Document:

EX-10.3

 Exhibit 10.3 

SECOND AMENDMENT TO OFFICE LEASE AGREEMENT 

THIS SECOND AMENDMENT TO OFFICE LEASE AGREEMENT (“Amendment”) dated this 9th
day of November, 2017, is by and between ALACHUA FOUNDATION PARK HOLDING COMPANY, LLC, a Florida Limited Liability Company (“Landlord”) and APPLIED GENETIC TECHNOLOGIES CORPORATION, a Delaware corporation (“Tenant”). 

W I T N E S S E T H: 
 A.
Landlord and Tenant are parties to: (i) that certain Standard Form of Lease for Foundation Park dated on or about April 10, 2015 (the “Original Lease”) as amended by (ii) that certain Amendment to Office Lease Agreement
dated effective October 1, 2016 (the “First Amendment”). The Original Lease as amended by the First Amendment is referred to collectively as the “Lease”. Pursuant to the Lease, Tenant leases Suites 101 and 102, containing
21,590 square feet net rentable area (the “Premises”), in the building known as “Building #1” located at 14100 N. W 113th Terrace, Alachua, Florida in the buildings known as
Foundation Park (the “Project”). The initial term of the lease commenced on January 1, 2016, and expires on December 31, 2027. 

B. Landlord and Tenant wish to further modify the terms of the Lease to extend the Lease to certain adjacent space for use as storage or other
allowable use permitted by the terms of the Lease in connection with Tenant’s operations as more fully set forth herein; and 
 C.
Landlord is willing to agree to such modifications provided that this agreement is entered into, but not otherwise. 
 NOW, THEREFORE,
in consideration of the mutual promises herein contained and other good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged by the parties, Landlord and Tenant hereby agree as follows: 

1. Recitals. All recitals set forth above are true and correct and are incorporated hereby reference. 

2. Premises. The “Premises”, as such term is defined in the Lease, shall hereafter refer to Suite 101, containing 18,309
rentable square feet; Suite 102, containing 3,281 rentable square feet; and the adjacent space containing 1,994 rentable square feet as shown on Exhibit “A” attached hereto (the “Storage Space”) for a total of 23,584 rentable
square feet. Landlord agrees to (i) demise the Storage Space with metal stud walls and sheet rock installed on the exterior, (ii) install reasonable lighting and electrical receptacles in mutually agreed locations, and (iii) to
install two (2) sets of double doors in the locations shown on Exhibit “A”. The date that Landlord has completed such improvements and delivered the Storage Space to Tenant or the date Tenant begins using the Storage Space (whichever
occurs sooner) shall be referred to as the “Storage 
  

							
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 Space Delivery Date”, which date is estimated to be December 1, 2017. The Storage Space Delivery
Date shall not occur prior to December 1, 2017. Otherwise, Tenant accepts the Storage Space and the Premises “AS IS” and acknowledges that Landlord has no obligation to make any other repairs or alterations to the Premises as a
condition to this amendment. 
 3. Term. The Initial Term of the Lease shall not be modified, and shall continue to expire on
December 31, 2027. 
 4. Operating Expenses. Beginning on the Storage Space Delivery Date, as a result of Tenant’s lease of
the Storage Space, Tenant’s pro rata share shall be increased from fifty percent (50%) to fifty-four and six tenths percent (54.6%). Tenant shall be responsible for its pro rata share of Operating Expenses and Additional Rent for the Premises
in the same manner as set forth in the Lease. 
 5. Fixed Annual Rent for Premises. Exhibit “D” of the Lease, which sets
forth the Fixed Annual Rents for Suite 101 and 102, is hereby amended to include the supplemental rent schedule for the Storage Space attached hereto as Exhibit “D-1 (Supplement) and incorporated into the
Lease by reference. Fixed Annual Rents shall be as set forth in both Exhibit “D” of the Lease and Exhibit “D-1” of this Amendment. 

