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!
1 answer
This has been answered here on the Ensembl Dev mailing list.
In summary, the gene itself extends beyond the PAR region on Y, so is retained. One of its transcripts lies completely within the PAR region, but presumably the Ensembl annotation process makes its decision for inclusion based on the gene boundaries rather than the transcript boundaries.
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I've tried posting this question to the ensembl-dev mailing list, but it hasn't shown up yet, so I assume it's awaiting approval or something.