Codon phases shown on the Genome Browser

Gene transcript tracks, for example NCBI RefSeq and Gencode, show the codon phase of exons on mouse over. The text looks like this:

The codon phase specifies where in the coding sequence the intron falls in the codon that separates two exons:

• Phase 0: before the first nucleotide, cleanly between two codons.
• Phase 1: between the first and the second nucleotide
• Phase 2: between the second and third nucleotide

This means that:

• The start phase of an exon is always the same as the end phase of the previous exon.
• An exon where the end and start phases are identical can be removed without destroying the reading frame: in-frame exon.
• An exon where start and end phases differ cannot be removed without destroying the reading frame: out-of-frame exon.