6W7M Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6W7M_001 | 1/A/12:22 | No text annotation | homologous HL_5J7L_001 NA | |
| HL_6W7M_005 | 1/A/206:213 | No text annotation | ||
| HL_6W7M_006 | 1/A/259:267 | GNRA related | homologous HL_5J7L_006 NA | |
| HL_6W7M_007 | 1/A/296:301 | GNRA | homologous HL_5J7L_007 NA | |
| HL_6W7M_011 | 1/A/419:424 | UNCG | homologous HL_5J7L_011 NA | |
| HL_6W7M_013 | 1/A/522:527 | No text annotation | geometric HL_4WF9_003 HL_75660.6 | |
| HL_6W7M_014 | 1/A/617:623 | GNRA-like with tWH | homologous HL_4LFB_014 HL_92337.1 | |
| HL_6W7M_016 | 1/A/726:731 | GNRA | homologous HL_5J7L_016 NA | |
| HL_6W7M_019 | 1/A/862:867 | GNRA | homologous HL_4LFB_019 HL_34789.1 | |
| HL_6W7M_020 | 1/A/897:902 | GNRA | homologous HL_4LFB_020 HL_34789.1 | |
| HL_6W7M_021 | 1/A/963:972 | No text annotation | homologous HL_4LFB_021 HL_97521.1 | |
| HL_6W7M_034 | 1/A/1089:1096 | T-loop related | homologous HL_4LFB_025 HL_63894.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6W7M_002 | No text annotation | ||
| HL_6W7M_003 | GNRA | ||
| HL_6W7M_004 | GNRA | ||
| HL_6W7M_008 | No text annotation | ||
| HL_6W7M_009 | UNCG | ||
| HL_6W7M_010 | GNRA | ||
| HL_6W7M_012 | GNRA wlth extra near cWW | ||
| HL_6W7M_015 | No text annotation | ||
| HL_6W7M_033 | No text annotation | ||
| HL_6W7M_017 | No text annotation | ||
| HL_6W7M_018 | No text annotation | ||
| HL_6W7M_022 | No text annotation | ||
| HL_6W7M_023 | No text annotation | ||
| HL_6W7M_024 | GNRA | ||
| HL_6W7M_025 | No text annotation | ||
| HL_6W7M_026 | No text annotation | ||
| HL_6W7M_027 | GNRA | ||
| HL_6W7M_028 | GNRA | ||
| HL_6W7M_029 | T-loop with 3 stacked bulged bases | ||
| HL_6W7M_030 | No text annotation | ||
| HL_6W7M_031 | UNCG | ||
| HL_6W7M_032 | tRNA anticodon loop | ||
| HL_6W7M_035 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6W7M_001 | 1/A/30:32, 1/A/552:553 | Single bulged G | homologous IL_5J7L_001 NA | |
| IL_6W7M_002 | 1/A/44:45, 1/A/396:398 | Single bulged A | homologous IL_5J7L_002 NA | |
| IL_6W7M_003 | 1/A/47:52, 1/A/359:361 | No text annotation | homologous IL_5J7L_003 NA | |
| IL_6W7M_005 | 1/A/63:66, 1/A/103:104 | Multiple bulged bases | homologous IL_6CZR_117 NA | |
| IL_6W7M_009 | 1/A/128:131, 1/A/231:233 | Isolated non-canonical cWW pair | homologous IL_5J7L_009 NA | |
| IL_6W7M_010 | 1/A/132:136, 1/A/227:230 | Minor groove platform related | homologous IL_6CZR_120 NA | |
| IL_6W7M_014 | 1/A/242:247, 1/A/277:284 | Kink-turn with non-sequential stacking | geometric IL_4V88_402 NA | |
| IL_6W7M_015 | 1/A/249:252, 1/A/274:275 | No text annotation | homologous IL_5J7L_015 NA | |
| IL_6W7M_016 | 1/A/292:293, 1/A/304:308 | C-loop | homologous IL_4LFB_013 IL_06671.1 | |
| IL_6W7M_018 | 1/A/371:375, 1/A/389:390 | C-loop | geometric IL_6CZR_127 NA | |
| IL_6W7M_059 | 1/A/375:376, 1/A/387:389 | Single bulged G | homologous IL_5J7L_019 NA | |
| IL_6W7M_020 | 1/A/409:416, 1/A/427:433 | No text annotation | homologous IL_5J7L_020 NA | |
| IL_6W7M_021 | 1/A/440:442, 1/A/492:497 | No text annotation | homologous IL_5J7L_021 NA | |
| IL_6W7M_024 | 1/A/504:511, 1/A/540:541 | SSU/LSU pseudoknot | homologous IL_5J7L_024 NA | |
| IL_6W7M_025 | 1/A/515:521, 1/A/528:536 | Kink-turn related | geometric IL_4V88_415 NA | |
| IL_6W7M_026 | 1/A/569:575, 1/A/880:881 | No text annotation | homologous IL_6CZR_134 NA | |
| IL_6W7M_027 | 1/A/580:584, 1/A/757:761 | tSH-tHW-tHS | homologous IL_5J7L_027 NA | |
| IL_6W7M_030 | 1/A/605:612, 1/A/628:633 | No text annotation | homologous IL_5J7L_030 NA | |
| IL_6W7M_065 | 1/A/662:666, 1/A/740:743 | Tandem non-canonical cWW pairs | homologous IL_4LFB_029 IL_15225.1 | |
| IL_6W7M_038 | 1/A/887:895, 1/A/904:910 | 9x7 Sarcin-Ricin with inserted C; G-bulge | homologous IL_6CZR_146 NA | |
