SVAs contain many transcriptional start sites (TSSs). 5′ RACE was performed on total RNA extracted from 293T, HeLa, and nTera cell lines, along with chimp testes. A nested PCR was performed followed by Sanger sequencing of Topo clones. The 5′ RACE adaptor was identified, and the first nucleotide after it was annotated as the TSS. Human (red triangles) and chimp TSS (blue triangles) within SVA are aligned relative to the position in SVARep. The CCCTCT hexamer (Hex), Alu-like region, and part of the VNTR are shown. TSSs aligning upstream of SVA are displayed relative to the first nucleotide of the SVA insertion in the genome. Both human (red triangles) and chimp (blue triangles) TSSs identified by 5′ RACE are shown.
