Document:

EX-10.1

 Exhibit 10.1 

LEASE AGREEMENT 
 THIS
Lease Agreement, entered into this 19th day of Sept., 2011, between THOMPSON-DAVIS ENTERPRISES, LLC, a limited liability company organized under the laws of the State of Florida, hereinafter
referred to as Lessor, and APPLIED GENETIC TECHNOLOGICS, a corporation organized under the laws of the state of Delaware or its successor entity or entities, and assigns, hereinafter referred to as Lessee. 

IT IS UNDERSTOOD: 
  

	 	a)	That Lessee may change its name; 

  

	 	b)	That Lessor may convert to a partnership, corporation or limited liability corporation which may be owned in part by others; 

  

	 	c)	Actual monthly rental payments shall commence on the first day of the first month the premises are occupied and, if occupied on a day other than the first day of a month, shall be prorated for that first month;

  

	 	d)	This is an extension of a Lease originally entered into by the parties on March 28, 2006 with renewal date of January 1, 2012. 

WITNESSETH: That in consideration of the covenants herein contained, the parties hereto covenant and agree as follows: 

 

	 	1.	PREMISES LEASED AND TERM: The Lessor does hereby Lease to the Lessee the premises described in the Exhibit “A” attached hereto (a building with total square footage of 15,424), which said specific
premises shall consist of approximately 2,750 square feet of office space determined as follows: 

  

							
	a)	 	 2,066 useable square feet in pod located in southeast portion of building, or
	  	 	2,066	  
			
	b)	 	 Prorata share (18%) of center core space including reception, board room, bathrooms, staff lounge, etc. @ 3,800 total square feet, or
	  	 	684	  
		 	 [Note: 18% is calculated as follows: Total leasable square footage of each of the four specific space designated pods 11,376 (2844x4) divided into
2,066 specifically assigned Lease space or 2,066/11,376=18%]
	  			
			
		 	 Total square footage to be Leased by Lessee
	  	 	2,750	  
		 		  	  
	  
	 

 Lessee shall have the right to make use of all core space elements including, but not limited to, reception area, boardroom,
bathrooms and staff lounge. Lessee will have access to the boardroom upon advance reservation on a basis that is no less favorable than access given to any other building tenant. Lessee may also use office furniture currently in the interior offices
of leased space at the pleasure of Lessor. However, this furniture may be removed by Lessor at any time. 

  
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 The Lease shall be for the term of three (3) years and will commence on the first day of January, 2012, or,
if earlier, the day of the month as first occupied and will expire on December 31, 2014, which is hereby designated as the new Base Term. 

2. RENT: Lessee shall pay rent in lawful monies of the United States of America to Lessor, or Lessor’s designated agent. The rent
for the first year of the Base Term shall be computed at the rate of $16.00 per square foot. The rent per year shall be $44,000 (2,750 sq. ft. x $16.00). Monthly payments due on the first day of each month shall be $3,667.00 ($44,000/12), with all
such payments being due in advance on the first day of each month. In addition to the rent as specified, Lessee shall pay, with each monthly payment of rent, sales or use tax as imposed on commercial leases by the State of Florida, city and/or
county governments. A late charge of six percent (6%) of the payment due will be payable by Lessee on all payments received by Lessor no later than ten (10) days after the payment is due. “Received” shall mean received at the
office the Lessor at an address to be subsequently specified by the Lessor before occupancy by Lessee. The rent during the remainder of the Base Term shall be increased effective each subsequent January 1 by an amount equal to $16.00 per square
foot per year plus the cumulative percentage increase in the Consumer Price Index from January 1, 2012. 
 The rate for the existing lease will be
reduced to $16.00 per square foot effective the first day of the month following the date this renewal is signed by Lessee. 
 3.
OPTION: Provided Lessee is not in default under any provisions of this Lease, Lessee shall have the option and right to extend this Lease for an additional term of three (3) years following the Base Term. Such term shall be referred to
herein as the Option Term. In the event of the exercise of this option, this Lease shall be extended upon the same terms and conditions as the Base Term with the exception that Lessee shall have the right to cancel during this renewal term upon
giving twelve (12) months notice to Lessor. In order to exercise this renewal option, Lessee shall give written notice of Lessee’s election to extend the Lease at least six (6) months prior to the end of the Base Term. Within fifteen
days of receipt of this notice, Lessor shall inform Lessee of the rental applicable to the Option Term. 
 4. DEPOSIT MONEY: Lessor
herewith acknowledges that, inasmuch as Lessee made a deposit of $3,742.00 with initial lease, no additional deposit shall be required with this Lease renewal. 

5. MAINTENANCE: Lessor shall provide all maintenance on the Leased premises not caused by Lessee’s negligence or misuse. 

6. INSURANCE: Lessor shall maintain fire, windstorm and extended coverage on the premises. Lessee shall maintain insurance on its
improvements to the premises and its personal property located therein. Lessee shall maintain general liability 

  
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insurance, naming Lessor as an additional insured, in amounts not less than $300,000.00 for property damage and $100,000.00 per person for personal injury. In the event the premises are damaged
by fire or windstorm, the rent shall abate for such time as the premises are not in condition for the conduct of business in a reasonable manner and not occupied by Lessee. This Lease shall not be terminated if Lessor can restore or replace the
premises within a period of one hundred twenty (120) days after the occurrence. 
 7. UTILITIES, JANITORIAL AND REAL ESTATE
TAXES: Lessor represents that the building in which the premises are located contains 15,424 square feet of leasable area. Lessee, in addition to the rent as provided herein, shall pay monthly, and within ten (10) days after receipt of a
request for payment, an amount equal to the actual prorata share, based on the square footage percentage of the building leased by Lessee, of the costs of utilities, janitorial and real estate taxes for the premises. By way of example, if Lessee
leases 50% of the total leasable area, Lessee will pay 50% of such costs. Lessor will provide copies of statements for such services for the entire building. The percentage of space leased under this Lease by Lessee is eighteen percent (18%). 

8. SIGN: Lessee shall be permitted to place a sign on the space provided for tenant signs. The cost of preparing and installing the
sign shall be paid by Lessee. The sign, its location and installations shall be subject to Lessor’s approval. 
 9. POSSESSION:
If the Lessee shall default in the payment of the rent, or if the Lessee shall violate any of the covenants of this Lease, then the Lessor shall be immediately entitled to re-enter and re-take possession after giving notice as required by law and to
recover damages for any expense incurred, including reasonable attorney’s fees, interest and costs, in enforcing any of the terms or provisions of this Lease including, but not limited to, the eviction of the Lessee by judicial process or the
collection of rent due hereunder. 
 10. ASSIGNMENT AND SUBLETTING: Lessee shall not assign or sublet its space or any part thereof
without written consent of the Lessor. 
 11. ALTERATIONS, ADDITIONS OR REPAIRS: Lessee shall provide any improvements desired which
are beyond Lessor’s obligation to provide finished walls, ceiling, floors and lighting. After initial installation, Lessee shall do no redecorating or make any alterations, additions, or repairs without the written consent of the Lessor
obtained in advance in each case. All alterations, additions, and repairs shall become the property of the Lessor upon termination of this Lease unless Lessor elects otherwise. 

12. RIGHT OF ENTRY: The Lessor, or any of its agents, has the right to enter the Unit occupied by the Lessee during reasonable hours to
make inspections, repairs, additions or alterations as may be deemed necessary for the safety, comfort, or preservation thereof, of said building, and to enter at any time for emergency repairs necessary for the protection of any person or of the
building. 

  
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 13. RELEASE FROM LIABILITY: It is expressly agreed and understood that Lessee releases
Lessor and/or its agents from any and all damage or injury to person or property of Lessee suffered in the Leased space or upon the premises herein leased, and will hold the Lessor and/or agents harmless from all damages sustained during the Lease
term. 
 14. LESSEE SHALL: (a) Keep the Leased area in clean condition during its occupancy; (b) Not use any improperly
wired or unsafe electrical appliances or install any unsafe wiring in the Leased area; (c) Keep plumbing and drain lines in the Leased area clear and free from obstruction; (d) Report promptly to Lessor in writing any defects or damages to the
Leased area or any repairs needed for same; (e) Pay for cleaning and repairs necessitated by Lessee’s willful or accidental misuse of the Leased area; (f) Not block any common walkways or driveways; (g) Not place any signs in the
windows of the building or at any place on the premises without the prior written consent of the Lessor; (h) Not leave or store any disabled or non regularly used vehicle on the premises; (i) Not unreasonably interfere with the use of other
portions of the building and common areas by other lawful users of the premises; (j) Place all trash, except for normal janitorial service removal, in the dumpster provided on the premises; (k) Keep all interior portions of the leased
premises in a clean condition and surrender the premises at the end of the Lease in good condition, subject only to reasonable wear and use; and (l) Use the premises only for professional office use in conformity with applicable zoning. 

15. LESSOR SHALL: (a) Provide finished walls, ceiling, floors and lighting pursuant to approved plans; (b) Maintain the
exterior of the building and parking lots; (c) Repair heating and air conditioning, plumbing and electrical units at no cost to Lessee unless such repairs are caused by willful or negligent acts of Lessee’s employees or invitees;
(d) Pay real property ad valorem taxes and pay Lessee’s prorata share of utilities, janitorial and lawn maintenance, and see that such services are properly available to the premises pursuant to receipt of prorata share from Lessee. 

16. RIGHT TO SHOW PREMISES: During the last six (6) months of this Lease, Lessor shall have the right to show the premises to
prospective tenants so long as such activities shall not reasonably interfere with Lessee’s use of the premises. Lessor shall notify Lessee of the times of such showing of the premises. 

17. TIME IS OF THE ESSENCE: Time is of the essence for this Lease agreement. 

18. GOODS AND CHATTEL: All goods and chattel placed and stored in or about the premises are at the risk of the Lessee. 

19. REQUIRED DISPUTE RESOLUTION: If either party, the Lessor or Lessee, has disagreement under this Agreement, the disagreeing party
agrees to promptly bring such disagreement to the other party’s attention whereupon both parties agree to meet in an attempt to resolve differences. If differences are not resolved within thirty

  
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(30) days, it is agreed that either party may invoke the services of an impartial mediator under the auspices of the commercial mediation rules of the American Arbitration Association, the United
States Arbitration and Mediation Service, or any other national, neutral mediation service at the election of the party who first requests mediation. Such mediation shall be held in Gainesville, Florida. It is agreed that no claim shall be asserted
in court unless the foregoing procedures have first been followed. 
 20. BINDING ON HEIRS AND ASSIGNEES: All covenants and
agreements in this Lease shall be binding upon and inure to the benefit of the heirs, executors, administrators, successors and assigns of the Lessor and Lessee. 
  

									
	WITNESSES AS TO LESSOR:	 		 	LESSOR:
				
		 		 		 	THOMPSON-DAVIS ENTERPRISES, LLC
			
	 [Illegible]
	 		 	  /s/ DOUGLAS H. THOMPSON, JR.

