A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana

BMC Bioinformatics

Table 1 Experimental evidence for predicted ESE hexamers.

9mer ESE	ESE Score	Mutant ESE	Mutant Score	Contained Hexamer Motifs
GAAGAAGAA	5	GCAGAAAAA	-1	gaagaa, aagaag
TGCTGCTGG	5			tgctgc, gctgct
TGCAGCTGG	5			gcagct, cagctg
GAAGATGGA	5			gaagat, aagatg, gatgga
GAAGGAAGA	5			gaagga, aaggaa, ggaaga
GAGAAGAAG	5			gagaag, gaagaa, aagaag
TTGGAGCAA	5			ttggag, ggagca
AGCTGCTGG	4			agctgc, gctgct
TGCTGGTGG	4			tggtgg
TGCTGCAGG	4			tgctgc, ctgcag
TGCTGCTCG	4			tgctgc, gctgct
TGCTGCTGC	4	TACTTCTGC	-3	tgctgc, gctgct
GAGGATTGA	4	GAGAATTGA	-1	gaggat
TGCAGATGA	4			gcagat, cagatg
CAAGAAACA	4			aagaaa
GAAGAGAAA	4	GCAGAAAAA	-1	aagaga
AAAGGAGAT	4			aaggag, aggaga, ggagat
GAAGAAAGA	4			gaagaa, aagaaa
GAGCAGAAG	4			gagcag
TGCTGCCGC	4			tgctgc
TTGAAGAAG	3	TTGAAAAAG	-3	ttgaag, tgaaga, gaagaa, aagaag
TTGAAGCTG	3	TTAAAGCTG	-3	ttgaag, tgaagc, gaagct, aagctg
GAAGATTGA	3	GAGAATTGA	-1	gaagat
TTTGGTGGA	3			tggtgg, ggtgga
ATGGAGAAA	3	ATTGAGAAA	-3	atggag, tggaga, ggagaa

Hexamer motifs that are contained within experimentally confirmed 9-mers with ESE activity (column 5). Experiments to confirm 9-mers are described elsewhere (S. Mount et al., manuscript in preparation). Column 1 shows the containing ESE ninemer, and column 3 shows ninemers without ESE activity, which are situated within 1–2 bp edit distance from the ESE ninemer. The ESE activity of each 9-mer in the table is shown by a score equal to log₂(inclusion/skipping) [34].

ISSN: 1471-2105