7AFL Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_7AFL_001 | 1/A/12:22 | No text annotation | homologous HL_4LFB_001 HL_73535.1 | |
| HL_7AFL_004 | 1/A/186:191 | GNRA | homologous HL_5J7L_004 NA | |
| HL_7AFL_006 | 1/A/259:267 | GNRA related | homologous HL_5J7L_006 NA | |
| HL_7AFL_025 | 1/A/296:301 | GNRA | homologous HL_4LFB_007 HL_34789.2 | |
| HL_7AFL_008 | 1/A/320:333 | No text annotation | homologous HL_5J7L_008 NA | |
| HL_7AFL_009 | 1/A/342:347 | UNCG | homologous HL_6CZR_080 NA | |
| HL_7AFL_010 | 1/A/379:384 | GNRA | homologous HL_5J7L_010 NA | |
| HL_7AFL_023 | 1/A/522:527 | GNRA variation | homologous HL_5J7L_205 NA | |
| HL_7AFL_014 | 1/A/617:623 | GNRA-like with tWH | homologous HL_5J7L_014 NA | |
| HL_7AFL_016 | 1/A/726:731 | GNRA | homologous HL_5J7L_016 NA | |
| HL_7AFL_017 | 1/A/786:796 | No text annotation | geometric HL_7KI3_001 HL_75660.7 | |
| HL_7AFL_019 | 1/A/862:867 | GNRA | homologous HL_4LFB_019 HL_34789.2 | |
| HL_7AFL_020 | 1/A/897:902 | GNRA | homologous HL_5J7L_020 NA | |
| HL_7AFL_022 | 1/A/1515:1520 | GNRA | homologous HL_5J7L_031 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_7AFL_002 | No text annotation | ||
| HL_7AFL_003 | GNRA | ||
| HL_7AFL_005 | UNCG | ||
| HL_7AFL_007 | GNRA with extra cWW | ||
| HL_7AFL_011 | UNCG | ||
| HL_7AFL_012 | GNRA wlth extra near cWW | ||
| HL_7AFL_013 | No text annotation | ||
| HL_7AFL_015 | No text annotation | ||
| HL_7AFL_024 | GNRA with extra near cWW | ||
| HL_7AFL_018 | No text annotation | ||
| HL_7AFL_021 | UNCG |
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 | homologous IL_5J7L_001 NA | |
| IL_7AFL_002 | 1/A/44:45, 1/A/396:398 | Single bulged A | homologous IL_5J7L_002 NA | |
| IL_7AFL_003 | 1/A/47:52, 1/A/359:361 | No text annotation | geometric IL_5J7L_003 NA | |
| IL_7AFL_004 | 1/A/54:56, 1/A/356:357 | Minor groove platform | homologous IL_4LFB_004 IL_34520.2 | |
| IL_7AFL_005 | 1/A/63:66, 1/A/103:104 | Multiple bulged bases | homologous IL_4LFB_005 IL_71421.2 | |
| IL_7AFL_006 | 1/A/67:69, 1/A/99:102 | Minor groove platform with extra cWW | homologous IL_5J7L_006 NA | |
| IL_7AFL_009 | 1/A/128:131, 1/A/231:233 | Isolated non-canonical cWW pair | homologous IL_5J7L_009 NA | |
| IL_7AFL_010 | 1/A/132:136, 1/A/227:230 | Minor groove platform related | homologous IL_5J7L_010 NA | |
| IL_7AFL_011 | 1/A/144:146, 1/A/176:178 | Isolated cWH basepair | homologous IL_5J7L_011 NA | |
| IL_7AFL_012 | 1/A/147:153, 1/A/168:175 | tWH-tWH-tHW-tHW | homologous IL_5J7L_012 NA | |
| IL_7AFL_014 | 1/A/242:247, 1/A/277:284 | Kink-turn with non-sequential stacking | homologous IL_5J7L_014 NA | |
| IL_7AFL_047 | 1/A/249:252, 1/A/274:275 | No text annotation | homologous IL_4LFB_012 IL_22002.1 | |
| IL_7AFL_016 | 1/A/292:293, 1/A/304:308 | C-loop | homologous IL_6CZR_125 NA | |
| IL_7AFL_017 | 1/A/367:369, 1/A/392:393 | Single bulged U | geometric IL_4V88_407 NA | |
| IL_7AFL_018 | 1/A/371:375, 1/A/389:390 | C-loop | homologous IL_5J7L_018 NA | |
| IL_7AFL_019 | 1/A/375:376, 1/A/387:389 | Single bulged G | geometric IL_5J7L_019 NA | |
| IL_7AFL_020 | 1/A/409:416, 1/A/427:433 | No text annotation | homologous IL_5J7L_020 NA | |
| IL_7AFL_021 | 1/A/440:442, 1/A/492:497 | No text annotation | homologous IL_5J7L_021 NA | |
| IL_7AFL_022 | 1/A/446:450, 1/A/483:488 | tSH-tHW-tWW | geometric IL_5J7L_022 NA | |
| IL_7AFL_023 | 1/A/450:455, 1/A/477:483 | No text annotation | homologous IL_5J7L_023 NA | |
