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The prototype, EF65 1000 and over, made its debut in 1969 and pulled various cars ranging from blue (sleeper) trains to freight cars in DC electrified zones on plains throughout Japan. Different from EF65 0 and over and 500 and over, this version has a through door in its front to facilitate double locomotive driving. The equipment against cold weather and snow is also reinforced in consideration of winter use in snowy Tohoku and Jo-etsu Mainlines. Of 139 cars produced in total, they are different among themselves, depending on the production epochs and special specifications in the appearance.

EF65 1000 and over Early JR Freight Color has light and dark blue and white color painting on the body, a remarkable character of the locomotive which was renovated by JR Freight for longer use.