3JCD Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_3JCD_001 | 1/8/13:22 | No text annotation Not in a motif group | geometric HL_2ZZN_004 HL_09136.1 | |
| HL_3JCD_002 | 1/8/30:40 | No text annotation Not in a motif group | geometric HL_4UYK_001 HL_36684.1 | |
| HL_3JCD_003 | 1/8/53:61 | T-loop with 2 stacked bulged bases Not in a motif group | geometric HL_3WFS_003 HL_71309.1 | |
| HL_3JCD_004 | 1/9/13:22 | No text annotation Not in a motif group | geometric HL_3AMU_001 HL_25462.2 | |
| HL_3JCD_005 | 1/9/30:40 | No text annotation Not in a motif group | ||
| HL_3JCD_006 | 1/9/53:61 | No text annotation Not in a motif group | geometric HL_5TBW_051 HL_90642.6 | |
| HL_3JCD_007 | 1/A/59:68 | No text annotation Not in a motif group | homologous HL_5J7L_134 HL_18177.1 | |
| HL_3JCD_008 | 1/A/87:95 | No text annotation Not in a motif group | homologous HL_5J7L_135 HL_84193.1 | |
| HL_3JCD_009 | 1/A/123:128 | No text annotation Not in a motif group | homologous HL_4WF9_003 HL_75407.1 | |
| HL_3JCD_010 | 1/A/136:143 | No text annotation Not in a motif group | ||
| HL_3JCD_011 | 1/A/158:168 | No text annotation Not in a motif group | homologous HL_5J7L_138 HL_81820.1 | |
| HL_3JCD_012 | 1/A/194:201 | No text annotation Not in a motif group | homologous HL_5J7L_139 HL_06192.2 | |
| HL_3JCD_013 | 1/A/225:230 | No text annotation Not in a motif group | homologous HL_5J7L_140 HL_27930.1 | |
| HL_3JCD_014 | 1/A/246:252 | No text annotation Not in a motif group | homologous HL_5J7L_141 HL_67216.7 | |
| HL_3JCD_015 | 1/A/305:312 | T-loop with 1 bulged base Not in a motif group | homologous HL_5J7L_142 HL_89380.2 | |
| HL_3JCD_016 | 1/A/319:323 | No text annotation Not in a motif group | homologous HL_4WF9_011 HL_75407.1 | |
| HL_3JCD_017 | 1/A/327:335 | No text annotation Not in a motif group | homologous HL_5J7L_144 HL_08002.8 | |
| HL_3JCD_018 | 1/A/381:393 | No text annotation Not in a motif group | ||
| HL_3JCD_019 | 1/A/409:418 | No text annotation Not in a motif group | geometric HL_4V83_139 HL_53597.2 | |
| HL_3JCD_020 | 1/A/462:467 | No text annotation Not in a motif group | homologous HL_7A0S_015 HL_42097.1 | |
| HL_3JCD_021 | 1/A/487:493 | No text annotation Not in a motif group | homologous HL_5J7L_148 HL_42097.1 | |
| HL_3JCD_022 | 1/A/543:550 | No text annotation Not in a motif group | homologous HL_5J7L_149 HL_79531.1 | |
| HL_3JCD_023 | 1/A/566:575 | T-loop with 2 stacked bulged bases Not in a motif group | geometric HL_5J7L_150 HL_89380.2 | |
| HL_3JCD_024 | 1/A/611:617 | No text annotation Not in a motif group | homologous HL_5J7L_151 HL_90617.2 | |
| HL_3JCD_025 | 1/A/629:634 | GNRA Not in a motif group | homologous HL_5J7L_152 HL_42097.1 | |
| HL_3JCD_026 | 1/A/641:647 | No text annotation Not in a motif group | homologous HL_5J7L_153 HL_77805.2 | |
| HL_3JCD_029 | 1/A/779:785 | No text annotation Not in a motif group | homologous HL_5J7L_156 HL_74322.1 | |
