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:
Transcript: ENST00000297261.7
Strand: -
Exon: Exon 2 of 3
Codon phase: start 0, end 1: out-of-frame exon
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.