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annotating to pseudogenes

Suzanna Lewis suzi at fruitfly.org
Tue Mar 14 13:45:41 PST 2006


Right, it is in the traditional sense that we are using the term 
"pseudogene" (our 1 single definition). The others erstwhile 
"pseudogenes" are horses of a different color entirely and we must not 
confuse the two.

-S

On Mar 14, 2006, at 9:02 AM, Matthew Berriman wrote:

>
> the key thing here is that they are not necessarily decayed genes.  
> They are "stored" in an inactive form, so that they can be assembled 
> by gene conversion etc into "functional" genes when transcribed.  They 
> do, therefore, indirectly encode gene products.  I would argue that in 
> this case, they do indirectly have a function and should receive some 
> kind of GO annotation. A pragmatic consideration is that >10% of the 
> genome is dedicated to evading the mammalian immune system and that 
> this should be annotated.  Unfortunately, the situation is complicated 
> by the fact that amongst the large repertoire of "functional" 
> pseudogenes, there are some that may have been used in previous 
> generations and are therefore pseudogenes in the more traditional 
> sense.
> cheers
> Matt
>
>
> On 14 Mar 2006, at 8:53 am, Jane Lomax wrote:
>
>> Hi Christine - when you say you assigned GO terms to your 
>> pseudogenes, do
>> you mean you assigned the function the pseudogene would have had 
>> before it
>> became a pseudogene?
>>
>> jane
>>
>>
>> On Tue, 14 Mar 2006, 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
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>> -- 
>>> 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
>>>
>>>
>>>
>>
>> Dr Jane Lomax
>> GO Editorial Office
>> EMBL-EBI
>> Wellcome Trust Genome Campus
>> Hinxton
>> Cambridgeshire, UK
>> CB10 1SD
>>
>> p: +44 1223 492516
>> f: +44 1223 494468
>>
>>
>




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