[ensembl-dev] Takifugu rubripes - Genenames

[Ewan Birney]

Just to briefly expand on this;

   It is well known that the bony fish (telosts) went through another
genome duplication (on top of the 2 that happened at the root of the
vertebrate tree), and this means that for many mammalian genes, there
are >1 orthologs (co-orthologs), related by this duplication, in  
telosts.

   If we sticked to strict 1-1 orthologs, we'd have ended up with very
few names transfered in telosts.


On 11 Mar 2011, at 09:21, Glenn Proctor wrote:

> Hi Elsa
>
> For some species, we project gene names from highly-annotated species
> (e.g. human) onto the target species, based on Compara homologies. In
> nearly all cases we use the Compara 1:1 homologies. However for fish
> we also use the 1:many homologies, and add a suffix (1 of 2 or
> whatever) to the projected name to indicate this.
>
> The projections done for the fish are:
>
> human -> zebrafish
> human -> medaka
> human -> tetraodon
> human -> fugu
> human -> stickleback
>
> I hope this clarifies things.
>
> Glenn.
>
> On Fri, Mar 11, 2011 at 9:10 AM, Elsa Chacko <elsa.chacko at mq.edu.au>  
> wrote:
>> Hi
>>
>> I am a bit confused as to why there is a (1 of 2) and (2 of 2)  
>> along with
>> the geneNames for the genes in the species Takifugu rubripes . For  
>> example:
>> for gene ID: ENSTRUG00000002307, the geneName is ZNF395 (2 of 2)  
>> and for
>> gene ID: ENSTRUG00000003845 the geneNme is ZNF395 (1 of 2). I have  
>> however
>> not seen this naming system in species like human, mouse or chicken.
>>
>> kindly assist
>> Elsa
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>>
>
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