Motif HL_80459.6 Version HL_80459.6 of this group appears in releases 1.16 to 1.16
| #S | Loop id | PDB | Disc | #Non-core | Annotation | Chain(s) | Standardized name for chain | 1 | 2 | 3 | 4 | 5 | 1-5 | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | HL_1VWW_032 | 1VWW | 0.3277 | 7 | 5 | 28S ribosomal RNA | A | 2420 | C | 2422 | A | 2423 | G | 2424 | U | 2426 | cWW | |
| 2 | HL_4NVV_036 | 4NVV | 0.2506 | 2 | A | 23S Ribosomal RNA | G | 1538 | A | 1540 | A | 1541 | A | 1542 | C | 1544 | cWW | |
| 3 | HL_4A1B_031 | 4A1B | 0.2758 | 2 | 1 | 26S RRNA | A | 1532 | C | 1534 | A | 1535 | A | 1536 | U | 1538 | cWW | |
| 4 | HL_3U5H_032 | 3U5H | 0.2344 | 2 | 5 | 25S rRNA | A | 1506 | C | 1508 | A | 1509 | G | 1510 | U | 1512 | cWW | |
| 5 | HL_4CUV_032 | 4CUV | 0.2008 | 2 | 1 | 25S RRNA | A | 1506 | C | 1508 | A | 1509 | G | 1510 | U | 1512 | cWW | |
| 6 | HL_4IOA_032 | 4IOA | 0.0000 | 2 | X | LSU rRNA | G | 1337 | U | 1339 | C | 1340 | G | 1341 | C | 1343 | cWW | |
| 7 | HL_4NVV_032 | 4NVV | 0.0847 | 2 | A | 23S Ribosomal RNA | G | 1370 | U | 1372 | C | 1373 | G | 1374 | C | 1376 | cWW | |
| 8 | HL_1S72_035 | 1S72 | 0.2464 | 2 | Pseudoknot geometry with 3' bulge (H) | 0 | LSU rRNA | G | 1430 | U | 1432 | G | 1433 | A | 1434 | C | 1436 | cWW |
| 9 | HL_2QBG_035 | 2QBG | 0.2820 | 2 | B | 23S rRNA | G | 1324 | U | 1326 | A | 1327 | A | 1328 | C | 1330 | cWW | |
| 10 | HL_4IOA_040 | 4IOA | 0.6017 | 1 | X | LSU rRNA | U | 1647 | C | 1648 | A | 1649 | A | 1650 | G | 1652 | cWW | |
| 11 | HL_4NVV_039 | 4NVV | 0.6533 | 1 | A | 23S Ribosomal RNA | C | 1677 | A | 1678 | A | 1679 | G | 1680 | G | 1682 | cWW |
3D structures
Complete motif including flanking bases
| Sequence | Counts |
|---|---|
| AGCAGUU | 2 |
| GGUCGUC | 2 |
| GGUUCAGAUCCC | 1 |
| GCAAAUC | 1 |
| AGCAAUU | 1 |
| GCUGAUC | 1 |
| GUUAAUC | 1 |
| UCAAUG | 1 |
| CAAGAG | 1 |
Non-Watson-Crick part of the motif
| Sequence | Counts |
|---|---|
| GCAGU | 2 |
| GUCGU | 2 |
| GUUCAGAUCC | 1 |
| CAAAU | 1 |
| GCAAU | 1 |
| CUGAU | 1 |
| UUAAU | 1 |
| CAAU | 1 |
| AAGA | 1 |
Release history
| Release | 1.16 |
|---|---|
| Date | 2014-07-26 |
| Status | Updated, 1 parent |
Parent motifs
| Parent motif | Common motif instances | Only in HL_80459.6 | Only in the parent motif |
|---|---|---|---|
| HL_80459.5 Compare | HL_4NVV_036, HL_3U5H_032, HL_1S72_035, HL_2QBG_035, HL_4NVV_032, HL_4CUV_032, HL_4A1B_031, HL_4NVV_039, HL_4IOA_032, HL_4IOA_040 | HL_1VWW_032 |
Children motifs
| Child motif | Common motif instances | Only in HL_80459.6 | Only in the child motif |
|---|---|---|---|
| HL_80459.7 Compare | HL_4IOA_040, HL_3U5H_032, HL_1S72_035, HL_2QBG_035, HL_4CUV_032, HL_4A1B_031, HL_4IOA_032, HL_1VWW_032 | HL_4NVV_036, HL_4NVV_032, HL_4NVV_039 | HL_4QCN_032, HL_4QCN_039, HL_4QCN_036 |
- Annotations
-
- (10)
- Pseudoknot geometry with 3' bulge (H) (1)
- Basepair signature
- cWW-R-R
- Heat map statistics
- Min 0.08 | Avg 0.36 | Max 0.76
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