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Welcome to MSY Breakpoint Mapper, a database of sequence-tagged sites (STSs) and a user interface for mapping partial deletions in the male-specific region of the human Y chromosome (MSY).

Naturally occurring partial deletions in the human Y chromosome are associated with diverse phenotypes including male infertility, sex reversal, Turner syndrome, and germ cell tumor formation. With the complete sequence of the euchromatic Y chromosome in hand, it is now possible to precisely demarcate each deletion and the repertoire of genes lost, and to propose mechanisms of deletion.

Detailed DNA-sequence analysis of MSY deletions is most readily accomplished with Y-specific STS assays, which employ the polymerase chain reaction (PCR). Each such STS assay provides a straightforward means of determining the presence or absence, in a sample of human genomic DNA, of a specific point along the length of the Y chromosome. In the course of analyzing normal and aberrant Y chromosomes over the past two decades, we and our colleagues have generated robust, Y-specific STSs at an average spacing of less than 14 kilobases across the MSY euchromatin.

MSY Breakpoint Mapper provides information about these STSs and is useful for efficiently and systematically defining the breakpoint(s) of virtually any Y chromosome deletion.


We request that use of this website be cited as:

MSY Breakpoint Mapper, a database of sequence-tagged sites useful in defining naturally occurring deletions in the human Y chromosome.
Lange J, Skaletsky H, Bell, GW, Page DC (2008) Nucleic Acids Res 36(Database issue): D809-D814.


September 2014: We have updated STS positions and genome coordinates to NCBI Build 38.


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