53.0%GC3 content

55.2Effective codons (Nc)

249Coding sequences

18/26GC3 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 Horse is glutamine: of its 2 synonymous codons, CAG takes 71% of the family. Aspartate sits at the other end, spread almost evenly across its options (evenness 1.00 against 0.87 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 Koala (r = 0.997) and least with M. tuberculosis (r = 0.722). 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, Horse leans hardest on TGT (+0.049 against the mean) and avoids CCG most (-0.063). 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	0.378	1.51	GCG	0.098	0.39
Arginine R	AGA	0.246	1.47	CGT	0.083	0.50
Asparagine N	AAC	0.507	1.01	AAT	0.493	0.99
Aspartate D	GAT	0.501	1.00	GAC	0.499	1.00
Cysteine C	TGT	0.509	1.02	TGC	0.490	0.98
Glutamate E	GAG	0.545	1.09	GAA	0.455	0.91
Glutamine Q	CAG	0.706	1.41	CAA	0.294	0.59
Glycine G	GGC	0.323	1.29	GGT	0.175	0.70
Histidine H	CAC	0.522	1.04	CAT	0.478	0.96
Isoleucine I	ATC	0.435	1.31	ATA	0.194	0.58
Leucine L	CTG	0.358	2.15	CTA	0.068	0.41
Lysine K	AAG	0.544	1.09	AAA	0.456	0.91
Phenylalanine F	TTT	0.504	1.01	TTC	0.496	0.99
Proline P	CCT	0.314	1.25	CCG	0.095	0.38
Serine S	AGC	0.229	1.37	TCG	0.047	0.28
Threonine T	ACC	0.337	1.35	ACG	0.110	0.44
Tyrosine Y	TAC	0.518	1.04	TAT	0.482	0.96
Valine V	GTG	0.424	1.70	GTA	0.127	0.51

Full codon usage table

Amino acid	Codon	Frequency	RSCU
Alanine A	GCC	0.3775	1.510
	GCT	0.2960	1.184
	GCA	0.2284	0.914
	GCG	0.0981	0.392
Arginine R	AGA	0.2456	1.474
	AGG	0.2305	1.383
	CGG	0.1753	1.052
	CGC	0.1628	0.977
	CGA	0.1032	0.619
	CGT	0.0826	0.496
Asparagine N	AAC	0.5073	1.015
Asparagine N	AAT	0.4927	0.985
Aspartate D	GAT	0.5013	1.003
Aspartate D	GAC	0.4987	0.997
Cysteine C	TGT	0.5095	1.019
Cysteine C	TGC	0.4905	0.981
Glutamate E	GAG	0.5447	1.089
Glutamate E	GAA	0.4553	0.911
Glutamine Q	CAG	0.7061	1.412
Glutamine Q	CAA	0.2939	0.588
Glycine G	GGC	0.3234	1.294
	GGA	0.2708	1.083
	GGG	0.2313	0.925
	GGT	0.1746	0.698
Histidine H	CAC	0.5217	1.043
Histidine H	CAT	0.4783	0.957
Isoleucine I	ATC	0.4351	1.305
	ATT	0.3714	1.114
	ATA	0.1936	0.581
Leucine L	CTG	0.3577	2.146
	CTC	0.1844	1.106
	TTG	0.1466	0.880
	CTT	0.1451	0.871
	TTA	0.0983	0.590
	CTA	0.0678	0.407
Lysine K	AAG	0.5439	1.088
Lysine K	AAA	0.4561	0.912
Methionine M	ATG	1.0000	1.000
Phenylalanine F	TTT	0.5040	1.008
Phenylalanine F	TTC	0.4960	0.992
Proline P	CCT	0.3137	1.255
	CCC	0.3051	1.220
	CCA	0.2865	1.146
	CCG	0.0946	0.378
Serine S	AGC	0.2290	1.374
	TCT	0.2085	1.251
	TCC	0.2040	1.224
	AGT	0.1684	1.010
	TCA	0.1429	0.857
	TCG	0.0471	0.283
Threonine T	ACC	0.3371	1.348
	ACT	0.2764	1.106
	ACA	0.2762	1.105
	ACG	0.1103	0.441
Tryptophan W	TGG	1.0000	1.000
Tyrosine Y	TAC	0.5183	1.037
Tyrosine Y	TAT	0.4817	0.963
Valine V	GTG	0.4238	1.695
	GTC	0.2450	0.980
	GTT	0.2046	0.818
	GTA	0.1266	0.506

Provenance

Computed from 249 RefSeq coding sequences for Equus caballus, 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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