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[SO-devel] Re: annotating to pseudogenes

Richard Durbin rd at sanger.ac.uk
Sun Mar 19 04:27:58 PST 2006


Thank you for this thoughtful analysis and proposal. 
I support the revised definition as well.  

Richard

Michael Ashburner (Genetics) wrote:

>I could live with that changed definition.
>Michael
>
>  
>
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>>Cc: ruth at galton.ucl.ac.uk, Karen Eilbeck <eilbeck at fruitfly.org>, 
>>    
>>
>...
>  
>
>>List-Archive: <http://sourceforge.net/mailarchive/forum.php?forum=song-devel>
>>Date: Wed, 15 Mar 2006 09:46:15 -0800 (PST)
>>
>>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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