The pseudoautosomal region (PAR) of mammalian sex chromosomes is a small re
gion of sequence identity that is the site of an obligatory pairing and rec
ombination event between the X and Y chromosomes during male meiosis. Durin
g female meiosis, X chromosomes can pair and recombine along their entire l
ength; recombination in the PAR is therefore similar to 10x greater in male
meiosis compared with female meiosis. A consequence of the presence of the
PAR in two copies in males and females is that genes in the region escape
the process of X-Inactivation. Although the structure and gene content of t
he human PAR at Xq/Yq is well understood, the mouse PAR, which appears to b
e of independent evolutionary origin, is poorly characterized. Here we desc
ribe a yeast artificial chromosome (YAC) contig covering the distal part of
the Mouse X chromosome, which we have used to define the pseudoautosomal b
oundary, that is, the point of divergence of X-specific and X-Y-identical s
equences. In addition, we have investigated the size of the mouse PAR by in
tegrating a unique restriction endonuclease recognition site just proximal
to the pseudoautosomal boundary by homologous recombination. Restriction di
gestion of this modified DNA and pulsed field gel electrophoresis reveal th
at the PAR in these cells is similar to 700 kb. Thus, the Mouse PAR, althou
gh small in size, has retained essential sex chromosome pairing functions d
espite its rapid rate of evolution.