An exhaustive search for tandem repeats and long duplicated chromosomal regions within the mouse genome

Y. Wada

Faculty of Agriculture
Saga University
1 Honjyo
Saga city, 840-8502
JAPAN

ywada@cc.saga-u.ac.jp
FAX +81-952-28-8787

Abstract

       Traces of ancient duplications of extensive chromosomal regions are being discovered 
within the human genome.  For example, the MHC (major histocompatibility complex) gene region 
on chromosome 6 (6p21.3) encodes a cluster of genes that are homologous to those on chromosome 
9 (9q33-q34).  These regions appear to have arisen from regional duplication around the time of 
vertebrate emergence.  To elucidate the evolution of mammalian genomes, it is crucial to search 
for duplicated chromosomal regions in the mouse genome.  In this study, we searched for long 
duplicated chromosomal regions in the mouse genome using the map information derived from 
the Mouse Genome Database and the numerous homologous gene pairs from GenBank.  To identify 
the regions, we searched for homologous gene pairs among the genomic sequences extracted 
from GenBank (r.118).  We defined the candidates of duplicated regions as those having more than 
two homologous gene pairs located within 5cM on each chromosome.  We conducted a statistical test 
considering the distribution of homologous gene pairs and tandem repeats in the mouse genome.  
Twenty-seven pairs of duplicated regions were found in this study. Seven procollagen genes, 
three Hox gene clusters, six integrin genes, three fibroblast growth factor receptor genes 
and three eye absent homolog genes were located in the duplicated regions.



                                                        Journal of Animal Genetics 30, 3-10, 2002