| HL_3JCD_030 | 1/A/826:831 | No text annotation Not in a motif group | homologous HL_4WF9_025 HL_64365.1 | |
| HL_3JCD_032 | 1/A/955:962 | GNRA Not in a motif group | homologous HL_4WF9_027 HL_42097.1 | |
| HL_3JCD_033 | 1/A/978:985 | No text annotation Not in a motif group | homologous HL_4WF9_028 HL_64430.2 | |
| HL_3JCD_036 | 1/A/1172:1177 | No text annotation Not in a motif group | ||
| HL_3JCD_037 | 1/A/1222:1227 | Other HL Not in a motif group | homologous HL_5J7L_164 HL_87030.2 | |
| HL_3JCD_038 | 1/A/1281:1289 | T-loop with 2 stacked bulged bases Not in a motif group | homologous HL_5J7L_165 HL_89380.2 | |
| HL_3JCD_039 | 1/A/1324:1330 | No text annotation Not in a motif group | homologous HL_5J7L_166 HL_46680.1 | |
| HL_3JCD_040 | 1/A/1363:1368 | No text annotation Not in a motif group | homologous HL_7RQB_035 HL_87030.2 | |
| HL_3JCD_041 | 1/A/1389:1398 | No text annotation Not in a motif group | homologous HL_5J7L_168 HL_69023.2 | |
| HL_3JCD_042 | 1/A/1451:1459 | No text annotation Not in a motif group | geometric HL_5U30_001 HL_53837.1 | |
| HL_3JCD_043 | 1/A/1492:1498 | No text annotation Not in a motif group | homologous HL_5J7L_170 HL_46680.1 | |
| HL_3JCD_044 | 1/A/1529:1542 | No text annotation Not in a motif group | ||
| HL_3JCD_045 | 1/A/1565:1568 | No text annotation Not in a motif group | homologous HL_7RQB_039 HL_38927.2 | |
| HL_3JCD_046 | 1/A/1612:1619 | No text annotation Not in a motif group | homologous HL_4WF9_038 HL_64430.2 | |
| HL_3JCD_047 | 1/A/1630:1636 | GNRA with one bulged base Not in a motif group | homologous HL_5J7L_174 HL_42097.1 | |
| HL_3JCD_049 | 1/A/1728:1731 | No text annotation Not in a motif group | geometric HL_5J7L_176 HL_98426.1 | |
| HL_3JCD_050 | 1/A/1752:1756 | No text annotation Not in a motif group | homologous HL_7RQB_044 HL_76539.2 | |
| HL_3JCD_056 | 1/A/2027:2036 | No text annotation Not in a motif group | homologous HL_7RQB_050 HL_90642.6 | |
| HL_3JCD_070 | 1/A/2658:2663 | No text annotation Not in a motif group | ||
| HL_3JCD_071 | 1/A/2701:2706 | Ribsomal LSU H95 Not in a motif group | homologous HL_5J7L_198 HL_46680.1 | |
| HL_3JCD_072 | 1/A/2745:2759 | No text annotation Not in a motif group | homologous HL_5J7L_199 HL_56677.7 | |
| HL_3JCD_073 | 1/A/2796:2799 | No text annotation Not in a motif group | geometric HL_4V88_192 HL_53837.1 | |
| HL_3JCD_074 | 1/A/2819:2827 | No text annotation Not in a motif group | homologous HL_5J7L_201 HL_27930.1 | |
| HL_3JCD_075 | 1/A/2856:2861 | Other HL Not in a motif group | homologous HL_5J7L_202 HL_42097.1 | |
| HL_3JCD_076 | 1/B/38:44 | No text annotation Not in a motif group | geometric HL_4V9F_071 HL_87939.1 | |
| HL_3JCD_077 | 1/B/86:90 | No text annotation Not in a motif group | homologous HL_5J7L_204 HL_38927.2 | |
| HL_3JCD_078 | 1/a/12:22 | No text annotation Not in a motif group | homologous HL_5J7L_001 HL_89881.2 | |
