Custom PCIE x1 card

Possibly a silly question, but I dont know where else to ask, so here goes...



I'm currently building a custom fan and led controller using an arduino. And thus far, its working quite well, but its currently connected to a usb header, that I actually need for my card reader...



So, I've been thinking, if its not too hard (or costly) I could make my own PCIEx1 card instead.



What I need to do, is make a PCIE card, that acts as a USB port, and then I can connect to that... My problem is, I dont know where to start? And googling doesnt show up anything :(



With PCIE mini, there are usb D+ and D- lines that I could use... but not on the standard size cards... Any ideas?



thanks



dan