MPEP § 2412.04 — Use of Sequence Identifiers to Denote Sequences Disclosed in the Description, Drawings or Claims (Annotated Rules)

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

USPTO MPEP version: BlueIron's Update: 2025-12-31

This page consolidates and annotates all enforceable requirements under MPEP § 2412.04, including statutory authority, regulatory rules, examiner guidance, and practice notes. It is provided as guidance, with links to the ground truth sources. This is information only, it is not legal advice.

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

This section addresses Use of Sequence Identifiers to Denote Sequences Disclosed in the Description, Drawings or Claims. Primary authority: 35 U.S.C. 112, 35 U.S.C. 112(a), and 35 U.S.C. 112(b). Contains: 2 requirements, 1 guidance statement, 3 permissions, and 4 other statements.

Key Rules

Topic

Sequence Listing Content

5 rules
StatutoryInformativeAlways
[mpep-2412-04-9fbb80fe1f327982a41be134]
Requirement for Nucleotide and Amino Acid Sequence Disclosure
Note:
This rule requires the disclosure of nucleotide and amino acid sequences in applications filed on or after July 1, 2022.

[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b). Formatting representations of XML (eXtensible Markup Language) elements in this section appear different than shown in Standard ST.26, which may be accessed at: www.wipo.int /export/sites/www/ standards/en/pdf/03-26-01.pdf.]

37 CFR 1.77 · 37 CFR 1.831(b)Sequence Listing ContentSequence Listing RequirementsSequence Listing Format
StatutoryRequiredAlways
[mpep-2412-04-e3835251aaab1e13aebe56e8]
Patent Description Must Use Sequence Identifiers
Note:
The description and claims of a patent application must reference sequences listed in the 'Sequence Listing XML' using ‘SEQ ID NO:’ identifiers, even if the sequence is embedded in the text.

(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. *****

Jump to MPEP Source · 37 CFR 1.832(a)Sequence Listing ContentSequence Listing FormatSequence Listing Requirements
StatutoryRequiredAlways
[mpep-2412-04-a059786b4e957277d28378fa]
Requirement for Identifying Sequences in Drawings
Note:
When a sequence is presented in a drawing, it must be referenced using its sequence identifier (SEQ ID NO) either in the drawing or in the Brief Description of the Drawings.

(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. *****

Jump to MPEP Source · 37 CFR 1.832(a)Sequence Listing ContentSequence Listing FormatSequence Listing Requirements
StatutoryRequiredAlways
[mpep-2412-04-d0df5e0b874424c1bfcc65a5]
Sequence Identifiers Must Be Used for Nucleotide and Amino Acid Sequences in Description and Claims
Note:
Each nucleotide and amino acid sequence must be referenced by a sequence identifier preceded by 'SEQ ID NO:' when it appears in the description or claims.

37 CFR 1.831(c) requires that each nucleotide and/or amino acid sequence set forth in a “Sequence Listing XML” in accordance with 37 CFR § 1.831(a) must be referenced by a sequence identifier as defined in 37 CFR 1.832(a) (see MPEP § 2412.05(a)), preceded by the notation “SEQ ID NO:” or the like, when the sequence appears in the description or claims. Additionally, where a sequence set forth in a “Sequence Listing XML” is presented in a drawing, reference must be made using the sequence identifier preceded by the notation “SEQ ID NO:” or the like, either in the drawing or in the Brief Description of the Drawings. The sequence identifiers in the disclosure must correspond to sequence identifiers set forth in the “Sequence Listing XML” as defined in 37 CFR 1.832(a).

Jump to MPEP Source · 37 CFR 1.831(c)Sequence Listing ContentSequence Listing FormatSequence Listing Requirements
StatutoryInformativeAlways
[mpep-2412-04-fc40765bfc5062cf2608d47d]
Sequence Identifiers Do Not Alter 112 Requirements
Note:
This rule confirms that sequence identifiers in patent applications do not change the disclosure and claiming requirements under 35 U.S.C. 112.

