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annotating to pseudogenes

Suzanna Lewis suzi at
Tue Mar 14 13:43:33 PST 2006

On Mar 14, 2006, at 8:35 AM, Fiona McCarthy wrote:

> Hi All,
> I recent found a microarray tiling paper (PMID: 15876366) where the
> authors estimated that one fifth of human pseudogenes on chr22 are
> potentially transcribed. It seems to me that there must be a reason for
> this level of transcription, even if we don't know what it is.
> I think it would be reasonable to annotate pseudogenes to GO, even if 
> we
> have to use function unknown in most cases. Otherwise, we would be
> implying that *all* pseudogenes have no function, and this may not be 
> the
> case.

See Peter's reply.

But to repeat.

All pseudogenes are, by our definition, things that you believe are 
truly and sincerely, completely, uttterly dead (shades of the dead 
parrot skit).

If, in your scientific judgment, they may have some function (including 
latent, waiting for recombination, function a la inactive, cold-storage 
units) then they are not pseudogenes: in our shared, common definition.

We have agreed that it is useful to have clear definitions, and that we 
will use the same terms to mean precisely the same thing. We must not 
fall away from this.

While we are aware that there are entire communities that use the term 
"pseudogene", but mean something different, we must be consistent 
ourselves. Which means that we must have other terms (with the synonym 
"pseudogene") to describe these different phenomena.

Now, part 2.

Given that this thing has a function, then you get into the issue of 
what is that function. Once you have agreed that the function is in 
there, it is perfectly fine to say "unknown".


> As for the SO definition of a pseudogene, I am not sure that I would 
> say
> that all pseudogenes are non-functional.
> Fiona
> AgBase Biocurator
> Department of Basic Sciences
> Box 6100
> MS 39762-6100
> Mississippi State University
> Tel:   (+ 1) 662 325 5859
> Fax:  (+ 1) 662 325 1031

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