42.1%GC3 content

55.4Effective codons (Nc)

250Coding sequences

25/26GC3 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 Asian elephant is alanine: of its 4 synonymous codons, GCT takes 35% of the family. Lysine sits at the other end, spread almost evenly across its options (evenness 0.99 against 0.91 for alanine). 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 Ferret (r = 0.995) and least with M. tuberculosis (r = 0.475). 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, Asian elephant leans hardest on AAT (+0.164 against the mean) and avoids AAC most (-0.164). 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	GCT	0.346	1.38	GCG	0.060	0.24
Arginine R	AGA	0.313	1.88	CGC	0.107	0.64
Asparagine N	AAT	0.626	1.25	AAC	0.374	0.75
Aspartate D	GAT	0.619	1.24	GAC	0.382	0.76
Cysteine C	TGT	0.578	1.16	TGC	0.422	0.84
Glutamate E	GAA	0.600	1.20	GAG	0.400	0.80
Glutamine Q	CAG	0.623	1.25	CAA	0.377	0.75
Glycine G	GGA	0.340	1.36	GGG	0.183	0.73
Histidine H	CAT	0.562	1.12	CAC	0.438	0.88
Isoleucine I	ATT	0.446	1.34	ATA	0.239	0.72
Leucine L	CTG	0.257	1.54	CTA	0.092	0.55
Lysine K	AAA	0.555	1.11	AAG	0.445	0.89
Phenylalanine F	TTT	0.576	1.15	TTC	0.424	0.85
Proline P	CCT	0.369	1.48	CCG	0.078	0.31
Serine S	TCT	0.230	1.38	TCG	0.039	0.23
Threonine T	ACA	0.351	1.41	ACG	0.071	0.29
Tyrosine Y	TAT	0.563	1.13	TAC	0.437	0.87
Valine V	GTG	0.343	1.37	GTA	0.190	0.76

Full codon usage table

Amino acid	Codon	Frequency	RSCU
Alanine A	GCT	0.3457	1.383
	GCA	0.3014	1.206
	GCC	0.2932	1.173
	GCG	0.0596	0.238
Arginine R	AGA	0.3132	1.879
	AGG	0.2120	1.272
	CGA	0.1384	0.830
	CGT	0.1193	0.716
	CGG	0.1105	0.663
	CGC	0.1066	0.640
Asparagine N	AAT	0.6264	1.253
Asparagine N	AAC	0.3736	0.747
Aspartate D	GAT	0.6185	1.237
Aspartate D	GAC	0.3815	0.763
Cysteine C	TGT	0.5782	1.156
Cysteine C	TGC	0.4218	0.844
Glutamate E	GAA	0.5998	1.200
Glutamate E	GAG	0.4002	0.800
Glutamine Q	CAG	0.6231	1.246
Glutamine Q	CAA	0.3769	0.754
Glycine G	GGA	0.3396	1.358
	GGC	0.2451	0.980
	GGT	0.2327	0.931
	GGG	0.1826	0.730
Histidine H	CAT	0.5623	1.125
Histidine H	CAC	0.4377	0.875
Isoleucine I	ATT	0.4463	1.339
	ATC	0.3146	0.944
	ATA	0.2391	0.717
Leucine L	CTG	0.2569	1.541
	CTT	0.1970	1.182
	TTG	0.1755	1.053
	TTA	0.1409	0.845
	CTC	0.1376	0.826
	CTA	0.0922	0.553
Lysine K	AAA	0.5547	1.109
Lysine K	AAG	0.4453	0.891
Methionine M	ATG	1.0000	1.000
Phenylalanine F	TTT	0.5763	1.153
Phenylalanine F	TTC	0.4237	0.847
Proline P	CCT	0.3692	1.477
	CCA	0.3446	1.378
	CCC	0.2082	0.833
	CCG	0.0780	0.312
Serine S	TCT	0.2301	1.381
	TCA	0.2006	1.204
	AGT	0.1939	1.163
	AGC	0.1787	1.072
	TCC	0.1583	0.950
	TCG	0.0386	0.232
Threonine T	ACA	0.3515	1.406
	ACT	0.3031	1.212
	ACC	0.2739	1.096
	ACG	0.0715	0.286
Tryptophan W	TGG	1.0000	1.000
Tyrosine Y	TAT	0.5634	1.127
Tyrosine Y	TAC	0.4366	0.873
Valine V	GTG	0.3428	1.371
	GTT	0.2769	1.108
	GTC	0.1903	0.761
	GTA	0.1900	0.760

Provenance

Computed from 250 RefSeq coding sequences for Elephas maximus, 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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