Motif HL_86880.4 Version HL_86880.4 of this group appears in releases 3.48 to 3.53
| #S | Loop id | PDB | Disc | #Non-core | Annotation | Chain(s) | Standardized name for chain | 1 | 2 | 3 | 4 | 5 | 1-5 | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | HL_4Y4O_139 | 4Y4O | 0.2499 | 2 | 2A | LSU rRNA | G | 1492 | A | 1494 | A | 1495 | A | 1496 | C | 1498 | cWW | |
| 2 | HL_5J7L_170 | 5J7L | 0.1953 | 2 | Pseudoknot geometry with 3' bulge | DA | LSU rRNA | G | 1492 | A | 1494 | A | 1495 | A | 1496 | C | 1498 | cWW |
| 3 | HL_5TBW_032 | 5TBW | 0.2478 | 2 | Pseudoknot geometry with 3' bulge | 1 | LSU rRNA | A | 1506 | C | 1508 | A | 1509 | G | 1510 | U | 1512 | cWW |
| 4 | HL_7A0S_033 | 7A0S | 0.1276 | 2 | Pseudoknot geometry with 3' bulge | X | LSU rRNA | G | 1337 | U | 1339 | C | 1340 | G | 1341 | C | 1343 | cWW |
| 5 | HL_4Y4O_135 | 4Y4O | 0.0796 | 2 | 2A | LSU rRNA | G | 1324 | U | 1326 | C | 1327 | G | 1328 | C | 1330 | cWW | |
| 6 | HL_4WF9_033 | 4WF9 | 0.0000 | 2 | Pseudoknot geometry with 3' bulge | X | LSU rRNA | G | 1361 | U | 1363 | C | 1364 | G | 1365 | C | 1367 | cWW |
| 7 | HL_5J7L_166 | 5J7L | 0.2604 | 2 | Pseudoknot geometry with 3' bulge | DA | LSU rRNA | G | 1324 | U | 1326 | A | 1327 | A | 1328 | C | 1330 | cWW |
| 8 | HL_4V9F_035 | 4V9F | 0.1923 | 2 | Pseudoknot geometry with 3' bulge | 0 | LSU rRNA | G | 1430 | U | 1432 | G | 1433 | A | 1434 | C | 1436 | cWW |
| 9 | HL_5VJ9_003 | 5VJ9 | 0.4971 | 1 | Pseudoknot geometry with 3' bulge | C | RNA (16-mer) | G | 6 | A | 7 | C | 8 | G | 9 | C | 11 | cWW |
| 10 | HL_5NDH_001 | 5NDH | 0.5359 | 1 | Pseudoknot geometry with 3' bulge | A | RNA (16-mer) | G | 6 | A | 7 | C | 8 | G | 9 | C | 11 | cWW |
| 11 | HL_5NDI_002 | 5NDI | 0.5351 | 1 | Pseudoknot geometry with 3' bulge | B | RNA (20-mer) | G | 8 | A | 9 | C | 10 | G | 11 | C | 13 | cWW |
| 12 | HL_4Y4O_143 | 4Y4O | 0.6247 | 1 | 2A | LSU rRNA | C | 1631 | A | 1631|||A | A | 1632 | G | 1633 | G | 1635 | cWW |
3D structures
Complete motif including flanking bases
| Sequence | Counts |
|---|---|
| GACGAC | 3 |
| GCAAAUC | 2 |
| GGUCGUC | 2 |
| AGCAGUU | 1 |
| GCUCGUC | 1 |
| GUUAAUC | 1 |
| GCUGAUC | 1 |
| CAAGAG | 1 |
Non-Watson-Crick part of the motif
| Sequence | Counts |
|---|---|
| ACGA | 3 |
| CAAAU | 2 |
| GUCGU | 2 |
| GCAGU | 1 |
| CUCGU | 1 |
| UUAAU | 1 |
| CUGAU | 1 |
| AAGA | 1 |
- Annotations
-
- Pseudoknot geometry with 3' bulge (9)
- (3)
- Basepair signature
- cWW-R-R
- Heat map statistics
- Min 0.07 | Avg 0.39 | Max 0.78
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