	Witness Signature	 		 	DOUGLAS H. THOMPSON, JR.
		 		 		 	As Its Managing Director
					
	Date:	 	9/19/11	 		 	Date:	 	9/19/11
				
	  /s/ Laura E. Bess
	 		 		 	
	Witness Signature	 		 	
				
	Date:	 	9/19/11	 		 	
				
		 		 		 	LESSEE:
			
	WITNESSES AS TO LESSEE:	 		 	APPLIED GENETIC TECHNOLOGIES
				
	 [Illegible]
	 		 	By:	 	 [Illegible]

	Witness Signature	 		 	As Its	 	President and CEO
					
	Date:	 	9/19/11	 		 	Date:	 	9/19/11
				
	 [Illegible]
	 		 		 	
	Witness Signature	 		 		 	
					
	Date:	 	9/19/11	 		 		 	

  
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 ADVANCING SCIENCE, SAFETY & INNOVATION 

November 16, 2012 
 Applied Genetic Technologies 

11801 Research Drive 
 Alachua, FL 32615 

Attention: Susan B. Washer, President 
  

	RE:	Lease dated September 19, 2011 

 Dear Ms. Washer: 

As of November 16, 2012, Thompson-Davis Enterprises, LLC (the “Former Owner”), has transferred all of its interest (including your
security deposit) in and to RTI Biologics, Inc. (the “New Owner”). 
 Consequently, the New Owner is now the “landlord” or
“lessor” under the lease with respect to your office space. 
 Future rental payments with respect to your office space should be made payable to
“RTI Biologics, Inc.” and should be mailed to 11621 Research Circle, Alachua, Florida 32615. 
  

					
	 Sincerely,
	 	
		
	NEW OWNER:	 	
	 RTI BIOLOGICS, INC.,
 A
Delaware corporation
	 	
			
	By:	 	  /s/ Thomas F. Rose
	 	
		 	Thomas F. Rose	 	
		 	Chief Operating Officer	 	
		
	FORMER OWNER:	 	
	THOMPSON-DAVIS ENTERPRISES, LLC,	 	
	A Florida limited liability company	 	
			
	By:	 	  /s/ Douglas H. Thompson, Jr.
	 	
		 	Douglas H. Thompson, Jr.	 	
		 	Manager	 	

  
 11621 Research Circle
 Ÿ  Alachua, FL 32615 

Tel  386.418.8888 Ÿ  877.343.6832 Ÿ  Fax  386.418.0342 Ÿ  Customer Service 800.624.7238 Ÿ  www.rtix.com 

 TENANT ESTOPPEL CERTIFICATE 

 

	TO:	RTI BIOLOGICS, INC., 11621 Research Circle, Alachua, Florida 32615 (together with its successors and assigns, collectively “Purchaser”) 

THIS IS TO CERTIFY THAT: 
 I. The undersigned is executing this
Tenant Estoppel Certificate with the understanding that it will assist RTI Biologics, Inc. in acquiring the real property, on which the Premises is a part, from Thompson-Davis Enterprises, LLC. The undersigned agrees that RTI Biologics, Inc. is
relying on the accuracy of the statements contained herein. 
 2. The undersigned APPLIED GENETIC TECHNOLOGIES, a Delaware corporation, is the tenant
(“Tenant”) under that certain lease dated as of September 19, 2011 and any memorandum thereof recorded in Alachua County, Florida (“Lease”) by and between THOMPSON-DAVIS ENTERPRISES, LLC, a Florida
limited liability company, as landlord (“Landlord”) and Tenant, covering those certain premises containing 2,750 square feet (the “Premises”) commonly known and designated 11801 Research Drive, Alachua, Florida
32615, all a described in the Lease. 
 3. The Lease has not been modified, changed, altered, assigned, supplemented or amended in any respect and
replaces the lease of March 28, 2006. The Lease is valid and in full force and effect on the date hereof. The Lease is the only lease or agreement between Tenant and Landlord affecting or relating to the Premises and represents the entire
agreement between Landlord and Tenant with respect to the Premises. The Initial Term of the Lease ends on 11:59 pm December 31, 2014. 
 4. All rents,
additional rents and other sums due and payable under the Lease have been paid in full and no rents, additional rents and other sums payable under the Lease have been paid for more than one (1) month in advance of the due dates thereof. The
current annual fixed rent (excluding additional rent, impositions, or pass-through charges) payable to Landlord under the Lease is $ 44,000.00. The Lease more accurately describes the rent and the calculation thereof from time to time. The
current monthly rental payment (including all additional rent, impositions and pass-through charges, if any) due under the Lease in the amount of $3,887 has been paid for the month of Nov, 2012. Tenant has deposited the security deposit set forth in
the Lease with Landlord. 
 5. Tenant is not in default under the Lease, Tenant as of the date hereof knows of no uncured default by the Landlord under the
Lease. Tenant has no existing defenses or offsets against the enforcement of the Lease by Landlord, including, without limitation, the collection of rents, additional rents, pass-through charges and other sums due and payable thereunder. Neither
Tenant nor, to Tenant’s knowledge, Landlord has commenced any action or given or received any notice for the purpose of terminating the Lease. 

 6. Tenant has received payment or credit for all Tenant improvement work or allowances except NONE [if none,
write NONE]. The Premises have been completed and Tenant has taken possession of the same on a rent-paying basis. 
 7. The Lease contains, and Tenant has,
an option to extend the Initial Term of the Lease. 
 8. Tenant is not insolvent and is able to pay its debts as they mature. No actions, whether voluntary
or otherwise, are pending against Tenant or any general partner of Tenant under the bankruptcy or insolvency laws of the United States or any state thereof. 

9. Tenant has not sublet the Premises to any sublessee and has not assigned any of its rights under the Lease. 

10. In the event that RTI Biologics, Inc. shall become the owner of the property of which the Premises are a part, Tenant shall attorn to RTI Biologics, Inc.
as landlord under the Lease. 
 This certification is made for use by RTI Biologics, Inc. for disbursing certain funds. 

Dated this 13th day of November, 2012. 

 

							
		 	CORPORATE:	 		 	 APPLIED GENETIC
 TECHNOLOGIES, a
Delaware corporation

				
		 	TENANT:	 		 	
				
		 		 	By:	 	  /s/ Susan B. Washer

		 		 		 	Print Name: Susan B. Washer
		 		 		 	President
				
		 		 		 	Address:
				
		 		 		 	11801 Research Drive, Suite D
		 		 		 	Alachua, Florida 32615EX-10.14

 Exhibit 10.14 

APPLIED GENETIC TECHNOLOGIES CORPORATION 

2011 STOCK INCENTIVE PLAN 
  

	1.	Purpose 

 The purpose of this 2011 Stock Incentive Plan (the “Plan”) of
Applied Genetic Technologies Corporation, a Delaware corporation (the “Company”), is to advance the interests of the Company’s stockholders by enhancing the Company’s ability to attract, retain and motivate persons who are
expected to make important contributions to the Company and by providing such persons with equity ownership opportunities and performance-based incentives that are intended to align their interests with those of the Company’s stockholders.
Except where the context otherwise requires, the term “Company” includes the Company’s present or future parent or subsidiary corporations as defined in Sections 424(e) or (f) of the Internal Revenue Code of 1986, as
amended, and any regulations promulgated thereunder (the “Code”) and other business ventures (including, without limitation, any joint venture or limited liability company) in which the Company has a controlling interest, as
determined by the Board of Directors of the Company (the “Board”). 
  

	2.	Eligibility 

 All of the Company’s employees, officers, directors, and individual
consultants and advisors (each a “Service Provider”) are eligible to receive options, restricted stock, restricted stock units and other stock-based awards (each, an “Award”) under the Plan. Each person who receives
an Award under the Plan is deemed a “Participant.” 
  

	3.	Administration and Delegation 

 (a) Administration by Board of Directors. The Plan
shall be administered by the Board. The Board shall have authority to grant Awards and to adopt, amend and repeal such administrative rules, guidelines and practices relating to the Plan as it shall deem advisable. The Board may correct any defect,
supply any omission or reconcile any inconsistency in the Plan or any Award in the manner and to the extent it shall deem expedient to carry the Plan into effect and it shall be the sole and final judge of such expediency. All decisions by the Board
shall be made in the Board’s sole discretion and shall be final and binding on all persons having or claiming any interest in the Plan or in any Award. No director or person acting pursuant to the authority delegated by the Board shall be
liable for any action or determination relating to or under the Plan made in good faith. 
 (b) Appointment of Committees. To the
extent permitted by applicable law, the Board may delegate any or all of its powers under the Plan to one or more committees or subcommittees of the Board (a “Committee”). All references in the Plan to the “Board”
shall mean the Board or a Committee of the Board to the extent that the Board’s powers or authority under the Plan have been delegated to such Committee. 
  

	4.	Stock Available for Awards. 

 (a) Subject to adjustment under Section 8, Awards may
be made under the Plan for up to 5,446,341 shares of the common stock of the Company, $0.001 par value per share (the “Common Stock”); provided, however, that initially, only 830.754 shares of Common Stock are
authorized for issuance under the Plan, which number shall be increased automatically from time to time, up to an 

 
aggregate of 5,446,341 shares of Common Stock, with one additional share becoming available for grant with respect to each option to purchase a share of Common Stock outstanding under the
Company’s Stock Option Plan as of the date of the adoption of this Amendment which is terminated, surrendered or cancelled without having been exercised. If any Award issued under this Plan expires or is terminated, surrendered or canceled
without having been fully exercised or is forfeited in whole or in part (including as the result of shares of Common Stock subject to such Award being repurchased by the Company at the original issuance price pursuant to a contractual repurchase
right) or results in any Common Stock not being issued, the unused Common Stock covered by such Award shall again be available for the grant of Awards under the Plan. Further, shares of Common Stock tendered to the Company by a Participant to
exercise an Award shall be added to the number of shares of Common Stock available for the grant of Awards under the Plan. However, in the case of Incentive Stock Options (as hereinafter defined), the foregoing provisions shall be subject to any
limitations under the Code. Shares issued under the Plan may consist in whole or in part of authorized but unissued shares or treasury shares. At no time while there is any Option (as defined below) outstanding and held by a Participant who was a
resident of the State of California on the date of grant of such Option, shall the total number of shares of Common Stock issuable upon exercise of all outstanding options and the total number of shares provided for under any stock bonus or similar
plan or agreement of the Company exceed the applicable percentage as calculated in accordance with the conditions and exclusions of Section 260.140.45 of the California Code of Regulations, as amended (the “California
Regulations”), based on the shares of the Company which are outstanding at the time the calculation is made unless the Plan complies with all conditions of Rule 701 of the Securities Act of 1933, as amended. 

(b) Substitute Awards. In connection with a merger or consolidation of an entity with the Company or the acquisition by the Company of
property or stock of an entity, the Board may grant Awards in substitution for any options or other stock or stock-based awards granted by such entity or an affiliate thereof. Substitute Awards may be granted on such terms as the Board deems
appropriate in the circumstances, notwithstanding any limitations on Awards contained in the Plan. Substitute Awards shall not count against the overall share limit set forth in Section 4(a), except as may be required by reason of
Section 422 and related provisions of the Code. 
  

