International Mammalian Genome Society


The 13th International Mouse Genome Conference
October 31-November 3, 1999

Table of Contents * Structure * Bioinformatics * Sequence * Mapping * New Tools * Gene Discovery * Developmental * Mutagenesis * Functional Genomics

D8 Novel Gene Identification in the Bare-Patches (Bpa)/ Striated (Str) Region of the Mouse X Chromosome Using a Mouse-Human Comparative Approach

Bate, R.1, Mallon, A-M.1, Denny, P.1, Strivens, M. A.1, Botcherby, M. R. M.2, Straw, R.2, Clarke, D.2, Weston, P.2, Greystrong, J.2, Gilbert, M.2, Dangel, A.3, Cunningham, D.3, Herman, G.E.3, Miller, W.4, Platzer, M.5, Rosenthal, A.5,, Rhodes, M.2, Brown, S. D. M.1 1MRC UK Mouse Genome Centre and Mammalian Genetics Unit, Harwell, Oxon, UK; 2MRC Human Genome Mapping Project Resource Centre, Hinxton, Cambridge, UK; 3Department of Pediatrics and Children's Research Institute, Ohio State University, Columbus, Ohio 43205, USA; 4Department of Computer Science, The Pennsylvania State University, University Park PA 16802, USA; 5Institut für Molekulare Biotechnologie, Beutenbergstaße 11, D-07745 Jena, Germany

A comparative sequencing approach has been undertaken to study several regions of the mouse X chromosome between the Ids and Dmd loci. Comparison of mouse and homologous human sequence allows us to use sequence conservation, together with gene and exon prediction packages, to identify genes. The region of interest encompasses two murine X-linked dominant male lethal mutations, bare patches (Bpa) and striated (Str). We have completed the sequencing of approximately 0.5Mb from this region (ftp://www.hgmp.mrc.ac.uk/pub/mouseseq). This sequence has been compared to the homologous human sequence on Xq28 (http://genome.imb-jena.de) by pairwise alignment.

The specificity of exon prediction has been considerably improved by combining pairwise alignments with exon prediction methods. Conserved regions, identified by pairwise alignment to homologous human sequence, with percentage identities greater than 80% have been selected for further study, and a number of these conserved elements have been shown to be transcribed.

A number of other mouse genes were identified in the region through database searches and gene prediction packages including (1) a zinc-finger gene, (2) a member of the murine-specific X-linked lymphocyte regulated (Xlr) gene family identified by homology to other known members of the family, and (3) a putative gene predicted by a number of exon and gene structure packages in NIX. RT-PCR experiments were carried out, which confirmed the predicted exons and identified expression in testis. Additional analysis of this gene has identified weak homology to the Xlr gene family; 24% at the protein level.

This work is part of a larger project to sequence around 6 Mb of the mouse X chromosome (e.g. see abstract by Straw et al) and to test the value of comparative sequencing as a tool for the identification of genes and regulatory elements.

 


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