Macaca mulatta
Synonymous codon usage in Rhesus macaque (Macaca mulatta), computed from 248 RefSeq coding sequences. Third positions are 59.5% G or C, above the median across the 26 organisms catalogued on this site, making it 7th of 26 by that measure. An effective number of codons of 52.9 indicates weak bias: the closer that value sits to 61, the more evenly an organism spreads its synonymous choices.
NCBI table 1 (Standard). Do not apply these frequencies to mitochondrial genes, where AGA, AGG, ATA and TGA carry different meanings. The four reassignments.
The most constrained choice in Rhesus macaque is glutamine: of its 2 synonymous codons, CAG takes 75% of the family. Phenylalanine sits at the other end, spread almost evenly across its options (evenness 0.99 against 0.81 for glutamine). Those two families are where a codon-optimizer has the most and the least room to move.
Measured across all 59 sense codons, this table correlates most closely with Pig (r = 0.998) and least with Ferret (r = 0.811). A sequence tuned for the first would need little adjustment to move here; one tuned for the second would need a great deal.
Relative to the average across the 26 organisms on this site, Rhesus macaque leans hardest on TGC (+0.054 against the mean) and avoids TGT most (-0.054). Those two are the codons that most distinguish this table from the others.
| Amino acid | Preferred | Freq | RSCU | Avoided | Freq | RSCU |
|---|---|---|---|---|---|---|
| Alanine A | GCC | 0.432 | 1.73 | GCG | 0.119 | 0.48 |
| Arginine R | CGG | 0.216 | 1.30 | CGT | 0.078 | 0.47 |
| Asparagine N | AAC | 0.567 | 1.13 | AAT | 0.433 | 0.87 |
| Aspartate D | GAC | 0.569 | 1.14 | GAT | 0.431 | 0.86 |
| Cysteine C | TGC | 0.594 | 1.19 | TGT | 0.406 | 0.81 |
| Glutamate E | GAG | 0.600 | 1.20 | GAA | 0.400 | 0.80 |
| Glutamine Q | CAG | 0.751 | 1.50 | CAA | 0.249 | 0.50 |
| Glycine G | GGC | 0.349 | 1.39 | GGT | 0.160 | 0.64 |
| Histidine H | CAC | 0.611 | 1.22 | CAT | 0.389 | 0.78 |
| Isoleucine I | ATC | 0.499 | 1.50 | ATA | 0.161 | 0.48 |
| Leucine L | CTG | 0.428 | 2.57 | CTA | 0.066 | 0.40 |
| Lysine K | AAG | 0.589 | 1.18 | AAA | 0.411 | 0.82 |
| Phenylalanine F | TTC | 0.543 | 1.09 | TTT | 0.457 | 0.91 |
| Proline P | CCC | 0.349 | 1.39 | CCG | 0.131 | 0.52 |
| Serine S | AGC | 0.253 | 1.52 | TCG | 0.058 | 0.35 |
| Threonine T | ACC | 0.367 | 1.47 | ACG | 0.125 | 0.50 |
| Tyrosine Y | TAC | 0.591 | 1.18 | TAT | 0.409 | 0.82 |
| Valine V | GTG | 0.480 | 1.92 | GTA | 0.100 | 0.40 |
| Amino acid | Codon | Frequency | RSCU | Share of family |
|---|---|---|---|---|
| Alanine A | GCC | 0.4323 | 1.729 | |
| GCT | 0.2374 | 0.950 | ||
| GCA | 0.2114 | 0.846 | ||
| GCG | 0.1189 | 0.476 | ||
| Arginine R | CGG | 0.2165 | 1.299 | |
| CGC | 0.2102 | 1.261 | ||
| AGG | 0.2074 | 1.244 | ||
| AGA | 0.1808 | 1.085 | ||
| CGA | 0.1074 | 0.644 | ||
| CGT | 0.0777 | 0.466 | ||
| Asparagine N | AAC | 0.5674 | 1.135 | |
| AAT | 0.4326 | 0.865 | ||
| Aspartate D | GAC | 0.5688 | 1.138 | |
| GAT | 0.4312 | 0.862 | ||
| Cysteine C | TGC | 0.5942 | 1.188 | |
| TGT | 0.4058 | 0.812 | ||
| Glutamate E | GAG | 0.5999 | 1.200 | |
| GAA | 0.4001 | 0.800 | ||
| Glutamine Q | CAG | 0.7507 | 1.501 | |
| CAA | 0.2493 | 0.499 | ||
| Glycine G | GGC | 0.3486 | 1.394 | |
| GGG | 0.2642 | 1.057 | ||
| GGA | 0.2274 | 0.910 | ||
| GGT | 0.1597 | 0.639 | ||
| Histidine H | CAC | 0.6106 | 1.221 | |
| CAT | 0.3894 | 0.779 | ||
| Isoleucine I | ATC | 0.4986 | 1.496 | |
| ATT | 0.3403 | 1.021 | ||
| ATA | 0.1611 | 0.483 | ||
| Leucine L | CTG | 0.4279 | 2.567 | |
| CTC | 0.2024 | 1.214 | ||
| TTG | 0.1158 | 0.695 | ||
| CTT | 0.1158 | 0.695 | ||
| TTA | 0.0722 | 0.433 | ||
| CTA | 0.0661 | 0.397 | ||
| Lysine K | AAG | 0.5894 | 1.179 | |
| AAA | 0.4106 | 0.821 | ||
| Methionine M | ATG | 1.0000 | 1.000 | |
| Phenylalanine F | TTC | 0.5433 | 1.087 | |
| TTT | 0.4567 | 0.913 | ||
| Proline P | CCC | 0.3487 | 1.395 | |
| CCT | 0.2705 | 1.082 | ||
| CCA | 0.2501 | 1.000 | ||
| CCG | 0.1306 | 0.522 | ||
| Serine S | AGC | 0.2529 | 1.517 | |
| TCC | 0.2331 | 1.399 | ||
| TCT | 0.1791 | 1.075 | ||
| AGT | 0.1391 | 0.835 | ||
| TCA | 0.1377 | 0.826 | ||
| TCG | 0.0581 | 0.349 | ||
| Threonine T | ACC | 0.3675 | 1.470 | |
| ACA | 0.2740 | 1.096 | ||
| ACT | 0.2332 | 0.933 | ||
| ACG | 0.1253 | 0.501 | ||
| Tryptophan W | TGG | 1.0000 | 1.000 | |
| Tyrosine Y | TAC | 0.5913 | 1.183 | |
| TAT | 0.4087 | 0.817 | ||
| Valine V | GTG | 0.4797 | 1.919 | |
| GTC | 0.2593 | 1.037 | ||
| GTT | 0.1609 | 0.644 | ||
| GTA | 0.1002 | 0.401 |
Computed from 248 RefSeq coding sequences for Macaca mulatta, sampled and counted codon by codon. Frequencies are relative within each amino acid family. Page generated 2026-08-09.
The full derivation of GC3, RSCU and the effective number of codons, along with the limits of each, is set out once in the methods note rather than repeated on every page.
Nucleora codon-optimizes a coding sequence against this table directly, then folds the result and reports where structure would interfere with expression.
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