[Biojava-l] genes and things

[Niclas Jareborg]

At 18.00 -0700 00-09-27, Ann Loraine wrote:
>Why don't you attach Exons to SpliceVariants (or possibly
>transcipts) instead of Genes?
>
>It seems counter-intuitive to assign Exons to Genes directly, since
>an exon doesn't really make sense outside the context of spliced
>transcript.
>
>e.g.,
>
>(XXX = exonic, ---- = intronic)
>
>cartoon of gene w/ two splice variants:
>
>XXXXXXXXXXXXX-----XXXXXXXXX  SpliceVariant 1 (w/ exon 1 and 2)
>XXXXXXXXXXXXX---------XXXXX  SpliceVariant 2 (w/ exon 1 and 4)
>
>If you were to ask this Gene for all its exons, you'd get {1,3,4},
>which is okay, but doesn't make a ton of sense  because it doesn't
>say anything about how these exons fit together to make "legal" transcripts.
>
>That is, you can't get a transcript that has *both* exon 2 and 4, for
>instance.
>
>So wouldn't you rather get your exons from SpliceVariants instead of
>genes? Then you'd know which goes with which.
>
>This would also make interactive editing a lot easier to support.  For
>example, let's say you've built an editor and your user is looking at
>transcript 2 and decides to make its exon 1 longer on the 3' end. 
>
>If you're storing just one copy of exon 1 internally then your user
>will have mucked with transcript 1 as well as transcript 2.  Yuck!
>
>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).

In the following cartoon your model would have a gene with two 
transcripts, one of which contains two splice variants. In my model 
the gene would have three transcripts (or mRNA products, or whatever 
you want to call it)

XXXXXXXXXXXXX-----XXXXXXXXX  Trx 1, SpliceVariant 1
XXXXXXXXXXXXX---------XXXXX  Trx 1, SpliceVariant 2
      XXXXXXXX-----XXXXXXXXX  Trx 2, SpliceVariant 1

Just my few pennies worth.

-Nic
-- 
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
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