Hello

Could you please advise any database which contains coordinates of unique loci for every isoform of alternatively spliced genes? Or any tool which can count them?

Cufflinks' output contains information about isoforms' FPKM but there are now coordinates for these loci. MATS detects different splice event but gives no coordinates.
Try [the fly genome browser @ Ensembl][1]

 [1]: http://www.ensembl.org/Drosophila_melanogaster/Info/Index