Research Article
Compositional Constraint Is the Key Force in Shaping Codon Usage Bias in Hemagglutinin Gene in H1N1 Subtype of Influenza A Virus
Table 3
Synonymous codon usage pattern in 32 coding sequences.
| AA | Codon | RSCU* | Fop* | |
| Ala | GCA | 2.06 | 0.53 | 18 | GCC | 1.01 | 0.26 | 9 | GCG | 0.24 | 0.06 | 2 | GCT | 0.62 | 0.16 | 5 |
| Arg | CGT | 0.00 | 0.00 | 0 | CGC | 0.00 | 0.00 | 0 | CGA | 0.00 | 0.00 | 0 | CGG | 0.05 | 0.01 | 0 | AGA | 4.61 | 0.77 | 14 | AGG | 1.32 | 0.22 | 4 |
| Asn | AAT | 1.30 | 0.66 | 27 | AAC | 0.69 | 0.34 | 14 |
| Asp | GAT | 1.00 | 0.50 | 13 | GAC | 1.00 | 0.50 | 13 |
| Cys | TGT | 1.20 | 0.60 | 9 | TGC | 0.81 | 0.40 | 6 |
| Gln | CAA | 0.87 | 0.40 | 6 | CAG | 1.19 | 0.59 | 9 |
| Glu | GAA | 1.38 | 0.69 | 24 | GAG | 0.66 | 0.31 | 11 |
| Gly | GGT | 0.87 | 0.22 | 9 | GGC | 0.51 | 0.12 | 5 | GGA | 1.31 | 0.33 | 13 | GGG | 1.37 | 0.34 | 14 |
| His | CAT | 1.08 | 0.54 | 8 | CAC | 0.92 | 0.46 | 7 |
| Ile | ATT | 1.50 | 0.50 | 18 | ATC | 0.52 | 0.17 | 6 | ATA | 0.98 | 0.33 | 12 |
| Leu | TTA | 0.77 | 0.12 | 6 | TTG | 1.35 | 0.22 | 10 | CTT | 0.12 | 0.02 | 1 | CTC | 0.64 | 0.11 | 5 | CTA | 1.79 | 0.30 | 14 | CTG | 1.33 | 0.22 | 10 |
| Lys | AAA | 1.28 | 0.64 | 27 | AAG | 0.72 | 0.36 | 15 |
| Phe | TTT | 0.86 | 0.44 | 9 | TTC | 1.13 | 0.56 | 11 |
| Pro | CCT | 0.23 | 0.06 | 1 | CCC | 0.87 | 0.22 | 4 | CCA | 1.86 | 0.47 | 9 | CCG | 1.02 | 0.26 | 5 |
| Ser | TCT | 1.16 | 0.19 | 9 | TCC | 0.54 | 0.09 | 4 | TCA | 2.25 | 0.37 | 17 | TCG | 0.12 | 0.02 | 1 | AGT | 0.87 | 0.14 | 7 | AGC | 1.08 | 0.18 | 8 |
| Thr | ACT | 1.00 | 0.25 | 9 | ACC | 0.21 | 0.05 | 2 | ACA | 2.49 | 0.62 | 24 | ACG | 0.31 | 0.08 | 3 |
| Tyr | TAT | 0.96 | 0.48 | 13 | TAC | 1.04 | 0.52 | 14 |
| Val | GTT | 0.76 | 0.19 | 7 | GTC | 0.64 | 0.16 | 6 | GTA | 1.83 | 0.46 | 17 | GTG | 0.78 | 0.19 | 7 |
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Note: *All values are mean values; represents the number of codons; the preferentially used codons for each amino acid are described in bold.
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