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

[Allan Kamau]

On 5/27/12, Javier Herrero <jherrero at ebi.ac.uk> wrote:
> 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
>
>
> _______________________________________________
> 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/
>


Dear Javier,

Thank you for your corrective advise, incidentally I received the same
suggestion from another biologist at work. Thank for for confirming
that a transcript can be seen as a mRNA and that there can be more
than one variation of a gene.

Indeed your input has saved me from going in the wrong direction.
Now I will work directly with the provided transcripts per gene.

Allan.