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annotating to pseudogenes
dph at informatics.jax.org
Tue Mar 14 05:51:00 PST 2006
I agree with Suzi, 100%
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)."
> (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.
> On Mar 13, 2006, at 12:02 PM, Rama Balakrishnan wrote:
>> Hi Sue,
>> At SGD, we also annotate pseudogenes to unknown.
>> On Mar 13, 2006, at 11:49 AM, Pascale Gaudet wrote:
>>> Hi Sue,
>>> At dictyBase we annotate pseudogenes to unknown.
>>> 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,
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
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