6. Tenant Expansion Option. Tenant acknowledges that Tenant did not elect to exercise Tenant’s Expansion Option as set forth in
paragraph 8 of the First Amendment. Such option has now expired and is no longer effective. 
 7. Performance by Landlord and Tenant.
By execution of this Amendment, each party warrants, represents, acknowledges and agrees that the other party hereto has performed each and every obligation of such party pursuant to the Lease as same has been amended from time to time and that
there are no defaults (or circumstances which with notice and passage of time would constitute defaults) by either party under the Lease. 

8. Brokers. Landlord and Tenant warrant and represent to each other that neither party has had any dealings with any real estate
broker, finder or other person with respect to this Amendment to Lease. Tenant covenants and agrees that to the extent Tenant has a leasing representative who is due a fee hereon (other than as disclosed herein), such fee shall be paid directly by
Tenant. 
 9. Covenants Binding. It is mutually agreed that ail covenants, conditions and agreements set forth in the Lease (as
hereby amended) shall remain binding upon the parties and inure to the benefit of the parties hereto and their respective successors and assigns. 

10. Continuing Force and Effect. Except as modified hereby, all other terms and conditions of the Lease shall remain unchanged and in
full force and effect and are hereby ratified and confirmed by the parties hereto. 
  

							
		  		  	

	  	

 11. Defined Terms. Except as otherwise expressly provided herein, all defined terms
shall have the meanings ascribed to them in the Lease. 
 12. Conflicts/Amendment to Control. Any inconsistencies or conflicts
between the terms and provisions of the Lease and the terms and provisions of this Amendment shall be resolved in favor of the terms and provisions of this Amendment. 

13. Writing Required. This Amendment shall not be modified except in writing and signed by both parties hereto. 

IN WITNESS WHEREOF, the parties hereto have executed this Amendment to Lease on the date indicated above. 

 

									
	Witnesses:	 		 	Landlord:
			
	

	 		 	ALACHUA FOUNDATION PARK HOLDING COMPANY, LLC,
	Print Name:	 	

	 		 	a Florida Limited Liability Company
				
	

	 		 	By:	 	 

	 		 	Print Name:

	Print Name:	 	

	 		 	Its:

			
	Witnesses:	 		 	Tenant:
			
	

	 		 	APPLIED GENETIC TECHNOLOGIES CORPORATION, a Delaware corporation
	Print Name:	 	

	 		 		 	
					
		 		 		 	By:	 	

	

	 		 	Print Name:

	Print Name:	 	

	 		 	Its:

  

							
		  		  	

	  	

 EXHIBIT “D-1 (Supplement)” 

SCHEDULE OF ADJUSTMENTS IN FIXED ANNUAL RENT*** 

Storage Space, Building I, containing Approx. 1,994 Rentable Sq. Ft. 

Rents for the Storage Space shall begin on the Storage Space Delivery Date (estimated 11/15/17) and end December 31, 2027. 

The rent rates and Fixed Annual Rent for the Storage Space during the initial term and renewal terms, if exercised, shall be: 

 

													
	 Lease Months
	  	Fixed Annual
Rent*	 	  	Fixed Annual Rent
Per Square Foot	 	  	Fixed Annual Rent
Monthly Payment*	 
	 23* -144
	  	$	35,592.96	 	  	$	17.85	 	  	$	2,966.08	 
	 145 - 204**
	  	$	39,162.12	 	  	$	19.64	 	  	$	3,263.51	 
	 205 - 264**
	  	$	43,070.40	 	  	$	21.60	 	  	$	3,589.20	 
	 265 - 324**
	  	$	47,377.44	 	  	$	23.76	 	  	$	3,948.12	 

  

	*	 Rents for Storage Space estimated to begin 11/15/17, which, is the 23rd month of the Term. If the Storage Space Deliver Date occurs on a date other than the first day of a month, then the rent for such month shall be prorated based upon the foregoing monthly rent.. Does
not include sales tax, which shall be paid by Tenant with each installment of Rent. 

	**	 Reflects Initial Base Rent for Renewal Terms if applicable renewal option exercised by Tenant based upon the
ten percent (10%) increase for illustration purposes only, but actual increase shall be based upon the methodology set forth in Section 3(G) of the Lease. 

