[ensembl-dev] phase of first exon in transcript is 1 or 2

[Giulietta]

Hi Jeff,

These cases result from alignments of the protein/cDNA/EST to the genome 
in which there is a good alignment for most of the transcript, but not 
at the start site.  I.e. the transcript is believed to be there,  but 
the EST and cDNA evidence does not provide the correct nucleotides to 
annotate the start (ATG).  All the transcripts that do start with phase 
1 or 2 are from Havana manual curation.

Michael's previous answer to your question last year explains this a bit 
more:

http://lists.ensembl.org/pipermail/dev/2011-January/000768.html

Regards,
Giulietta


On 30/07/2012 21:01, Jeff Hussmann wrote:
> Hello all -
>
> The API documentation for Bio::EnsEMBL::Exon::phase says: 'The Ensembl
> phase convention can be thought of as "the number of bases of the
> first codon which are on the previous exon".'
>
> Given this, I was surprised to find that a large number of human
> transcripts have a first exon with a starting phase of 1 or 2. Why is
> this the case? Of course, first exons do not have a previous exon. I
> am having trouble imagining experimental evidence that would lead to
> frequent annotations of this kind.
>
> Thanks,
> Jeff
>
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