[BioC] About ensembl genes

Paul Leo p.leo at uq.edu.au
Thu Aug 9 02:28:47 CEST 2012

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.

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

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