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

Table 3 Origin of previously described MSRV sequences

MSRV sequences	HERV-W source locus/loci	Number of nucleotide mismatches
env		no recombinations	recombinations
AF127227 (544 bp)	3q23	1 (1.84/kb)	n.a.
AF127228 (1932 bp)	Xq22.3	4 (2.07/kb)	n.a.
AF127229 (2004 bp)	3p12.3/18q21.32	94 (46.91/kb)	3 (1.5/kb)
AF123882 (2477 bp)	15q21.3	5 (2.02/kb)	n.a.
AF331500 (1629 bp)	Xq22.3/5p12	31 (19.03/kb)	5 (3.07/kb)
gag
AF123881 (1511 bp)	3q26.32	2 (1.32/kb)	n.a.

Previously published MSRV sequences were assigned by BLAT searches to corresponding HERV-W elements in the human genome. The accession number and length (base pairs, bp) of published MSRV clones are provided in the left column. The best matching HERV-W locus or loci (in case of recombined sequences) are indicated in column 2, and the number of nucleotide mismatches between MSRV sequences and the best matching genomic HERV-W elements in column 3. Note that for the recombined sequences, the number of nucleotide mismatches after assuming recombinations is markedly reduced. The average number of nucleotide differences of the 6 analyzed MSRV sequences to their best matching genomic HERV-W locus/loci was 1.97/kb. n.a., not applicable

ISSN: 1742-4690