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Clean Energy Jobs Act of 2012 - Amends the Internal Revenue Code to allow additional allocations of credits under the qualifying advanced energy project (i.e., the project for the production of renewable and alternative energy resources) in 2012. Limits or repeals certain tax benefits for major integrated oil companies (defined as companies with annual gross receipts over $1 billion and an average daily worldwide production of crude oil of at least 500,000 barrels), including: (1) the foreign tax credit; (2) the tax deduction for income attributable to oil, natural gas, or primary products thereof; (3) the tax deduction for intangible drilling and development costs; (4) the percentage depletion allowance for oil and gas wells; and (5) the tax deduction for qualified tertiary injectant expenses. Amends the Energy Policy Act of 2005 to repeal royalty relief (suspension of royalties) for: (1) natural gas production from deep wells in shallow waters of the Gulf of Mexico; and (2) deep water oil and gas production in the Western and Central Planning Area of the Gulf (including the portion of the Eastern Planning Area encompassing whole lease blocks lying west of 87 degrees, 30 minutes west longitude). Dedicates any increased revenue generated by this Act to the reduction of a federal budget deficit or the federal debt. Provides for compliance of the budgetary effects of this Act with the Statutory Pay-As-You-Go Act of 2010.