Fig. 4

Alternative transcript from the At1g76880 gene is highly expressed under heat stress. a Schematic of the putative ORFs of the At1g76880 gene. Black, CDS; gray, 5′ or 3′ UTRs; gray dashed line, intron, and arrow heads above the gene model: locations of the qRT-PCR primers. b In addition to the main transcript, a transcript encoding 88-amino acids long peptide is detected in both ribosome profiling and RNA-Seq data sets (plots on the left) as highly expressed at both transcriptional (mRNA reads, gray) and translational level (RPF reads, red) under heat stress. The dashed vertical line denotes the start of this additional ORF. Note the different scale of the coverage profile in the heat vs. control condition. qRT-PCR verification of the expression of the alternative transcript under stress (right panel) using primer pairs spanning the main and alternative transcript designated in panel a (arrow heads). c Three distinct recurring motifs are present within 1 kb-region upstream of the initiation of the alternative ORF (upstream 2100 nt) and multiple heat shock responsive genes as revealed by MEME motif analysis