[Biojava-l] genes and things

[Ann Loraine]

I didn't even consider trans-splicing and operons...I guess
I'm too human-centric.  Does trans-splicing happen in humans?
(that we know of :-)

-Ann

---

Ann E. Loraine
http://www.loraine.net

On Thu, 28 Sep 2000, Matthew Pocock wrote:

> Hi Niclas - hope everything is going well with you.
> 
> Niclas Jareborg wrote:
> 
> > At 18.00 -0700 00-09-27, Ann Loraine wrote:
> > >In general,
> > >
> > >       -A gene has 1 or more transcripts (due to alternate
> > >               transcriptional start sites)
> > >
> > >       -A transcript has 1 or more mRNA splice variants (due to
> > >               alternative splicing)
> >
> > I agree that this makes biological sense. But, does it make sense
> > "modeling-wise"? Is there any advantage to destiguish between
> > transcripts and splice variants? The way I think about it a gene has
> > one or more 'mRNA products' that will have at least parts of exons in
> > common (otherwise I'd call it two genes).
> >
> > -Nic
> 
> Bacterial (and C.Elegans) operons could be modeled as transcripts with with a set
> of non-overlapping TranslatedRegion objects (or for c-elegans, SpliceVariants
> with multiple TranslatedRegion thingys) - one per 'gene' . This kind of destroys
> the meaning of the 'Gene' interface, though. Mabey the top-level thing is
> ExpressedRegion (promoter stuff & transcripts), or Expresson, or Regulon or
> something, and 'Gene' information is mixed in somewhere? Pants. I think for the
> C.Elegans operons, we would end up using each level of the hierachy to add
> information.
> 
> For bacterial genes, I guess we drop the splice-variant layer, or have a standard
> view of each Transcript producing a default SpliceVariant that contains the whole
> of itself.
> 
> Trans-splicing is a whole other tin of worms.
> 
> >
> > --
> > Niclas Jareborg, PhD                         Center for Genomics Research
> > niclas.jareborg@cgr.ki.se                    Karolinska institutet
> > http://www.cgr.ki.se/cgr/groups/jareborg     S-171 77 Stockholm, Sweden
> > Tel:+46-8-728 69 20    Mob:+46-70-7630461    Fax:+46-8-337983
> > ------------------------------------------------------------------------
> > "Reeling and Writhing, of course, to begin with," the Mock Turtle replied;
> > "and then the different branches of Arithmetic - Ambition, Distraction,
> > Uglification, and Derision."    -"Alice in Wonderland" by Lewis Carroll
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> --
> Joon: You're out of your tree
> Sam:  It wasn't my tree
>                                                  (Benny & Joon)
> 
> 
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