Re: Alternative Splicing


Larry Moran wrote:

<< ... >>
> As you can see, we're dealing with someone who doesn't even understand
> the correct meaning of the Central Dogma of Molecular Biology. That's
> just the beginning of his conceptual errors. It gets much worse.

> With respect to alternative splicing, it is important to show that the
> alternative splice patterns are conserved in different species (e.g.,
> mouse and humans) in order to demonstrate that they are real and not
> artifacts. As it turns out, these alternative splice variants are NOT
> conserved and that would normally be interpreted as a bad thing. It
> suggests that the variants are species-specific artifacts. This isn't
> a surprise since almost all of the alernative splicing predictions are
> based on EST data that data is clearly flawed.

Well I think EST data generally sucks too but,

The pattern I want to see is where a splice variant is tissue specific
and
where the tissue specificity is conserved across species.

Clearly, if 10 exons for proteinX are conserved for all studied
vertibrate
genomes, suggesting that a splice variant is mostly unique to one
species is dubious. But I do forsee some wonderfull papers that I hope
will soon be published "Most variable splice claims are bunk". Wish
I could take a few months off to do the work and write it.

I'd start with this paper

http://www.pubmedcentral.gov/articlerender.fcgi?pubmedid=12202761

and check it versus EST data on chimp and rhesus. They are only
claiming 667 tissue specific forms so an accounting could readily
be made, though the lack of evidence could be written off to incomplete
EST data in these other species. I guess I'd do rat and mouse too.
For some subset of the 667 I'd want to do some wetwork. Anybody
funding GarageGrants?

.