[annotation] RNA trimethylguanosine cap binding query

[Harold Drabkin]

I actually noticed that the core term, binding, with def of :    The 
selective, often stoichiometric, interaction of a molecule with one or 
more specific sites on another molecule.
is missing the non-covalent idea; fixing it in this term should suffice 
for it's children


The Oxford bible: binding: the act or process by which one molecule 
attaches to another by noncovalent forces.


Valerie Wood wrote:
> yes thanks it seems obvious now, although I think I have some rogue annotations to fix for GPI binding to fix.! This might be obvious to everyone, but it might be worth adding 'non covalent' to all of the binding term defs just to emphasise. Its quite clear when you read the 'RNA trimethylguanosine cap 
> binding def, but I'm not sure that it is for some of the others. 
>
> thanks
>
> val
>
>
> Karen Christie <kchris at genome.stanford.edu> wrote: 
>   
>> Hi Val,
>>
>> Yea, I agree with Harold that the term 'RNA trimethylguanosine cap 
>> binding' should only be used for things that bind to the cap, once it's 
>> been created.
>>
>> What you're talking about, annotating the modification that occurs on the 
>> RNA, is completely different, and I think perhaps, completely outside the 
>> scope of GO.
>>
>> -Karen
>>
>>
>> On Wed, 16 Jan 2008, Harold Drabkin wrote:
>>
>>     
>>> Valerie Wood wrote:
>>>       
>>>> I recently used the term RNA trimethylguanosine cap binding  to annotate 
>>>> pombe telomerase RNA and represent the fact that this is trimethylguanosine 
>>>> capped, but on re-reading the definition  I'm not sure if this is correct?
>>>> Can I use this for the modification itself?  or is it for gene products 
>>>> which interact with a capped product?
>>>>         
>>> It represents some gene product that binds to the triMeG cap present on an 
>>> mRNA. Not the gene product that makes the cap. A binding term should never be 
>>> used for a covalent bond. Binding implies a reversible reaction at STP, with 
>>> a Ka and Kd.
>>>
>>> GPI anchor binding it meant to be used for something that binds the the GPI 
>>> anchor and not covalently linked to it.
>>>
>>>       
>>>> There do not appear to be any other annotations to this term despite  the 
>>>> fact that many RNAs are capped which is another reason which made me 
>>>> suspect my usage may be wrong.
>>>>
>>>> Should  the binding terms should only be used for non-covalent 
>>>> modifications (although this is only in some of the binding defs?), and 
>>>> does not represent the use of some terms. For instance GPI anchor binding 
>>>> is used for a number of proteins which are GPI anchored, in addition to 
>>>> proteins which bins the GPI moiety during GPI anchor biosynthesis.
>>>>
>>>> Cheers
>>>>
>>>> Val
>>>>
>>>> Def:
>>>> Interacting selectively with the trimethylguanosine (m(3)(2,2,7)-GTP) 
>>>> moiety located at the 5' end of some RNA molecules. Such trimethylated cap 
>>>> structures, generally produced by posttranscriptional modification of a 
>>>> 7-methylguanosine cap, are often found on snRNAs and snoRNAs transcribed by 
>>>> RNA polymerase II, but have also be found on snRNAs transcribed by RNA 
>>>> polymerase III. They have also been found on a subset of the mRNA 
>>>> population in some species, e.g. C. elegans.
>>>>
>>>>
>>>>         
>>     
>
>