Generally, in the case of a corporation, the underpayment rate is the federal short-term rate plus 3 percentage points and the overpayment rate is the federal short-term rate plus 2 percentage points. The rate for large corporate underpayments is the federal short-term rate plus 5 percentage points.
Back taxes have a baseline rate that grows at certain increments of lateness but is ultimately capped. I don't think it's in any way tied to the base or prime rate.
Based on what happens in my country, it could be both penalty + some interest rates based on the reference rate (which definitely haven't been zero for the past two years btw) but not equal to it.
The IRS says Microsoft owes an additional $28.9 billion -- in tax for 2004 to 2013 plus penalties and interest
For an SEC filing they really should be declaring the actual value of their liability - the interest on the bill is going to be $10bn+