7D4I Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_7D4I_005 | 1/SA/64:86 | No text annotation Not in a motif group | ||
| HL_7D4I_006 | 1/SA/154:160 | Other HL Not in a motif group | homologous HL_4V88_188 HL_43074.18 | |
| HL_7D4I_007 | 1/SA/190:195 | No text annotation Not in a motif group | ||
| HL_7D4I_008 | 1/SA/230:235 | No text annotation Not in a motif group | geometric HL_6QN3_003 HL_79299.11 | |
| HL_7D4I_009 | 1/SA/243:250 | T-loop with 1 bulged base Not in a motif group | homologous HL_4V88_191 HL_68493.6 | |
| HL_7D4I_010 | 1/SA/276:279 | No text annotation Not in a motif group | geometric HL_5TBW_068 HL_46546.1 | |
| HL_7D4I_011 | 1/SA/330:338 | No text annotation Not in a motif group | homologous HL_4V88_193 HL_93727.5 | |
| HL_7D4I_012 | 1/SA/450:456 | No text annotation Not in a motif group | homologous HL_4V88_197 HL_50374.1 | |
| HL_7D4I_013 | 1/SA/491:496 | No text annotation Not in a motif group | geometric HL_5NFV_001 HL_58912.1 | |
| HL_7D4I_014 | 1/SA/520:532 | No text annotation Not in a motif group | geometric HL_4V88_199 HL_17086.2 | |
| HL_7D4I_015 | 1/SA/561:566 | No text annotation Not in a motif group | geometric HL_5NFV_001 HL_58912.1 | |
| HL_7D4I_017 | 1/SA/764:772 | No text annotation Not in a motif group | homologous HL_4V88_203 HL_72066.1 | |
| HL_7D4I_018 | 1/SA/777:783 | No text annotation Not in a motif group | geometric HL_1WZ2_007 HL_05692.1 | |
| HL_7D4I_020 | 1/SA/900:909 | No text annotation Not in a motif group | homologous HL_4V88_206 HL_87219.4 | |
| HL_7D4I_021 | 1/SA/937:942 | Other HL Not in a motif group | homologous HL_4V88_207 HL_43074.18 | |
| HL_7D4I_022 | 1/SA/1055:1064 | No text annotation Not in a motif group | geometric HL_4V88_198 HL_30541.1 | |
| HL_7D4I_023 | 1/SA/1129:1139 | No text annotation Not in a motif group | ||
| HL_7D4I_028 | 1/SA/1594:1602 | No text annotation Not in a motif group | ||
| HL_7D4I_029 | 1/SA/1629:1636 | No text annotation Not in a motif group | ||
| HL_7D4I_030 | 1/SA/1698:1703 | No text annotation Not in a motif group | ||
| HL_7D4I_031 | 1/SA/1777:1784 | No text annotation Not in a motif group |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_7D4I_001 | No text annotation | ||
| HL_7D4I_002 | No text annotation | ||
| HL_7D4I_003 | No text annotation | ||
| HL_7D4I_004 | No text annotation | ||
| HL_7D4I_016 | No text annotation | ||
| HL_7D4I_019 | No text annotation | ||
| HL_7D4I_024 | No text annotation | ||
| HL_7D4I_025 | No text annotation | ||
| HL_7D4I_026 | GNRA | ||
| HL_7D4I_027 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_7D4I_001 | 1/3A/6:7, 1/SA/1117:1119 | Single bulged G Not in a motif group | geometric IL_3IGI_004 IL_59137.10 | |
| IL_7D4I_002 | 1/3A/11:13, 1/SA/1112:1113 | Single stack bend Not in a motif group | geometric IL_5J7L_032 IL_04038.4 | |
| IL_7D4I_003 | 1/3A/47:51, 1/5A/465:471 | No text annotation Not in a motif group | ||
| IL_7D4I_004 | 1/3A/78:85, 1/3A/325:329 | Kink-turn Not in a motif group | geometric IL_3NVI_002 IL_68057.1 | |
| IL_7D4I_005 | 1/3A/97:98, 1/3A/317:319 | Single bulged U Not in a motif group | geometric IL_7KVT_002 IL_83039.11 | |
| IL_7D4I_006 | 1/3A/111:115, 1/3A/252:259 | Kink-turn Not in a motif group | geometric IL_5G4U_006 IL_29549.9 | |
| IL_7D4I_007 | 1/3A/200:207, 1/3A/242:249 | No text annotation Not in a motif group | ||
| IL_7D4I_009 | 1/5A/497:499, 1/5A/539:542 | No text annotation Not in a motif group | ||
| IL_7D4I_010 | 1/5A/501:503, 1/5A/533:537 | No text annotation Not in a motif group | ||
