Figure 4

HERV structure and breakpoint distribution of HERV-mediated CNVs. Structures of the HERV elements involved at each locus are presented compared to the consensus HERV-H sequence from RepBase. Gaps in the consensus represent insertions in the genomic HERV elements mediating the CNVs. Gaps in the genomic HERVs represent deletions compared to the reference. The color of the genomic HERV elements denotes identity at that position when aligned with its partner element over a 50-bp window. Blue represents 0% sequence identity (i.e. caused by a large insertion or deletion) while orange represents perfect identity. The region of the crossover for each patient is presented as a colored X with the size of the X representing the uncertainty bounded by informative cis-morphisms. Red X’s indicate deletions; green X’s indicate duplications; the purple X represents breakpoints for two patients that occurred between the same two cis-morphisms. Recombination hotspot motifs in each HERV element are annotated along the HERV sequences as black H’s. The relative positions of the genes encoded in the HERV genome are annotated along the top of the first consensus. * Previously published locus. CNV, copy-number variation; HERV, human endogenous retrovirus; LTR, long tandem repeat.