The motherboard doesn't determine if you need a low profile card or not, the case does!
Small compact cases often don't have room for a full sized card. If your machine is built an a standard mid tower case you should be fine.
Also PCIe 2.0 x 16 should run any graphics card out there- the thing that limits you is your power supply. Different cards have different power requirements, and mid to high end boards require special direct connectors from your PSU.
If your unsure about this, one of the safest options is the Geforce GTX 750 as that is the fastest card you can buy that runs only off the power from the PCIe slot on the motherboard.