HL_3JCJ_084 | 1/g/522:527 | No text annotation Not in a motif group | geometric HL_4WF9_003 HL_75407.1 | |
| HL_3JCJ_085 | 1/g/617:623 | No text annotation Not in a motif group | homologous HL_5J7L_014 HL_26881.1 | |
| HL_3JCJ_086 | 1/g/689:698 | No text annotation Not in a motif group | homologous HL_5J7L_015 HL_12326.1 | |
| HL_3JCJ_087 | 1/g/726:731 | Other HL Not in a motif group | homologous HL_5J7L_016 HL_87030.2 | |
| HL_3JCJ_088 | 1/g/786:796 | No text annotation Not in a motif group | homologous HL_5J7L_017 HL_12326.1 | |
| HL_3JCJ_089 | 1/g/840:846 | No text annotation Not in a motif group | ||
| HL_3JCJ_090 | 1/g/862:867 | GNRA Not in a motif group | homologous HL_5J7L_019 HL_42097.1 | |
| HL_3JCJ_091 | 1/g/897:902 | GNRA Not in a motif group | homologous HL_4LFB_020 HL_42097.1 | |
| HL_3JCJ_092 | 1/g/963:972 | No text annotation Not in a motif group | homologous HL_5J7L_021 NA | |
| HL_3JCJ_093 | 1/g/1012:1017 | GNRA Not in a motif group | homologous HL_4LFB_022 HL_42097.1 | |
| HL_3JCJ_094 | 1/g/1028:1033 | No text annotation Not in a motif group | geometric HL_4V88_198 HL_56691.2 | |
| HL_3JCJ_095 | 1/g/1076:1081 | GNRA Not in a motif group | homologous HL_5J7L_023 HL_42097.1 | |
| HL_3JCJ_096 | 1/g/1089:1096 | No text annotation Not in a motif group | homologous HL_4LFB_025 HL_71554.2 | |
| HL_3JCJ_097 | 1/g/1134:1140 | No text annotation Not in a motif group | homologous HL_5J7L_025 HL_03562.2 | |
| HL_3JCJ_098 | 1/g/1165:1171 | No text annotation Not in a motif group | homologous HL_5J7L_026 HL_90617.2 | |
| HL_3JCJ_099 | 1/g/1265:1270 | Other HL Not in a motif group | homologous HL_4LFB_028 HL_42097.1 | |
| HL_3JCJ_100 | 1/g/1314:1323 | No text annotation Not in a motif group | homologous HL_5J7L_028 HL_89380.2 | |
| HL_3JCJ_101 | 1/g/1355:1367 | No text annotation Not in a motif group | ||
| HL_3JCJ_102 | 1/g/1449:1454 | UNCG Not in a motif group | homologous HL_5J7L_030 HL_03562.2 | |
| HL_3JCJ_103 | 1/g/1515:1520 | No text annotation Not in a motif group | homologous HL_6CZR_103 NA | |
| HL_3JCJ_104 | 1/v/13:22 | No text annotation Not in a motif group | ||
| HL_3JCJ_105 | 1/v/31:39 | tRNA anticodon loop Not in a motif group | homologous HL_6UFG_007 HL_53597.2 | |
| HL_3JCJ_106 | 1/v/52:62 | No text annotation Not in a motif group | homologous HL_4WQ1_225 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_3JCJ_023 | No text annotation | ||
| HL_3JCJ_024 | No text annotation | ||
| HL_3JCJ_027 | No text annotation | ||
| HL_3JCJ_030 | No text annotation | ||
| HL_3JCJ_031 | No text annotation | ||
| HL_3JCJ_044 | UNCG | ||
| HL_3JCJ_047 | No text annotation | ||
| HL_3JCJ_048 | No text annotation | ||
| HL_3JCJ_049 | Other HL | ||
| HL_3JCJ_050 | No text annotation | ||
| HL_3JCJ_051 | No text annotation | ||
| HL_3JCJ_053 | No text annotation | ||
| HL_3JCJ_054 | No text annotation | ||
| HL_3JCJ_055 | No text annotation | ||
| HL_3JCJ_056 | No text annotation | ||
| HL_3JCJ_057 | No text annotation | ||
