[ensembl-dev] Genes, transcripts and exons and mRNA

Javier Herrero jherrero at ebi.ac.uk
Sun May 27 12:56:15 BST 2012


Dear Allan

The idea of having just one messenger RNA per gene does not make much 
biological sense. Each gene may have one or several alternative 
transcripts and each transcript is essentially an mRNA.

Your aim might be slightly different from reconstructing the mRNAs. For 
instance, maybe you want to look at the codon usage per gene and don't 
care much about the transcripts. In that case, I would probably get the 
longest exons when two or more exons overlap, but bear in mind that 
concatenating all these exons might not be biologically correct.

Again, if you want the actual mRNAs, just take each transcript separately.

I hope this helps

Javier

On 26/05/12 11:38, Allan Kamau wrote:
> Hi,
> I am trying to reconstruct messenger RNA sequences (in DNA format)
> using transcript and exon data obtained using ensembl API.
> I have read on the Ensembl API documentation that transcripts are
> groups of exons and (protein based) genes are groups of transcripts,
> and that these transcripts may be overlapping (within a given Gene)
> and that exons may also overlap.
>
> So for a given gene, I am trying to flatten out it's exons by using
> their start and end positions. I have noticed that some exons from
> different transcripts may have the same start position but different
> end positions, or different start positions and same end position or
> that these exons may have the identical start and end positions.
>
> Should I make use of the longer exons (and ignore the shorter ones)
> when there are more than one exon for a given region for the same
> gene?
>
> Is my overall understanding and approach to reconstruction of message
> RNA correct?
>
> Allan.
>
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-- 
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK





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