37 CFR 1.833 - Requirements for a “Sequence Listing XML” for nucleotide and/or amino acid sequences as part of a patent application filed on or after July 1, 2022.

For the purposes of these regulations pertaining to the deposit of biological material for purposes of patents for inventions under 35 U.S.C. 101,the. Representative examples include bacteria, fungi including yeast, algae, protozoa, eukaryotic cells, cell lines, hybridomas, plasmids, viruses, plant tissue cells, lichens and seeds. Viruses, vectors, cell organelles and other non-living material existing in and reproducible from a living cell may be deposited by deposit of the host cell capable of reproducing the non-living material.

§ 1.802 - Need or opportunity to make a deposit.

(a) Where an invention is, or relies on, a biological material, the disclosure may include reference to a deposit of such biological material.

(b) Biological material need not be deposited unless access to such material is necessary for the satisfaction of the statutory requirements for patentability under 35 U.S.C. 112. If a deposit is necessary, it shall be acceptable if made in accordance with these regulations. Biological material need not be deposited, inter alia, if it is known and readily avaliable to the public or can be made or isolated without undue experimentation. Once deposited in a depository complying with these regulations, a biological material will be considered to be readily available even though some requirement of law or regulation of the United States or of the country in which the depository institution is located permits access to the material only under conditions imposed for safety, public health or similar reasons.

(c) The reference to a biological material in a specification disclosure or the actual deposit of such material by an applicant or patent owner does not create any presumption that such material is necessary to satisfy 35 U.S.C. 112 or that deposit in accordance with these regulations is or was required.

§ 1.803 - Acceptable depository.

(a) A deposit shall be recognized for the purposes of these regulations if made in

(1) Any International Depositary Authority (IDA) as established under the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure, or

(2) Any other depository recognized to be suitable by the Office. Suitability will be determined by the Director on the basis of the administrative and technical competence, and agreement of the depository to comply with the terms and conditions applicable to deposits for patent purposes. The Director may seek the advice of impartial consultants on the suitability of a depository. The depository must:

(i) Have a continuous existence;

(ii) Exist independent of the control of the depositor;

(iii) Possess the staff and facilities sufficient to examine the viability of a deposit and store the deposit in a manner which ensures that it is kept viable and uncontaminated;

(iv) Provide for sufficient safety measures to minimize the risk of losing biological material deposited with it;

(v) Be impartial and objective;

(vi) Furnish samples of the deposited material in an expeditious and proper manner; and

(vii) Promptly notify depositors of its inability to furnish samples, and the reasons why.

(b) A depository seeking status under paragraph (a)(2) of this section must direct a communication to the Director which shall:

(1) Indicate the name and address of the depository to which the communication relates;

(2) Contain detailed information as to the capacity of the depository to comply with the requirements of paragraph (a)(2) of this section, including information on its legal status, scientific standing, staff and facilities;

(3) Indicate that the depository intends to be available, for the purposes of deposit, to any depositor under these same conditions;

(4) Where the depository intends to accept for deposit only certain kinds of biological material, specify such kinds;

(5) Indicate the amount of any fees that the depository will, upon acquiring the status of suitable depository under paragraph (a)(2) of this section, charge for storage, viability statements and furnishings of samples of the deposit.

(c) A depository having status under paragraph (a)(2) of this section limited to certain kinds of biological material may extend such status to additional kinds of biological material by directing a communication to the Director in accordance with paragraph (b) of this section. If a previous communication under paragraph (b) of this section is of record, items in common with the previous communication may be incorporated by reference.

(d) Once a depository is recognized to be suitable by the Director or has defaulted or discontinued its performance under this section, notice thereof will be published in the Office Gazette of the Patent and Trademark Office.

§ 1.804 - Time of making an original deposit.

(a) Whenever a biological material is specifically identified in an application for patent as filed, an original deposit thereof may be made at any time before filing the application for patent or, subject to § 1.809, during pendency of the application for patent.

(b) When the original deposit is made after the effective filing date of an application for patent, the applicant must promptly submit a statement from a person in a position to corroborate the fact, stating that the biological material which is deposited is a biological material specifically identified in the application as filed.

[54 FR 34880, Aug. 22, 1989, as amended at 62 FR 53202, Oct. 10, 1997]

§ 1.805 - Replacement or supplement of deposit.

(a) A depositor, after receiving notice during the pendency of an application for patent, application for reissue patent or reexamination proceeding, that the depository possessing a deposit either cannot furnish samples thereof or can furnish samples thereof but the deposit has become contaminated or has lost its capability to function as described in the specification, shall notify the Office in writing, in each application for patent or patent affected. In such a case, or where the Office otherwise learns, during the pendency of an application for patent, application for reissue patent or reexamination proceeding, that the depository possessing a deposit either cannot furnish samples thereof or can furnish samples thereof but the deposit has become contaminated or has lost its capability to function as described in the specification, the need for making a replacement or supplemental deposit will be governed by the same considerations governing the need for making an original deposit under the provisions set forth in § 1.802(b). A replacement or supplemental deposit made during the pendency of an application for patent shall not be accepted unless it meets the requirements for making an original deposit under these regulations, including the requirement set forth under § 1.804(b). A replacement or supplemental deposit made in connection with a patent, whether or not made during the pendency of an application for reissue patent or a reexamination proceeding or both, shall not be accepted unless a certificate of correction under § 1.323 is requested by the patent owner which meets the terms of paragraphs (b) and (c) of this section.

(b) A request for certificate of correction under this section shall not be granted unless the certificate identifies:

(1) The accession number for the replacement or supplemental deposit;

(2) The date of the deposit; and

(3) The name and address of the depository.

(c) A request for a certificate of correction under this section shall not be granted unless the request is made promptly after the replacement or supplemental deposit has been made and the request:

(1) Includes a statement of the reason for making the replacement or supplemental deposit;

(2) Includes a statement from a person in a position to corroborate the fact, and stating that the replacement or supplemental deposit is of a biological material which is identical to that originally deposited;

(3) Includes a showing that the patent owner acted diligently—

(i) In the case of a replacement deposit, in making the deposit after receiving notice that samples could no longer be furnished from an earlier deposit; or

(ii) In the case of a supplemental deposit, in making the deposit after receiving notice that the earlier deposit had become contaminated or had lost its capability to function as described in the specification;

(4) Includes a statement that the term of the replacement or supplemental deposit expires no earlier than the term of the deposit being replaced or supplemented; and

(5) Otherwise establishes compliance with these regulations.

(d) A depositor's failure to replace a deposit, or in the case of a patent, to diligently replace a deposit and promptly thereafter request a certificate of correction which meets the terms of paragraphs (b) and (c) of this section, after being notified that the depository possessing the deposit cannot furnish samples thereof, shall cause the application or patent involved to be treated in any Office proceeding as if no deposit were made.

(e) In the event a deposit is replaced according to these regulations, the Office will apply a rebuttable presumption of identity between the original and the replacement deposit where a patent making reference to the deposit is relied upon during any Office proceeeding.

(f) A replacement or supplement deposit made during the pendency of an application for patent may be made for any reason.

(g) In no case is a replacement or supplemental deposit of a biological material necessary where the biological material, in accordance with § 1.802(b), need not be deposited.

(h) No replacement deposit of a biological material is necessary where a depository can furnish samples thereof but the depository for national security, health or environmental safety reasons is unable to provide samples to requesters outside of the jurisdiction where the depository is located.

(i) The Office will not recognize in any Office proceeding a replacement deposit of a biological material made by a patent owner where the depository could furnish samples of the deposit being replaced.

[54 FR 34880, Aug. 22, 1989, as amended at 62 FR 53202, Oct. 10, 1997]

§ 1.806 - Term of deposit.

A deposit made before or during pendency of an application for patent shall be made for a term of at least thirty (30) years and at least five (5) years after the most recent request for the furnishing of a sample of the deposit was received by the depository. In any case, samples must be stored under agreements that would make them available beyond the enforceable life of the patent for which the deposit was made.

§ 1.807 - Viability of deposit.

(a) A deposit of biological material that is capable of self-replication either directly or indirectly must be viable at the time of deposit and during the term of deposit. Viability may be tested by the depository. The test must conclude only that the deposited material is capable of reproduction. No evidence is necessarily required regarding the ability of the deposited material to perform any function described in the patent application.

(b) A viability statement for each deposit of a biological material defined in paragraph (a) of this section not made under the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure must be filed in the application and must contain:

(1) The name and address of the depository;

(2) The name and address of the depositor;

(3) The date of deposit;

(4) The identity of the deposit and the accession number given by the depository;

(5) The date of the viability test;

(6) The procedures used to obtain a sample if the test is not done by the depository; and

(7) A statement that the deposit is capable of reproduction.

(c) If a viability test indicates that the deposit is not viable upon receipt, or the examiner cannot, for scientific or other valid reasons, accept the statement of viability received from the applicant, the examiner shall proceed as if no deposit has been made. The examiner will accept the conclusion set forth in a viability statement issued by a depository recognized under § 1.803(a).

