From what I have seen, pins 3 & 6 of the RJ-45 are TX and RX, and pin 4 is signal ground. On the RJ-45 to DB-9 adaptor, they are often the Black, Yellow, and Red wires.
Here are the RJ-45 jack to wire colors on all of the adaptors I have used:
1 BLUE
2 ORANGE
3 BLACK
4 RED
5 GREEN
6 YELLOW
7 BROWN
8 WHITE
When pinning out the DB-9 connector, I typically start with BLACK on pin 2 and YELLOW on pin 3, RED always goes to pin 5. I usually do not use handshaking for my serial connections. If you are crossing TX & RX, swap the YELLOW and BLACK leads into the DB-9