title: Recent amplification of rat ID sequences.
abstract: The rodent identifier (ID) family of repeats has amplified at an extremely high rate in the rat genome in recent evolutionary time, resulting in 130,000 copies per haploid genome. Statistical analyses support the grouping of 119 individual rat ID elements into four major and three minor subfamilies based on six diagnostic nucleotide positions. The consensus sequence of the oldest subfamily is identical to the ID region of the rat BC1 RNA gene, suggesting that the BC1 gene has dominated the early amplification of rat ID elements. The other six subfamilies share at least one diagnostic mutation in relation to the BC1 gene and show much less nucleotide sequence divergence, indicating that the recent large amplification of rat ID elements has been driven by another lineage of master gene(s) in the rat genome. This is consistent with the formation of a new lineage of master elements for ID amplification in rat. The formation of most rat ID elements appears to have occurred during the past three million years based on the results that four out of five randomly chosen ID elements are present only in the genome of one rat species and not in other closely related species.
authors.affiliation: Department of Biochemistry and Molecular Biology, Louisiana State University Medical Center, New Orleans, USA.
authors.forename: J
authors.initials: J
authors.lastname: Kim
authors.forename: P L
authors.initials: PL
authors.lastname: Deininger
mesh_terms: D000818:Animals; D001483:Base Sequence; D004268:DNA-Binding Proteins / Q000235:genetics*; D019143:Evolution, Molecular; D005784:Gene Amplification; D016678:Genome; D008969:Molecular Sequence Data; D009154:Mutation; D062085:RNA, Long Noncoding; D022661:RNA, Untranslated; D051381:Rats / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D012261:Ribonucleoproteins / Q000235:genetics*; D020736:Ribonucleoproteins, Small Cytoplasmic; D016415:Sequence Alignment; D017421:Sequence Analysis
chemical_list: C489663:Bc1 long-non-coding RNA, rat; D004268:DNA-Binding Proteins; D062085:RNA, Long Noncoding; D022661:RNA, Untranslated; D012261:Ribonucleoproteins; D020736:Ribonucleoproteins, Small Cytoplasmic