6ZVJ Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6ZVJ_001 | 1/2/7:17 | No text annotation | homologous HL_4V88_186 NA | |
| HL_6ZVJ_002 | 1/2/69:80 | No text annotation | ||
| HL_6ZVJ_003 | 1/2/156:162 | GNRA related | homologous HL_4V88_188 NA | |
| HL_6ZVJ_004 | 1/2/195:204 | No text annotation | geometric HL_2Y8W_001 HL_81100.2 | |
| HL_6ZVJ_005 | 1/2/288:295 | T-loop with 1 bulged base | geometric HL_4V88_191 NA | |
| HL_6ZVJ_006 | 1/2/320:331 | No text annotation | geometric HL_2Y9H_005 HL_86870.2 | |
| HL_6ZVJ_007 | 1/2/377:387 | No text annotation | ||
| HL_6ZVJ_008 | 1/2/414:423 | No text annotation | geometric HL_5TBW_015 NA | |
| HL_6ZVJ_009 | 1/2/441:452 | No text annotation | homologous HL_4V88_195 NA | |
| HL_6ZVJ_010 | 1/2/462:467 | UNCG | homologous HL_4V88_196 NA | |
| HL_6ZVJ_011 | 1/2/498:504 | No text annotation | homologous HL_4V88_197 NA | |
| HL_6ZVJ_012 | 1/2/535:549 | No text annotation | geometric HL_4WF9_011 HL_75660.5 | |
| HL_6ZVJ_013 | 1/2/569:581 | No text annotation | homologous HL_4V88_199 NA | |
| HL_6ZVJ_014 | 1/2/618:623 | GNRA variation | homologous HL_4V88_200 NA | |
| HL_6ZVJ_015 | 1/2/711:716 | GNRA | geometric HL_4WF9_060 HL_37824.8 | |
| HL_6ZVJ_035 | 1/2/747:796 | No text annotation | ||
| HL_6ZVJ_016 | 1/2/820:828 | No text annotation | homologous HL_4V88_203 NA | |
| HL_6ZVJ_017 | 1/2/833:841 | No text annotation | geometric HL_8Y0B_001 HL_69752.2 | |
| HL_6ZVJ_018 | 1/2/883:903 | No text annotation | geometric HL_2Y8W_001 HL_81100.2 | |
| HL_6ZVJ_019 | 1/2/957:966 | No text annotation | homologous HL_4V88_206 NA | |
| HL_6ZVJ_020 | 1/2/994:999 | GNRA | homologous HL_4V88_207 NA | |
| HL_6ZVJ_021 | 1/2/1054:1064 | No text annotation | homologous HL_4V88_208 NA | |
| HL_6ZVJ_037 | 1/2/1113:1120 | No text annotation | ||
| HL_6ZVJ_023 | 1/2/1141:1146 | GNRA | homologous HL_4V88_210 NA | |
| HL_6ZVJ_024 | 1/2/1178:1183 | GNRA | homologous HL_4V88_211 NA | |
| HL_6ZVJ_025 | 1/2/1245:1254 | No text annotation | geometric HL_2ZNI_001 HL_75660.5 | |
| HL_6ZVJ_026 | 1/2/1295:1304 | Anticodon loop related | homologous HL_4V88_213 NA | |
| HL_6ZVJ_027 | 1/2/1353:1358 | GNRA | homologous HL_4V88_214 NA | |
| HL_6ZVJ_028 | 1/2/1366:1373 | No text annotation | homologous HL_4V88_215 NA | |
| HL_6ZVJ_029 | 1/2/1460:1466 | GNRA | homologous HL_4V88_217 NA | |
| HL_6ZVJ_030 | 1/2/1565:1570 | GNRA | homologous HL_4V88_218 NA | |
| HL_6ZVJ_031 | 1/2/1614:1625 | No text annotation | homologous HL_4V88_219 NA | |
