Example of AS event observed by RNA-seq and RT-PCR. Top, gene model for Poptr_0001s00260 (annotated as encoding a transaldolase) from the Phyotzome browser of P. trichocarpa genome, v. 2.2 (http://www.phytozome.net). Exons are numbered 1–13. The 11th intron is retained in a splice variant. The average coverage is shown for the retained intron and adjacent exons in sample PT19. The mapped reads are presented below the illustrated retained intron and adjacent exons by short black lines, and the junction reads are denoted by the broken reads below the gene structure models. Bottom, RT-PCR analysis of Poptr_0001s00260 transcripts in RNA samples from individual poplar trees. Arrow indicates longer RNA isoform due to intron retention.