ArticleGenome research2005
Short interspersed elements (SINEs) are a major source of canine genomic diversity.
Article in Genome research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed, 128 citations in OpenAlex.
- Recent Dominant Transposition Events Affect Gene Regulatory Regions, but Not Coding Sequences, in Polar and Brown Bear Genomes.Current issues in molecular biology · 2026Article
- Diploid dual assemblies reveal the telocentric structure and extensive allelic heterogeneity of canine genomes.NAR genomics and bioinformatics · 2026Article
- A phylogenetic estimate of canine retrotransposition rates based on genome assembly comparisons.Mobile DNA · 2026Article
- Family C of Short Interspersed Elements in the Genomes of Lagomorphs: Structure, Evolution, Transcription and Transcript Polyadenylation.Animals : an open access journal from MDPI · 2026Article
- Influence of homozygosity on genomic structural variation analyses for predicting ACL rupture risk in the Labrador Retriever and Rottweiler.Frontiers in genetics · 2026Article
- A phylogenetic estimate of canine retrotransposition rates based on genome assembly comparisons.bioRxiv : the preprint server for biology · 2025Article
- Integrative Genotyping and Analysis of Canine Structural Variation Using Long-read and Short-read Data.Genome biology and evolution · 2025Article
- Analysis of RNA Transcribed by RNA Polymerase III from B2 SINEs in Mouse Cells.Non-coding RNA · 2025Article
- SINE retrotransposons import polyadenylation signals to 3'UTRs in dog (Canis familiaris).Mobile DNA · 2025Article
- Analyses of theInternational journal of molecular sciences · 2024Article
- Unraveling the DNA methylation landscape in dog blood across breeds.BMC genomics · 2024Article
- Article
- Ere, a Family of Short Interspersed Elements in the Genomes of Odd-Toed Ungulates (Perissodactyla).Animals : an open access journal from MDPI · 2024Article
- Duplications and Retrogenes Are Numerous and Widespread in Modern Canine Genomic Assemblies.Genome biology and evolution · 2024Article
- A naturally occurring canine model of syndromic congenital microphthalmia.G3 (Bethesda, Md.) · 2024Article
- Structural genomic variation in the inbred Scandinavian wolf population contributes to the realized genetic load but is positively affected by immigration.Evolutionary applications · 2024Article
- Genome-wide methylation patterns from canine nanopore assemblies.G3 (Bethesda, Md.) · 2023Article
- SINEs as Potential Expression Cassettes: Impact of Deletions and Insertions on Polyadenylation and Lifetime of B2 and Ves SINE Transcripts Generated by RNA Polymerase III.International journal of molecular sciences · 2023Article
- Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture.Genome biology · 2023Article
- Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat,NAR genomics and bioinformatics · 2023Article
19 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
SINEs are retrotransposons that have enjoyed remarkable reproductive success during the course of mammalian evolution, and have played a major role in shaping mammalian genomes. Previously, an analysis of survey-sequence data from an individual dog (a poodle) indicated that canine genomes harbor a high frequency of alleles that differ only by the absence or presence of a SINEC_Cf repeat. Comparison of this survey-sequence data with a draft genome sequence of a distinct dog (a boxer) has confirmed this prediction, and revealed the chromosomal coordinates for >10,000 loci that are bimorphic for SINEC_Cf insertions. Analysis of SINE insertion sites from the genomes of nine additional dogs indicates that 3%-5% are absent from either the poodle or boxer genome sequences--suggesting that an additional 10,000 bimorphic loci could be readily identified in the general dog population. We describe a methodology that can be used to identify these loci, and could be adapted to exploit these bimorphic loci for genotyping purposes. Approximately half of all annotated canine genes contain SINEC_Cf repeats, and these elements are occasionally transcribed. When transcribed in the antisense orientation, they provide splice acceptor sites that can result in incorporation of novel exons. The high frequency of bimorphic SINE insertions in the dog population is predicted to provide numerous examples of allele-specific transcription patterns that will be valuable for the study of differential gene expression among multiple dog breeds.
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