7D5S Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_7D5S_003 | 1/5A/4:9 | No text annotation | geometric HL_5U3G_001 HL_75660.5 | |
| HL_7D5S_005 | 1/5A/120:125 | GNRA | geometric HL_4QLM_001 HL_37824.7 | |
| HL_7D5S_006 | 1/5A/196:201 | GNRA | geometric HL_2OIU_001 HL_37824.7 | |
| HL_7D5S_007 | 1/5A/251:257 | Mini UNCG | geometric HL_5U30_001 HL_48778.2 | |
| HL_7D5S_008 | 1/5A/301:305 | Mini UNCG | geometric HL_4V9F_021 HL_48778.2 | |
| HL_7D5S_009 | 1/5A/360:365 | GNRA related | geometric HL_5J7L_179 HL_04783.2 | |
| HL_7D5S_010 | 1/5A/424:433 | No text annotation | ||
| HL_7D5S_011 | 1/5A/514:521 | No text annotation | geometric HL_7RQB_022 NA | |
| HL_7D5S_013 | 1/SA/491:496 | GNRA | geometric HL_4V9F_040 HL_37824.7 | |
| HL_7D5S_014 | 1/SA/520:532 | No text annotation | geometric HL_4V88_199 NA | |
| HL_7D5S_015 | 1/SA/561:566 | No text annotation | geometric HL_5NFV_001 HL_69752.2 | |
| HL_7D5S_016 | 1/SA/900:909 | No text annotation | homologous HL_4V88_206 NA | |
| HL_7D5S_017 | 1/SA/937:942 | GNRA | homologous HL_4V88_207 NA | |
| HL_7D5S_018 | 1/SA/997:1007 | No text annotation | homologous HL_4V88_208 NA | |
| HL_7D5S_019 | 1/SA/1129:1139 | No text annotation | ||
| HL_7D5S_022 | 1/SA/1501:1506 | GNRA | homologous HL_4V88_218 NA | |
| HL_7D5S_023 | 1/SA/1594:1602 | Mini UNCG | geometric HL_4OOG_001 HL_56334.1 | |
| HL_7D5S_024 | 1/SA/1629:1636 | No text annotation | geometric HL_4LX6_002 HL_31585.3 | |
| HL_7D5S_025 | 1/SA/1698:1703 | GNRA | geometric HL_6UFH_004 HL_37824.7 | |
| HL_7D5S_026 | 1/SA/1778:1783 | No text annotation | geometric HL_2Y8W_001 HL_81100.2 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_7D5S_001 | No text annotation | ||
| HL_7D5S_002 | No text annotation | ||
| HL_7D5S_004 | No text annotation | ||
| HL_7D5S_012 | No text annotation | ||
| HL_7D5S_027 | No text annotation | ||
| HL_7D5S_020 | No text annotation | ||
| HL_7D5S_021 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_7D5S_001 | 1/3A/6:7, 1/SA/1117:1119 | Single bulged G | geometric IL_3IGI_004 IL_00225.13 | |
| IL_7D5S_002 | 1/3A/48:50, 1/5A/466:470 | No text annotation | geometric IL_4V9F_053 IL_09990.4 | |
| IL_7D5S_003 | 1/3A/78:85, 1/3A/325:329 | No text annotation | ||
| IL_7D5S_068 | 1/3A/85:96, 1/3A/320:325 | No text annotation | ||
| IL_7D5S_004 | 1/3A/97:98, 1/3A/317:319 | No text annotation | ||
| IL_7D5S_005 | 1/3A/111:115, 1/3A/252:259 | No text annotation | ||
| IL_7D5S_007 | 1/5A/17:18, 1/5A/62:64 | Single bulged G | geometric IL_3NDB_004 IL_00225.13 | |
| IL_7D5S_076 | 1/5A/94:95, 1/5A/149:156 | No text annotation | ||
| IL_7D5S_009 | 1/5A/97:99, 1/5A/145:147 | Isolated cWH basepair | geometric IL_3R1C_012 IL_10167.5 | |
| IL_7D5S_010 | 1/5A/100:104, 1/5A/140:144 | No text annotation | ||
| IL_7D5S_011 | 1/5A/107:110, 1/5A/136:137 | Single stack bend | geometric IL_4C7O_002 IL_90729.1 | |
| IL_7D5S_012 | 1/5A/116:117, 1/5A/128:130 | Single bulged U | geometric IL_4V88_469 NA | |
| IL_7D5S_013 | 1/5A/167:173, 1/5A/223:228 | No text annotation | ||
| IL_7D5S_069 | 1/5A/175:178, 1/5A/219:221 | No text annotation | ||
| IL_7D5S_070 | 1/5A/187:189, 1/5A/208:210 | Isolated non-canonical cWW pair | geometric IL_3DIL_006 IL_87907.2 | |
