Table 1. Codon usage for genes located in the leading and lagging strands on the C.trachomatis genome, and preferred codons on highly expressed sequences.
| AA | Codon | Leading | Lagging | ||
|---|---|---|---|---|---|
| N | RSCU | N | RSCU | ||
| Phe | TTT* | 5450 | 1.37 | 4149 | 1.16 |
| TTC- | 2491 | 0.63 | 3008 | 0.84 | |
| Leu | TTA* | 5922 | 1.96 | 4215 | 1.49 |
| TTG* | 4254 | 1.41 | 1930 | 0.68 | |
| CTT- | 3311 | 1.10 | 3835 | 1.36 | |
| CTC- | 1241 | 0.41 | 2568 | 0.91 | |
| CTA- | 1846 | 0.61 | 2817 | 1.00 | |
| CTG | 1553 | 0.51 | 1563 | 0.55 | |
| Ile | ATT* | 5793 | 1.69 | 5105 | 1.48 |
| ATC- | 2555 | 0.74 | 3652 | 1.06 | |
| ATA* | 1954 | 0.57 | 1567 | 0.46 | |
| Met | ATG | 3747 | 1.00 | 2623 | 1.00 |
| Val | GTT* | 4843 | 1.56 | 2702 | 1.41 |
| GTC- | 1616 | 0.52 | 1618 | 0.85 | |
| GTA | 3228 | 1.04 | 2046 | 1.07 | |
| GTG* | 2709 | 0.87 | 1291 | 0.67 | |
| Tyr | TAT* | 3742 | 1.46 | 2724 | 1.23 |
| TAC- | 1398 | 0.54 | 1705 | 0.77 | |
| TER | TAA | 250 | 1.50 | 243 | 1.85 |
| TAG | 182 | 1.09 | 87 | 0.66 | |
| His | CAT* | 2654 | 1.53 | 2436 | 1.31 |
| CAC- | 804 | 0.47 | 1296 | 0.69 | |
| Gln | CAA- | 3868 | 1.14 | 4612 | 1.47 |
| CAG* | 2935 | 0.86 | 1651 | 0.53 | |
| Asn | AAT* | 3981 | 1.48 | 3588 | 1.29 |
| AAC- | 1391 | 0.52 | 1966 | 0.71 | |
| Lys | AAA- | 6034 | 1.24 | 6503 | 1.58 |
| AAG* | 3707 | 0.76 | 1743 | 0.42 | |
| Asp | GAT* | 6422 | 1.62 | 4417 | 1.43 |
| GAC- | 1516 | 0.38 | 1741 | 0.57 | |
| Glu | GAA- | 6931 | 1.15 | 6250 | 1.46 |
| GAG* | 5101 | 0.85 | 2317 | 0.54 | |
| Ser | TCT | 5270 | 2.49 | 5237 | 2.49 |
| TCC- | 1418 | 0.67 | 2403 | 1.14 | |
| TCA | 1499 | 0.71 | 1474 | 0.70 | |
| TCG* | 1238 | 0.58 | 883 | 0.42 | |
| Pro | CCT | 3584 | 2.24 | 3950 | 2.19 |
| CCC- | 639 | 0.40 | 1153 | 0.64 | |
| CCA* | 1476 | 0.92 | 1531 | 0.85 | |
| CCG* | 701 | 0.44 | 589 | 0.33 | |
| Thr | ACT | 2453 | 1.32 | 2842 | 1.33 |
| ACC- | 1016 | 0.55 | 1818 | 0.85 | |
| ACA | 2450 | 1.32 | 2813 | 1.32 | |
| ACG* | 1495 | 0.81 | 1079 | 0.50 | |
| Ala | GCT* | 6299 | 1.96 | 4926 | 1.86 |
| GCC- | 1388 | 0.43 | 1818 | 0.69 | |
| GCA | 3335 | 1.04 | 2766 | 1.04 | |
| GCG* | 1861 | 0.58 | 1085 | 0.41 | |
| Cys | TGT* | 1969 | 1.41 | 1219 | 1.07 |
| TGC- | 832 | 0.59 | 1059 | 0.93 | |
| TER | TGA | 67 | 0.40 | 64 | 0.49 |
| Trp | TGG | 1728 | 1.00 | 1256 | 1.00 |
| Arg | CGT* | 2626 | 1.75 | 1445 | 1.43 |
| CGC- | 944 | 0.63 | 1459 | 1.44 | |
| CGA | 1734 | 1.15 | 1235 | 1.22 | |
| CGG* | 943 | 0.63 | 382 | 0.38 | |
| Ser | AGT* | 2085 | 0.98 | 1176 | 0.56 |
| AGC- | 1207 | 0.57 | 1431 | 0.68 | |
| Arg | AGA | 2164 | 1.44 | 1342 | 1.33 |
| AGG* | 604 | 0.40 | 203 | 0.20 | |
| Gly | GGT* | 2408 | 0.82 | 1446 | 0.71 |
| GGC- | 1284 | 0.44 | 1405 | 0.69 | |
| GGA- | 4826 | 1.65 | 3772 | 1.86 | |
| GGG* | 3180 | 1.09 | 1474 | 0.73 | |
AA, amino acid; N, count of codons. Codons marked with an * or - are statistically more frequent in the leading or lagging strand of replication, respectively (P < 0.01). Underlined codons are those more frequent (P < 0.05) in highly expressed sequences.