Fig. 1
From: LINE-1 ORF1p does not determine substrate preference for human/orangutan SVA and gibbon LAVA
General structure of VNTR composite retrotransposons and SVA/LAVA subfamilies in hominoid primates. a Structure of SVA/LAVA. The elements are composed of (from 5′) hexameric repeats (TCTCCC)n, an Alu-like region, variable number of 36-49 bp tandem repeats (VNTR) and either a retrovirus-derived SINE (SINE-R in SVA) or a 3′ domain containing L1 and Alu fragments (LA in LAVA). They terminate with a poly A tail (AAA)n. b Currently active LAVA and SVA subfamilies in hominoid primates. Blue and yellow bars indicate short deletions relative to the ancestral SVA_A sequence. Tildes represent the apparently unstructured central part of gibbon LAVA. The VNTR subunit code is that described in Lupan et al. [4]. TR represents the invariable tandem repeats at the VNTR 5′ end. Note that the type and sequence of subunits in this part is not identical among subfamilies (for details see [4]). The overall structure of SVA_D elements in gorilla and chimpanzee corresponds to that shown for humans. LAVA_F, OU3, OU4, H19_27 and H8_43 denote the LAVA/SVA elements used in the study. The position indicates their subfamily affiliation. c Non-canonical SVAs in human and chimpanzee. In SVA_F1 and pt_SVA_D6 the hexameric repeat and larger part of the Alu-like regions are replaced by the first exons of MAST2 and STK40, respectively