Fig. 3

Examples of alternatively spliced transcripts represented by two oligos on the NSF45K array. a Example of alternative splicing for light-induced transcripts, Os01g63270.1 and Os01g63270.2. b Example of alternative splicing for dark-induced transcripts, Os01g14100.1, Os01g14100.2, and Os01g14100.3. The left panels of a and b show the primary structures of the TIGR/RGAP version 5 gene models for the two tested loci. The positions of the NSF45K array oligos, TR070452 (a), TR034207 (a), TR030998 (b), and TR070173 (b), are indicated as dark triangles. Arrows indicate the positions and directions of primers used, light blue boxes indicate exons, and the lines between the boxes indicate introns. Scale bar is 0.5 kb. The center panels display light vs. dark NSF45K microarray data. Oligo_id on the x-axis indicates the name of NSF45K oligo; transcript refers to the TIGR/RGAP version 5.0 gene model for the locus under examination; FDR is the adjusted p value. The y-axis indicates normalized spot intensity from the NSF45K light vs. dark experiment. The right panels show RT-PCR data for each locus. Genomic DNA shows the results of PCR with genomic DNA as a positive control to check primers. Transcript refers to the TIGR/RGAP version 5.0 gene model for the locus under examination; the number of PCR cycles is indicated. IL IR24 leaf harvested in the light, ID IR24 leaf harvested in the dark, TL Taipei 309 leaf harvested in the light, TD Taipei 309 leaf harvested in the dark, NL Nipponbare leaf harvested in the light, ND Nipponbare leaf harvested in the dark, KL Kitaake leaf harvested in the light, KD Kitaake leaf harvested in the dark. Actin 1 and Ubq1 were used as controls for RT-PCR [11].