<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0306</schemaVersion>

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    <periodOfReport>2022-11-30</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0001273636</issuerCik>
        <issuerName>APPLIED GENETIC TECHNOLOGIES CORP</issuerName>
        <issuerTradingSymbol>AGTC</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001511991</rptOwnerCik>
            <rptOwnerName>Potter Stephen W</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O APPLIED GENETIC TECHNOLOGIES CORP.</rptOwnerStreet1>
            <rptOwnerStreet2>14193 NW 119TH TERRACE, SUITE #10</rptOwnerStreet2>
            <rptOwnerCity>ALACHUA</rptOwnerCity>
            <rptOwnerState>FL</rptOwnerState>
            <rptOwnerZipCode>32615</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Chief Business Officer</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

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            <expirationDate>
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            <underlyingSecurity>
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                <underlyingSecurityShares>
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        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
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            <expirationDate>
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        <derivativeTransaction>
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            <conversionOrExercisePrice>
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            <expirationDate>
                <value>2029-08-15</value>
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            <underlyingSecurity>
                <underlyingSecurityTitle>
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        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
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        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
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            <transactionDate>
                <value>2022-11-30</value>
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                <transactionPricePerShare>
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            <expirationDate>
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                <underlyingSecurityTitle>
                    <value>Common Stock</value>
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                    <value>60000</value>
                </underlyingSecurityShares>
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                <directOrIndirectOwnership>
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        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>0.40</value>
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            <transactionDate>
                <value>2022-11-30</value>
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                <transactionShares>
                    <value>133100</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F3"/>
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                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
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            <exerciseDate>
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            <expirationDate>
                <value>2032-08-21</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>133100</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
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        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">At the effective time of the Merger, each issued and outstanding Share was cancelled in exchange for (1) $0.34 per share of common stock of the Issuer (&quot;Common Stock&quot;), without interest and less any applicable withholding taxes  (the &quot;Cash Consideration&quot;); and (2) one contingent value right (&quot;CVR&quot;) per share of Common Stock representing the right to receive potential milestone payments, currently estimated to be up to approximately $0.73 per CVR in the aggregate (without interest and less any applicable withholding taxes) (the Cash Consideration plus one CVR, collectively, as such amount may be increased in accordance with the terms of the Merger Agreement, the &quot;Offer Price&quot;). Pursuant to the terms of the Merger Agreement, the Shares were tendered and disposed of at the Acceptance Time (as defined in the Merger Agreement) in exchange for the right to receive the Offer Price.</footnote>
        <footnote id="F2">At the effective time of the Merger, each outstanding restricted stock unit of the Issuer, whether vested or unvested, was cancelled and converted into the right to receive the Offer Price.</footnote>
        <footnote id="F3">At the effective time of the Merger, each outstanding option of the Issuer with an exercise price equal to or greater than $0.34 was cancelled without any consideration in respect of such cancelled option.</footnote>
    </footnotes>

    <remarks>Pursuant to the Agreement and Plan of Merger (the &quot;Merger Agreement&quot;), dated as of October 23, 2022, by and among Applied Genetic Technologies Corporation (the &quot;Issuer&quot;), Alliance Holdco Limited (&quot;Parent&quot;) and Alliance Acquisition Sub, Inc., a wholly owned subsidiary of Parent (&quot;Purchaser&quot;), on November 30, 2022, Purchaser completed a tender offer for shares of common stock of the Issuer (each, a &quot;Share&quot;) and thereafter merged with and into the Issuer, with the Issuer continuing as the surviving corporation and a wholly owned subsidiary of Parent (the &quot;Merger&quot;).</remarks>

    <ownerSignature>
        <signatureName>/s/ Stacie Aarestad, Attorney-in-fact</signatureName>
        <signatureDate>2022-12-01</signatureDate>
    </ownerSignature>
</ownershipDocument>
