Comparative genome sequence analysis of the Bpa/Str region in mouse and Man

Genome Res. 2000 Jun;10(6):758-75. doi: 10.1101/gr.10.6.758.


The progress of human and mouse genome sequencing programs presages the possibility of systematic cross-species comparison of the two genomes as a powerful tool for gene and regulatory element identification. As the opportunities to perform comparative sequence analysis emerge, it is important to develop parameters for such analyses and to examine the outcomes of cross-species comparison. Our analysis used gene prediction and a database search of 430 kb of genomic sequence covering the Bpa/Str region of the mouse X chromosome, and 745 kb of genomic sequence from the homologous human X chromosome region. We identified 11 genes in mouse and 13 genes and two pseudogenes in human. In addition, we compared the mouse and human sequences using pairwise alignment and searches for evolutionary conserved regions (ECRs) exceeding a defined threshold of sequence identity. This approach aided the identification of at least four further putative conserved genes in the region. Comparative sequencing revealed that this region is a mosaic in evolutionary terms, with considerably more rearrangement between the two species than realized previously from comparative mapping studies. Surprisingly, this region showed an extremely high LINE and low SINE content, low G+C content, and yet a relatively high gene density, in contrast to the low gene density usually associated with such regions.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • 3-Hydroxysteroid Dehydrogenases / genetics
  • Amino Acid Sequence
  • Animals
  • Antigens, Neoplasm / genetics
  • Antigens, Neoplasm / isolation & purification
  • Calcium-Binding Proteins / genetics
  • Chromosomal Proteins, Non-Histone*
  • Cytoskeletal Proteins
  • DNA-Binding Proteins / genetics
  • Genomic Library
  • Humans
  • LIM Domain Proteins
  • Melanoma-Specific Antigens
  • Mice
  • Molecular Sequence Data
  • Multigene Family
  • Neoplasm Proteins / genetics
  • Nuclear Proteins / genetics
  • Sequence Analysis, DNA*
  • Sequence Homology, Nucleic Acid
  • X Chromosome / genetics*
  • Zinc Fingers / genetics


  • Antigens, Neoplasm
  • Calcium-Binding Proteins
  • Chromosomal Proteins, Non-Histone
  • Cytoskeletal Proteins
  • DNA-Binding Proteins
  • LIM Domain Proteins
  • Melanoma-Specific Antigens
  • Neoplasm Proteins
  • Nuclear Proteins
  • ZNF185 protein, human
  • Zfp185 protein, mouse
  • Zinc finger protein 275, mouse
  • caltractin
  • Xlr3 protein, mouse
  • 3-Hydroxysteroid Dehydrogenases

Associated data

  • GENBANK/AL021127
  • GENBANK/AL049866
  • GENBANK/AL136328
  • GENBANK/AL136329
  • GENBANK/U82670
  • GENBANK/U82671
  • GENBANK/U82695