Analysis of transcribed human endogenous retrovirus W env loci clarifies the origin of multiple sclerosis-associated retrovirus envsequences

Table 1 Characteristics of HERV-W env loci identified in this study as transcribed in human PBMC

HERV-W env locus	strand	location of amplicon in genome		5' LTR	3' LTR	processed pseudogene	full-length Env ORF
5q11.2	-	56852791	56853425	absent	Δ325–780	+	-
6q21	+	106788519	106789159	Δ1–255	Δ327–780	+	-
7q21.2 (ERVWE1)	-	91936808	91937448	complete	complete	-	+ (538 aa)
14q21.3	-	44559628	44559996	absent	Δ327–780	+	-
15q21.3	-	53385554	53386189	Δ1–255	Δ327–780	+	-
17q12	+	32765922	32766546	absent	Δ327–780	+	-
Xq22.3	-	106183197	106183837	absent	Δ327–780	+	-*

The chromosomal location of transcriptionally active HERV-W env loci is indicated in the first column. Nucleotide positions of amplicons on the respective chromosomes (human genome sequence March 2006 assembly) are indicated. Structures of the 5' and 3' LTRs of transcribed HERV-W env loci are given with respect to the 780-bp HERV-W LTR consensus sequence (LTR17) obtained from Repbase http://girinst.org/repbase/update/[37]. Missing nucleotides (Δ) in the LTRs as compared to the consensus LTR sequence are indicated. All but one locus represent processed pseudogenes. Presence of full length ORFs for HERV-W Env proteins is given in the final column.
* The Xq22.3 locus contains an ORF for a hypothetical N-terminally truncated 475 amino acid HERV-W Env protein.

ISSN: 1742-4690