Additional file 3 of LINE-1 ORF1p does not determine substrate preference for human/orangutan SVA and gibbon LAVA

Additional file 3: Subgroups of human SVA_E elements containing both fixed and polymorphic elements. SVA_E3: VNTR subunit structure of SVA_E subgroup E3 containing four fixed and four polymorphic elements. Based on divergence from subgroup consensus (div; Alu-like region and SINE-R) and VNTR structure the two fixed elements on chromosome 1 would be candidates to test for activity. AF - allele frequency as provided in Stewart C, Kural D, Strömberg MP, Walker JA, Konkel MK, et al. (2011) A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans. PLoS Genet 7(8): e1002236. Arrays of VNTR subunits are boxed. Polymorphic elements are highlighted in yellow. SVA_E4: VNTR subunit structure of SVA_E subgroup E4 containing eight fixed and three polymorphic elements. Candidates to test for activity based on divergence from subgroup consensus (div; Alu-like region and SINE-R) and VNTR structure are indicated. AF - allele frequency; Sources: chr1:112,834,947–112,837,733–1000 Genomes Phase 3 Integrated Variant Calls track of the UCSC genome browser; chr2:223760192–223,762,683 - Stewart C, Kural D, Strömberg MP, Walker JA, Konkel MK, et al. (2011) A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans. PLoS Genet 7(8): e1002236; chr5:43,086,412-43,089,307 - dbRIP. Arrays of VNTR subunits are boxed. Polymorphic elements are highlighted in yellow.