§ 1.808 - Furnishing of samples.

(a) A deposit must be made under conditions that assure that:

(1) Access to the deposit will be available during pendency of the patent application making reference to the deposit to one determined by the Director to be entitled thereto under § 1.14 and 35 U.S.C. 122,and,all.

(b) The depositor may contract with the depository to require that samples of a deposited biological material shall be furnished only if a request for a sample, during the term of the patent:

(1) Is in writing or other tangible form and dated;

(2) Contains the name and address of the requesting party and the accession number of the deposit; and

(3) Is communicated in writing by the depository to the depositor along with the date on which the sample was furnished and the name and address of the party to whom the sample was furnished.

(c) Upon request made to the Office, the Office will certify whether a deposit has been stated to have been made under conditions which make it available to the public as of the issue date of the patent grant provided the request contains:

(1) The name and address of the depository;

(2) The accession number given to the deposit;

(3) The patent number and issue date of the patent referring to the deposit; and

(4) The name and address of the requesting party.

§ 1.809 - Examination procedures.

(a) The examiner shall determine pursuant to § 1.104 in each application for patent, application for reissue patent or reexamination proceeding if a deposit is needed, and if needed, if a deposit actually made is acceptable for patent purposes. If a deposit is needed and has not been made or replaced or supplemented in accordance with these regulations, the examiner, where appropriate, shall reject the affected claims under the appropriate provision of 35 U.S.C. 112,explaining.

(b) The applicant for patent or patent owner shall reply to a rejection under paragraph (a) of this section by—

(1) In the case of an applicant for patent, either making an acceptable original, replacement, or supplemental deposit, or assuring the Office in writing that an acceptable deposit will be made; or, in the case of a patent owner, requesting a certificate of correction of the patent which meets the terms of paragraphs (b) and (c) of § 1.805, or

(2) Arguing why a deposit is not needed under the circumstances of the application or patent considered and/or why a deposit actually made should be accepted. Other replies to the examiner's action shall be considered nonresponsive. The rejection will be repeated until either paragraph (b)(1) of this section is satisfied or the examiner is convinced that a deposit is not needed.

(c) If an application for patent is otherwise in condition for allowance except for a needed deposit and the Office has received a written assurance that an acceptable deposit will be made, the Office may notify the applicant in a notice of allowability and set a three-month period of time from the mailing date of the notice of allowability within which the deposit must be made in order to avoid abandonment. This time period is not extendable under § 1.136 (see § 1.136(c)).

(d) For each deposit made pursuant to these regulations, the specification shall contain:

(1) The accession number for the deposit;

(2) The date of the deposit;

(3) A description of the deposited biological material sufficient to specifically identify it and to permit examination; and

(4) The name and address of the depository.

(e) Any amendment required by paragraphs (d)(1), (d)(2) or (d)(4) of this section must be filed before or with the payment of the issue fee (see § 1.312).

[54 FR 34880, Aug. 22, 1989, as amended at 66 FR 21092, Apr. 27, 2001; 78 FR 62408, Oct. 21, 2013]

APPLICATION DISCLOSURES CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCES

§ 1.821 - Nucleotide and/or amino acid sequence disclosures in patent applications.

(a) Nucleotide and/or amino acid sequences, as used in §§ 1.821 through 1.825, are interpreted to mean an unbranched sequence of 4 or more amino acids or an unbranched sequence of 10 or more nucleotides. Branched sequences are specifically excluded from this definition. Sequences with fewer than four specifically defined nucleotides or amino acids are specifically excluded from this section. “Specifically defined” means those amino acids other than “Xaa” and those nucleotide bases other than “n,” defined in accordance with Appendices A through F to this subpart. Nucleotides and amino acids are further defined as follows:

(1) Nucleotides. Nucleotides are intended to embrace only those nucleotides that can be represented using the symbols set forth in Appendix A to this subpart. Modifications (e.g., methylated bases) may be described as set forth in Appendix B to this subpart but shall not be shown explicitly in the nucleotide sequence.

(2) Amino acids. Amino acids are those L-amino acids commonly found in naturally occurring proteins and are listed in appendix C to this subpart. Those amino acid sequences containing D-amino acids are not intended to be embraced by this definition. Any amino acid sequence that contains post-translationally modified amino acids may be described as the amino acid sequence that is initially translated using the symbols shown in appendix C to this subpart, with the modified positions (e.g., hydroxylations or glycosylations) being described as set forth in appendix D to this subpart, but these modifications shall not be shown explicitly in the amino acid sequence. Any peptide or protein that can be expressed as a sequence using the symbols in appendix C to this subpart, in conjunction with a description in the Feature section, to describe, for example, modified linkages, cross links and end caps, non-peptidyl bonds, etc., is embraced by this definition.

Note 1 to paragraph (a):

Appendices A through F to this subpart contain Tables 1-6 of the World Intellectual Property Organization (WIPO) Handbook on Industrial Property Information and Documentation, Standard ST.25: Standard for the Presentation of Nucleotide and Amino Acid Sequence Listings in Patent Applications (2009).

(b) Patent applications which contain disclosures of nucleotide and/or amino acid sequences, in accordance with the definition in paragraph (a) of this section, shall, with regard to the manner in which the nucleotide and/or amino acid sequences are presented and described, conform exclusively to the requirements of §§ 1.821 through 1.825.

(c) Patent applications that contain disclosures of nucleotide and/or amino acid sequences, as defined in paragraph (a) of this section, must contain a “Sequence Listing,” which is a separate part of the specification containing each of those nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of §§ 1.822 and 1.823. The “Sequence Listing” must be submitted as follows, except for a national stage entry under § 1.495(b)(1), where the “Sequence Listing” has been previously communicated by the International Bureau or originally filed in the United States Patent and Trademark Office and complies with Patent Cooperation Treaty (PCT) Rule 5.2:

(1) As an ASCII plain text file, in compliance with § 1.824, submitted via the USPTO patent electronic filing system or on a read-only optical disc under § 1.52(e), accompanied by an incorporation by reference statement of the ASCII plain text file, in a separate paragraph of the specification, in accordance with § 1.77(b)(5);

(2) As a PDF file via the USPTO patent electronic filing system; or

(3) On physical sheets of paper.

(d) Where the description or claims of a patent application discuss a sequence that is set forth in the “Sequence Listing,” in accordance with paragraph (c) of this section, reference must be made to the sequence by use of a sequence identifier (§ 1.823(a)(5)), preceded by “SEQ ID NO:” or the like, in the text of the description or claims, even if the sequence is also embedded in the text of the description or claims of the patent application. Where a sequence is presented in a drawing, reference must be made to the sequence by use of the sequence identifier (§ 1.823(a)(5)), either in the drawing or in the Brief Description of the Drawings, where the correlation between multiple sequences in the drawing and their sequence identifiers (§ 1.823(a)(5)) in the Brief Description is clear.

(e)(1) If the “Sequence Listing” under paragraph (c) of this section is submitted in an application filed under 35 U.S.C. 111(a) as a PDF file (§ 1.821(c)(2)) via the USPTO patent electronic filing system or on physical sheets of paper (§ 1.821(c)(3)), then the following must be submitted:

(i) A CRF of the “Sequence Listing,” in accordance with the requirements of § 1.824; and

(ii) A statement that the sequence information contained in the CRF submitted under paragraph (e)(1)(i) of this section is identical to the sequence information contained in the “Sequence Listing” under paragraph (c) of this section.

(2) If the “Sequence Listing” under paragraph (c) of this section in an application submitted under 35 U.S.C. 371 is a PDF file (paragraph (c)(2) of this section) or on physical sheets of paper (paragraph (c)(3) of this section), and not also as an ASCII plain text file, in compliance with § 1.824 (paragraph (c)(1) of this section), then the following must be submitted:

(i) A CRF of the “Sequence Listing,” in accordance with the requirements of § 1.824; and

(ii) A statement that the sequence information contained in the CRF submitted under paragraph (e)(2)(i) of this section is identical to the sequence information contained in the “Sequence Listing” under paragraph (c)(2) or (3) of this section.

(3) If a “Sequence Listing” in ASCII plain text format, in compliance with § 1.824, has not been submitted for an international application under the PCT, and that application contains disclosures of nucleotide and/or amino acid sequences, as defined in paragraph (a) of this section, and is to be searched by the United States International Searching Authority or examined by the United States International Preliminary Examining Authority, then the following must be submitted:

(i) A CRF of the “Sequence Listing,” in accordance with the requirements of § 1.824;

(ii) The late furnishing fee for providing a “Sequence Listing” in response to an invitation, as set forth in § 1.445(a)(5); and

(iii) A statement that the sequence information contained in the CRF, submitted under paragraph (e)(3)(i) of this section, does not go beyond the disclosure in the international application as filed, or a statement that the information recorded in the ASCII plain text file, submitted under paragraph (e)(3)(i) of this section, is identical to the sequence listing contained in the international application as filed, as applicable.

