# How many codons are there?

> There are 64 codons in the standard genetic code. Sixty-one specify the 20 standard amino acids, and three, UAA, UAG, and UGA, are stop codons.

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](/app/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. During translation, a [ribosome](/guides/how-many-ribosomes-are-in-a-cell) 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.

  <caption><strong>Table 1. The standard codon table.</strong> All 64 mRNA codons, read 5′ to 3′, with the three-letter abbreviation of the amino acid each one encodes. Table 2 gives the full amino acid names. Assignments follow NCBI translation table 1. Source: Elzanowski and Ostell, NCBI.</caption>
  <thead>
    <tr>
      <th scope="col">First base</th>
      <th scope="col">Second base U</th>
      <th scope="col">Second base C</th>
      <th scope="col">Second base A</th>
      <th scope="col">Second base G</th>
      <th scope="col">Third base</th>
    </tr>
  </thead>
  <tbody>
    <tr>
      <td>U</td>
      <td>UUU Phe</td>
      <td>UCU Ser</td>
      <td>UAU Tyr</td>
      <td>UGU Cys</td>
      <td>U</td>
    </tr>
    <tr>
      <td>U</td>
      <td>UUC Phe</td>
      <td>UCC Ser</td>
      <td>UAC Tyr</td>
      <td>UGC Cys</td>
      <td>C</td>
    </tr>
    <tr>
      <td>U</td>
      <td>UUA Leu</td>
      <td>UCA Ser</td>
      <td>UAA Stop</td>
      <td>UGA Stop</td>
      <td>A</td>
    </tr>
    <tr>
      <td>U</td>
      <td>UUG Leu</td>
      <td>UCG Ser</td>
      <td>UAG Stop</td>
      <td>UGG Trp</td>
      <td>G</td>
    </tr>
    <tr>
      <td>C</td>
      <td>CUU Leu</td>
      <td>CCU Pro</td>
      <td>CAU His</td>
      <td>CGU Arg</td>
      <td>U</td>
    </tr>
    <tr>
      <td>C</td>
      <td>CUC Leu</td>
      <td>CCC Pro</td>
      <td>CAC His</td>
      <td>CGC Arg</td>
      <td>C</td>
    </tr>
    <tr>
      <td>C</td>
      <td>CUA Leu</td>
      <td>CCA Pro</td>
      <td>CAA Gln</td>
      <td>CGA Arg</td>
      <td>A</td>
    </tr>
    <tr>
      <td>C</td>
      <td>CUG Leu</td>
      <td>CCG Pro</td>
      <td>CAG Gln</td>
      <td>CGG Arg</td>
      <td>G</td>
    </tr>
    <tr>
      <td>A</td>
      <td>AUU Ile</td>
      <td>ACU Thr</td>
      <td>AAU Asn</td>
      <td>AGU Ser</td>
      <td>U</td>
    </tr>
    <tr>
      <td>A</td>
      <td>AUC Ile</td>
      <td>ACC Thr</td>
      <td>AAC Asn</td>
      <td>AGC Ser</td>
      <td>C</td>
    </tr>
    <tr>
      <td>A</td>
      <td>AUA Ile</td>
      <td>ACA Thr</td>
      <td>AAA Lys</td>
      <td>AGA Arg</td>
      <td>A</td>
    </tr>
    <tr>
      <td>A</td>
      <td>AUG Met (start)</td>
      <td>ACG Thr</td>
      <td>AAG Lys</td>
      <td>AGG Arg</td>
      <td>G</td>
    </tr>
    <tr>
      <td>G</td>
      <td>GUU Val</td>
      <td>GCU Ala</td>
      <td>GAU Asp</td>
      <td>GGU Gly</td>
      <td>U</td>
    </tr>
    <tr>
      <td>G</td>
      <td>GUC Val</td>
      <td>GCC Ala</td>
      <td>GAC Asp</td>
      <td>GGC Gly</td>
      <td>C</td>
    </tr>
    <tr>
      <td>G</td>
      <td>GUA Val</td>
      <td>GCA Ala</td>
      <td>GAA Glu</td>
      <td>GGA Gly</td>
      <td>A</td>
    </tr>
    <tr>
      <td>G</td>
      <td>GUG Val</td>
      <td>GCG Ala</td>
      <td>GAG Glu</td>
      <td>GGG Gly</td>
      <td>G</td>
    </tr>
  </tbody>

### Why 61 codons make only 20 amino acids

The 61 sense codons encode only [20 standard amino acids](/guides/how-many-amino-acids-are-there) 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.

