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Hang on! There's no 12th precinct in the NYPD!
That's true, there isn't anymore. There is, however, an old tradition of TV Cops working out of the 12th precinct -- from Barney Miller to CSI: NY.
According to the Manhattan South page on policeny.com the real 12th precinct was abolished in 1916, and the building was used as a police storehouse after that. This picture, taken from that page, shows the building as of 1998.
This shot from 1x01 establishes the frontage of Castle's version of the 12th precinct.
If you look closely at the window, however, you can see it's actually the real 9th precinct stationhouse (below), which covers the East Village and Alphabet City. This site was refurbished in 2007.
The (9)12th precinct frontage pictured here is used from the pilot, up until the middle of Season 3.
In Sucker Punch (3x13) we see the facade below for the first time. Presumably, this is remains the 12th precinct's home throughout S4.