MPEP § 2423 — MPEP § 2423
Current through: 2022-07-01

2423-Symbols and Format To Be Used for Nucleotide and/or Amino Acid Sequence Data for WIPO ST.25 
 
 

 
 
 
 
 
 
 
 

 

 
 
 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

 
 
 
 
 

 
 
 
 
 
 
 
 
 
 
 

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 Chapter 2400 

 Section 2423 
 

 
 
 
 
 
 2423 Symbols and Format To Be Used for Nucleotide and/or Amino Acid
 Sequence Data for WIPO ST.25 [R-07.2022]
 

 [Editor Note: This section is not applicable to applications filed on or after
 July 1, 2022, having disclosures of nucleotide and/or amino acid sequences as defined in
 37 CFR
 1.831(b) . See MPEP §§
 2412 - 2419 for guidance on WIPO ST.26
 requirements for applications filed on or after July 1, 2022.] 

 
 37 CFR 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): 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).
 

 (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): 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).
 

 (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 upper case 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): 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).
 

 (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.
 

 
 

 Appendices A through F referenced in 37 CFR
 1.822 are reproduced in MPEP § 2422(I) .
 

 
 2423.01 Format and Symbols To Be Used in a “Sequence Listing” [R-07.2022]

 [Editor Note: This section is not applicable to applications filed on or after
 July 1, 2022, having disclosures of nucleotide and/or amino acid sequences as defined
 in 37
 CFR 1.831(b) . See MPEP §§
 2412 - 2419 for guidance on WIPO ST.26
 requirements for applications filed on or after July 1, 2022.] 

 37 CFR
 1.822 sets forth the format and symbols to be used for listing
 nucleotide and/or amino acid sequence data. The symbols for representing the nucleotide
 and/or amino acid characters in the sequences are set forth in Appendices A and C to
 Subpart G of Part 1 of the CFR. See MPEP § 2422 (I). No other symbols shall
 be used in nucleotide and amino acid sequences. The “modified base” and “modified and
 unusual amino acid” symbols appearing in Appendices B and D to Subpart G of Part 1 of
 the CFR (see 37 CFR 1.822 and
 MPEP §
 2422 (I)) are not to be set forth in the sequences recited in
 the "Sequence Listing”. However, “modified base” or “modified and unusual amino acid”
 symbols may be used in the written description and/or drawing portions of the
 specification. To properly enter notations for modified bases or amino acids in the
 “Sequence Listing”, the Feature section of the “Sequence Listing” should be used. That
 is, a modified base or amino acid may be presented in a given sequence as the
 corresponding unmodified base or amino acid if the modified base or amino acid is one of
 those listed in Appendices B and D to Subpart G of Part 1 of the CFR and the
 modification is also set forth in the Feature section of the “Sequence Listing”.
 Otherwise, all nucleotide bases or amino acids not appearing in Appendices A and C to
 Subpart G of Part 1 of the CFR must be listed in a given sequence as “n” or “Xaa,”
 respectively, with further information given in the Feature section of the “Sequence
 Listing” by including one or more feature keys listed in Appendices E and F to Subpart G
 of Part 1 of the CFR. See 37 CFR 1.822(b) .
 

 In 37 CFR 1.822(b) and 37 CFR 1.822(d) , the use of
 three-letter symbols for amino acids is required in the “Sequence Listing”. The
 three-letter symbols must be presented using the upper case for the first character and
 lower case for the remaining two characters. Applicants are encouraged to use the
 three-letter symbols for amino acids throughout the disclosure, instead of the
 one-letter symbols, for easier reading of the application and any patent issuing
 therefrom.
 

 37 CFR
 1.822(c) through (e) set forth the format for
 presenting sequence data. These paragraphs set forth the manner in which the characters
 in sequences are to be grouped, spaced, presented and numbered. 
 

 

 
 2423.02 Depiction of Coding Regions [R-07.2022]

 [Editor Note: This section is not applicable to applications filed on or after
 July 1, 2022, having disclosures of nucleotide and/or amino acid sequences as defined
 in 37
 CFR 1.831(b) . See MPEP §§
 2412 - 2419 for guidance on WIPO ST.26
 requirements for applications filed on or after July 1, 2022.] 

 If applicant chooses to depict coding regions, 37 CFR 1.822(c)(3) 
 requires the amino acids corresponding to the codons in the coding parts of a nucleotide
 sequence to be listed immediately below the corresponding codons. Further, in
 37 CFR
 1.822(c)(3) , the situation in which a codon spans an intron has
 been addressed. In those situations, the “amino acid symbol shall be listed below the
 portion of the codon containing two nucleotides.” This requirement clarifies the
 representation of an amino acid that corresponds to a codon that spans an intron.
 

