Table 1.

Significant AS Events in Core Clock Genes

GeneAS EventSequencingTAIRAS EventNMD
LHYUAS4Sanger/NGSTAIR.2IR1 (5′UTR)NMD (P < 0.05)a
AS5Sanger/NGSTAIR.5Alt 3′ss and alt 5′ss adds alternative exon of 82 nucleotidesNMD (P < 0.01)a
AS9Sanger/NGSAlt 3′ss in exon 8 removes 3 nucleotides (TAG/CAG)In frame, no NMD observed
CCA1AS5Sanger/NGS/Filichkin et al. (2010)IR4No NMD observed
AS14UnknownUnknownNot determined
PRR9AS2SangerTAIR.2Alt 5′ss in IVS2 adds 8 nucleotidesNMD possible (P < 0.1)
AS4Sanger/NGSIR3No NMD observed
PRR7AS1SangerES Ex4NMD (P < 0.01)
AS3SangerIR3No NMD observed
PRR5AS1PredictedbAlt 5′ss in exon 1 or alt 3′ss in exon 2 each could remove nine nucleotidesNo NMD observed
AS3SangerAlt 3′ss in IVS3 adds 47 nucleotidesNMD (P < 0.01)
PRR3UAS1NGSAlt 3′ss removes seven nucleotides from exon 2; uORF increased from nine to 29 amino acidsNo NMD observed
UAS2UnknownUnknownNot determined
AS3Sanger/NGSIR8No NMD observed
  • Features of the 15 AS events that change significantly after transfer of plants to 4°C. ASn, AS variant where n is the number to identify the product; UASn, unspliced transcript; ES, exon skip; ss, splice sites. The P values are for differences between Col-0, upf1-5, and upf3-1 by analysis of variance; n = 3.

  • a NMD only observed in some conditions.

  • b Predicted from size of RT-PCR product, sizes of introns, skipped exons, and positions of putative alternative 5′ or 3′splice sites.