Amino Acid Codon Table

Amino Acid Codon Table

Complete reference table of 64 codons mapping to 20 amino acids plus stop signals, with degeneracy classes, wobble rules, and frequency data for human and E. coli expression systems.

Codon Table

Phenylalanine (F) — 2 codons

Codon	Amino Acid	Degeneracy	Human Freq	E. coli Freq
UUU	Phe	2-fold	45.6%	57.4%
UUC	Phe	2-fold	54.4%	42.6%

Leucine (L) — 6 codons

Codon	Amino Acid	Degeneracy	Human Freq	E. coli Freq
UUA	Leu	6-fold	7.1%	13.0%
UUG	Leu	6-fold	12.7%	13.2%
CUU	Leu	6-fold	12.7%	11.5%
CUC	Leu	6-fold	19.5%	10.8%
CUA	Leu	6-fold	7.0%	3.8%
CUG	Leu	6-fold	39.6%	52.8%

Isoleucine (I) — 3 codons

Codon	Amino Acid	Degeneracy	Human Freq	E. coli Freq
AUU	Ile	3-fold	36.0%	30.0%
AUC	Ile	3-fold	46.8%	21.8%
AUA	Ile	3-fold	17.2%	4.4%

Methionine (M) — 1 codon (start)

Codon	Amino Acid	Degeneracy	Human Freq	E. coli Freq
AUG	Met	1-fold	22.0%	27.2%

Valine (V) — 4 codons

Codon	Amino Acid	Degeneracy	Human Freq	E. coli Freq
GUU	Val	4-fold	17.9%	18.0%
GUC	Val	4-fold	19.3%	15.1%
GUA	Val	4-fold	11.4%	11.1%
GUG	Val	4-fold	51.4%	55.8%

Serine (S) — 6 codons

Codon	Amino Acid	Degeneracy	Human Freq	E. coli Freq
UCU	Ser	6-fold	18.2%	14.9%
UCC	Ser	6-fold	18.8%	8.7%
UCA	Ser	6-fold	14.8%	7.0%
UCG	Ser	6-fold	6.8%	8.8%
AGU	Ser	6-fold	14.7%	8.6%
AGC	Ser	6-fold	26.7%	20.0%

Proline (P) — 4 codons

Codon	Amino Acid	Degeneracy	Human Freq	E. coli Freq
CCU	Pro	4-fold	20.0%	17.3%
CCC	Pro	4-fold	19.6%	13.2%
CCA	Pro	4-fold	19.8%	8.1%
CCG	Pro	4-fold	40.6%	61.4%

Threonine (T) — 4 codons

Codon	Amino Acid	Degeneracy	Human Freq	E. coli Freq
ACU	Thr	4-fold	24.1%	15.4%
ACC	Thr	4-fold	28.4%	22.6%
ACA	Thr	4-fold	27.8%	6.9%
ACG	Thr	4-fold	19.7%	55.1%

Alanine (A) — 4 codons

Codon	Amino Acid	Degeneracy	Human Freq	E. coli Freq
GCU	Ala	4-fold	25.8%	15.2%
GCC	Ala	4-fold	28.2%	25.3%
GCA	Ala	4-fold	22.5%	21.6%
GCG	Ala	4-fold	23.5%	37.9%

Tyrosine (Y) — 2 codons

Codon	Amino Acid	Degeneracy	Human Freq	E. coli Freq
UAU	Tyr	2-fold	43.6%	54.9%
UAC	Tyr	2-fold	56.4%	45.1%

Histidine (H) — 2 codons

Codon	Amino Acid	Degeneracy	Human Freq	E. coli Freq
CAU	His	2-fold	41.3%	57.3%
CAC	His	2-fold	58.7%	42.7%

Glutamine (Q) — 2 codons

Codon	Amino Acid	Degeneracy	Human Freq	E. coli Freq
CAA	Gln	2-fold	26.3%	14.6%
CAG	Gln	2-fold	73.7%	85.4%

Asparagine (N) — 2 codons

Codon	Amino Acid	Degeneracy	Human Freq	E. coli Freq
AAU	Asn	2-fold	46.7%	46.8%
AAC	Asn	2-fold	53.3%	53.2%

Lysine (K) — 2 codons

Codon	Amino Acid	Degeneracy	Human Freq	E. coli Freq
AAA	Lys	2-fold	42.3%	74.0%
AAG	Lys	2-fold	57.7%	26.0%

Aspartic Acid (D) — 2 codons

Codon	Amino Acid	Degeneracy	Human Freq	E. coli Freq
GAU	Asp	2-fold	45.5%	62.6%
GAC	Asp	2-fold	54.5%	37.4%

