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So it appears the 486 motherboard has PCI - not all do as you may know.
Just remember that just because it's got PCI, it's not necessarily going to mean it will work before consideration of the drivers.
My real world example was a couple of years ago or so, I was building a 486 from scratch and managed to buy a new PCI based motherboard. I bought a new 8 MB ATI Rage XL PCI video card so I could run WFW at higher resolutions with decent colour depth. The PC wouldn't start at all and it took a while to figure out as the BIOS beep codes weren't giving me the right answers. At a later stage I bought from eBay a 4 MB Matrox Millenium II PCI card and soon as I plugged it into the 486 board it just worked. The 8 MB ATI card was fine, after testing it in a Pentium 200 and Pentium III. I put it down to the PCI specification that went from 2.0 to 2.1 that occurred with the original Pentiums.
So if you manage to find one of these Matrox Millenium cards or a Diamond Viper, I'd recommend it if you want to upgrade it. Some people have placed an early 3D PCI card into a 486, though that was really to see whether it would work. Generally there's little value if it does, as many 3D games require a Pentium as a minimum and the 486 processor becomes the bottleneck.