(4) The CRF may not be retained as a part of the patent application file.

(f) [Reserved]

(g) If any of the requirements of paragraphs (b) through (e) of this section are not satisfied at the time of filing under 35 U.S.C. 111(a) or at the time of entering the national stage under 35 U.S.C. 371,the. Any amendment to add or replace a “Sequence Listing” and CRF copy thereof in reply to a requirement under this paragraph must be submitted in accordance with the requirements of § 1.825.

(h) If any of the requirements of paragraph (e)(3) of this section are not satisfied at the time of filing an international application under the PCT, and the application is to be searched by the United States International Searching Authority or examined by the United States International Preliminary Examining Authority, the applicant may be sent a notice necessitating compliance with the requirements within a prescribed time period. Where a “Sequence Listing” under PCT Rule 13ter is provided in reply to a requirement under this paragraph, it must be accompanied by a statement that the information recorded in the ASCII plain text file under paragraph (e)(3)(i) of this section is identical to the sequence listing contained in the international application as filed, or does not go beyond the disclosure in the international application as filed, as applicable. It must also be accompanied by the late furnishing fee, as set forth in § 1.445(a)(5). If the applicant fails to timely provide the required CRF, the United States International Searching Authority shall search only to the extent that a meaningful search can be performed without the CRF, and the United States International Preliminary Examining Authority shall examine only to the extent that a meaningful examination can be performed without the CRF.

[63 FR 29634, June 1, 1998, as amended at 65 FR 54680, Sept. 8, 2000; 69 FR 18803, Apr. 9, 2004; 70 FR 10489, Mar. 4, 2005; 86 FR 57048, Oct. 14, 2021]

§ 1.822 - Symbols and format to be used for nucleotide and/or amino acid sequence data.

(a) The symbols and format to be used for nucleotide and/or amino acid sequence data shall conform to the requirements of paragraphs (b) through (e) of this section.

(b) The code for representing the nucleotide and/or amino acid sequence characters shall conform to the code set forth in appendices A and C to this subpart. No code other than that specified in these sections shall be used in nucleotide and amino acid sequences. A modified base or modified or unusual amino acid may be presented in a given sequence as the corresponding unmodified base or amino acid if the modified base or modified or unusual amino acid is one of those listed in appendices B and D to this subpart, and the modification is also set forth in the Feature section. Otherwise, each occurrence of a base or amino acid not appearing in appendices A and C, shall be listed in a given sequence as “n” or “Xaa,” respectively, with further information, as appropriate, given in the Feature section, by including one or more feature keys listed in appendices E and F to this subpart.

Note 1 to paragraph (b):

(c) Format representation of nucleotides. (1) A nucleotide sequence shall be listed using the lowercase letter for representing the one-letter code for the nucleotide bases set forth in appendix A to this subpart.

(2) The bases in a nucleotide sequence (including introns) shall be listed in groups of 10 bases except in the coding parts of the sequence. Leftover bases, fewer than 10 in number, at the end of noncoding parts of a sequence shall be grouped together and separated from adjacent groups of 10 or 3 bases by a space.

(3) The bases in the coding parts of a nucleotide sequence shall be listed as triplets (codons). The amino acids corresponding to the codons in the coding parts of a nucleotide sequence shall be listed immediately below the corresponding codons. Where a codon spans an intron, the amino acid symbol shall be listed below the portion of the codon containing two nucleotides.

(4) A nucleotide sequence shall be listed with a maximum of 16 codons or 60 bases per line, with a space provided between each codon or group of 10 bases.

(5) A nucleotide sequence shall be represented, only by a single strand, in the 5 to 3 direction, from left to right.

(6) The enumeration of nucleotide bases shall start at the first base of the sequence with number 1. The enumeration shall be continuous through the whole sequence in the direction 5 to 3. The enumeration shall appear in the right margin, next to the line containing the one-letter codes for the bases and giving the number of the last base of that line.

(7) For those nucleotide sequences that are circular in configuration, the enumeration method set forth in paragraph (c)(6) of this section remains applicable with the exception that the designation of the first base of the nucleotide sequence may be made at the option of the applicant.

Note 2 to paragraph (c):

(d) Representation of amino acids. (1) The amino acids in a protein or peptide sequence shall be listed using the three-letter abbreviation, with the first letter as an uppercase character, as in Appendix C to this subpart.

(2) A protein or peptide sequence shall be listed with a maximum of 16 amino acids per line, with a space provided between each amino acid.

(3) An amino acid sequence shall be represented in the amino to carboxy direction, from left to right, and the amino and carboxy groups shall not be represented in the sequence.

(4) The enumeration of amino acids may start at the first amino acid of the first mature protein, with the number 1. When represented, the amino acids preceding the mature protein (e.g., pre-sequences, pro-sequences, pre-pro-sequences, and signal sequences) shall have negative numbers, counting backwards starting with the amino acid next to number 1. Otherwise, the enumeration of amino acids shall start at the first amino acid at the amino terminal as number 1, and shall appear below every five amino acids of the sequence. The enumeration method for amino acid sequences that is set forth in this section remains applicable for amino acid sequences that are circular in configuration, with the exception that the designation of the first amino acid of the sequence may be made at the option of the applicant.

(5) An amino acid sequence that contains internal terminator symbols (e.g., “Ter,” “*,” or “.,” etc.) may not be represented as a single amino acid sequence but shall be represented as separate amino acid sequences.

Note 3 to paragraph (d):

(e) A sequence with a gap or gaps shall be represented as a plurality of separate sequences, with separate sequence identifiers (§ 1.823(a)(5)), with the number of separate sequences being equal in number to the number of continuous strings of sequence data. A sequence composed of one or more noncontiguous segments of a larger sequence or segments from different sequences shall be presented as a separate sequence.

[63 FR 29635, June 1, 1998, as amended at 69 FR 18803, Apr. 9, 2004; 70 FR 10489, Mar. 4, 2005; 86 FR 57050, Oct. 14, 2021]

§ 1.823 - Requirements for content of a “Sequence Listing” part of the specification.

(a) The “Sequence Listing” must comply with the following:

(1) The order and presentation of the items of information in the “Sequence Listing” shall conform to the arrangement in appendix G to this subpart. The submission of those items of information designated with an “M” is mandatory. The submission of those items of information designated with an “O” is optional.

(2) Each item of information shall begin on a new line, with the numeric identifier enclosed in angle brackets, as shown in appendix G to this subpart.

(3) Set forth numeric identifiers <110> through <170> at the beginning of the “Sequence Listing.”

(4) Include each disclosed nucleotide and/or amino acid sequence, as defined in § 1.821(a).

(5) Assign a separate sequence identifier to each sequence, beginning with 1 and increasing sequentially by integers, and include the sequence identifier in numeric identifier <210>.

(6) Use the code “000” in place of the sequence where no sequence is present for a sequence identifier.

(7) Include the total number of SEQ ID NOs in numeric identifier <160>, as defined in appendix G to this subpart, whether followed by a sequence or by the code “000.”

(8) Must not contain more than 74 characters per line.

(b)(1) Unless paragraph (b)(2) of this section applies, if the “Sequence Listing” required by § 1.821(c) is submitted as an ASCII plain text file via the USPTO patent electronic filing system or on a read-only optical disc, in compliance with § 1.52(e), then the specification must contain a statement in a separate paragraph (see § 1.77(b)(5)) that incorporates by reference the material in the ASCII plain text file identifying:

(i) The name of the file;

(ii) The date of creation; and

(iii) The size of the file in bytes.

(2) If the “Sequence Listing” required by § 1.821(c) is submitted as an ASCII plain text file via the USPTO patent electronic filing system or on a read-only optical disc, in compliance with § 1.52(e) for an international application during the international stage, then incorporation by reference of the material in the ASCII plain text file is not required.

(3) A “Sequence Listing” required by § 1.821(c) that is submitted as a PDF file (§ 1.821(c)(2)) via the USPTO patent electronic filing system or on physical sheets of paper (§ 1.821(c)(3)), setting forth the nucleotide and/or amino acid sequence and associated information in accordance with paragraph (a) of this section:

(i) Must begin on a new page;

(ii) Must be titled “Sequence Listing”;

(iii) Must not include material other than the “Sequence Listing” itself;

(iv) Must have sheets containing no more than 66 lines, with each line containing no more than 74 characters;

(v) Should have sheets numbered independently of the numbering of the remainder of the application; and

(vi) Should use a fixed-width font exclusively throughout.

[86 FR 57050, Oct. 14, 2021]

§ 1.824 - Form and format for a nucleotide and/or amino acid sequence submission as an ASCII plain text file.