| IL_7AFL_024 | 1/A/504:511, 1/A/540:541 | SSU/LSU pseudoknot | homologous IL_5J7L_024 NA | |
| IL_7AFL_025 | 1/A/515:521, 1/A/528:536 | Kink-turn related | homologous IL_5J7L_025 NA | |
| IL_7AFL_045 | 1/A/569:575, 1/A/880:881 | No text annotation | homologous IL_4LFB_022 IL_20847.1 | |
| IL_7AFL_026 | 1/A/579:584, 1/A/757:762 | tSH-tHW-tHS-cWW | geometric IL_3LQX_002 IL_35186.2 | |
| IL_7AFL_027 | 1/A/594:596, 1/A/644:645 | Major groove platform | homologous IL_5J7L_028 NA | |
| IL_7AFL_028 | 1/A/597:598, 1/A/640:643 | Major groove minor groove platform; mini C-loop | homologous IL_4LFB_025 IL_73108.2 | |
| IL_7AFL_029 | 1/A/605:612, 1/A/628:633 | No text annotation | homologous IL_5J7L_030 NA | |
| IL_7AFL_030 | 1/A/654:655, 1/A/751:754 | Major groove platform; stack outside cWW | homologous IL_4LFB_027 IL_74641.2 | |
| IL_7AFL_048 | 1/A/659:660, 1/A/745:747 | Single stack bend | homologous IL_5J7L_032 NA | |
| IL_7AFL_032 | 1/A/662:666, 1/A/740:743 | Tandem non-canonical cWW pairs | homologous IL_5J7L_033 NA | |
| IL_7AFL_033 | 1/A/673:678, 1/A/712:717 | No text annotation | homologous IL_4LFB_030 NA | |
| IL_7AFL_035 | 1/A/774:778, 1/A/804:805 | Left turn | homologous IL_4LFB_032 IL_29346.3 | |
| IL_7AFL_036 | 1/A/779:783, 1/A/799:803 | tSH-tHW-tHS | homologous IL_5J7L_037 NA | |
| IL_7AFL_037 | 1/A/887:894, 1/A/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_6CZR_364 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_7AFL_007 | Minor groove platform | ||
| IL_7AFL_008 | Single bulged G | ||
| IL_7AFL_013 | Minor groove platform | ||
| IL_7AFL_015 | No text annotation | ||
| IL_7AFL_031 | No text annotation | ||
| IL_7AFL_034 | No text annotation | ||
| IL_7AFL_049 | Kink-turn | ||
| IL_7AFL_038 | Single bulged A | ||
| IL_7AFL_039 | No text annotation | ||
| IL_7AFL_046 | Isolated tHS basepair with bulges | ||
| 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 | homologous J3_5J7L_001 NA | |
| J3_7AFL_005 | 1/A/46:52, 1/A/359:367, 1/A/393:395 | No text annotation | homologous J3_5J7L_050 NA | |
| J3_7AFL_002 | 1/A/586:588, 1/A/651:654, 1/A/754:755 | No text annotation | homologous J3_5J7L_002 NA | |
| J3_7AFL_006 | 1/A/586:588, 1/A/651:655, 1/A/751:755 | No text annotation | homologous J3_5J7L_051 NA | |
| J3_7AFL_003 | 1/A/671:673, 1/A/717:725, 1/A/732:735 | No text annotation | ||
| J3_7AFL_007 | 1/A/672:677, 1/A/713:725, 1/A/732:734 | No text annotation | ||
| J3_7AFL_004 | 1/A/826:829, 1/A/857:861, 1/A/868:874 | No text annotation | homologous J3_5J7L_004 NA | |
| J4_7AFL_001 | 1/A/115:122, 1/A/239:240, 1/A/286:289, 1/A/311:312 | No text annotation | homologous J4_5J7L_001 NA | |
| J4_7AFL_004 | 1/A/142:144, 1/A/178:184, 1/A/193:198, 1/A/219:221 | No text annotation | homologous J4_5J7L_002 NA | |
| J4_7AFL_003 | 1/A/575:577, 1/A/764:769, 1/A/810:821, 1/A/879:880 | No text annotation | homologous J4_5J7L_003 NA | |
| J5_7AFL_001 | 1/A/36:39, 1/A/403:406, 1/A/436:440, 1/A/497:500, 1/A/545:548 | No text annotation | homologous J5_5J7L_001 NA | |
| J5_7AFL_002 | 1/A/36:39, 1/A/403:406, 1/A/436:442, 1/A/492:500, 1/A/545:548 | No text annotation | homologous J5_5J7L_002 NA | |
| J5_7AFL_004 | 1/A/58:61, 1/A/106:113, 1/A/314:316, 1/A/337:339, 1/A/350:354 | No text annotation | homologous J5_5J7L_003 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J4_7AFL_002 | No text annotation | ||
| J5_7AFL_003 | No text annotation |
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