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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.

From: Integrating alternative splicing detection into gene prediction

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