(a) A “Sequence Listing” under § 1.821(c)(1) and the CRF required by § 1.821(e) submitted as an ASCII plain text file may be created by any means, such as text editors, nucleotide/amino acid sequence editors, or other custom computer programs; however, the ASCII plain text file must conform to the following requirements:

(1) Must have the following compatibilities:

(i) Computer compatibility: PC or Mac®; and

(ii) Operating system compatibility: MS-DOS®, MS-Windows®, Mac OS®, or Unix®/Linux®.

(2) Must be in ASCII plain text, where:

(i) All printable characters (including the space character) are permitted; and

(ii) No nonprintable (ASCII control) characters are permitted, except ASCII CRLF or LF as line terminators.

(3) Must be named as *.txt, where “*” is one character or a combination of characters limited to upper- or lowercase letters, numbers, hyphens, and underscores and does not exceed 60 characters in total, excluding the extension. No spaces or other types of characters are permitted in the file name.

(4) Must contain no more than 74 printable characters in each line.

(5) Pagination is not permitted; the ASCII plain text file must be one continuous file, with no “hard page break” codes and no page numbering.

(b) The ASCII plain text file must contain a copy of a single “Sequence Listing” in a single file and be submitted either:

(1) Electronically via the USPTO patent electronic filing system, where the file must not exceed 100 MB, and file compression is not permitted; or

(2) On a read-only optical disc(s), in compliance with § 1.52(e), where:

(i) A file that is not compressed must be contained on a single read-only optical disc;

(ii) The file may be compressed using WinZip®, 7-Zip, or Unix®/Linux® Zip;

(iii) A compressed file must not be self-extracting; and

(iv) A compressed ASCII plain text file that does not fit on a single read-only optical disc may be split into multiple file parts, in accordance with the target read-only optical disc size, and labeled in compliance with § 1.52(e)(5)(vi).

[86 FR 57051, Oct. 14, 2021]

§ 1.825 - Amendment to add or replace a “Sequence Listing” and CRF copy thereof.

(a) Any amendment adding a “Sequence Listing” (§ 1.821(c)) after the application filing date must include:

(1) A “Sequence Listing,” in accordance with the requirements of §§ 1.821 through 1.824, submitted as:

(i) An ASCII plain text file, under § 1.821(c)(1), via the USPTO patent electronic filing system or on a read-only optical disc, in compliance with § 1.52(e);

(ii) A PDF file via the USPTO patent electronic filing system; or

(iii) Physical sheets of paper;

(2) A request that the amendment be made:

(i) By incorporation by reference of the material in the ASCII plain text file, in a separate paragraph of the specification, identifying the name of the file, the date of creation, and the size of the file in bytes (see § 1.77(b)(5)), for a “Sequence Listing” submitted under § 1.821(c)(1), except when submitted to the United States International Preliminary Examining Authority for an international application; or

(ii) By inserting, after the abstract of the disclosure, a “Sequence Listing” submitted as a PDF file under § 1.821(c)(2) or submitted on physical sheets of paper under § 1.821(c)(3), except when submitted to the United States International Preliminary Examining Authority for an international application;

(3) A statement that indicates the basis for the amendment, with specific references to particular parts of the application (specification, claims, drawings) for all sequence data in the “Sequence Listing” in the application as originally filed;

(4) A statement that the “Sequence Listing” includes no new matter;

(5) A new or substitute CRF under § 1.821(e), if:

(i) The added “Sequence Listing” is submitted as a PDF file, under § 1.821(c)(2), or on physical sheets of paper, under § 1.821(c)(3); and

(ii) A CRF, under § 1.821(e), was not submitted, not compliant with § 1.824, or not the same as the “Sequence Listing”; and

(6) A statement that the sequence information contained in the CRF is the same as the sequence information contained in the added “Sequence Listing,” if submitted as a PDF file, under § 1.821(c)(2), or on physical sheets of paper, under § 1.821(c)(3).

(b) Any amendment to a “Sequence Listing” (§ 1.821(c)) must include:

(1) A replacement “Sequence Listing,” in accordance with the requirements of §§ 1.821 through 1.824, submitted as:

(i) An ASCII plain text file, under § 1.821(c)(1), via the USPTO patent electronic filing system, or on a read-only optical disc, in compliance with § 1.52(e), labeled as “REPLACEMENT MM/DD/YYYY” (with the month, day, and year of creation indicated);

(ii) A PDF file via the USPTO patent electronic filing system; or

(iii) Physical sheets of paper;

(2) A request that the amendment be made:

(i) By incorporation by reference of the material in the ASCII plain text file, in a separate paragraph of the specification (replacing any prior such paragraph, as applicable) identifying the name of the file, the date of creation, and the size of the file in bytes (see § 1.77(b)(5)) for a “Sequence Listing” under § 1.821(c)(1), except when submitted to the United States International Preliminary Examining Authority for an international application; or

(ii) By placing, after the abstract of the disclosure, a “Sequence Listing” submitted as a PDF file, under § 1.821(c)(2), or on physical sheets of paper, under § 1.821(c)(3) (replacing any prior “Sequence Listing,” as applicable), except when submitted to the United States International Preliminary Examining Authority for an international application;

(3) A statement that identifies the location of all deletions, replacements, or additions to the “Sequence Listing”;

(4) A statement that indicates the basis for the amendment, with specific references to particular parts of the application (specification, claims, drawings) as originally filed for all amended sequence data in the replacement “Sequence Listing”;

(5) A statement that the replacement “Sequence Listing” includes no new matter;

(6) A new or substitute CRF, under § 1.821(e), with the amendment incorporated therein, if:

(i) The replacement “Sequence Listing” is submitted as a PDF file, under § 1.821(c)(2), or on physical sheets of paper, under § 1.821(c)(3); and

(ii) A CRF, under § 1.821(e), was not submitted, not compliant with § 1.824, or not the same as the submitted “Sequence Listing”; and

(7) A statement that the sequence information contained in the CRF is the same as the sequence information contained in the replacement “Sequence Listing” when submitted as a PDF file, under § 1.821(c)(2), or on physical sheets of paper, under § 1.821(c)(3).

(c) The specification of a complete application, filed on the application filing date, with a “Sequence Listing” as an ASCII plain text file, under § 1.821(c)(1), without an incorporation by reference of the material contained in the ASCII plain text file, must be amended to contain a separate paragraph incorporating by reference the material contained in the ASCII plain text file, in accordance with § 1.77(b)(5), except for international applications during the international stage or national stage.

(d) Any appropriate amendments to the “Sequence Listing” in a patent (e.g., by reason of reissue, reexamination, or a certificate of correction) must comply with the requirements of paragraph (b) of this section.

[86 FR 57051, Oct. 14, 2021]

§ 1.831 - Requirements for patent applications filed on or after July 1, 2022, having nucleotide and/or amino acid sequence disclosures.

(a) Patent applications disclosing a nucleotide and/or amino acid sequence(s) by enumeration of its residues, as defined in paragraph (b) of this section, must contain, as a separate part of the disclosure, a computer readable Sequence Listing in XML format (a “Sequence Listing XML”). Disclosed nucleotide or amino acid sequences that do not meet the definition in paragraph (b) of this section must not be included in the “Sequence Listing XML.” The “Sequence Listing XML” contains the information of the nucleotide and/or amino acid sequence(s) disclosed in the patent application using the symbols and format in accordance with the requirements of §§ 1.832 through 1.834.

(b) Nucleotide and/or amino acid sequences, as used in this section and §§ 1.832 through 1.835, encompass:

(1) An unbranched sequence or linear region of a branched sequence containing 4 or more specifically defined amino acids, wherein the amino acids form a single peptide backbone; or

(2) An unbranched sequence or linear region of a branched sequence of 10 or more specifically defined nucleotides, wherein adjacent nucleotides are joined by:

(i) A 3′ to 5′ (or 5′ to 3′) phosphodiester linkage; or

(ii) Any chemical bond that results in an arrangement of adjacent nucleobases that mimics the arrangement of nucleobases in naturally occurring nucleic acids (i.e., nucleotide analogs).

(c) Where the description or claims of a patent application discuss a sequence that is set forth in the “Sequence Listing XML” in accordance with paragraph (a) of this section, reference must be made to the sequence by use of the sequence identifier, preceded by “SEQ ID NO:” or the like in the text of the description or claims, even if the sequence is also embedded in the text of the description or claims of the patent application. Where a sequence is presented in a drawing, reference must be made to the sequence by use of the sequence identifier (§ 1.832(a)), either in the drawing or in the Brief Description of the Drawings, where the correlation between multiple sequences in the drawing and their sequence identifiers (§ 1.832(a)) in the Brief Description is clear.

(d) “Enumeration of its residues” means disclosure of a nucleotide or amino acid sequence in a patent application by listing, in order, each residue of the sequence, where the residues are represented in the manner as defined in paragraph 3(c)(i) or (ii) of WIPO Standard ST.26 (incorporated by reference, see § 1.839).

(e) “Specifically defined” means any amino acid or nucleotide as defined in paragraph 3(k) of WIPO Standard ST.26.

(f) “Amino acid” includes any D- or L-amino acid or modified amino acid as defined in paragraph 3(a) of WIPO Standard ST.26.

