Codon and Base Coloring for Alignment Tracks

The Genome Browser's codon coloring feature allows users to quickly validate and compare alignment tracks, including mRNAs. To turn on codon coloring, select the desired option from the Color track by codons pull-down menu.

Color Options

Color Legend

  Genomic/mRNA codons Nonsynonymous mRNA codons mRNA bases/different mRNA bases
red "*" stop codons non-conservative codon substitutions base substitutions
yellow   conservative codon substitutions  
cyan spliced or truncated partial codons spliced or truncated partial codons  
green start codons incl. methionine    
black "X" truncated codons    


The codon reading frame is defined by the GenBank CDS annotation of the aligned sequence. Each codon is colored and labeled in the direction of transcription. A sequence without a CDS will not be colored; these can be non-protein coding RNAs or an mRNA where a CDS annotation was not provided in the original data.

The mRNA bases/different mRNA bases display options are colored and labeled in the direction of the genomic sequence. Note that it is possible to show the base complement, and thus change the base labeling, by clicking the arrow to the left of the base display or by clicking the "reverse" button.

When zoomed out past the base level, the browser will choose one color to represent many bases. The priority of display, from most important to least important, is: different mRNA base/nonsynonymous codon coloring (if enabled), and then alignment coloring (if enabled). The browser will not display genomic/mRNA codon coloring when viewing large regions of the genome. To view labeling, the track must be zoomed to within 3 times the base level.

For information about alignment insertion/deletion display options, click here.


Henikoff S and Henikoff JG. Amino acid substitution matrices from protein blocks. PNAS. 1992;89(22):10915-10919.