| HL_3JCJ_058 | No text annotation | ||
| HL_3JCJ_059 | Other HL | ||
| HL_3JCJ_060 | GNRA | ||
| HL_3JCJ_061 | No text annotation | ||
| HL_3JCJ_062 | No text annotation | ||
| HL_3JCJ_063 | No text annotation | ||
| HL_3JCJ_064 | No text annotation | ||
| HL_3JCJ_065 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_3JCJ_001 | 1/0/17:18, 1/0/65:67 | Major groove intercalation Not in a motif group | homologous IL_5J7L_355 IL_37497.2 | |
| IL_3JCJ_002 | 1/0/23:28, 1/0/56:60 | No text annotation Not in a motif group | homologous IL_5J7L_356 IL_18472.2 | |
| IL_3JCJ_003 | 1/0/30:32, 1/0/50:54 | No text annotation Not in a motif group | homologous IL_4WF9_114 IL_10810.1 | |
| IL_3JCJ_004 | 1/0/33:38, 1/0/44:49 | No text annotation Not in a motif group | geometric IL_7A0S_105 IL_93630.2 | |
| IL_3JCJ_005 | 1/0/71:79, 1/0/97:105 | Bacterial 5S Loop E Not in a motif group | homologous IL_5J7L_359 IL_56455.3 | |
| IL_3JCJ_006 | 1/A/24:30, 1/A/510:516 | Triple sheared with non-canonical cWW Not in a motif group | homologous IL_4WF9_001 IL_66414.6 | |
| IL_3JCJ_007 | 1/A/36:37, 1/A/442:444 | Single bulged A Not in a motif group | homologous IL_7RQB_002 IL_37497.2 | |
| IL_3JCJ_008 | 1/A/43:44, 1/A/434:436 | Minor groove platform Not in a motif group | homologous IL_5J7L_247 IL_42622.2 | |
| IL_3JCJ_009 | 1/A/81:85, 1/A/97:105 | No text annotation Not in a motif group | homologous IL_5J7L_248 IL_93699.1 | |
| IL_3JCJ_010 | 1/A/183:184, 1/A/212:214 | Single stack bend Not in a motif group | homologous IL_7A0S_005 IL_76488.2 | |
| IL_3JCJ_011 | 1/A/188:194, 1/A/201:208 | 8x7 Sarcin-Ricin; G-bulge Not in a motif group | homologous IL_5J7L_250 IL_04346.7 | |
| IL_3JCJ_012 | 1/A/239:245, 1/A/253:258 | 7x6 Sarcin-Ricin; G-bulge Not in a motif group | homologous IL_5J7L_251 IL_76042.2 | |
| IL_3JCJ_013 | 1/A/269:273, 1/A/364:370 | No text annotation Not in a motif group | ||
| IL_3JCJ_014 | 1/A/274:281, 1/A/359:363 | No text annotation Not in a motif group | homologous IL_5J7L_253 IL_77870.1 | |
| IL_3JCJ_015 | 1/A/293:295, 1/A/343:347 | No text annotation Not in a motif group | homologous IL_7RQB_013 IL_69440.1 | |
| IL_3JCJ_016 | 1/A/481:484, 1/A/496:509 | No text annotation Not in a motif group | homologous IL_7A0S_009 IL_60992.6 | |
| IL_3JCJ_017 | 1/A/536:539, 1/A/554:557 | Double sheared Not in a motif group | homologous IL_5J7L_256 IL_09705.9 | |
| IL_3JCJ_018 | 1/A/564:566, 1/A/575:577 | No text annotation Not in a motif group | homologous IL_5J7L_257 IL_95997.1 | |
| IL_3JCJ_019 | 1/A/606:610, 1/A/618:622 | AAA cross-strand stack Not in a motif group | homologous IL_5J7L_258 IL_17136.1 | |
| IL_3JCJ_020 | 1/A/672:674, 1/A/806:808 | No text annotation Not in a motif group | geometric IL_7RQB_017 IL_95997.1 | |
| IL_3JCJ_021 | 1/A/674:678, 1/A/799:806 | tHW-tHW cross-strand stack Not in a motif group | homologous IL_5J7L_260 IL_17470.6 | |
| IL_3JCJ_027 | 1/A/837:838, 1/A/940:942 | No text annotation Not in a motif group | ||
