Eyras Ribo Data Ensembl BLASTX
WORKFLOW
blastx against ensembl protein database
-Blast sequences with cassette exon spliced in and spliced out against the five four species and human
-Filter: the alignment must start in the upstream exon and end in the downstream exon
-Gap introduced cannot be larger than the cassette exon length / 3
-If there are blast results for both spliced in and spliced out sequences, then that splicing event is conserved
Number of total cassette splicing events: 6898
Number of genes involved: 4121
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 | 1531 (1228) | 3577 (2551) | 3295 |
| zebrafish | 1611 (1272) | 3404 (2492) | 3261 |
| fugu | 1451 (1181) | 3218 (2370) | 3098 |
| coelacanth | 1446 (1182) | 3624 (2556) | 3265 |
| human | 2775 (2029) | 3574 (2622) | 3894 |
Splicing Event Conservation:
upset(fromList(listInput), nsets = 5, order.by = "freq")
21 cassette splicing events that are conserved in all 5 fish species (not human)
19 genes have cassette splicing events that are conserved in all 5 fish species (not human)
783 cassette splicing events are conserved in all 5 fish species and human
674 (16.4%) genes have cassette splicing events that are conserved in all 5 fish species and human
2306 cassette splicing events from 1753 are conserved in at least one fish species