| IL_7D5S_016 | 1/5A/238:240, 1/5A/273:274 | Single bulged U | geometric IL_6JDV_003 IL_89505.4 | |
| IL_7D5S_017 | 1/5A/245:246, 1/5A/266:268 | Single bulged U | geometric IL_7KVT_002 IL_89505.4 | |
| IL_7D5S_018 | 1/5A/250:251, 1/5A/257:262 | Multiple bulged bases | geometric IL_1R3E_002 IL_84476.1 | |
| IL_7D5S_019 | 1/5A/337:340, 1/5A/386:387 | Major groove minor groove platform; mini C-loop | geometric IL_4V9F_068 IL_68140.4 | |
| IL_7D5S_020 | 1/5A/340:341, 1/5A/384:386 | Single bulged A | geometric IL_1JZV_002 IL_31462.5 | |
| IL_7D5S_021 | 1/5A/342:343, 1/5A/381:383 | Single bulged U | geometric IL_4FRG_002 IL_89505.4 | |
| IL_7D5S_022 | 1/5A/346:349, 1/5A/375:378 | Tandem non-canonical cWW pairs | geometric IL_280D_001 IL_77658.1 | |
| IL_7D5S_071 | 1/5A/352:355, 1/5A/371:372 | No text annotation | ||
| IL_7D5S_072 | 1/5A/352:356, 1/5A/369:372 | No text annotation | ||
| IL_7D5S_024 | 1/5A/355:356, 1/5A/369:371 | Stack outside cWW | geometric IL_1NTA_001 IL_66635.5 | |
| IL_7D5S_025 | 1/5A/402:407, 1/5A/449:455 | No text annotation | ||
| IL_7D5S_026 | 1/5A/413:414, 1/5A/441:443 | Single stack bend | geometric IL_4C7O_002 IL_90729.1 | |
| IL_7D5S_027 | 1/5A/414:415, 1/5A/439:441 | Single bulged U | geometric IL_7KVT_002 IL_89505.4 | |
| IL_7D5S_029 | 1/5A/497:499, 1/5A/539:542 | Isolated non-canonical cWW pair | geometric IL_3TD0_005 IL_57744.1 | |
| IL_7D5S_030 | 1/5A/501:503, 1/5A/533:537 | No text annotation | ||
| IL_7D5S_031 | 1/5A/505:507, 1/5A/529:531 | Isolated non-canonical cWW pair | geometric IL_5MSF_001 IL_87907.2 | |
| IL_7D5S_032 | 1/5A/510:511, 1/5A/524:526 | Single bulged U | geometric IL_6UFH_004 IL_89505.4 | |
| IL_7D5S_033 | 1/5A/550:552, 1/5A/585:587 | Isolated non-canonical cWW contact | geometric IL_5UNE_001 IL_44465.1 | |
| IL_7D5S_034 | 1/SA/24:26, 1/SA/600:601 | Single bulged C | geometric IL_7KGA_001 IL_61258.15 | |
| IL_7D5S_035 | 1/SA/482:483, 1/SA/504:506 | Single bulged A | homologous IL_4V88_409 NA | |
| IL_7D5S_036 | 1/SA/514:516, 1/SA/536:543 | No text annotation | homologous IL_8C3A_420 NA | |
| IL_7D5S_037 | 1/SA/517:520, 1/SA/532:535 | Tandem non-canonical cWW pairs | geometric IL_6JDV_001 IL_77658.1 | |
| IL_7D5S_038 | 1/SA/551:552, 1/SA/584:587 | No text annotation | geometric IL_5J7L_341 IL_42626.2 | |
| IL_7D5S_039 | 1/SA/552:559, 1/SA/568:584 | No text annotation | ||
| IL_7D5S_040 | 1/SA/627:631, 1/SA/969:972 | No text annotation | ||
| IL_7D5S_041 | 1/SA/631:632, 1/SA/967:969 | Single stack bend | geometric IL_7A0S_054 IL_26793.1 | |
| IL_7D5S_043 | 1/SA/865:866, 1/SA/962:965 | Major groove platform; stack outside cWW | geometric IL_4V88_428 NA | |
| IL_7D5S_077 | 1/SA/868:869, 1/SA/958:960 | Single bulged U | geometric IL_7KVT_002 IL_89505.4 | |
| IL_7D5S_045 | 1/SA/871:873, 1/SA/954:956 | Isolated non-canonical cWW pair | geometric IL_2R8S_001 IL_87907.2 | |
| IL_7D5S_046 | 1/SA/874:878, 1/SA/950:953 | Tandem non-canonical cWW pairs | homologous IL_4V88_431 NA | |
| IL_7D5S_047 | 1/SA/885:888, 1/SA/924:927 | Tandem non-canonical cWW pairs | homologous IL_4V88_432 NA | |
| IL_7D5S_048 | 1/SA/893:899, 1/SA/910:919 | Kink-turn related | homologous IL_8C3A_440 NA | |
| IL_7D5S_049 | 1/SA/985:990, 1/SA/1014:1016 | Other IL | geometric IL_4V88_435 NA | |