| IL_3JCJ_028 | 1/A/844:848, 1/A/930:934 | No text annotation Not in a motif group | ||
| IL_3JCJ_029 | 1/A/850:851, 1/A/926:928 | Single stack bend Not in a motif group | homologous IL_5J7L_269 IL_76488.2 | |
| IL_3JCJ_030 | 1/A/856:862, 1/A/915:921 | 7x7 Sarcin-Ricin with intercalated A; G-bulge Not in a motif group | homologous IL_5J7L_270 IL_93830.3 | |
| IL_3JCJ_031 | 1/A/862:863, 1/A/913:915 | Single bulged G Not in a motif group | geometric IL_5J7L_271 IL_00225.2 | |
| IL_3JCJ_036 | 1/A/994:996, 1/A/1159:1160 | Single bulged C Not in a motif group | homologous IL_7RQB_035 IL_61258.12 | |
| IL_3JCJ_037 | 1/A/998:1002, 1/A/1153:1157 | UAA/GAN Not in a motif group | homologous IL_7A0S_033 IL_89002.2 | |
| IL_3JCJ_038 | 1/A/1004:1011, 1/A/1150:1151 | SSU/LSU pseudoknot Not in a motif group | homologous IL_5J7L_278 IL_15861.7 | |
| IL_3JCJ_039 | 1/A/1011:1013, 1/A/1149:1150 | Single bulged U Not in a motif group | geometric IL_5J7L_279 IL_83039.13 | |
| IL_3JCJ_040 | 1/A/1018:1024, 1/A/1140:1144 | No text annotation Not in a motif group | geometric IL_5J7L_280 IL_57188.3 | |
| IL_3JCJ_041 | 1/A/1024:1030, 1/A/1124:1140 | No text annotation Not in a motif group | geometric IL_5J7L_281 IL_50715.1 | |
| IL_3JCJ_047 | 1/A/1196:1198, 1/A/1247:1250 | Isolated cWS basepair Not in a motif group | homologous IL_5J7L_286 IL_52767.2 | |
| IL_3JCJ_048 | 1/A/1202:1206, 1/A/1240:1243 | No text annotation Not in a motif group | homologous IL_5J7L_287 IL_91920.1 | |
| IL_3JCJ_049 | 1/A/1208:1215, 1/A/1234:1238 | Kink-turn Not in a motif group | homologous IL_5J7L_288 IL_70923.2 | |
| IL_3JCJ_050 | 1/A/1262:1269, 1/A/2011:2017 | 8x7 Sarcin-Ricin; G-bulge Not in a motif group | homologous IL_5J7L_289 IL_04346.7 | |
| IL_3JCJ_051 | 1/A/1319:1323, 1/A/1331:1333 | C-loop Not in a motif group | homologous IL_5J7L_291 IL_63596.6 | |
| IL_3JCJ_052 | 1/A/1351:1355, 1/A/1376:1380 | UAA/GAN Not in a motif group | homologous IL_5J7L_292 IL_89002.2 | |
| IL_3JCJ_053 | 1/A/1357:1361, 1/A/1370:1374 | tSH-tHW-tHS Not in a motif group | homologous IL_5J7L_293 IL_17136.1 | |
| IL_3JCJ_054 | 1/A/1415:1416, 1/A/1582:1587 | No text annotation Not in a motif group | homologous IL_5J7L_294 IL_90348.1 | |
| IL_3JCJ_055 | 1/A/1417:1421, 1/A/1577:1581 | UAA/GAN Not in a motif group | homologous IL_5J7L_295 IL_89002.2 | |
| IL_3JCJ_056 | 1/A/1432:1435, 1/A/1557:1561 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_5J7L_296 IL_55178.1 | |
| IL_3JCJ_057 | 1/A/1437:1440, 1/A/1551:1555 | tSH-tHW Not in a motif group | homologous IL_5J7L_297 IL_04059.1 | |
| IL_3JCJ_058 | 1/A/1450:1451, 1/A/1459:1461 | Single bulged U Not in a motif group | geometric IL_5J7L_298 IL_83039.13 | |
| IL_3JCJ_059 | 1/A/1467:1471, 1/A/1520:1525 | tSH-tHH-tHS Not in a motif group | geometric IL_4V9F_056 IL_62654.1 | |
| IL_3JCJ_060 | 1/A/1474:1479, 1/A/1512:1517 | No text annotation Not in a motif group | ||
| IL_3JCJ_061 | 1/A/1481:1482, 1/A/1507:1510 | No text annotation Not in a motif group | homologous IL_5J7L_301 IL_67474.4 | |
