FTP is a specific type of transfer system and is defined by a standards document (RFC 959). Unless you plan on implementing RFC 959RFC 959, your file transfer system won't be FTP and shouldn't be on port 21.
In fact, anything up to and including port 1023 is reserved for those types of well-known protocols. Ports 1024 and above are technically fair game for custom applications like yours, but there are a lot of registered port numbers in the 1024–49151 range and you may run into a conflict if you choose randomly.
Instead, I'd assign your application a port above 49151. You should generally be safe there.