| HL_6ZVJ_032 | 1/2/1658:1666 | No text annotation | homologous HL_4V88_220 NA | |
| HL_6ZVJ_033 | 1/2/1750:1784 | No text annotation | ||
| HL_6ZVJ_034 | 1/2/1847:1852 | GNRA variation | homologous HL_4V88_222 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6ZVJ_022 | No text annotation | ||
| HL_6ZVJ_036 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6ZVJ_001 | 1/2/23:25, 1/2/649:651 | Isolated non-canonical cWW pair | geometric IL_4M4O_001 IL_87907.2 | |
| IL_6ZVJ_002 | 1/2/34:36, 1/2/519:521 | Isolated non-canonical cWW pair | homologous IL_4V88_385 NA | |
| IL_6ZVJ_003 | 1/2/37:40, 1/2/514:518 | Double sheared | geometric IL_4WF9_016 IL_09705.15 | |
| IL_6ZVJ_004 | 1/2/41:47, 1/2/479:481 | No text annotation | homologous IL_4V88_387 NA | |
| IL_6ZVJ_005 | 1/2/49:51, 1/2/476:477 | Minor groove platform | homologous IL_4V88_388 NA | |
| IL_6ZVJ_006 | 1/2/57:62, 1/2/86:88 | No text annotation | homologous IL_4V88_389 NA | |
| IL_6ZVJ_007 | 1/2/63:68, 1/2/81:85 | No text annotation | homologous IL_4V88_390 NA | |
| IL_6ZVJ_008 | 1/2/108:110, 1/2/351:353 | Isolated non-canonical cWW pair | geometric IL_4P43_001 NA | |
| IL_6ZVJ_089 | 1/2/108:112, 1/2/349:353 | Partly complementary | geometric IL_7VYX_008 IL_49751.4 | |
| IL_6ZVJ_009 | 1/2/110:112, 1/2/349:351 | Isolated non-canonical cWW pair | geometric IL_4WF9_042 IL_87907.2 | |
| IL_6ZVJ_010 | 1/2/112:115, 1/2/348:349 | Major groove intercalation | geometric IL_4WF9_071 IL_82107.5 | |
| IL_6ZVJ_011 | 1/2/116:121, 1/2/343:347 | No text annotation | geometric IL_4V88_393 NA | |
| IL_6ZVJ_012 | 1/2/123:125, 1/2/338:341 | No text annotation | geometric IL_4V9F_053 IL_09990.4 | |
| IL_6ZVJ_013 | 1/2/130:144, 1/2/175:182 | No text annotation | ||
| IL_6ZVJ_014 | 1/2/145:151, 1/2/167:174 | tWH-tWH-tHW-tHW | homologous IL_4V88_394 NA | |
| IL_6ZVJ_015 | 1/2/152:154, 1/2/164:166 | Isolated cWH basepair | geometric IL_3R1C_012 IL_10167.6 | |
| IL_6ZVJ_016 | 1/2/188:192, 1/2/207:211 | Double sheared with non-canonical cWW | geometric IL_4V9F_085 IL_17948.2 | |
| IL_6ZVJ_017 | 1/2/216:219, 1/2/302:309 | No text annotation | ||
| IL_6ZVJ_018 | 1/2/219:221, 1/2/300:302 | Isolated non-canonical cWW pair | geometric IL_7A0S_026 IL_87907.2 | |
| IL_6ZVJ_019 | 1/2/223:288, 1/2/295:298 | No text annotation | ||
| IL_6ZVJ_020 | 1/2/312:314, 1/2/336:337 | Single bulged A | homologous IL_4V88_399 NA | |
| IL_6ZVJ_092 | 1/2/317:319, 1/2/332:333 | Single stack bend | geometric IL_5TBW_009 NA | |