 It should be noted that the sequence rules do not, in any way, require
 the depiction of coding regions or the amino acids corresponding to the codons in those
 coding regions. 37 CFR
 1.822(d) only requires that where amino acids corresponding to the
 codons in the coding parts of a nucleotide sequence are depicted, they must be depicted
 below the corresponding codons. There is absolutely no requirement in the rules to
 depict coding regions. However, when the coding parts of a nucleotide sequence and their
 corresponding amino acids have been enumerated by their residues, those amino acids must
 also be set forth as a separate sequence if the amino acid sequence meets the length
 thresholds in 37 CFR
 1.821(a) . 
 

 

 
 2423.03 Presentation and Numbering of Sequences [R-07.2022]

 [Editor Note: This section is not applicable to applications filed on or after
 July 1, 2022, having disclosures of nucleotide and/or amino acid sequences as defined
 in 37
 CFR 1.831(b) . See MPEP §§
 2412 - 2419 for guidance on WIPO ST.26
 requirements for applications filed on or after July 1, 2022.] 

 37 CFR
 1.822(c)(5) provides that nucleotide sequences shall only be
 represented by a single strand, in the 5′ to 3′ direction, from left to right. That is,
 double stranded nucleotides shall not be represented in the “Sequence Listing”. A double
 stranded nucleotide may be represented as two single stranded nucleotides, and any
 relationship between the two may be shown in the drawings. 
 

 The procedures for presenting and numbering amino acid sequences are
 set forth in 37 CFR
 1.822(d) . Two alternatives are presented for numbering amino acid
 sequences. Amino acid sequences may be numbered with respect to the identification of
 the first amino acid of the first mature protein or with respect to the first amino acid
 appearing at the amino terminal. The numbering procedure for nucleotides is set forth in
 37 CFR
 1.822(c)(6) . Sequences that are circular in configuration are
 intended to be encompassed by these rules, and the numbering procedures described above
 remain applicable with the exception that the designation of the first nucleotide base
 or amino acid of the sequence may be made at the option of the applicant. See
 37 CFR
 1.822(c)(7) and (d)(4) . 
 

 In 37
 CFR 1.822(e) the procedures for presenting and numbering hybrid
 and gapped sequences are set forth. A sequence with a gap or gaps shall be presented as
 a plurality of separate sequences, each having separate sequence identifiers, with the
 number of separate sequences being equal in number to the number of continuous strings
 of sequence data. The term “gap” is not intended to embrace a gap or gaps that is/are
 introduced into the presentation of otherwise continuous sequence information in, e.g.,
 a drawing figure, to show alignments or similarities with other sequences. The “gaps”
 referred to in this section are gaps representing unknown or undisclosed regions in a
 sequence between regions that are known or disclosed. On the other hand, a sequence that
 contains one or more regions of contiguous “n” or “Xaa” residues, wherein the exact
 number of “n” or “Xaa” residues in each region is disclosed, must be included in the
 “Sequence Listing” as a single sequence with a single sequence identifier. A sequence
 disclosed by enumeration of its residues that is constructed as a single continuous
 sequence from one or more non-contiguous segments of a larger sequence or segments from
 different sequences must be included in the “Sequence Listing” as a single sequence with
 a single sequence identifier. A fragment of a larger sequence need not be enumerated by
 its residues, and may be referred to in the specification, claims or drawings as, e.g.,
 “residues 2 through 33 of SEQ ID NO:12,” assuming that SEQ ID NO:12 has been properly
 included in the “Sequence Listing”.
 

 

 [top] 

 

 

 
 

 
 

 

 

 

 
 
 
 2401-Introduction 

 2402-The Deposit Rules 

 2403-Deposit of Biological Material 
 2403.01-Material Capable of Self- Replication 

 2403.02-Plant Material 

 
 

 2404-Need or Opportunity to Make a Deposit 
 2404.01-Biological Material That Is Known and Readily Available to the Public 

 2404.02-Biological Material That Can Be Made or Isolated Without Undue Experimentation 

 2404.03-Reference to a Deposit in the Specification 

 
 

 2405-Acceptable Depository 

 2406-Time of Making an Original Deposit 
 2406.01-Description in Application Specification 

