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In humans, the Y chromosome spans about 58 million base pairs (the building blocks of DNA) and represents approximately 2% of the total DNA in a male cell. The human Y chromosome contains 86 genes, which code for only 23 distinct proteins. Traits that are inherited via the Y chromosome are called holandric traits.The human Y chromosome is unable to recombine with the X chromosome, except for small pieces of pseudoautosomal regions at the telomeres (which comprise about 5% of the chromosome's length). These regions are relics of ancient homology between the X and Y chromosomes. The bulk of the Y chromosome which does not recombine is called the "NRY" or non-recombining region of the Y chromosome. It is the SNPs in this region which are used for tracing direct paternal ancestral lines.
SRY (Sex-determining region Y) is a sex-determining gene on the Y chromosome in the therians (placental mammals and marsupials).This intronless gene encodes a transcription factor that is a member of the SOX (SRY-like box) gene family of DNA-binding proteins. This protein is the therian testis determining factor (TDF), referred to as the sex-determining region Y protein or SRY protein which initiates male sex determination. Mutations in this gene give rise to XY females with gonadal dysgenesis (Swyer syndrome); translocation of part of the Y chromosome containing this gene to the X chromosome causes XX male syndrome.