| IL_7D4I_012 | 1/SA/35:37, 1/SA/471:473 | UC cWW Not in a motif group | homologous IL_4V88_385 IL_01312.13 | |
| IL_7D4I_013 | 1/SA/37:41, 1/SA/466:471 | No text annotation Not in a motif group | geometric IL_4V88_386 IL_53318.1 | |
| IL_7D4I_014 | 1/SA/50:52, 1/SA/428:429 | Minor groove platform Not in a motif group | homologous IL_4V88_388 IL_06437.11 | |
| IL_7D4I_015 | 1/SA/58:63, 1/SA/87:89 | No text annotation Not in a motif group | homologous IL_4V88_389 IL_96451.1 | |
| IL_7D4I_016 | 1/SA/109:112, 1/SA/302:305 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_391 IL_85877.10 | |
| IL_7D4I_017 | 1/SA/113:116, 1/SA/300:301 | Multiple bulged bases Not in a motif group | homologous IL_4V88_392 IL_13730.12 | |
| IL_7D4I_018 | 1/SA/117:122, 1/SA/295:299 | No text annotation Not in a motif group | homologous IL_4V88_393 IL_76386.1 | |
| IL_7D4I_019 | 1/SA/143:149, 1/SA/165:172 | tWH-tWH-tHW-tHW Not in a motif group | homologous IL_4V88_394 IL_92440.5 | |
| IL_7D4I_020 | 1/SA/150:153, 1/SA/161:164 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_5EW4_002 IL_85877.10 | |
| IL_7D4I_021 | 1/SA/186:189, 1/SA/196:199 | Double sheared Not in a motif group | homologous IL_4V88_396 IL_09705.7 | |
| IL_7D4I_022 | 1/SA/204:209, 1/SA/256:263 | No text annotation Not in a motif group | ||
| IL_7D4I_023 | 1/SA/265:267, 1/SA/288:289 | Single bulged A Not in a motif group | homologous IL_4V88_399 IL_80007.16 | |
| IL_7D4I_024 | 1/SA/270:273, 1/SA/283:285 | No text annotation Not in a motif group | homologous IL_4V88_400 IL_05922.1 | |
| IL_7D4I_025 | 1/SA/275:276, 1/SA/279:281 | Single bulged U Not in a motif group | homologous IL_4V88_401 IL_83039.11 | |
| IL_7D4I_026 | 1/SA/311:316, 1/SA/348:355 | Kink-turn with non-sequential stacking Not in a motif group | homologous IL_4V88_402 IL_29549.9 | |
| IL_7D4I_027 | 1/SA/318:323, 1/SA/345:346 | No text annotation Not in a motif group | homologous IL_4V88_403 IL_55658.1 | |
| IL_7D4I_028 | 1/SA/439:441, 1/SA/463:464 | Single bulged U Not in a motif group | homologous IL_4V88_407 IL_83039.11 | |
| IL_7D4I_029 | 1/SA/443:447, 1/SA/460:461 | C-loop Not in a motif group | geometric IL_4LFB_015 IL_63596.4 | |
| IL_7D4I_030 | 1/SA/447:448, 1/SA/458:460 | Single bulged G Not in a motif group | geometric IL_5J7L_019 IL_59137.10 | |
| IL_7D4I_031 | 1/SA/480:482, 1/SA/505:508 | No text annotation Not in a motif group | ||
| IL_7D4I_032 | 1/SA/514:516, 1/SA/536:543 | Isolated tHS basepair with bulges Not in a motif group | geometric IL_7RQB_082 IL_38958.6 | |
| IL_7D4I_033 | 1/SA/516:518, 1/SA/533:536 | Minor groove platform with extra cWW Not in a motif group | geometric IL_4V88_411 IL_87332.1 | |
| IL_7D4I_034 | 1/SA/518:520, 1/SA/532:533 | Minor groove platform Not in a motif group | geometric IL_4V88_412 IL_06437.11 | |
| IL_7D4I_035 | 1/SA/551:552, 1/SA/584:587 | No text annotation Not in a motif group | geometric IL_5J7L_341 IL_44093.1 | |
| IL_7D4I_036 | 1/SA/552:559, 1/SA/568:584 | No text annotation Not in a motif group | ||
| IL_7D4I_037 | 1/SA/624:626, 1/SA/973:975 | No text annotation Not in a motif group | homologous IL_4V88_417 IL_01312.13 | |
| IL_7D4I_038 | 1/SA/627:631, 1/SA/969:972 | No text annotation Not in a motif group | ||
| IL_7D4I_039 | 1/SA/631:632, 1/SA/967:969 | Single stack bend Not in a motif group | geometric IL_7A0S_054 IL_04038.4 | |
| IL_7D4I_040 | 1/SA/646:648, 1/SA/686:688 | No text annotation Not in a motif group | homologous IL_4V88_419 IL_01312.13 | |
| IL_7D4I_041 | 1/SA/658:659, 1/SA/669:671 | Single stack bend Not in a motif group | geometric IL_5J7L_032 IL_04038.4 | |
