Motif IL_60676.1 Version IL_60676.1 of this group appears in releases 3.12 to 3.14
| #S | Loop id | PDB | Disc | #Non-core | Annotation | Chain(s) | Standardized name for chain | 1 | 2 | 3 | break | 4 | 5 | 1-5 | 2-5 | 3-4 | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | IL_5TBW_070 | 5TBW | 0.7785 | 0 | Single stack bend | 1 | LSU rRNA | G | 1776 | U | 1777 | G | 1778 | * | C | 1670 | C | 1671 | cWW | cWW | |
| 2 | IL_4UYK_002 | 4UYK | 0.5764 | 0 | Not an internal loop | R | SRP RNA | G | 78 | C | 79 | G | 80 | * | C | 121 | C | 122 | ncwW | cWW | |
| 3 | IL_4Y4O_234 | 4Y4O | 0.5657 | 0 | Single stack bend (H) | 2A | LSU rRNA | G | 1448 | A | 1449 | G | 1450 | * | C | 1462 | C | 1463 | cWW | cWW | |
| 4 | IL_5J7L_269 | 5J7L | 0.6438 | 0 | Single stack bend | DA | LSU rRNA | G | 926 | A | 927 | A | 928 | * | U | 850 | C | 851 | cWW | cWW | |
| 5 | IL_4LFB_053 | 4LFB | 0.5103 | 0 | Not an internal loop | A | SSU rRNA | G | 1274 | A | 1275 | G | 1276 | * | C | 1259 | C | 1260 | ncWW | ntHS | cWW |
| 6 | IL_4IOA_066 | 4IOA | 0.4037 | 1 | Minor groove platform, major groove intercalation (H) | X | LSU rRNA | C | 1829 | G | 1831 | G | 1832 | * | C | 1885 | G | 1886 | cWW | cWW | |
| 7 | IL_4V9F_066 | 4V9F | 0.3415 | 1 | Minor groove platform, major groove intercalation | 0 | LSU rRNA | C | 1893 | A | 1895 | G | 1896 | * | C | 1943 | G | 1944 | cWW | cWW | |
| 8 | IL_4Y4O_244 | 4Y4O | 0.4412 | 1 | Minor groove platform, major groove intercalation (H) | 2A | LSU rRNA | C | 1837 | G | 1839 | G | 1840 | * | C | 1902 | G | 1903 | cWW | cWW | |
| 9 | IL_5TBW_084 | 5TBW | 0.3544 | 1 | Major groove intercalation | 1 | LSU rRNA | C | 2196 | A | 2198 | G | 2199 | * | C | 2245 | G | 2246 | cWW | cWW | |
| 10 | IL_4IOA_106 | 4IOA | 0.0000 | 1 | Y | 5S rRNA | G | 53 | C | 55 | G | 56 | * | C | 32 | C | 33 | cWW | ntHS | cWW | |
| 11 | IL_4TS2_002 | 4TS2 | 0.3578 | 3 | Minor groove platform | Y+X | Spinach aptamer RNA, bimolecular construct | U | 82 | A | 84 | C | 85 | * | G | 14 | A | 17 | cWW | cWS | cWW |
| 12 | IL_5TBW_374 | 5TBW | 0.4554 | 1 | Minor groove platform | AS | 5S rRNA | G | 49 | A | 51 | G | 52 | * | C | 28 | C | 29 | cWW | cWS | cWW |
3D structures
Complete motif including flanking bases
| Sequence | Counts |
|---|---|
| GAG*CC | 2 |
| CCGG*CG | 2 |
| CCAG*CG | 2 |
| GUG*CC | 1 |
| GCG*CC | 1 |
| GAA*UC | 1 |
| GUCG*CC | 1 |
| UAAC*GAAA | 1 |
| GUAG*CC | 1 |
Non-Watson-Crick part of the motif
| Sequence | Counts |
|---|---|
| A* | 3 |
| CG* | 2 |
| CA* | 2 |
| U* | 1 |
| C* | 1 |
| UC* | 1 |
| AA*AA | 1 |
| UA* | 1 |
- Annotations
-
- Minor groove platform, major groove intercalation (H) (2)
- Not an internal loop (2)
- Minor groove platform (2)
- Single stack bend (2)
- (1)
- Minor groove platform, major groove intercalation (1)
- Single stack bend (H) (1)
- Major groove intercalation (1)
- Basepair signature
- cWW-L-cWW
- Heat map statistics
- Min 0.12 | Avg 0.54 | Max 0.98
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