37 CFR 1.831(c) does not alter, in any way, the requirements of 35 U.S.C. 112. The implementation of this rule has had no effect on disclosure and/or claiming requirements. 37 CFR 1.831 – 1.835, in general, or the use of sequence identifiers throughout the specification and claims, specifically, should not raise any issues under 35 U.S.C. 112(a) or 35 U.S.C. 112(b) because the of sequence identifiers (preceded by “SEQ ID NO: or the like”) only provides a shorthand way for applicants to discuss and claim their inventions. These identifiers do not in any way restrict the manner in which an invention can be claimed.

Jump to MPEP Source · 37 CFR 1.831(c)Sequence Listing ContentSequence Listing RequirementsOptional Claim Content
Topic

Sequence Listing Format

4 rules
StatutoryPermittedAlways
[mpep-2412-04-2a93ddde3365f644dbcf0be5]
XML Elements Must Follow Specific Format
Note:
The rule requires that XML elements in sequence listings must adhere to a specific format as defined by Standard ST.26.

[Editor Note: This section is applicable to all applications with a filing date, or, for national phase applications, an international filing date, on or after July 1, 2022, having disclosure of one or more nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b). Formatting representations of XML (eXtensible Markup Language) elements in this section appear different than shown in Standard ST.26, which may be accessed at: www.wipo.int /export/sites/www/ standards/en/pdf/03-26-01.pdf.]

37 CFR 1.77 · 37 CFR 1.831(b)Sequence Listing FormatSequence Listing RequirementsSequence Listing Content
StatutoryRequiredAlways
[mpep-2412-04-d499bf0b9a42fb27454780a3]
Sequence Identifiers Must Match Listing XML
Note:
The sequence identifiers in the patent application must correspond to those listed in the Sequence Listing XML as defined by 37 CFR 1.832(a).

37 CFR 1.831(c) requires that each nucleotide and/or amino acid sequence set forth in a “Sequence Listing XML” in accordance with 37 CFR § 1.831(a) must be referenced by a sequence identifier as defined in 37 CFR 1.832(a) (see MPEP § 2412.05(a)), preceded by the notation “SEQ ID NO:” or the like, when the sequence appears in the description or claims. Additionally, where a sequence set forth in a “Sequence Listing XML” is presented in a drawing, reference must be made using the sequence identifier preceded by the notation “SEQ ID NO:” or the like, either in the drawing or in the Brief Description of the Drawings. The sequence identifiers in the disclosure must correspond to sequence identifiers set forth in the “Sequence Listing XML” as defined in 37 CFR 1.832(a).

Jump to MPEP Source · 37 CFR 1.831(c)Sequence Listing FormatSequence Listing RequirementsSequence Listing Content
StatutoryInformativeAlways
[mpep-2412-04-6d0e141c8d302b99a57abdf2]
Use of Sequence Identifiers for Describing Sequences
Note:
Permits referencing sequences in the application using assigned identifiers without enumerating them.

37 CFR 1.831(c) is also intended to permit references in the application (e.g., specification, claims, or drawings) to sequences set forth in the “Sequence Listing XML” by the use of assigned sequence identifiers without enumerating the sequence. Sequence identifiers can also be used to discuss and/or claim parts or fragments of a properly presented sequence. For example, language such as “residues 14 to 243 of SEQ ID NO:23” is permissible and the fragment need not be separately presented in the “Sequence Listing XML.”

Jump to MPEP Source · 37 CFR 1.831(c)Sequence Listing FormatSequence Listing RequirementsSequence Listing Content
StatutoryPermittedAlways
[mpep-2412-04-7c24ae46a7631ca5b8ec4132]
Sequence Identifiers Can Denote Sequence Fragments
Note:
Permits using sequence identifiers to refer to parts of disclosed sequences without separately presenting them.

37 CFR 1.831(c) is also intended to permit references in the application (e.g., specification, claims, or drawings) to sequences set forth in the “Sequence Listing XML” by the use of assigned sequence identifiers without enumerating the sequence. Sequence identifiers can also be used to discuss and/or claim parts or fragments of a properly presented sequence. For example, language such as “residues 14 to 243 of SEQ ID NO:23” is permissible and the fragment need not be separately presented in the “Sequence Listing XML.”

