Income Taxes (Tables)

12 Months Ended

Jun. 30, 2015

Income Taxes

Reconciliation of the Company's expected tax benefit, as computed by applying the U.S. federal corporate tax rate to loss before the benefit for income taxes, and actual tax

The difference between the Company's expected tax benefit, as computed by applying the U.S. federal corporate tax rate of 34% to loss before the benefit for income taxes, and actual tax is reconciled in the following chart (in thousands):

	Year Ended June 30,
	2015			2014			2013
Loss before income tax expense	$	(60,739	)	$	(71,364	)	$	(72,811	)
Expected tax benefit at 34%	$	(20,651	)	$	(24,264	)	$	(24,756	)
Permanent differences		2,766			1,953			1,540
State tax benefit net of federal benefit		(3,252	)		(4,062	)		(3,921	)
Increase in valuation allowance, net		27,940			26,011			25,624
Federal research credit		(1,407	)		(1,002	)		(2,260	)
Federal orphan drug credit		(5,471	)		—			—
Expired loss and credit carryforwards		75			1,364			3,773
Benefit for income taxes	$	—		$	—		$	—

Schedule of significant components of deferred tax assets

Significant components of the Company's deferred tax assets and liabilities as of June 30, 2015 and 2014 are as follows (in thousands):

	June 30,
	2015			2014
Deferred tax assets:
Net operating loss carryforwards	$	89,362		$	144,230
Federal and state tax credit carryforwards		25,131			14,453
Property and other intangible assets		2,532			2,386
Deferred revenue		16,179			24,095
Stock-based compensation		11,379			9,047
Deferred lease incentive		4,279			3,908
Other liabilities		3,177			1,234
Royalty sale		78,427			—
Total deferred tax assets	$	230,466		$	199,353
Deferred tax liabilities:
Accounting method change		(983	)		—
Royalty sale transaction costs		(2,190	)		—
Total deferred tax liabilities	$	(3,173	)	$	—
Valuation allowance		(227,293	)		(199,353	)
Net deferred tax assets/(liabilities)	$	—		$	—