	5.	Stock Options 

 (a) General. The Board may grant options to purchase Common Stock
(each, an “Option”) and determine the number of shares of Common Stock to be covered by each Option, the exercise price of each Option and the conditions and limitations applicable to the exercise of each Option, including
conditions relating to applicable federal or state securities laws, as it considers necessary or advisable. An Option, or portion of an Option, which is not intended to be or fails to qualify as an Incentive Stock Option (as hereinafter defined)
shall be designated a “Nonstatutory Stock Option.” 
 (b) Incentive Stock Options. An Option that the Board intends
to be an “incentive stock option” as defined in Section 422 of the Code (an “Incentive Stock Option”) shall only be granted to employees of the Company and any other entities the employees of which are eligible to
receive Incentive Stock Options under the Code, and shall be subject to and shall be construed consistently with the requirements of Section 422 of the Code. A Participant who owns more than 10% of the total combined voting power of all classes
of outstanding stock of the Company shall not be eligible for the grant of an Incentive Stock Option unless (i) the exercise price is at least 110% of the Fair Market Value (as defined below) on the date the Option is granted and (ii) such
Incentive Stock Option by its terms is not exercisable after the expiration of five years from the date the Option is granted. The Company shall have no liability to a Participant, or any other party, if an Option (or any part thereof) that is
intended to be an Incentive Stock Option is not an Incentive Stock Option or for any action taken by the Board pursuant to Section 9(f), including without limitation the conversion of an Incentive Stock Option to a Nonstatutory Stock Option.

  
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 (c) Exercise Price. The Board shall establish the exercise price of each Option and
specify such exercise price in the applicable option agreement. The exercise price shall be not less than 100% of the Fair Market Value on the date the Option is granted unless the Board specifically determines that the exercise price is intended to
be less than such Fair Market Value, in which case the option agreement shall contain provisions complying with Section 409A of the Code; provided that if the Board approves the grant of an Option with an exercise price to be determined on a
future dale, the exercise price shall be not less than 100% of the Fair Market Value on such future date. The term “Fair Market Value” shall mean, as of a given date: (i) if the Common Stock is listed on a national securities
exchange, the last sale price of the Common Stock in the principal trading market for the Common Stock on such date; (ii) if the Common Stock is not listed on a national securities exchange, but is traded in the over-the counter market, the
closing bid price for the Common Stock on such date, as reported by the OTC Bulletin Board or the National Quotation Bureau, Incorporated or similar publisher of such quotations; or (iii) if the Common Stock is not listed on a national
securities exchange or traded in the over-the-counter market, such price as shall be determined by (or in a manner approved by) the Board in good faith and in compliance with applicable provisions of the Code and the regulations issued thereunder.

 (d) Duration of Options. Each Option shall be exercisable at such times and subject to such terms and conditions as the Board may
specify in the applicable option agreement. 
 (e) Exercise of Option. Options may be exercised by delivery to the Company of a
written notice of exercise signed by the proper person or by any other form of notice (including electronic notice) approved by the Board together with payment in full as specified in Section 5(f) for the number of shares of Common Stock for
which the Option is exercised. Shares of Common Stock subject to the Option will be delivered by the Company following exercise either as soon as practicable or, subject to such conditions as the Board shall specify, on a deferred basis (with the
Company’s obligation to be evidenced by an instrument providing for future delivery of the deferred shares at the time or times specified by the Board). 

(f) Payment Upon Exercise. Common Stock purchased upon the exercise of an Option granted under the Plan shall be paid for as follows:

 (1) in cash or by check, payable to the order of the Company; 

(2) except as may otherwise be provided in the applicable option agreement, by (i) delivery of an irrevocable and unconditional
undertaking by a creditworthy broker to deliver promptly to the Company sufficient funds to pay the exercise price and any required tax withholding or (ii) delivery by the Participant to the Company of a copy of irrevocable and unconditional
instructions to a creditworthy broker to deliver promptly to the Company cash or a check sufficient to pay the exercise price and any required tax withholding; 

(3) when the Common Stock is registered under the Securities Exchange Act of 1934, as amended (the “Exchange Act”) and to the
extent provided for in the applicable option agreement or approved by the Board, in its sole discretion, by delivery (either by actual delivery or attestation) of shares of Common Stock owned by the Participant valued at their Fair Market Value,
provided (i) such method of payment is then permitted under applicable law, (ii) such Common Stock, if acquired directly from the Company, was owned by the Participant for such minimum period of time, if any, as may be established by the
Board in its discretion and (iii) such Common Stock is not subject to any repurchase, forfeiture, unfulfilled vesting or other similar requirements; 

  
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 (4) to the extent permitted by applicable law and provided for in the applicable option agreement
or approved by the Board, in its sole discretion, by (i) delivery of a promissory note of the Participant to the Company on terms determined by the Board, or (ii) payment of such other lawful consideration as the Board may determine; or

 (5) by any combination of the above permitted forms of payment. 

 

	6.	Restricted Stock; Restricted Stock Units 

 (a) General. The Board may grant Awards
entitling recipients to acquire shares of Common Stock (“Restricted Stock”), subject to the right of the Company to repurchase all or part of such shares at their issue price or other stated or formula price (or to require
forfeiture of such shares if issued at no cost) from the recipient in the event that conditions specified by the Board in the applicable Award are not satisfied prior to the end of the applicable restriction period or periods established by the
Board for such Award. Instead of granting Awards for Restricted Stock, the Board may grant Awards entitling the recipient to receive shares of Common Stock to be delivered at the time such shares of Common Stock vest (“Restricted Stock
Units”) (Restricted Stock and Restricted Stock Units are each referred to herein as a “Restricted Stock Award”). 

(b) Terms and Conditions. The Board shall determine the terms and conditions of a Restricted Stock Award, including the conditions for
repurchase (or forfeiture) and the issue price, if any. 
 (c) Additional Provisions Relating to Restricted Stock. 

(1) Dividends. Participants holding shares of Restricted Stock will be entitled to all ordinary cash dividends paid with respect to
such shares, unless otherwise provided by the Board. If any such dividends or distributions are paid in shares, or consist of a dividend or distribution to holders of Common Stock other than an ordinary cash dividend, the shares, cash or other
property will be subject to the same restrictions on transferability and forfeitability as the shares of Restricted Stock with respect to which they were paid. Each dividend payment will be made no later than the end of the calendar year in which
the dividends are paid to stockholders of that class of stock or, if later, the 15th day of the third month following the dale the dividends are paid to stockholders of that class of stock. 

(2) Stock Certificates. The Company may require that any stock certificates issued in respect of a Restricted Stock Award shall be
registered in the name of the Participant and be deposited by the Participant, together with a stock power endorsed in blank, with the Company (or its designee). After the expiration of the applicable restriction periods, upon request of a
Participant or as otherwise determined by the Company, the Company (or such designee) shall deliver the certificates no longer subject to such restrictions to the Participant or if the Participant has died, to the beneficiary designated, in a manner
determined by the Board, by a Participant to receive amounts due or exercise rights of the Participant in the event of the Participant’s death (the “Designated Beneficiary”). In the absence of an effective designation by a
Participant, “Designated Beneficiary” shall mean the Participant’s then living spouse, or, if none, the Participant’s estate. 

  
 4 

	7.	Other Stock-Based Awards 

 Other Awards of shares of Common Stock, and other Awards that
are valued in whole or in part by reference to, or are otherwise based on, shares of Common Stock or other property, may be granted hereunder to Participants (“Other Stock-Based Awards”), including without limitation stock
appreciation rights and Awards entitling recipients to receive shares of Common Stock to be delivered in the future. Such Other Stock-Based Awards shall also be available as a form of payment in the settlement of other Awards granted under the Plan
or as payment in lieu of compensation to which a Participant is otherwise entitled. Other Stock-Based Awards may be paid in shares of Common Stock or cash, as the Board shall determine. Subject to the provisions of the Plan, the Board shall
determine the conditions of each Other Stock-Based Award, including any purchase price applicable thereto. 
  

	8.	Adjustments for Changes in Common Stock and Certain Other Events 

 (a) Changes in
Capitalization. In the event of any stock split, reverse stock split, stock dividend, recapitalization, combination of shares, reclassification of shares, spin-off or other similar change in capitalization or event, or any dividend or
distribution to holders of Common Stock other than an ordinary cash dividend, (i) the number and class of securities available under this Plan, (ii) the number and class of securities and exercise price per share of each outstanding
Option, (iii) the number of shares subject to and the repurchase price per share subject to each outstanding Restricted Stock Award, and (iv) the terms of each other outstanding Award shall be equitably adjusted by the Company (or
substituted Awards may be made, if applicable) in the manner determined by the Board. Without limiting the generality of the foregoing, in the event the Company effects a split of the Common Stock by means of a stock dividend and the exercise price
of and the number of shares subject to an outstanding Option are adjusted as of the date of the distribution of the dividend (rather than as of the record date for such dividend), then an optionee who exercises an Option between the record date and
the distribution date for such stock dividend shall be entitled to receive, on the distribution date, the stock dividend with respect to the shares of Common Stock acquired upon such Option exercise, notwithstanding the fact that such shares were
not outstanding as of the close of business on the record date for such stock dividend. 
 (b) Change in Control 

(1) Definition. Unless otherwise specifically provided in an Award agreement, a “Change in Control” shall be deemed to
have occurred upon the first to occur of: 
 (i) any “person” (as such term is used in sections 13(d) and 14(d) of the Exchange
Act) becoming a “beneficial owner” (as defined in Rule 13d-3 under the Exchange Act), directly or indirectly, of securities of the Company representing either (A) more than a majority of the voting power of the then outstanding
securities of the Company, or (B) more than a majority of the aggregate fair market value of the then outstanding securities of the Company; provided, however, that a Change in Control shall not be deemed to occur as a result of
(x) a transaction in which the Company becomes a subsidiary of another corporation and in which the stockholders of the Company, immediately prior to the transaction, will beneficially own, immediately after the transaction, shares entitling
such stockholders to more than majority of all votes to which all stockholders of the parent corporation would be entitled in the election of directors, or (y) a transaction in which the person acquires newly issued securities of the Company in
exchange for an investment in the Company; or 
 (ii) the consummation of either: (A) a merger, share exchange, consolidation or
reorganization of the Company where the stockholders of the Company, immediately prior to the merger or consolidation, will not beneficially own, immediately after the merger, share exchange, consolidation or reorganization, shares entitling such
stockholders to either (x) more than a majority of all votes to which all stockholders of the surviving corporation would be entitled in the election of directors, or (y) more than a majority of the aggregate fair market value of then
outstanding securities of the Company; or (B) a sale or other disposition of all or substantially all of the assets of the Company. 

  
 5 

 (2) Consequences of a Change in Control on Awards Other than Restricted Stock Awards. In
connection with a Change in Control, the Board may take any one or more of the following actions as to all (or any portion of) outstanding Awards other than Restricted Stock Awards on such terms as the Board determines: (i) provide that Awards
shall be assumed, or substantially equivalent Awards shall be substituted, by the acquiring or succeeding corporation (or an affiliate thereof) in compliance with the applicable provisions of the Code, including Code Sections 409A, 422 and 424,
(ii) upon written notice to a Participant, provide that the Participant’s unexercised Options or other unexercised Awards will terminate immediately prior to the consummation of such Change in Control unless exercised by the Participant
within a specified period following the date of such notice, (iii) provide that outstanding Awards shall become exercisable, realizable or deliverable, or restrictions applicable to an Award shall lapse, in whole or in part prior to or upon
such Change in Control, (iv) in the event of a Change in Control under the terms of which holders of Common Stock will receive upon consummation thereof a cash payment for each share surrendered in the Change in Control (the
“Acquisition Price”), make or provide for a cash payment to a Participant equal to the excess, if any, of (A) the Acquisition Price times the number of shares of Common Stock subject to the Participant’s Options or other
Awards (to the extent the exercise price does not exceed the Acquisition Price) less (B) the aggregate exercise price of all such outstanding Options or other Awards and any applicable tax withholdings, in exchange for the termination of such
Options or other Awards, (v) provide that, in connection with a liquidation or dissolution of the Company, Awards shall convert into the right to receive liquidation proceeds (if applicable, net of the exercise price thereof) and (vi) any
combination of the foregoing. In taking any of the actions permitted under this Section 8(b), the Board shall not be obligated by the Plan to treat all Awards, or all Awards of the same type, identically. 

