[BiO BB] looking for reference on DSCAM exon locations.

[Mike Marchywka]

As it turns out, to answer most of my earlier question,

http://www.mail-archive.com/bbb@bioinformatics.org/msg00026.html

the exon locations are reasonably well described at NCBI following the links contained here,

http://genomebiology.com/2006/7/1/R2

( or here, I can't get figures to render at above link, 
     http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1431710&blobtype=pdf    )

Variable window binding for mutually exclusive alternative splicing
Dimitris Anastassiou , Hairuo Liu  and Vinay Varadan 
Center for Computational Biology and Bioinformatics, and Department of Electrical Engineering, Columbia University, New York, NY 07670, USA
 author email corresponding author email
Genome Biology 2006, 7:R2doi:10.1186/gb-2006-7-1-r2

"Because the Dscam gene of four out of the six Drosophila spp. had not previously been annotated [11], we first generated the missing annotations for all exons of cluster 6 using the existing annotations as benchmarks and ensuring that exons are located in open reading frames. The resulting annotated sequences for D. yakuba, D. ananassae, D. mojavensis and D. pseudoobscura have been deposited in GenBank under accession numbers DQ317106, DQ317107, DQ317108 and DQ317109, respectively. These can be accessed in addition to the previously available annotated sequences for D. melanogaster (accession number AF260530) and D. virilis (accession number AY686597)."

for mealnogaster, this would be here

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=8072216

Not sure how I missed this earlier but, anyway DSCAM does seem like a good test case and example to follow for splicing literature.

And I was able to verify that I can use my reverse-complement and rule code to find the patterns
previously reported by the authors. I'm still trying to determine what, if any, significance there may be to
the pattern I mentioned earlier.  I did some surveys on random genome segments and it does come
up pretty often but it doesn't seem to be completed excluded from DSCAM exon clusters.


Mike Marchywka
586 Saint James Walk
Marietta GA 30067-7165
404-788-1216 (C)<- leave message
989-348-4796 (P)<- emergency only
marchywka at hotmail.com
Note: Hotmail is blocking my mom's entire
ISP claiming it is to reduce spam but probably
to force users to use hotmail. Please DON'T
assume I am ignoring you and try
me on marchywka at yahoo.com if no reply
here. Thanks.


_________________________________________________________________
Climb to the top of the charts! Play the word scramble challenge with star power.
http://club.live.com/star_shuffle.aspx?icid=starshuffle_wlmailtextlink_jan