Table 1

Analysis of the AS cases detected by EuGène-M in the AraSet genes data set. First, sequence IDs, genes and EST involved are reported. The TIGR and AtGDB columns indicate if each AS case is reported in these databases. The AS status is described as follows: ACC = alternative acceptor splice site, DON = alternative donor splice site, -EX = exon skipping (an entire exon lacks in the reported variant), +IN = intron inclusion (an internal part of an exon is spliced), FP = false positive AS. nt = nucleotide. Some ESTs of the At2g39780 gene in seq16 are not correctly aligned: the use of either GeneSeqer or sim4 with default options leads to a missed 4 nt exon (not involved in AS). In seq50, the 168 nt additional (+IN) intron from the EST CF652136 is flanked by GC-CT (instead of the canonical GT-AG). In seq62, the EST AV542276 from the gene At4g37040 overlaps with an intron of EST AV562725 from the neighboring gene At4g37050. In seq65, the EST BE521212 is not spliced between the exon 5 and 6 of the gene At2g44100 (intron retention case), and is thus suspected of incomplete maturation. Except for CF652136, all alignments can be browsed on the AtGDB site.

AraSet sequence

Gene ID

EST evidence

TIGR

AtGDB

AS status

Note

seq14

At2g47640

AI998209

Y

N

ACC

skip 3 nt

seq16

At2g39780

AV832175

N

N

-EX

incorrect alignments

seq50

At5g46290

CF652136

N

N

+IN

non consensus splice sites

seq53

At3g51800

AV544387

Y

Y

ACC

add 27 nt

seq62

At4g37070

AU236122

Y

Y

DON

add 33 nt

seq62

At4g37050

AV542276

N

N

FP

overlapping genes

seq65

At2g44100

BE521212

N

N

FP

incomplete splicing

seq65

At2g44120

BE524396

Y

N

ACC

skip 33 nt

seq69

At4gl4350

AV547538

Y

Y

+IN

skip 105 nt

Foissac and Schiex BMC Bioinformatics 2005 6:25   doi:10.1186/1471-2105-6-25