[ensembl-dev] human transcripts with non 'AUG' start

[Magali]

Hi Uma,

An initiator_codon_variant is a sequence ontology term used in the
variation annotation.
We map variations to the reference genome and calculate consequences for
this variation.
In this case, it is a missense variation that affects the first codon of
the transcript.
More information can be found here:
http://www.ensembl.org/info/genome/variation/predicted_data.html

The transcripts you are looking at come from the Havana manual annotation.
They are protein-coding transcripts but we lack evidence to annotate the
full length CDS, hence the incomplete sequence.
This can happen for example if the biological evidence (proteins, mRNAs)
are not publicly available or if there is an error in the genome
sequence, preventing us from correctly aligning said evidence.


Hope that helps,
Magali

On 12/09/13 20:37, Paila, Uma Devi (udp3f) wrote:
> Hi,
>  I would greatly appreciated if anybody could tell me what it means by
> an initiator codon in ENSEMBL? If it refers to the translational start
> site, why some of the HUMAN transcripts in ENSEMBL  show an initiator
> codon other than 'AUG' ? Considering this
> example, http://www.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?g=ENSG00005917;r=2:20449625-20512017;t=ENST00000440577;transcript=ENST0000044057,
> this transcript shows a translation with 'R' as the first amino acid
> whereas you would expect to see a 'M' as in this
> example http://www.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db=core;g=ENSG00000055917;r=2:20449625-20512017;t=ENST00000442400 
>
> I see the first example shows its CDS as incomplete. Does that mean it
> is actually missing some transcript info? My other question is, how is
> the initiator_codon_variant defined? Does this mean a variation in the
> translational start or the transcription start site?
>
> regards,
> uma 
>
>
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