title: Carnivore-specific SINEs (Can-SINEs): distribution, evolution, and genomic impact.
abstract: Short interspersed nuclear elements (SINEs) are a type of class 1 transposable element (retrotransposon) with features that allow investigators to resolve evolutionary relationships between populations and species while providing insight into genome composition and function. Characterization of a Carnivora-specific SINE family, Can-SINEs, has, has aided comparative genomic studies by providing rare genomic changes, and neutral sequence variants often needed to resolve difficult evolutionary questions. In addition, Can-SINEs constitute a significant source of functional diversity with Carnivora. Publication of the whole-genome sequence of domestic dog, domestic cat, and giant panda serves as a valuable resource in comparative genomic inferences gleaned from Can-SINEs. In anticipation of forthcoming studies bolstered by new genomic data, this review describes the discovery and characterization of Can-SINE motifs as well as describes composition, distribution, and effect on genome function. As the contribution of noncoding sequences to genomic diversity becomes more apparent, SINEs and other transposable elements will play an increasingly large role in mammalian comparative genomics.
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, PA, USA. kwalt@sas.upenn.edu
authors.forename: Kathryn B
authors.initials: KB
authors.lastname: Walters-Conte
authors.forename: Diana L E
authors.initials: DL
authors.lastname: Johnson
authors.forename: Marc W
authors.initials: MW
authors.lastname: Allard
authors.forename: Jill
authors.initials: J
authors.lastname: Pecon-Slattery
mesh_terms: D000818:Animals; D001483:Base Sequence; D002335:Carnivora / Q000235:genetics*; D014644:Genetic Variation; D023281:Genomics / Q000379:methods*; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment; D020086:Short Interspersed Nucleotide Elements / Q000235:genetics*; D013045:Species Specificity