Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

annotating to pseudogenes

Alexander Diehl adiehl at informatics.jax.org
Tue Mar 14 07:38:14 PST 2006


As David and others alluded to earlier, not all pseudogenes are created 
equal.  Some may function as the source of anti-sense RNA to regulate 
gene function.  Some may serve as the source of material for 
gene-conversion processes.  And some may simply be evolutionary relics 
not subject to positive selection whatsoever.

The first role may be appropriate for GO, as there is a gene-product 
involved.  In the other two cases, I think no annotation at all is 
appropriate, until and unless an identifiable gene product is found.

-- Alex


Christiane Hertz-Fowler wrote:
> Hi,
>
> we have also been struggeling with this for a while during the
> annotation of pathogen genomes. Particularly in the case of the
> Trypanosoma brucei genome which encodes in excess of 1,000 pseudogenes
> (out of approx. 9,000 genes). There is experimental evidence that
> fragments/parts of pseudogenes can recombine to produce functional genes
> which are expressed. We have assigned GO terms to these pseudogenes,
> though this is was more for internal purposes at this stage and these
> associations don't make it either into GeneDB or (obviously) the gene
> association files. The definition of a pseudogene as listed below is
> probably in line with this but could possibly be extended to capture
> this oddity. However, I would disagree with not being able to assign GO
> terms to pseudogenes  ...
> contrary to the last couple of e-mails.
>
> Regards,
>
> Christiane
>
>
> -----Original Message-----
> From: owner-annotation at genome.stanford.edu
> [mailto:owner-annotation at genome.stanford.edu] On Behalf Of David Hill
> Sent: 14 March 2006 13:51
> To: Suzanna Lewis
> Cc: Rama Balakrishnan; Sue Rhee; song-devel at lists.sourceforge.net;
> Pascale Gaudet; Barry Smith; GO Annotation list
> Subject: Re: annotating to pseudogenes
>
>
> 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
>>>>>           
>>>>         
>
>
>   

-- 
Alexander Diehl, Ph.D.
Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609

email:  adiehl at informatics.jax.org
work:  +1 (207) 288-6427
fax:  +1 (207) 288-6131 




More information about the go-discuss mailing list