 

							
		  		  	

	  	

 EXHIBIT “A”EX-10.28

 Exhibit 10.28 

RESTRICTED STOCK UNIT AGREEMENT 

Granted by 
 Applied Genetic
Technologies Corporation 
 Under the 2013 Equity and Incentive Plan 

Applied Genetic Technologies Corporation (the “Company”) hereby grants to the person named below (the “Recipient”)
restricted stock units (“Restricted Stock Units”), with each such unit representing the right to receive one share of the Company’s common stock, par value $0.001 per share (the “Common Stock”), pursuant to the terms set
forth below (the “Award”). The Award is and shall be subject in every respect to the provisions of the Company’s 2013 Equity and Incentive Plan, as amended from time to time (the “Plan”), which is incorporated herein by
reference and made a part hereof. The Recipient hereby accepts this Award subject to all the terms and provisions of the Plan and agrees that (a) in the event of any conflict between the terms hereof and those of the Plan, the latter shall
prevail, and (b) all decisions under and interpretations of the Plan by the Board or the Committee shall be final, binding and conclusive upon the Recipient and his or her heirs and legal representatives. Capitalized terms used herein but not
defined shall have the meaning set forth in the Plan. 
  

	1.	 Name of Recipient:  

 

	2.	 Date of Grant:  

 

	3.	 Maximum Number of Restricted Stock Units: 

 

	4.	 Vesting of Restricted Stock Units: 

 

	5.	 Payment. Upon each vesting date, the Recipient shall receive one share of Stock for each vested
Restricted Stock Unit; provided, however, that the number of shares issued shall be reduced by the number of shares sufficient to satisfy the minimum tax withholding obligations as set forth in Section 6 below. 

 

	6.	 Withholding Obligation; Sell to Cover. 

(a) The Recipient expressly acknowledges and agrees that the Recipient’s rights hereunder, including the right to be issued shares of
Common Stock upon the vesting of the Award (or any portion thereof), are subject to the Recipient’s promptly paying to the Company in cash (or by such other means as may be acceptable to the Administrator in its discretion) all taxes required
to be withheld, if any, relating to the Award (the “Withholding Obligation”). 
 (b) By accepting this Award, the Recipient hereby
acknowledges and agrees that he or she elects to sell shares of Common Stock issued in respect of the Award and to allow the Agent to remit the cash proceeds of such sale to the Company (“Sell to Cover”) to satisfy the Withholding
Obligation, to the extent that such cash proceeds are sufficient to satisfy the Withholding Obligation. 

 (c) In order to implement a Sell to Cover, the Recipient hereby irrevocably appoints Stifel,
Nicolaus & Company, Incorporated, or such other registered broker-dealer that is a member of the Financial Industry Regulatory Authority as the Company may select, as the Recipient’s agent (the “Agent”), and the Recipient
authorizes and directs the Agent to: (i) sell on the open market at the then prevailing market price(s), on the Recipient’s behalf, as soon as practicable on or after the date on which the shares of Common Stock are delivered to the
Recipient pursuant to Section 4 hereof in connection with the vesting of the Restricted Stock Units, the number (rounded up to the next whole number) of shares of Common Stock sufficient to generate proceeds to cover (A) the satisfaction
of the Withholding Obligation arising from the vesting of the Restricted Stock Units and the related issuance and delivery of shares of Common Stock to the Recipient and (B) all applicable fees and commissions due to, or required to be
collected by, the Agent with respect thereto; (ii) remit directly to the Company the proceeds from the sale of the shares of Common Stock referred to in clause (i) above necessary to satisfy the Withholding Obligation; (iii) retain
the amount required to cover all applicable fees and commissions due to, or required to be collected by, the Agent, relating directly to the sale of the shares of Common Stock referred to in clause (i) above; and (iv) maintain any
remaining funds from the sale of the shares of Common Stock referred to in clause (i) above in the Recipient’s account with the Agent. The Recipient hereby authorizes the Company and the Agent to cooperate and communicate with one another
to determine the number of shares of Common Stock that must be sold to satisfy the Recipient’s obligations hereunder and to otherwise effect the purpose and intent of this Agreement and satisfy the rights and obligations hereunder. 

