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[SO-devel] Re: annotating to pseudogenes

Karen Eilbeck eilbeck at fruitfly.org
Sun Mar 19 09:52:33 PST 2006


Before we all agree on the proposed definition for pseudogenes, we need  
to address some issues.
Firstly if we use this definition, then a region that is a pseudogene  
that turns out to also be a functional non-coding RNA, will also be a  
ncRNA.
I'm not sure if this will affect supporting software.

Secondly the definition is supposed the explicitly describe the  
feature, and the phrase "that is thought to be" adds vagueness rather  
than clarity.

I'm sure there will ample discussion of this term in St Croix.

--Karen



On Mar 19, 2006, at 5:27 AM, Richard Durbin wrote:

> 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
>>
>>
>>> Envelope-to: ma11 at gen.cam.ac.uk
>>> Delivery-date: Wed, 15 Mar 2006 18:44:22 +0000
>>> X-Cam-SpamDetails: scanned, SpamAssassin (score=0)
>>> X-Cam-AntiVirus: No virus found
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>>> From: Karen Christie <kchris at genome.stanford.edu>
>>> To: Hubert Renauld <hjr at sanger.ac.uk>
>>> 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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>>
>>
>>
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>
>



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