51.1%GC3 content

54.7Effective codons (Nc)

248Coding sequences

22/26GC3 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 African elephant is glutamine: of its 2 synonymous codons, CAG takes 71% of the family. Asparagine 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 Lion (r = 0.982) and least with M. tuberculosis (r = 0.655). 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, African elephant leans hardest on TGT (+0.213 against the mean) and avoids TGC most (-0.213). 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	0.403	1.61	GCG	0.113	0.45
Arginine R	AGA	0.286	1.72	CGT	0.084	0.51
Asparagine N	AAT	0.503	1.01	AAC	0.497	0.99
Aspartate D	GAC	0.533	1.07	GAT	0.467	0.93
Cysteine C	TGT	0.673	1.35	TGC	0.327	0.65
Glutamate E	GAA	0.527	1.05	GAG	0.473	0.95
Glutamine Q	CAG	0.712	1.42	CAA	0.288	0.58
Glycine G	GGA	0.303	1.21	GGT	0.154	0.62
Histidine H	CAC	0.527	1.05	CAT	0.473	0.95
Isoleucine I	ATC	0.400	1.20	ATA	0.218	0.65
Leucine L	CTG	0.335	2.01	CTA	0.065	0.39
Lysine K	AAG	0.509	1.02	AAA	0.491	0.98
Phenylalanine F	TTC	0.512	1.02	TTT	0.488	0.98
Proline P	CCT	0.350	1.40	CCG	0.105	0.42
Serine S	TCC	0.208	1.25	TCG	0.054	0.32
Threonine T	ACT	0.319	1.28	ACG	0.117	0.47
Tyrosine Y	TAT	0.520	1.04	TAC	0.480	0.96
Valine V	GTG	0.435	1.74	GTA	0.131	0.52

Full codon usage table

Amino acid	Codon	Frequency	RSCU
Alanine A	GCC	0.4028	1.611
	GCT	0.2640	1.056
	GCA	0.2208	0.883
	GCG	0.1125	0.450
Arginine R	AGA	0.2859	1.715
	AGG	0.2739	1.643
	CGG	0.1340	0.804
	CGC	0.1281	0.769
	CGA	0.0939	0.563
	CGT	0.0842	0.505
Asparagine N	AAT	0.5034	1.007
Asparagine N	AAC	0.4966	0.993
Aspartate D	GAC	0.5334	1.067
Aspartate D	GAT	0.4666	0.933
Cysteine C	TGT	0.6731	1.346
Cysteine C	TGC	0.3269	0.654
Glutamate E	GAA	0.5267	1.053
Glutamate E	GAG	0.4733	0.947
Glutamine Q	CAG	0.7120	1.424
Glutamine Q	CAA	0.2880	0.576
Glycine G	GGA	0.3032	1.213
	GGG	0.2741	1.096
	GGC	0.2685	1.074
	GGT	0.1542	0.617
Histidine H	CAC	0.5271	1.054
Histidine H	CAT	0.4729	0.946
Isoleucine I	ATC	0.3996	1.199
	ATT	0.3825	1.147
	ATA	0.2179	0.654
Leucine L	CTG	0.3348	2.009
	CTC	0.2279	1.367
	CTT	0.1528	0.917
	TTG	0.1337	0.802
	TTA	0.0862	0.517
	CTA	0.0646	0.388
Lysine K	AAG	0.5093	1.019
Lysine K	AAA	0.4907	0.981
Methionine M	ATG	1.0000	1.000
Phenylalanine F	TTC	0.5122	1.024
Phenylalanine F	TTT	0.4878	0.976
Proline P	CCT	0.3505	1.402
	CCC	0.2755	1.102
	CCA	0.2690	1.076
	CCG	0.1050	0.420
Serine S	TCC	0.2077	1.246
	AGT	0.2048	1.229
	AGC	0.1876	1.126
	TCA	0.1873	1.124
	TCT	0.1591	0.955
	TCG	0.0536	0.322
Threonine T	ACT	0.3193	1.277
	ACC	0.3093	1.237
	ACA	0.2545	1.018
	ACG	0.1169	0.468
Tryptophan W	TGG	1.0000	1.000
Tyrosine Y	TAT	0.5203	1.041
Tyrosine Y	TAC	0.4797	0.959
Valine V	GTG	0.4346	1.738
	GTC	0.2529	1.012
	GTT	0.1819	0.728
	GTA	0.1306	0.522

Provenance

Computed from 248 RefSeq coding sequences for Loxodonta africana, 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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