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annotating to pseudogenes

David Hill dph at informatics.jax.org
Tue Mar 14 05:51:00 PST 2006


I agree with Suzi, 100%

David

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
>>>
>>>
>>
>


-- 
David P. Hill, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
Gene Ontology Consortium
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609-1500
tel:207-288-6430
htpp://www.informatics.jax.org
http://www.geneontology.org




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