| HL_3JCD_090 | 1/a/522:527 | No text annotation Not in a motif group | geometric HL_5J7L_143 HL_75407.1 | |
| HL_3JCD_097 | 1/a/897:902 | No text annotation Not in a motif group | ||
| HL_3JCD_101 | 1/a/1076:1081 | GNRA Not in a motif group | homologous HL_4LFB_024 HL_42097.1 | |
| HL_3JCD_109 | 1/a/1515:1520 | No text annotation Not in a motif group | homologous HL_4LFB_032 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_3JCD_027 | No text annotation | ||
| HL_3JCD_028 | No text annotation | ||
| HL_3JCD_031 | No text annotation | ||
| HL_3JCD_034 | No text annotation | ||
| HL_3JCD_035 | No text annotation | ||
| HL_3JCD_048 | UNCG | ||
| HL_3JCD_051 | No text annotation | ||
| HL_3JCD_052 | No text annotation | ||
| HL_3JCD_053 | Other HL | ||
| HL_3JCD_054 | No text annotation | ||
| HL_3JCD_055 | No text annotation | ||
| HL_3JCD_057 | No text annotation | ||
| HL_3JCD_058 | No text annotation | ||
| HL_3JCD_059 | No text annotation | ||
| HL_3JCD_060 | No text annotation | ||
| HL_3JCD_061 | No text annotation | ||
| HL_3JCD_062 | No text annotation | ||
| HL_3JCD_063 | Other HL | ||
| HL_3JCD_064 | GNRA | ||
| HL_3JCD_065 | No text annotation | ||
| HL_3JCD_066 | No text annotation | ||
| HL_3JCD_067 | No text annotation | ||
| HL_3JCD_068 | No text annotation | ||
| HL_3JCD_069 | No text annotation | ||
| HL_3JCD_079 | No text annotation | ||
| HL_3JCD_080 | GNRA | ||
| HL_3JCD_081 | No text annotation | ||
| HL_3JCD_082 | No text annotation | ||
| HL_3JCD_083 | No text annotation | ||
| HL_3JCD_084 | GNRA | ||
| HL_3JCD_085 | No text annotation | ||
| HL_3JCD_086 | UNCG | ||
| HL_3JCD_087 | GNRA | ||
| HL_3JCD_088 | UNCG | ||
| HL_3JCD_089 | No text annotation | ||
| HL_3JCD_091 | No text annotation | ||
| HL_3JCD_092 | No text annotation | ||
| HL_3JCD_093 | Other HL | ||
| HL_3JCD_094 | No text annotation | ||
| HL_3JCD_095 | No text annotation | ||
| HL_3JCD_096 | GNRA | ||
| HL_3JCD_098 | No text annotation | ||
| HL_3JCD_099 | GNRA | ||
| HL_3JCD_100 | No text annotation | ||
| HL_3JCD_102 | No text annotation | ||
| HL_3JCD_103 | No text annotation | ||
| HL_3JCD_104 | No text annotation | ||
| HL_3JCD_105 | Other HL | ||
| HL_3JCD_106 | No text annotation | ||
| HL_3JCD_107 | No text annotation | ||
| HL_3JCD_108 | UNCG |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_3JCD_001 | 1/A/24:30, 1/A/510:516 | Triple sheared with non-canonical cWW Not in a motif group | geometric IL_7RQB_001 IL_66414.6 | |
| IL_3JCD_002 | 1/A/36:37, 1/A/442:444 | Single bulged A Not in a motif group | homologous IL_7RQB_002 IL_37497.2 | |
| IL_3JCD_003 | 1/A/81:85, 1/A/97:105 | No text annotation Not in a motif group | homologous IL_5J7L_248 IL_93699.1 | |
| IL_3JCD_004 | 1/A/183:184, 1/A/212:214 | Single stack bend Not in a motif group | homologous IL_5J7L_249 IL_76488.2 | |
