Fig. 3
Functional impact and genomic features of differentially spliced events in A. thaliana. a Percentage of exon skipping (left), intron retention (middle), and alternative splice donor and acceptor sites (ALT splice sites, right) of events belonging to the different AS core sets located in UTRs or CDS gene regions. Among the latter category, the percentage of events that potentially affect protein levels or produce alternative protein isoforms is indicated (see “Methods” for details). Arrows indicate whether the levels of proteins are expected to increase or decrease in the stress or tissue-specific condition. b Log2 of the fold change in the expression values of upf1/upf3 double mutant (upf13) compared to WT for genes belonging to the different AS core sets. Data from [10]. c Percentage of events for which the inclusion of the alternative sequence is up- or downregulated from each AS core set that occur in the 5′ UTR of their respective genes. a–c “Genome” contains all multi-exonic A. thaliana genes fulfilling the coverage criteria used for the corresponding AS analysis. d Percentage of events from each subcategory that occur in genes with uORFs. Data from [42]. e Distributions of the lowest 5′ splice site (left) or 3′ splice site (right) strength per gene for each AS and GE core set. Values correspond to the splice site with the lowest maximum entropy score in each gene, calculated as in [43] (see “Methods”). f Number of binding sites of A. thaliana transcription factors (TF) per gene’s promoter (left) and promoter length for each gene (right). Promoter information was obtained from [44]. e, f AS-all and GE-all sets contain genes fulfilling the coverage criteria used for GE and AS analyses (see “Methods” for details). p values indicate statistical significance as assessed by two-sided Fisher’s exact tests (a), one-sided Fisher’s exact tests (c,d), or Wilcoxon rank-sum test (b,e). P < 0.05 (*); P < 0.01 (**); P < 0.001 (***). AS-NR, alternative spliced-non-regulated; n.s., not significant; w/, with; wo/, without