Motif HL_66853.3 Version HL_66853.3 of this group appears in releases 3.85 to 3.87
| #S | Loop id | PDB | Disc | #Non-core | Annotation | Chain(s) | Standardized name for chain | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 1-7 | 2-6 | 4-5 | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | HL_8KAH_003 | 8KAH | 0.9402 | 0 | I | tracrRNA | C | 86 | G | 87 | A | 88 | G | 89 | U | 90 | C | 91 | G | 92 | cWW | |||
| 2 | HL_7MDL_001 | 7MDL | 0.6786 | 1 | E | Selenocysteine transfer RNA | A | 14||A | G | 15||A | U | 16||A | G | 19||A | U | 20||A | C | 20||A|A | U | 21||A | cWW | ncWW | ncSW | |
| 3 | HL_4MGN_002 | 4MGN | 0.3247 | 2 | tRNA D-loop | B | tRNA | C | 13 | A | 14 | G | 15 | G | 18 | U | 19 | A | 20 | G | 21 | cWW | ncWS | cSH |
| 4 | HL_8UO6_005 | 8UO6 | 0.2691 | 3 | B | HIV-1 Rev Response Element Stem-Loop II with tRNA scaffold | C | 13 | A | 14 | G | 15 | G | 19 | U | 20 | A | 21 | G | 22 | cWW | ncWS | cSH | |
| 5 | HL_8UO6_001 | 8UO6 | 0.2732 | 3 | A | HIV-1 Rev Response Element Stem-Loop II with tRNA scaffold | C | 13 | A | 14 | G | 15 | G | 19 | U | 20 | A | 21 | G | 22 | cWW | ncWS | cSH | |
| 6 | HL_4YCO_001 | 4YCO | 0.2971 | 3 | D | tRNA | C | 13 | A | 14 | G | 15 | G | 19 | U | 20 | A | 21 | G | 22 | cWW | cWS | cSH | |
| 7 | HL_6CU1_003 | 6CU1 | 0.2954 | 2 | tRNA D-loop | A | Y RNA-like | C | 58 | A | 59 | A | 60 | G | 63 | U | 64 | A | 65 | G | 66 | cWW | cWS | cSH |
| 8 | HL_8S95_001 | 8S95 | 0.2693 | 3 | C | Enterovirus 5' cloverleaf cis-acting replication element | C | 13 | A | 14 | G | 15 | G | 19 | U | 20 | A | 21 | G | 22 | cWW | ncWS | ncSH | |
| 9 | HL_4WJ4_001 | 4WJ4 | 0.0000 | 3 | tRNA D-loop | B | tRNA | C | 13 | A | 14 | G | 15 | G | 19 | U | 20 | A | 21 | G | 22 | cWW | ncSW | |
| 10 | HL_7E8O_001 | 7E8O | 0.2615 | 2 | X | tRNA | C | 13 | A | 14 | G | 15 | G | 18 | U | 19 | A | 20 | G | 21 | cWW | cSH | ||
| 11 | HL_7UZ0_001 | 7UZ0 | 0.2643 | 2 | A | tRNA | C | 13 | A | 14 | G | 15 | G | 18 | U | 19 | A | 20 | G | 21 | cWW | ncSH | ||
| 12 | HL_1H4S_001 | 1H4S | 0.2901 | 4 | tRNA D-loop | T | tRNA | C | 13 | A | 14 | G | 15 | G | 19 | U | 20 | A | 21 | G | 22 | cWW | cSH |
3D structures
Complete motif including flanking bases
| Sequence | Counts |
|---|---|
| CAGUCGGUAG | 5 |
| CAGUGGUAG | 3 |
| CGAGUCG | 1 |
| AGUGGUCU | 1 |
| CAAUGGUAG | 1 |
| CAGCCCGGUAG | 1 |
Non-Watson-Crick part of the motif
| Sequence | Counts |
|---|---|
| AGUCGGUA | 5 |
| AGUGGUA | 3 |
| GAGUC | 1 |
| GUGGUC | 1 |
| AAUGGUA | 1 |
| AGCCCGGUA | 1 |
- Annotations
-
- (8)
- tRNA D-loop (4)
- Basepair signature
- cWW-cWS-F-cSH
- Heat map statistics
- Min 0.09 | Avg 0.42 | Max 0.97
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