Table 1.
Relative synonymous codon usage (RSCU) analysis of the various codons of all coding sequences (G, F, M, N, L, P, C, V, and W) belonging to six genes of Nipah virus (NiV) genome.
| S. no. | Amino acid | Codons | Coding sequences (CDSs) |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| C | F | G | M | N | P | L | W | V | |||
| (1) | Phenylalanine (F) | UUU | 0.50 | 1.56 | 0.94 | 0.91 | 1.13 | 1.16 | 1.17 | 1.47 | 1.45 |
| UUC | 1.50 | 0.44 | 1.06 | 1.09 | 0.87 | 0.84 | 0.83 | 0.53 | 0.55 | ||
| (2) | Leucine (L) | UUA | 1.09 | 1.34 | 0.94 | 0.24 | 0.46 | 0.47 | 1.46 | 0.25 | 0.24 |
| UUG | 1.91 | 1.20 | 1.13 | 1.19 | 0.96 | 1.17 | 1.25 | 1.13 | 1.06 | ||
| CUU | 0.55 | 0.90 | 0.87 | 1.22 | 0.99 | 1.27 | 1.13 | 0.84 | 0.90 | ||
| CUC | 0.55 | 0.73 | 0.21 | 1.41 | 1.82 | 0.44 | 0.54 | 0.49 | 0.49 | ||
| CUA | 0.82 | 0.88 | 1.37 | 0.86 | 1.14 | 0.89 | 0.95 | 1.47 | 1.46 | ||
| CUG | 1.09 | 0.97 | 1.48 | 1.09 | 0.63 | 1.75 | 0.67 | 1.82 | 1.85 | ||
| (3) | Isoleucine (I) | AUU | 0.63 | 1.15 | 0.90 | 1.39 | 0.86 | 1.48 | 0.90 | 1.60 | 1.57 |
| AUC | 1.97 | 0.87 | 1.10 | 1.19 | 1.29 | 0.83 | 0.85 | 0.72 | 0.78 | ||
| AUA | 0.39 | 0.97 | 1.00 | 0.42 | 0.86 | 0.70 | 1.25 | 0.68 | 0.66 | ||
| (4) | Valine (V) | GUU | 0.50 | 1.62 | 1.47 | 1.78 | 1.43 | 1.70 | 1.25 | 1.71 | 1.63 |
| GUC | 0.50 | 0.92 | 0.64 | 0.64 | 0.95 | 0.77 | 0.69 | 0.49 | 0.55 | ||
| GUA | 1.32 | 0.89 | 1.23 | 0.76 | 0.54 | 0.67 | 1.30 | 0.76 | 0.79 | ||
| GUG | 1.68 | 0.56 | 0.66 | 0.82 | 1.08 | 0.85 | 0.75 | 1.04 | 1.02 | ||
| (5) | Serine (S) | UCU | 0.00 | 1.03 | 1.38 | 1.47 | 1.03 | 1.45 | 1.57 | 1.49 | 1.48 |
| UCC | 0.00 | 0.21 | 0.40 | 0.78 | 0.24 | 0.68 | 0.71 | 0.53 | 0.55 | ||
| UCA | 4.00 | 1.67 | 1.88 | 1.30 | 1.66 | 1.90 | 1.97 | 1.66 | 1.69 | ||
| UCG | 0.00 | 0.47 | 0.13 | 0.00 | 0.06 | 0.48 | 0.31 | 0.32 | 0.31 | ||
| AGU | 2.00 | 1.13 | 1.04 | 1.61 | 1.93 | 0.79 | 1.00 | 0.93 | 0.91 | ||
| AGC | 0.00 | 1.49 | 1.17 | 0.83 | 1.07 | 0.71 | 0.45 | 1.07 | 1.05 | ||
| (6) | Proline (P) | CCU | 0.75 | 1.93 | 1.79 | 1.44 | 1.16 | 1.32 | 1.89 | 1.35 | 1.29 |
| CCC | 0.46 | 0.62 | 0.76 | 0.30 | 0.50 | 0.99 | 0.63 | 0.98 | 1.02 | ||
| CCA | 1.86 | 0.94 | 1.20 | 1.66 | 1.50 | 1.11 | 1.05 | 1.24 | 1.18 | ||
| CCG | 0.93 | 0.51 | 0.25 | 0.60 | 0.84 | 0.57 | 0.43 | 0.44 | 0.50 | ||
| (7) | Threonine (T) | ACU | 1.00 | 1.12 | 1.02 | 1.00 | 1.80 | 1.80 | 1.49 | 1.80 | 1.78 |
| ACC | 1.12 | 0.49 | 1.16 | 1.33 | 0.84 | 0.74 | 0.52 | 0.67 | 0.62 | ||
| ACA | 1.21 | 2.11 | 1.63 | 1.63 | 1.36 | 1.32 | 1.70 | 1.53 | 1.60 | ||
