53.0%GC3 content

54.5Effective codons (Nc)

241Coding sequences

17/26GC3 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 Chimpanzee is glutamine: of its 2 synonymous codons, CAG takes 74% of the family. Cysteine sits at the other end, spread almost evenly across its options (evenness 1.00 against 0.82 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 = 0.992) and least with M. tuberculosis (r = 0.721). 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, Chimpanzee leans hardest on TAT (+0.085 against the mean) and avoids TAC most (-0.085). 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	0.366	1.46	GCG	0.119	0.47
Arginine R	AGA	0.273	1.64	CGT	0.078	0.47
Asparagine N	AAT	0.524	1.05	AAC	0.476	0.95
Aspartate D	GAT	0.517	1.03	GAC	0.482	0.96
Cysteine C	TGC	0.512	1.02	TGT	0.488	0.98
Glutamate E	GAG	0.588	1.18	GAA	0.412	0.82
Glutamine Q	CAG	0.743	1.49	CAA	0.257	0.51
Glycine G	GGC	0.295	1.18	GGT	0.199	0.79
Histidine H	CAT	0.520	1.04	CAC	0.480	0.96
Isoleucine I	ATC	0.450	1.35	ATA	0.195	0.58
Leucine L	CTG	0.401	2.41	CTA	0.065	0.39
Lysine K	AAG	0.560	1.12	AAA	0.440	0.88
Phenylalanine F	TTC	0.550	1.10	TTT	0.450	0.90
Proline P	CCA	0.329	1.32	CCG	0.105	0.42
Serine S	AGC	0.242	1.45	TCG	0.045	0.27
Threonine T	ACC	0.329	1.32	ACG	0.132	0.53
Tyrosine Y	TAT	0.529	1.06	TAC	0.471	0.94
Valine V	GTG	0.432	1.73	GTA	0.133	0.53

Full codon usage table

Amino acid	Codon	Frequency	RSCU
Alanine A	GCC	0.3657	1.463
	GCA	0.2655	1.062
	GCT	0.2501	1.000
	GCG	0.1187	0.475
Arginine R	AGA	0.2732	1.639
	AGG	0.2230	1.338
	CGG	0.1833	1.100
	CGC	0.1480	0.888
	CGA	0.0949	0.569
	CGT	0.0776	0.466
Asparagine N	AAT	0.5236	1.047
Asparagine N	AAC	0.4764	0.953
Aspartate D	GAT	0.5175	1.035
Aspartate D	GAC	0.4825	0.965
Cysteine C	TGC	0.5118	1.024
Cysteine C	TGT	0.4882	0.976
Glutamate E	GAG	0.5883	1.177
Glutamate E	GAA	0.4117	0.823
Glutamine Q	CAG	0.7426	1.485
Glutamine Q	CAA	0.2574	0.515
Glycine G	GGC	0.2947	1.179
	GGA	0.2727	1.091
	GGG	0.2340	0.936
	GGT	0.1987	0.795
Histidine H	CAT	0.5198	1.040
Histidine H	CAC	0.4802	0.960
Isoleucine I	ATC	0.4504	1.351
	ATT	0.3550	1.065
	ATA	0.1946	0.584
Leucine L	CTG	0.4010	2.406
	CTC	0.1730	1.038
	TTG	0.1526	0.916
	CTT	0.1257	0.754
	TTA	0.0824	0.494
	CTA	0.0652	0.391
Lysine K	AAG	0.5598	1.120
Lysine K	AAA	0.4402	0.880
Methionine M	ATG	1.0000	1.000
Phenylalanine F	TTC	0.5503	1.101
Phenylalanine F	TTT	0.4497	0.899
Proline P	CCA	0.3290	1.316
	CCT	0.3165	1.266
	CCC	0.2491	0.996
	CCG	0.1054	0.422
Serine S	AGC	0.2424	1.454
	TCT	0.2106	1.264
	TCC	0.1766	1.060
	AGT	0.1695	1.017
	TCA	0.1559	0.935
	TCG	0.0450	0.270
Threonine T	ACC	0.3291	1.316
	ACT	0.2883	1.153
	ACA	0.2511	1.004
	ACG	0.1315	0.526
Tryptophan W	TGG	1.0000	1.000
Tyrosine Y	TAT	0.5294	1.059
Tyrosine Y	TAC	0.4706	0.941
Valine V	GTG	0.4320	1.728
	GTC	0.2296	0.918
	GTT	0.2056	0.822
	GTA	0.1329	0.532

Provenance

Computed from 241 RefSeq coding sequences for Pan troglodytes, 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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