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SCHEDULE 13D/A 0001091823 XXXXXXXX LIVE 20 Common Stock 09/17/2025 false 0001356090 46122T102 PRECIGEN, INC. 20374 Seneca Meadows Parkway Germantown MD 20876 Third Security, LLC 5406337900 1881 Grove Avenue Attention: April D. Jones Radford VA 24141 John Owen Gwathmey, Esq. 8046971239 Troutman Pepper Locke Building 1001 Haxall Point Richmond VA 23219 David I. Meyers, Esq. 8046971239 Troutman Pepper Locke Building 1001 Haxall Point Richmond VA 23219 Troutman Pepper Locke, LLP 8046971239 Troutman Pepper Locke Building 1001 Haxall Point Richmond VA 23219 0001091823 N RANDAL J. KIRK b PF N X1 146295359.00 0.00 146295359.00 0.00 146295359.00 N 39.4 IN The indicated amount of Common Stock beneficially owned by Mr. Kirk assumes the full conversion of (i) 25,000 shares of Preferred Stock, as that term is defined herein (ii) 906,512 Options to Purchase Common Stock, which are fully vested and exercisable at the discretion of Mr. Kirk, and (iii) 16,666,667 Warrants to Purchase Common Stock, which are fully vested and exercisable at the discretion of Mr. Kirk. Y R.J. KIRK DECLARATION OF TRUST b PF N X1 98831434.00 0.00 98831434.00 0.00 98831434.00 N 26.6 OO OO - trust; The indicated amount of Common Stock beneficially owned by RJ DOT assumes the full conversion of (i) 25,000 shares of Preferred Stock, as that term is defined herein and (ii) 16,666,667 Warrants to Purchase Common Stock, which are fully vested and exercisable at the discretion of Mr. Kirk. Y SUNSET 2020 LLC b WC N DE 16406828.00 0.00 16406828.00 0.00 16406828.00 N 4.4 OO OO - limited liability company Y THIRD SECURITY, LLC b WC N VA 27454284.00 0.00 27454284.00 0.00 27454284.00 N 7.4 OO OO - limited liability company Common Stock PRECIGEN, INC. 20374 Seneca Meadows Parkway Germantown MD 20876 This Amendment No. 20 (the "Amendment") amends and supplements the Statement on Schedule 13D, dated March 27, 2014 and filed on April 7, 2014, as amended by Amendment No. 1 dated December 31, 2014 and filed on January 5, 2015, by Amendment No. 2 dated May 31, 2016 and filed June 2, 2016, by Amendment No. 3 dated July 24, 2017 and filed July 26, 2017, by Amendment No. 4 dated October 16, 2017 and filed October 23, 2017, by Amendment No. 5 dated December 29, 2017 and filed on January 2, 2018, by Amendment No. 6 dated January 19, 2018 and filed January 22, 2018, by Amendment No. 7 dated July 3, 2018 and filed July 6, 2018, by Amendment No. 8 dated May 13, 2019 and filed May 15, 2019, by Amendment No. 9 dated May 24, 2019 and filed on May 24, 2019, by Amendment No. 10 dated June 6, 2019 and filed on June 10, 2019, by Amendment No. 11 dated January 1, 2020 and filed on January 6, 2020, by Amendment No. 12 dated January 31, 2020 and filed on February 4, 2020, by Amendment No. 13 dated August 11, 2020 and filed on August 13, 2020, by Amendment No. 14 dated December 17, 2020 and filed on December 21, 2020, by Amendment No. 15 dated October 6, 2022 and filed on October 7, 2022, by Amendment No. 16 dated January 27, 2023 and filed on January 31, 2023, by Amendment No. 17 dated May 2, 2024 and filed on May 3, 2024, by Amendment No. 18 dated August 9, 2024 and filed on August 13, 2024, and by Amendment No. 19 dated and filed on December 30, 2024 (the "Original Schedule 13D"), relating to the Common Stock, no par value per share (the "Common Stock"), of Precigen, Inc., formerly known as Intrexon Corporation, a Virginia corporation (the "Company"). Mr. Randal J. Kirk ("Mr. Kirk"), the R.J. Kirk Declaration of Trust, a revocable trust established by Mr. Kirk ("RJ DOT"), Third Security, LLC, a Virginia limited liability company that is controlled by Mr. Kirk ("Third Security"), and Sunset 2020 LLC, a Delaware limited liability company that is controlled by Mr. Kirk ("Sunset 2020" and, together with Mr. Kirk, the RJ DOT, and Third Security, the "Reporting Persons") are filing this Amendment to disclose (i) the receipt on September 17, 2025 of 17,385,257 shares of Common Stock by RJ DOT following the election to convert 25,000 shares of 8.00% Series A Convertible Perpetual Preferred Stock ("Preferred Stock"), which Preferred