(g) “Modified amino acid” includes any amino acid as described in paragraph 3(e) of WIPO Standard ST.26.

(h) “Nucleotide” includes any nucleotide, nucleotide analog, or modified nucleotide as defined in paragraphs 3(f) and 3(g) of WIPO Standard ST.26.

(i) “Modified nucleotide” includes any nucleotide as described in paragraph 3(f) of WIPO Standard ST.26.

(j) A “Sequence listing XML” must not include any sequences having fewer than 10 specifically defined nucleotides, or fewer than 4 specifically defined amino acids.

[87 FR 30818, May 20, 2022, as amended at 88 FR 34091, May 26, 2023]

§ 1.832 - Representation of nucleotide and/or amino acid sequence data in the “Sequence Listing XML” part of a patent application filed on or after July 1, 2022.

(a) Each disclosed nucleotide or amino acid sequence that meets the requirements of § 1.831(b) must appear separately in the “Sequence Listing XML.” Each sequence set forth in the “Sequence Listing XML” must be assigned a separate sequence identifier. The sequence identifiers must begin with 1 and increase sequentially by integers as defined in paragraph 10 of WIPO Standard ST.26 (incorporated by reference, see § 1.839).

(b) The representation and symbols for nucleotide sequence data shall conform to the requirements of paragraphs (b)(1) through (4) of this section.

(1) A nucleotide sequence must be represented in the manner described in paragraphs 11-12 of WIPO Standard ST.26.

(2) All nucleotides, including nucleotide analogs, modified nucleotides, and “unknown” nucleotides, within a nucleotide sequence must be represented using the symbols set forth in paragraphs 13-16, 19, and 21 of WIPO Standard ST.26.

(3) Modified nucleotides within a nucleotide sequence must be described in the manner discussed in paragraphs 17, 18, and 19 of WIPO Standard ST.26.

(4) A region containing a known number of contiguous “a,” “c,” “g,” “t,” or “n” residues for which the same description applies may be jointly described in the manner described in paragraph 22 of WIPO Standard ST.26.

(c) The representation and symbols for amino acid sequence data shall conform to the requirements of paragraphs (c)(1) through (4) of this section.

(1) The amino acids in an amino acid sequence must be represented in the manner described in paragraphs 24 and 25 of WIPO Standard ST.26.

(2) All amino acids, including modified amino acids and “unknown” amino acids, within an amino acid sequence must be represented using the symbols set forth in paragraphs 26-29 and 32 of WIPO Standard ST.26.

(3) Modified amino acids within an amino acid sequence must be described in the manner discussed in paragraphs 29 and 30 of WIPO Standard ST.26.

(4) A region containing a known number of contiguous “X” residues for which the same description applies may be jointly described in the manner described in paragraph 34 of WIPO Standard ST.26.

(d) A nucleotide and/or amino acid sequence that is constructed as a single continuous sequence derived from one or more non-contiguous segments of a larger sequence or of segments from different sequences must be listed in the “Sequence Listing XML” in the manner described in paragraph 35 of WIPO Standard ST.26.

(e) A nucleotide and/or amino acid sequence that contains regions of specifically defined residues separated by one or more regions of contiguous “n” or “X” residues, wherein the exact number of “n” or “X” residues in each region is disclosed, must be listed in the “Sequence Listing XML” in the manner described in paragraph 36 of WIPO Standard ST.26.

(f) A nucleotide and/or amino acid sequence that contains regions of specifically defined residues separated by one or more gaps of an unknown or undisclosed number of residues must be listed in the “Sequence Listing XML” in the manner described in paragraph 37 of WIPO Standard ST.26.

[87 FR 30818, May 20, 2022]

§ 1.833 - Requirements for a “Sequence Listing XML” for nucleotide and/or amino acid sequences as part of a patent application filed on or after July 1, 2022.

(a) The “Sequence Listing XML” as required by § 1.831(a) must be presented as a single file in XML 1.0 encoded using Unicode UTF-8, where the character set complies with paragraphs 40 and 41 and Annex IV of WIPO Standard ST.26 (incorporated by reference, see § 1.839).

(b) The “Sequence Listing XML” presented in accordance with paragraph (a) of this section must further:

(1) Be valid according to the Document Type Definition (DTD) as presented in WIPO Standard ST.26, Annex II.

(2) Comply with the requirements of WIPO Standard ST.26 to include:

(i) An XML declaration as defined in paragraph 39(a) of WIPO Standard ST.26;

(ii) A document type (DOCTYPE) declaration as defined in paragraph 39(b) of WIPO Standard ST.26;

(iii) A root element as defined in paragraph 43 of WIPO Standard ST.26;

(iv) A general information part that complies with the requirements of paragraphs 45, 47, and 48, as applicable, of WIPO Standard ST.26; and

(v) A sequence data part that complies with the requirements of paragraphs 50-55, 57, 58, 60-69, 71-78, 80-87, 89-98, and 100, as applicable, of WIPO Standard ST.26 representing the nucleotide and/or amino acid sequences according to § 1.832.

(3) Include an INSDQualifier__value element with a value in English for any language-dependent free text qualifier as defined by paragraphs 76 and 85-87 of WIPO Standard ST.26, and as required by § 1.52(b)(1)(ii).

[87 FR 30818, May 20, 2022]

§ 1.834 - Form and format for nucleotide and/or amino acid sequence submissions as the “Sequence Listing XML” in patent applications filed on or after July 1, 2022.

(a) A “Sequence Listing XML” encoded using Unicode UTF-8, created by any means (e.g., text editors, nucleotide/amino acid sequence editors, or other custom computer programs) in accordance with §§ 1.831 through 1.833, must:

(1) Have the following compatibilities:

(i) Computer compatibility: PC or Mac®; and

(ii) Operating system compatibility: MS-DOS®, MS-Windows®, Mac OS®, or Unix®/Linux®.

(2) Be in XML format, where all permitted printable characters (including the space character) and non-printable (control) characters are defined in paragraph 40 of WIPO Standard ST.26 (incorporated by reference, see § 1.839).

(3) Be named as *.xml, where “*” is one character or a combination of characters limited to upper- or lowercase letters, numbers, hyphens, and underscores, and the name does not exceed 60 characters in total, excluding the extension. No spaces or other types of characters are permitted in the file name.

(b) The “Sequence Listing XML” must be in a single file containing the sequence information and be submitted either:

(1) Electronically via the USPTO patent electronic filing system, where the file size must not exceed 100 MB, and file compression is not permitted; or

(2) On read-only optical disc(s) in compliance with § 1.52(e), where:

(i) A file that is not compressed must be contained on a single read-only optical disc;

(ii) The file may be compressed using WinZip®, 7-Zip, or Unix®/Linux® Zip;

(iii) A compressed file must not be self-extracting; or

(iv) A compressed XML file that does not fit on a single read-only optical disc may be split into multiple file parts, in accordance with the target read-only optical disc size, and labeled in compliance with § 1.52(e)(5)(vi);

(c)(1) Unless paragraph (c)(2) of this section applies, when the “Sequence Listing XML” required by § 1.831(a) is submitted in XML file format via the USPTO patent electronic filing system or on a read-only optical disc (in compliance with § 1.52(e)), then the specification must contain a statement in a separate paragraph (see § 1.77(b)(5)) that incorporates by reference the material in the XML file identifying:

(i) The name of the file;

(ii) The date of creation; and

(iii) The size of the file in bytes; or

(2) If the “Sequence Listing XML” required by § 1.831(a) is submitted in XML file format via the USPTO patent electronic filing system or on a read-only optical disc (in compliance with § 1.52(e)) for an international application during the international stage, then an incorporation by reference statement of the material in the XML file is not required.

[87 FR 30818, May 20, 2022]

§ 1.835 - Amendment to add or replace a “Sequence Listing XML” in patent applications filed on or after July 1, 2022.

(a) Any amendment to a patent application adding an initial submission of a “Sequence Listing XML” as required by § 1.831(a) after the application filing date must include:

(1) A “Sequence Listing XML” in accordance with §§ 1.831 through 1.834, submitted as an XML file:

(i) Via the USPTO patent electronic filing system; or

(ii) On a read-only optical disc, in compliance with § 1.52(e);

(2) A request to amend the specification to include an incorporation by reference statement of the material in the “Sequence Listing XML” file, identifying the name of the file, the date of creation, and the size of the file in bytes (see § 1.77(b)(5)(ii)), except when submitted to the United States International Preliminary Examining Authority for an international application;

(3) A statement that indicates the basis for the amendment, with specific references to particular parts of the application as originally filed (specification, claims, drawings) for all sequence data in the “Sequence Listing XML”; and

(4) A statement that the “Sequence Listing XML” includes no new matter.