| IL_3JCJ_062 | 1/A/1489:1491, 1/A/1499:1500 | Single bulged A Not in a motif group | homologous IL_5J7L_302 IL_37497.2 | |
| IL_3JCJ_063 | 1/A/1526:1529, 1/A/1542:1546 | UAA/GAN variation Not in a motif group | homologous IL_5J7L_303 IL_07235.1 | |
| IL_3JCJ_064 | 1/A/1651:1656, 1/A/2004:2006 | No text annotation Not in a motif group | homologous IL_4WF9_062 IL_12566.2 | |
| IL_3JCJ_065 | 1/A/1663:1665, 1/A/1995:1997 | Isolated tWW turn Not in a motif group | homologous IL_5J7L_305 IL_54997.7 | |
| IL_3JCJ_066 | 1/A/1666:1669, 1/A/1993:1994 | Major groove platform; stack outside cWW Not in a motif group | geometric IL_7RQB_066 IL_50694.2 | |
| IL_3JCJ_067 | 1/A/1669:1674, 1/A/1990:1993 | Intercalated tWH Not in a motif group | homologous IL_4WF9_065 IL_82842.2 | |
| IL_3JCJ_069 | 1/A/1712:1718, 1/A/1742:1746 | 6x5 Sarcin-Ricin; G-bulge Not in a motif group | homologous IL_5J7L_309 IL_88269.3 | |
| IL_3JCJ_070 | 1/A/1720:1725, 1/A/1735:1740 | Triple sheared with non-canonical cWW Not in a motif group | geometric IL_7A0S_018 IL_86929.2 | |
| IL_3JCJ_079 | 1/A/2050:2052, 1/A/2617:2618 | Major groove platform Not in a motif group | homologous IL_5J7L_320 IL_27635.1 | |
| IL_3JCJ_080 | 1/A/2054:2056, 1/A/2612:2615 | No text annotation Not in a motif group | ||
| IL_3JCJ_097 | 1/A/2636:2640, 1/A/2774:2782 | No text annotation Not in a motif group | homologous IL_5J7L_345 IL_04638.1 | |
| IL_3JCJ_098 | 1/A/2652:2658, 1/A/2663:2668 | Sarcin-Ricin target in LSU H95; G-bulge Not in a motif group | geometric IL_7RQB_103 IL_16458.1 | |
| IL_3JCJ_099 | 1/A/2679:2685, 1/A/2724:2728 | No text annotation Not in a motif group | geometric IL_4LFB_048 IL_85222.1 | |
| IL_3JCJ_100 | 1/A/2687:2691, 1/A/2718:2722 | No text annotation Not in a motif group | homologous IL_5J7L_348 IL_08296.3 | |
| IL_3JCJ_101 | 1/A/2695:2696, 1/A/2711:2714 | Multiple bulged bases Not in a motif group | homologous IL_4WF9_103 IL_71530.2 | |
| IL_3JCJ_102 | 1/A/2737:2742, 1/A/2762:2767 | UAA/GAN with extra cWW Not in a motif group | homologous IL_5J7L_350 IL_49767.5 | |
| IL_3JCJ_103 | 1/A/2806:2811, 1/A/2889:2892 | No text annotation Not in a motif group | geometric IL_5J7L_351 IL_49460.2 | |
| IL_3JCJ_104 | 1/A/2838:2839, 1/A/2878:2880 | Major groove intercalation Not in a motif group | homologous IL_5J7L_352 IL_16396.2 | |
| IL_3JCJ_105 | 1/A/2843:2846, 1/A/2870:2874 | Multiple bulged bases with non-canonical cWW Not in a motif group | homologous IL_5J7L_353 IL_58764.3 | |
| IL_3JCJ_106 | 1/A/2847:2852, 1/A/2865:2869 | No text annotation Not in a motif group | homologous IL_7RQB_110 IL_83162.5 | |
| IL_3JCJ_107 | 1/g/30:32, 1/g/552:553 | Single bulged G Not in a motif group | homologous IL_6CZR_113 IL_00225.2 | |
| IL_3JCJ_108 | 1/g/44:45, 1/g/396:398 | Single bulged A Not in a motif group | homologous IL_5J7L_002 IL_37497.2 | |
| IL_3JCJ_109 | 1/g/47:52, 1/g/359:361 | No text annotation Not in a motif group | geometric IL_5J7L_003 IL_11178.1 | |
