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[SO-devel] Re: annotating to pseudogenes

val at sanger.ac.uk val at sanger.ac.uk
Tue Mar 14 01:13:00 PST 2006


But there is alway one....

PMID: 12721631

Nature. 2003 May 1;423(6935):91-6.	
 
An expressed pseudogene regulates the messenger-RNA stability of its homologous 
coding gene.
Hirotsune S, Yoshida N, Chen A, Garrett L, Sugiyama F, Takahashi S, Yagami K, 
Wynshaw-Boris A, Yoshiki A





Quoting chris mungall <cjm at fruitfly.org>:

> 
> Yes, I agree. pseudogenes have no function by definition, so they would  
> have no GO annotation.
> 
> On Mar 13, 2006, at 3:48 PM, 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
> >>>
> >>
> >
> >
> >
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