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annotating to pseudogenes

Mike Cherry cherry at stanford.edu
Wed Mar 15 12:55:46 PST 2006


There is a site devoted to pseudogenes, their identification and  
analysis, Mark Gerstein's lab at Yale.

http://pseudogene.org/

On this page you'll find some definitions:

http://pseudogene.org/background.php

-Mike

On Mar 15, 2006, at 9:46 AM, Karen Christie wrote:

> Hi,
>
> My comment here is more about the SO definition of pseudogene, than  
> about
> whether or not to use GO terms to annotate features given that label.
>
> I was thinking about the SO definition of pseudogene this morning  
> and was
> wondering if part of the problem is that the definition may have been
> written from a protein-centric view of genes and what the possible
> functions of genes are. If I understand correctly, and Rama and  
> some of
> the other people who are more up on pseudogenes may correct me, most
> pseudogenes have been designated as such by virtue of being 1)  
> similar to
> a known protein-coding gene and 2) being thought to NOT express that
> particular protein that might have been expected based on its  
> similarity
> to a known protein coding gene. In other words, most people when
> designating something as a pseudogene were only thinking about it's
> protein coding ability. It seems that all of the cases that people  
> have
> mentioned in this thread where a pseudogene is expressed result in the
> production of an RNA from a pseudogene that resesmbles a protein,  
> thus the
> pseudogene is not producing the gene product that it might have been
> expected to have based on its sequence similarity to a protein coding
> gene. It seems to me that even when it has been discovered that a
> "pseudogene" produces an RNA transcript that may have activity in
> regulating the gene it is related to, that the community still  
> calls these
> "pseudogenes" because they do not produce the protein product expected
> based on sequence similarity to the known functional gene.
>
> It seems possible that there may be pseudogenes of ncRNA genes as  
> well of
> protein coding genes, but perhaps we can revise the definition of
> pseudogene to be a little more accurate. While GO and SO do need to be
> precise and rigorous, often more so than the literature, we also do  
> need
> to reflect the community usage of terms.
>
> Here's my thoughts on a possible revision of the SO def of  
> pseudogene; the
> current SO def is below.
>
> Possible revision:
>
> def: "A sequence that closely resembles a known functional gene, at
> another locus within a genome, that is thought to be non- 
> functional, with
> respect to producing the expected gene product based on sequence
> similarity with the known functional gene, 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://www.ucl.ac.uk/ ~ ucbhjow/b241/glossary.html] subset: SOFA
>
>
> Current SO def:
>
> def: "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://www.ucl.ac.uk/ ~ ucbhjow/b241/ 
> glossary.html]
> subset: SOFA
>




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