 2406.02-Deposit After Filing Date - Corroboration 

 2406.03-Possible Loss of U.S. Filing Date in Other Countries 

 
 

 2407-Replacement or Supplement of Deposit 
 2407.01-In a Pending Application 

 2407.02-After a Patent Has Issued 

 2407.03-Failure to Replace 

 2407.04-Treatment of Replacement 

 2407.05-Exemption From Replacement 

 2407.06-Replacement May Not Be Recognized 

 
 

 2408-Term of Deposit 

 2409-Viability of Deposit 

 2410-Furnishing of Samples 
 2410.01-Conditions of Deposit 

 2410.02-Certification of Statement of Availability of Deposit 

 
 

 2411-Examination Procedures 
 2411.01-Rejections Based on Deposit Issue 

 2411.02-Replies to Rejections Based on Deposit Issue 

 2411.03-Application in Condition for Allowance Except for Deposit 

 2411.04-[Reserved] 

 2411.05-Content of Application with Respect to Deposited Material 

 
 

 2412-The Requirements for Patent Applications Containing Nucleotide Sequence and/or Amino Acid Sequence Disclosures to Include
 a Sequence Listing in XML file format 
 2412.01-Overview of the Sequence Rules 

 2412.02-Definition of “Sequence Listing XML” 
 2412.02(a)-“Enumeration of its residues” 

 
 

 2412.03-Nucleotides and Amino Acids Included and Excluded From a “Sequence Listing XML” 
 2412.03(a)-“Specifically Defined” 

 2412.03(b)-“Amino Acid” 

 2412.03(c)-“Modified Amino Acid” 

 2412.03(d)-“Nucleotide” 

 2412.03(e)-“Modified Nucleotide” 

 
 

 2412.04-Use of Sequence Identifiers to Denote Sequences Disclosed in the Description, Drawings or Claims 

 2412.05-Representation and Symbols for Nucleotide and/or Amino Acid Sequences 
 2412.05(a)-Use of Sequentially Numbered Sequence Identifiers in the “Sequence Listing XML” 

 2412.05(b)-Representation and Symbols of Nucleotide Sequence Data 

 2412.05(c)-Representation and Inclusion of Variants 

 2412.05(d)-Representation and Symbols of Amino Acid Sequence Data 

 2412.05(e)-Presentation of Special Situations 

 
 

 2412.06-The Requirement for Exclusive Conformance; Sequences Presented in Drawing Figures 

 2412.07-Examination of Patent Applications Claiming Large Numbers of Nucleotide Sequences 

 
 

 2413-Content of a “Sequence Listing XML” and Form and Format of the “Sequence Listing XML” File 
 2413.01-Parts of the “Sequence Listing XML” 
 2413.01(a)-The “Sequence Listing XML” is a Single File Encoded Using Unicode UTF-8 

 2413.01(b)-The “Sequence Listing XML” Must Be Valid According To the DTD 

 2413.01(c)-The “Sequence Listing XML” Must Contain an XML Declaration 

 2413.01(d)-The “Sequence Listing XML” Must Contain a DOCTYPE Declaration 

 2413.01(e)-The “Sequence Listing XML” Must Contain a Root Element 

 2413.01(f)-The “Sequence Listing XML” Must Contain a General Information Part 

 2413.01(g)-The “Sequence Listing XML” Must Contain a Sequence Data Part 

 2413.01(h)-Language Dependent Free Text Qualifier Values in the English Language 

 2413.01(i)-Title Element in “Sequence Listing XML” 

 
 

 2413.02-Form and Format of the XML file containing the “Sequence Listing XML” 

 2413.03-How to Submit the “Sequence Listing XML” 

 2413.04-Requirements Regarding Incorporation By Reference of the “Sequence Listing XML” 

 2413.05-Presumptions Regarding Compliance 

 
 

 2414-Notification of a Failure to Comply with Sequence Listing Requirements and Amendments Relating to “Sequence Listing XML” Files
 Under 37 CFR 1.835 
 2414.01-Issuance of a Notice Relating to the Requirements For Patent Applications Containing Nucleotide and/or Amino Acid Sequence
 Disclosures 

 2414.02-Amendment to Add an Initial “Sequence Listing XML” under 37 CFR 1.835(a) 

 2414.03-Amendment Adding to, Deleting from, or Replacing Sequence Information in a “Sequence Listing XML” under 37 CFR 1.835(b) 

 2414.04-Translation of “Sequence Listing XML” is Not an Amended “Sequence Listing XML” under 37 CFR 1.835(b) 