| IL_3JCD_005 | 1/A/188:194, 1/A/201:208 | 8x7 Sarcin-Ricin; G-bulge Not in a motif group | geometric IL_7A0S_006 IL_04346.7 | |
| IL_3JCD_006 | 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_3JCD_007 | 1/A/269:273, 1/A/364:370 | No text annotation Not in a motif group | ||
| IL_3JCD_008 | 1/A/274:281, 1/A/359:363 | No text annotation Not in a motif group | homologous IL_5J7L_253 IL_77870.1 | |
| IL_3JCD_009 | 1/A/293:295, 1/A/343:347 | No text annotation Not in a motif group | homologous IL_5J7L_254 IL_69440.1 | |
| IL_3JCD_010 | 1/A/481:484, 1/A/496:509 | No text annotation Not in a motif group | homologous IL_5J7L_255 IL_60992.6 | |
| IL_3JCD_011 | 1/A/536:539, 1/A/554:557 | Double sheared Not in a motif group | homologous IL_5J7L_256 IL_09705.9 | |
| IL_3JCD_012 | 1/A/564:566, 1/A/575:577 | No text annotation Not in a motif group | homologous IL_7A0S_011 IL_95997.1 | |
| IL_3JCD_013 | 1/A/606:610, 1/A/618:622 | AAA cross-strand stack Not in a motif group | homologous IL_7RQB_016 IL_17136.1 | |
| IL_3JCD_014 | 1/A/672:674, 1/A/806:808 | No text annotation Not in a motif group | homologous IL_7A0S_014 IL_95997.1 | |
| IL_3JCD_015 | 1/A/674:678, 1/A/799:806 | tHW-tHW cross-strand stack Not in a motif group | geometric IL_5J7L_260 IL_17470.6 | |
| IL_3JCD_021 | 1/A/837:838, 1/A/940:942 | Single stack bend Not in a motif group | homologous IL_5J7L_266 IL_92001.1 | |
| IL_3JCD_022 | 1/A/844:847, 1/A/933:934 | Other IL Not in a motif group | geometric IL_5J7L_267 IL_92001.1 | |
| IL_3JCD_023 | 1/A/847:848, 1/A/930:933 | Stack outside cWW Not in a motif group | homologous IL_5J7L_268 IL_37629.1 | |
| IL_3JCD_024 | 1/A/849:851, 1/A/926:929 | No text annotation Not in a motif group | geometric IL_4P3T_002 IL_46796.1 | |
| IL_3JCD_025 | 1/A/856:862, 1/A/915:921 | 7x7 Sarcin-Ricin with intercalated A; G-bulge Not in a motif group | geometric IL_5J7L_270 IL_93830.3 | |
| IL_3JCD_026 | 1/A/862:863, 1/A/913:915 | Single bulged G Not in a motif group | homologous IL_5J7L_271 IL_00225.2 | |
| IL_3JCD_029 | 1/A/994:996, 1/A/1159:1160 | Single bulged C Not in a motif group | homologous IL_7RQB_035 IL_61258.12 | |
| IL_3JCD_030 | 1/A/998:1002, 1/A/1153:1157 | UAA/GAN Not in a motif group | homologous IL_7RQB_036 IL_89002.2 | |
| IL_3JCD_031 | 1/A/1003:1011, 1/A/1150:1152 | No text annotation Not in a motif group | ||
| IL_3JCD_032 | 1/A/1011:1013, 1/A/1149:1150 | No text annotation Not in a motif group | ||
| IL_3JCD_033 | 1/A/1018:1024, 1/A/1140:1144 | No text annotation Not in a motif group | homologous IL_4WF9_039 IL_57188.3 | |
| IL_3JCD_034 | 1/A/1024:1030, 1/A/1124:1140 | No text annotation Not in a motif group | geometric IL_5J7L_281 IL_50715.1 | |
| IL_3JCD_040 | 1/A/1196:1199, 1/A/1246:1250 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_3WBM_002 IL_30621.2 | |
| IL_3JCD_041 | 1/A/1202:1207, 1/A/1239:1243 | No text annotation Not in a motif group | ||