Jump to MPEP Source · 37 CFR 1.831(c)Sequence Listing FormatSequence Listing RequirementsSequence Listing Content
Topic

Claims

2 rules
StatutoryInformativeAlways
[mpep-2412-04-f8493399e2c8c28cfa55a70f]
No Effect on Disclosure and Claiming Requirements
Note:
The rule does not alter the disclosure and claiming requirements for patent applications with sequence identifiers.

37 CFR 1.831(c) does not alter, in any way, the requirements of 35 U.S.C. 112. The implementation of this rule has had no effect on disclosure and/or claiming requirements. 37 CFR 1.831 – 1.835, in general, or the use of sequence identifiers throughout the specification and claims, specifically, should not raise any issues under 35 U.S.C. 112(a) or 35 U.S.C. 112(b) because the of sequence identifiers (preceded by “SEQ ID NO: or the like”) only provides a shorthand way for applicants to discuss and claim their inventions. These identifiers do not in any way restrict the manner in which an invention can be claimed.

Jump to MPEP Source · 37 CFR 1.831(c)Sequence Listing ContentSequence Listing Requirements
StatutoryRecommendedAlways
[mpep-2412-04-0cbc16722905dd9bbd2a3404]
Use of Sequence Identifiers Does Not Raise Claim Issues
Note:
The use of sequence identifiers (e.g., SEQ ID NO:) in the specification and claims does not raise issues under 35 U.S.C. 112(a) or 112(b) as they provide a shorthand for discussing inventions without restricting claim scope.

37 CFR 1.831(c) does not alter, in any way, the requirements of 35 U.S.C. 112. The implementation of this rule has had no effect on disclosure and/or claiming requirements. 37 CFR 1.831 – 1.835, in general, or the use of sequence identifiers throughout the specification and claims, specifically, should not raise any issues under 35 U.S.C. 112(a) or 35 U.S.C. 112(b) because the of sequence identifiers (preceded by “SEQ ID NO: or the like”) only provides a shorthand way for applicants to discuss and claim their inventions. These identifiers do not in any way restrict the manner in which an invention can be claimed.

Jump to MPEP Source · 37 CFR 1.831(c)Sequence Listing FormatPatent Application Content
Topic

Optional Claim Content

1 rules
StatutoryPermittedAlways
[mpep-2412-04-47b7e049fbe1f262aec98416]
Sequence Identifiers Do Not Restrict Claiming
Note:
These identifiers provide a shorthand for discussing and claiming inventions but do not limit the manner in which an invention can be claimed.

37 CFR 1.831(c) does not alter, in any way, the requirements of 35 U.S.C. 112. The implementation of this rule has had no effect on disclosure and/or claiming requirements. 37 CFR 1.831 – 1.835, in general, or the use of sequence identifiers throughout the specification and claims, specifically, should not raise any issues under 35 U.S.C. 112(a) or 35 U.S.C. 112(b) because the of sequence identifiers (preceded by “SEQ ID NO: or the like”) only provides a shorthand way for applicants to discuss and claim their inventions. These identifiers do not in any way restrict the manner in which an invention can be claimed.

Jump to MPEP Source · 37 CFR 1.831(c)Optional Claim ContentSequence Listing Content

Citations

Primary topicCitation
Claims
Optional Claim Content
Sequence Listing Content
35 U.S.C. § 112
Claims
Optional Claim Content
Sequence Listing Content
35 U.S.C. § 112(a)
Claims
Optional Claim Content
Sequence Listing Content
35 U.S.C. § 112(b)
Claims
Optional Claim Content
Sequence Listing Content
37 CFR § 1.831
Sequence Listing Content
Sequence Listing Format
37 CFR § 1.831(a)
Sequence Listing Content
Sequence Listing Format
37 CFR § 1.831(b)
Claims
Optional Claim Content
Sequence Listing Content
Sequence Listing Format
37 CFR § 1.831(c)
Sequence Listing Content
Sequence Listing Format
37 CFR § 1.832(a)
Sequence Listing Content
Sequence Listing Format
MPEP § 2412.05(a)

Source Text from USPTO’s MPEP

This is an exact copy of the MPEP from the USPTO. It is here for your reference to see the section in context.

BlueIron Last Updated: 2025-12-31