[ensembl-dev] missing transcript
amonida at ebi.ac.uk
Tue Jul 29 14:04:42 BST 2014
Sorry for the delay in getting back to you.
The mouse annotation changed in e68 when a new mouse assembly (GRCm38)
was released by GRC. As a consequence of assembly change, the annotation
of the Fign gene has also changed. More specifically, the BC059266.1 
cDNA sequence that was used as the evidence for ENSMUST00000166144
doesn't align well to the new assembly, most likely it fell below the
set alignment threshold and hence was not included as transcript
Hope this explains the missing transcript.
On 29/07/2014 10:20, Nathalie Conte wrote:
> Hello, Could I have some help on this? Thanks Nathalie
> On 24 Jul 2014, at 15:31, Nathalie Conte <nconte at ebi.ac.uk> wrote:
>> Hi Dev team,
>> In Ensembl, there is only one protein coding transcript for Fign
>> gene: ENSMUST00000131615
>>The ATG is here in exon-2.
>> However, historically there has been a second protein coding
>> annotated in Ensembl, ENSMUST00000166144, which has been removed at
>> some point. For this second transcript the ATG starts in the last
>> exon (in frame and 33 bp downstream of the ATG in exon-2)
>>There seems to have biological evidence that this second transcript
>> exist and it would be therefore very useful to understand as to why
>> this transcript has been removed and is not considered protein
>> coding by Ensembl any more.
>> Thanks for any info,
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