The study by Filichkin et al. investigates alternative splicing in *Arabidopsis thaliana* using high-throughput RNA sequencing (RNA-seq) to map the transcriptome at single-base resolution. The authors confirm a majority of annotated introns and identify thousands of novel alternatively spliced mRNA isoforms, suggesting that at least 42% of intron-containing genes in *Arabidopsis* are alternatively spliced, which is significantly higher than previous estimates based on cDNA/EST sequencing. They find that a substantial proportion of novel introns detected by RNA-seq carry non-consensus terminal dinucleotide splice signals and that many alternatively spliced isoforms contain premature termination codons (PTCs). These PTC-containing transcripts are likely to be targeted for nonsense-mediated mRNA decay (NMD) or regulated by the unproductive splicing and translation (RUST) mechanism. The study also demonstrates that the relative abundance of unproductive isoforms can be regulated by abiotic stress conditions, indicating that RUST may play a significant role in regulating gene expression in plants. Additionally, the authors show that intron retention in the circadian clock gene *CCA1* is evolutionarily conserved among diverse plant species and is regulated by different stress conditions. The findings suggest that alternative splicing in plants is more extensive and complex than previously thought, and that NMD and RUST may be widespread mechanisms for regulating gene expression.The study by Filichkin et al. investigates alternative splicing in *Arabidopsis thaliana* using high-throughput RNA sequencing (RNA-seq) to map the transcriptome at single-base resolution. The authors confirm a majority of annotated introns and identify thousands of novel alternatively spliced mRNA isoforms, suggesting that at least 42% of intron-containing genes in *Arabidopsis* are alternatively spliced, which is significantly higher than previous estimates based on cDNA/EST sequencing. They find that a substantial proportion of novel introns detected by RNA-seq carry non-consensus terminal dinucleotide splice signals and that many alternatively spliced isoforms contain premature termination codons (PTCs). These PTC-containing transcripts are likely to be targeted for nonsense-mediated mRNA decay (NMD) or regulated by the unproductive splicing and translation (RUST) mechanism. The study also demonstrates that the relative abundance of unproductive isoforms can be regulated by abiotic stress conditions, indicating that RUST may play a significant role in regulating gene expression in plants. Additionally, the authors show that intron retention in the circadian clock gene *CCA1* is evolutionarily conserved among diverse plant species and is regulated by different stress conditions. The findings suggest that alternative splicing in plants is more extensive and complex than previously thought, and that NMD and RUST may be widespread mechanisms for regulating gene expression.