Motif HL_25462.3 Version HL_25462.3 of this group appears in releases 3.84 to 3.87
| #S | Loop id | PDB | Disc | #Non-core | Annotation | Chain(s) | Standardized name | 1 | 2 | 3 | 4 | 1-4 | 2-3 | 2-4 | 3-4 | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | HL_8C3A_012 | 8C3A | 0.5855 | 4 | 1 | LSU rRNA | G | 539 | C | 540 | C | 543 | C | 546 | cWW | ncWw | |||
| 2 | HL_3AKZ_010 | 3AKZ | 0.3098 | 5 | tRNA D-loop | E | tRNAGln | U | 13 | A | 14 | A | 21 | G | 22 | cWW | cWS | ||
| 3 | HL_3AL0_001 | 3AL0 | 0.2211 | 5 | tRNA D-loop | E | tRNA | U | 13 | A | 14 | A | 21 | G | 22 | cWW | cWS | ||
| 4 | HL_4WT8_215 | 4WT8 | 0.2898 | 7 | tRNA D-loop | D4 | tRNA | C | 13 | A | 14 | A | 22 | G | 23 | cWW | ncWS | ||
| 5 | HL_5B63_003 | 5B63 | 0.2156 | 7 | tRNA D-loop | D | tRNA | C | 913 | A | 914 | A | 922 | G | 923 | cWW | ncWS | ||
| 6 | HL_4TUE_033 | 4TUE | 0.2631 | 7 | tRNA D-loop | QV | tRNA | C | 12 | A | 13 | A | 21 | G | 22 | cWW | cWS | ||
| 7 | HL_6CFJ_106 | 6CFJ | 0.2810 | 7 | tRNA D-loop | 1x | tRNA | C | 13 | A | 14 | A | 21 | G | 22 | cWW | cWS | ||
| 8 | HL_4V9Q_213 | 4V9Q | 0.2529 | 7 | tRNA D-loop | DV | tRNA | C | 13 | A | 14 | A | 21 | G | 22 | cWW | ncSH | ||
| 9 | HL_4WT8_135 | 4WT8 | 0.4135 | 6 | tRNA D-loop | C3 | tRNA | C | 13 | A | 14 | A | 21 | G | 22 | ncWW | |||
| 10 | HL_3TUP_001 | 3TUP | 0.1818 | 6 | tRNA D-loop | T | tRNA | C | 13 | A | 14 | A | 21 | G | 22 | cWW | ncWS | ||
| 11 | HL_3FOZ_004 | 3FOZ | 0.2421 | 6 | tRNA D-loop | D | tRNA(Phe) | C | 13 | A | 14 | A | 21 | G | 22 | cWW | cWS | ||
| 12 | HL_7MRL_001 | 7MRL | 0.2561 | 6 | tRNA D-loop | A | tRNA | C | 13 | A | 14 | A | 21 | G | 22 | cWW | ncWS | ||
| 13 | HL_5AXM_001 | 5AXM | 0.2503 | 6 | tRNA D-loop | P | tRNA | C | 13 | A | 14 | A | 21 | G | 22 | cWW | ncWS | ||
| 14 | HL_8SP9_001 | 8SP9 | 0.3046 | 6 | tRNA D-loop | C | Enterovirus 5' cloverleaf cis-acting replication element | C | 13 | A | 14 | A | 21 | G | 22 | cWW | ncWS | ||
| 15 | HL_7LYF_001 | 7LYF | 0.2864 | 6 | tRNA D-loop | A | Dengue virus SLA | C | 13 | A | 14 | A | 21 | G | 22 | cWW | ncWS | ||
| 16 | HL_3EPH_001 | 3EPH | 0.1510 | 5 | tRNA D-loop | E | tRNA | C | 13 | A | 14 | A | 21 | G | 22 | cWW | cWS | ||
| 17 | HL_2AZX_004 | 2AZX | 0.0000 | 5 | tRNA D-loop | D | 72-MER | C | 513 | A | 514 | A | 521 | G | 522 | cWW | cWS | ||
| 18 | HL_1J1U_001 | 1J1U | 0.2185 | 7 | tRNA D-loop | B | tRNA(Tyr) | C | 513 | A | 514 | A | 522 | G | 523 | cWW | ncWS | ||
| 19 | HL_6JXM_001 | 6JXM | 0.2727 | 5 | tRNA D-loop | B | tRNA | C | 13 | A | 14 | A | 20 | G | 21 | cWW | ncWS | ||
| 20 | HL_3AMU_001 | 3AMU | 0.4451 | 8 | tRNA D-loop | B | tRNA | U | 13 | A | 14 | A | 21|||C | G | 22 | cWW | ncWS | ||
| 21 | HL_2ZUE_001 | 2ZUE | 0.3067 | 8 | tRNA D-loop | B | tRNA-Arg | U | 913 | A | 914 | A | 921 | G | 922 | cWW | cWS | ||
| 22 | HL_4M6D_004 | 4M6D | 1.1714 | 1 | D-loop related | H | aptamer | C | 32 | U | 33 | A | 35 | G | 36 | cWW | cWS | ||
| 23 | HL_4M4O_001 | 4M4O | 1.1808 | 1 | D-loop related | B | RNA (59-MER) | C | 32 | U | 33 | A | 35 | G | 36 | cWW | cWS |
3D structures
Complete motif including flanking bases
| Sequence | Counts |
|---|---|
| CAGCCUGGUAG | 5 |
| CAGUCGGUAG | 5 |
| UAACGGUAG | 2 |
| CAGUGGUAG | 2 |
| CUUAG | 2 |
| GCUUCUGC | 1 |
| CAAUUGGAUAG | 1 |
| CAGUUGGUAG | 1 |
| CAGUUGGGAG | 1 |
| CAAUGGUAG | 1 |
| UAGCCAGGUCAG | 1 |
| UAGCCAGGACAG | 1 |
Non-Watson-Crick part of the motif
| Sequence | Counts |
|---|---|
| AGCCUGGUA | 5 |
| AGUCGGUA | 5 |
| AACGGUA | 2 |
| AGUGGUA | 2 |
| UUA | 2 |
| CUUCUG | 1 |
| AAUUGGAUA | 1 |
| AGUUGGUA | 1 |
| AGUUGGGA | 1 |
| AAUGGUA | 1 |
| AGCCAGGUCA | 1 |
| AGCCAGGACA | 1 |
- Annotations
-
- tRNA D-loop (20)
- D-loop related (2)
- (1)
- Basepair signature
- cWW-cWS
- Heat map statistics
- Min 0.08 | Avg 0.49 | Max 1.36
Coloring options: