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 (e-value threshold = 0.1 and identity % >= 30 and query coverage >= 70)
-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: 19015

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
lamprey 3499 (427) 3260 (697) 969
spotted gar 7358 (899) 3875 (1036) 1628
zebrafish 6783 (889) 3806 (972) 1559
fugu 6372 (825) 3865 (938) 1486
coelacanth 5496 (938) 4071 (1016) 1619
human 10495 (1559) 3672 (994) 2128
C. elegans 1794 (145) 1655 (427) 506

Splicing Event Conservation:

upset(fromList(listInput), nsets = 7, order.by = "freq")

  • i.e 94 mouse genes / 300 (31%) have cassette splicing events that are conserved in all 5 fish species, human and C. elegans
    300 mouse genes / 693 (43%) have cassette splicing events that are conserved in all 5 fish species, human and C. elegans

TODO: blast against other mammals
-take the first hit (the one with the highest bit score)
-legnth vs bit