For purposes of clause (i) above, an Option shall be considered assumed if, following consummation of the Change in Control, the Option
confers the right to purchase, for each share of Common Stock subject to the Option immediately prior to the consummation of the Change in Control, the consideration (whether cash, securities or other property) received as a result of the Change in
Control by holders of Common Stock for each share of Common Stock held immediately prior to the consummation of the Change in Control (and if holders were offered a choice of consideration, the type of consideration chosen by the holders of a
majority of the outstanding shares of Common Stock); provided, however, that if the consideration received as a result of the Change in Control is not solely common stock of the acquiring or succeeding corporation (or an affiliate
thereof), the Company may, with the consent of the acquiring or succeeding corporation, provide for the consideration to be received upon the exercise of Options to consist solely of common stock of the acquiring or succeeding corporation (or an
affiliate thereof) with equivalent in value (as determined by the Board) to the per share consideration received by holders of outstanding shares of Common Stock as a result of the Change in Control. 

(3) Consequences of a Change in Control on Restricted Stock Awards. Upon the occurrence of a Change in Control other than a liquidation
or dissolution of the Company, the repurchase and other rights of the Company under each outstanding Restricted Stock Award shall inure to the benefit of the Company’s successor and shall, unless the Board determines otherwise, apply to the
cash, securities or other property which the Common Stock was converted into or exchanged for pursuant to such Change in Control in the same manner and to the same extent as they applied to the Common Stock subject to such Restricted Stock Award.
Upon the occurrence of a Change in Control involving the liquidation or dissolution of the Company, except to the extent specifically provided to the contrary in the instrument evidencing any Restricted Stock Award or any other agreement between a
Participant and the Company, all restrictions and conditions on all Restricted Stock Awards then outstanding shall automatically be deemed terminated or satisfied. 

  
 6 

	9.	General Provisions Applicable to Awards 

 (a) Transferability of Awards. Except as
the Board may otherwise expressly determine or provide in an Award, Awards shall not be sold, assigned, transferred, pledged or otherwise encumbered by the person to whom they are granted, either voluntarily or by operation of law, except by will or
the laws of descent and distribution or, other than in the case of an Incentive Stock Option, pursuant to a qualified domestic relations order, and, during the life of the Participant, shall be exercisable only by the Participant. References to a
Participant, to the extent relevant in the context, shall include references to authorized transferees. 
 (b) Documentation. Unless
otherwise expressly determined by the Board, each Incentive Stock Option shall be evidenced by a Notice of Incentive Stock Option and Incentive Stock Option Agreement substantially in the form attached as Exhibit A, each Nonstatutory
Stock Option shall be evidenced by a Notice of Nonstatutory Stock Option and Nonstatutory Stock Option Agreement substantially in the form attached as Exhibit B, and each Restricted Stock Award shall be evidenced by a Summary of
Restricted Stock Purchase and Restricted Stock Purchase Agreement substantially in the form attached as Exhibit C. Each Award may contain terms and conditions in addition to those set forth in the Plan. 

(c) Board Discretion. Except as otherwise provided by the Plan, each Award may be made alone or in addition or in relation to any other
Award. The terms of each Award need not be identical, and the Board need not treat Participants uniformly. 
 (d) Termination of
Status. The Board shall determine the effect on an Award of the disability, death, termination of employment, authorized leave of absence or other change in the employment or other status of a Participant and the extent to which, and the period
during which, the Participant, or the Participant’s legal representative, conservator, guardian or Designated Beneficiary, may exercise rights under the Award. 

(e) Withholding. The Participant must satisfy all applicable federal, state, and local or other income and employment tax withholding
obligations before the Company will deliver stock certificates or otherwise recognize ownership of Common Stock under an Award. The Company may decide to satisfy the withholding obligations through additional withholding on salary or wages. If the
Company elects not to or cannot withhold from other compensation, the Participant must pay the Company the full amount, if any, required for withholding or have a broker tender to the Company cash equal to the withholding obligations. Payment of
withholding obligations is due before the Company will issue any shares on exercise or release from forfeiture of an Award or, if the Company so requires, at the same time as is payment of the exercise price unless the Company determines otherwise.
If provided for in an Award or approved by the Board in its sole discretion, a Participant may satisfy such tax obligations in whole or in part by delivery of shares of Common Stock, including shares retained from the Award creating the tax
obligation, valued at their Fair Market Value; provided, however, except as otherwise provided by the Board, that the total tax withholding where stock is being used to satisfy such tax obligations cannot exceed the Company’s
minimum statutory withholding obligations (based on minimum statutory withholding rates for federal and state tax purposes, including payroll taxes, that are applicable to such supplemental taxable income). Shares surrendered to satisfy tax
withholding requirements cannot be subject to any repurchase, forfeiture, unfulfilled vesting or other similar requirements. 

  
 7 

 (f) Amendment of Award. 

(1) The Board may amend, modify or terminate any outstanding Award, including but not limited to, substituting therefor another Award of the
same or a different type, changing the date of exercise or realization, and converting an Incentive Stock Option to a Nonstatutory Stock Option, provided that the Participant’s consent to such action shall be required unless the Board
determines that the action, taking into account any related action, would not materially and adversely affect the Participant. 
 (2) The
Board may, without stockholder approval, amend any outstanding Award granted under the Plan to provide an exercise price per share that is lower than the then-current exercise price per share of such outstanding Award provided that such amended
exercise price is at least equal to the then-current Fair Market Value. The Board may also, without stockholder approval, cancel any outstanding award (whether or not granted under the Plan) and grant in substitution new Awards under the Plan
covering the same or a different number of shares of Common Stock and having an exercise price per share lower than the then-current exercise price per share of the cancelled award. 

(g) Conditions on Delivery of Stock. The Company will not be obligated to deliver any shares of Common Stock pursuant to the Plan or to
remove restrictions from shares previously delivered under the Plan until (i) all conditions of the Award have been met or removed to the satisfaction of the Company, (ii) in the opinion of the Company’s counsel, all other legal
matters in connection with the issuance and delivery of such shares have been satisfied, including any applicable securities laws and any applicable stock exchange or stock market rules and regulations, and (iii) the Participant has executed
and delivered to the Company such representations or agreements as the Company may consider appropriate to satisfy the requirements of any applicable laws, rules, regulations or contracts of the Company. 

(h) Acceleration. The Board may at any time provide that any Award shall become immediately exercisable in full or in part, free of
some or all restrictions or conditions, or otherwise realizable in full or in part, as the case may be. 
  

	10.	Miscellaneous 

 (a) No Right To Employment or Other Status. No person shall have
any claim or right to be granted an Award, and the grant of an Award shall not be construed as giving a Participant the right to continued employment or any other relationship with the Company. The Company expressly reserves the right at any time to
dismiss or otherwise terminate its relationship with a Participant free from any liability or claim under the Plan, except as expressly provided in the applicable Award. 

(b) No Rights As Stockholder. Subject to the provisions of the applicable Award, no Participant or Designated Beneficiary shall have
any rights as a stockholder with respect to any shares of Common Stock to be distributed with respect to an Award until becoming the record holder of such shares. Notwithstanding the foregoing, in the event the Company effects a split of the Common
Stock by means of a stock dividend or otherwise and the exercise price of and the number of shares subject to such Option are adjusted as of the effective date of the stock dividend or split (rather than as of the record date for such stock dividend
or split), then an optionee who exercises an Option between the record date and the distribution date for such stock dividend or split shall be entitled to receive, on the distribution date, the stock dividend or split with respect to the shares of
Common Stock acquired upon such Option exercise, notwithstanding the fact that such shares were not outstanding as of the close of business on the record date for such stock dividend or split. 

  
 8 

 (c) Effective Date and Term of Plan. The Plan shall become effective on the date on which
it is adopted by the Board. No Awards shall be granted under the Plan after the expiration of 10 years from the earlier of (i) the date on which the Plan was adopted by the Board or (ii) the date the Plan was approved by the Company’s
stockholders, but Awards previously granted may extend beyond that date. 
 (d) Amendment of Plan. The Board may amend, suspend or
terminate the Plan or any portion thereof at any time; provided, however, that if at any time the approval of the Company’s stockholders is required as to any modification or amendment under Section 422 of the Code or any
successor provision with respect to Incentive Stock Options, the Board may not effect such modification or amendment without such approval. Unless otherwise specified in the amendment, any amendment to the Plan adopted in accordance with this
Section 10(d) shall apply to, and be binding on the holders of, all Awards outstanding under the Plan at the time the amendment is adopted, provided the Board determines that such amendment does not materially and adversely affect the rights of
Participants under the Plan. 
 (e) Authorization of Sub-Plans. The Board may from time to time establish one or more sub-plans under
the Plan for purposes of satisfying applicable blue sky, securities or tax law’s of various jurisdictions. The Board shall establish such sub-plans by adopting supplements to this Plan containing (i) such limitations on the Board’s
discretion under the Plan as the Board deems necessary or desirable or (ii) such additional terms and conditions not otherwise inconsistent with the Plan as the Board shall deem necessary or desirable. All supplements adopted by the Board shall be
deemed to be part of the Plan, but each supplement shall apply only to Participants within the affected jurisdiction and the Company shall not be required to provide copies of any supplement to Participants in any jurisdiction which is not the
subject of such supplement. 
 (f) Compliance with Code Section 409A. It is intended that all Awards granted hereunder be either
exempt from, or issued in compliance with, Code Section 409A. The Company shall have no liability to a Participant, or any other party, if an Award that is intended to be exempt from, or compliant with, Code Section 409A is not so exempt
or compliant, or for any action taken by the Board. 
 (g) Governing Law. The provisions of the Plan and all Awards made hereunder
shall be governed by and construed in accordance with the General Corporation Law of the State of Delaware, as to matters within the scope thereof, and the internal laws of the State of Florida (without reference to conflict of law provisions), as
to all other matters. 
 *  *  *  *  *  *  *  * 

  
 9 

 APPLIED GENETIC TECHNOLOGIES CORPORATION 

2011 STOCK INCENTIVE PLAN 

CALIFORNIA SUPPLEMENT 

Pursuant to Section 10(e) of the Plan, the Board has adopted this supplement for purposes of satisfying the requirements of
Section 25102(o) of the California Corporations Code, as amended: 
 Any Awards granted under the Plan to a Participant who is a
resident of the State of California on the date of grant (a “California Participant”) shall be subject to the following additional limitations, terms and conditions: 

1. Additional Limitations on Awards. 

(a) Generally. The terms of all Awards granted to a California Participant under Sections 5, 6 or 7 of the Plan shall comply, to the
extent applicable, with Section 260.140.41 or Section 260.140.42 of the California Regulations. 
 (b) Maximum Duration of
Options. No Options granted to California Participants shall have a term in excess of 10 years measured from the Option grant date. 

