[SO-devel] Re: annotating to pseudogenes

[Jane Lomax]

yes, that's what I was just thinking - sometimes the mRNA of a pseudogene 
has a function, even if the final protein doesn't. In that case I guess 
you'd annotate the RNA function and make no annotation for the protein. I 
agree that 'unknown' shouldn't be used...

jane

On Tue, 14 Mar 2006 val at sanger.ac.uk wrote:

> 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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> 
> 
> 
> 

Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

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