Coloring Gene Predictions and Annotations by Codon

The Genome Browser's codon coloring feature allows users to quickly validate and compare gene predictions and annotations. To turn on codon coloring, select the genomic codons option from the Color track by codons pull-down menu.

Color Legend

  • bright green codons/lines: methionine, including start codons
  • cyan text/lines: partial codon, either spliced or truncated
  • red "*": stop codons
  • black "X": error (e.g. truncated last codon)

All other codons are shown in the original track color, with codon boundaries indicated by alternating lighter and darker shades.

Each codon is colored and labeled in the direction of transcription. This coloring applies only to gene prediction and annotation tracks; thus the codon sequence is colored in reference to the genome and not the associated mRNA. A gene prediction without a CDS will not be colored; these can be non-protein-coding RNAs or predictions where a CDS annotation was not provided in the original data.

To view codon coloring, the option must be turned on, the track must be in squish, pack, or full display mode, and the browser must be zoomed-in to a level at which there is at least one pixel per codon. When zoomed out to large regions of the genome, the browser will not display codon coloring. To view labeling, the track must be zoomed to within 3 times the base level.