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Vol. 10, Issue 6, 758-775, June 2000

LETTER
Comparative Genome Sequence Analysis of the Bpa/Str Region in Mouse and Man

A.-M. Mallon,1,7 M. Platzer,2,7 R. Bate,1 G. Gloeckner,2 M.R.M. Botcherby,3 G. Nordsiek,2 M.A. Strivens,1 P. Kioschis,4 A. Dangel,5 D. Cunningham,5 R.N.A. Straw,3 P. Weston,3 M. Gilbert,3 S. Fernando,3 K. Goodall,3 G. Hunter,3 J.S. Greystrong,3 D. Clarke,3 C. Kimberley,3 M. Goerdes,2 K. Blechschmidt,2 A. Rump,2 B. Hinzmann,2 C.R. Mundy,3 W. Miller,6 A. Poustka,4 G.E. Herman,5 M. Rhodes,3 P. Denny,1 A. Rosenthal,2,8 and S.D.M. Brown1,8,9

1 MRC UK Mouse Genome Centre and Mammalian Genetics Unit, Harwell, Oxon, UK; 2 Institut für Molekulare Biotechnologie, D-07745 Jena, Germany; 3 MRC Human Genome Mapping Project Resource Centre, Hinxton, Cambridge, UK; 4 Deutsches Krebsforschungszentrum, Molekulare Genomanalyse, Heidelberg, 69120, Germany; 5 Children's Research Institute, Ohio State University, Columbus, Ohio 43205 USA; 6 Department of Computer Science, The Pennsylvania State University, University Park, PA 16802 USA

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.

[The sequence data described in this paper have been submitted to EMBL under the following accession nos.: Mouse Genomic Sequence: Mouse contig A (AL021127), Mouse contig B (AL049866), BAC41M10 (AL136328), PAC303O11(AL136329). Human Genomic Sequence: Human contig 1 (U82671, U82670), Human contig 2 (U82695).]

7 These authors contributed equally to this work.

8 Joint senior authors.

9 Corresponding author.

10:758-775 ©2000 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/00 $5.00
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