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annotating to pseudogenes
jane at ebi.ac.uk
Tue Mar 14 07:53:06 PST 2006
Hi Christine - when you say you assigned GO terms to your pseudogenes, do
you mean you assigned the function the pseudogene would have had before it
became a pseudogene?
On Tue, 14 Mar 2006, Christiane Hertz-Fowler wrote:
> we have also been struggeling with this for a while during the
> annotation of pathogen genomes. Particularly in the case of the
> Trypanosoma brucei genome which encodes in excess of 1,000 pseudogenes
> (out of approx. 9,000 genes). There is experimental evidence that
> fragments/parts of pseudogenes can recombine to produce functional genes
> which are expressed. We have assigned GO terms to these pseudogenes,
> though this is was more for internal purposes at this stage and these
> associations don't make it either into GeneDB or (obviously) the gene
> association files. The definition of a pseudogene as listed below is
> probably in line with this but could possibly be extended to capture
> this oddity. However, I would disagree with not being able to assign GO
> terms to pseudogenes ...
> contrary to the last couple of e-mails.
> -----Original Message-----
> From: owner-annotation at genome.stanford.edu
> [mailto:owner-annotation at genome.stanford.edu] On Behalf Of David Hill
> Sent: 14 March 2006 13:51
> To: Suzanna Lewis
> Cc: Rama Balakrishnan; Sue Rhee; song-devel at lists.sourceforge.net;
> Pascale Gaudet; Barry Smith; GO Annotation list
> Subject: Re: annotating to pseudogenes
> I agree with Suzi, 100%
> Suzanna Lewis wrote:
> > Hmm, this seems to me to raise some questions regarding dual uses for
> > unknown. It the case of gene products where you simply do not *yet*
> > known the function they are annotated to 'unknown'. But conversely, if
> > we look at the definition from the SO, a pseudogene is clearly
> > something that has *no* function:
> > "Pseudogene: A sequence that closely resembles a known functional
> > gene, at another locus within a genome, that is *non-functional* as a
> > consequence of (usually several) mutations that prevent either its
> > transcription or translation (or both). In general, pseudogenes result
> > from either reverse transcription of a transcript of their "normal"
> > paralog (SO:0000043) (in which case the pseudogene typically lacks
> > introns and includes a poly(A) tail) or from recombination
> > (SO:0000044) (in which case the pseudogene is typically a tandem
> > duplication of its "normal" paralog)."
> > http://song.sourceforge.net/SO_view/index.html
> > (caution, may take some time to load)
> > Annotating pseudogenes to "unknown" implies that they have a function
> > (but it is not yet known), but pseudogenes have no function by
> > definition, so there is a contradiction.
> > -S
> > On Mar 13, 2006, at 12:02 PM, Rama Balakrishnan wrote:
> >> Hi Sue,
> >> At SGD, we also annotate pseudogenes to unknown.
> >> rama
> >> On Mar 13, 2006, at 11:49 AM, Pascale Gaudet wrote:
> >>> Hi Sue,
> >>> At dictyBase we annotate pseudogenes to unknown.
> >>> Pascale
> >>> At 11:45 AM 3/13/2006 -0800, Sue Rhee wrote:
> >>>> Hi all:
> >>>> We are discussing whether/how to annotate to pseudogenes at TAIR.
> >>>> We are debating whether to annotate them to 'unknown' terms or not
> >>>> annotate them at all. I'd like to know how the other MODs are
> >>>> handling them.
> >>>> Thanks for your input,
> >>>> Sue
> David P. Hill, Ph.D.
> Senior Scientific Curator
> Mouse Genome Informatics
> Gene Ontology Consortium
> The Jackson Laboratory
> 600 Main Street
> Bar Harbor, ME 04609-1500
Dr Jane Lomax
GO Editorial Office
Wellcome Trust Genome Campus
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