SeqBench

Zebrafish (D. rerio) Codon Usage

For every amino acid with more than one synonymous codon, Zebrafish (D. rerio)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
AlanineAAlaGCT32%preferred
AlanineAAlaGCC30%
AlanineAAlaGCA25%
AlanineAAlaGCG13%
ArginineRArgCGT13%
ArginineRArgCGC18%
ArginineRArgCGA12%
ArginineRArgCGG12%
ArginineRArgAGA26%preferred
ArginineRArgAGG19%
AsparagineNAsnAAT40%
AsparagineNAsnAAC60%preferred
Aspartic acidDAspGAT47%
Aspartic acidDAspGAC53%preferred
CysteineCCysTGT50%preferred
CysteineCCysTGC50%
Glutamic acidEGluGAA36%
Glutamic acidEGluGAG64%preferred
GlutamineQGlnCAA26%
GlutamineQGlnCAG74%preferred
GlycineGGlyGGT22%
GlycineGGlyGGC28%
GlycineGGlyGGA34%preferred
GlycineGGlyGGG16%
HistidineHHisCAT42%
HistidineHHisCAC58%preferred
IsoleucineIIleATT34%
IsoleucineIIleATC50%preferred
IsoleucineIIleATA16%
LeucineLLeuTTA8%
LeucineLLeuTTG13%
LeucineLLeuCTT14%
LeucineLLeuCTC18%
LeucineLLeuCTA7%
LeucineLLeuCTG41%preferred
LysineKLysAAA49%
LysineKLysAAG51%preferred
MethionineMMetATG100%preferred
PhenylalanineFPheTTT47%
PhenylalanineFPheTTC53%preferred
ProlinePProCCT31%preferred
ProlinePProCCC24%
ProlinePProCCA30%
ProlinePProCCG15%
SerineSSerTCT20%
SerineSSerTCC18%
SerineSSerTCA16%
SerineSSerTCG7%
SerineSSerAGT16%
SerineSSerAGC22%preferred
ThreonineTThrACT26%
ThreonineTThrACC29%
ThreonineTThrACA31%preferred
ThreonineTThrACG13%
TryptophanWTrpTGG100%preferred
TyrosineYTyrTAT43%
TyrosineYTyrTAC57%preferred
ValineVValGTT22%
ValineVValGTC23%
ValineVValGTA11%
ValineVValGTG44%preferred
Stop*StopTAA36%
Stop*StopTAG18%
Stop*StopTGA46%

Optimize a protein for Zebrafish

Paste a protein sequence and every residue is rewritten with its preferred Zebrafish 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 Zebrafish?

The codon with the highest usage fraction for that amino acid in Zebrafish (D. rerio) — 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 Zebrafish?

CTA (Leucine) is used only 7% of the time among its synonymous codons in Zebrafish (D. rerio) — a run of codons like this can slow translation if the matching tRNA is scarce.

How do I codon-optimize a gene for Zebrafish?

Paste the protein sequence into the tool below (or the full Codon Optimizer), and every residue is rewritten with its most-used codon in Zebrafish (D. rerio) — 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 Zebrafish (D. rerio). For critical work, verify against your specific expression system rather than treating any single table as definitive.