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[SO-devel] Re: annotating to pseudogenes

chris mungall cjm at
Mon Mar 13 20:07:20 PST 2006

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)."
> (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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