IONIS PHARMACEUTICALS INC — Director's Dealing 2014

Jan 31, 2014

SEC Form 4 — Statement of Changes in Beneficial Ownership

Issuer: ISIS PHARMACEUTICALS INC (ISIS)
CIK: 0000874015
Period of Report: 2014-01-29

Reporting Person: PARSHALL B LYNNE (Director, COO)

Non-Derivative Transactions

Date	Security	Code	Shares	Price	A/D	Holdings After	Ownership
2014-01-29	Common Stock	M	3972	$11.27	Acquired	7994	Direct
2014-01-29	Common Stock	S	3972	$48.807	Disposed	4022	Direct
2014-01-29	Common Stock	M	31028	$10.29	Acquired	35050	Direct
2014-01-29	Common Stock	S	31028	$48.807	Disposed	4022	Direct
2014-01-29	Common Stock	M	5000	$7.25	Acquired	5000	Indirect
2014-01-29	Common Stock	S	5000	$48.807	Disposed	0	Indirect
2014-01-29	Common Stock	M	5000	$7.25	Acquired	5000	Indirect
2014-01-29	Common Stock	S	5000	$48.807	Disposed	0	Indirect
2014-01-29	Common Stock	M	5000	$7.25	Acquired	5000	Indirect
2014-01-29	Common Stock	S	5000	$48.807	Disposed	0	Indirect
2014-01-30	Common Stock	M	23635	$10.29	Acquired	27657	Direct
2014-01-30	Common Stock	S	23635	$50.364	Disposed	4022	Direct
2014-01-30	Common Stock	M	15875	$7.25	Acquired	19897	Direct
2014-01-30	Common Stock	S	15875	$50.364	Disposed	4022	Direct

Derivative Transactions

Date	Security	Exercise Price	Code	Shares	A/D	Expiration	Underlying	Ownership
2014-01-29	Employee Stock Option (right to buy)	$11.27	M	3972	Disposed	2017-01-03	Common Stock (3972)	Direct
2014-01-29	Employee Stock Option (right to buy)	$10.29	M	31028	Disposed	2018-01-02	Common Stock (31028)	Direct
2014-01-29	Employee Stock Option (right to buy)	$7.25	M	5000	Disposed	2019-01-02	Common Stock (5000)	Indirect
2014-01-29	Employee Stock Option (right to buy)	$7.25	M	5000	Disposed	2019-01-02	Common Stock (5000)	Indirect
2014-01-29	Employee Stock Option (right to buy)	$7.25	M	5000	Disposed	2019-01-02	Common Stock (5000)	Indirect
2014-01-30	Employee Stock Option (right to buy)	$10.29	M	23635	Disposed	2018-01-02	Common Stock (23635)	Direct
2014-01-30	Employee Stock Option (right to buy)	$7.25	M	15875	Disposed	2019-01-02	Common Stock (15875)	Direct

Footnotes

F1: Acquired as a result of exercising a stock option pursuant to a Rule 10b5-1 Trading Plan. The purchase and sale reported on this Form 4 was effective pursuant to a Rule 10b5-1 Trading Plan adopted by the reporting person on 12/30/13.

F2: Grant of 1/3/11 to reporting person of stock options under the Isis Pharmaceuticals, Inc. 1989 Stock Option Plan. 25% of the shares subject to the option vested and became exercisable on 1/3/12. Thereafter, the remaining shares subject to the option vest and become exercisable in 36 equal monthly installments, at the rate of 18,221 shares per year. The option shall be fully vested and exercisable on 1/3/15. The option was exercisable as to 54,663 shares on 1/29/14.

F3: Grant of 1/3/12 to reporting person of stock options under the Isis Pharmaceuticals, Inc. 1989 Stock Option Plan. 25% of the shares subject to the option vested and became exercisable on 1/3/13. Thereafter, the remaining shares subject to the option vest and become exercisable in 36 equal monthly installments, at the rate of 15,437 shares per year. The option shall be fully vested and exercisable on 1/3/16. The option was exercisable as to 15,875 shares on 1/30/14.