![The number of standard amino acids encoded by one, two, three, four, or six synonymous codons](/images/charts/amino-acids-by-codon-degeneracy.webp '**Figure 1. Amino acids grouped by their number of codons.** Standard genetic code, NCBI translation table 1. Source: [Elzanowski and Ostell, NCBI](https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi).')

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. 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.

  <caption><strong>Table 2. Codons for each amino acid.</strong> Standard genetic code in mRNA notation, ordered by the number of synonymous codons. Source: Elzanowski and Ostell, NCBI.</caption>
  <thead>
    <tr>
      <th scope="col">Amino acid</th>
      <th scope="col">Abbreviations</th>
      <th scope="col">Number of codons</th>
      <th scope="col">Codons</th>
    </tr>
  </thead>
  <tbody>
    <tr>
      <td>Methionine</td>
      <td>Met, M</td>
      <td>1</td>
      <td>AUG</td>
    </tr>
    <tr>
      <td>Tryptophan</td>
      <td>Trp, W</td>
      <td>1</td>
      <td>UGG</td>
    </tr>
    <tr>
      <td>Asparagine</td>
      <td>Asn, N</td>
      <td>2</td>
      <td>AAU, AAC</td>
    </tr>
    <tr>
      <td>Aspartic acid</td>
      <td>Asp, D</td>
      <td>2</td>
      <td>GAU, GAC</td>
    </tr>
    <tr>
      <td>Cysteine</td>
      <td>Cys, C</td>
      <td>2</td>
      <td>UGU, UGC</td>
    </tr>
    <tr>
      <td>Glutamic acid</td>
      <td>Glu, E</td>
      <td>2</td>
      <td>GAA, GAG</td>
    </tr>
    <tr>
      <td>Glutamine</td>
      <td>Gln, Q</td>
      <td>2</td>
      <td>CAA, CAG</td>
    </tr>
    <tr>
      <td>Histidine</td>
      <td>His, H</td>
      <td>2</td>
      <td>CAU, CAC</td>
    </tr>
    <tr>
      <td>Lysine</td>
      <td>Lys, K</td>
      <td>2</td>
      <td>AAA, AAG</td>
    </tr>
    <tr>
      <td>Phenylalanine</td>
      <td>Phe, F</td>
      <td>2</td>
      <td>UUU, UUC</td>
    </tr>
    <tr>
      <td>Tyrosine</td>
      <td>Tyr, Y</td>
      <td>2</td>
      <td>UAU, UAC</td>
    </tr>
    <tr>
      <td>Isoleucine</td>
      <td>Ile, I</td>
      <td>3</td>
      <td>AUU, AUC, AUA</td>
    </tr>
    <tr>
      <td>Alanine</td>
      <td>Ala, A</td>
      <td>4</td>
      <td>GCU, GCC, GCA, GCG</td>
    </tr>
    <tr>
      <td>Glycine</td>
      <td>Gly, G</td>
      <td>4</td>
      <td>GGU, GGC, GGA, GGG</td>
    </tr>
    <tr>
      <td>Proline</td>
      <td>Pro, P</td>
      <td>4</td>
      <td>CCU, CCC, CCA, CCG</td>
    </tr>
    <tr>
      <td>Threonine</td>
      <td>Thr, T</td>
      <td>4</td>
      <td>ACU, ACC, ACA, ACG</td>
    </tr>
    <tr>
      <td>Valine</td>
      <td>Val, V</td>
      <td>4</td>
      <td>GUU, GUC, GUA, GUG</td>
    </tr>
    <tr>
      <td>Arginine</td>
      <td>Arg, R</td>
      <td>6</td>
      <td>CGU, CGC, CGA, CGG, AGA, AGG</td>
    </tr>
    <tr>
      <td>Leucine</td>
      <td>Leu, L</td>
      <td>6</td>
      <td>UUA, UUG, CUU, CUC, CUA, CUG</td>
    </tr>
    <tr>
      <td>Serine</td>
      <td>Ser, S</td>
      <td>6</td>
      <td>UCU, UCC, UCA, UCG, AGU, AGC</td>
    </tr>
    <tr>
      <td>Stop signal</td>
      <td>None</td>
      <td>3</td>
      <td>UAA, UAG, UGA</td>
    </tr>
  </tbody>

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](/app/protein-to-dna) back-translation has to choose among synonymous codons for 18 of the 20 amino acids. [Codon optimization](/app/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.

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.

## 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.

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. In practice, bacteria rely mostly on the first three. Among known *E. coli* genes, AUG starts 83%, GUG 14%, and UUG 3%. An [ORF finder](/app/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. 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](/guides/how-many-mitochondria-are-in-a-cell), 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.

Termination in [human mitochondrial DNA](/guides/how-many-genes-in-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. The possible triplets still number 64, but “61 sense plus three stop” describes the standard code, not every genome.