Arse is slang for ass or butt. "A pain in the ass" is an expression which means something is really difficult or troublesome.
A person can be a pain in the arse, a job can be a pain in the arse, anything can be a pain in the ass if it is difficult or it causes you problems. For a person, a pain in the ass is the same as a jerk.
My boss is making me work on Saturday, what a pain in the ass/arse.
I can't open this coconut, what a pain in the ass/arse.