60.2%GC3 content

52.5Effective codons (Nc)

250Coding sequences

6/26GC3 rank here

Scope: nuclear genes only

NCBI table 1 (Standard). Do not apply these frequencies to mitochondrial genes, where AGA, AGG, ATA and TGA carry different meanings. The four reassignments.

What distinguishes this table

The most constrained choice in Red fox is glutamine: of its 2 synonymous codons, CAG takes 74% of the family. Aspartate sits at the other end, spread almost evenly across its options (evenness 0.99 against 0.83 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 Rhesus macaque (r = 0.997) and least with Ferret (r = 0.805). 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, Red fox leans hardest on CAC (+0.071 against the mean) and avoids CAT most (-0.071). Those two are the codons that most distinguish this table from the others.

Preferred and avoided codons

Amino acid	Preferred	Freq	RSCU	Avoided	Freq	RSCU
Alanine A	GCC	0.451	1.80	GCG	0.140	0.56
Arginine R	AGG	0.218	1.31	CGT	0.068	0.41
Asparagine N	AAC	0.547	1.09	AAT	0.453	0.91
Aspartate D	GAC	0.544	1.09	GAT	0.456	0.91
Cysteine C	TGC	0.578	1.16	TGT	0.422	0.84
Glutamate E	GAG	0.602	1.20	GAA	0.398	0.80
Glutamine Q	CAG	0.741	1.48	CAA	0.259	0.52
Glycine G	GGC	0.363	1.45	GGT	0.165	0.66
Histidine H	CAC	0.635	1.27	CAT	0.365	0.73
Isoleucine I	ATC	0.522	1.57	ATA	0.147	0.44
Leucine L	CTG	0.431	2.59	TTA	0.057	0.34
Lysine K	AAG	0.590	1.18	AAA	0.410	0.82
Phenylalanine F	TTC	0.558	1.12	TTT	0.442	0.88
Proline P	CCC	0.368	1.47	CCG	0.139	0.56
Serine S	AGC	0.251	1.50	TCG	0.069	0.41
Threonine T	ACC	0.392	1.57	ACG	0.151	0.60
Tyrosine Y	TAC	0.579	1.16	TAT	0.421	0.84
Valine V	GTG	0.498	1.99	GTA	0.101	0.41

Full codon usage table

Amino acid	Codon	Frequency	RSCU
Alanine A	GCC	0.4511	1.804
	GCT	0.2333	0.933
	GCA	0.1752	0.701
	GCG	0.1403	0.561
Arginine R	AGG	0.2184	1.310
	AGA	0.2153	1.292
	CGG	0.2124	1.274
	CGC	0.1980	1.188
	CGA	0.0876	0.526
	CGT	0.0682	0.409
Asparagine N	AAC	0.5468	1.094
Asparagine N	AAT	0.4532	0.906
Aspartate D	GAC	0.5444	1.089
Aspartate D	GAT	0.4556	0.911
Cysteine C	TGC	0.5784	1.157
Cysteine C	TGT	0.4216	0.843
Glutamate E	GAG	0.6016	1.203
Glutamate E	GAA	0.3984	0.797
Glutamine Q	CAG	0.7408	1.482
Glutamine Q	CAA	0.2592	0.518
Glycine G	GGC	0.3633	1.453
	GGG	0.2484	0.994
	GGA	0.2232	0.893
	GGT	0.1651	0.660
Histidine H	CAC	0.6350	1.270
Histidine H	CAT	0.3650	0.730
Isoleucine I	ATC	0.5224	1.567
	ATT	0.3307	0.992
	ATA	0.1469	0.441
Leucine L	CTG	0.4311	2.587
	CTC	0.2059	1.235
	TTG	0.1236	0.742
	CTT	0.1194	0.716
	CTA	0.0629	0.377
	TTA	0.0572	0.343
Lysine K	AAG	0.5898	1.180
Lysine K	AAA	0.4102	0.820
Methionine M	ATG	1.0000	1.000
Phenylalanine F	TTC	0.5576	1.115
Phenylalanine F	TTT	0.4424	0.885
Proline P	CCC	0.3678	1.471
	CCT	0.2481	0.992
	CCA	0.2452	0.981
	CCG	0.1390	0.556
Serine S	AGC	0.2505	1.503
	TCC	0.2320	1.392
	TCT	0.1780	1.068
	TCA	0.1446	0.868
	AGT	0.1258	0.755
	TCG	0.0691	0.415
Threonine T	ACC	0.3916	1.566
	ACA	0.2295	0.918
	ACT	0.2282	0.913
	ACG	0.1508	0.603
Tryptophan W	TGG	1.0000	1.000
Tyrosine Y	TAC	0.5793	1.159
Tyrosine Y	TAT	0.4207	0.841
Valine V	GTG	0.4978	1.991
	GTC	0.2468	0.987
	GTT	0.1541	0.616
	GTA	0.1013	0.405

Provenance

Computed from 250 RefSeq coding sequences for Vulpes vulpes, 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.

Use this table

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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