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Rules for Assigning Start and End Phase to Coding Exons

Hello everyone,

I need to calculate the start and end phase for each exon across all transcripts of a specific gene. I understand that the phase indicates how the exon aligns with the codon reading frame, but I need clarification on how to determine the start phase of the first exon in a transcript that contains coding sequence and the end phase of the last exon that contains coding sequence. I’ve noticed that in many cases, these phases are assigned as -1, similar to non-coding sequences, but this is not always consistent. As I couldn't manage to find this information in Ensembl documentation, I’d appreciate it if someone could clarify the precise rules for assigning these phases, especially in cases where variations occur.

Thanks in advance!

stare_phase reading_frame end_phase
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updated by Jorge - Ensembl • Jorge - Ensembl • written by Milica • Milica

1 answer

Hi Milica! Here is the information from the Ensembl Glossary on exon phases:

" The position of an exon/intron boundary within a codon. A phase of zero means the boundary falls between codons, one means between the first and second base and two means between the second and third base. Exons have a start and end phase, whereas introns have just one phase. A boundary in a non-coding region has a phase of -1. "

https://www.ensembl.org/info/website/glossary.html

For exon phases assigned -1, those would be untranslated

Hope that helps! Cheers Jorge

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written by Jorge - Ensembl • Jorge - Ensembl

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