Genome-wide nucleotide composition, gene structure and gene annotation biases for TEV occurrence. (a) Having accounted for these GC biases, TEVs are substantially and significantly depleted (red shades) in exons and introns, with the notable exception of SINEs that are enriched (green shades) in intronic regions. Both SINE and ERV TEVs are enriched in 5 kb upstream and downstream flanking regions of genes, while LINEs are depleted. (b, c) Gene annotations that are significantly enriched (green shades) or depleted (red shades) in intronic or intergenic TEV insertions having accounted for GC content, and intronic or intergenic lengths, and after adjusting for multiple tests. Gene annotations are from either the Gene Ontology (slim set) (b) or the Mouse Genome Informatics phenotypes associated with gene disruptions (c), and are shown when at least one significant association (P < 10-6) was observed. SINE TEVs show a pattern of enrichments and depletions that is the complement of the patterns for LINE and ERV TEVs. * Sequence-Specific DNA binding Transcription Factor activity.