Examples of ggRibo plots with Arabidopsis and tomato genes. The Arabidopsis seedling Ribo-seq and RNA-seq data are from Wu et al. (2024a). The tomato Ribo-seq and RNA-seq data are from Wu et al. (2019). Data presentations are as described in the Figure 3 legend. (A) Gene view of PAE7 shows that both isoforms are translated. Note that the RNA-seq coverage reveals that the 14th exon (highlighted) is longer than the annotated exon range for this isoform. The inferred exon 14 extension is shown with a blue dashed box (added with Adobe Illustrator). (B,C) A gene view and zoom-in view show the strong minimum uORF (i.e., AUG-stop) in SnRK2.2. In C, the Ribo-seq reads precisely map to the “A” and “T” of the start codon. Orange solid and dashed vertical lines represent the translation start and stop, respectively, for the uORF. (D) A small ORF is translated within TAS3, an annotated noncoding RNA (ncRNA). Robust 3 nt periodicity is detected in the 50-aa small ORF region. (E) A nested ORF (nORF) using the blue reading frame is detected in the Arabidopsis ALP2 gene. The nORF range is highlighted with an orange box in the gene model. (F) A nORF using the blue reading frame is detected in a tomato G protein-coupled receptor beta subunit gene. The nORF range is highlighted with an orange box in the gene model.