Try reseating the gpu in the original slot. If it still doesn't work, RMA the board.
PCIE is the high speed interconnect bus for peripheral components (gpu, sound card, etc). In today's boards the different versions start at pcie, then pcie-1, -2, -3. Each ascending number is basically an upgrade in speed capability. While your card is designed for -3, it will work fine on -2 as the versions are generally backward compatible. Generally, today's cards cannot saturate -2, but that will change quickly.
Regardless, if the lane isn't working, I'd send the board back.
Mark