annotating to pseudogenes

[Suzanna Lewis]

Hmm, this seems to me to raise some questions regarding dual uses for 
unknown. It the case of gene products where you simply do not *yet* 
known the function they are annotated to 'unknown'. But conversely, if 
we look at the definition from the SO, a pseudogene is clearly 
something that has *no* function:

"Pseudogene: 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://song.sourceforge.net/SO_view/index.html
(caution, may take some time to load)

Annotating pseudogenes to "unknown" implies that they have a function 
(but it is not yet known), but pseudogenes have no function by 
definition, so there is a contradiction.

-S

On Mar 13, 2006, at 12:02 PM, Rama Balakrishnan wrote:

> Hi Sue,
>
> At SGD, we also annotate pseudogenes to unknown.
>
> rama
>
> On Mar 13, 2006, at 11:49 AM, Pascale Gaudet wrote:
>
>> Hi Sue,
>>
>> At dictyBase we annotate pseudogenes to unknown.
>>
>> Pascale
>>
>>
>> At 11:45 AM 3/13/2006 -0800, Sue Rhee wrote:
>>> Hi all:
>>>
>>> We are discussing whether/how to annotate to pseudogenes at TAIR. We 
>>> are debating whether to annotate them to 'unknown' terms or not 
>>> annotate them at all. I'd like to know how the other MODs are 
>>> handling them.
>>>
>>> Thanks for your input,
>>> Sue
>>
>