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.
- bright green codons/lines: methionine, including start
- 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.