Examples of recombined HERV-W env cDNA sequences. A multiple alignment of the genomic DNA sequences (March 2006 human genome assembly) of the seven HERV-W env loci identified as transcriptionally active in human PBMC in this study is shown. HERV-W env loci are designated according to their chromosomal location. The 7q21.2 HERV-W env locus (ERVWE1) serves as reference sequence. Note that the 7 HERV-W env loci can be distiguished by unique nucleotides and/or indels. Two of the cloned HERV-W env cDNA sequences, MS-III-K11 (from a patient with MS) and KO-IV-K6 (from a healthy control) are shown as examples of recombined cDNAs. The proviral origin of cDNA sequence portions is indicated by a color code. Gray shaded areas represent regions in which recombination events have taken place. Sequences of the primers used in this study are underlined.