(b) Any amendment adding to, deleting from, or replacing sequence information in a “Sequence Listing XML” submitted as required by § 1.831(a) must include:

(1) A replacement “Sequence Listing XML” in accordance with the requirements of §§ 1.831 through 1.834 containing the entire “Sequence Listing XML,” including any additions, deletions, or replacements of sequence information, which shall be submitted:

(i) Via the USPTO patent electronic filing system; or

(ii) On a read-only optical disc, in compliance with § 1.52(e), labeled as “REPLACEMENT MM/DD/YYYY” (with the month, day, and year of creation indicated);

(2) A request to amend the specification to include an incorporation by reference statement of the material in the replacement “Sequence Listing XML” file that identifies the name of the file, the date of creation, and the size of the file in bytes (see § 1.77(b)(5)(ii)), except when the replacement “Sequence Listing XML” is submitted to the United States International Preliminary Examining Authority for an international application;

(3) A statement that identifies the location of all additions, deletions, or replacements of sequence information relative to the replaced “Sequence Listing XML”;

(4) A statement that indicates the support for the additions, deletions, or replacements of the sequence information, with specific references to particular parts of the application as originally filed (specification, claims, drawings) for all amended sequence data in the replacement “Sequence Listing XML”; and

(5) A statement that the replacement “Sequence Listing XML” includes no new matter.

(c) The specification of a complete application, filed on the application filing date, with a “Sequence Listing XML” as required under § 1.831(a), without an incorporation by reference of the material contained in the “Sequence Listing XML” file, must be amended to include a separate paragraph incorporating by reference the material contained in the “Sequence Listing XML” file, in accordance with § 1.77(b)(5)(ii), except for international applications.

(d)(1) If any of the requirements of §§ 1.831 through 1.834 are not satisfied in an application under 35 U.S.C. 111(a) or in a national stage application under 35 U.S.C. 371,the. Subject to paragraph (d)(2) of this section, any amendment to add or replace a “Sequence Listing XML” or add an incorporation by reference of the material contained in the “Sequence Listing XML” in response to a requirement under this paragraph (d)(1) must be submitted in accordance with the requirements of paragraphs (a) through (c) of this section.

(2) Compliance with paragraphs (a) through (c) of this section is not required for submission of a “Sequence Listing XML” that is solely an English translation of a previously submitted “Sequence Listing XML” that contains non-English values for any language-dependent free text elements (as per § 1.833(b)(3)). The required submission will be a translated “Sequence Listing XML” in compliance with §§ 1.831 through 1.834. Updated values for attributes in the root element (§ 1.833(b)(2)(iii)) or elements of the general information part (§ 1.833(b)(2)(iv)) are not considered amendments for purposes of complying with paragraphs (a) through (c) of this section.

(e) If any of the requirements of §§ 1.831 through 1.834 are not satisfied at the time of filing an international application under the PCT, where the application is to be searched by the United States International Searching Authority or examined by the United States International Preliminary Examining Authority, the applicant may be sent a notice necessitating compliance with the requirements within a prescribed time period. Under PCT Rule 13ter, the applicant can provide, in response to such a requirement or otherwise, a sequence listing that is a “Sequence Listing XML” in accordance with § 1.831(a). The “Sequence Listing XML” must be accompanied by a statement that the information recorded does not go beyond the disclosure in the international application as filed. In response to such a requirement, the late furnishing fee set forth in § 1.445(a)(5) is also required. If the applicant fails to timely provide the required “Sequence Listing XML,” the United States International Searching Authority shall search only to the extent that a meaningful search can be performed without the “Sequence Listing XML,” and the United States International Preliminary Examining Authority shall examine only to the extent that a meaningful examination can be performed without the “Sequence Listing XML.”

(f) Any appropriate amendments to the “Sequence Listing XML” in a patent (e.g., by reason of reissue, reexamination, or certificate of correction) must comply with the requirements of paragraph (b) of this section.

[87 FR 30818, May 20, 2022]

§ 1.839 - Incorporation by reference.

(a) Certain material is incorporated by reference into this subpart with the approval of the Director of the Federal Register under 5 U.S.C. 552(a) and 1 CFR part 51. All approved incorporation by reference (IBR) material is available for inspection at the USPTO and at the National Archives and Records Administration (NARA). Contact the USPTO's Office of Patent Legal Administration at 571-272-7701. For information on the availability of this material at NARA, email [email protected] or go to www.archives.gov/federal-register/cfr/ibr-locations.html. The material may be obtained from the source(s) in paragraph (b) of this section.

(b) World Intellectual Property Organization (WIPO), 34 chemin des Colombettes, 1211 Geneva 20 Switzerland, www.wipo.int.

(1) WIPO Standard ST.26. WIPO Handbook on Intellectual Property Information and Documentation, Standard ST.26: Recommended Standard for the Presentation of Nucleotide and Amino Acid Sequence Listings Using XML (eXtensible Markup Language) including Annexes I-VII, version 1.7, approved December 8, 2023; IBR approved for §§ 1.831 through 1.834.

(2) [Reserved]

[87 FR 30818, May 20, 2022, as amended at 88 FR 34091, May 26, 2023; 89 FR 36679, May 3, 2024]

Appendix Appendix A - Appendix A to Subpart G of Part 1—List of Nucleotides

Source: World Intellectual Property Organization (WIPO) Handbook on Industrial Property Information and Documentation, Standard ST.25: Standard for the Presentation of Nucleotide and Amino Acid Sequence Listings in Patent Applications (2009).

Symbol	Meaning	Origin of designation
a	a	adenine.
g	g	guanine.
c	c	cytosine.
t	t	thymine.
u	u	uracil.
r	g or a	purine.
y	t/u or c	pyrimidine.
m	a or c	amino.
k	g or t/u	keto.
s	g or c	strong interactions 3H-bonds.
w	a or t/u	weak interactions 2H-bonds.
b	g or c or t/u	not a.
d	a or g or t/u	not c.
h	a or c or t/u	not g.
v	a or g or c	not t, not u.
n	a or g or c or t/u, unknown, or other	any.

[86 FR 57052, Oct. 14, 2021]

Appendix Appendix B - Appendix B to Subpart G of Part 1—List of Modified Nucleotides

Symbol	Meaning
ac4c	4-acetylcytidine.
chm5u	5-(carboxyhydroxymethyl)uridine.
cm	2′-O-methylcytidine.
cmnm5s2u	5-carboxymethylaminomethyl-2-thiouridine.
cmnm5u	5-carboxymethylaminomethyluridine.
d	dihydrouridine.
fm	2′-O-methylpseudouridine.
gal q	beta, D-galactosylqueuosine.
gm	2′-O-methylguanosine.
i	inosine.
i6a	N6-isopentenyladenosine.
m1a	1-methyladenosine.
m1f	1-methylpseudouridine.
m1g	1-methylguanosine.
m1i	1-methylinosine.
m22g	2,2-dimethylguanosine.
m2a	2-methyladenosine.
m2g	2-methylguanosine.
m3c	3-methylcytidine.
m5c	5-methylcytidine.
m6a	N6-methyladenosine.
m7g	7-methylguanosine.
mam5u	5-methylaminomethyluridine.
mam5s2u	5-methoxyaminomethyl-2-thiouridine.
man q	beta, D-mannosylqueuosine.
mcm5s2u	5-methoxycarbonylmethyl-2-thiouridine.
mcm5u	5-methoxycarbonylmethyluridine.
mo5u	5-methoxyuridine.
ms2i6a	2-methylthio-N6-isopentenyladenosine.
ms2t6a	N-((9-beta-D-ribofuranosyl-2-methylthiopurine-6-yl)carbamoyl)threonine.
mt6a	N-((9-beta-D-ribofuranosylpurine-6-yl)N-methylcarbamoyl)threonine.
mv	uridine-5-oxyacetic acid-methylester.
o5u	uridine-5-oxyacetic acid.
osyw	wybutoxosine.
p	pseudouridine.
q	queuosine.
s2c	2-thiocytidine.
s2t	5-methyl-2-thiouridine.
s2u	2-thiouridine.
s4u	4-thiouridine.
t	5-methyluridine.
t6a	N-((9-beta-D-ribofuranosylpurine-6-yl)-carbamoyl)threonine.
tm	2′-O-methyl-5-methyluridine.
um	2′-O-methyluridine.
yw	wybutosine.
x	3-(3-amino-3-carboxy-propyl)uridine, (acp3)u.

[86 FR 57052, Oct. 14, 2021]

Appendix Appendix C - Appendix C to Subpart G of Part 1—List of Amino Acids

Symbol	Meaning
Ala	Alanine.
Cys	Cysteine.
Asp	Aspartic Acid.
Glu	Glutamic Acid.
Phe	Phenylalanine.
Gly	Glycine.
His	Histidine.
Ile	Isoleucine.
Lys	Lysine.
Leu	Leucine.
Met	Methionine.
Asn	Asparagine.
Pro	Proline.
Gln	Glutamine.
Arg	Arginine.
Ser	Serine.
Thr	Threonine.
Val	Valine.
Trp	Tryptophan.
Tyr	Tyrosine.
Asx	Asp or Asn.
Glx	Glu or Gln.
Xaa	unknown or other.

