[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.
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
--
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK
More information about the Dev
mailing list