 2414.05-Notifications for Failure to Submit a “Sequence Listing XML” in an International Application under the PCT to be Searched
 by the United States International Searching Authority or Examined by International Preliminary Examination Authority 

 2414.06-Amendment of a “Sequence Listing XML” in a Patent 

 
 

 2415-Applicability date of “Sequence Listing XML” Requirements to Applications Based on Filing Date of Application and Procedures
 for Failure to Submit Correct Format of Sequence Listing 
 2415.01-Determining if a “Sequence Listing XML” Must be Submitted 

 2415.02-Provisional Applications Containing Disclosures of Nucleotides and/or Amino Acids, Compliance with 37 CFR 1.831-1.834 

 2415.03-Improper Submissions of “Sequence Listing” under 1.821(c) When a “Sequence Listing XML” was Required 

 
 

 2416-Form Paragraphs 

 2417-Helpful Hints for Sequence Rules Compliance under WIPO Standard ST.26 

 2418-WIPO Sequence Tool 

 2419-Publishing of Patent Grants and Patent Application Publications with a “Sequence Listing XML” 
 2419.01-Patent Grants and Patent Application Publications Containing a Non-Lengthy “Sequence Listing XML” 

 2419.02-Patent Grants and Patent Application Publications Containing a Lengthy “Sequence Listing XML” 

 2419.03-Patent Grants and Patent Application Publications Containing a “Sequence Listing XML” of 1GB or Larger 

 
 

 2420-The Requirements for Patent Applications Containing Nucleotide Sequence and/or Amino Acid Sequence Disclosures under World
 Intellectual Property Office Standard ST.25 (WIPO ST.25) - the Sequence Rules 

 2421-Overview of the Sequence Rules under WIPO ST.25 
 2421.01-Definition of “Sequence Listing” and Computer Readable Form (CRF) 

 2421.02-Summary of the Requirements of the Sequence Rules 

 2421.03-Notification of a Failure to Comply 

 2421.04-[Reserved] 

 
 

 2422-Nucleotide and/or Amino Acid Sequence Disclosures in Patent Applications Subject to WIPO ST.25 
 2422.01-Nucleotide and/or Amino Acids Disclosures Requiring a “Sequence Listing” 

 2422.02-The Requirement for Exclusive Conformance; Sequences Presented in Drawing Figures 

 2422.03-Sequence Listing Submission 

 2422.03(a)-“Sequence Listing” Submitted as ASCII Plain Text Files 

 2422.04-The Requirement for a Computer Readable Copy of the “Sequence Listing” 

 2422.05-[Reserved] 

 2422.06-Requirement for Statement Regarding Information Contained in the “Sequence Listing” and Separate Computer Readable Form 

 2422.07-Requirements for Compliance and Consequences of Non-Compliance 

 2422.08-Presumptions Regarding Compliance 

 2422.09-[Reserved] 

 
 

 2423-Symbols and Format To Be Used for Nucleotide and/or Amino Acid Sequence Data for WIPO ST.25 
 2423.01-Format and Symbols To Be Used in a “Sequence Listing” 

 2423.02-Depiction of Coding Regions 

 2423.03-Presentation and Numbering of Sequences 

 
 

 2424-Requirements for Content of a “Sequence Listing” Part of the Specification under WIPO ST.25. 
 2424.01-Informational Requirements for the “Sequence Listing” 

 2424.02-“Sequence Listing” Numeric Identifiers 

 2424.03-Additional Miscellaneous Requirements 

 
 

 2425-Form and Format for a Nucleotide and/or Amino Acid Sequence Submission as an ASCII Plain Text File under WIPO ST.25 

 2426-Amendments to Add or Replace a “Sequence Listing” and CRF Copy Thereof Subject to WIPO ST. 25 

 2427-Form Paragraphs for Applications Subject to WIPO ST.25 

 2428-Sample Statements under WIPO ST.25 

 2429-Helpful Hints for Sequence Rules Compliance under WIPO ST.25 

 2430-PatentIn Information 

 2431-Sample “Sequence Listing” under WIPO ST.25 

 2432-[Reserved] 

 2433-Box Sequence; Hand Delivery of a “Sequence Listing” and Computer Readable Forms 

 2434-Examination of Patent Applications Claiming Large Numbers of Nucleotide Sequences 

 2435-Publishing of Patents and Patent Application Publications with a Lengthy “Sequence Listing” 

 

 

 
 

 
 
 

 
 

 

 
 
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 Last Modified: 
 
 03/09/2026 20:50:46