| IL_6W7M_051 | 1/A/1255:1258, 1/A/1277:1282 | 180 degree turn | homologous IL_4LFB_052 IL_08849.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6W7M_004 | Minor groove platform | ||
| IL_6W7M_006 | Minor groove platform with extra cWW | ||
| IL_6W7M_007 | Minor groove platform | ||
| IL_6W7M_008 | Stack outside cWW | ||
| IL_6W7M_011 | Isolated cWH basepair | ||
| IL_6W7M_012 | tWH-tWH-tHW-tHW | ||
| IL_6W7M_013 | Minor groove platform | ||
| IL_6W7M_017 | Single bulged U | ||
| IL_6W7M_019 | Single bulged G, near cWW | ||
| IL_6W7M_022 | tSH-tHW-tWW | ||
| IL_6W7M_023 | No text annotation | ||
| IL_6W7M_060 | No text annotation | ||
| IL_6W7M_028 | Major groove platform | ||
| IL_6W7M_029 | Major groove minor groove platform; mini C-loop | ||
| IL_6W7M_031 | Major groove platform; stack outside cWW | ||
| IL_6W7M_032 | Single stack bend | ||
| IL_6W7M_033 | No text annotation | ||
| IL_6W7M_066 | Triple non-canonical cWW pairs | ||
| IL_6W7M_034 | No text annotation | ||
| IL_6W7M_035 | Kink-turn related | ||
| IL_6W7M_061 | Left turn | ||
| IL_6W7M_036 | Other IL | ||
| IL_6W7M_037 | tSH-tHW-tHS | ||
| IL_6W7M_039 | Minor groove platform | ||
| IL_6W7M_062 | No text annotation | ||
| IL_6W7M_040 | Minor groove platform | ||
| IL_6W7M_041 | Minor groove platform | ||
| IL_6W7M_042 | Single stack bend | ||
| IL_6W7M_043 | Single bulged U | ||
| IL_6W7M_044 | Tandem non-canonical cWW pairs | ||
| IL_6W7M_045 | Minor groove platform | ||
| IL_6W7M_046 | Single bulged U | ||
| IL_6W7M_047 | Isolated non-canonical cWW pair | ||
| IL_6W7M_048 | No text annotation | ||
| IL_6W7M_049 | Minor groove platform | ||
| IL_6W7M_050 | No text annotation | ||
| IL_6W7M_052 | Double sheared with non-canonical cWW | ||
| IL_6W7M_053 | No text annotation | ||
| IL_6W7M_054 | No text annotation | ||
| IL_6W7M_063 | Double sheared | ||
| IL_6W7M_055 | Double sheared with non-canonical cWW | ||
| IL_6W7M_064 | No text annotation | ||
| IL_6W7M_056 | Triple sheared related | ||
| IL_6W7M_057 | Single bulged A | ||
| IL_6W7M_058 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6W7M_001 | 1/A/46:47, 1/A/361:367, 1/A/393:395 | No text annotation | homologous J3_5J7L_001 NA | |
| J3_6W7M_002 | 1/A/586:588, 1/A/651:654, 1/A/754:755 | No text annotation | homologous J3_6CZR_016 NA | |
| J3_6W7M_014 | 1/A/586:588, 1/A/651:655, 1/A/751:755 | No text annotation | homologous J3_4LFB_015 J3_17385.5 | |
| J3_6W7M_004 | 1/A/826:829, 1/A/857:861, 1/A/868:874 | No text annotation | homologous J3_5J7L_004 NA | |
| J3_6W7M_007 | 1/A/955:962, 1/A/973:984, 1/A/1221:1225 | No text annotation | homologous J3_5J7L_006 NA | |
| J3_6W7M_010 | 1/A/1063:1068, 1/A/1107:1113, 1/A/1187:1193 | No text annotation | homologous J3_5J7L_008 NA | |
| J3_6W7M_011 | 1/A/1073:1075, 1/A/1082:1087, 1/A/1098:1102 | No text annotation | ||
| J4_6W7M_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_6W7M_005 | 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_6W7M_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_6W7M_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_6W7M_003 | 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_4LFB_002 J5_58574.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6W7M_003 | No text annotation | ||
| J3_6W7M_005 | No text annotation | ||
| J3_6W7M_006 | No text annotation | ||
| J3_6W7M_008 | No text annotation | ||
| J3_6W7M_015 | No text annotation | ||
| J3_6W7M_016 | No text annotation | ||
| J3_6W7M_009 | No text annotation | ||
| J3_6W7M_017 | No text annotation | ||
| J3_6W7M_012 | No text annotation | ||
| J3_6W7M_013 | No text annotation | ||
| J4_6W7M_004 | No text annotation | ||
| J4_6W7M_002 | No text annotation | ||
| J4_6W7M_003 | No text annotation |
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