Fig. 4

Discovery of SR45-associated transcripts and motifs in inflorescence. a Discovery of enriched motifs with highest occurrence in SR45-associated transcripts. SAR genes identified by Salmon and LG12 separately were compared, and the common genes were submitted to XXmotif to solicit enriched motifs in control (pC) and two independent SR45.1-GFP lines (p1 & p9). The 215 common motifs between p1 and p9, but not in pC were isolated and used for motif distribution analysis in the SAR genes. The locations of the top four highly occurring motifs around a splicing event were visualized as the ratio of the number of one particular Motif at a particular location /the number of total motifs observed in this particular location. b qPCR confirmation of SARs. n = 3. Error bars present Standard Error of Mean (SEM). * p < 0.05; ** p < 0.01; *** p < 0.001. c Venn diagram showing a comparison of SAR genes between seedling (Xing, 2015) and inflorescence and their GO enrichment. All selected GO terms have p-value < 1.0E-05 and fold of enrichment >2.0. d Venn Diagram showing SAR genes that are also subject to SR45-dependent alternative splicing, and/or NMD. e qPCR confirmation of SAR examples of NMD targets. GAPDH was used as control. n = 3. Letters a-c denote statistically significant difference among Col-0, sr45–1 and upf3–1 analyzed by Student t-test with Bonferroni correction. p < 0.05. f Intronless SARs identified by TAIR10 and/or AtRTD2