Fig. 5: Annotation with constrained, non-conserved regions (CNCRs) is highly granular and shows APOE to have a high density of CNCRs throughout its length especially in association with an intron-3 retention event in the human hippocampus. | Nature Communications

Fig. 5: Annotation with constrained, non-conserved regions (CNCRs) is highly granular and shows APOE to have a high density of CNCRs throughout its length especially in association with an intron-3 retention event in the human hippocampus.

From: Human-lineage-specific genomic elements are associated with neurodegenerative disease and APOE transcript usage

Fig. 5

The first track represents the genomic location of APOE within chromosome 19. The second track shows the known transcripts, currently within annotation in Ensembl v.92. The mean coverage (MC) (log10 scale) in the hippocampus shown here is greater than zero (denoted by the grey shaded area) across intron-3 highlighting an intron-3 retention event (mean coverage data derived from GTEx v.7). In the fourth track, CNC scores above the black dashed line and shaded in red fulfil criteria for a constrained, non-conserved region (CNCR) are shown. The intron-3 retention event has the highest CNCR density among all intronic regions of APOE. The fifth track labelled “CNCR” depicts regions fulfilling criteria for CNCR. PC20 represents the mean phastCons20 score. The black dashed line within this track represents a mean phastCons20 score of 0. CDTS represents the context-dependent tolerance score as a measure of constraint with the black dashed line showing a CDTS of 0. Within the CDTS track, the blue dotted line represents a region with no CDTS annotation.

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