Table 2.
Codon usage in RV-A strains of different genotypes, expressed by RSCU values.
| AA | Cod | HC | OC | IM | IC | NSP | Full | AA | Cod | HC | OC | IM | IC | NSP | Full |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Phe | UUU | 0.92 | 1.53 | 1.58 | 1.52 | 1.52 | 1.51 | Ser | UCU | 1.14 | 1.30 | 1.02 | 1.13 | 1.66 | 1.30 |
| UUC | 1.08 | 0.47 | 0.42 | 0.48 | 0.48 | 0.49 | UCC | 1.32 | 0.26 | 0.43 | 0.29 | 0.28 | 0.28 | ||
| Leu | UUA | 0.48 | 2.74 | 1.41 | 2.59 | 1.89 | 2.33 | UCA | 0.90 | 2.84 | 3.07 | 3.26 | 2.29 | 2.93 | |
| UUG | 0.78 | 0.99 | 1.25 | 1.14 | 1.32 | 1.17 | UCG | 0.30 | 0.54 | 0.55 | 0.62 | 0.54 | 0.57 | ||
| CUU | 0.78 | 0.47 | 1.37 | 0.60 | 0.92 | 0.70 | Pro | CCU | 1.16 | 0.61 | 0.26 | 0.43 | 0.90 | 0.54 | |
| CUC | 1.20 | 0.29 | 0.32 | 0.18 | 0.39 | 0.25 | CCC | 1.28 | 0.27 | 0.02 | 0.12 | 0.20 | 0.15 | ||
| CUA | 0.42 | 1.09 | 1.18 | 1.04 | 1.03 | 1.07 | CCA | 1.12 | 2.68 | 3.34 | 2.85 | 2.55 | 2.81 | ||
| CUG | 2.40 | 0.42 | 0.48 | 0.46 | 0.45 | 0.48 | CCG | 0.44 | 0.44 | 0.38 | 0.60 | 0.35 | 0.51 | ||
| Ile | AUU | 1.08 | 1.13 | 1.80 | 1.02 | 1.80 | 1.24 | Thr | ACU | 1.00 | 1.14 | 1.35 | 1.35 | 1.64 | 1.35 |
| AUC | 1.41 | 0.22 | 0.30 | 0.23 | 0.27 | 0.24 | ACC | 1.44 | 0.24 | 0.12 | 0.24 | 0.24 | 0.23 | ||
| AUA | 0.51 | 1.65 | 0.90 | 1.75 | 0.93 | 1.51 | ACA | 1.12 | 1.73 | 2.11 | 1.63 | 1.52 | 1.66 | ||
| Met | AUG | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | ACG | 0.44 | 0.89 | 0.43 | 0.78 | 0.61 | 0.76 | |
| Val | GUU | 0.72 | 0.95 | 1.09 | 1.36 | 1.67 | 1.33 | Ala | GCU | 1.08 | 1.25 | 1.57 | 1.44 | 1.34 | 1.40 |
| GUC | 0.96 | 0.33 | 0.71 | 0.38 | 0.32 | 0.37 | GCC | 1.60 | 0.26 | 0.32 | 0.33 | 0.17 | 0.28 | ||
| GUA | 0.48 | 1.77 | 1.46 | 1.46 | 1.11 | 1.43 | GCA | 0.92 | 1.76 | 1.36 | 1.62 | 2.03 | 1.69 | ||
| GUG | 1.84 | 0.94 | 0.74 | 0.80 | 0.90 | 0.86 | GCG | 0.44 | 0.73 | 0.75 | 0.61 | 0.45 | 0.63 | ||
| Tyr | UAU | 0.88 | 1.46 | 1.13 | 1.47 | 1.33 | 1.43 | Cys | UGU | 0.92 | 1.35 | 1.80 | 1.39 | 1.17 | 1.31 |
| UAC | 1.12 | 0.54 | 0.87 | 0.53 | 0.67 | 0.57 | UGC | 1.08 | 0.65 | 0.20 | 0.61 | 0.83 | 0.69 | ||
| TER | UAA | ** | ** | ** | ** | ** | ** | TER | UGA | ** | ** | ** | ** | ** | ** |
| UAG | ** | ** | ** | ** | ** | ** | Trp | UGG | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | 1.00 | |
| His | CAU | 0.84 | 1.69 | 1.80 | 1.66 | 1.48 | 1.62 | Arg | CGU | 0.48 | 0.12 | 0.46 | 0.60 | 0.74 | 0.53 |
| CAC | 1.16 | 0.31 | 0.20 | 0.34 | 0.52 | 0.38 | CGC | 1.08 | 0.22 | 0.12 | 0.23 | 0.06 | 0.18 | ||
| Gln | CAA | 0.54 | 1.20 | 1.28 | 1.28 | 1.38 | 1.29 | CGA | 0.66 | 0.87 | 0.31 | 0.50 | 0.59 | 0.56 | |
| CAG | 1.46 | 0.80 | 0.72 | 0.72 | 0.62 | 0.71 | CGG | 1.20 | 0.29 | 0.00 | 0.15 | 0.18 | 0.18 | ||
| Asn | AAU | 0.94 | 1.53 | 1.38 | 1.52 | 1.56 | 1.51 | Ser | AGU | 0.90 | 0.85 | 0.55 | 0.58 | 0.92 | 0.71 |
| AAC | 1.06 | 0.47 | 0.62 | 0.48 | 0.44 | 0.49 | AGC | 1.44 | 0.22 | 0.39 | 0.11 | 0.31 | 0.21 | ||
| Lys | AAA | 0.86 | 1.52 | 1.66 | 1.49 | 1.48 | 1.49 | Arg | AGA | 1.26 | 3.75 | 4.98 | 3.86 | 3.50 | 3.85 |
| AAG | 1.14 | 0.48 | 0.34 | 0.51 | 0.52 | 0.57 | AGG | 1.26 | 0.75 | 0.12 | 0.67 | 0.92 | 0.70 | ||
| Asp | GAU | 0.92 | 1.38 | 1.54 | 1.43 | 1.63 | 1.47 | Gly | GGU | 0.64 | 1.44 | 1.03 | 1.31 | 1.45 | 1.34 |
| GAC | 1.08 | 0.62 | 0.46 | 0.57 | 0.37 | 0.53 | GGC | 1.36 | 0.34 | 0.34 | 0.26 | 0.20 | 0.28 | ||
| Glu | GAA | 0.84 | 1.30 | 1.46 | 1.46 | 1.47 | 1.43 | GGA | 1.00 | 1.90 | 2.40 | 2.02 | 2.04 | 2.01 | |
| GAG | 1.16 | 0.70 | 0.54 | 0.54 | 0.53 | 0.57 | GGG | 1.00 | 0.32 | 0.23 | 0.41 | 0.31 | 0.37 | ||
RSCU, relative synonymous codon usage; AA, amino acid; Cod, codons; HC, human cells; OC, outer capsid shell proteins; IM, intermediate protein shell; IC, inner capsid shell proteins; NSP, non-structural proteins; Full, full genome; TER, termination codon. More frequent codons with respect to human cells found in all genome regions studied are shown in bold. Frequencies sharply reduced with respect to frequencies found in human cells are shown in italics.