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annotating to pseudogenes

Christiane Hertz-Fowler chf at
Tue Mar 14 07:50:57 PST 2006

... but realistically you will not be able to prove that each one of in
excess of 1,000 pseudogenes and fragments is able to recombine and be
expressed considering that these switching events are seen in the
mamalian host during a parasitic infection and very difficult to mirror
experimentally in the lab. It is of course an extrapolation but I would
have thought a valid one with the appropriate evidence code?


-----Original Message-----
From: Alexander Diehl [mailto:adiehl at] 
Sent: 14 March 2006 15:38
To: Christiane Hertz-Fowler
Cc: David Hill; Suzanna Lewis; Rama Balakrishnan; Sue Rhee;
song-devel at; Pascale Gaudet; Barry Smith; GO
Annotation list; Matthew Berriman; hjr at
Subject: Re: annotating to pseudogenes

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

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