37 CFR § 1.822 — Symbols and format to be used for nucleotide (MPEP Coverage Index) – BlueIron IP
37 CFR § 1.822 Symbols and format to be used for nucleotide
This page consolidates MPEP guidance interpreting 37 CFR § 1.822, including 86 rules from the Manual of Patent Examining Procedure. It is provided as guidance, with links to the ground truth sources. This is information only, it is not legal advice.
Summary
This section outlines the requirements for nucleotide sequence listings in patent applications, including the use of standardized symbols and formats, and the submission of a separate computer readable form (CRF).
What this section covers
- Defines the scope of this section, which covers sequence listings and their computer readable form (CRF) requirements.
Key obligations
- Patent applications containing nucleotide sequences must include a separate computer readable form (CRF) of the sequence listing.
- The sequence listing must be a separate part of the patent application, as defined in paragraph (a) of this section.
Practice notes
- Draft the sequence listing using standardized symbols and formats as specified in this section to avoid common pitfalls.
- Ensure all required sequence information is included and use non-standard symbols in the sequence listing to avoid rejection.
Official MPEP § 1.822 — Symbols and format to be used for nucleotide
Source: USPTOLast Modified: 10/30/2024 08:50:22
1.822 Symbols and format to be used for nucleotide and/or amino acid sequence data.
[Editor Note: This rule is applicable to applications containing a nucleotide and/or amino acid sequence filed prior to July 1, 2022. See §§ 1.831 through 1.835 for rules applicable on or after July 1, 2022.]
- (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.
[Added, 55 FR 18230, May 1, 1990, effective Oct. 1, 1990; revised, 63 FR 29620, June 1, 1998, effective, July 1, 1998; para. (b) revised, 70 FR 10488, Mar. 4, 2005, effective Mar. 4, 2005; paras. (b), (c)(1), (3), (5) and (6), (d)(1) and (3) through (5) and (e) revised, para. (c) added note 2; para. (d) added note 3, 86 FR 57035, Oct. 14, 2021, effective Nov. 15, 2021]
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