can they run the same cards?

Yes. PCI-E cards are backward compatible, but on highest-end card it will bottleneck a little. In case of most cards, though, the bandwidth bottleneck is insignificant... what card are you planning to run?
 
just remember the PCIE 2.0 is more updated then the standard PCIE and may run slightly quicker. Make sure you have the latest manufacturer driver for both the motherboard and the video card to eliminate any problems
 
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