Motif HL_89167.4 Version HL_89167.4 of this group appears in releases 4.10 to 4.12
| #S | Loop id | PDB | Disc | #Non-core | Annotation | Chain(s) | Standardized name for chain | 1 | 2 | 3 | 4 | 1-4 | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | HL_8UO6_007 | 8UO6 | 0.7672 | 3 | B | HIV-1 Rev Response Element Stem-Loop II with tRNA scaffold | A | 77 | A | 78 | U | 80 | U | 83 | cWW | |
| 2 | HL_5E08_001 | 5E08 | 0.3715 | 2 | N | RNA | C | 6 | A | 7 | A | 9 | G | 11 | cWW | |
| 3 | HL_1H4S_002 | 1H4S | 0.3852 | 3 | tRNA anticodon loop with synthetase | T | tRNA | U | 32 | U | 33 | C | 34 | A | 38 | cWW |
| 4 | HL_4LFB_004 | 4LFB | 0.2155 | 2 | A | SSU rRNA | C | 190|||B | C | 190|||C | U | 190|||D | G | 190|||G | cWW | |
| 5 | HL_5AMQ_001 | 5AMQ | 0.2329 | 3 | C | RNA | U | 3 | A | 4 | G | 5 | A | 9 | cWW | |
| 6 | HL_6XH2_001 | 6XH2 | 0.2988 | 1 | D | TRANS-ACTIVATION RESPONSE ELEMENT | C | 30 | U | 31 | G | 32 | G | 34 | cWW | |
| 7 | HL_9BZC_001 | 9BZC | 0.3459 | 3 | A | RNA (87-MER) | G | 24 | A | 25 | G | 26 | C | 30 | cWW | |
| 8 | HL_6DTD_001 | 6DTD | 0.2971 | 3 | C | RNA (37-MER) | C | 16 | U | 17 | U | 20 | G | 22 | cWW | |
| 9 | HL_8GLP_043 | 8GLP | 0.3412 | 2 | L5 | LSU rRNA | G | 2705 | G | 2706 | U | 2708 | C | 2710 | cWW | |
| 10 | HL_9PN5_093 | 9PN5 | 0.3478 | 3 | B5 | SSU rRNA | C | 777 | G | 778 | A | 780 | G | 783 | cWW | |
| 11 | HL_8CRE_202 | 8CRE | 0.3242 | 3 | CM | SSU rRNA | C | 448 | G | 449 | C | 451 | G | 454 | cWW | |
| 12 | HL_2C4Q_001 | 2C4Q | 0.2898 | 2 | R | RNA (19-mer) | G | 8||||P_1 | A | 9||||P_1 | PYO | 11||||P_1 | C | 13||||P_1 | cWW | |
| 13 | HL_2IZN_001 | 2IZN | 0.3096 | 2 | R | RNA (19-mer) | G | 8||||P_1 | A | 9||||P_1 | U | 11||||P_1 | C | 13||||P_1 | cWW | |
| 14 | HL_7MSF_001 | 7MSF | 0.3398 | 2 | R | RNA (14-mer) | C | 5||||P_1 | A | 6||||P_1 | C | 8||||P_1 | G | 10||||P_1 | cWW | |
| 15 | HL_5MSF_001 | 5MSF | 0.3340 | 2 | R | RNA (18-mer) | G | 7||||P_1 | A | 8||||P_1 | C | 10||||P_1 | C | 12||||P_1 | cWW | |
| 16 | HL_5UD5_001 | 5UD5 | 0.2507 | 3 | tRNA D-loop | C | tRNA | C | 13 | A | 14 | U | 15 | G | 21 | cWW |
| 17 | HL_6D12_002 | 6D12 | 0.1559 | 3 | C | human 7SK RNA stem-loop 4 | C | 328 | A | 329 | U | 330 | G | 334 | cWW | |
| 18 | HL_6D12_001 | 6D12 | 0.0000 | 3 | C | human 7SK RNA stem-loop 4 | C | 309 | A | 310 | U | 311 | G | 315 | cWW | |
| 19 | HL_7VTI_001 | 7VTI | 0.1754 | 3 | B | crRNA | C | 15 | G | 16 | A | 17 | G | 21 | cWW | |
| 20 | HL_8CRE_220 | 8CRE | 0.3515 | 2 | CM | SSU rRNA | C | 1344 | A | 1345 | U | 1346 | G | 1349 | cWW |
3D structures
Complete motif including flanking bases
| Sequence | Counts |
|---|---|
| CAUGUGG | 2 |
| AAUUAUU | 1 |
| CAUAGG | 1 |
| UUCGGGA | 1 |
| CCUUGG | 1 |
| UAGUGUA | 1 |
| CUGGG | 1 |
| GAGUUAC | 1 |
| CUUUUUG | 1 |
| GGUUCC | 1 |
| CGUAUUG | 1 |
| CGACACG | 1 |
| GAU(PYO)AC | 1 |
| GAUUAC | 1 |
| CAACAG | 1 |
| GAUCAC | 1 |
| CAUGUAG | 1 |
| CGAUUUG | 1 |
| CAUUUG | 1 |
Non-Watson-Crick part of the motif
| Sequence | Counts |
|---|---|
| AUGUG | 2 |
| AUUAU | 1 |
| AUAG | 1 |
| UCGGG | 1 |
| CUUG | 1 |
| AGUGU | 1 |
| UGG | 1 |
| AGUUA | 1 |
| UUUUU | 1 |
| GUUC | 1 |
| GUAUU | 1 |
| GACAC | 1 |
| AU(PYO)A | 1 |
| AUUA | 1 |
| AACA | 1 |
| AUCA | 1 |
| AUGUA | 1 |
| GAUUU | 1 |
| AUUU | 1 |
- Annotations
-
- (18)
- tRNA anticodon loop with synthetase (1)
- tRNA D-loop (1)
- Basepair signature
- cWW-F-F
- Heat map statistics
- Min 0.08 | Avg 0.39 | Max 0.88
Coloring options: