About ensembl genes

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chris Jhon ▴ 260

@chris-jhon-5047

Last seen 10.2 years ago

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 [[alternative HTML version deleted]]

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ADD COMMENT • link updated 12.3 years ago by Paul Leo ▴ 970 • written 12.3 years ago by chris Jhon ▴ 260

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Paul Leo ▴ 970

@paul-leo-2092

Last seen 10.2 years ago

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 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD COMMENT • link 12.3 years ago Paul Leo ▴ 970

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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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]

ADD REPLY • link 12.3 years ago chris Jhon ▴ 260

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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 at uq.edu.au Web: http://www.di.uq.edu.au -----Original Message----- From: chris Jhon <cjhon217@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 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD REPLY • link 12.3 years ago Paul Leo ▴ 970

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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 > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]]

ADD REPLY • link 12.3 years ago chris Jhon ▴ 260

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