53.8%GC3 content

53.6Effective codons (Nc)

247Coding sequences

15/26GC3 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 Axolotl is glutamine: of its 2 synonymous codons, CAG takes 72% of the family. Cysteine 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 Chimpanzee (r = 0.965) and least with M. tuberculosis (r = 0.715). 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, Axolotl leans hardest on CAT (+0.150 against the mean) and avoids CAC most (-0.150). 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	0.320	1.28	GCG	0.112	0.45
Arginine R	AGA	0.318	1.91	CGT	0.056	0.34
Asparagine N	AAC	0.558	1.12	AAT	0.442	0.88
Aspartate D	GAC	0.545	1.09	GAT	0.455	0.91
Cysteine C	TGC	0.509	1.02	TGT	0.491	0.98
Glutamate E	GAG	0.591	1.18	GAA	0.409	0.82
Glutamine Q	CAG	0.715	1.43	CAA	0.285	0.57
Glycine G	GGG	0.321	1.28	GGT	0.167	0.67
Histidine H	CAT	0.587	1.17	CAC	0.413	0.83
Isoleucine I	ATC	0.504	1.51	ATA	0.169	0.51
Leucine L	CTG	0.354	2.12	TTA	0.075	0.45
Lysine K	AAG	0.537	1.07	AAA	0.463	0.93
Phenylalanine F	TTC	0.613	1.23	TTT	0.388	0.78
Proline P	CCA	0.337	1.35	CCG	0.121	0.48
Serine S	AGC	0.273	1.64	TCG	0.039	0.24
Threonine T	ACT	0.348	1.39	ACG	0.091	0.36
Tyrosine Y	TAC	0.642	1.28	TAT	0.358	0.72
Valine V	GTG	0.373	1.49	GTA	0.136	0.54

Full codon usage table

Amino acid	Codon	Frequency	RSCU
Alanine A	GCC	0.3204	1.282
	GCT	0.2872	1.149
	GCA	0.2804	1.122
	GCG	0.1120	0.448
Arginine R	AGA	0.3181	1.909
	AGG	0.3024	1.814
	CGA	0.1219	0.731
	CGC	0.1121	0.673
	CGG	0.0891	0.535
	CGT	0.0563	0.338
Asparagine N	AAC	0.5576	1.115
Asparagine N	AAT	0.4424	0.885
Aspartate D	GAC	0.5451	1.090
Aspartate D	GAT	0.4549	0.910
Cysteine C	TGC	0.5090	1.018
Cysteine C	TGT	0.4910	0.982
Glutamate E	GAG	0.5911	1.182
Glutamate E	GAA	0.4089	0.818
Glutamine Q	CAG	0.7154	1.431
Glutamine Q	CAA	0.2846	0.569
Glycine G	GGG	0.3207	1.283
	GGA	0.3042	1.217
	GGC	0.2085	0.834
	GGT	0.1665	0.666
Histidine H	CAT	0.5866	1.173
Histidine H	CAC	0.4134	0.827
Isoleucine I	ATC	0.5045	1.514
	ATT	0.3264	0.979
	ATA	0.1691	0.507
Leucine L	CTG	0.3541	2.125
	CTC	0.2055	1.233
	CTT	0.1323	0.794
	TTG	0.1289	0.773
	CTA	0.1038	0.623
	TTA	0.0754	0.452
Lysine K	AAG	0.5374	1.075
Lysine K	AAA	0.4626	0.925
Methionine M	ATG	1.0000	1.000
Phenylalanine F	TTC	0.6125	1.225
Phenylalanine F	TTT	0.3875	0.775
Proline P	CCA	0.3365	1.346
	CCT	0.3063	1.225
	CCC	0.2365	0.946
	CCG	0.1208	0.483
Serine S	AGC	0.2725	1.635
	TCC	0.2405	1.443
	TCT	0.1615	0.969
	TCA	0.1579	0.947
	AGT	0.1284	0.770
	TCG	0.0392	0.235
Threonine T	ACT	0.3481	1.392
	ACA	0.3080	1.232
	ACC	0.2529	1.012
	ACG	0.0911	0.364
Tryptophan W	TGG	1.0000	1.000
Tyrosine Y	TAC	0.6422	1.284
Tyrosine Y	TAT	0.3578	0.716
Valine V	GTG	0.3727	1.491
	GTC	0.2683	1.073
	GTT	0.2234	0.894
	GTA	0.1356	0.542

Provenance

Computed from 247 RefSeq coding sequences for Ambystoma mexicanum, 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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