(c) Minimum Exercise Period Following Termination. Unless a California Participant’s employment is terminated for cause (as
defined by applicable law, the terms of any contract of employment between the Company and such Participant, or in the instrument evidencing the grant of such Participant’s Option), in the event of termination of employment of such Participant,
such Participant shall have the right to exercise an Option, to the extent that he or she was otherwise entitled to exercise such Option on the date employment terminated, until the earlier of the Option expiration date or: (i) at least six
months from the date of termination, if termination was caused by such Participant’s death or “permanent and total disability” (within the meaning of Section 22(e)(3) of the Code) and (ii) at least 30 days from the
date of termination, if termination was caused other than by such Participant’s death or “permanent and total disability” (within the meaning of Section 22(e)(3) of the Code). 

2. Additional Requirement to Provide Information to California Participants. Unless the Plan or agreement complies with all conditions of Rule 701 of
the Securities Act of 1933, as amended (“Rule 701”), the Company shall provide to each California Participant and to each California Participant who acquires Common Stock pursuant to the Plan, not less frequently than annually,
copies of annual financial statements (which need not be audited). The Company shall not be required to provide such statements to key employees whose duties in connection with the Company assure their access to equivalent information or when the
Plan or agreement complies with all conditions of Rule 701. 
 3. Additional Limitations on Timing of Awards. No Award granted to a California
Participant shall become exercisable, vested or realizable, as applicable to such Award, unless the Plan has been approved by the holders of at least a majority of the Company’s outstanding voting securities by the later of (i) within 12
months before or after the date the Plan was adopted by the Board or the agreement entered into; and (ii) prior to or within 12 months of the granting of any option or issuance of any security under the Plan or agreement to a California
Participant. 
 4. Additional Restriction Regarding Recapitalizations, Stock Splits, Etc. For purposes of Section 8 of the Plan, in the event of
a stock split, reverse stock split, stock dividend, recapitalization, combination, 

 
reclassification or other distribution of the Company’s securities, the number of securities allocated to each California Participant must be adjusted proportionately and without the receipt
by the Company of any consideration from any California Participant. 

  
 A - 2 

 EXHIBIT A 

Notice of Incentive Stock Option 

and 
 Incentive Stock
Option Agreement 

 APPLIED GENETIC TECHNOLOGIES CORPORATION 

NOTICE OF INCENTIVE STOCK OPTION 

2011 STOCK INCENTIVE PLAN 

Applied Genetic Technologies Corporation, a Delaware corporation (the “Company”) grants to the undersigned (the
“Participant”) the following incentive stock option to purchase shares (the “Shares”) of the common stock of the Company, par value $0.001 per share (the “Common Stock”), pursuant to the
Company’s 2011 Stock Incentive Plan (the “Plan”): 
  

			
	Participant:	  	*[Participant Name]
		
	Total Number of Shares:	  	*[Number of Shares]
		
	Grant Date:	  	*[Grant Date]
		
	Exercise Price per Share:	  	$*[Exercise Price]
		
	Vesting Commencement Date:	  	*[Vesting Date]
		
	Vesting Schedule:	  	*[ 25% of the Total Number of Shares shall vest and become exercisable on the 1 year anniversary of the Vesting Commencement Date and 1/48 of the Total Number of Shares shall vest and become exercisable on the corresponding
day of each month thereafter, or on the last day of each month, to the extent each month thereafter does not have the corresponding day. until all of the Shares have vested on the fourth anniversary of the Vesting Commencement Date, subject to
Participant continuing to be a Service Provider through each such date.] *[In addition, this Option may vest and become exercisable on an accelerated basis under Section 2 of the Incentive Stock Option Agreement.]
		
	Final Exercise Date:	  	*[Expiration Date]. This Option may expire earlier pursuant to Section 3 of the Incentive Stock Option Agreement if the Participant’s relationship with the Company is terminated or pursuant to Section 8 of the
Plan.

 This incentive stock option is granted under and governed by the terms and conditions of the Plan and the
Incentive Stock Option Agreement, both of which are incorporated herein by reference. By signing below, the Participant accepts this incentive stock option, acknowledges receipt of a copy of the Plan and the Incentive Stock Option Agreement, and
agrees to the terms thereof. 
  

									
	*[PARTICIPANT NAME]:	 		 	APPLIED GENETIC TECHNOLOGIES CORPORATION:
				
	  
	 		 	By:	 	  

	(Signature)	 		 		 	
		 		 		 	Name:	 	  

					
	Address:	 	  
	 		 	Title:	 	  

				
	  
	 		 	Date:	 	  

 THE OPTION GRANTED PURSUANT TO THIS AGREEMENT AND THE SHARES ISSUABLE UPON THE EXERCISE THEREOF HAVE NOT BEEN
REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR ANY STATE SECURITIES LAWS, AND MAY NOT BE SOLD, PLEDGED OR OTHERWISE TRANSFERRED WITHOUT AN EFFECTIVE REGISTRATION THEREOF UNDER SUCH ACT OR APPLICABLE LAWS OR AN OPINION OF COUNSEL
SATISFACTORY TO THE COMPANY AND ITS COUNSEL THAT SUCH REGISTRATION IS NOT REQUIRED. 
 APPLIED GENETIC TECHNOLOGIES CORPORATION

 INCENTIVE STOCK OPTION AGREEMENT 

Granted under 2011 Stock Incentive Plan 

1. Grant of Option. 
 This Incentive
Stock Option Agreement (the “Agreement”) evidences the grant by Applied Genetic Technologies Corporation, a Delaware corporation (the “Company”), on the Grant Date to the Participant, an employee of the Company, of
an option (this “Option”) to purchase, in whole or in part, on the terms provided herein and in the Plan, the Total Number of Shares at the Exercise Price per Share, all as defined and set forth in the accompanying Notice of
Incentive Stock Option (the “Notice”). Capitalized terms that are not otherwise defined herein or in the Notice shall have the meanings given to such terms in the Plan. 

It is intended that this Option shall be an incentive stock option as defined in Section 422 of the Internal Revenue Code of 1986, as
amended, and any regulations promulgated thereunder (the “Code”). If for any reason the Option, or any portion thereof, does not meet the requirements of Section 422 of the Code, then the Option, or any portion thereof, as
necessary, shall be deemed a nonstatutory stock option granted under the Plan. Except as otherwise indicated by the context, the term “Participant,” as used in this Agreement, shall include any person who acquires the right to exercise
this Option validly under its terms. 
 2. Vesting Schedule. 

This Option shall vest and become exercisable at the time or times set forth in the accompanying Notice. [In addition, this Option may
vest and become exercisable on an accelerated basis as follows: 
 * [ Insert any applicable acceleration provisions, such as one of
the following examples.] 
 *[If, prior to the Final Exercise Date, the Participant’s status as a Service Provider is
terminated by the Company without Cause (as defined in Section 3(e) below), then, immediately upon the effective date of such termination, this Option shall become exercisable as to [partial acceleration: that portion of the Total
Number of Shares that otherwise would have vested during the *[            ] month period following the effective date of such termination, it being understood that in no
event shall the Participant be entitled to exercise the Option to purchase greater than the Total Number of Shares as a result of this provision.] OR [full acceleration: 100% of the Total Number of Shares, it being understood
that in no event shall the Participant be entitled to exercise the Option to purchase greater than the Total Number of Shares as a result of this provision.] 

[Single Trigger] *[Immediately prior to the effective date of a Change in Control, this Option shall vest and become exercisable
as to [partial acceleration: that portion of the Total Number of Shares 

 
that otherwise would have vested during the *[            ] month period following the effective date of such Change in
Control, it being understood that in no event shall the Participant be entitled to exercise the Option to purchase greater than the Total Number of Shares as a result of this provision.] OR [full acceleration: 100% of the Total Number of
Shares, it being understood that in no event shall the Participant be entitled to exercise the Option to purchase greater than the Total Number of Shares as a result of this provision.] 

[Double Trigger] *[If (a) upon the consummation of a Change in Control this Option is assumed, or a substantially
equivalent award is substituted, by the acquiring or succeeding corporation (in accordance with Section 8(b)(2)(i) of the Plan) and (b) within *[12] months following such Change in Control the Participant’s status as a Service
Provider is terminated by the acquiring or succeeding corporation without Cause (as defined in Section 3(e) below), then, immediately upon the effective date of such termination, this Option shall vest and become exercisable as to [partial
acceleration: that portion of the Total Number of Shares that otherwise would have vested during the *[            ] month period following the effective date of such
termination, it being understood that in no event shall the Participant be entitled to exercise the Option to purchase greater than the Total Number of Shares as a result of this provision.] OR [full acceleration: 100% of the Total Number of
Shares, it being understood that in no event shall the Participant be entitled to exercise the Option to purchase greater than the Total Number of Shares as a result of this provision.] 

3. Exercise of Option. 
 (a) Form of
Exercise. Each election to exercise this Option shall be in writing in substantially the form of the Notice of Stock Option Exercise attached to this Agreement as Exhibit A, signed by the Participant, and received by the Company at
its principal office, accompanied by this Agreement, and payment in full in the manner provided in the Plan. The Participant may purchase less than the number of Shares subject to this Option; provided that, no partial exercise of this
Option may be for any fractional share. 
 (b) Continuous Relationship with the Company Required. Except as otherwise provided in
this Section 3, this Option may not be exercised unless the Participant, at the time of the exercise of this Option, is, and has been at all times since the Grant Date, a Service Provider to or of the Company or any subsidiary of the Company as
defined in Section 424 (f) of the Code (an “Eligible Participant”). 
 (c) Termination of Relationship with
the Company. If the Participant ceases to be an Eligible Participant for any reason, then, except as provided in paragraphs (d) and (e) below, the right to exercise this Option shall terminate three months after such cessation (but in
no event after the Final Exercise Date); provided that, this Option shall be exercisable only to the extent that the Participant was entitled to exercise this Option on the date of such cessation. Notwithstanding the foregoing, if the
Participant, prior to the Final Exercise Date, violates the non-competition or confidentiality provisions of any employment agreement, confidentiality and nondisclosure agreement, or other agreement between the Participant and the Company, the right
to exercise this Option shall terminate immediately upon such violation. 
 (d) Exercise Period Upon Death or Disability. If the
Participant dies or becomes disabled (within the meaning of Section 22(e)(3) of the Code) prior to the Final Exercise Date while the Participant is an Eligible Participant and the Company has not terminated such relationship for
“Cause” (as defined below), this Option shall be exercisable, within the period of one year following the date of death or disability of the Participant, by the Participant (or in the case of death by an authorized transferee);
provided that, this Option shall be exercisable only to the extent that this Option was exercisable by the Participant on the date of the Participant’s death or disability, and further provided that this Option shall not be
exercisable after the Final Exercise Date. 

