How many codons are there?

There are 64 codons in the standard genetic code. Sixty-one of them specify the 20 standard amino acids, and the other three, UAA, UAG, and UGA, are stop codons that end a protein. AUG, the codon for methionine, is where translation usually starts.

The total is 64 because a codon is three bases long and each position can hold one of four RNA bases: 4 × 4 × 4 = 64. Translating a gene, by hand or with a DNA-to-protein translator, means reading the sequence three bases at a time and looking up each triplet in the table below.

The standard codon table

The standard genetic code assigns each of the 64 codons either to one of 20 amino acids or to a stop signal, giving 61 sense codons and three stop codons.^[1][2] During translation, a ribosome reads the mRNA from its 5′ end toward its 3′ end, and each triplet either adds an amino acid to the growing protein or tells translation to stop.

To find a codon in Table 1, take its first base from the first column, its second base from the column heading, and its third base from the last column. The table uses mRNA notation, so U (uracil) stands where a DNA sequence would have T.

First base	Second base U	Second base C	Second base A	Second base G	Third base
U	UUU Phe	UCU Ser	UAU Tyr	UGU Cys	U
U	UUC Phe	UCC Ser	UAC Tyr	UGC Cys	C
U	UUA Leu	UCA Ser	UAA Stop	UGA Stop	A
U	UUG Leu	UCG Ser	UAG Stop	UGG Trp	G
C	CUU Leu	CCU Pro	CAU His	CGU Arg	U
C	CUC Leu	CCC Pro	CAC His	CGC Arg	C
C	CUA Leu	CCA Pro	CAA Gln	CGA Arg	A
C	CUG Leu	CCG Pro	CAG Gln	CGG Arg	G
A	AUU Ile	ACU Thr	AAU Asn	AGU Ser	U
A	AUC Ile	ACC Thr	AAC Asn	AGC Ser	C
A	AUA Ile	ACA Thr	AAA Lys	AGA Arg	A
A	AUG Met (start)	ACG Thr	AAG Lys	AGG Arg	G
G	GUU Val	GCU Ala	GAU Asp	GGU Gly	U
G	GUC Val	GCC Ala	GAC Asp	GGC Gly	C
G	GUA Val	GCA Ala	GAA Glu	GGA Gly	A
G	GUG Val	GCG Ala	GAG Glu	GGG Gly	G

Why 61 codons make only 20 amino acids

The 61 sense codons encode only 20 standard amino acids because the code is degenerate: several codons can specify the same amino acid. The redundancy is uneven. Leucine, serine, and arginine each have six codons, while methionine and tryptophan have only one.

Across the standard table, two amino acids have one codon, nine have two, one has three, five have four, and three have six. Together they account for the 61 sense codons, and the three stop codons bring the total to 64.^[3] Synonymous codons usually differ only in their third base, which is why the four codons of alanine, glycine, proline, threonine, and valine share their first two letters.

Amino acid	Abbreviations	Number of codons	Codons
Methionine	Met, M	1	AUG
Tryptophan	Trp, W	1	UGG
Asparagine	Asn, N	2	AAU, AAC
Aspartic acid	Asp, D	2	GAU, GAC
Cysteine	Cys, C	2	UGU, UGC
Glutamic acid	Glu, E	2	GAA, GAG
Glutamine	Gln, Q	2	CAA, CAG
Histidine	His, H	2	CAU, CAC
Lysine	Lys, K	2	AAA, AAG
Phenylalanine	Phe, F	2	UUU, UUC
Tyrosine	Tyr, Y	2	UAU, UAC
Isoleucine	Ile, I	3	AUU, AUC, AUA
Alanine	Ala, A	4	GCU, GCC, GCA, GCG
Glycine	Gly, G	4	GGU, GGC, GGA, GGG
Proline	Pro, P	4	CCU, CCC, CCA, CCG
Threonine	Thr, T	4	ACU, ACC, ACA, ACG
Valine	Val, V	4	GUU, GUC, GUA, GUG
Arginine	Arg, R	6	CGU, CGC, CGA, CGG, AGA, AGG
Leucine	Leu, L	6	UUA, UUG, CUU, CUC, CUA, CUG
Serine	Ser, S	6	UCU, UCC, UCA, UCG, AGU, AGC
Stop signal	None	3	UAA, UAG, UGA

Degeneracy makes translation unambiguous in one direction and open-ended in the other. A protein sequence fixes the amino acids but not the codons, so a protein-to-DNA back-translation has to choose among synonymous codons for 18 of the 20 amino acids. Codon optimization makes that choice deliberately, favoring the codons that an expression host such as E. coli uses most.

How many stop codons are there in the genetic code?

There are three stop codons in the standard genetic code: UAA, UAG, and UGA.^[1][2]

Stop codons do not add one of the 20 standard amino acids. They recruit release factors that end translation and release the completed protein. In DNA coding-strand notation, the same three signals are TAA, TAG, and TGA.

The count of three applies to the standard code. Some organisms and organelles reassign these triplets. UGA, for example, specifies tryptophan in the vertebrate mitochondrial code rather than acting as a stop.^[3]

How many start codons are there?

AUG is the primary start codon, but how many other codons can start translation depends on the organism and the genetic code it uses.^[3]

At the start of an open reading frame, AUG recruits an initiator tRNA and is read as methionine. The same AUG encountered inside that reading frame also encodes methionine, but it does not start a new protein unless the surrounding sequence supports initiation.

NCBI's standard table also allows UUG and CUG as alternative starts, and its bacterial, archaeal, and plant plastid table (table 11) allows seven: AUG, GUG, UUG, CUG, AUU, AUC, and AUA.^[3] In practice, bacteria rely mostly on the first three. Among known E. coli genes, AUG starts 83%, GUG 14%, and UUG 3%.^[4] An ORF finder therefore needs both the sequence and the correct genetic-code and start-codon rules.

A sensitive experiment detected low-level initiation from 47 of the 64 codons in E. coli, but the noncanonical starts produced only 0.007% to 3% as much translation as AUG.^[4] That result shows that initiation is not an all-or-nothing property of a triplet. It does not mean that every organism routinely uses 47 annotated start codons.

Are there always 64 mRNA and DNA codons?

There are always 64 possible three-base combinations in a four-letter mRNA or DNA alphabet, but their biological assignments can change.

Codons are usually written as mRNA because the ribosome reads mRNA directly. RNA uses A, C, G, and U; a DNA coding strand uses A, C, G, and T. Thus mRNA AUG corresponds to DNA ATG, and mRNA UGA corresponds to DNA TGA. A DNA-to-protein translation must also use the correct strand and reading frame.

The standard table covers most nuclear genes, but NCBI currently lists 26 alternative genetic codes alongside it, used by mitochondria, plastids, and some bacteria, archaea, protists, and fungi. In NCBI's vertebrate mitochondrial table, AUA changes from isoleucine to methionine, UGA changes from stop to tryptophan, and AGA and AGG are assigned as termination signals rather than arginine.^[3]

Termination in human mitochondrial DNA is more specific still. NCBI notes that humans do not read AGA and AGG as stops; the mitochondrial ribosome instead shifts back one base at the ends of the two affected genes, putting a standard UAG stop in frame.^[3] The possible triplets still number 64, but “61 sense plus three stop” describes the standard code, not every genome.