| IL_6ZVJ_022 | 1/2/359:364, 1/2/396:403 | Kink-turn with non-sequential stacking | homologous IL_4V88_402 NA | |
| IL_6ZVJ_023 | 1/2/366:371, 1/2/393:394 | No text annotation | geometric IL_5Y58_001 IL_59877.1 | |
| IL_6ZVJ_024 | 1/2/411:413, 1/2/424:429 | No text annotation | homologous IL_4V88_404 NA | |
| IL_6ZVJ_025 | 1/2/437:439, 1/2/454:456 | Isolated cWH basepair | homologous IL_4V88_405 NA | |
| IL_6ZVJ_026 | 1/2/459:461, 1/2/468:470 | Isolated near basepair | homologous IL_4V88_406 NA | |
| IL_6ZVJ_027 | 1/2/487:489, 1/2/511:512 | Single bulged U | geometric IL_4V88_407 NA | |
| IL_6ZVJ_028 | 1/2/491:495, 1/2/508:509 | C-loop | geometric IL_6CZR_127 NA | |
| IL_6ZVJ_029 | 1/2/495:496, 1/2/506:508 | Single bulged G | geometric IL_5J7L_019 IL_00225.14 | |
| IL_6ZVJ_030 | 1/2/529:530, 1/2/554:556 | Single bulged A | homologous IL_4V88_409 NA | |
| IL_6ZVJ_031 | 1/2/563:565, 1/2/585:592 | No text annotation | homologous IL_8C3A_420 NA | |
| IL_6ZVJ_032 | 1/2/566:569, 1/2/581:584 | Tandem non-canonical cWW pairs | geometric IL_402D_001 IL_77658.1 | |
| IL_6ZVJ_033 | 1/2/599:606, 1/2/636:637 | SSU/LSU pseudoknot | homologous IL_4V88_413 NA | |
| IL_6ZVJ_034 | 1/2/606:608, 1/2/635:636 | Single bulged U | geometric IL_5TBW_146 NA | |
| IL_6ZVJ_035 | 1/2/611:617, 1/2/624:632 | Kink-turn related | homologous IL_4V88_415 NA | |
| IL_6ZVJ_036 | 1/2/673:675, 1/2/1030:1032 | Isolated non-canonical cWW pair | homologous IL_4V88_417 NA | |
| IL_6ZVJ_037 | 1/2/676:680, 1/2/1025:1029 | tSH-tHW-tHS | homologous IL_4V88_418 NA | |
| IL_6ZVJ_038 | 1/2/692:694, 1/2/736:738 | No text annotation | ||
| IL_6ZVJ_039 | 1/2/694:696, 1/2/734:736 | Isolated non-canonical cWW pair | geometric IL_5J7L_050 IL_28037.2 | |
| IL_6ZVJ_040 | 1/2/705:708, 1/2/719:725 | No text annotation | ||
| IL_6ZVJ_041 | 1/2/801:803, 1/2/860:864 | No text annotation | ||
| IL_6ZVJ_042 | 1/2/805:807, 1/2/856:858 | Isolated non-canonical cWW pair | homologous IL_4V88_424 NA | |
| IL_6ZVJ_043 | 1/2/807:815, 1/2/849:856 | No text annotation | homologous IL_4V88_425 NA | |
| IL_6ZVJ_044 | 1/2/874:876, 1/2/910:912 | Isolated non-canonical cWW pair | geometric IL_4E59_001 IL_87907.2 | |
| IL_6ZVJ_045 | 1/2/877:879, 1/2/907:909 | Isolated non-canonical cWW pair | geometric IL_5TBW_042 NA | |
| IL_6ZVJ_046 | 1/2/922:923, 1/2/1019:1022 | Major groove platform; stack outside cWW | homologous IL_4V88_428 NA | |
| IL_6ZVJ_100 | 1/2/925:926, 1/2/1015:1017 | Single bulged U | geometric IL_8P9A_427 IL_89505.4 | |