  
 2 

 (e) Termination for Cause. If, prior to the Final Exercise Date, the Participant’s
status as a Service Provider is terminated by the Company for Cause (as defined below), the right to exercise this Option shall terminate immediately upon the effective date of such termination. If the Participant is party to an agreement with the
Company that contains an applicable definition of “cause”, “Cause” shall have the meaning ascribed to such term in such agreement. Otherwise, “Cause” shall mean willful misconduct by the Participant or
willful failure by the Participant to perform the Participant’s responsibilities to the Company (including, without limitation, breach by the Participant of any provision of any employment, consulting, advisory, nondisclosure, non-competition
or other similar agreement between the Participant and the Company), as determined by the Company, which determination shall be conclusive. The Participant shall be considered to have been discharged for Cause if the Company determines, within 30
days after the Participant’s resignation, that discharge for cause was warranted. 
 4. Restrictions on Transfer; Rights of First Refusal and
Stockholder Agreements. 
 (a) Bylaws. The Participant acknowledges and agrees that the Shares are subject to the provisions of
the Company’s Bylaws, as amended from time to time (the “Bylaws”), including without limitation, all restrictions on transfer and rights of first refusal described in the Bylaws. The Participant may inspect the Bylaws at the
Company’s principal office. 
 (b) Legend. Any certificate representing Shares shall bear a legend substantially in the
following form (in addition to, or in combination with, any legend required by applicable federal and state securities laws and agreements relating to the transfer and/or voting of the Company securities): 

“The securities represented by this certificate, and the transfer thereof, are subject to the restriction on transfer provisions of the
Bylaws of the Company, a copy of which is on file in, and may be examined at, the principal office of the Company” 
 (c)
Stockholder Agreements. The Participant acknowledges and agrees that the Company may condition the issuance of the Shares upon the Participant joining and becoming a party to such stockholder agreements, which may impose certain contractual
rights and obligations on the Shares, as may be entered into from time to time by and among the Company and certain holders of the Company’s capital stock. 

5. Agreement in Connection with Public Offering. The Participant agrees, in connection with the initial underwritten public offering of the
Company’s securities pursuant to a registration statement under the Securities Act of 1933, as amended (the “Securities Act”): (i) not to sell, make short sale of, loan, grant any options for the purchase of, or otherwise
dispose of any shares of Common Stock held by the Participant (other than those shares included in the offering) without the prior written consent of the Company or the underwriters managing such initial underwritten public offering of the
Company’s securities for a period of 180 days from the effective date of such registration statement, which period may be extended upon the request of the underwriters for an additional period of up to fifteen (15) days if the Company
issues or proposes to issue an earnings or other public release within fifteen (15) days of the expiration of the 180-day lockup period, and (ii) to execute any agreement reflecting clause (i) above as may be requested by the Company
or the managing underwriters at the time of such offering. 
 The Participant agrees to execute and deliver such other agreements as may be
reasonably requested by the Company or the underwriters of such offering which are consistent with the foregoing or 

  
 3 

 
which are necessary to give further effect thereto. In addition, if requested, by the Company or the underwriters of such offering, the Participant shall provide, within 10 days of such request,
such information as may be required by the Company or such underwriters in connection with the completion of any public offering of the Company’s securities pursuant to a registration statement filed under the Securities Act. The obligations
described in this Section 5 shall not apply to a registration relating solely to employee benefits plans on Form S-1 or Form S-8 or similar forms that may be promulgated in the future, or a registration relating solely to a Commission Rule 145
transaction on Form S-4 or similar forms that may be promulgated in the future. The Company may impose stop-transfer instructions with respect to the shares of Common Stock (or other securities) subject to the foregoing restriction until the end of
the applicable period. Participant agrees that any transferee of this Option or Shares pursuant to this Agreement shall be bound by this Section 5. 

6. Tax Matters. 
 (a) Withholding.
No Shares shall be issued pursuant to the exercise of this Option unless and until the Participant pays to the Company, or makes provision satisfactory to the Company for payment of, any federal, state or local withholding taxes required by law to
be withheld in respect of this Option. 
 (b) Disqualifying Disposition. If the Participant disposes of Shares acquired upon exercise
of this Option within two years from the Grant Date or one year after such Shares were acquired pursuant to exercise of this Option, the Participant shall immediately notify the Company in writing of such disposition and shall timely satisfy all
resulting tax obligations and shall hold the Company harmless with respect to any such tax obligations. 
 (c) Code
Section 409A. The Exercise Price is intended to be the Fair Market Value of the Common Stock on the Grant Date. The Company has determined the Fair Market Value of the Common Stock in good faith and using the reasonable application of a
reasonable valuation method, for purposes of determining the Exercise Price. Notwithstanding this, the Internal Revenue Service may assert that the Fair Market Value of the Common Stock on the Grant Date was greater than the Exercise Price. Under
Code Section 409A, if the Exercise Price is less than the Fair Market Value of the Common Stock as of the Grant Date, this Option may be treated as a form of deferred compensation and the Participant may be subject to an additional twenty
percent (20%) tax, plus interest and possible penalties. The Participant acknowledges that the Company has advised the Participant to consult with a tax adviser regarding the potential impact of Code Section 409A and that the Company, in
the exercise of its sole discretion and without the consent of the Participant, may amend or modify this Agreement in any manner and delay the payment of any amounts payable pursuant to this Agreement to the minimum extent necessary to meet the
requirements of Code Section 409A, as amplified by any Internal Revenue Service or U.S. Treasury Department regulations or guidance as the Company deems appropriate or advisable. 

7. Nontransferability of Option. This Option may not be sold, assigned, transferred, pledged or otherwise encumbered by the Participant, either
voluntarily or by operation of law, except by will or the laws of descent and distribution, and, during the lifetime of the Participant, this Option shall be exercisable only by the Participant. 

8. Provisions of the Plan. This Option is subject to the provisions of the Plan, a copy of which is furnished to the Participant with this Option. 

9 Entire Agreement; Governing Law. The Plan and the accompanying Notice are incorporated herein by reference. This Agreement, the Notice and the Plan
constitute the entire agreement between the Company and the Participant with respect to the subject matter hereof and supersede in their entirety all prior undertakings and agreements of the Company and the Participant with respect to the subject
matter hereof. This Agreement shall be governed by and construed in accordance with the General Corporation Law of the State of Delaware, as to matters within the scope thereof, and the internal laws of the State of Florida. 

  
 4 

 10. Amendment. Except as set forth in Section 6(c), this Agreement may not be modified or amended in
any manner adverse to the Participant’s interest except by means of a writing signed by the Company and Participant. 
 11. No Guarantee of
Continued Service. THE PARTICIPANT ACKNOWLEDGES AND AGREES THAT THE VESTING OF OPTIONS PURSUANT TO THE VESTING SCHEDULE SET FORTH HEREIN AND IN THE NOTICE ARE EARNED ONLY BY CONTINUING SERVICE AT THE WILL OF THE COMPANY (NOT THROUGH THE ACT OF
BEING HIRED, BEING GRANTED THIS OPTION OR ACQUIRING SHARES HEREUNDER). THE PARTICIPANT FURTHER ACKNOWLEDGES AND AGREES THAT THIS AGREEMENT, THE TRANSACTIONS CONTEMPLATED HEREUNDER AND THE VESTING SCHEDULE SET FORTH HEREIN DO NOT CONSTITUTE AN
EXPRESS OR IMPLIED PROMISE OF CONTINUED SERVICE FOR THE VESTING PERIOD, FOR ANY PERIOD, OR AT ALL, AND SHALL NOT INTERFERE IN ANY WAY WITH PARTICIPANT’S RIGHT OR THE COMPANY’S RIGHT TO TERMINATE PARTICIPANT’S SERVICE WITH OR WITHOUT
CAUSE. 

*            *           
 * 

  
 5 

 Exhibit A 

APPLIED GENETIC TECHNOLOGIES CORPORATION 

NOTICE OF INCENTIVE STOCK OPTION EXERCISE 

2011 STOCK INCENTIVE PLAN 

The undersigned (the “Participant”) has previously been awarded an incentive stock option (the “Option”) to
purchase shares (the “Shares”) of the common stock of Applied Genetic Technologies Corporation, a Delaware corporation (the “Company”), pursuant to the Company’s 2011 Stock Incentive Plan (the
“Plan”), and hereby notifies the Company of the Participant’s desire to exercise the Option on the terms set forth herein: 
  

													
	PARTICIPANT INFORMATION:	  		  	OPTION INFORMATION:	  	
							
	Name:	 	  
	  		  		  	Grant Date:	  	  
	  	
							
	Address:	 	  
	  		  		  	Exercise Price Per Share:	  	$            	  	
							
		 	  
	  		  		  		  		  	
							
	Taxpayer	 		  		  		  	Total Shares Covered	  		  	
	ID #:	 	  
	  		  		  	by Option:	  	  
	  	

 EXERCISE INFORMATION: 
  

					
	Number of Shares Being Purchased:	 	  
	 	
			
	Aggregate Exercise Price:	 	$            	 	
		
	Form of Payment (check all that apply):	 	 ̈ Check for $             made payable to “Applied Genetic Technologies Corporation”
		 	  
  ̈ Cash in the amount of
$            
	 	

					
			
	Please register the Shares in my name as follows:	 	  
	 	
		 	(Print name as it is to appear on stock certificate)	 	
		 		 	

 REPRESENTATIONS AND WARRANTIES OF THE PARTICIPANT: 

The Participant hereby represents and warrants to the Company that, as of the date hereof: 

1. I am purchasing the Shares for my own account for investment only, and not with a view to, or for sale in connection with, any distribution of the Shares
in violation of the Securities Act of 1933 (the “Securities Act”), or any rule or regulation under the Securities Act. 
 2. I have had
such opportunity as I have deemed adequate to obtain from representatives of the Company such information as is necessary to permit me to evaluate the merits and risks of my investment in the Company. 

3. I have sufficient experience in business, financial and investment matters to be able to evaluate the risks involved in the purchase of the Shares and to
make an informed investment decision with respect to such purchase. 
 4. I can afford a complete loss of the value of the Shares and am able to bear the
economic risk of holding such Shares for an indefinite period. 
 5. I acknowledge that I am acquiring the Shares subject to all other terms of the Plan,
including the Notice of Incentive Stock Option and related Incentive Stock Option Agreement. 
 6. I acknowledge that the Company has encouraged me to
consult my own adviser to determine the tax consequences of acquiring the Shares at this time. I acknowledge that the Company has encouraged me to consult my own adviser to determine the form of ownership that is appropriate for me. 

7. I acknowledge that the Shares remain subject to the Company’s right of first refusal and the market stand-off (sometimes referred to as the
“lock-up”), all in accordance with the applicable Notice of Incentive Stock Option and related Incentive Stock Option Agreement. 
 8. I
understand that (i) the Shares have not been registered under the Securities Act and are “restricted securities” within the meaning of Rule 144 under the Securities Act, (ii) the Shares cannot be sold, transferred or otherwise
disposed of unless they are subsequently registered under the Securities Act or an exemption from registration is then available; (iii) in any event, the exemption from registration under Rule 144 will not be available for at least six months
or one year (depending on whether the Company is subject to the reporting obligations of the Securities Exchange Act of 1934, as amended) and even then will not be available unless applicable terms and conditions of Rule 144 are complied with; and
(iv) there is now no registration statement on file with the Securities and Exchange Commission with respect to any stock of the Company and the Company has no obligation or current intention to register the Shares under the Securities Act.

