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I'm looking into developing a device that will be installed in a PCIe slot but not communicate with the CPU. It will be a standalone device using either the 3v3 or 12v supplies at fairly low current(~150mA).

Does the PCIe 1x slot provide any power when the system is shutdown?

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Depends on the system implementation -- the specification calls out an auxiliary 3.3V rail that is present, in addition to regular 3.3V and 12V. The motherboard vendor may or may not have decided to implement that rail using a simple regulator from +5VSB. If they did, you'll get power on that pin, if not, no worries.

Simplest thing for you to do would be to not connect to the 3.3V aux pin(s) at all.

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