Full-length HERV-H elements with env SU open reading frames in the human genome.
Human endogenous retroviruses (HERVs) are estimated to represent at least 1% of the human genome. An HERV-H env SU sequence (HERV-H19) was used to screen the high-throughput (htgs) and nonredundant (nr) databases for other HERV-H SU open reading frames (ORFs) and thus possible functional proteins. Using PCR with primers derived from HERV-H19 SU, we also obtained several new sequences with ORFs from a human DNA sample. In a phylogenetic analysis, ORF-containing sequences clustered with HERV-H sequences from chromosomes 1 and 2. SU ORF- and non-SU ORF-containing elements had about the same difference between 5' and 3' long terminal repeats (LTRs) (about 4%), indicating a similar time of integration. SU ORF sequences had a moderately high number of synonymous-versus-nonsynonymous mutations, which indicates a selection for maintenance of the HERV-H SU ORFs.
Jern
Patric
P
Section of Virology, Department of Medical Science, Uppsala University, SE-751 85 Uppsala, Sweden. Patric.Jern@medsci.uu.se
Lindeskog
Mats
M
Karlsson
Damita
D
Blomberg
Jonas
J
D000595:Amino Acid Sequence; D002878:Chromosomes, Human, Pair 1; D002889:Chromosomes, Human, Pair 2; D020077:Endogenous Retroviruses / Q000235:genetics*; D015686:Gene Products, env / Q000235:genetics*; D015894:Genome, Human; D006801:Humans; D008969:Molecular Sequence Data; D005810:Multigene Family; D009154:Mutation; D016366:Open Reading Frames / Q000235:genetics; D012191:Retroviridae Proteins / Q000235:genetics*; D017386:Sequence Homology, Amino Acid
D015686:Gene Products, env; C464079:HERV-H19 protein, human; D012191:Retroviridae Proteins