53.7%GC3 content

55.5Effective codons (Nc)

250Coding sequences

16/26GC3 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 Cattle is glutamine: of its 2 synonymous codons, CAG takes 72% of the family. Aspartate sits at the other end, spread almost evenly across its options (evenness 1.00 against 0.86 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 Horse (r = 0.996) and least with M. tuberculosis (r = 0.744). 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, Cattle leans hardest on GAA (+0.033 against the mean) and avoids CCG most (-0.053). 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	0.383	1.53	GCG	0.099	0.40
Arginine R	AGA	0.230	1.38	CGT	0.078	0.47
Asparagine N	AAC	0.508	1.02	AAT	0.492	0.98
Aspartate D	GAC	0.508	1.02	GAT	0.492	0.98
Cysteine C	TGC	0.549	1.10	TGT	0.451	0.90
Glutamate E	GAG	0.520	1.04	GAA	0.480	0.96
Glutamine Q	CAG	0.718	1.44	CAA	0.282	0.56
Glycine G	GGC	0.312	1.25	GGT	0.172	0.69
Histidine H	CAC	0.558	1.12	CAT	0.442	0.88
Isoleucine I	ATC	0.447	1.34	ATA	0.190	0.57
Leucine L	CTG	0.355	2.13	CTA	0.068	0.41
Lysine K	AAG	0.532	1.06	AAA	0.468	0.94
Phenylalanine F	TTC	0.514	1.03	TTT	0.486	0.97
Proline P	CCC	0.302	1.21	CCG	0.104	0.42
Serine S	TCT	0.209	1.25	TCG	0.053	0.32
Threonine T	ACC	0.327	1.31	ACG	0.119	0.48
Tyrosine Y	TAC	0.542	1.08	TAT	0.458	0.92
Valine V	GTG	0.437	1.75	GTA	0.126	0.50

Full codon usage table

Amino acid	Codon	Frequency	RSCU
Alanine A	GCC	0.3826	1.530
	GCT	0.2734	1.094
	GCA	0.2446	0.978
	GCG	0.0993	0.397
Arginine R	AGA	0.2295	1.377
	AGG	0.2068	1.241
	CGG	0.1940	1.164
	CGC	0.1700	1.020
	CGA	0.1221	0.733
	CGT	0.0777	0.466
Asparagine N	AAC	0.5081	1.016
Asparagine N	AAT	0.4919	0.984
Aspartate D	GAC	0.5079	1.016
Aspartate D	GAT	0.4921	0.984
Cysteine C	TGC	0.5491	1.098
Cysteine C	TGT	0.4509	0.902
Glutamate E	GAG	0.5198	1.040
Glutamate E	GAA	0.4802	0.960
Glutamine Q	CAG	0.7178	1.436
Glutamine Q	CAA	0.2822	0.564
Glycine G	GGC	0.3121	1.248
	GGA	0.2728	1.091
	GGG	0.2428	0.971
	GGT	0.1723	0.689
Histidine H	CAC	0.5583	1.117
Histidine H	CAT	0.4417	0.883
Isoleucine I	ATC	0.4469	1.341
	ATT	0.3627	1.088
	ATA	0.1904	0.571
Leucine L	CTG	0.3550	2.130
	CTC	0.1829	1.097
	CTT	0.1521	0.913
	TTG	0.1403	0.842
	TTA	0.1021	0.613
	CTA	0.0676	0.406
Lysine K	AAG	0.5322	1.064
Lysine K	AAA	0.4678	0.936
Methionine M	ATG	1.0000	1.000
Phenylalanine F	TTC	0.5139	1.028
Phenylalanine F	TTT	0.4861	0.972
Proline P	CCC	0.3017	1.207
	CCT	0.2994	1.198
	CCA	0.2945	1.178
	CCG	0.1043	0.417
Serine S	TCT	0.2086	1.252
	AGC	0.2078	1.247
	TCC	0.1924	1.154
	AGT	0.1721	1.033
	TCA	0.1661	0.997
	TCG	0.0530	0.318
Threonine T	ACC	0.3265	1.306
	ACA	0.2873	1.149
	ACT	0.2672	1.069
	ACG	0.1189	0.476
Tryptophan W	TGG	1.0000	1.000
Tyrosine Y	TAC	0.5421	1.084
Tyrosine Y	TAT	0.4579	0.916
Valine V	GTG	0.4372	1.749
	GTC	0.2334	0.934
	GTT	0.2033	0.813
	GTA	0.1261	0.504

Provenance

Computed from 250 RefSeq coding sequences for Bos taurus, 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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