Hello,
to my knowledge, PCI clamp diode is available for all Cyclone pins, the same with Cyclone II: It can be enabled in Assignment Editor or Pin Planner (after activating the PCI-IO column). But I never used it, mainly for the following restriction, that makes the option effectively useless in interfacing 5V signals to my opinion:
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Because 5.0-V tolerance in Cyclone devices require the use of the PCI clamping diode, and the clamping diode is only available after configuration has finished, be careful not to connect 5.0-V signals to the device. (From Cyclone devive handbook)
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I suggest to use resistive dividers or 74LVC buffers instead.
Regards,
Frank