Fig. 2

Genomic structure of ERV sequences. Panel a shows a schematic representation of a generalised retroviral provirus. The four coding domains found in all exogenous retroviruses are indicated. The precise organization of these domains varies among retrovirus lineages, and some viruses also encode additional genes. The long terminal repeat (LTR) sequences are comprised of three distinct subregions that are named according to their organization in the genomic RNA: unique 3′ region (U3), repeat region (R), and unique 5′ region (U5). Panel b shows a schematic representation of processes that modify ERV sequences. (1) Recombination between the two LTRs of a single provirus resulting in the formation of a solo LTR. (2) Recombination between the 3′ and 5′ LTRs of a given provirus leading to a tandem duplicated provirus. (3) Adaptation to intracellular retrotransposition, resulting in the loss of the envelope gene. (4) LINE1-mediated retrotransposition, resulting in loss of the 5′ U3 sequence, and the 3′ U5 sequence. Variants with larger 5′ truncations may also occur. Poly-A tails at the 3′ end and L1-typical target site duplications flanking the retrotransposed sequence are usually found for these forms.