Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence homology

Table 1 Mutually exclusive exons in the Drosophila species Dscam genes

exon	Dm	AF260530	Dse^a	Dy	Der	Da	Dp	Drp^a	Dw	Dmo	Dv	Dg
4	12	12	12	12	12	12	12	10	12	12	12	12
6^b	46/47	47/48	46^c	39/40	44	47	49	49	48/49	50	52	53
9	32	33	29	32	33	33	32	29	29	32	32	32
17	2	2	2	2	2	2	2	2	2	2	2	2
total	92/93	94/95	90	85/86	91	94	95	90	91/92	96	98	99
[16, 46]	95	95	95	87	94	93	94	95	95	95	98	94
[15]	95	95		88		93	94			95	98

Dm = Drosophila melanogaster; Dse = Drosophila sechellia Rob3c; Dy = Drosophila yakuba Tai18E2; Der = Drosophila erecta TSC#14021-0224.01; Da = Drosophila ananassae TSC#14024-0371.13; Dp = Drosophila pseudoobscura MV2-25; Drp = Drosophila persimilis MSH-3; Dw = Drosophila willistoni TSC#14030-0811.24;
Dmo = Drosophila mojavensis TSC#15081-1352.22; Dv = Drosophila virilis TSC#15010-1051.87; Dg = Drosophila grimshawi TSC#15287-2541.00.
^a Genomes are fragmented and contain gaps in the Dscam genes.
^b The first number corresponds to a search with standard parameters, the second to searches with one round of recursion.
^c One of the exons is a pseudo-exon because it misses the last forth of the exon because of an in-frame stop codon.

ISSN: 1471-2105