Hi Leo,

Thank you very much.

Best Regards,
Chris

On Thu, Aug 9, 2012 at 12:50 PM, Paul Leo <p.leo@uq.edu.au> wrote:

> 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
> ---------------------------------------------------------------------
> Level 4, R Wing
> Princess Alexandra Hospital
> Ipswich Rd
> Woolloongabba QLD 4102
> Tel: +61 7 3346 1759  Mob: 041 303 8691  Fax: +61 7 3240 5946
> Email: p.leo@uq.edu.au   Web: http://www.di.uq.edu.au
>
> -----Original Message-----
> From: chris Jhon <cjhon217@gmail.com>
> To: p.leo@uq.edu.au
> Cc: Bioconductor mailing list <bioconductor@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@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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