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To imprison or confine someone or an animal inside of a pen or a similarly small, restricted space. We pen these convicts up with other criminals for years at a time, and you expect them all to become reformed citizens as a result? The man had penned up dozens of wild animals in a disused corner of his company's warehouse.
pen (someone or an animal) up
to confine someone to a confined space or an animal to a pen. He said he didn't want them to pen him up in an office all day. They penned up the dog during the day.