Expression pattern analysis of transcribed HERV sequences is complicated by recombination-0

<p><b>Copyright information:</b></p><p>Taken from "Expression pattern analysis of transcribed HERV sequences is complicated by recombination"</p><p>http://www.retrovirology.com/content/4/1/39</p><p>Retrovirology 2007;4():39-39.</p><p>Published online 6 Jun 2007</p><p>PMCID:PMC1904241.</p><p></p> genome. The majority of cDNAs displayed between zero and a few differences to the best match, and were thus assignable to specific HML-2 loci. A minority of cDNAs displayed a greater number of dissimilarities to the best match and were thus not assignable with confidence to specific HML-2 loci. HERV-KX sequences were defined as displaying 18 or more nucleotide differences to the best matching HML-2 locus. (B) Sequence divergence of HERV-KX sequences in comparison to selected HML-2 reference sequences from the human genome, depicted as a neighbour joining-tree of the absolute number of nucleotide differences between sequences. For the sake of clarity, phylogenetically more distant HML-2 reference sequences were not included in the tree, as they were less similar to HERV-KX sequences than the reference sequences included in the tree. Proviral reference sequences are given as "xx_xxx" (see text). Positions with gaps were excluded in pairwise sequence comparisons

Expression pattern analysis of transcribed HERV sequences is complicated by recombination-3

<p><b>Copyright information:</b></p><p>Taken from "Expression pattern analysis of transcribed HERV sequences is complicated by recombination"</p><p>http://www.retrovirology.com/content/4/1/39</p><p>Retrovirology 2007;4():39-39.</p><p>Published online 6 Jun 2007</p><p>PMCID:PMC1904241.</p><p></p> genome. The majority of cDNAs displayed between zero and a few differences to the best match, and were thus assignable to specific HML-2 loci. A minority of cDNAs displayed a greater number of dissimilarities to the best match and were thus not assignable with confidence to specific HML-2 loci. HERV-KX sequences were defined as displaying 18 or more nucleotide differences to the best matching HML-2 locus. (B) Sequence divergence of HERV-KX sequences in comparison to selected HML-2 reference sequences from the human genome, depicted as a neighbour joining-tree of the absolute number of nucleotide differences between sequences. For the sake of clarity, phylogenetically more distant HML-2 reference sequences were not included in the tree, as they were less similar to HERV-KX sequences than the reference sequences included in the tree. Proviral reference sequences are given as "xx_xxx" (see text). Positions with gaps were excluded in pairwise sequence comparisons

Expression pattern analysis of transcribed HERV sequences is complicated by recombination-1

<p><b>Copyright information:</b></p><p>Taken from "Expression pattern analysis of transcribed HERV sequences is complicated by recombination"</p><p>http://www.retrovirology.com/content/4/1/39</p><p>Retrovirology 2007;4():39-39.</p><p>Published online 6 Jun 2007</p><p>PMCID:PMC1904241.</p><p></p>een transcripts from different HML-2 proviral loci. Three examples of HERV-KX sequences were multiply aligned with HML-2 proviral sequences, the transcripts of which served as template for recombination events. HERV-KX sequence "93" was generated by one recombination event involving two loci. HERV-KX sequence "B270" was generated by two recombination events involving three loci. HERV-KX sequence "94" was generated by two recombination events involving two different proviral templates. Probable recombination regions are indicated by medium grey background. Light and dark grey background indicates proviral templates. Localization of the RT-PCR amplicon and the 96 bp sequence (see text) within the HML-2 gag gene/provirus is depicted above the sequence comparisons