The state last night rejected the MTA’s $28 billion budget for big-ticket transit projects like the Second Avenue Subway, sending agency officials back to the drawing board.

The two sticking points were a $10 billion funding gap in the plan, and the fact that the budget to finance upstate roads and bridges hasn’t been finished yet.

Gov. Paterson’s representative on the four-person board that oversees capital budgets, state Transportation Commissioner Stanley Gee, cast the sole “no” vote. But under MTA rules, his veto is enough to sink the plan.