| IL_3JCD_042 | 1/A/1208:1215, 1/A/1234:1238 | Kink-turn Not in a motif group | homologous IL_7RQB_047 IL_70923.2 | |
| IL_3JCD_043 | 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_3JCD_044 | 1/A/1319:1323, 1/A/1331:1333 | C-loop Not in a motif group | homologous IL_5J7L_291 IL_63596.6 | |
| IL_3JCD_045 | 1/A/1351:1355, 1/A/1376:1380 | UAA/GAN Not in a motif group | homologous IL_5J7L_292 IL_89002.2 | |
| IL_3JCD_046 | 1/A/1357:1361, 1/A/1370:1374 | tSH-tHW-tHS Not in a motif group | homologous IL_5J7L_293 IL_17136.1 | |
| IL_3JCD_047 | 1/A/1413:1415, 1/A/1587:1589 | CA cWW Not in a motif group | geometric IL_5ED2_004 IL_95997.1 | |
| IL_3JCD_048 | 1/A/1415:1416, 1/A/1582:1587 | No text annotation Not in a motif group | geometric IL_5J7L_294 IL_90348.1 | |
| IL_3JCD_049 | 1/A/1417:1421, 1/A/1577:1581 | UAA/GAN Not in a motif group | homologous IL_5J7L_295 IL_89002.2 | |
| IL_3JCD_050 | 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_3JCD_051 | 1/A/1437:1441, 1/A/1550:1555 | No text annotation Not in a motif group | ||
| IL_3JCD_052 | 1/A/1450:1451, 1/A/1459:1461 | Single bulged U Not in a motif group | homologous IL_5J7L_298 IL_83039.13 | |
| IL_3JCD_053 | 1/A/1468:1471, 1/A/1520:1524 | No text annotation Not in a motif group | homologous IL_5J7L_299 IL_68574.2 | |
| IL_3JCD_054 | 1/A/1474:1479, 1/A/1512:1517 | No text annotation Not in a motif group | ||
| IL_3JCD_055 | 1/A/1480:1483, 1/A/1506:1511 | No text annotation Not in a motif group | ||
| IL_3JCD_056 | 1/A/1489:1491, 1/A/1499:1500 | Single bulged A Not in a motif group | homologous IL_5J7L_302 IL_37497.2 | |
| IL_3JCD_057 | 1/A/1526:1529, 1/A/1542:1546 | UAA/GAN variation Not in a motif group | homologous IL_5J7L_303 IL_07235.1 | |
| IL_3JCD_058 | 1/A/1651:1656, 1/A/2004:2006 | No text annotation Not in a motif group | homologous IL_7RQB_064 IL_12566.2 | |
| IL_3JCD_059 | 1/A/1663:1665, 1/A/1995:1997 | Isolated tWW turn Not in a motif group | homologous IL_4WF9_063 IL_54997.7 | |
| IL_3JCD_060 | 1/A/1666:1669, 1/A/1993:1994 | Major groove platform; stack outside cWW Not in a motif group | geometric IL_5J7L_306 IL_50694.2 | |
| IL_3JCD_061 | 1/A/1669:1674, 1/A/1990:1993 | Intercalated tWH Not in a motif group | homologous IL_7A0S_062 IL_82842.2 | |
| IL_3JCD_063 | 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_3JCD_064 | 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_3JCD_065 | 1/A/1727:1728, 1/A/1731:1733 | Single bulged C Not in a motif group | homologous IL_5J7L_311 IL_61258.12 | |
| IL_3JCD_074 | 1/A/2050:2053, 1/A/2616:2618 | No text annotation Not in a motif group | geometric IL_6CZR_136 IL_05564.2 | |
| IL_3JCD_075 | 1/A/2054:2056, 1/A/2612:2615 | No text annotation Not in a motif group | homologous IL_5J7L_321 IL_54678.5 | |
| IL_3JCD_096 | 1/A/2636:2640, 1/A/2774:2782 | No text annotation Not in a motif group | homologous IL_5J7L_345 IL_04638.1 | |
