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Filing Details

Issuer

Cik	Name	Symbol	Sector (SIC)	IRS No
874015	Isis Pharmaceuticals Inc	ISIS	Pharmaceutical Preparations (2834)	330336973

Insiders

Cik	Name	Reported Address	Insider Title	Director	Officer	Large Shareholder	Other
897667	T Stanley Crooke	C/O Isis Pharmaceuticals, Inc. 2855 Gazelle Court Carlsbad CA 92010	Chairman, Ceo And President	Yes	Yes	No	No

Reported Non-Derivative Transactions

Sec. Name	Acquisiton - Disposition	Date	Amount	Price	Remaning Holdings	Equity Swap Involved	Form Type	Code	Nature of Ownership	Explanation
Common Stock	Acquisiton	2012-09-04	30,000	$5.25	30,000	No	4	M	Direct
Common Stock	Disposition	2012-09-04	30,000	$14.11	0	No	4	S	Direct
Common Stock	Acquisiton	2012-09-05	15,000	$5.25	15,000	No	4	M	Direct
Common Stock	Disposition	2012-09-05	15,000	$14.82	0	No	4	S	Direct
Common Stock	Acquisiton	2012-09-06	8,694	$5.25	8,694	No	4	M	Direct
Common Stock	Disposition	2012-09-06	8,694	$15.00	0	No	4	S	Direct
Common Stock	Acquisiton	2012-09-06	8,694	$5.25	8,694	No	4	M	Direct
Common Stock	Disposition	2012-09-06	8,694	$15.04	0	No	4	S	Direct
Common Stock	Acquisiton	2012-09-06	1,925	$6.84	1,925	No	4	M	Indirect	By wife
Common Stock	Disposition	2012-09-06	1,925	$15.04	0	No	4	S	Indirect	By wife
Common Stock	Acquisiton	2012-09-06	4,381	$5.25	4,381	No	4	M	Indirect	By wife
Common Stock	Disposition	2012-09-06	4,381	$15.04	0	No	4	S	Indirect	By wife
Common Stock	Acquisiton	2012-09-06	306	$5.25	306	No	4	M	Indirect	By wife
Common Stock	Disposition	2012-09-06	306	$15.00	0	No	4	S	Indirect	By wife
Common Stock	Acquisiton	2012-09-06	6,000	$5.25	6,000	No	4	M	Indirect	By wife
Common Stock	Disposition	2012-09-06	6,000	$15.00	0	No	4	S	Indirect	By wife

Equity Swap Involved	Form Type	Code	Nature of Ownership	Explanation
No	4	M	Direct
No	4	S	Direct
No	4	M	Direct
No	4	S	Direct
No	4	M	Direct
No	4	S	Direct
No	4	M	Direct
No	4	S	Direct
No	4	M	Indirect	By wife
No	4	S	Indirect	By wife
No	4	M	Indirect	By wife
No	4	S	Indirect	By wife
No	4	M	Indirect	By wife
No	4	S	Indirect	By wife
No	4	M	Indirect	By wife
No	4	S	Indirect	By wife

Reported Derivative Transactions

Sec. Name	Sec. Type	Acquisiton - Disposition	Date	Amount	Price	Amount - 2	Price - 2
Common Stock	Employee Stock Option (right to buy)	Disposition	2012-09-04	30,000	$0.00	30,000	$5.25
Common Stock	Employee Stock Option (right to buy)	Disposition	2012-09-05	15,000	$0.00	15,000	$5.25
Common Stock	Employee Stock Option (right to buy)	Disposition	2012-09-06	17,388	$0.00	17,388	$5.25
Common Stock	Employee Stock Option (right to buy)	Disposition	2012-09-06	1,925	$0.00	1,925	$6.84
Common Stock	Employee Stock Option (right to buy)	Disposition	2012-09-06	4,687	$0.00	4,687	$5.25
Common Stock	Employee Stock Option (right to buy)	Disposition	2012-09-06	6,000	$0.00	6,000	$5.25

Remaning Holdings	Exercise Date	Expiration Date	Equity Swap Involved	Transaction Form Type	Transaction Code	Nature of Ownership
98,924	2010-01-03	2013-01-02	No	4	M	Direct
83,924	2010-01-03	2013-01-02	No	4	M	Direct
66,536	2010-01-03	2013-01-02	No	4	M	Direct
0	2007-01-02	2013-01-01	No	4	M	Indirect
0	2007-05-07	2013-05-06	No	4	M	Indirect
0	2010-01-03	2013-01-02	No	4	M	Indirect

Reported Non-Derivative Holdings

Sec. Name	Remaning Holdings	Nature of Ownership	Explanation
Common Stock	875,391	Indirect	By Trust

Footnotes

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 6/27/2012.
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's wife on 6/27/2012.