[86 FR 57052, Oct. 14, 2021]

Appendix Appendix D - Appendix D to Subpart G of Part 1—List of Modified and Unusual Amino Acids

Symbol	Meaning
Aad	2-Aminoadipic acid.
bAad	3-Aminoadipic acid.
bAla	beta-Alanine, beta-Aminopropionic acid.
Abu	2-Aminobutyric acid.
4Abu	4-Aminobutyric acid, piperidinic acid.
Acp	6-Aminocaproic acid.
Ahe	2-Aminoheptanoic acid.
Aib	2-Aminoisobutyric acid.
bAib	3-Aminoisobutyric acid.
Apm	2-Aminopimelic acid.
Dbu	2,4 Diaminobutyric acid.
Des	Desmosine.
Dpm	2,2′-Diaminopimelic acid.
Dpr	2,3-Diaminopropionic acid.
EtGly	N-Ethylglycine.
EtAsn	N-Ethylasparagine.
Hyl	Hydroxylysine.
aHyl	allo-Hydroxylysine.
3Hyp	3-Hydroxyproline.
4Hyp	4-Hydroxyproline.
Ide	Isodesmosine.
aIle	allo-Isoleucine.
MeGly	N-Methylglycine, sarcosine.
MeIle	N-Methylisoleucine.
MeLys	6-N-Methyllysine.
MeVal	N-Methylvaline.
Nva	Norvaline.
Nle	Norleucine.
Orn	Ornithine.

[86 FR 57052, Oct. 14, 2021]

Appendix Appendix E - Appendix E to Subpart G of Part 1—List of Feature Keys Related to Nucleotide Sequences

Key	Description
allele	a related individual or strain contains stable, alternative forms of the same gene, which differs from the presented sequence at this location (and perhaps others).
attenuator	(1) region of DNA at which regulation of termination of transcription occurs, which controls the expression of some bacterial operons; (2) sequence segment located between the promoter and the first structural gene that causes partial termination of transcription.
C__region	constant region of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains; includes one or more exons depending on the particular chain.
CAAT__signal	CAAT box; part of a conserved sequence located about 75 bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG (C or T) CAATCT.
CDS	coding sequence; sequence of nucleotides that corresponds with the sequence of amino acids in a protein (location includes stop codon); feature includes amino acid conceptual translation.
conflict	independent determinations of the “same” sequence differ at this site or region.
D-loop	displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein.
D-segment	diversity segment of immunoglobulin heavy chain, and T-cell receptor beta chain.
enhancer	a cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter.
exon	region of genome that codes for portion of spliced mRNA; may contain 5′UTR, all CDSs, and 3′UTR.
GC__signal	GC box; a conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG.
gene	region of biological interest identified as a gene and for which a name has been assigned.
iDNA	intervening DNA; DNA which is eliminated through any of several kinds of recombination.
intron	a segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it.
J__segment	joining segment of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains.
LTR	long terminal repeat, a sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses.
mat__peptide	mature peptide or protein coding sequence; coding sequence for the mature or final peptide or protein product following post-translational modification; the location does not include the stop codon (unlike the corresponding CDS).
misc__binding	site in nucleic acid which covalently or non-covalently binds another moiety that cannot be described by any other Binding key (primer__bind or protein__bind).
misc__difference	feature sequence is different from that presented in the entry and cannot be described by any other Difference key (conflict, unsure, old__sequence, mutation, variation, allele, or modified__base).
misc__feature	region of biological interest which cannot be described by any other feature key; a new or rare feature.
misc__recomb	site of any generalized, site-specific or replicative recombination event where there is a breakage and reunion of duplex DNA that cannot be described by other recombination keys (iDNA and virion) or qualifiers of source key (/insertion__seq, /transposon, /proviral).
misc__RNA	any transcript or RNA product that cannot be defined by other RNA keys (prim__transcript, precursor__RNA, mRNA, 5′clip, 3′clip, 5′UTR, 3′UTR, exon, CDS, sig__peptide, transit__peptide, mat__peptide, intron, polyA__site, rRNA, tRNA, scRNA, and snRNA).
misc__signal	any region containing a signal controlling or altering gene function or expression that cannot be described by other Signal keys (promoter, CAAT__signal, TATA__signal, -35__signal, -10__signal, GC__signal, RBS, polyA__signal, enhancer, attenuator, terminator, and rep__origin).
misc__structure	any secondary or tertiary structure or conformation that cannot be described by other Structure keys (stem__loop and D-loop).
modified__base	the indicated nucleotide is a modified nucleotide and should be substituted for by the indicated molecule (given in the mod__base qualifier value).
mRNA	messenger RNA; includes 5′ untranslated region (5′UTR), coding sequences (CDS, exon) and 3′ untranslated region (3′UTR).
mutation	a related strain has an abrupt, inheritable change in the sequence at this location.
N__region	extra nucleotides inserted between rearranged immunoglobulin segments.
old__sequence	the presented sequence revises a previous version of the sequence at this location.
polyA__signal	recognition region necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA.
polyA__site	site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation.
precursor__RNA	any RNA species that is not yet the mature RNA product; may include 5′ clipped region (5′clip), 5′ untranslated region (5′UTR), coding sequences (CDS, exon), intervening sequences (intron), 3′ untranslated region (3′UTR), and 3′ clipped region (3′clip).
prim__transcript	primary (initial, unprocessed) transcript; includes 5′ clipped region (5′clip), 5′ untranslated region (5′UTR), coding sequences (CDS, exon), intervening sequences (intron), 3′ untranslated region (3′UTR), and 3′ clipped region (3′clip).
primer__bind	non-covalent primer binding site for initiation of replication, transcription, or reverse transcription; includes site(s) for synthetic, for example, PCR primer elements.
promoter	region on a DNA molecule involved in RNA polymerase binding to initiate transcription.
protein__bind	non-covalent protein binding site on nucleic acid.
RBS	ribosome binding site.
repeat__region	region of genome containing repeating units.
repeat__unit	single repeat element.
rep__origin	origin of replication; starting site for duplication of nucleic acid to give two identical copies.
rRNA	mature ribosomal RNA; the RNA component of the ribonucleoprotein particle (ribosome) which assembles amino acids into proteins.
S__region	switch region of immunoglobulin heavy chains; involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin class from the same B-cell.
satellite	many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.
scRNA	small cytoplasmic RNA; any one of several small cytoplasmic RNA molecules present in the cytoplasm and (sometimes) nucleus of a eukaryote.
sig__peptide	signal peptide coding sequence; coding sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane; leader sequence.
snRNA	small nuclear RNA; any one of many small RNA species confined to the nucleus; several of the snRNAs are involved in splicing or other RNA processing reactions.
source	identifies the biological source of the specified span of the sequence; this key is mandatory; every entry will have, as a minimum, a single source key spanning the entire sequence; more than one source key per sequence is permissible.
stem__loop	hairpin; a double-helical region formed by base-pairing between adjacent (inverted) complementary sequences in a single strand of RNA or DNA.
STS	Sequence Tagged Site; short, single-copy DNA sequence that characterizes a mapping landmark on the genome and can be detected by PCR; a region of the genome can be mapped by determining the order of a series of STSs.
TATA__signal	TATA box; Goldberg-Hogness box; a conserved AT-rich septamer found about 25 bp before the start point of each eukaryotic RNA polymerase II transcript unit which may be involved in positioning the enzyme for correct initiation; consensus=TATA(A or T)A(A or T).
terminator	sequence of DNA located either at the end of the transcript or adjacent to a promoter region that causes RNA polymerase to terminate transcription; may also be site of binding of repressor protein.
transit__peptide	transit peptide coding sequence; coding sequence for an N-terminal domain of a nuclear-encoded organellar protein; this domain is involved in post-translational import of the protein into the organelle.
tRNA	mature transfer RNA, a small RNA molecule (75-85 bases long) that mediates the translation of a nucleic acid sequence into an amino acid sequence.
unsure	author is unsure of exact sequence in this region.
V__region	variable region of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains; codes for the variable amino terminal portion; can be made up from V__segments, D__segments, N__regions, and J__segments.
V__segment	variable segment of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains; codes for most of the variable region (V__region) and the last few amino acids of the leader peptide.
variation	a related strain contains stable mutations from the same gene (for example, RFLPs, polymorphisms, etc.) which differ from the presented sequence at this location (and possibly others).
3′clip	3′-most region of a precursor transcript that is clipped off during processing.
3′UTR	region at the 3′ end of a mature transcript (following the stop codon) that is not translated into a protein.
5′clip	5′-most region of a precursor transcript that is clipped off during processing.
5′UTR	region at the 5′ end of a mature transcript (preceding the initiation codon) that is not translated into a protein.
−10__signal	pribnow box; a conserved region about 10 bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT.
−35__signal	a conserved hexamer about 35 bp upstream of the start point of bacterial transcription units; consensus=TTGACa [ ] or TGTTGACA [ ].

