Mota was born in Santo Domingo, Dominican Republic and is the son of former major league player Manny Mota, as well as the brother of José Mota and cousin of José Báez.
Mota attended Golden West College. He then attended California State University, Fullerton.
He was initially drafted in the sixth round of the 1985 amateur draft by the Kansas City Royals, but did not sign. In 1987 he was drafted by the Houston Astros in the twelfth round. Mota amassed just 90 at-bats in 27 games at second base for the Astros in 1991, batting .189.

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