TABLE 1.
Prime positions in the binding sites of sRNAs
| sRNAa | Number of targets | Length of binding site | Prime position (within binding site on target) | Number of binding sites with prime position in N1 | Number of binding sites with prime position in N2 | Number of binding sites with prime position in N3 | Nucleotide in sRNA | Nucleotide in target | Coincidence with frequent codon? (N3)b | Percentage of frequent codons (N3)c |
|---|---|---|---|---|---|---|---|---|---|---|
| CyaR | 98 | 15 | 11 | 34 | 8 | 56 | C | 98G | 47 | 0.8392 |
| FliX | 5 | 11 | 7 | 0 | 1 | 4 | A | 5U | 0 | 0 |
| MicA | 14 | 15 | 10 | 6 | 2 | 6 | G | 14C | 6 | 1 |
| UhpU | 13 | 8 | 6 | 3 | 2 | 8 | G | 13C | 7 | 0.875 |
| DsrA | 6 | 11 | 7 | 1 | 4 | 1 | C | 6G | 1 | 1 |
| RprA | 19 | 9 | 3 | 5 | 10 | 4 | G | 17C, 2U | 1 | 0.25 |
| RprA | 19 | 9 | 6 | 5 | 10 | 4 | G | 18C, 1U | 4 | 1 |
| ArcZ | 87 | 13 | 6 | 52 | 7 | 28 | G | 1A, 85C, 1U | 20 | 0.7142 |
| ArcZ | 87 | 13 | 8 | 7 | 28 | 52 | C | 1A, 85G, 1U | 50 | 0.9615 |
| CpxQ | 44 | 15 | 6 | 4 | 29 | 11 | A | 44U | 3 | 0.2727 |
| CpxQ | 44 | 15 | 7 | 11 | 4 | 29 | C | 44G | 19 | 0.6551 |
| SdhX | 7 | 11 | 4 | 1 | 4 | 2 | A | 7U | 1 | 0.5 |
| SdhX | 7 | 11 | 5 | 2 | 1 | 4 | C | 7G | 4 | 1 |
| GadF | 7 | 8 | 4 | 1 | 0 | 6 | C | 7G | 6 | 1 |
| GadF | 7 | 8 | 5 | 6 | 1 | 0 | A | 7G | 0 | 0 |
| Spf | 5 | 8 | 1 | 1 | 3 | 1 | U | 5A | 1 | 1 |
| Spf | 5 | 8 | 2 | 1 | 1 | 3 | U | 5A | 3 | 1 |
| Spf | 5 | 8 | 7 | 1 | 3 | 1 | G | 5C | 0 | 0 |
| RyhB | 55 | 11 | 3 | 40 | 8 | 7 | G | 55C | 1 | 0.1429 |
| RyhB | 55 | 11 | 4 | 7 | 40 | 8 | A | 55U | 0 | 0 |
| RyhB | 55 | 11 | 5 | 8 | 7 | 40 | C | 55G | 40 | 1 |
| MgrR | 14 | 8 | 1 | 7 | 7 | 0 | C | 14G | 0 | 0 |
| MgrR | 14 | 8 | 3 | 7 | 0 | 7 | U | 14A | 0 | 0 |
| MgrR | 14 | 8 | 4 | 7 | 7 | 0 | A | 14U | 0 | 0 |
| MgrR | 14 | 8 | 5 | 0 | 7 | 7 | C | 14G | 7 | 1 |
| MgrR | 14 | 8 | 6 | 7 | 0 | 7 | C | 14G | 7 | 1 |
-
asRNAs are ordered by the number of prime positions they have.
-
bNumber of targets in which the prime positions that align with a third codon position coincide with the frequent codon.
-
cFraction of targets in which the prime positions that align with a third codon position coincide with the frequent codon.
