[ensembl-dev] a question about nonsense_mediated_decay in Homo_sapiens

[Bronwen Aken]

Hello,

Ensembl release 62 was released last week, and the three transcripts you listed have all been updated.

ENST00000511104 is no longer available in e62. In e61 it was labelled as protein-coding. Its prediction method was "Ensembl genebuild". The Ensembl genebuild does not currently distinguish between protein-coding and NMD transcripts, so all coding transcripts from the Ensembl genebuild are called 'protein_coding'.

ENST00000393966 is protein_coding in e62. Its prediction method is "Ensembl genebuild" meaning that, as for ENST00000511104, its biotype will be protein-coding even if the transcript is NMD by the defintiion.

ENST00000433422 is a processed_transcript in e62. In e61 is was labelled as NMD. The prediction method of this transcript is manual annotation by Havana, meaning that the exon structure and biotype were set by Havana. It looks like the biotype was set incorrectly for this transcript in e61.

Thanks,
Bronwen


On 19 Apr 2011, at 03:51, 李雪楠 wrote:

> I am a student in bioinformatics who is eager to know where is your data about  nonsense_mediated_decay in Homo_sapiens from, automatically annotation or experiment data ?
> as the definition of NMD is that If the coding sequence (following the appropriate reference) of a transcript finishes >50bp from a downstream splice site then it is tagged as NMD. If the variant does not cover the full reference coding sequence then it is annotated as NMD if NMD is unavoidable i.e. no matter what the exon structure of the missing portion is the transcript will be subject to NMD. 
> so i design perl programs to find the NMD. 
> for example ENST00000511104,ENST00000393966 ENST00000433422 these data's transcript type in your website are different from my perl programs result  so i need your help to work out my confusing,   thanks a lot. 
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