| IL_3JCD_097 | 1/A/2652:2658, 1/A/2663:2668 | No text annotation Not in a motif group | ||
| IL_3JCD_098 | 1/A/2678:2685, 1/A/2724:2729 | No text annotation Not in a motif group | ||
| IL_3JCD_099 | 1/A/2687:2691, 1/A/2718:2722 | No text annotation Not in a motif group | homologous IL_4WF9_102 IL_08296.3 | |
| IL_3JCD_100 | 1/A/2695:2696, 1/A/2711:2714 | Multiple bulged bases Not in a motif group | homologous IL_5J7L_349 IL_71530.2 | |
| IL_3JCD_101 | 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_3JCD_102 | 1/A/2795:2796, 1/A/2799:2801 | Single bulged A Not in a motif group | geometric IL_7RQB_019 IL_37497.2 | |
| IL_3JCD_103 | 1/A/2806:2811, 1/A/2889:2892 | No text annotation Not in a motif group | homologous IL_5J7L_351 IL_49460.2 | |
| IL_3JCD_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_3JCD_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_3JCD_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_3JCD_107 | 1/B/17:18, 1/B/65:67 | Major groove intercalation Not in a motif group | homologous IL_5J7L_355 IL_37497.2 | |
| IL_3JCD_108 | 1/B/23:28, 1/B/56:60 | No text annotation Not in a motif group | homologous IL_5J7L_356 IL_18472.2 | |
| IL_3JCD_109 | 1/B/30:31, 1/B/51:54 | Major groove minor groove platform; mini C-loop Not in a motif group | homologous IL_7RQB_113 IL_09061.6 | |
| IL_3JCD_110 | 1/B/34:38, 1/B/44:48 | Symmetric double minor groove platform Not in a motif group | homologous IL_5J7L_358 IL_58103.6 | |
| IL_3JCD_111 | 1/B/71:79, 1/B/97:105 | Bacterial 5S Loop E Not in a motif group | homologous IL_5J7L_359 IL_56455.3 | |
| IL_3JCD_112 | 1/a/30:32, 1/a/552:553 | Single bulged G Not in a motif group | homologous IL_5J7L_001 IL_00225.2 | |
| IL_3JCD_131 | 1/a/504:511, 1/a/540:541 | SSU/LSU pseudoknot Not in a motif group | homologous IL_4LFB_020 IL_15861.7 | |
| IL_3JCD_132 | 1/a/515:521, 1/a/528:536 | No text annotation Not in a motif group | geometric IL_4V88_415 IL_55871.1 | |
| IL_3JCD_133 | 1/a/569:575, 1/a/880:881 | No text annotation Not in a motif group | homologous IL_6CZR_134 IL_69996.1 | |
| IL_3JCD_144 | 1/a/887:895, 1/a/904:910 | 9x7 Sarcin-Ricin with inserted C; G-bulge Not in a motif group | homologous IL_6CZR_146 IL_68633.1 | |
| IL_3JCD_145 | 1/a/922:924, 1/a/1392:1395 | Isolated non-canonical cWW with bulges Not in a motif group | geometric IL_3TD0_002 IL_82068.2 | |
| IL_3JCD_146 | 1/a/925:927, 1/a/1390:1391 | Single bulged G Not in a motif group | homologous IL_5J7L_040 IL_00225.2 | |
| IL_3JCD_152 | 1/a/1057:1059, 1/a/1198:1203 | No text annotation Not in a motif group | geometric IL_3OXE_002 IL_18471.2 | |
| IL_3JCD_160 | 1/a/1399:1401, 1/a/1501:1504 | No text annotation Not in a motif group | homologous IL_5J7L_058 IL_36143.3 | |
| IL_3JCD_161 | 1/a/1401:1404, 1/a/1497:1501 | No text annotation Not in a motif group | geometric IL_4V88_464 IL_99670.1 | |