| IL_6ZVJ_101 | 1/2/928:931, 1/2/1010:1013 | Tandem non-canonical cWW pairs | homologous IL_8CRE_433 IL_85033.2 | |
| IL_6ZVJ_049 | 1/2/931:935, 1/2/1007:1010 | Tandem non-canonical cWW pairs | homologous IL_4V88_431 NA | |
| IL_6ZVJ_050 | 1/2/942:945, 1/2/981:984 | Tandem non-canonical cWW pairs | homologous IL_4V88_432 NA | |
| IL_6ZVJ_051 | 1/2/951:956, 1/2/967:975 | Kink-turn | geometric IL_4LFB_031 IL_95727.1 | |
| IL_6ZVJ_052 | 1/2/1041:1047, 1/2/1071:1074 | No text annotation | ||
| IL_6ZVJ_053 | 1/2/1047:1051, 1/2/1067:1071 | tSH-tHW-tHS | geometric IL_4V88_436 NA | |
| IL_6ZVJ_102 | 1/2/1091:1093, 1/2/1152:1158 | No text annotation | homologous IL_8P9A_425 IL_82706.1 | |
| IL_6ZVJ_055 | 1/2/1098:1103, 1/2/1129:1134 | No text annotation | geometric IL_6O5F_001 NA | |
| IL_6ZVJ_056 | 1/2/1108:1110, 1/2/1123:1124 | Minor groove platform | geometric IL_4V88_412 NA | |
| IL_6ZVJ_057 | 1/2/1168:1175, 1/2/1186:1191 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_4V88_440 NA | |
| IL_6ZVJ_103 | 1/2/1203:1204, 1/2/1694:1696 | Single bulged A | homologous IL_8CRE_443 IL_31462.7 | |
| IL_6ZVJ_104 | 1/2/1206:1208, 1/2/1691:1692 | No text annotation | homologous IL_8CRE_444 IL_00225.14 | |
| IL_6ZVJ_060 | 1/2/1213:1217, 1/2/1681:1686 | C-loop with extra cWW pair | geometric IL_4V88_408 NA | |
| IL_6ZVJ_094 | 1/2/1230:1232, 1/2/1526:1528 | Isolated non-canonical cWW pair | homologous IL_8C3A_450 NA | |
| IL_6ZVJ_105 | 1/2/1235:1236, 1/2/1521:1523 | Minor groove platform | homologous IL_8CRE_447 IL_51454.3 | |
| IL_6ZVJ_063 | 1/2/1281:1290, 1/2/1309:1316 | No text annotation | homologous IL_8P9A_470 IL_28304.1 | |
| IL_6ZVJ_064 | 1/2/1291:1294, 1/2/1305:1308 | Tandem non-canonical cWW pairs | geometric IL_6DTD_001 IL_25872.4 | |
| IL_6ZVJ_065 | 1/2/1325:1327, 1/2/1502:1503 | Single bulged U | homologous IL_4V88_449 NA | |
| IL_6ZVJ_066 | 1/2/1329:1333, 1/2/1498:1500 | Isolated cWS basepair | geometric IL_4LFB_044 IL_76319.5 | |
| IL_6ZVJ_095 | 1/2/1329:1335, 1/2/1492:1500 | No text annotation | homologous IL_8P9A_439 IL_86012.1 | |
| IL_6ZVJ_067 | 1/2/1333:1335, 1/2/1492:1498 | Minor groove platform with extra cWW | homologous IL_4V88_451 NA | |
| IL_6ZVJ_068 | 1/2/1337:1338, 1/2/1488:1490 | Single bulged A | homologous IL_4V88_452 NA | |
| IL_6ZVJ_069 | 1/2/1347:1349, 1/2/1380:1382 | Isolated cWH basepair | homologous IL_4V88_453 NA | |
| IL_6ZVJ_070 | 1/2/1363:1365, 1/2/1374:1375 | Minor groove platform | homologous IL_4V88_454 NA | |
| IL_6ZVJ_071 | 1/2/1395:1399, 1/2/1447:1450 | Tandem non-canonical cWW pairs | geometric IL_5LQO_002 IL_85033.2 | |