| IL_7D5S_050 | 1/SA/990:994, 1/SA/1010:1014 | tSH-tHW-tHS | homologous IL_4V88_436 NA | |
| IL_7D5S_051 | 1/SA/1157:1160, 1/SA/1617:1621 | C-loop | homologous IL_4V88_443 NA | |
| IL_7D5S_052 | 1/SA/1173:1174, 1/SA/1464:1466 | Single stack bend | geometric IL_7RQB_058 NA | |
| IL_7D5S_053 | 1/SA/1174:1176, 1/SA/1463:1464 | Minor groove platform | geometric IL_5TBW_039 NA | |
| IL_7D5S_054 | 1/SA/1212:1216, 1/SA/1448:1451 | No text annotation | ||
| IL_7D5S_055 | 1/SA/1268:1270, 1/SA/1440:1441 | No text annotation | ||
| IL_7D5S_074 | 1/SA/1480:1493, 1/SA/1514:1527 | No text annotation | ||
| IL_7D5S_057 | 1/SA/1495:1498, 1/SA/1509:1512 | Tandem non-canonical cWW pairs | homologous IL_4V88_461 NA | |
| IL_7D5S_058 | 1/SA/1649:1652, 1/SA/1748:1751 | Tandem non-canonical cWW pairs | geometric IL_5J7L_283 IL_85033.2 | |
| IL_7D5S_078 | 1/SA/1653:1658, 1/SA/1742:1747 | No text annotation | ||
| IL_7D5S_060 | 1/SA/1659:1664, 1/SA/1737:1741 | No text annotation | ||
| IL_7D5S_061 | 1/SA/1665:1667, 1/SA/1734:1736 | Isolated non-canonical cWW pair | homologous IL_4V88_470 NA | |
| IL_7D5S_062 | 1/SA/1669:1672, 1/SA/1729:1732 | Double sheared | homologous IL_4V88_471 NA | |
| IL_7D5S_063 | 1/SA/1672:1674, 1/SA/1727:1729 | Isolated non-canonical cWW pair | geometric IL_3D0U_006 IL_87907.2 | |
| IL_7D5S_064 | 1/SA/1675:1678, 1/SA/1723:1726 | Tandem non-canonical cWW pairs | geometric IL_6JDV_001 IL_77658.1 | |
| IL_7D5S_075 | 1/SA/1675:1682, 1/SA/1719:1726 | No text annotation | ||
| IL_7D5S_065 | 1/SA/1678:1682, 1/SA/1719:1723 | Triple sheared | homologous IL_4V88_474 NA | |
| IL_7D5S_066 | 1/SA/1688:1690, 1/SA/1711:1713 | Single stack bend | geometric IL_5J7L_269 IL_26793.1 | |
| IL_7D5S_067 | 1/SA/1693:1695, 1/SA/1706:1708 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_7D5S_006 | No text annotation | ||
| IL_7D5S_008 | Isolated non-canonical cWW pair | ||
| IL_7D5S_014 | No text annotation | ||
| IL_7D5S_015 | Tandem non-canonical cWW pairs | ||
| IL_7D5S_023 | No text annotation | ||
| IL_7D5S_028 | Single bulged A | ||
| IL_7D5S_042 | No text annotation | ||
| IL_7D5S_073 | Isolated non-canonical cWW pair | ||
| IL_7D5S_044 | Tandem non-canonical cWW pairs | ||
| IL_7D5S_056 | No text annotation | ||
| IL_7D5S_059 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_7D5S_002 | 1/SA/881:884, 1/SA/928:936, 1/SA/943:947 | No text annotation | homologous J3_4V88_033 NA | |
| J3_7D5S_003 | 1/SA/1150:1151, 1/SA/1627:1629, 1/SA/1636:1640 | No text annotation | ||
| J3_7D5S_006 | 1/SA/1161:1164, 1/SA/1581:1587, 1/SA/1609:1616 | No text annotation | homologous J3_8C3A_038 NA | |
| J3_7D5S_004 | 1/SA/1168:1171, 1/SA/1468:1470, 1/SA/1574:1577 | No text annotation | homologous J3_4V88_036 NA | |
| J5_7D5S_001 | 1/3A/54:62, 1/5A/291:299, 1/5A/307:333, 1/5A/391:397, 1/5A/460:462 | No text annotation | ||
| J5_7D5S_002 | 1/SA/31:37, 1/SA/471:479, 1/SA/509:514, 1/SA/543:546, 1/SA/592:595 | No text annotation | ||
| J5_7D5S_003 | 1/SA/31:37, 1/SA/471:479, 1/SA/509:516, 1/SA/536:546, 1/SA/592:595 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_7D5S_001 | No text annotation | ||
| J3_7D5S_005 | No text annotation |
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