| IL_3JCD_162 | 1/a/1405:1407, 1/a/1494:1496 | No text annotation Not in a motif group | geometric IL_4V9F_017 IL_95997.1 | |
| IL_3JCD_163 | 1/a/1407:1409, 1/a/1491:1494 | Not an internal loop Not in a motif group | geometric IL_5VCI_005 IL_82842.2 | |
| IL_3JCD_164 | 1/a/1412:1414, 1/a/1486:1488 | No text annotation Not in a motif group | homologous IL_5J7L_061 IL_95997.1 | |
| IL_3JCD_165 | 1/a/1416:1419, 1/a/1481:1484 | Double sheared Not in a motif group | homologous IL_5J7L_062 IL_09705.9 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_3JCD_016 | Single bulged A | ||
| IL_3JCD_017 | Single bulged G | ||
| IL_3JCD_018 | Triple sheared | ||
| IL_3JCD_019 | Major groove platform | ||
| IL_3JCD_020 | Multiple bulged bases | ||
| IL_3JCD_027 | C-loop with extra cWW pair | ||
| IL_3JCD_028 | Tandem non-canonical cWW pairs | ||
| IL_3JCD_035 | Isolated non-canonical cWW with bulges | ||
| IL_3JCD_036 | Tandem non-canonical cWW pairs | ||
| IL_3JCD_037 | Kink-turn | ||
| IL_3JCD_038 | No text annotation | ||
| IL_3JCD_039 | No text annotation | ||
| IL_3JCD_062 | tSH-tSH-tHH-tHS | ||
| IL_3JCD_066 | Single bulged A | ||
| IL_3JCD_067 | Kink-turn related | ||
| IL_3JCD_068 | Major groove outside cWW, minor groove, intercalation pocket | ||
| IL_3JCD_069 | No text annotation | ||
| IL_3JCD_070 | Minor groove platform | ||
| IL_3JCD_071 | Triple sheared related | ||
| IL_3JCD_072 | Multiple bulged bases | ||
| IL_3JCD_073 | No text annotation | ||
| IL_3JCD_076 | Single bulged U | ||
| IL_3JCD_077 | Minor groove platform | ||
| IL_3JCD_078 | Isolated tHS basepair with bulges | ||
| IL_3JCD_079 | No text annotation | ||
| IL_3JCD_080 | Single stack bend | ||
| IL_3JCD_081 | Single stack bend | ||
| IL_3JCD_082 | No text annotation | ||
| IL_3JCD_083 | No text annotation | ||
| IL_3JCD_084 | Single bulged U | ||
| IL_3JCD_085 | Double sheared | ||
| IL_3JCD_086 | No text annotation | ||
| IL_3JCD_087 | Major groove platform | ||
| IL_3JCD_088 | Major groove platform | ||
| IL_3JCD_089 | Major groove minor groove platform with extra cWW | ||
| IL_3JCD_090 | Triple sheared | ||
| IL_3JCD_091 | Major groove platform | ||
| IL_3JCD_092 | Isolated non-canonical cWW with bulges | ||
| IL_3JCD_093 | No text annotation | ||
| IL_3JCD_094 | Minor groove platform with intercalation | ||
| IL_3JCD_095 | Single bulged A | ||
| IL_3JCD_113 | No text annotation | ||
| IL_3JCD_114 | Minor groove platform | ||
| IL_3JCD_115 | Multiple bulged bases | ||
| IL_3JCD_116 | No text annotation | ||
| IL_3JCD_117 | Tandem non-canonical cWW pairs | ||
| IL_3JCD_118 | Minor groove platform related | ||
| IL_3JCD_119 | Isolated cWH basepair | ||
| IL_3JCD_120 | tWH-tWH-tHW-tHW | ||
| IL_3JCD_121 | Minor groove platform | ||
| IL_3JCD_122 | No text annotation | ||
| IL_3JCD_123 | No text annotation | ||
| IL_3JCD_124 | No text annotation | ||
| IL_3JCD_125 | C-loop | ||
| IL_3JCD_126 | Single bulged G | ||
