Table 2.
Codon usage in the nPPR and PPRa
| Genotype and frequency | nPPR |
PPR |
||
|---|---|---|---|---|
| Codon (aa) | Frequency | Codon (aa) | Frequency | |
| Genotype 1 | ||||
| Most frequent | GCC(A) | 5.31 | GCC(A) | 12.59 |
| GAG(E) | 4.29 | CCU(P) | 9.93 | |
| GGC(G) | 3.75 | UCU(S) | 6.15 | |
| GCU(A) | 3.37 | CCC(P) | 6.15 | |
| CGC(R) | 3.07 | CCG(P) | 5.87 | |
| ACC(T) | 3.04 | ACC(T) | 3.92 | |
| CUC(L) | 2.95 | GAG(E) | 3.92 | |
| CAG(Q) | 2.90 | GCU(A) | 3.64 | |
| GUU(V) | 2.65 | AUA(I) | 2.94 | |
| GUC(V) | 2.37 | GCG(A) | 2.94 | |
| GAU(D) | 2.37 | GAU(D) | 2.52 | |
| UUU(F) | 2.35 | AGU(S) | 2.38 | |
| Least frequent | ACG(T) | 0.68 | CGA(R) | 0.14 |
| UCA(S) | 0.67 | UCG(S) | 0.00 | |
| AGU(S) | 0.62 | UAC(Y) | 0.00 | |
| AUA(I) | 0.53 | AAU(N) | 0.00 | |
| GUA(V) | 0.49 | AAA(K) | 0.00 | |
| AGC(S) | 0.45 | AAG(K) | 0.00 | |
| AAA(K) | 0.44 | UGU(C) | 0.00 | |
| CAA(Q) | 0.41 | UGC(C) | 0.00 | |
| UUA(L) | 0.35 | UGG(W) | 0.00 | |
| AGA(R) | 0.24 | CGC(R) | 0.00 | |
| CGA(R) | 0.20 | AGA(R) | 0.00 | |
| GGA(G) | 0.19 | GGA(G) | 0.00 | |
| Genotype 3 | ||||
| Most frequent | GAG(E) | 4.42 | CCC(P) | 9.05 |
| GCC(A) | 4.35 | CCU(P) | 7.15 | |
| GCU(A) | 3.22 | CCA(P) | 7.04 | |
| GGC(G) | 3.21 | CCG(P) | 6.59 | |
| CAG(Q) | 2.76 | GCC(A) | 4.58 | |
| GUU(V) | 2.67 | UCU(S) | 4.13 | |
| CUU(L) | 2.48 | GCU(A) | 3.91 | |
| UUU(F) | 2.47 | GAG(E) | 3.35 | |
| CCU(P) | 2.43 | AGU(S) | 2.79 | |
| GAU(D) | 2.41 | UCC(S) | 2.57 | |
| GUG(V) | 2.21 | ACC(T) | 2.46 | |
| CGU(R) | 2.16 | ACA(T) | 2.46 | |
| Least frequent | UCA(S) | 0.87 | AUG(M) | 0.22 |
| CUA(L) | 0.86 | AAU(N) | 0.22 | |
| AGG(R) | 0.77 | AAA(K) | 0.22 | |
| AAA(K) | 0.74 | UAC(Y) | 0.11 | |
| UCG(S) | 0.73 | CAU(H) | 0.11 | |
| AGU(S) | 0.67 | CAA(Q) | 0.11 | |
| CAA(Q) | 0.61 | UGU(C) | 0.11 | |
| AGC(S) | 0.60 | CGG(R) | 0.11 | |
| CGA(R) | 0.52 | AGA(R) | 0.11 | |
| GUA(V) | 0.46 | CAC(H) | 0.00 | |
| GGA(G) | 0.44 | UGC(C) | 0.00 | |
| AGA(R) | 0.39 | CGA(R) | 0.00 | |
| Genotype 4 | ||||
| Most frequent | GAG(E) | 4.40 | CCC(P) | 7.13 |
| GCC(A) | 3.73 | CCA(P) | 6.42 | |
| GCU(A) | 3.29 | CCU(P) | 5.83 | |
| CUU(L) | 3.08 | CCG(P) | 4.88 | |
| GGC(G) | 3.02 | GCU(A) | 4.76 | |
| GUU(V) | 2.87 | UCU(S) | 4.40 | |
| CAG(Q) | 2.75 | GUG(V) | 3.92 | |
| UUU(F) | 2.66 | GAU(D) | 3.45 | |
| GAU(D) | 2.57 | GCC(A) | 3.33 | |
| CCU(P) | 2.41 | GUU(V) | 3.21 | |
| GGU(G) | 2.25 | GAG(E) | 2.85 | |
| GUC(V) | 2.21 | GGC(G) | 2.62 | |
| Least frequent | UCG(S) | 0.88 | ACG(T) | 0.24 |
| ACG(T) | 0.84 | CAU(H) | 0.24 | |