(d) The Recipient acknowledges that the Agent is under no obligation to arrange for the sale of Common Stock at any particular price under a
Sell to Cover and that the Agent may affect sales under any Sell to Cover in one or more sales and that the average price for executions resulting from bunched orders may be assigned to the Recipient’s account. The Recipient further
acknowledges that he or she will be responsible for all brokerage fees and other costs of sale associated with any Sell to Cover or transaction contemplated by this Section 6 and agrees to indemnify and hold the Company harmless from any
losses, costs, damages, or expenses relating to any such sale. In addition, the Recipient acknowledges that it may not be possible to sell shares of Common Stock as provided for in this Section 6 due to various circumstances. If it is not
possible to sell shares of Common Stock in a Sell to Cover, the Company will assist the Recipient in determining additional alternatives available to the Recipient. In the event of the Agent’s inability to sell shares of Common Stock, the
Recipient will continue to be responsible for the timely payment to the Company of all federal, state, local and foreign taxes that are required by applicable laws and regulations to be paid or withheld with respect to the Restricted Stock Units or
the Award. In such event, or in the event that the Company determines that the cash proceeds from a Sell to Cover are insufficient to meet the Withholding Obligation, the Recipient authorizes the Company and its subsidiaries to withhold such amounts
from any amounts otherwise owed to the Recipient, but nothing in this sentence shall be construed as relieving the Recipient of any liability for satisfying his or her obligations under the preceding provisions of this Section. 

  
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 (e) The Recipient hereby agrees to execute and deliver to the Agent or the Company any other
agreements or documents as the Agent or the Company reasonably deem necessary or appropriate to carry out the purposes and intent of this Agreement, including without limitation, any agreement intended to ensure the Sell to Cover and the
corresponding authorization and instruction to the Agent set forth in this Section 6 to sell Common Stock to satisfy the Withholding Obligation comply with the requirements of Rule 10b5-1(c) under
the Exchange Act. The Agent is a third-party beneficiary of this Section 6. 
 (f) The Recipient’s election to Sell to Cover to
satisfy the Withholding Obligation is irrevocable. Upon acceptance of the Award, the Recipient has elected to Sell to Cover to satisfy the Withholding Obligation, and the Recipient acknowledges that he or she may not change this election at any time
in the future. 
  

	7.	 No Rights to Shares or as a Stockholder; No 83(b) Election. The Recipient shall not have any right in,
or with respect to, any of the shares of Common Stock issuable under the Award (including voting rights) unless and until the Award vests and is settled by issuance of the shares to the Recipient. The Recipient expressly acknowledges that because
the Award consists of an unfunded and unsecured promise by the Company to deliver Common Stock in the future, subject to the terms hereof, it is not possible to make a so-called “83(b) election” for
tax purposes with respect to the Award. 

  

	8.	 Nontransferability. The Restricted Stock Units are personal to the Recipient and shall not be
transferable or assignable, other than by will or the laws of descent and distribution, and any such purported transfer or assignment shall be null and void. 

  

	9.	 Termination of Employment. If the Recipient’s employment with or service for the Company is
terminated, for any reason or no reason, with or without cause, all unvested Restricted Stock Units shall immediately terminate and be of no further force or effect. 

 

	10.	 Notice. Any notice to be given to the Company hereunder shall be deemed sufficient if addressed to the
Company and delivered to the office of the Company, Applied Genetic Technologies Corporation, 14193 NW 119th Terrace, Alachua, FL 32615, attention of the chief financial officer, or such other
address as the Company may hereafter designate. 

 Any notice to be given to the Recipient hereunder shall be deemed
sufficient if addressed to and delivered in person to the Recipient at his or her address furnished to the Company or when deposited in the mail, postage prepaid, addressed to the Recipient at such address. 

  
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 IN WITNESS WHEREOF, the parties have executed this Award, or caused this Award to be
executed, as of the Date of Grant. 
  

			
	Applied Genetic Technologies Corporation
		
	By:	 	 

 The undersigned Recipient hereby acknowledges receipt of a copy of the Plan and this Award, and agrees to the terms of
this Award and the Plan. 
  

                          
                                   

[Name of Recipient] 

  
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