| IL_3JCD_127 | No text annotation | ||
| IL_3JCD_128 | No text annotation | ||
| IL_3JCD_129 | tSH-tHW-tWW | ||
| IL_3JCD_130 | No text annotation | ||
| IL_3JCD_134 | tSH-tHW-tHS | ||
| IL_3JCD_135 | Major groove platform | ||
| IL_3JCD_136 | No text annotation | ||
| IL_3JCD_137 | No text annotation | ||
| IL_3JCD_138 | Major groove platform; stack outside cWW | ||
| IL_3JCD_139 | Single stack bend | ||
| IL_3JCD_140 | Tandem non-canonical cWW pairs | ||
| IL_3JCD_141 | Kink-turn | ||
| IL_3JCD_142 | Left turn | ||
| IL_3JCD_143 | tSH-tHW-tHS | ||
| IL_3JCD_147 | Minor groove platform | ||
| IL_3JCD_148 | No text annotation | ||
| IL_3JCD_149 | No text annotation | ||
| IL_3JCD_150 | Single bulged U | ||
| IL_3JCD_151 | Isolated cWS basepair | ||
| IL_3JCD_153 | No text annotation | ||
| IL_3JCD_154 | Minor groove platform | ||
| IL_3JCD_155 | No text annotation | ||
| IL_3JCD_156 | No text annotation | ||
| IL_3JCD_157 | No text annotation | ||
| IL_3JCD_158 | Triple sheared | ||
| IL_3JCD_159 | No text annotation | ||
| IL_3JCD_166 | Triple sheared related | ||
| IL_3JCD_167 | Minor groove platform | ||
| IL_3JCD_168 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_3JCD_001 | 1/A/30:31, 1/A/474:481, 1/A/509:510 | No text annotation Not in a motif group | ||
| J3_3JCD_002 | 1/A/55:57, 1/A/70:76, 1/A/110:115 | No text annotation Not in a motif group | ||
| J3_3JCD_006 | 1/A/1298:1303, 1/A/1625:1627, 1/A/1639:1642 | No text annotation Not in a motif group | homologous J3_5J7L_041 NA | |
| J3_3JCD_007 | 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_3JCD_008 | 1/A/1343:1349, 1/A/1382:1385, 1/A/1402:1404 | No text annotation Not in a motif group | ||
| J3_3JCD_013 | 1/A/2789:2791, 1/A/2805:2806, 1/A/2892:2894 | No text annotation Not in a motif group | ||
| J3_3JCD_014 | 1/A/2812:2815, 1/A/2831:2836, 1/A/2882:2888 | No text annotation Not in a motif group | ||
| J3_3JCD_015 | 1/B/10:16, 1/B/68:70, 1/B/106:110 | No text annotation Not in a motif group | homologous J3_5J7L_049 NA | |
| J3_3JCD_024 | 1/a/1073:1074, 1/a/1083:1088, 1/a/1097:1102 | No text annotation Not in a motif group |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_3JCD_003 | No text annotation | ||
| J3_3JCD_004 | No text annotation | ||
| J3_3JCD_005 | No text annotation | ||
| J3_3JCD_009 | No text annotation | ||
| J3_3JCD_010 | No text annotation | ||
| J3_3JCD_011 | No text annotation | ||
| J3_3JCD_012 | No text annotation | ||
| J3_3JCD_016 | No text annotation | ||
| J3_3JCD_017 | No text annotation | ||
| J3_3JCD_018 | No text annotation | ||
| J3_3JCD_019 | No text annotation | ||
| J3_3JCD_020 | No text annotation | ||
| J3_3JCD_021 | No text annotation | ||
| J3_3JCD_022 | No text annotation | ||
| J3_3JCD_023 | No text annotation | ||
| J3_3JCD_025 | No text annotation | ||
| J3_3JCD_026 | No text annotation |
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