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[SO-devel] Re: annotating to pseudogenes

Peter D'Eustachio eustachi at cshl.edu
Tue Mar 14 05:33:56 PST 2006


Right, but in that case it's not really a pseudogene as GO/SO (but not the 
authors of the data in question) use that word. There are also a number of 
instances in mammals of intronless but otherwise perfect open reading 
frames, where it's truly unclear whether the entity is transcribed and 
translated or not, but again, that's a case where the real biological object 
doesn't fir the GO/SO definition of pseudogene, not an argument for 
attributing possible functions to true GO/SO pseudogenes.

Peter D'Eustachio
Reactome

----- Original Message ----- 
From: "Jane Lomax" <jane at ebi.ac.uk>
To: <val at sanger.ac.uk>
Cc: "chris mungall" <cjm at fruitfly.org>; <song-devel at lists.sourceforge.net>; 
"Sue Rhee" <rhee at acoma.Stanford.EDU>; "Pascale Gaudet" 
<pgaudet at northwestern.edu>; "Rama Balakrishnan" <rama at genome.stanford.edu>; 
"Barry Smith" <phismith at buffalo.edu>; "GO Annotation list" 
<annotation at genome.stanford.edu>
Sent: Tuesday, March 14, 2006 5:46 AM
Subject: Re: [SO-devel] Re: annotating to pseudogenes


>
> 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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>> > > _______________________________________________
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>> >
>>
>>
>>
>>
>
> Dr Jane Lomax
> GO Editorial Office
> EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridgeshire, UK
> CB10 1SD
>
> p: +44 1223 492516
> f: +44 1223 494468
>
> 



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