[SO-devel] Re: annotating to pseudogenes

[Suzanna Lewis]

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

I agree with the above.

The mechanism by which it arose is not the issue.

If is has a function, then it is not a pseudogene by definition.
period.

This is not withstanding Trypanosome community usage of the term. Where  
we will do need to do some extra work to deal with this in the  
ontology.

-S

On Mar 14, 2006, at 7:56 AM, Judith Blake wrote:
>
> 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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