| CUA(L) | 0.83 | AAA(K) | 0.24 | |
| AGC(S) | 0.76 | GGA(G) | 0.24 | |
| AGG(R) | 0.75 | AAC(N) | 0.12 | |
| GUA(V) | 0.63 | AAG(K) | 0.12 | |
| CGA(R) | 0.62 | UAU(Y) | 0.00 | |
| AGU(S) | 0.60 | UAC(Y) | 0.00 | |
| UUA(L) | 0.57 | UGG(W) | 0.00 | |
| CAA(Q) | 0.57 | CGA(R) | 0.00 | |
| GGA(G) | 0.36 | AGA(R) | 0.00 | |
| AGA(R) | 0.17 | AGG(R) | 0.00 | |
| Avian | ||||
| Most frequent | GAG(E) | 3.66 | CCG(P) | 6.86 |
| GUG(V) | 3.61 | CCA(P) | 5.26 | |
| GCC(A) | 3.41 | CCU(P) | 5.03 | |
| CAG(Q) | 3.20 | CCC(P) | 4.58 | |
| GAU(D) | 3.19 | GCA(A) | 4.58 | |
| GUU(V) | 3.06 | GAG(E) | 3.89 | |
| GGG(G) | 2.53 | GGU(G) | 3.66 | |
| GAC(D) | 2.51 | GGC(G) | 3.66 | |
| UUG(L) | 2.41 | CAG(Q) | 3.43 | |
| GCU(A) | 2.38 | GCU(A) | 3.20 | |
| GCG(A) | 2.34 | GCC(A) | 3.20 | |
| GGC(G) | 2.31 | CGC(R) | 2.75 | |
| Least frequent | AGG(R) | 0.84 | AAG(K) | 0.46 |
| CUC(L) | 0.83 | UGU(C) | 0.46 | |
| AUC(I) | 0.75 | AGG(R) | 0.46 | |
| UCC(S) | 0.75 | GUG(V) | 0.23 | |
| UCG(S) | 0.72 | ACA(T) | 0.23 | |
| CAA(Q) | 0.71 | UGC(C) | 0.23 | |
| CGA(R) | 0.69 | AGU(S) | 0.23 | |
| AGC(S) | 0.68 | AGA(R) | 0.23 | |
| AGU(S) | 0.66 | UUU(F) | 0.00 | |
| UCA(S) | 0.64 | UAU(Y) | 0.00 | |
| GGA(G) | 0.33 | UAC(Y) | 0.00 | |
| AGA(R) | 0.28 | UGG(W) | 0.00 | |
| Rubivirus | ||||
| Most frequent | GCC(A) | 7.80 | CCC(P) | 10.38 |
| CGC(R) | 6.58 | CCG(P) | 10.21 | |
| GGC(G) | 4.90 | GCC(A) | 8.15 | |
| CUC(L) | 4.55 | GCG(A) | 7.79 | |
| GAG(E) | 4.52 | GAC(D) | 7.70 | |
| GAC(D) | 4.48 | CGC(R) | 6.45 | |
| GCG(A) | 4.37 | GGC(G) | 4.12 | |
| CCC(P) | 3.78 | CCA(P) | 3.49 | |
| ACC(T) | 3.22 | AGC(S) | 2.78 | |
| GUC(V) | 3.13 | GCA(A) | 2.51 | |
| UGC(C) | 2.99 | GUC(V) | 2.42 | |
| CAC(H) | 2.80 | GAG(E) | 2.33 | |
| Least frequent | UAU(Y) | 0.34 | CAU(H) | 0.09 |
| ACA(T) | 0.33 | UUU(F) | 0.00 | |
| UUU(F) | 0.31 | UUC(F) | 0.00 | |
| AGG(R) | 0.30 | UUA(L) | 0.00 | |
| GGA(G) | 0.29 | AUA(I) | 0.00 | |
| UCU(S) | 0.26 | AUG(M) | 0.00 | |
| UCA(S) | 0.25 | UAU(Y) | 0.00 | |
| UGU(C) | 0.24 | AAA(K) | 0.00 | |
| AGA(R) | 0.24 | UGU(C) | 0.00 | |
| CUA(L) | 0.23 | UGG(W) | 0.00 | |
| UUA(L) | 0.13 | AGA(R) | 0.00 | |
| AUA(I) | 0.12 | GGA(G) | 0.00 | |
a
The table lists codons, the amino acid (aa) encoded by the codon (in parentheses), and frequency of use (as a percentage). Codons are listed from most to least frequent. The space in the table separates the 12 most frequently and the 12 least frequently used codons for each genotype. Termination codons have been removed from the table.