[86 FR 57052, Oct. 14, 2021]

Appendix Appendix F - Appendix F to Subpart G of Part 1—List of Feature Keys Related to Protein Sequences

Key	Description
CONFLICT	different papers report differing sequences.
VARIANT	authors report that sequence variants exist.
VARSPLIC	description of sequence variants produced by alternative splicing.
MUTAGEN	site which has been experimentally altered.
MOD__RES	post-translational modification of a residue.
ACETYLATION	N-terminal or other.
AMIDATION	generally at the C-terminal of a mature active peptide.
BLOCKED	undetermined N- or C-terminal blocking group.
FORMYLATION	of the N-terminal methionine.
GAMMA-CARBOXYGLUTAMIC ACID HYDROXYLATION	of asparagine, aspartic acid, proline, or lysine.
METHYLATION	generally of lysine or arginine.
PHOSPHORYLATION	of serine, threonine, tyrosine, aspartic acid or histidine.
PYRROLIDONE CARBOXYLIC ACID	N-terminal glutamate which has formed an internal cyclic lactam.
SULFATATION	generally of tyrosine.
LIPID	covalent binding of a lipidic moiety.
MYRISTATE	myristate group attached through an amide bond to the N-terminal glycine residue of the mature form of a protein or to an internal lysine residue.
PALMITATE	palmitate group attached through a thioether bond to a cysteine residue or through an ester bond to a serine or threonine residue.
FARNESYL	farnesyl group attached through a thioether bond to a cysteine residue.
GERANYL-GERANYL	geranyl-geranyl group attached through a thioether bond to a cysteine residue.
GPI-ANCHOR	glycosyl-phosphatidylinositol (GPI) group linked to the alpha- carboxyl group of the C-terminal residue of the mature form of a protein.
N-ACYL DIGLYCERIDE	N-terminal cysteine of the mature form of a prokaryotic lipoprotein with an amide-linked fatty acid and a glyceryl group to which two fatty acids are linked by ester linkages.
DISULFID	disulfide bond; the `FROM' and `TO' endpoints represent the two residues which are linked by an intra-chain disulfide bond; if the `FROM' and `TO' endpoints are identical, the disulfide bond is an interchain one and the description field indicates the nature of the cross-link.
THIOLEST	thiolester bond; the `FROM' and `TO' endpoints represent the two residues which are linked by the thiolester bond.
THIOETH	thioether bond; the `FROM' and `TO' endpoints represent the two residues which are linked by the thioether bond.
CARBOHYD	glycosylation site; the nature of the carbohydrate (if known) is given in the description field.
METAL	binding site for a metal ion; the description field indicates the nature of the metal.
BINDING	binding site for any chemical group (co-enzyme, prosthetic group, etc.); the chemical nature of the group is given in the description field.
SIGNAL	extent of a signal sequence (prepeptide).
TRANSIT	extent of a transit peptide (mitochondrial, chloroplastic, or for a microbody).
PROPEP	extent of a propeptide.
CHAIN	extent of a polypeptide chain in the mature protein.
PEPTIDE	extent of a released active peptide.
DOMAIN	extent of a domain of interest on the sequence; the nature of that domain is given in the description field.
CA__BIND	extent of a calcium-binding region.
DNA__BIND	extent of a DNA-binding region.
NP__BIND	extent of a nucleotide phosphate binding region; the nature of the nucleotide phosphate is indicated in the description field.
TRANSMEM	extent of a transmembrane region.
ZN__FING	extent of a zinc finger region.
SIMILAR	extent of a similarity with another protein sequence; precise information, relative to that sequence, is given in the description field.
REPEAT	extent of an internal sequence repetition.
HELIX	secondary structure: Helices, for example, Alpha-helix, 3(10) helix, or Pi-helix.
STRAND	secondary structure: Beta-strand, for example, Hydrogen bonded beta-strand, or Residue in an isolated beta-bridge.
TURN	secondary structure Turns, for example, H-bonded turn (3-turn, 4-turn, or 5-turn).
ACT__SITE	amino acid(s) involved in the activity of an enzyme.
SITE	any other interesting site on the sequence.
INIT__MET	the sequence is known to start with an initiator methionine.
NON__TER	the residue at an extremity of the sequence is not the terminal residue; if applied to position 1, this signifies that the first position is not the N-terminus of the complete molecule; if applied to the last position, it signifies that this position is not the C-terminus of the complete molecule; there is no description field for this key.
NON__CONS	non consecutive residues; indicates that two residues in a sequence are not consecutive and that there are a number of unsequenced residues between them.
UNSURE	uncertainties in the sequence; used to describe region(s) of a sequence for which the authors are unsure about the sequence assignment.

[86 FR 57052, Oct. 14, 2021]

Appendix Appendix G - Appendix G to Subpart G of Part 1—Numeric Identifiers

Numeric identifier	Definition	Comments and format	Mandatory (M) or optional (O)
<110>	Applicant	If Applicant is inventor, then preferably max. of 10 names; one name per line; preferable format: Surname, Other Names and/or Initials	M.
<120>	Title of Invention		M.
<130>	File Reference	Personal file reference	M when filed prior to assignment or appl. number.
<140>	Current Application Number	Specify as: US 09/999,999 or PCT/US09/99999	M, if available.
<141>	Current Filing Date	Specify as: yyyy-mm-dd	M, if available.
<150>	Prior Application Number	Specify as: US 09/999,999 or PCT/US09/99999	M, if applicable include priority documents under 35 U.S.C. 119 and 120.
<151>	Prior Application Filing Date	Specify as: yyyy-mm-dd	M, if applicable.
<160>	Number of SEQ ID NOs	Count includes total number of SEQ ID NOs	M.
<170>	Software	Name of software used to create the “Sequence Listing”	O.
<210>	SEQ ID NO:#:	Response shall be an integer representing the SEQ ID NO shown	M.
<211>	Length	Respond with an integer expressing the number of bases or amino acid residues	M.
<212>	Type	Whether presented sequence molecule is DNA, RNA, or PRT (protein). If a nucleotide sequence contains both DNA and RNA fragments, the type shall be “DNA.” In addition, the combined DNA/RNA molecule shall be further described in the <220> to <223> feature section	M.
<213>	Organism	Scientific name, i.e., Genus/species, Unknown or Artificial Sequence. In addition, the “Unknown” or “Artificial Sequence” organisms shall be further described in the <220> to <223> feature section	M.
<220>	Feature	Leave blank after <220>. <221-223> provide for a description of points of biological significance in the sequence	M, under the following conditions: If “n,” “Xaa,” or a modified or unusual L-amino acid or modified base was used in a sequence; if ORGANISM is “Artificial Sequence” or “Unknown”; if molecule is combined DNA/RNA.
<221>	Name/Key	Provide appropriate identifier for feature, from WIPO Standard ST.25 (2009), Appendices E and F to this subpart	M, under the following conditions: If “n,” “Xaa,” or a modified or unusual L-amino acid or modified base was used in a sequence.
<222>	Location	Specify location within sequence; where appropriate, state number of first and last bases/amino acids in feature	M, under the following conditions: If “n,” “Xaa,” or a modified or unusual L-amino acid or modified base was used in a sequence.
<223>	Other Information	Other relevant information; four lines maximum	M, under the following conditions: If “n,” “Xaa,” or a modified or unusual L-amino acid or modified base was used in a sequence; if ORGANISM is “Artificial Sequence” or “Unknown”; if molecule is combined DNA/RNA.
<300>	Publication Information	Leave blank after <30>	O.
<301>	Authors	Preferably max. of 10 named authors of publication; specify one name per line; preferable format: Surname, Other Names and/or Initials	O.
<302>	Title		O.
<303>	Journal		O.
<304>	Volume		O.
<305>	Issue		O.
<306>	Pages		O.
<307>	Date	Journal date on which data published; specify as yyyy-mm-dd, MMM-yyyy or Season-yyyy	O.
<308>	Database Accession Number	Accession number assigned by database, including database name	O.
<309>	Database Entry Date	Date of entry in database; specify as yyyy-mm-dd or MMM-yyyy	O.
<310>	Patent Document Number	Document number; for patent-type citations only. Specify as, for example, US 09/999,999	O.
<311>	Patent Filing Date	Document filing date, for patent-type citations only; specify as yyyy-mm-dd	O.
<312>	Publication Date	Document publication date, for patent-type citations only; specify as yyyy-mm-dd	O.
<313>	Relevant Residues	FROM (position) TO (position)	O.
<400>	Sequence	SEQ ID NO should follow the numeric identifier and should appear on the line preceding the actual sequence	M.

[86 FR 57052, Oct. 14, 2021]

authority: 35 U.S.C. 2(b)(2), unless otherwise noted

source: 24 FR 10332, Dec. 22, 1959, unless otherwise noted.

cite as: 37 CFR 1.833