| ACG | 0.67 | 0.29 | 0.20 | 0.04 | 0.00 | 0.14 | 0.30 | 0.00 | 0.00 | ||
| (8) | Alanine (A) | GCU | 0.24 | 1.39 | 1.30 | 1.79 | 1.77 | 1.07 | 1.53 | 1.30 | 1.31 |
| GCC | 1.76 | 0.65 | 0.51 | 1.27 | 0.62 | 0.32 | 0.70 | 0.29 | 0.35 | ||
| GCA | 2.00 | 1.86 | 1.63 | 0.88 | 1.47 | 2.13 | 1.45 | 2.41 | 2.34 | ||
| GCG | 0.00 | 0.10 | 0.56 | 0.07 | 0.14 | 0.48 | 0.32 | 0.00 | 0.00 | ||
| (9) | Tyrosine (Y) | UAU | 1.33 | 1.30 | 0.96 | 0.76 | 1.36 | 0.95 | 1.24 | 0.73 | 0.71 |
| UAC | 0.67 | 0.70 | 1.04 | 1.24 | 0.64 | 1.05 | 0.76 | 1.27 | 1.29 | ||
| (10) | Histidine (H) | CAU | 2.00 | 1.69 | 0.93 | 1.01 | 1.00 | 0.95 | 1.25 | 1.20 | 1.35 |
| CAC | 0.00 | 0.31 | 1.07 | 0.99 | 1.00 | 1.05 | 0.75 | 0.80 | 0.65 | ||
| (11) | Glutamine (Q) | CAA | 0.83 | 1.16 | 1.31 | 0.87 | 1.15 | 1.23 | 1.39 | 1.24 | 1.23 |
| CAG | 1.17 | 0.84 | 0.69 | 1.13 | 0.85 | 0.77 | 0.61 | 0.76 | 0.77 | ||
| (12) | Asparagine (N) | AAU | 0.67 | 1.14 | 1.47 | 0.94 | 1.22 | 1.23 | 1.35 | 1.00 | 1.00 |
| AAC | 1.33 | 0.86 | 0.53 | 1.06 | 0.78 | 0.77 | 0.65 | 1.00 | 1.00 | ||
| (13) | Lysine (K) | AAA | 0.88 | 1.19 | 1.36 | 0.84 | 1.08 | 1.12 | 1.20 | 1.20 | 1.18 |
| AAG | 1.12 | 0.81 | 0.64 | 1.16 | 0.92 | 0.88 | 0.80 | 0.80 | 0.82 | ||
| (14) | Aspartic acid (D) | GAU | 1.50 | 1.14 | 0.86 | 1.57 | 1.03 | 1.26 | 1.33 | 1.31 | 1.32 |
| GAC | 0.50 | 0.86 | 1.14 | 0.43 | 0.97 | 0.74 | 0.67 | 0.69 | 0.68 | ||
| (15) | Glutamic acid (E) | GAA | 0.87 | 1.09 | 1.02 | 0.69 | 1.18 | 1.25 | 1.13 | 1.20 | 1.24 |
| GAG | 1.13 | 0.91 | 0.98 | 1.31 | 0.82 | 0.75 | 0.87 | 0.80 | 0.76 | ||
| (16) | Cysteine (C) | UGU | 1.13 | 1.14 | 1.24 | 1.87 | 0.00 | 1.18 | 1.33 | 1.09 | 1.13 |
| UGC | 0.87 | 0.86 | 0.76 | 0.13 | 0.00 | 0.82 | 0.67 | 0.91 | 0.87 | ||
| (17) | Arginine (R) | CGU | 0.00 | 0.00 | 0.58 | 0.61 | 0.32 | 0.38 | 0.56 | 0.60 | 0.64 |
| CGC | 0.00 | 0.00 | 0.00 | 0.27 | 0.00 | 0.39 | 0.02 | 0.00 | 0.00 | ||
| CGA | 0.55 | 1.03 | 0.49 | 0.71 | 0.29 | 0.86 | 0.56 | 1.25 | 1.18 | ||
| CGG | 0.00 | 0.04 | 0.10 | 0.39 | 0.27 | 0.52 | 0.07 | 0.50 | 0.58 | ||
| AGA | 3.47 | 3.02 | 3.68 | 2.24 | 3.50 | 2.92 | 3.33 | 2.35 | 2.39 | ||
| AGG | 1.98 | 1.90 | 1.16 | 1.78 | 1.63 | 0.92 | 1.46 | 1.30 | 1.21 | ||
| (18) | Glycine (G) | GGU | 0.57 | 1.17 | 0.96 | 0.97 | 0.61 | 0.52 | 1.12 | 0.29 | 0.32 |
| GGC | 0.00 | 0.37 | 0.32 | 0.82 | 0.86 | 0.60 | 0.41 | 0.73 | 0.69 | ||
| GGA | 0.94 | 1.21 | 1.63 | 1.25 | 1.73 | 2.08 | 1.24 | 2.43 | 2.47 | ||
| GGG | 2.49 | 1.25 | 1.08 | 0.96 | 0.80 | 0.80 | 1.24 | 0.55 | 0.52 | ||
The values of preferred codon for different coding sequences have been shown bold and highlighted.