Hi Leo ,
Thank you very much for your kind help.
I appreciate if you can explain this more
A  protein coding gene on the
other stand has exons in the introns of the other protein coding gene.

what do you think the solution for such cases?is it fine just to consider
longest gene geneA in previous example and just ignore geneB??

Thank you
Chris

On Thu, Aug 9, 2012 at 9:28 AM, Paul Leo <p.leo@uq.edu.au> wrote:

> HI Chris,
> This is not uncommon in mammalian genomes. A  protein coding gene on the
> other stand has exons in the introns of the other protein coding gene.
>
> The will Also be may instances of Ensemble gene ids within a gene on the
> same stand. There are often non-coding RNA's
>
> And sometimes there is just inconsistent nomenclature where there should
> be one  geneid but for historical reasons (or other) alternative
> transcripts from the same gene have been given their own geneid...
>
> The same will happen in refseq too. So you will have to take it into
> account. Being biology the only rule is there is always an exception to
> the rule.
>
> Cheers
> Paul Leo
>
> Hi All,
>
> when i looked to mouse ensembl genes i found some genes  located inside
> another gene ,for example , geneA on chromosome # starts @ 1000 pb and
> ends@3500 bp,geneB on same chromosome,same strand starts @1050 bp and ends
> @1650bp,is gene B a predicted gene?
>
> Is there any recommendation to use for instance refseg genes rather than
> enseml or vice versa??
>
> thank you for your help in advance
> Best,
> Chris
>
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