Stock was issued to RJ DOT pursuant to a Securities Purchase Agreement entered into by and between the Company and certain existing and new investors in a private placement transaction that closed on December 30, 2024 (the "Offering") and (ii) the sale of an aggregate of 5,000,252 shares of Common Stock by Kapital Joe, LLC, a Virginia limited liability company under the common control of Mr. Kirk ("Kapital Joe"), in open market transactions between September 18, 2025 and September 19, 2025. See Original Schedule 13D See Original Schedule 13D See Original Schedule 13D See Original Schedule 13D See Original Schedule 13D See Original Schedule 13D Item 4 of the Original Schedule 13D is hereby amended and supplemented as follows: The information set forth in Items 3 and 6 is incorporated herein by reference. In the Offering, the Company issued 79,000 shares of Preferred Stock of the Company to certain new and existing investors, including RJ DOT, on the terms and conditions set forth in that certain Securities Purchase Agreement, filed as Exhibit 10.1 to the Company's Current Report on Form 8-K dated December 27, 2024 and filed on December 30, 2024. The Preferred Stock was convertible into shares of common stock of the Company (i) at the option of the holder at any time on or after the later of the six-month anniversary of the issue date and the date on which the issuer has, among other things, obtained shareholder approval, which requisite shareholder approval was obtained on June 26, 2025 and (ii) at an initial conversion price of approximately $1.125 per share, which conversion price was subject to upward adjustment based on the valuation of the common stock from time to time. On September 17, 2025, RJ DOT received 17,385,257 shares of Common Stock following its election to convert 25,000 shares of Preferred Stock. RJ DOT acquired these shares for investment purposes. Kapital Joe sold a total of 5,000,252 shares of Common Stock in open market transactions between September 18, 2025 and September 19, 2025, for aggregate net proceeds of approximately $18,648,905.62. The responses to Items 11 and 13 of the cover pages, as well as the applicable comments thereto, to this Amendment No. 20 are incorporated herein. The percentage ownership is calculated based on 297,972,920 shares of Common Stock issued and outstanding as of August 8, 2025, as disclosed in the Company's Form S-3 Registration Statement dated and filed on August 19, 2025, increased by (i) 54,937,411 shares of Common Stock issued by the Company pursuant to the conversion of the Preferred Stock, as disclosed by the Company on its Form 8-K filed on September 17, 2025, of which Mr. Kirk received 17,385,257 shares of Common Stock issued to RJ DOT (ii) 16,666,667 shares of Common Stock issuable to Mr. Kirk upon exercise of Warrants to Purchase Common Stock, which are exercisable within sixty (60) days; (iii) 906,512 shares of Common Stock issuable to Mr. Kirk upon exercise of Options to Purchase Common Stock, which are exercisable within sixty (60) days, and (iv) 1,154,000 shares of Common Stock issued on September 12, 2025 to certain executive officers of the Company pursuant to vested Performance Stock Units, as reported by the Company in Forms 4 filed on September 16, 2025. The responses to Items 7, 8, 9 and 10 of the cover pages to this Amendment No. 20 are incorporated herein. Except as disclosed in the Original Schedule 13D and this Amendment No. 20, the Reporting Persons have not engaged in any transactions within the previous sixty (60) days. Not applicable Not applicable Item 6 of the Original Schedule 13D is hereby amended and supplemented to include the responses in Item 4 above. Exhibit 1 Joint Filing Agreement, dated as of September 19, 2025, by and among Randal J. Kirk, R.J. Kirk Declaration of Trust, Sunset 2020 LLC, and Third Security, LLC. RANDAL J. KIRK /s/ Randal J. Kirk Randal J. Kirk 09/19/2025 R.J. KIRK DECLARATION OF TRUST /s/ Randal J. Kirk Randal J. Kirk Trustee 09/19/2025 SUNSET 2020 LLC /s/ Randal J. Kirk Randal J. Kirk Manager 09/19/2025 THIRD SECURITY, LLC /s/ Randal J. Kirk Randal J. Kirk Managing Member 09/19/2025