Figure 4.

Alternative end-joining in the formation of an adjacent segmental duplication. (A) Overview of the duplication. A 22.7 kb fragment consisting of several nested and partial CR1s, a CR2 solo LTR and a genomic repeat (gray) was duplicated locally (Figure S3D). Two full-length CR2 elements subsequently inserted into the downstream duplication (boxed). CR1 LTRs blue, CR2 LTRs red and CDS tan. (B) A 5 nt match between the polyprotein coding region at the 5′ end of the initial 22.7 kb fragment (top sequence) and the CR1 LTR (represented by the 3′ end of the duplicated region, bottom sequence) likely mediated this tandem duplication by alternative end-joining DNA repair following a double-strand DNA break. JV annotations: CR1 LTRs blue, CDS tan.