  

			
	  

	(Print Participant Name)
	
	  

	(Signature)
		
	Date:	 	  

 EXHIBIT B 

Notice of Nonstatutory Stock Option 

and 
 Nonstatutory Stock
Option Agreement 

 APPLIED GENETIC TECHNOLOGIES CORPORATION 

NOTICE OF NONSTATUTORY STOCK OPTION 

2011 STOCK INCENTIVE PLAN 

Applied Genetic Technologies Corporation, a Delaware corporation (the “Company”) grants to the undersigned (the
“Participant”) the following nonstatutory stock option to purchase shares (the “Shares”) of the common stock of the Company, par value $0.001 per share (the “Common Stock”) pursuant to the
Company’s 2011 Stock Incentive Plan (the “Plan”): 
  

			
	Participant:	  	*[Participant Name]
		
	Total Number of Shares:	  	*[Number of Shares]
		
	Grant Date:	  	*[Grant Date]
		
	Exercise Price per Share:	  	$*[Exercise Price]
		
	Vesting Commencement Date:	  	*[Vesting Date]
		
	Vesting Schedule:	  	*[25% of the Total Number of Shares shall vest and become exercisable on the 1 year anniversary of the Vesting Commencement Date and 1/48 of the Total Number of Shares shall vest and become exercisable on the corresponding
day of each month thereafter, or on the last day of each month, to the extent each month thereafter does not have the corresponding day, until all of the Shares have vested on the fourth anniversary of the Vesting Commencement Date, subject to
Participant continuing to be a Service Provider through each such date.] *[In addition, this option may vest and become exercisable on an accelerated basis under Section 2 of the Nonstatutory Stock Option Agreement.]
		
	Final Exercise Date:	  	*[Expiration Date]. This option may expire earlier pursuant to Section 3 of the Nonstatutory Stock Option Agreement if the Participant’s relationship with the Company is terminated, or pursuant to Section 8 of the
Plan.

 This nonstatutory stock option is granted under and governed by the terms and conditions of the Plan and the
Nonstatutory Stock Option Agreement, both of which are incorporated herein by reference. By signing below, the Participant accepts this nonstatutory stock option, acknowledges receipt of a copy of the Plan and the Nonstatutory Stock Option
Agreement, and agrees to the terms thereof. 
  

									
	[PARTICIPANT NAME]:	 		 	APPLIED GENETIC TECHNOLOGIES CORPORATION:
				
	  
	 		 	By:	 	  

	(Signature)	 		 		 	
				
		 		 	Name:	 	  

					
	Address:	 	  
	 		 	Title:	 	  

				
	  
	 		 	Date:	 	  

 THE OPTION GRANTED PURSUANT TO THIS AGREEMENT AND THE SHARES ISSUABLE UPON THE EXERCISE THEREOF HAVE NOT BEEN
REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR ANY STATE SECURITIES LAWS, AND MAY NOT BE SOLD, PLEDGED OR OTHERWISE TRANSFERRED WITHOUT AN EFFECTIVE REGISTRATION THEREOF UNDER SUCH ACT OR APPLICABLE LAWS OR AN OPINION OF COUNSEL
SATISFACTORY TO THE COMPANY AND ITS COUNSEL THAT SUCH REGISTRATION IS NOT REQUIRED. 
 APPLIED GENETIC TECHNOLOGIES CORPORATION

 NONSTATUTORY STOCK OPTION AGREEMENT 

Granted Under 2011 Stock Incentive Plan 

1. Grant of Option. 
 This Nonstatutory
Stock Option Agreement (the “Agreement”) evidences the grant by Applied Genetic Technologies Corporation, a Delaware corporation (the “Company”), on the Grant Date to the Participant, a[n]
*[employee/officer/director/consultant/advisor] of the Company, of an option (this “Option”) to purchase, in whole or in part, on the terms provided herein and in the Plan, the Total Number of Shares of Common Stock at
the Exercise Price per Share, all as defined and set forth in the accompanying Notice of Nonstatutory Stock Option (the “Notice”). Capitalized terms that are not otherwise defined herein or in the Notice shall have the meanings
given to such terms in the Plan. 
 It is intended that this Option shall not be an incentive stock option as defined in Section 422 of
the Internal Revenue Code of 1986, as amended, and any regulations promulgated thereunder (the “Code”). Except as otherwise indicated by the context, the term “Participant,” as used in this Agreement, shall include any
person who acquires the right to exercise this Option validly under its terms. 
 2. Vesting Schedule. 

This Option shall vest and become exercisable at the time or times set forth in the accompanying Notice. [In addition, the Option may
vest and become exercisable on an accelerated basis as follows: 
 *[Insert any applicable acceleration provisions.] 

*[If, prior to the Final Exercise Date, the Participant’s status as a Service Provider is terminated by the Company without Cause
(as defined in Section 3(e) below), then, immediately upon the effective date of such termination, this Option shall become exercisable as to [partial acceleration: that portion of the Total Number of Shares that otherwise would have
vested during the *[            ] month period following the effective date of such termination, it being understood that in no event shall the Participant be entitled to
exercise the Option to purchase greater than the Total Number of Shares as a result of this provision.) OR [full acceleration: 100% of the Total Number of Shares, it being understood that in no event shall the Participant be entitled to
exercise the Option to purchase greater than the Total Number of Shares as a result of this provision.] 
 [Single Trigger]
*[Immediately prior to the effective date of a Change in Control, this Option shall vest and become exercisable as to [partial acceleration: that portion of the Total Number of Shares that otherwise would have vested during the
*[            ] month period following the effective date of such Change in Control, it being understood that in no event shall the Participant be entitled to exercise the
Option to purchase greater than the Total Number of Shares as a result of this provision.] OR [full acceleration: 100% of the Total Number of Shares, it being understood that in no event shall the Participant be entitled to exercise the
Option to purchase greater than the Total Number of Shares as a result of this provision.] 

 [Double Trigger] *[If (a) upon the consummation of a Change in Control this
Option is assumed, or a substantially equivalent award is substituted, by the acquiring or succeeding corporation (in accordance with Section 8(b)(2)(i) of the Plan) and (b) within *[12] months following such Change in Control the
Participant’s status as a Service Provider is terminated by the acquiring or succeeding corporation without Cause (as defined in Section 3(e) below), then, immediately upon the effective date of such termination, this Option shall vest and
become exercisable as to [partial acceleration: that portion of the Total Number of Shares that otherwise would have vested during the *[            ] month period
following the effective date of such termination, it being understood that in no event shall the Participant be entitled to exercise the Option to purchase greater than the Total Number of Shares as a result of this provision.] OR [full
acceleration: 100% of the Total Number of Shares, it being understood that in no event shall the Participant be entitled to exercise the Option to purchase greater than the Total Number of Shares as a result of this provision.] 

3. Exercise of Option. 
 (a) Form of
Exercise. Each election to exercise this Option shall be in writing in substantially the form of the Notice of Stock Option Exercise attached to this Agreement as Exhibit A, signed by the Participant, and received by the Company at
its principal office, accompanied by this Agreement, and payment in full in the manner provided in the Plan. The Participant may purchase less than the number of Shares subject to this Option; provided that, no partial exercise of this
Option may be for any fractional share. 
 (b) Continuous Relationship with the Company Required. Except as otherwise provided in
this Section 3, this Option may not be exercised unless the Participant, at the time of the exercise of this Option, is, and has been at all times since the Grant Date, a Service Provider to or of the Company or any subsidiary of the Company as
defined in Section 424 (f) of the Code (an “Eligible Participant”). 
 (c) Termination of Relationship with
the Company. If the Participant ceases to be an Eligible Participant for any reason, then, except as provided in paragraphs (d) and (e) below, the right to exercise this Option shall terminate *[three months] after such
cessation (but in no event after the Final Exercise Date); provided that, this Option shall be exercisable only to the extent that the Participant was entitled to exercise this Option on the date of such cessation. Notwithstanding the
foregoing, if the Participant, prior to the Final Exercise Date, violates the non-competition or confidentiality provisions of any employment agreement, confidentiality and nondisclosure agreement, or other agreement between the Participant and the
Company, the right to exercise this Option shall terminate immediately upon such violation. 
 (d) Exercise Period Upon Death or
Disability. If the Participant dies or becomes disabled (within the meaning of Section 22(e)(3) of the Code) prior to the Final Exercise Date while the Participant is an Eligible Participant and the Company has not terminated such
relationship for “Cause” (as defined below), this Option shall be exercisable, within the period of one year following the date of death or disability of the Participant, by the Participant (or in the case of death by an authorized
transferee); provided that, this Option shall be exercisable only to the extent that this Option was exercisable by the Participant on the date of the Participant’s death or disability, and further provided that this Option shall
not be exercisable after the Final Exercise Date. 
 (e) Termination for Cause. If, prior to the Final Exercise Date, the
Participant’s status as a Service Provider is terminated by the Company for Cause (as defined below), the right to exercise this Option shall terminate immediately upon the effective date of such termination. If the Participant is party

  
 2 

 
to an agreement with the Company that contains an applicable definition of “cause”, “Cause” shall have the meaning ascribed to such term in such agreement. Otherwise,
“Cause” shall mean willful misconduct by the Participant or willful failure by the Participant to perform the Participant’s responsibilities to the Company (including, without limitation, breach by the Participant of any
provision of any employment, consulting, advisory, nondisclosure, non-competition or other similar agreement between the Participant and the Company), as determined by the Company, which determination shall be conclusive. The Participant shall be
considered to have been discharged for “Cause” if the Company determines, within 30 days after the Participant’s resignation, that discharge for cause was warranted. 

4. Restrictions on Transfer; Rights of First Refusal and Stockholder Agreements. 

(a) Bylaws. The Participant acknowledges and agrees that the Shares are subject to the provisions of the Company’s Bylaws, as
amended from time to time (the “Bylaws”), including without limitation, all restrictions on transfer and rights of first refusal described in the Bylaws. The Participant may inspect the Bylaws at the Company’s principal office. 

(b) Legend. Any certificate representing Shares shall bear a legend substantially in the following form (in addition to, or in
combination with, any legend required by applicable federal and state securities laws and agreements relating to the transfer and/or voting of the Company securities): 

“The securities represented by this certificate, and the transfer thereof, are subject to the restriction on transfer provisions of the
Bylaws of the Company, a copy of which is on file in, and may be examined at, the principal office of the Company.” 
 (c)
Stockholder Agreements. The Participant acknowledges and agrees that [the Company may condition the issuance of the Shares upon the Participant joining and becoming a party to such stockholder agreements, which may impose certain contractual
rights and obligations on the Shares, as may be entered into from time to time by and among the Company and certain holders of the Company’s capital stock. 