| IL_6ZVJ_106 | 1/2/1402:1405, 1/2/1441:1444 | No text annotation | homologous IL_8P9A_445 IL_78800.1 | |
| IL_6ZVJ_073 | 1/2/1412:1413, 1/2/1427:1429 | Single bulged G | geometric IL_5J7L_019 IL_00225.14 | |
| IL_6ZVJ_074 | 1/2/1537:1539, 1/2/1594:1596 | Isolated non-canonical cWW pair | geometric IL_4ZC7_001 IL_87907.2 | |
| IL_6ZVJ_097 | 1/2/1541:1550, 1/2/1582:1592 | No text annotation | ||
| IL_6ZVJ_075 | 1/2/1550:1558, 1/2/1577:1582 | 180 degree turn | geometric IL_5J7L_055 IL_11344.2 | |
| IL_6ZVJ_076 | 1/2/1560:1562, 1/2/1573:1575 | Isolated non-canonical cWW pair | geometric IL_4V88_470 NA | |
| IL_6ZVJ_077 | 1/2/1604:1610, 1/2/1629:1635 | No text annotation | homologous IL_8C3A_469 NA | |
| IL_6ZVJ_078 | 1/2/1700:1702, 1/2/1833:1836 | No text annotation | homologous IL_4V88_463 NA | |
| IL_6ZVJ_079 | 1/2/1702:1705, 1/2/1829:1833 | No text annotation | geometric IL_4V88_464 NA | |
| IL_6ZVJ_080 | 1/2/1706:1708, 1/2/1826:1828 | Isolated non-canonical cWW pair | geometric IL_5MWI_002 IL_87907.2 | |
| IL_6ZVJ_081 | 1/2/1708:1713, 1/2/1820:1826 | No text annotation | ||
| IL_6ZVJ_082 | 1/2/1714:1716, 1/2/1817:1819 | Isolated non-canonical cWW pair | geometric IL_4V88_467 NA | |
| IL_6ZVJ_098 | 1/2/1714:1720, 1/2/1813:1819 | No text annotation | ||
| IL_6ZVJ_083 | 1/2/1716:1720, 1/2/1813:1817 | Double sheared with non-canonical cWW | geometric IL_1U6B_002 IL_17948.2 | |
| IL_6ZVJ_084 | 1/2/1720:1727, 1/2/1807:1813 | No text annotation | ||
| IL_6ZVJ_085 | 1/2/1729:1731, 1/2/1803:1805 | Isolated non-canonical cWW pair | homologous IL_4V88_470 NA | |
| IL_6ZVJ_086 | 1/2/1733:1736, 1/2/1798:1801 | Double sheared | homologous IL_4V88_471 NA | |
| IL_6ZVJ_087 | 1/2/1739:1741, 1/2/1793:1795 | Isolated non-canonical cWW pair | geometric IL_4E48_004 IL_87907.2 | |
| IL_6ZVJ_088 | 1/2/1742:1746, 1/2/1788:1792 | Triple sheared | homologous IL_4V88_474 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6ZVJ_090 | No text annotation | ||
| IL_6ZVJ_091 | No text annotation | ||
| IL_6ZVJ_021 | No text annotation | ||
| IL_6ZVJ_093 | No text annotation | ||
| IL_6ZVJ_047 | Single bulged G, near cWW | ||
| IL_6ZVJ_048 | No text annotation | ||
| IL_6ZVJ_054 | No text annotation | ||
| IL_6ZVJ_058 | Isolated non-canonical cWW with bulges | ||
| IL_6ZVJ_059 | No text annotation | ||
| IL_6ZVJ_061 | Tandem non-canonical cWW pairs | ||
| IL_6ZVJ_062 | Isolated non-canonical cWW with bulges | ||
| IL_6ZVJ_072 | No text annotation | ||
