In the past if you are able to check-in through the parent airline you can use on-board check-in. For example, if you have a USAir flight you can check-in on American's (the parent company) website.
If you are ticketed through one of the airlines listed as participating, even if the flight is operated by a regional carrier, yes, you can use Onboard Airline check in as long as all the other requirements are met (domestic flight departing after 11:30 am on date of disembarkation, using DCL transfers, you sign up for the service, etc.)
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