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[SO-devel] Re: annotating to pseudogenes

Suzanna Lewis suzi at fruitfly.org
Sun Mar 19 18:21:26 PST 2006


On Mar 19, 2006, at 9:52 AM, Karen Eilbeck wrote:

> 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.

Non, non, mon cheri.

If it turns out to be a functional non-coding RNA then it is *not* a  
pseudogene (even with this modified definition). The annotation calling  
it a "pseudogene" would necessarily have to be updated (removed) as  
soon as proof of functionality is found.

-S

>
> 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
>>>> X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/
>>>> 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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