| IL_6ZVJ_096 | No text annotation | ||
| IL_6ZVJ_099 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6ZVJ_001 | 1/2/40:41, 1/2/481:487, 1/2/512:514 | No text annotation | homologous J3_8P9A_068 J3_67856.4 | |
| J3_6ZVJ_012 | 1/2/807:819, 1/2/829:831, 1/2/843:856 | No text annotation | ||
| J3_6ZVJ_002 | 1/2/937:941, 1/2/985:993, 1/2/1000:1005 | No text annotation | ||
| J3_6ZVJ_003 | 1/2/1094:1096, 1/2/1136:1140, 1/2/1147:1151 | No text annotation | ||
| J3_6ZVJ_013 | 1/2/1214:1221, 1/2/1645:1651, 1/2/1673:1685 | No text annotation | ||
| J3_6ZVJ_004 | 1/2/1218:1222, 1/2/1644:1651, 1/2/1673:1680 | No text annotation | ||
| J3_6ZVJ_005 | 1/2/1223:1228, 1/2/1530:1532, 1/2/1638:1643 | No text annotation | ||
| J3_6ZVJ_014 | 1/2/1237:1245, 1/2/1254:1266, 1/2/1516:1520 | No text annotation | ||
| J3_6ZVJ_007 | 1/2/1270:1277, 1/2/1320:1324, 1/2/1504:1512 | No text annotation | ||
| J3_6ZVJ_015 | 1/2/1337:1345, 1/2/1384:1389, 1/2/1481:1490 | No text annotation | ||
| J3_6ZVJ_008 | 1/2/1338:1345, 1/2/1384:1389, 1/2/1481:1488 | No text annotation | ||
| J3_6ZVJ_009 | 1/2/1350:1351, 1/2/1360:1363, 1/2/1375:1379 | No text annotation | homologous J3_8C3A_085 NA | |
| J3_6ZVJ_010 | 1/2/1391:1395, 1/2/1450:1456, 1/2/1470:1479 | No text annotation | ||
| J3_6ZVJ_011 | 1/2/1532:1536, 1/2/1597:1604, 1/2/1635:1638 | No text annotation | homologous J3_8C3A_044 NA | |
| J4_6ZVJ_001 | 1/2/98:106, 1/2/355:357, 1/2/405:409, 1/2/431:432 | No text annotation | homologous J4_8P9A_021 J4_15241.1 | |
| J4_6ZVJ_003 | 1/2/663:675, 1/2/1030:1037, 1/2/1078:1089, 1/2/1160:1164 | No text annotation | ||
| J5_6ZVJ_001 | 1/2/30:34, 1/2/521:527, 1/2/558:563, 1/2/592:595, 1/2/641:644 | No text annotation | homologous J5_8C3A_018 NA | |
| J5_6ZVJ_002 | 1/2/30:34, 1/2/521:527, 1/2/558:565, 1/2/585:595, 1/2/641:644 | No text annotation | ||
| J5_6ZVJ_003 | 1/2/53:56, 1/2/89:96, 1/2/434:436, 1/2/457:459, 1/2/470:474 | No text annotation | homologous J5_8C3A_020 NA | |
| J5_6ZVJ_005 | 1/2/123:129, 1/2/183:185, 1/2/214:215, 1/2/310:314, 1/2/336:341 | No text annotation | ||
| J6_6ZVJ_001 | 1/2/682:691, 1/2/739:747, 1/2/796:800, 1/2/865:874, 1/2/912:922, 1/2/1022:1023 | No text annotation | ||
| J6_6ZVJ_002 | 1/2/682:691, 1/2/739:747, 1/2/796:800, 1/2/865:874, 1/2/912:923, 1/2/1019:1023 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6ZVJ_006 | No text annotation | ||
| J4_6ZVJ_002 | No text annotation | ||
| J5_6ZVJ_004 | No text annotation |
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