Where to get splicing sites of D.melanogaster?

[holywoool]

Hi,
I'm looking for splicing annotation of Drosophila melanogaster.I've searched D.melanogaster's database from UCSC Download page and there is no file contains splicing annotation.Anyone knows where to get the data?

Thanks

[mudshark]

FlyBase is the curator of D. melanogaster genome annotations. Look in the GFF Files they provide: http://flybase.org/static_pages/down...bulkdata7.html

[holywoool]

Thanks,
I've downloaded a file in GFF format,however,the data are not about splicing annotation but annotation about EST.The FLYBASE ftp does have so many data about D.melanogaster,sadly,none meets my need.
I'm Keeping finding ...

[mudshark]

ftp://flybase.net/genomes/Drosophila...l-r5.32.gff.gz

contains all the information you need and much more. you will find all transcripts and their exons. this should constitute a rather large set of splice sites. of course you will have to parse the gff for the information you need. but simple perl scripts will pull you the lines with the interesting information such as..

#!/usr/bin/perl

while (defined(my $line = <>)) {
chomp($line);
my @line_items = split(/\t/, $line);
print $line."\n" if ($line_items[2] =~ /exon/);
}

[steven]

What are you looking for exactly? From any transcript annotation it should be possible to obtain the splice sites.. Depending on the format you want, you will certainly have to do some parsing anyway.
I would suggest the following:
Go to the UCSC table browser, select Insect/Drosophila/genes/FlyBase, and BED output format. Then once you click "get output" select the "introns" category. By definition, each position in this file correspond to a splice site.
I find it easier to extract them from the introns, because in the exonic boundaries you also have Transcription Start Sites and polyadenylation sites.

[holywoool]

Oh,thanks
With your scripts I see some lines that describe exon,I didn't notice this at first.
The coordinates appeared in the corresponding lines should be exon's 5' and 3' ends,this shall be confirmed with UCSC genome browser.
Thank you!

[holywoool]

Thanks,steven
You've taught me a new methord to use UCSC.With your instruction,I obtained all introns with terminal coordinates.And this will help me reconstruct splicing sites.
Thank you!