Table 1. Differences in codon usage between Oryza sativa, native FLP, and S. cerevisiae and codons used for mFLP gene synthesis.
| Amino acid | Codon | RCSU | Amino | Codon | RCSU | ||||
|---|---|---|---|---|---|---|---|---|---|
| O. sativa | FLP | S. cerevisiae | acid | O. sativa | FLP | S. cerevisiae | |||
| Ala | GCA+ | 0.73 | 1.83 | 1.15 | Ser | AGC*+ | 1.22 | 1.46 | 0.66 |
| GCC* | 1.31 | 0.67 | 0.90 | AGU+ | 0.67 | 1.02 | 0.95 | ||
| GCG* | 1.13 | 0.17 | 0.44 | UCA+ | 0.95 | 1.76 | 1.26 | ||
| GCU+ | 0.83 | 1.33 | 1.51 | UCC* | 1.24 | 0.15 | 0.96 | ||
| Cys | UGC* | 1.33 | - | 0.74 | UCG | 0.95 | 0.73 | 0.58 | |
| UGU+ | 0.67 | 2.00 | 1.26 | UCU | 0.97 | 0.88 | 1.59 | ||
| Asn | AAC*+ | 1.10 | 1.43 | 0.82 | Tyr | UAC*+ | 1.21 | 1.05 | 0.88 |
| AAU | 0.90 | 0.57 | 1.18 | UAU | 0.79 | 0.95 | 1.12 | ||
| Pro | CCA+ | 0.99 | 1.86 | 1.67 | Val | GUA+ | 0.41 | 1.05 | 0.84 |
| CCC | 0.83 | 0.27 | 0.62 | GUC* | 1.21 | 0.85 | 0.84 | ||
| CCG* | 1.24 | 0.27 | 0.48 | GUG*+ | 1.45 | 1.05 | 0.76 | ||
| CCU+ | 0.94 | 1.60 | 1.23 | GUU+ | 0.93 | 1.05 | 1.56 | ||
| Lys | AAA+ | 0.66 | 1.11 | 1.15 | Thr | ACA+ | 0.95 | 1.86 | 1.21 |
| AAG* | 1.34 | 0.89 | 0.85 | ACC* | 1.23 | 0.43 | 0.87 | ||
| Asp | GAC* | 1.05 | 0.13 | 0.70 | ACG | 0.94 | 0.43 | 0.54 | |
| GAU+ | 0.95 | 1.87 | 1.30 | ACU+ | 0.88 | 1.28 | 1.38 | ||
| Leu | CUA+ | 0.51 | 1.35 | 0.85 | Arg | AGA+ | 0.90 | 2.10 | 2.89 |
| CUC* | 1.71 | 0.15 | 0.34 | AGG*+ | 1.38 | 2.10 | 1.25 | ||
| CUG* | 1.39 | 0.60 | 0.66 | CGA | 0.55 | 0.60 | 0.40 | ||
| CUU* | 1.01 | 0.90 | 0.78 | CGC* | 1.39 | 0.30 | 0.35 | ||
| UUA+ | 0.41 | 1.65 | 1.65 | CGG* | 1.16 | 0.30 | 0.24 | ||
| UUG+ | 0.97 | 1.35 | 1.72 | CGU | 0.62 | 0.60 | 0.87 | ||
| His | CAC* | 1.10 | 0.89 | 0.73 | Gly | GGA+ | 0.82 | 2.00 | 0.86 |
| CAU+ | 0.90 | 1.11 | 1.27 | GGC* | 1.53 | 0.75 | 0.77 | ||
| Phe | UUC* | 1.26 | 0.80 | 0.83 | GGG | 0.88 | 0.25 | 0.48 | |
| UUU+ | 0.74 | 1.20 | 1.17 | GGU | 0.77 | 1.00 | 1.89 | ||
| Gln | CAA | 0.79 | 0.94 | 1.39 | Ile | AUA+ | 0.62 | 1.42 | 0.82 |
| CAG*+ | 1.21 | 1.06 | 0.61 | AUC* | 1.38 | 0.75 | 0.79 | ||
| Glu | GAA+ | 0.72 | 1.15 | 1.41 | AUU | 1.00 | 0.83 | 1.39 | |
| GAG* | 1.28 | 0.85 | 0.59 | ||||||
An asterisk (*) after the codon indicates a favored codon (RCSU > 1) in genes of coding DNA sequences in the rice genome, and a plus sign (+) indicates a favored codon (RCSU > 1) in the native FLP gene. Codons used for synthesis of the mFLP gene are shown as bold text and were favored codons in high-GC genes within the rice genome [30]. Relative synonymous codon usage (RSCU) was defined as the ratio of the observed frequency of codons to the expected frequency given that all synonymous codons for the same amino acids were used equally.