Motif IL_64417.2 Version IL_64417.2 of this group appears in releases 3.85 to 3.87
| #S | Loop id | PDB | Disc | #Non-core | Annotation | Chain(s) | Standardized name | 1 | 2 | 3 | break | 4 | 5 | 1-5 | 3-4 | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | IL_1ZZ5_003 | 1ZZ5 | 0.3846 | 2 | Decoding loop related | D+C | RNA (14-mer) | C | 26 | A | 27 | C | 28 | * | G | 7 | G | 10 | cWW | cWW |
| 2 | IL_1ZZ5_001 | 1ZZ5 | 0.3617 | 2 | Decoding loop related | B+A | RNA (14-mer) | C | 26 | A | 27 | C | 28 | * | G | 7 | G | 10 | cWW | cWW |
| 3 | IL_3C3Z_003 | 3C3Z | 0.4683 | 2 | Decoding loop related | A+B | HIV-1 subtype F genomic RNA | C | 15 | A | 16 | C | 17 | * | G | 7 | G | 10 | cWW | cWW |
| 4 | IL_4PDQ_002 | 4PDQ | 0.4493 | 2 | A+B | RNA (23-mer) | C | 7 | A | 8 | C | 9 | * | G | 39 | G | 42 | cWW | cWW | |
| 5 | IL_3C3Z_002 | 3C3Z | 0.1607 | 2 | Decoding loop related | B+A | HIV-1 subtype F genomic RNA | C | 15 | A | 16 | C | 17 | * | G | 7 | G | 10 | cWW | cWW |
| 6 | IL_2ET8_002 | 2ET8 | 0.1845 | 2 | Decoding loop related | A+B | RNA (22-mer) | C | 6 | A | 7 | C | 8 | * | G | 38 | G | 41 | cWW | cWW |
| 7 | IL_2O3X_002 | 2O3X | 0.1322 | 2 | Decoding loop related | A+B | RNA (23-mer) | C | 7 | A | 8 | C | 9 | * | G | 39 | G | 42 | cWW | cWW |
| 8 | IL_4ZC7_003 | 4ZC7 | 0.0000 | 2 | Decoding loop related | B+A | RNA duplex | C | 30 | G | 31 | U | 32 | * | A | 16 | G | 19 | cWW | ncWW |
| 9 | IL_5Z1I_003 | 5Z1I | 0.2573 | 2 | Decoding loop related | A | RNA (21-mer) | C | 7||||8_555 | G | 8||||8_555 | C | 9||||8_555 | * | G | 16 | G | 19 | cWW | cWW |
| 10 | IL_5Z1I_002 | 5Z1I | 0.2573 | 2 | Decoding loop related | A | RNA (21-mer) | C | 7 | G | 8 | C | 9 | * | G | 16||||8_555 | G | 19||||8_555 | cWW | cWW |
| 11 | IL_1T0E_001 | 1T0E | 0.4623 | 2 | Decoding loop related | C+A | RNA (17-mer) | C | 16 | A | 17 | C | 18 | * | G | 7 | G | 10||A | cWW | cWW |
| 12 | IL_1ZX7_003 | 1ZX7 | 0.5650 | 2 | Decoding loop related | D+C | RNA (14-mer) | C | 26 | A | 27 | C | 28 | * | G | 7 | G | 10 | cWW | cWW |
| 13 | IL_1ZX7_005 | 1ZX7 | 0.5929 | 2 | Decoding loop related | F+E | RNA (14-mer) | C | 26 | A | 27 | C | 28 | * | G | 7 | G | 10 | cWW | cWW |
| 14 | IL_5VCI_005 | 5VCI | 0.4390 | 0 | Not an internal loop | A+B | RNA (22-mer) + RNA (12-mer) | G | 13 | C | 14 | C | 15 | * | G | 22 | C | 1 | cWW | cWW |
| 15 | IL_2O3X_001 | 2O3X | 0.5090 | 1 | Stack and bulge | B+A | RNA (23-mer) | G | 42 | U | 43 | C | 44 | * | G | 5 | C | 7 | cWW | cWW |
| 16 | IL_2ET8_001 | 2ET8 | 0.5283 | 1 | Stack and bulge | B+A | RNA (22-mer) | G | 41 | U | 42 | C | 43 | * | G | 4 | C | 6 | cWW | cWW |
| 17 | IL_7A0S_044 | 7A0S | 0.5192 | 1 | Intercalated cWW | X | LSU rRNA | G | 1241 | A | 1242 | G | 1243 | * | U | 1232 | C | 1234 | cWW | cWW |
| 18 | IL_4WF9_047 | 4WF9 | 0.6726 | 1 | Intercalated cWW | X | LSU rRNA | G | 1266 | A | 1267 | C | 1268 | * | G | 1257 | U | 1259 | cWW | cWW |
3D structures
Complete motif including flanking bases
| Sequence | Counts |
|---|---|
| CAC*GAAG | 9 |
| CGC*GAAG | 2 |
| GUC*GUC | 2 |
| CGU*AAAG | 1 |
| GAAG*CAC | 1 |
| GCC*GC | 1 |
| GAG*UAC | 1 |
| GAC*GAU | 1 |
Non-Watson-Crick part of the motif
| Sequence | Counts |
|---|---|
| A*AA | 9 |
| G*AA | 3 |
| U*U | 2 |
| A*A | 2 |
| AA*A | 1 |
| C* | 1 |
- Annotations
-
- Decoding loop related (12)
- Stack and bulge (2)
- Intercalated cWW (2)
- (1)
- Not an internal loop (1)
- Basepair signature
- cWW-L-cWW
- Heat map statistics
- Min 0.00 | Avg 0.36 | Max 0.75
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