| IL_3JCJ_110 | 1/g/54:56, 1/g/356:357 | Minor groove platform Not in a motif group | homologous IL_4LFB_004 IL_93353.1 | |
| IL_3JCJ_111 | 1/g/63:67, 1/g/102:104 | No text annotation Not in a motif group | geometric IL_4V88_426 IL_95997.1 | |
| IL_3JCJ_112 | 1/g/67:69, 1/g/99:102 | Minor groove platform with extra cWW Not in a motif group | geometric IL_5J7L_006 IL_65006.1 | |
| IL_3JCJ_113 | 1/g/70:73, 1/g/97:98 | Minor groove platform Not in a motif group | homologous IL_5J7L_007 IL_15052.1 | |
| IL_3JCJ_114 | 1/g/75:76, 1/g/93:95 | Major groove intercalation Not in a motif group | geometric IL_5J7L_352 IL_16396.2 | |
| IL_3JCJ_115 | 1/g/79:82, 1/g/88:90 | No text annotation Not in a motif group | ||
| IL_3JCJ_116 | 1/g/82:83, 1/g/86:88 | No text annotation Not in a motif group | ||
| IL_3JCJ_117 | 1/g/128:131, 1/g/231:233 | No text annotation Not in a motif group | ||
| IL_3JCJ_118 | 1/g/132:136, 1/g/227:230 | No text annotation Not in a motif group | homologous IL_4LFB_008 IL_58764.3 | |
| IL_3JCJ_119 | 1/g/144:146, 1/g/176:178 | Isolated cWH basepair Not in a motif group | homologous IL_5J7L_011 IL_51629.2 | |
| IL_3JCJ_120 | 1/g/147:153, 1/g/168:175 | tWH-tWH-tHW-tHW Not in a motif group | homologous IL_5J7L_012 IL_80604.2 | |
| IL_3JCJ_121 | 1/g/242:247, 1/g/277:284 | Kink-turn with non-sequential stacking Not in a motif group | homologous IL_5J7L_014 IL_45067.2 | |
| IL_3JCJ_122 | 1/g/249:253, 1/g/273:275 | No text annotation Not in a motif group | homologous IL_6CZR_124 IL_38684.1 | |
| IL_3JCJ_123 | 1/g/292:293, 1/g/304:308 | C-loop Not in a motif group | homologous IL_4LFB_013 IL_37712.2 | |
| IL_3JCJ_124 | 1/g/371:375, 1/g/389:390 | C-loop Not in a motif group | homologous IL_5J7L_018 IL_75255.1 | |
| IL_3JCJ_125 | 1/g/375:376, 1/g/387:389 | Single bulged G Not in a motif group | geometric IL_5J7L_019 IL_00225.2 | |
| IL_3JCJ_126 | 1/g/409:416, 1/g/427:433 | No text annotation Not in a motif group | homologous IL_5J7L_020 IL_28026.1 | |
| IL_3JCJ_127 | 1/g/440:442, 1/g/492:497 | No text annotation Not in a motif group | homologous IL_5J7L_021 IL_22248.1 | |
| IL_3JCJ_128 | 1/g/446:450, 1/g/483:488 | tSH-tHW-tWW Not in a motif group | homologous IL_5J7L_022 IL_88269.3 | |
| IL_3JCJ_129 | 1/g/450:455, 1/g/477:483 | No text annotation Not in a motif group | geometric IL_5J7L_023 IL_70801.1 | |
| IL_3JCJ_130 | 1/g/504:511, 1/g/540:541 | SSU/LSU pseudoknot Not in a motif group | homologous IL_5J7L_024 IL_15861.7 | |
| IL_3JCJ_131 | 1/g/515:521, 1/g/528:536 | No text annotation Not in a motif group | ||
| IL_3JCJ_132 | 1/g/569:575, 1/g/880:881 | No text annotation Not in a motif group | homologous IL_6CZR_134 IL_69996.1 | |
| IL_3JCJ_133 | 1/g/580:584, 1/g/757:761 | tSH-tHW-tHS Not in a motif group | homologous IL_5J7L_027 IL_17136.1 | |
| IL_3JCJ_134 | 1/g/594:596, 1/g/644:645 | Major groove platform Not in a motif group | homologous IL_5J7L_028 IL_27635.1 | |
| IL_3JCJ_135 | 1/g/597:598, 1/g/640:643 | Major groove minor groove platform; mini C-loop Not in a motif group | homologous IL_5J7L_029 IL_09061.6 | |
| IL_3JCJ_136 | 1/g/605:612, 1/g/628:633 | No text annotation Not in a motif group | homologous IL_5J7L_030 IL_78349.1 | |
| IL_3JCJ_137 | 1/g/654:655, 1/g/751:754 | Major groove platform; stack outside cWW Not in a motif group | geometric IL_5J7L_031 IL_50694.2 | |
| IL_3JCJ_138 | 1/g/658:659, 1/g/746:748 | Single stack bend Not in a motif group | homologous IL_5J7L_032 IL_76488.2 | |
| IL_3JCJ_139 | 1/g/662:666, 1/g/740:743 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_5J7L_033 IL_71110.1 | |
| IL_3JCJ_140 | 1/g/683:688, 1/g/699:707 | Kink-turn Not in a motif group | homologous IL_4LFB_031 IL_37722.1 | |
| IL_3JCJ_141 | 1/g/774:778, 1/g/804:805 | Left turn Not in a motif group | homologous IL_5J7L_036 IL_29346.1 | |
| IL_3JCJ_142 | 1/g/779:783, 1/g/799:803 | tSH-tHW-tHS Not in a motif group | homologous IL_4LFB_033 IL_17136.1 | |
| IL_3JCJ_143 | 1/g/887:894, 1/g/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge Not in a motif group | homologous IL_5J7L_038 IL_24606.2 | |
| IL_3JCJ_144 | 1/g/922:923, 1/g/1393:1395 | Single bulged A Not in a motif group | homologous IL_5J7L_039 IL_37497.2 | |
| IL_3JCJ_145 | 1/g/925:927, 1/g/1390:1391 | Single bulged G Not in a motif group | homologous IL_4LFB_036 IL_00225.2 | |
| IL_3JCJ_146 | 1/g/933:935, 1/g/1380:1384 | Minor groove platform Not in a motif group | homologous IL_4LFB_037 IL_47078.1 | |
| IL_3JCJ_147 | 1/g/953:954, 1/g/1226:1228 | No text annotation Not in a motif group | homologous IL_6CZR_150 NA | |
| IL_3JCJ_148 | 1/g/993:997, 1/g/1044:1045 | Minor groove platform Not in a motif group | homologous IL_5J7L_043 IL_47078.1 | |
| IL_3JCJ_149 | 1/g/998:999, 1/g/1041:1043 | Single stack bend Not in a motif group | homologous IL_5J7L_044 IL_76488.2 | |
| IL_3JCJ_150 | 1/g/1048:1050, 1/g/1208:1209 | Single bulged U Not in a motif group | homologous IL_5J7L_046 IL_83039.13 | |
| IL_3JCJ_151 | 1/g/1052:1056, 1/g/1204:1206 | Isolated cWS basepair Not in a motif group | homologous IL_4LFB_044 IL_76319.2 | |
| IL_3JCJ_152 | 1/g/1057:1058, 1/g/1199:1203 | Minor groove platform Not in a motif group | homologous IL_4LFB_045 IL_93353.1 | |
| IL_3JCJ_153 | 1/g/1060:1061, 1/g/1195:1197 | Single bulged A Not in a motif group | homologous IL_5J7L_049 IL_37497.2 | |
| IL_3JCJ_154 | 1/g/1061:1063, 1/g/1193:1195 | No text annotation Not in a motif group | geometric IL_5J7L_050 IL_95997.1 | |
| IL_3JCJ_155 | 1/g/1124:1128, 1/g/1144:1149 | No text annotation Not in a motif group | homologous IL_5J7L_051 IL_93211.1 | |
| IL_3JCJ_156 | 1/g/1129:1132, 1/g/1142:1143 | Minor groove platform Not in a motif group | homologous IL_5J7L_052 IL_15052.1 | |
| IL_3JCJ_157 | 1/g/1158:1161, 1/g/1175:1181 | No text annotation Not in a motif group | homologous IL_4LFB_050 IL_42032.1 | |
| IL_3JCJ_158 | 1/g/1246:1253, 1/g/1284:1291 | No text annotation Not in a motif group | ||
| IL_3JCJ_159 | 1/g/1255:1258, 1/g/1277:1282 | No text annotation Not in a motif group | homologous IL_5J7L_055 IL_75461.4 | |
