title: Discovery of a novel long terminal repeat (LTR2i_SS) in Sus Scrofa.
abstract: Long terminal repeat (LTR) retrotransposons are transposable elements flanked by 5'/3' LTRs. They have a structure similar to endogenous retroviruses, but they lack the envelope (env) gene making them non-infectious. Long terminal repeats are motif-rich sequences and can act as bidirectional promoters or enhancers to regulate or inactivate genes by insertion. In this study, we identified a new chimeric LTR subfamily, LTR2i_SS, in the pig genome. This chimeric LTR family appears to be the ancestral form of the previously described LTR2_SS family. LTR2_SS appears to have deleted ~300 bp of un-annotated, ancestral sequence from LTR2i_SS. We identified no functional provirus sequences for either of these LTR types. LTR2i_SS sequences have been exapted into the untranslated regions of two protein-coding gene mRNAs. Both of these genes lie within previously mapped pig quantitative trait loci.
authors.affiliation: School of Molecular and Biomedical Science, The University of Adelaide, North Terrace, Adelaide, 5005, SA, Australia.
authors.forename: Sim L
authors.initials: SL
authors.lastname: Lim
authors.forename: R Daniel
authors.initials: RD
authors.lastname: Kortschak
authors.forename: David L
authors.initials: DL
authors.lastname: Adelson
mesh_terms: D000818:Animals; D020077:Endogenous Retroviruses / Q000235:genetics / Q000378:metabolism; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D011533:Proviruses / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D034421:Sus scrofa / Q000235:genetics*; D020079:Terminal Repeat Sequences
keywords: exaptation; long terminal repeat; repetitive elements; retrotransposon; retrovirus