| IL_7D4I_042 | 1/SA/746:751, 1/SA/798:805 | No text annotation Not in a motif group | ||
| IL_7D4I_043 | 1/SA/822:825, 1/SA/844:847 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_3WBM_002 IL_85877.10 | |
| IL_7D4I_044 | 1/SA/865:866, 1/SA/962:965 | Major groove platform; stack outside cWW Not in a motif group | homologous IL_4V88_428 IL_70995.6 | |
| IL_7D4I_045 | 1/SA/866:870, 1/SA/957:962 | No text annotation Not in a motif group | geometric IL_4V88_422 IL_79670.1 | |
| IL_7D4I_046 | 1/SA/871:873, 1/SA/954:956 | No text annotation Not in a motif group | geometric IL_5TBW_068 IL_01312.13 | |
| IL_7D4I_047 | 1/SA/874:878, 1/SA/950:953 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_431 IL_85877.10 | |
| IL_7D4I_048 | 1/SA/885:888, 1/SA/924:927 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_432 IL_85877.10 | |
| IL_7D4I_049 | 1/SA/893:899, 1/SA/910:919 | No text annotation Not in a motif group | ||
| IL_7D4I_050 | 1/SA/1041:1044, 1/SA/1074:1077 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_438 IL_85877.10 | |
| IL_7D4I_051 | 1/SA/1051:1053, 1/SA/1066:1067 | Single stack bend Not in a motif group | geometric IL_4C7O_002 IL_72766.2 | |
| IL_7D4I_052 | 1/SA/1157:1160, 1/SA/1617:1621 | C-loop Not in a motif group | homologous IL_4V88_443 IL_63596.4 | |
| IL_7D4I_053 | 1/SA/1173:1176, 1/SA/1463:1466 | Double sheared Not in a motif group | geometric IL_4ZNP_002 IL_09705.7 | |
| IL_7D4I_059 | 1/SA/1650:1652, 1/SA/1748:1750 | AA cWW Not in a motif group | homologous IL_4V88_467 IL_01312.13 | |
| IL_7D4I_060 | 1/SA/1653:1657, 1/SA/1744:1747 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_5J7L_283 IL_85877.10 | |
| IL_7D4I_061 | 1/SA/1664:1667, 1/SA/1734:1737 | No text annotation Not in a motif group | ||
| IL_7D4I_062 | 1/SA/1669:1672, 1/SA/1729:1732 | Double sheared Not in a motif group | geometric IL_4V88_468 IL_09705.7 | |
| IL_7D4I_063 | 1/SA/1672:1674, 1/SA/1727:1729 | No text annotation Not in a motif group | homologous IL_4V88_472 IL_01312.13 | |
| IL_7D4I_064 | 1/SA/1688:1690, 1/SA/1711:1713 | Single stack bend Not in a motif group | geometric IL_5VSU_003 IL_06437.11 | |
| IL_7D4I_065 | 1/SA/1692:1695, 1/SA/1706:1709 | No text annotation Not in a motif group |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_7D4I_008 | Single bulged G | ||
| IL_7D4I_011 | No text annotation | ||
| IL_7D4I_054 | No text annotation | ||
| IL_7D4I_055 | Single stack bend | ||
| IL_7D4I_056 | No text annotation | ||
| IL_7D4I_057 | Tandem non-canonical cWW pairs | ||
| IL_7D4I_058 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_7D4I_001 | 1/3A/106:111, 1/3A/259:263, 1/3A/308:309 | No text annotation Not in a motif group | ||
| J3_7D4I_002 | 1/SA/41:48, 1/SA/431:439, 1/SA/464:466 | No text annotation Not in a motif group | ||
| J3_7D4I_003 | 1/SA/633:635, 1/SA/861:865, 1/SA/965:966 | No text annotation Not in a motif group | ||
| J3_7D4I_004 | 1/SA/881:884, 1/SA/928:936, 1/SA/943:947 | No text annotation Not in a motif group | homologous J3_4V88_033 NA | |
| J3_7D4I_005 | 1/SA/1150:1151, 1/SA/1627:1629, 1/SA/1636:1640 | No text annotation Not in a motif group | ||
| J3_7D4I_006 | 1/SA/1168:1171, 1/SA/1468:1470, 1/SA/1574:1577 | No text annotation Not in a motif group | ||
| J3_7D4I_008 | 1/SA/1470:1474, 1/SA/1533:1540, 1/SA/1571:1574 | No text annotation Not in a motif group |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_7D4I_007 | No text annotation |
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