| IL_3JCJ_160 | 1/g/1259:1263, 1/g/1272:1276 | Triple sheared Not in a motif group | homologous IL_5J7L_056 IL_56467.8 | |
| IL_3JCJ_161 | 1/g/1303:1308, 1/g/1329:1334 | No text annotation Not in a motif group | geometric IL_5J7L_057 IL_19954.2 | |
| IL_3JCJ_162 | 1/g/1399:1401, 1/g/1501:1504 | No text annotation Not in a motif group | homologous IL_5J7L_058 IL_36143.3 | |
| IL_3JCJ_163 | 1/g/1401:1404, 1/g/1497:1501 | No text annotation Not in a motif group | geometric IL_4V88_464 IL_99670.1 | |
| IL_3JCJ_164 | 1/g/1405:1407, 1/g/1494:1496 | No text annotation Not in a motif group | geometric IL_4V88_465 IL_95997.1 | |
| IL_3JCJ_165 | 1/g/1407:1409, 1/g/1491:1494 | Isolated non-canonical cWW with bulges Not in a motif group | geometric IL_5J7L_009 IL_82068.2 | |
| IL_3JCJ_166 | 1/g/1412:1415, 1/g/1485:1488 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_6CZR_168 IL_67743.1 | |
| IL_3JCJ_167 | 1/g/1416:1419, 1/g/1481:1484 | Double sheared Not in a motif group | homologous IL_6CZR_169 IL_09705.9 | |
| IL_3JCJ_168 | 1/g/1430:1435, 1/g/1466:1470 | Triple sheared related Not in a motif group | homologous IL_5J7L_063 IL_64879.2 | |
| IL_3JCJ_169 | 1/g/1440:1442, 1/g/1460:1461 | Minor groove platform Not in a motif group | homologous IL_5J7L_064 IL_42622.2 | |
| IL_3JCJ_170 | 1/g/1445:1448, 1/g/1455:1457 | No text annotation Not in a motif group | homologous IL_5J7L_065 IL_02284.5 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_3JCJ_022 | Single bulged A | ||
| IL_3JCJ_023 | Single bulged G | ||
| IL_3JCJ_024 | Triple sheared | ||
| IL_3JCJ_025 | No text annotation | ||
| IL_3JCJ_026 | Multiple bulged bases | ||
| IL_3JCJ_032 | C-loop | ||
| IL_3JCJ_033 | Isolated cWS basepair | ||
| IL_3JCJ_034 | Triple sheared | ||
| IL_3JCJ_035 | No text annotation | ||
| IL_3JCJ_042 | Isolated non-canonical cWW with bulges | ||
| IL_3JCJ_043 | Tandem non-canonical cWW pairs | ||
| IL_3JCJ_044 | Kink-turn | ||
| IL_3JCJ_045 | No text annotation | ||
| IL_3JCJ_046 | No text annotation | ||
| IL_3JCJ_068 | tSH-tSH-tHH-tHS | ||
| IL_3JCJ_071 | Single bulged A | ||
| IL_3JCJ_072 | Kink-turn related | ||
| IL_3JCJ_073 | Major groove outside cWW, minor groove, intercalation pocket | ||
| IL_3JCJ_074 | Isolated non-canonical cWW with bulges | ||
| IL_3JCJ_075 | Minor groove platform | ||
| IL_3JCJ_076 | UAA/GAN related | ||
| IL_3JCJ_077 | No text annotation | ||
| IL_3JCJ_078 | No text annotation | ||
| IL_3JCJ_081 | Single bulged U | ||
| IL_3JCJ_082 | Minor groove platform | ||
| IL_3JCJ_083 | Isolated tHS basepair with bulges | ||
| IL_3JCJ_084 | No text annotation | ||
| IL_3JCJ_085 | Single bulged U | ||
| IL_3JCJ_086 | Double sheared | ||
| IL_3JCJ_087 | No text annotation | ||
| IL_3JCJ_088 | Major groove platform | ||
| IL_3JCJ_089 | Major groove platform with extra pair | ||
| IL_3JCJ_090 | Major groove minor groove platform with extra cWW | ||
| IL_3JCJ_091 | Triple sheared | ||
