Table 2

Ratios of the number of transcripts supporting the alternative splicing classes of skipped exon (SE), initiation within intron (IWI), termination within intron (TWI), and retained intron (RI).

Variation

Prevalence

Rice

Arabidopsis


SE

Minor

1,603 (61.0%)

284 (54.2%)

Equal

118 (4.5%)

28 (5.3%)

Major

909 (34.5%)

212 (40.5%)

IWI

Minor

3,570 (94.5%)

763 (90.6%)

Equal

61 (1.6%)

21 (2.5%)

Major

146 (3.9%)

58 (6.9%)

TWI

Minor

3,988 (94.8%)

804 (93.9%)

Equal

58 (1.4%)

14 (1.6%)

Major

162 (3.8%)

38 (4.5%)

RI

Minor

7,713 (70.0%)

3,574 (76.6%)

Equal

546 (5.0%)

163 (3.5%)

Major

2,755 (25.0%)

926 (19.9%)


These counts and ratios were calculated from pairwise comparisons between PASA assemblies. Cases where only a single transcript supports a variation were excluded. For each variation type, SE, IWI, TWI and RI, the prevalence of evidence indicates that it is the minor variation for the majority of cases examined. Note that the cognate isoform for SE is the retained exon (RE) and the cognate isoform for RI is the spliced intron (SI).

Campbell et al. BMC Genomics 2006 7:327   doi:10.1186/1471-2164-7-327

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