Glutamic Acid (E) — 2 codons

Codon	Amino Acid	Degeneracy	Human Freq	E. coli Freq
GAA	Glu	2-fold	42.1%	68.4%
GAG	Glu	2-fold	57.9%	31.6%

Cysteine (C) — 2 codons

Codon	Amino Acid	Degeneracy	Human Freq	E. coli Freq
UGU	Cys	2-fold	44.6%	52.4%
UGC	Cys	2-fold	55.4%	47.6%

Tryptophan (W) — 1 codon

Codon	Amino Acid	Degeneracy	Human Freq	E. coli Freq
UGG	Trp	1-fold	100%	100%

Arginine (R) — 6 codons

Codon	Amino Acid	Degeneracy	Human Freq	E. coli Freq
CGU	Arg	6-fold	8.4%	20.7%
CGC	Arg	6-fold	18.4%	21.5%
CGA	Arg	6-fold	10.8%	3.5%
CGG	Arg	6-fold	20.2%	5.5%
AGA	Arg	6-fold	20.7%	2.6%
AGG	Arg	6-fold	21.5%	1.2%

Glycine (G) — 4 codons

Codon	Amino Acid	Degeneracy	Human Freq	E. coli Freq
GGU	Gly	4-fold	24.5%	24.5%
GGC	Gly	4-fold	20.4%	28.7%
GGA	Gly	4-fold	25.3%	8.1%
GGG	Gly	4-fold	29.7%	11.2%

Stop Codons

Codon	Name	Human Freq	E. coli Freq
UAA	Ochre	27.8%	63.0%
UAG	Amber	20.4%	29.0%
UGA	Opal	51.8%	8.0%

Degeneracy Summary

Amino Acid	1-Letter	3-Letter	Codons	Degeneracy Class
Phenylalanine	F	Phe	2	2-fold
Leucine	L	Leu	6	6-fold (NNT/C only)
Isoleucine	I	Ile	3	3-fold
Methionine	M	Met	1	Unique (start)
Valine	V	Val	4	4-fold
Serine	S	Ser	6	6-fold (split)
Proline	P	Pro	4	4-fold
Threonine	T	Thr	4	4-fold
Alanine	A	Ala	4	4-fold
Tyrosine	Y	Tyr	2	2-fold
Histidine	H	His	2	2-fold
Glutamine	Q	Gln	2	2-fold
Asparagine	N	Asn	2	2-fold
Lysine	K	Lys	2	2-fold
Aspartic Acid	D	Asp	2	2-fold
Glutamic Acid	E	Glu	2	2-fold
Cysteine	C	Cys	2	2-fold
Tryptophan	W	Trp	1	Unique
Arginine	R	Arg	6	6-fold (split)
Glycine	G	Gly	4	4-fold
STOP	—	—	3	Signal

Wobble Rules

The third codon position (wobble position) tolerates non-standard base pairing:

5’ Base (tRNA)	3’ Base (mRNA)	Pairing
G	U or C	Standard wobble
C	G or A	Standard wobble
A	U	Standard (rare in wobble)
U	A or G	Wobble pairing
I (inosine)	U, C, or A	Expanded wobble

Inosine in the tRNA wobble position can pair with three different bases, explaining why organisms with high inosine content use fewer tRNA species.

Codon Optimization Guidelines

For Human Expression

• Prefer codons with >30% frequency in human genes
• Avoid rare codons (frequency <10%)
• Consider CpG suppression for regulatory elements
• Optimize mRNA secondary structure around start codon

For E. coli Expression

• Use codons favored by E. coli (e.g., CUG for Leu, GCG for Ala)
• Avoid rare codons that cause ribosomal pausing (AGA/AGG for Arg)
• Consider tRNA availability — Arg (AGA/AGG) is limiting
• Balance codon usage across the coding sequence

For Cell-Free Expression

• Similar to E. coli but with fewer tRNA constraints
• Avoid codons that form stable mRNA secondary structures
• Consider including rare tRNAs in the extract

References

1. Codon Usage Database: https://www.kazusa.or.jp/codon/
2. Sharp PM, Li WH. “The codon adaptation index — a measure of directional synonymous codon usage bias.” Nucleic Acids Res 1987;15:1281-1291.
3. Plotkin JB, Kudla G. “Synonymous but not the same: the causes and consequences of codon bias.” Nat Rev Genet 2011;12:20-32.
4. GC含量 (GC content) varies by organism and affects codon preference.
5. Wobble base pairing was first described by Francis Crick in 1966.