Genetic code

Codon usage table of chromosome 2 from a mouse strain. The first three characters are the codon, the second character in parentheses is the amino acid coded for by the codon, and the percentage is the relative usage of that codon in the genome across all CDSs.

Codon usage table of mitochondrion Mus musculus domesticus (western European house mouse) strain AKR/J.

The genetic code is the translation framwork of mRNA nucleotide sequence to protein amino acid sequence. mRNAs are read 5' to 3' using triplets of nucleotides. These triplets of nucleotides are called codons, and each codon codes for a single amino acid or a stop signal to end translation. While there are 64 possible codons (4x4x4), there are 20-21 amino acids and a stop signal. Thus, multiple codons can code for the same amino acids or stop signal, and the genetic code is redundant. While much of the genetic code is constant across all major domains of life, there are several modifications that are used by different groups of organisms. For example, compare the genetic codes from the mouse genome and the mouse mitochondria. Notice that the codon TGA codes for stop (*) in the mouse genome and Tryptophan (W) in the mouse mitochondria. Other difference are AGA and AGG, which code from Arginine (R) in the mouse genome and stop (*) in the mouse mitochondria; ATA which codes from isoleucine (I) in the mouse genome and methionine (M) in the mouse mitochondria.

It is easy to generate codon usage tables for entire genomes or chromosomes in CoGe through OrganismView, or for a genomic feature in FeatView and FeatList.