Figure 1. Examples of changing alternative splicing (AS) patterns in overexpressing lines of SR proteins. (a) Schematic diagram showing AS pattern schemes for two repair endonuclease genes (RAD1 and RAD23). The open boxes refer to exon sequences, and black bars to intron sequence. The smaller open box shows the alternatively selected sequence, as indicated by lines labeled with AS1 and AS2, to indicate the events giving rise to different AS isoforms; (b) The * refers to a novel previously unannotated alternative splice site, while the black arrows indicate primers used for RT‐PCR to generate the AS profiles from three different SR protein overexpressing (OE) lines, RSp31, RSZ33, and SRp30. wt = wild‐type plant, and AS1, AS2 and * correspond to the alternatively spliced products indicated in the schematic diagram in panel (a); (c) Plots showing the percentage of spliced products for AS1 and AS2.

Figure 2. Characterizing novel alternatively spliced events. (a) Genemapper profile of region of At5g13730, showing expected alternatively spliced transcripts AS1 and AS2 and an unknown product (*); (b) Colony PCR amplification identified clones that contain the novel alternatively spliced product (*). A 500 bp marker band is shown; (c) Gene transcript models derived from sequence analysis and alignment of cloned products. The alternative use of 3′ splice sites is indicated (Alt 3′ss), and the novel intron retained product is shown (IR). Gene length is indicated by the bar at the top of the gene model in steps of 500 bp. Open boxes refer to coding exon sequences, and are numbered. Black lines between the boxes show the intron sequence. The black bars indicate 5′ and 3′UTR sequences, and the lines below the splice type label (Alt 3′ss) indicate the splicing event. Newly discovered AS events are labeled as Novel; (d) Full‐length cDNA sequencing of transcripts from the HY2 gene (At3g09150). The multiple exon skipping event is indicated (ES), and the intron retained transcript is shown (IR). Gene length is indicated by the bar at the top of the gene model in steps of 500 bp. Open boxes refer to coding exon sequences and are numbered. Black lines between the boxes show intron sequence. The black bars indicate 5′ and 3′UTR sequences, and the lines above the splice type label (ES) indicate the splicing event. Newly discovered alternative splicing events are labeled as Novel.