SVA subfamily F1 can be subdivided into four transduction groups. (A) Transduction group 1 members carry exclusively MAST2 sequences as 5′ transduction. They could be direct descendants of source elements 1A, 1B, 2, or 3 (Fig. 8) except for H17_2 and H15_5. The latter can only be derived from source elements 1A or B due to the extension of their transduced MAST2 sequence. In theory, within this group any given SVA_F1 member could have served as a source element of any other SVA_F1 member whose MAST2 sequence is equal in length or shorter than its own. Source elements and polymorphic SVA_F1 members are marked by red and blue lettering, respectively. Yellow boxes; MAST2 sequence; red boxes, TSDs flanking AluY insertion; *, element was originally described by Bennett et al. 2004 and named as denoted in brackets. (B) Transduction group 2. In addition to MAST2 sequences, members of this group include heterologous sequences (pink boxes) as part of their 5′ transductions. Heterologous sequences indicating consecutive transduction events are derived from source locus 2 (Fig. 8B) on chromosome 9p13.3 (H10_1, H19_56, and H6_17), from sequences of non-LTR retrotransposons or endogenous retroviruses whose source loci could be identified (H6_2, H8_F116, H9_2, H22_17, H3_5, and H12_3), or they represent nonrepetitive genomic DNA fragments ranging from 21–107 bp (H1_F_67, H12_2, H1_F_163, H8_2). TSD-flanked intact Alu elements in sense orientation are part of H10_1, H19_56, and H22_17. H3_5 displays secondary (AluY) and tertiary (NPEPPS exon sequences) transduction events. Numbers indicate extensions of different modules of 5′-transduced heterologous (pink boxes) and MAST2 (yellow boxes) sequences and VNTRs. TSDs flanking AluSc and AluSp elements (red arrowheads), as well as all remaining Alu sequences (blue bars) are shown. Open boxes indicate genomic DNA flanking the SVA insertion. (C) Members of transduction group 3 include 3′ transductions. SVA_F1 members with 3′ transductions and their source elements are shown. Primary 3′ transductions of HX_4 and H9_1 originate from SVA-free source loci (data not shown). The source element of H6_6 is H1_F_160 (in brackets), a member of transduction group 1 (Fig. 7A). MER57A represents internal portions of the nonautonomous endogenous retrovirus 1 (ERV1) family. Yellow boxes depict 5′-transduced MAST2 sequences and/or 3′ transductions, respectively. Numbers denote the length of 5′- and 3′-transduced sequences, their components, and VNTR regions in nucleotides. Red ovals, TSDs flanking SVA elements; blue ovals, TSD sequence of the respective source element that became part of 3′ or 5′ transductions. (D) Members of transduction group 4 are derivatives of source element H10_1. Structures of the 13 identified members of transduction group 4 and their source element H10_1 are shown. Two consecutive transcriptional termination signals (asterisks) in the 3′-flanking sequence of H10_1 resulted in 3′ transductions of 400 and 479 bp, respectively. The 3′ TSD of the source element is overlapping with the 5′ TSD of AluSp. Lengths of 5′-truncated VNTRs of H10_7, H15_2, H15_3, and H6_5 range from 241–2098 bp. H19_47 is a source element of H1_F_163 (Fig. 7B); Black bars, extension of query sequences 1 and 2.
