Fig. 3: Validation with isoform-specific regions.

a Isoform-specific sequence regions (pink) are defined as the parts of an isoform ORF not present in any other isoform from the same gene. Isoform-specific ORFs (green) are defined as a region shared between two isoforms, but with a different frame in each isoform. b Density of Ribo-seq reads per nucleotide over the isoform-specific sequence regions for isoforms with ≥1 unique mapping read for mouse glia (mmu glia n = 13,541) and hippocampus (mmu hipp n = 18,015) samples. Distributions are given for predicted translated isoforms, for isoforms that did not pass the threshold of uniformity and periodicity (not-translated), and for the isoforms with low expression (TPM < 0.1) (not evaluated). Other samples are shown in Supplementary Fig. 13a. Box boundaries correspond to the first and the third quartiles, the median is indicated by a thick black line, top and bottom whiskers extend up to 1.5 times the interquartile range to the highest and smallest values, respectively, and outliers are indicated as black dots. c Percentage of regions with ≥10 uniquely mapping Ribo-seq reads in isoform-specific sequence regions, for mouse glia (mmu glia) and hippocampus (mmu hipp) samples. Other samples are shown in Supplementary Fig. 13b. d Density of Ribo-seq reads per nucleotide over the specific ORF regions for isoforms with ≥1 P-site position count, for mouse glia (mmu glia n = 1143) and hippocampus (mmu hipp n = 1445) samples. Other samples are shown in Supplementary Fig. 13c. e Percentage of sequence- and ORF-specific regions with one or more mass-spectrometry peptides, separated according to region length, for mouse glia (mmu glia) and hippocampus (mmu hipp) samples. Box boundaries correspond to the first and the third quartiles, the median is indicated by a thick black line, top and bottom whiskers extend up to 1.5 times the interquartile range to the highest and smallest values, respectively, and outliers are indicated as black dots. f Proportion of isoforms expressed (TPM > 0.1) predicted to be translated and validated with one or more sources of evidence: conservation, unique regions, and counts per base or peptides in specific ORF regions.