WORKFLOW

-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 (e-value threshold = 0.1 and identity % >= 30)
-If there are blast results for both spliced in and spliced out sequences, then that splicing event is conserved

Number of total cassette exons: 5051
Number of genes with cassette exons: 3037

Number of total cassette splicing events: 19009

BLAST RESULTS:

Species Number of Conserved Cassette Splicing Events Number of Non-conserved Cassette Splicing Events Number of genes with conserved splicing events
lamprey 13015 2363 2121
spotted gar 15862 1106 2470
zebrafish 14510 1968 2192
fugu 14824 1612 2318
coelacanth 14989 1522 2383

Splicing Event Conservation:

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

  • i.e 1620 mouse genes have cassette splicing events that are conserved in all 5 fish species
    TODO: blast against other mammals