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annotating to pseudogenes

Christiane Hertz-Fowler chf at sanger.ac.uk
Tue Mar 14 07:27:17 PST 2006


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
>>>
>>>
>>
>


-- 
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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