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: partial codon, either spliced or truncated
• red "*": stop codons
• black "X": error (e.g. truncated last codon)
• orange codons, with "!" after the codon number: the codon number counted along the genome is not the number the transcript itself uses (see below)

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

Details
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.

Codons where the two numberings disagree
Because codons are counted along the genome, a transcript whose own sequence differs from the genome by an insertion or a deletion will be numbered differently here than it is by the sequence provider. Every codon after the difference is shifted by one codon for each three bases involved. RefSeq transcripts are aligned to the genome rather than being derived from it, so this happens wherever the RefSeq sequence and the assembly disagree; it is uncommon in human but much more frequent in other assemblies, and more frequent the less complete the assembly is.

Codons affected this way are drawn in orange with a "!" after the codon number, and their mouseover gives both numbers — the one counted along the genome, which is what this track has always shown, and the one counted on the transcript, which is what NCBI and other resources report for that transcript. For a RefSeq track, the underlying difference can be seen in the RefSeq Alignments and RefSeq Diffs subtracks.

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.