7BOD Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
3D | Loop id | Location | Annotation; motif group | Mapped info |
---|---|---|---|---|
HL_7BOD_001 | 1/A/12:22 | No text annotation Not in a motif group | homologous HL_5J7L_001 HL_89881.2 | |
HL_7BOD_003 | 1/A/158:163 | GNRA Not in a motif group | homologous HL_5J7L_003 HL_42097.1 | |
HL_7BOD_004 | 1/A/186:191 | GNRA Not in a motif group | homologous HL_5J7L_004 HL_42097.1 | |
HL_7BOD_006 | 1/A/259:267 | No text annotation Not in a motif group | homologous HL_5J7L_006 HL_69023.2 | |
HL_7BOD_007 | 1/A/296:301 | GNRA Not in a motif group | homologous HL_5J7L_007 HL_42097.1 | |
HL_7BOD_008 | 1/A/320:333 | No text annotation Not in a motif group | homologous HL_5J7L_008 HL_81205.2 | |
HL_7BOD_009 | 1/A/342:347 | UNCG Not in a motif group | homologous HL_4LFB_009 HL_03562.2 | |
HL_7BOD_010 | 1/A/379:384 | GNRA Not in a motif group | homologous HL_5J7L_010 HL_42097.1 | |
HL_7BOD_011 | 1/A/419:424 | UNCG Not in a motif group | homologous HL_4LFB_011 HL_03562.2 | |
HL_7BOD_013 | 1/A/521:528 | No text annotation Not in a motif group | homologous HL_4LFB_013 NA | |
HL_7BOD_014 | 1/A/617:623 | No text annotation Not in a motif group | homologous HL_4LFB_014 HL_26881.1 | |
HL_7BOD_016 | 1/A/726:731 | Other HL Not in a motif group | homologous HL_5J7L_016 HL_87030.2 | |
HL_7BOD_019 | 1/A/862:867 | GNRA Not in a motif group | homologous HL_5J7L_019 HL_42097.1 | |
HL_7BOD_020 | 1/A/897:902 | GNRA Not in a motif group | homologous HL_4LFB_020 HL_42097.1 |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
HL_7BOD_002 | No text annotation | ||
HL_7BOD_005 | No text annotation | ||
HL_7BOD_012 | No text annotation | ||
HL_7BOD_015 | No text annotation | ||
HL_7BOD_017 | No text annotation | ||
HL_7BOD_018 | No text annotation | ||
HL_7BOD_021 | UNCG | ||
HL_7BOD_022 | No text annotation |
Valid loops
3D | Loop id | Location | Annotation; motif group | Mapped info |
---|---|---|---|---|
IL_7BOD_001 | 1/A/30:32, 1/A/552:553 | Single bulged G Not in a motif group | homologous IL_4LFB_001 IL_00225.2 | |
IL_7BOD_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_7BOD_003 | 1/A/47:52, 1/A/359:361 | No text annotation Not in a motif group | homologous IL_5J7L_003 IL_11178.1 | |
IL_7BOD_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_7BOD_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_7BOD_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_7BOD_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_7BOD_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_7BOD_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_7BOD_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_7BOD_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_7BOD_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_7BOD_015 | 1/A/249:252, 1/A/274:275 | No text annotation Not in a motif group | homologous IL_4LFB_012 IL_48100.2 | |
IL_7BOD_016 | 1/A/292:293, 1/A/304:308 | C-loop Not in a motif group | homologous IL_4LFB_013 IL_37712.2 | |
IL_7BOD_017 | 1/A/367:369, 1/A/392:393 | Single bulged U Not in a motif group | homologous IL_5J7L_017 IL_83039.13 | |
IL_7BOD_018 | 1/A/371:375, 1/A/389:390 | C-loop Not in a motif group | homologous IL_5J7L_018 IL_75255.1 | |
IL_7BOD_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_7BOD_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_7BOD_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_7BOD_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_7BOD_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_7BOD_025 | 1/A/515:521, 1/A/528:536 | No text annotation Not in a motif group | geometric IL_4V88_415 IL_55871.1 | |
IL_7BOD_026 | 1/A/580:584, 1/A/757:761 | tSH-tHW-tHS Not in a motif group | homologous IL_5J7L_027 IL_17136.1 | |
IL_7BOD_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_7BOD_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_7BOD_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_7BOD_030 | 1/A/654:655, 1/A/751:754 | Major groove platform; stack outside cWW Not in a motif group | homologous IL_5J7L_031 IL_50694.2 | |
IL_7BOD_031 | 1/A/659:660, 1/A/745:747 | Single stack bend Not in a motif group | homologous IL_5J7L_032 IL_76488.2 | |
IL_7BOD_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_7BOD_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_7BOD_035 | 1/A/774:778, 1/A/804:805 | Left turn Not in a motif group | homologous IL_4LFB_032 IL_29346.1 | |
IL_7BOD_037 | 1/A/887:894, 1/A/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge Not in a motif group | homologous IL_5J7L_038 IL_24606.2 | |
IL_7BOD_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_7BOD_039 | 1/A/925:927, 1/A/1390:1391 | Single bulged G Not in a motif group | homologous IL_5J7L_040 IL_00225.2 |
Problematic loops
# | loop id | Problem | Sequence |
---|---|---|---|
IL_7BOD_007 | Minor groove platform | ||
IL_7BOD_013 | Minor groove platform | ||
IL_7BOD_021 | No text annotation | ||
IL_7BOD_034 | Kink-turn | ||
IL_7BOD_036 | tSH-tHW-tHS | ||
IL_7BOD_040 | No text annotation | ||
IL_7BOD_041 | No text annotation | ||
IL_7BOD_042 | No text annotation | ||
IL_7BOD_043 | No text annotation | ||
IL_7BOD_044 | Double sheared | ||
IL_7BOD_045 | Triple sheared related | ||
IL_7BOD_046 | Minor groove platform | ||
IL_7BOD_047 | No text annotation |
Valid loops
3D | Loop id | Location | Annotation; motif group | Mapped info |
---|---|---|---|---|
J3_7BOD_001 | 1/A/46:47, 1/A/361:367, 1/A/393:395 | No text annotation Not in a motif group | ||
J3_7BOD_002 | 1/A/586:588, 1/A/651:654, 1/A/754:755 | No text annotation Not in a motif group | ||
J3_7BOD_003 | 1/A/672:673, 1/A/717:725, 1/A/732:734 | No text annotation Not in a motif group | ||
J3_7BOD_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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