A long-range repeat family of more than 50 kb repeat size is clustered in Chromosomes (Chr) 1 of Mus musculus and M. spretus. In M. musculus this long-range repeat family shows considerable variation of copy-number frequency and contains coding regions for at least two genes. In an intron of a gene, which is part of the repeat, a B2 small interspersed repetitive element (SINE) is inserted at identical positions. The B2 element is present in all copies of the long-range repeat family; it was presumably a component of the ancestral single-copy precursor sequence that gave rise by amplification to the repeat family.
Copies of the long-range repeat family vary with respect to the number of TAAA tandem repeats in the A-rich 3' end region of the B2 element. As inferred from polymerase chain reaction (PCR) data, presence and frequency of repeat number variants in the (TAAA)n block are strain and species specific. The B2 element and its flanking regions were sequenced from two copies of the long-range repeat family. Sequence divergence between the two copies (only non-CG base substitutions and deletions/insertions) was determined to be 2.6%. Based on the drift rate in human Alu elements and a correction for the higher drift rates in rodents, an estimate for the divergence time of 1.7 million years was calculated. Since the long-range repeat family is present in M. musculus and M. spretus, it must have evolved by amplification before the separation of the two species about 1-4 million years ago. family), which is clustered in the D band of Chr 1 (Purmann et al. 1992;Traut et al. 1992). Coding regions for two transcripts of 1.3 and 4.5 kb length are part of the repeat sequence (Eckert et al. 1991). Cloned DNA sequences from at least four different copies of the family were identified. They varied with respect to gross rearrangements, e.g., insertions and/ or deletions of DNA sequences several kilobases in size, and to point mutations causing restriction site variability (Purmann et al. 1992).
The long-range repeat family is chromosomally inconspicuous in the laboratory strain C57BL, where it consists of about 50 copies per haploid genome ('HSR-genome'). In individuals from wild-mouse populations of M. musculus, variants of this cluster with higher copy numbers (for example, 800 copies) were found, which are visible as homogeneously staining regions (HSRs) in metaphase chromosomes (HSR + genome, Traut et al. 1984;Purmann et al. 1992). During evolution, a progenitor sequence of the long-range repeat family was amplified to establish the low-copy repeat cluster that subsequently underwent dynamic evolution leading to high-copy-number variants (Winking et al. 1991).
Here, we investigate the sequence variability among different copies of the long-range repeat family in and around a B2 element which is a SINE (Singer 1982) inserted in an intron of the 1.3-kb RNA coding gene.