Fig. 3

Transcriptional potential and selection of ERV-ORFs. a Proportion of ERV-ORFs downstream of TSS as obtained from FANTOM datasets in each 1000 bp bin (all: light blue, transcriptional potential (tp): pink). ERVs without ORFs (non-ERV-ORFs) are shown for comparison (gray). The x-axis represents the distance between ERV-ORFs and the closest TSS. An asterisk (*) indicates statistically significant differences when comparing numbers of the observed ERV-ORF to those expected using proportions of the non-ERV-ORF for each bin (p -value < 0.001, chi-squared test, FDR corrected). b Top: PCA plot for TSSs from CAGE datasets, located upstream of ERV-ORFs. Colors represent different tissues/cell lines. COBLa_rind, COBL-a (a cell line established from human umbilical cord blood) infected by rinderpest; H9EB/ES, H9 embryoid bodies/embryonic stem cells; MSC, mesenchymal stem cells; RPE, retinal pigment epithelium. Bottom: PCA plot for TSSs from CAGE datasets, located upstream of non-ERV-ORFs. Colors are the same to the panel c. c The number of ERV-ORFs in mammalian species showing synteny with the human ERV-ORFs. The total number of syntenic ERV-ORFs is shown in gray and non-gray. For the total number of syntenic ERV-ORFs with length > 90% of the human ERV-ORF, each species is shown with a different color. An enlarged graph for the numbers of non-primate species (highlighted with a pink bar on the right side of species names) are shown as an inset. d Boxplots of pairwise dN/dS ratios for syntenic ERV-ORFs with length > 90% of human ERV-ORFs. Horizontal lines in the middle of each box represent the median value, and edges of boxes are lower and upper quartiles with whiskers as 1.5 times the interquartile range. Single points are beyond the range. e Divergence of all ERV-ORFs and ERV-ORFs with transcriptional potential in human-chimpanzee pairs. The scatter plot shows Kimura 2-parameter divergence to Repbase reference sequences (x-axis) and dN/dS ratios (y-axis) of ERV-ORFs. ERV-ORFs with transcriptional potential of dN/dS < 1, and all ERV-ORFs were shown in blue and gray, respectively. Histograms of divergence and dN/dS ratios are shown on the bottom and right of the scatter plot, respectively. For the histogram of divergence, median values of ERV-ORFs with transcriptional potential of dN/dS < 1, and all ERV-ORFs are shown in blue and gray, respectively. For the histogram of dN/dS ratio, gray and pink represent all ERV-ORFs and ERV-ORFs with transcriptional potential, respectively