[SO-devel] Re: annotating to pseudogenes

[Judith Blake]

I think that what we have here is the fact that the same object can be 
classified in different ways.  In regards to structural yet not 
functional similarity to a functional gene, we classify something as a 
'pseudogene'.  This seems to be a instance of a genome feature that has 
a function in a different way that that associated with its homolog.

So in one classification/definition it is a 'gene' [functional genome 
feature].  In another, it's a pseudogene [see definition below].

I would think perhaps that when a feature classified as a pseudogene is 
determined to have a function, it would be reclassified......

Judy

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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