SeqBench

Arabidopsis (A. thaliana) Codon Usage

For every amino acid with more than one synonymous codon, Arabidopsis (A. thaliana)uses some codons far more often than others. The table below shows each codon's usage fraction — the share of that amino acid's codons it accounts for — with the preferred (most-used) codon highlighted.

Amino acid1-letter3-letterCodonFraction
AlanineAAlaGCT43%preferred
AlanineAAlaGCC16%
AlanineAAlaGCA27%
AlanineAAlaGCG14%
ArginineRArgCGT17%
ArginineRArgCGC7%
ArginineRArgCGA12%
ArginineRArgCGG9%
ArginineRArgAGA35%preferred
ArginineRArgAGG20%
AsparagineNAsnAAT52%preferred
AsparagineNAsnAAC48%
Aspartic acidDAspGAT68%preferred
Aspartic acidDAspGAC32%
CysteineCCysTGT60%preferred
CysteineCCysTGC40%
Glutamic acidEGluGAA52%preferred
Glutamic acidEGluGAG48%
GlutamineQGlnCAA56%preferred
GlutamineQGlnCAG44%
GlycineGGlyGGT34%
GlycineGGlyGGC14%
GlycineGGlyGGA37%preferred
GlycineGGlyGGG16%
HistidineHHisCAT61%preferred
HistidineHHisCAC39%
IsoleucineIIleATT41%preferred
IsoleucineIIleATC35%
IsoleucineIIleATA24%
LeucineLLeuTTA14%
LeucineLLeuTTG22%
LeucineLLeuCTT26%preferred
LeucineLLeuCTC17%
LeucineLLeuCTA11%
LeucineLLeuCTG11%
LysineKLysAAA49%
LysineKLysAAG51%preferred
MethionineMMetATG100%preferred
PhenylalanineFPheTTT51%preferred
PhenylalanineFPheTTC49%
ProlinePProCCT38%preferred
ProlinePProCCC11%
ProlinePProCCA33%
ProlinePProCCG18%
SerineSSerTCT28%preferred
SerineSSerTCC13%
SerineSSerTCA20%
SerineSSerTCG10%
SerineSSerAGT16%
SerineSSerAGC13%
ThreonineTThrACT34%preferred
ThreonineTThrACC20%
ThreonineTThrACA31%
ThreonineTThrACG15%
TryptophanWTrpTGG100%preferred
TyrosineYTyrTAT52%preferred
TyrosineYTyrTAC48%
ValineVValGTT40%preferred
ValineVValGTC19%
ValineVValGTA15%
ValineVValGTG26%
Stop*StopTAA36%
Stop*StopTAG20%
Stop*StopTGA44%

Optimize a protein for Arabidopsis

Paste a protein sequence and every residue is rewritten with its preferred Arabidopsis codon — the same engine behind the full Codon Optimizer tool, scoped to this one organism.

Frequently asked questions

What is the preferred codon for each amino acid in Arabidopsis?

The codon with the highest usage fraction for that amino acid in Arabidopsis (A. thaliana) — highlighted in green in the table below. It's the codon a codon optimizer picks when rewriting a gene for this host.

What's a rare codon to avoid in Arabidopsis?

CGC (Arginine) is used only 7% of the time among its synonymous codons in Arabidopsis (A. thaliana) — a run of codons like this can slow translation if the matching tRNA is scarce.

How do I codon-optimize a gene for Arabidopsis?

Paste the protein sequence into the tool below (or the full Codon Optimizer), and every residue is rewritten with its most-used codon in Arabidopsis (A. thaliana) — the encoded protein is unchanged, only the DNA sequence changes.

Are these values exact?

These fractions are reference approximations derived from the Kazusa Codon Usage Database for Arabidopsis (A. thaliana). For critical work, verify against your specific expression system rather than treating any single table as definitive.