Re: [Gusdev-gusdev] Re: Alternative-splicing discussion

[Chris S. <sto...@SN...>]

Hi Arnaud,
> I'd like to illustrate the alternative splicing discussion by the worst 
> case scenario Bart could up with: the major immediate early (MIE) 
> region of the  Human Cytomegalovirus (HCMV).
>
> See attached the map of this region. Briefly, the upstream gene has 5 
> exons and gives, after splicing, 5 transcript variants and consequently 
> 5 proteins whose size differs quite a lot. In this situation all exons 
> can have both behaviour, coding/non-coding, depending on which RNA 
> variant they're attached to.
> Besides, note that the 5th exon can be splited into 2 smaller exons and 
> an intron, so it's not only the behaviour of the exon which changes but 
> it's internal structure as well !!!!
This is scary.

> What we would like is the flexibility of either attaching the RNA 
> variants to separate gene feature entries or to a unique gene feature 
> entry. As long as we have this flexibility, the underlying schema is 
> fine with us.
Yes. Each RNA variant can be a separate gene if desired. Note that each 
ExonFeature can only have one parent_id (i.e., can belong to only one 
gene). So any common exons would have to be duplicated for each gene.

> At the ExonFeature level, you're mentioning that the annotation of the 
> exons (first/last/middle - coding/non-coding) could move to the 
> RNAFeatureExon table. Would it replace the duplication of the exons ?
>
This would not prevent duplication of exons due to being shared by 
different genes but it would prevent duplication of exons shared by RNAs 
from the same gene.

Chris