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 3505 (847) 8451 (1664) 2103
zebrafish 3685 (885) 8256 (1587) 2078
fugu 3576 (791) 7911 (1526) 1969
coelacanth 3241 (800) 8383 (1697) 2117
human 4755 (1300) 9183 (1711) 2460

Splicing Event Conservation:

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

Denominator: 2961 genes

57 cassette splicing events that are conserved in all 5 fish species (not human)
20 genes have cassette splicing events that are conserved in all 5 fish species (not human)
2262 cassette splicing events are conserved in all 5 fish species and human
480 genes have cassette splicing events that are conserved in all 5 fish species and human
4729 cassette splicing events from 1150 are conserved in at least one fish species