GA-990FXA-UD3 not recognizing GPU

[al94]

I was having a problem with my PC booting up after installing some new fans so I took out my GPU and my first PCIEX16 broke so I moved it to my second PCIEX16 and now my GPU is not being recognized on my PC. I can boot up and use the PC fine the only problem is the GPU. How do I know if my GPU is broken or there is a problem with the motherboard? My GPU is XFX R9 280x and my motherboard is GA-990FXA-UD3.

[AgentFXA]

How can you boot up fine when the GPU is not recognized - oxymoron?
Have you told the sys bios in which slot the GPU is? (First Init)

 

[shadowsports]

..... and my first PCIEX16 broke ......

Sorry, have to ask... is there more to this story you haven't shared?  How do you know the first slot is broken?  If it is, that's where this story should end.  Repair or replace.  Are you really interested in limping along?