You're referring to the Boeing 747-400D (Domestic) which has basically an entirely economy layout and can typically carry up to 560 passengers or more. There aren't many of them, but you're right - those that exist are in Japan.

Japan Airlines have some, as do All Nippon. Other than that, it's a little used model.

These have no upperdeck galley and you can spot them because of the extra windows at the rear of the upperdeck where the galley would normall be but where seats have been installed instead!