WORKFLOW

blastx against ensembl protein database

-For each cassette exons, find the upstream and downstream exons
-Blast sequences with cassette exon spliced in and spliced out against the five fish species
-If there are blast results for both spliced in and spliced out sequences, then that splicing event is conserved

Number of total cassette exons: 4926
Number of genes with cassette exons: 2961

Number of total cassette splicing events: 18354

Non-conserved means blast hits for either the spliced in or spliced out sequences (exclusive or)

BLAST RESULTS:

Species Number of Conserved Cassette Splicing Events (# of genes) Number of Non-conserved Cassette Splicing Events (# of genes) Number of genes with at least one conserved isoform
spotted gar 4979 (860) 7812 (1668) 2103
zebrafish 5126 (901) 7646 (1590) 2078
fugu 5003 (805) 7350 (1529) 1969
coelacanth 4581 (815) 7963 (1698) 2117
human 6439 (1310) 8376 (1715) 2460

Splicing Event Conservation:

upset(fromList(listInput), nsets = 5, order.by = "freq")

Denominator: 2961 genes

78 cassette splicing events that are conserved in all 5 fish species (not human)
21 genes have cassette splicing events that are conserved in all 5 fish species (not human)
3263 cassette splicing events are conserved in all 5 fish species and human
496 genes have cassette splicing events that are conserved in all 5 fish species and human
6587 cassette splicing events from 1160 are conserved in at least one fish species