Essentially they are seperate entities owned by the same parent company.
I had a single ticket with both Alaska and Horizon flights. Even if it were merely a code share arrangement and not an even closer relationship (like being owned by the same company), e.g., if I had flown Alaska connecting to American, I would have expected the agent to be more helpful (e.g., "American gates are on concourse XYZ, or try their ticket counter for assistance") than the QX agent actually was.