| IL_3JCJ_092 | Major groove platform | ||
| IL_3JCJ_093 | Isolated non-canonical cWW with bulges | ||
| IL_3JCJ_094 | No text annotation | ||
| IL_3JCJ_095 | Minor groove platform with intercalation | ||
| IL_3JCJ_096 | Single bulged A |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_3JCJ_001 | 1/0/10:16, 1/0/68:70, 1/0/106:110 | No text annotation Not in a motif group | homologous J3_5J7L_049 NA | |
| J3_3JCJ_002 | 1/A/30:31, 1/A/474:481, 1/A/509:510 | No text annotation Not in a motif group | ||
| J3_3JCJ_003 | 1/A/55:57, 1/A/70:76, 1/A/110:115 | No text annotation Not in a motif group | ||
| J3_3JCJ_007 | 1/A/1298:1303, 1/A/1625:1627, 1/A/1639:1642 | No text annotation Not in a motif group | homologous J3_7A0S_006 NA | |
| J3_3JCJ_008 | 1/A/1306:1309, 1/A/1605:1611, 1/A/1620:1622 | No text annotation Not in a motif group | homologous J3_7A0S_007 NA | |
| J3_3JCJ_009 | 1/A/1344:1349, 1/A/1382:1385, 1/A/1402:1403 | No text annotation Not in a motif group | homologous J3_5J7L_043 NA | |
| J3_3JCJ_013 | 1/A/2789:2791, 1/A/2805:2806, 1/A/2892:2894 | No text annotation Not in a motif group | homologous J3_5J7L_047 NA | |
| J3_3JCJ_014 | 1/A/2812:2815, 1/A/2831:2836, 1/A/2882:2888 | No text annotation Not in a motif group | homologous J3_5J7L_048 NA | |
| J3_3JCJ_015 | 1/g/46:47, 1/g/361:369, 1/g/392:395 | No text annotation Not in a motif group | ||
| J3_3JCJ_016 | 1/g/586:588, 1/g/651:654, 1/g/754:755 | No text annotation Not in a motif group | homologous J3_5J7L_002 NA | |
| J3_3JCJ_017 | 1/g/826:829, 1/g/857:861, 1/g/868:874 | No text annotation Not in a motif group | homologous J3_5J7L_004 NA | |
| J3_3JCJ_018 | 1/g/936:939, 1/g/1344:1350, 1/g/1372:1379 | No text annotation Not in a motif group | homologous J3_4LFB_002 NA | |
| J3_3JCJ_019 | 1/g/943:946, 1/g/1235:1237, 1/g/1337:1340 | No text annotation Not in a motif group | homologous J3_5J7L_005 NA | |
| J3_3JCJ_020 | 1/g/955:962, 1/g/973:984, 1/g/1221:1225 | No text annotation Not in a motif group | ||
| J3_3JCJ_021 | 1/g/990:993, 1/g/1045:1047, 1/g/1210:1215 | No text annotation Not in a motif group | ||
| J3_3JCJ_022 | 1/g/1002:1006, 1/g/1023:1028, 1/g/1033:1038 | No text annotation Not in a motif group | ||
| J3_3JCJ_023 | 1/g/1063:1068, 1/g/1107:1113, 1/g/1187:1193 | No text annotation Not in a motif group | ||
| J3_3JCJ_024 | 1/g/1073:1074, 1/g/1083:1087, 1/g/1098:1102 | No text annotation Not in a motif group | homologous J3_5J7L_009 NA | |
| J3_3JCJ_025 | 1/g/1116:1118, 1/g/1155:1158, 1/g/1181:1184 | No text annotation Not in a motif group | ||
| J3_3JCJ_026 | 1/g/1237:1241, 1/g/1296:1303, 1/g/1334:1337 | No text annotation Not in a motif group |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_3JCJ_004 | No text annotation | ||
| J3_3JCJ_005 | No text annotation | ||
| J3_3JCJ_006 | No text annotation | ||
| J3_3JCJ_010 | No text annotation | ||
| J3_3JCJ_011 | No text annotation | ||
| J3_3JCJ_012 | No text annotation |
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