5. Agreement in Connection with Public Offering. 

The Participant agrees, in connection with the initial underwritten public offering of the Company’s securities pursuant to a
registration statement under the Securities Act of 1933, as amended (the “Securities Act”): (i) not to sell, make short sale of, loan, grant any options for the purchase of, or otherwise dispose of any shares of Common Stock
held by the Participant (other than those shares included in the offering) without the prior written consent of the Company or the underwriters managing such initial underwritten public offering of the Company’s securities for a period of 180
days from the effective date of such registration statement, which period may be extended upon the request of the underwriters for an additional period of up to fifteen (15) days if the Company issues or proposes to issue an earnings or other
public release within fifteen (15) days of the expiration of the 180-day lockup period, and (ii) to execute any agreement reflecting clause (i) above as may be requested by the Company or the managing underwriters at the time of such
offering. 
 The Participant agrees to execute and deliver such other agreements as may be reasonably requested by the Company or the
underwriters of such offering which are consistent with the foregoing or which are necessary to give further effect thereto. In addition, if requested, by the Company or the underwriters of such offering, the Participant shall provide, within 10
days of such request, such information as may be required by the Company or such underwriters in connection with the completion of any public offering of the Company’s securities pursuant to a registration statement filed under the Securities
Act. The obligations described in this Section 5 shall not apply to a registration relating solely 

  
 3 

 
to employee benefits plans on Form S-1 or Form S-8 or similar forms that may be promulgated in the future, or a registration relating solely to a Commission Rule 145 transaction on Form S-4 or
similar forms that may be promulgated in the future. The Company may impose stop-transfer instructions with respect to the shares of Common Stock (or other securities) subject to the foregoing restriction until the end of the applicable period.
Participant agrees that any transferee of this Option or Shares pursuant to this Agreement shall be bound by this Section 5. 
 6. Tax Matters.

 (a) Withholding. No Shares shall be issued pursuant to the exercise of this Option unless and until the Participant pays to the
Company, or makes provision satisfactory to the Company for payment of, any federal, state or local withholding or other taxes required by law to be withheld in respect of this Option. 

(b) Code Section 409A. The Exercise Price is intended to be not less than the Fair Market Value of the Common Stock on the Grant
Date. The Company has determined the Fair Market Value of the Common Stock in good faith and using the reasonable application of a reasonable valuation method, for purposes of determining the Exercise Price. Notwithstanding this, the Internal
Revenue Service may assert that the Fair Market Value of the Common Stock on the Grant Date was greater than the Exercise Price. Under Code Section 409A, if the Exercise Price is less than the Fair Market Value of the Common Stock as of the
Grant Date, this Option may be treated as a form of deferred compensation and the Participant may be subject to an additional twenty percent (20%) tax, plus interest and possible penalties. The Participant acknowledges that the Company has
advised the Participant to consult with a tax adviser regarding the potential impact of Code Section 409A and that the Company, in the exercise of its sole discretion and without the consent of the Participant, may amend or modify this
Agreement in any manner and delay the payment of any amounts payable pursuant to this Agreement to the minimum extent necessary to meet the requirements of Code Section 409A, as amplified by any Internal Revenue Service or U.S. Treasury
Department regulations or guidance as the Company deems appropriate or advisable. 
 7. Nontransferability of Option. This Option may not be sold,
assigned, transferred, pledged or otherwise encumbered by the Participant, either voluntarily or by operation of law, except by will or the laws of descent and distribution, and, during the lifetime of the Participant, this Option shall be
exercisable only by the Participant. 
 8. Provisions of the Plan. This Option is subject to the provisions of the Plan, a copy of which is furnished
to the Participant with this Option. 
 9 Entire Agreement; Governing Law. The Plan and the Notice are incorporated herein by reference. This
Agreement, the Notice and the Plan constitute the entire agreement between the Company and the Participant with respect to the subject matter hereof and supersede in their entirety all prior undertakings and agreements of the Company and the
Participant with respect to the subject matter hereof. This Agreement shall be governed by and construed in accordance with the General Corporation Law of the State of Delaware, as to matters within the scope thereof, and the internal laws of the
State of Florida (without reference to conflict of law provisions), as to all other matters. 
 10. Amendment. Except as set forth in
Section 6(b), this Agreement may not be modified or amended in any manner adverse to the Participant’s interest except by means of a writing signed by the Company and Participant. 

11. No Guarantee of Continued Service. THE PARTICIPANT ACKNOWLEDGES AND AGREES THAT THE VESTING OF OPTIONS PURSUANT TO THE VESTING SCHEDULE SET FORTH
HEREIN AND IN THE NOTICE ARE EARNED ONLY BY CONTINUING SERVICE AT THE WILL OF THE COMPANY (NOT THROUGH THE ACT OF BEING HIRED, BEING GRANTED THIS 

  
 4 

 
OPTION OR ACQUIRING SHARES HEREUNDER). THE PARTICIPANT FURTHER ACKNOWLEDGES AND AGREES THAT THIS AGREEMENT, THE TRANSACTIONS CONTEMPLATED HEREUNDER AND THE VESTING SCHEDULE SET FORTH HEREIN DO
NOT CONSTITUTE AN EXPRESS OR IMPLIED PROMISE OF CONTINUED SERVICE FOR THE VESTING PERIOD, FOR ANY PERIOD, OR AT ALL, AND SHALL NOT INTERFERE IN ANY WAY WITH PARTICIPANT’S RIGHT OR THE COMPANY’S RIGHT TO TERMINATE PARTICIPANT’S SERVICE
WITH OR WITHOUT CAUSE. 

*  *  *  *  *  *  *  *  *  *  * 

  
 5 

 Exhibit A 

APPLIED GENETIC TECHNOLOGIES CORPORATION 

NOTICE OF NONSTATUTORY STOCK OPTION EXERCISE 

2011 STOCK INCENTIVE PLAN 

The undersigned (the “Participant”) has previously been awarded a nonstatutory stock option (the “Option”)
to purchase shares (the “Shares”) of the common stock of Applied Genetic Technologies Corporation, a Delaware corporation (the “Company”), pursuant to the Company’s 2011 Stock Incentive Plan (the
“Plan”), and hereby notifies the Company of the Participant’s desire to exercise the Option on the terms set forth herein: 
  

													
	PARTICIPANT INFORMATION:	  		  		  	OPTION INFORMATION:	 	
							
	Name:	 	  
	  		  		  	Grant Date:	 	  
	 	
							
	Address:	 	  
	  		  		  	 Exercise Price Per
 Share:
	 	$             	 	
							
		 	  
	  		  		  		 		 	
							
	Taxpayer	 		  		  		  	Total Shares Covered	 		 	
	ID#:	 	  
	  		  		  	by Option:	 	  
	 	

  

					
	EXERCISE INFORMATION:	 	
			
	Number of Shares Being Purchased:	 	  
	 	
			
	Aggregate Exercise Price:	 	$             	 	
		
	Form of Payment (check all that apply):	 	  ̈ Check for
$             made payable to “Applied Genetic Technologies Corporation”
  

 ̈ Cash in the amount of
$            

					
			
	Please register the Shares in my name as follows:	 	  
	 	
		 	(Print name as it is to appear on stock certificate)

 REPRESENTATIONS AND WARRANTIES OF THE PARTICIPANT: 

The Participant hereby represents and warrants to the Company that, as of the date hereof: 

1. I am purchasing the Shares for my own account for investment only, and not with a view to, or for sale in connection with, any distribution of the Shares
in violation of the Securities Act of 1933 (the “Securities Act”), or any rule or regulation under the Securities Act. 
 2. I have had
such opportunity as I have deemed adequate to obtain from representatives of the Company such information as is necessary to permit me to evaluate the merits and risks of my investment in the Company. 

3. I have sufficient experience in business, financial and investment matters to be able to evaluate the risks involved in the purchase of the Shares and to
make an informed investment decision with respect to such purchase. 
 4. I can afford a complete loss of the value of the Shares and am able to bear the
economic risk of holding such Shares for an indefinite period. 
 5. I acknowledge that I am acquiring the Shares subject to all other terms of the Plan,
including the Notice of Nonstatutory Stock Option and related Nonstatutory Stock Option Agreement. 
 6. I acknowledge that the Company has encouraged me to
consult my own adviser to determine the tax consequences of acquiring the Shares at this time. I acknowledge that the Company has encouraged me to consult my own adviser to determine the form of ownership that is appropriate for me. 

7. I acknowledge that the Shares remain subject to the Company’s right of first refusal and the market stand-off (sometimes referred to as the
“lock-up”), all in accordance with the applicable Notice of Nonstatutory Stock Option and related Nonstatutory Stock Option Agreement. 
 8. I
understand that (i) the Shares have not been registered under the Securities Act and are “restricted securities” within the meaning of Rule 144 under the Securities Act, (ii) the Shares cannot be sold, transferred or otherwise
disposed of unless they are subsequently registered under the Securities Act or an exemption from registration is then available; (iii) in any event, the exemption from registration under Rule 144 will not be available for at least six months
or one year (depending on whether the Company is subject to the reporting obligations of the Securities Exchange Act of 1934, as amended) and even then will not be available unless applicable terms and conditions of Rule 144 are complied with; and
(iv) there is now no registration statement on file with the Securities and Exchange Commission with respect to any stock of the Company and the Company has no obligation or current intention to register the Shares under the Securities Act.

  

			
	  

	(Print Participant Name)
	
	  

	(Signature)
		
		 	
	Date:	 	  

 EXHIBIT C 

Summary of Restricted Stock Purchase and Restricted Stock 

Purchase Agreement 

 AMENDMENT NO. 1 

TO THE 
 APPLIED GENETIC
TECHNOLOGIES CORPORATION 
 2011 STOCK INCENTIVE PLAN 

Effective November 14, 2012, in accordance with resolutions adopted by (i) the Board of Directors of Applied Genetic Technologies
Corporation, a Delaware corporation (the “Company”), on November 14, 2012, and (ii) the stockholders of the Company on November 14, 2012, the Applied Genetic Technologies Corporation 2011 Stock Incentive Plan (the
“Plan”), is hereby amended as follows: 
 Section 4(a) of the Plan is amended by deleting the first sentence in its
entirety and substituting the following in lieu thereof: 
 “(a) Subject to adjustment under Section 8, Awards may be made under
the Plan for up to 11,644,489 shares of the common stock of the Company, $0.001 par value per share (the “Common Stock”).” 

 AMENDMENT NO. 2 

TO THE 
 APPLIED GENETIC
TECHNOLOGIES CORPORATION 
 2011 STOCK INCENTIVE PLAN 

Effective April 9, 2013, in accordance with resolutions adopted by (i) the Board of Directors of Applied Genetic Technologies
Corporation, a Delaware corporation (the “Company”), on April 9, 2013, and (ii) the stockholders of the Company on April 9, 2013, the Applied Genetic Technologies Corporation 2011 Stock Incentive Plan (the
“Plan”), is hereby amended as follows: 
 Section 4(a) of the Plan is amended by deleting the first sentence in its
entirety and substituting the following in lieu thereof: 
 “(a) Subject to adjustment under Section 8, Awards may be made under
the Plan for up to 25,283,337 shares of the common stock of the Company, $0.001 par value per share (the “Common Stock”).” 

 AMENDMENT NO. 3 

TO THE 
 APPLIED GENETIC
TECHNOLOGIES CORPORATION 
 2011 STOCK INCENTIVE PLAN 

Effective November 5, 2013, in accordance with resolutions adopted by (i) the Board of Directors of Applied Genetic Technologies Corporation,
a Delaware corporation (the “Company”), on October 28, 2013, and (ii) the stockholders of the Company on October 28, 2013, the Applied Genetic Technologies Corporation 2011 Stock Incentive Plan (the “Plan”), is
hereby amended as follows: 
 Section 4(a) of the Plan is amended by deleting the first sentence in its entirety and substituting the
following in lieu thereof: 
 “(a) Subject to adjustment under Section 8, Awards may be made under the Plan for up to 31,818,548 shares
of the common stock of the Company, $0.001 par value per share (the “Common Stock”).”

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