[BioC] About ensembl genes

[Paul Leo]

HI Chris,
That is really just a biology question , there are lots of examples (ok
mainly UTR overlaps) but others intron-exon.

Articles like:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC139260/

(and others you might get for searching very broadly with "overlapping
genes in mouse examples") will help you.

I think if you take a few specific examples from those papers and
visualise them with (for example) the UCSC genome browser 
http://genome.cse.ucsc.edu/

you will get a feel  for the field and come up with solutions   that
best suit your research.

Best if Luck
Paul




Dr Paul Leo
Senior Bioinformatician
UQ Diamantina Institute for Cancer, Immunology and Metabolic Medicine 
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-----Original Message-----
From: chris Jhon <cjhon217 at gmail.com>
To: p.leo at uq.edu.au
Cc: Bioconductor mailing list <bioconductor at r-project.org>
Subject: Re: [BioC] About ensembl genes
Date: Thu, 9 Aug 2012 10:00:05 +0900

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 at 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 at 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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