Atmega2560 usb-serial programming doubt

Hi All,

I am using Atmega2560 on custom PCB. In schematics Arduino Mega, FTDI converter(FT232RQ) is connected to TX0/RX0 (PE0 &PE1) for USB-serial programming, Unfortunately i have connected it to RX3/TX3 (PJ0 &PJ1) in custom PCB. Is it okay to function? I tested. But i failed to upload. May i ask you that do we need to change any register value in Atmega2560 to function RX/TX. Or only TX0/RX0 is compatible for programming via USB-serial FTDI converter?

If TX3/RX3 is compatible for programming, why did i fail to upload?

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