45.2%GC3 content

55.6Effective codons (Nc)

250Coding sequences

23/26GC3 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 California condor is threonine: of its 4 synonymous codons, ACA takes 37% of the family. Tyrosine sits at the other end, spread almost evenly across its options (evenness 1.00 against 0.92 for threonine). 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 Asian elephant (r = 0.988) and least with M. tuberculosis (r = 0.553). 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, California condor leans hardest on GAT (+0.113 against the mean) and avoids ATC most (-0.147). 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	GCA	0.329	1.32	GCG	0.094	0.38
Arginine R	AGA	0.320	1.92	CGT	0.093	0.56
Asparagine N	AAT	0.547	1.09	AAC	0.453	0.91
Aspartate D	GAT	0.580	1.16	GAC	0.420	0.84
Cysteine C	TGT	0.516	1.03	TGC	0.484	0.97
Glutamate E	GAA	0.556	1.11	GAG	0.444	0.89
Glutamine Q	CAG	0.648	1.30	CAA	0.352	0.70
Glycine G	GGA	0.330	1.32	GGT	0.192	0.77
Histidine H	CAT	0.526	1.05	CAC	0.474	0.95
Isoleucine I	ATT	0.424	1.27	ATA	0.246	0.74
Leucine L	CTG	0.297	1.78	CTA	0.087	0.52
Lysine K	AAA	0.542	1.08	AAG	0.458	0.92
Phenylalanine F	TTT	0.549	1.10	TTC	0.451	0.90
Proline P	CCT	0.348	1.39	CCG	0.116	0.47
Serine S	TCT	0.220	1.32	TCG	0.038	0.23
Threonine T	ACA	0.374	1.49	ACG	0.086	0.34
Tyrosine Y	TAT	0.509	1.02	TAC	0.491	0.98
Valine V	GTG	0.356	1.43	GTC	0.186	0.75

Full codon usage table

Amino acid	Codon	Frequency	RSCU
Alanine A	GCA	0.3289	1.316
	GCT	0.3179	1.272
	GCC	0.2590	1.036
	GCG	0.0942	0.377
Arginine R	AGA	0.3202	1.921
	AGG	0.2331	1.399
	CGG	0.1250	0.750
	CGC	0.1210	0.726
	CGA	0.1073	0.644
	CGT	0.0934	0.560
Asparagine N	AAT	0.5468	1.094
Asparagine N	AAC	0.4532	0.906
Aspartate D	GAT	0.5802	1.160
Aspartate D	GAC	0.4198	0.840
Cysteine C	TGT	0.5156	1.031
Cysteine C	TGC	0.4844	0.969
Glutamate E	GAA	0.5557	1.111
Glutamate E	GAG	0.4443	0.889
Glutamine Q	CAG	0.6484	1.297
Glutamine Q	CAA	0.3516	0.703
Glycine G	GGA	0.3296	1.318
	GGC	0.2634	1.054
	GGG	0.2153	0.861
	GGT	0.1916	0.766
Histidine H	CAT	0.5256	1.051
Histidine H	CAC	0.4744	0.949
Isoleucine I	ATT	0.4240	1.272
	ATC	0.3297	0.989
	ATA	0.2463	0.739
Leucine L	CTG	0.2966	1.780
	CTT	0.1823	1.094
	TTG	0.1735	1.041
	CTC	0.1429	0.857
	TTA	0.1176	0.706
	CTA	0.0872	0.523
Lysine K	AAA	0.5422	1.084
Lysine K	AAG	0.4578	0.916
Methionine M	ATG	1.0000	1.000
Phenylalanine F	TTT	0.5493	1.099
Phenylalanine F	TTC	0.4507	0.901
Proline P	CCT	0.3482	1.393
	CCA	0.3400	1.360
	CCC	0.1955	0.782
	CCG	0.1163	0.465
Serine S	TCT	0.2202	1.321
	AGC	0.2132	1.279
	AGT	0.1910	1.146
	TCA	0.1861	1.117
	TCC	0.1511	0.907
	TCG	0.0384	0.230
Threonine T	ACA	0.3737	1.495
	ACT	0.3218	1.287
	ACC	0.2189	0.876
	ACG	0.0856	0.342
Tryptophan W	TGG	1.0000	1.000
Tyrosine Y	TAT	0.5094	1.019
Tyrosine Y	TAC	0.4906	0.981
Valine V	GTG	0.3564	1.426
	GTT	0.2665	1.066
	GTA	0.1907	0.763
	GTC	0.1863	0.745

Provenance

Computed from 250 RefSeq coding sequences for Gymnogyps californianus, 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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