Unlike the GRCh37 assembly and the derived UCSC hg19, the derived Ensembl 59 masks the pseudo-autosomal regions (PAR-1 and PAR-2) on chromsome Y (but leaving them intact on chromsome X).
From what I can see, it annotates 35 genes on the PAR-1 on X, and 10 genes on the PAR-2 on X.
My question is why, in addition to this, it annotates a gene on the PAR-1 of Y? Doesn't this contradict the idea of a PAR region?
The gene in question is XGPY2 (ENSG00000249589), titled "Xg pseudogene, Y-linked 2". I suspect there's a clue in the title, but I can't figure it out!