What are all of the pins of the Beaglebone Black Rev. C serial (debug) header?
There is a schematic available here: http://elinux.org/Beagleboard:BeagleBoneBlack#LATEST_PRODUCTION_FILES_.28C.29

See page 4.  Looks like J1 (the UART0 serial port) has only three of the six pins connected - ground, TX, and RX.  The others are NC, so you can apply any reasonable voltage to them.  Looks like it is designed to work with a USB to TTL serial cable.  The TX and RX signals pass through a 74LVC2G241 dual tristate non-inverting buffer/driver that is powered by the 3.3 volt supply.  The inputs are 5v tolerant. 

The CTS pin of the UART is not connected while the RTS pin is brought out as TP9.  

By the way, those are some of the longest pin names that I have seen.