Can I use the second PCI Express x16 slot for my cpu without performance loss?

[npro]

Hello dear people,

I own the x79-ud3 motherboard that has:
2 x PCI Express x16 slots, running at x16 (PCIEX16_1, PCIEX16_2)

I am going to replace my gpu with a bigger one and and there is not room for installing the new gpu in the first slot (x16) so I would need to install it in the second x16 slot (PCIEX16_2). Thereof, I started wondering:
Will there be ANY possible loss when installing gpu in PCIEX16_2 instead of PCIEX16_2?
Please do not sugar code anything.

Thanks!

[ElectroStingz]

Hello,

A realistic answer, there will be no noticeable performance loss.
How is spacing below the lower slot, will the GFX card have enough airflow?