Motif HL_48417.1 Version HL_48417.1 of this group appears in releases 3.89 to 3.90
| #S | Loop id | PDB | Disc | #Non-core | Chain(s) | Standardized name | 1 | 2 | 3 | 4 | 1-4 | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | HL_8C3A_221 | 8C3A | 0.3993 | 2 | CM | SSU rRNA | C | 1344 | A | 1345 | U | 1346 | G | 1349 | cWW |
| 2 | HL_4V88_204 | 4V88 | 0.4132 | 3 | A6 | SSU rRNA | C | 777 | G | 778 | A | 780 | G | 783 | cWW |
| 3 | HL_8C3A_203 | 8C3A | 0.3563 | 3 | CM | SSU rRNA | C | 448 | G | 449 | C | 451 | G | 454 | cWW |
| 4 | HL_2C4Q_001 | 2C4Q | 0.2347 | 2 | R | RNA (19-mer) | G | 8||||P_1 | A | 9||||P_1 | PYO | 11||||P_1 | C | 13||||P_1 | cWW |
| 5 | HL_2IZN_001 | 2IZN | 0.2403 | 2 | R | RNA (19-mer) | G | 8||||P_1 | A | 9||||P_1 | U | 11||||P_1 | C | 13||||P_1 | cWW |
| 6 | HL_7MSF_001 | 7MSF | 0.2803 | 2 | R | RNA (14-mer) | C | 5||||P_1 | A | 6||||P_1 | C | 8||||P_1 | G | 10||||P_1 | cWW |
| 7 | HL_5MSF_001 | 5MSF | 0.2760 | 2 | R | RNA (18-mer) | G | 7||||P_1 | A | 8||||P_1 | C | 10||||P_1 | C | 12||||P_1 | cWW |
| 8 | HL_1U1Y_001 | 1U1Y | 0.2895 | 2 | R | RNA (17-mer) | G | 7||||P_1 | A | 8||||P_1 | C | 10||||P_1 | C | 12||||P_1 | cWW |
| 9 | HL_5UD5_001 | 5UD5 | 0.1413 | 3 | C | tRNA | C | 13 | A | 14 | U | 15 | G | 21 | cWW |
| 10 | HL_6D12_002 | 6D12 | 0.0000 | 3 | C | human 7SK RNA stem-loop 4 | C | 328 | A | 329 | U | 330 | G | 334 | cWW |
| 11 | HL_6D12_001 | 6D12 | 0.1559 | 3 | C | human 7SK RNA stem-loop 4 | C | 309 | A | 310 | U | 311 | G | 315 | cWW |
| 12 | HL_7VTI_001 | 7VTI | 0.1791 | 3 | B | crRNA | C | 15 | G | 16 | A | 17 | G | 21 | cWW |
| 13 | HL_6DTD_001 | 6DTD | 0.3648 | 3 | C | RNA (37-MER) | C | 16 | U | 17 | U | 20 | G | 22 | cWW |
| 14 | HL_5AMQ_001 | 5AMQ | 0.2675 | 3 | C | RNA | U | 3 | A | 4 | G | 5 | A | 9 | cWW |
| 15 | HL_6XH2_001 | 6XH2 | 0.3647 | 1 | D | TRANS-ACTIVATION RESPONSE ELEMENT | C | 30 | U | 31 | G | 32 | G | 34 | cWW |
| 16 | HL_4LFB_004 | 4LFB | 0.3043 | 2 | A | SSU rRNA | C | 190|||B | C | 190|||C | U | 190|||D | G | 190|||G | cWW |
| 17 | HL_6CZR_075 | 6CZR | 0.3364 | 2 | 1a | SSU rRNA | C | 187 | C | 188 | U | 189 | G | 192 | cWW |
| 18 | HL_1H4S_002 | 1H4S | 0.3835 | 3 | T | tRNA | U | 32 | U | 33 | C | 34 | A | 38 | cWW |
| 19 | HL_2Y9H_004 | 2Y9H | 0.3824 | 2 | H | RNA (19-mer) | C | 11 | G | 12 | C | 13 | G | 16 | cWW |
| 20 | HL_3SKL_007 | 3SKL | 0.3627 | 2 | B | RNA (66-MER) | A | 66 | C | 67 | C | 68 | U | 71 | ncWW |
| 21 | HL_3SKI_003 | 3SKI | 0.3378 | 2 | A | RNA (68-MER) | A | 67 | C | 68 | C | 69 | U | 72 | cWW |
| 22 | HL_5E08_001 | 5E08 | 0.3869 | 2 | N | RNA | C | 6 | A | 7 | A | 9 | G | 11 | cWW |
| 23 | HL_8UO6_007 | 8UO6 | 0.7335 | 3 | B | HIV-1 Rev Response Element Stem-Loop II with tRNA scaffold | A | 77 | A | 78 | U | 80 | U | 83 | cWW |
3D structures
Complete motif including flanking bases
| Sequence | Counts |
|---|---|
| GAUCAC | 2 |
| CAUGUGG | 2 |
| CCUUGG | 2 |
| ACCUAU | 2 |
| CAUUUG | 1 |
| CGUAUUG | 1 |
| CGACACG | 1 |
| GAU(PYO)AC | 1 |
| GAUUAC | 1 |
| CAACAG | 1 |
| CAUGUAG | 1 |
| CGAUUUG | 1 |
| CUUUUUG | 1 |
| UAGUGUA | 1 |
| CUGGG | 1 |
| UUCGGGA | 1 |
| CGCGUG | 1 |
| CAUAGG | 1 |
| AAUUAUU | 1 |
Non-Watson-Crick part of the motif
| Sequence | Counts |
|---|---|
| AUCA | 2 |
| AUGUG | 2 |
| CUUG | 2 |
| CCUA | 2 |
| AUUU | 1 |
| GUAUU | 1 |
| GACAC | 1 |
| AU(PYO)A | 1 |
| AUUA | 1 |
| AACA | 1 |
| AUGUA | 1 |
| GAUUU | 1 |
| UUUUU | 1 |
| AGUGU | 1 |
| UGG | 1 |
| UCGGG | 1 |
| GCGU | 1 |
| AUAG | 1 |
| AUUAU | 1 |
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