7AFL Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_7AFL_001 | 1/A/12:22 | No text annotation Not in a motif group | homologous HL_4LFB_001 HL_89881.2 | |
| HL_7AFL_003 | 1/A/158:163 | GNRA Not in a motif group | homologous HL_5J7L_003 HL_42097.1 | |
| HL_7AFL_004 | 1/A/186:191 | GNRA Not in a motif group | homologous HL_5J7L_004 HL_42097.1 | |
| HL_7AFL_006 | 1/A/259:267 | No text annotation Not in a motif group | homologous HL_5J7L_006 HL_69023.2 | |
| HL_7AFL_007 | 1/A/295:302 | No text annotation Not in a motif group | geometric HL_7A0S_056 HL_84085.2 | |
| HL_7AFL_008 | 1/A/320:333 | No text annotation Not in a motif group | homologous HL_5J7L_008 HL_81205.2 | |
| HL_7AFL_009 | 1/A/342:347 | No text annotation Not in a motif group | homologous HL_6CZR_080 HL_03562.2 | |
| HL_7AFL_010 | 1/A/379:384 | GNRA Not in a motif group | homologous HL_5J7L_010 HL_42097.1 | |
| HL_7AFL_011 | 1/A/419:424 | UNCG Not in a motif group | homologous HL_4LFB_011 HL_03562.2 | |
| HL_7AFL_013 | 1/A/521:528 | No text annotation Not in a motif group | homologous HL_5J7L_013 NA | |
| HL_7AFL_014 | 1/A/617:623 | No text annotation Not in a motif group | homologous HL_5J7L_014 HL_26881.1 | |
| HL_7AFL_016 | 1/A/726:731 | Other HL Not in a motif group | homologous HL_5J7L_016 HL_87030.2 | |
| HL_7AFL_019 | 1/A/862:867 | GNRA Not in a motif group | homologous HL_4LFB_019 HL_42097.1 | |
| HL_7AFL_020 | 1/A/897:902 | GNRA Not in a motif group | homologous HL_5J7L_020 HL_42097.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_7AFL_002 | No text annotation | ||
| HL_7AFL_005 | UNCG | ||
| HL_7AFL_012 | No text annotation | ||
| HL_7AFL_015 | No text annotation | ||
| HL_7AFL_017 | No text annotation | ||
| HL_7AFL_018 | No text annotation | ||
| HL_7AFL_021 | UNCG | ||
| HL_7AFL_022 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_7AFL_001 | 1/A/30:32, 1/A/552:553 | Single bulged G Not in a motif group | homologous IL_5J7L_001 IL_00225.2 | |
| IL_7AFL_002 | 1/A/44:45, 1/A/396:398 | Single bulged A Not in a motif group | homologous IL_5J7L_002 IL_37497.2 | |
| IL_7AFL_003 | 1/A/47:52, 1/A/359:361 | No text annotation Not in a motif group | geometric IL_5J7L_003 IL_11178.1 | |
| IL_7AFL_004 | 1/A/54:56, 1/A/356:357 | Minor groove platform Not in a motif group | homologous IL_4LFB_004 IL_93353.1 | |
| IL_7AFL_005 | 1/A/63:66, 1/A/103:104 | Multiple bulged bases Not in a motif group | homologous IL_4LFB_005 IL_76389.1 | |
| IL_7AFL_006 | 1/A/67:69, 1/A/99:102 | Minor groove platform with extra cWW Not in a motif group | homologous IL_5J7L_006 IL_65006.1 | |
| IL_7AFL_008 | 1/A/75:76, 1/A/93:95 | Single bulged G Not in a motif group | geometric IL_5DEA_002 IL_00225.2 | |
| IL_7AFL_009 | 1/A/128:131, 1/A/231:233 | Isolated non-canonical cWW with bulges Not in a motif group | homologous IL_5J7L_009 IL_82068.2 | |
| IL_7AFL_010 | 1/A/132:136, 1/A/227:230 | Minor groove platform related Not in a motif group | homologous IL_5J7L_010 IL_58764.3 | |
| IL_7AFL_011 | 1/A/144:146, 1/A/176:178 | Isolated cWH basepair Not in a motif group | homologous IL_5J7L_011 IL_51629.2 | |
| IL_7AFL_012 | 1/A/147:153, 1/A/168:175 | tWH-tWH-tHW-tHW Not in a motif group | homologous IL_5J7L_012 IL_80604.2 | |
| IL_7AFL_014 | 1/A/242:247, 1/A/277:284 | Kink-turn with non-sequential stacking Not in a motif group | homologous IL_5J7L_014 IL_45067.2 | |
| IL_7AFL_015 | 1/A/248:252, 1/A/274:276 | No text annotation Not in a motif group | ||
| IL_7AFL_016 | 1/A/292:293, 1/A/304:308 | C-loop Not in a motif group | homologous IL_6CZR_125 IL_37712.2 | |
| IL_7AFL_017 | 1/A/367:369, 1/A/392:393 | Single bulged U Not in a motif group | geometric IL_4V88_407 IL_83039.13 | |
| IL_7AFL_018 | 1/A/371:375, 1/A/389:390 | C-loop Not in a motif group | homologous IL_5J7L_018 IL_75255.1 | |
| IL_7AFL_019 | 1/A/375:376, 1/A/387:389 | Single bulged G Not in a motif group | geometric IL_5J7L_019 IL_00225.2 | |
| IL_7AFL_020 | 1/A/409:416, 1/A/427:433 | No text annotation Not in a motif group | homologous IL_5J7L_020 IL_28026.1 | |
| IL_7AFL_022 | 1/A/446:450, 1/A/483:488 | tSH-tHW-tWW Not in a motif group | geometric IL_5J7L_022 IL_88269.3 | |
| IL_7AFL_023 | 1/A/450:455, 1/A/477:483 | No text annotation Not in a motif group | homologous IL_5J7L_023 IL_70801.1 | |
| IL_7AFL_024 | 1/A/504:511, 1/A/540:541 | SSU/LSU pseudoknot Not in a motif group | homologous IL_5J7L_024 IL_15861.7 | |
| IL_7AFL_025 | 1/A/515:521, 1/A/528:536 | No text annotation Not in a motif group | ||
| IL_7AFL_026 | 1/A/579:584, 1/A/757:762 | tSH-tHW-tHS-cWW Not in a motif group | geometric IL_3LQX_002 IL_76308.4 | |
| IL_7AFL_027 | 1/A/594:596, 1/A/644:645 | Major groove platform Not in a motif group | homologous IL_5J7L_028 IL_27635.1 | |
| IL_7AFL_028 | 1/A/597:598, 1/A/640:643 | Major groove minor groove platform; mini C-loop Not in a motif group | homologous IL_4LFB_025 IL_09061.6 | |
| IL_7AFL_029 | 1/A/605:612, 1/A/628:633 | No text annotation Not in a motif group | homologous IL_5J7L_030 IL_78349.1 | |
| IL_7AFL_030 | 1/A/654:655, 1/A/751:754 | Major groove platform; stack outside cWW Not in a motif group | homologous IL_4LFB_027 IL_50694.2 | |
| IL_7AFL_031 | 1/A/658:660, 1/A/745:748 | No text annotation Not in a motif group | geometric IL_4N0T_004 IL_46796.1 | |
| IL_7AFL_032 | 1/A/662:666, 1/A/740:743 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_5J7L_033 IL_71110.1 | |
| IL_7AFL_033 | 1/A/673:678, 1/A/712:717 | No text annotation Not in a motif group | homologous IL_4LFB_030 IL_04668.1 | |
| IL_7AFL_035 | 1/A/774:778, 1/A/804:805 | Left turn Not in a motif group | homologous IL_4LFB_032 IL_29346.1 | |
| IL_7AFL_037 | 1/A/887:894, 1/A/905:910 | No text annotation Not in a motif group | ||
| IL_7AFL_038 | 1/A/922:923, 1/A/1393:1395 | Single bulged A Not in a motif group | homologous IL_5J7L_039 IL_37497.2 | |
| IL_7AFL_039 | 1/A/925:927, 1/A/1390:1391 | No text annotation Not in a motif group |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_7AFL_007 | Minor groove platform | ||
| IL_7AFL_013 | Minor groove platform | ||
| IL_7AFL_021 | No text annotation | ||
| IL_7AFL_034 | No text annotation | ||
| IL_7AFL_036 | tSH-tHW-tHS | ||
| IL_7AFL_040 | Isolated tHS basepair with bulges | ||
| IL_7AFL_041 | Double sheared | ||
| IL_7AFL_042 | Triple sheared related | ||
| IL_7AFL_043 | No text annotation | ||
| IL_7AFL_044 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_7AFL_001 | 1/A/46:47, 1/A/361:367, 1/A/393:395 | No text annotation Not in a motif group | homologous J3_5J7L_001 NA | |
| J3_7AFL_002 | 1/A/586:588, 1/A/651:654, 1/A/754:755 | No text annotation Not in a motif group | ||
| J3_7AFL_003 | 1/A/671:673, 1/A/717:725, 1/A/732:735 | No text annotation Not in a motif group | ||
| J3_7AFL_004 | 1/A/826:829, 1/A/857:861, 1/A/868:874 | No text annotation Not in a motif group | homologous J3_5J7L_004 NA |
Problematic loops
No problematic loops
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