WIPO Standard ST.25

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.1

STANDARD ST.25
STANDARD FOR THE PRESENTATION OF NUCLEOTIDE AND AMINO ACID
SEQUENCE LISTINGS IN PATENT APPLICATIONS
Revision adopted by the SCIT Standards and Documentation Working Group
at its eleventh session on October 30, 2009

It is recommended that Offices apply the provisions of the “Standard for the Presentation of Nucleotide and
Amino Acid Sequence Listings in International Patent Applications Under the Patent Cooperation Treaty (PCT)” as set
out in Annex C to the Administrative Instructions under the PCT, mutatis mutandis, to all patent applications other than
the PCT international applications, noting that certain provisions specific to PCT procedures and requirements may not
be applicable to patent applications other than PCT international applications (*) . The text of that PCT Standard is
reproduced on the following pages.

(*)

If, on July 1, 2009, the national law and practice applicable by an Office is not compatible with the provisions of
paragraph 3(i) of the “Standard for the Presentation of Nucleotide and Amino Acid Sequence Listings in International Patent
Applications Under the Patent Cooperation Treaty (PCT)” requiring that a sequence listing which is contained in the
international application as filed “shall be presented as a separate part of the description, be placed at the end of the
application, preferably be entitled ‘Sequence Listing’, begin on a new page and have independent page numbering”, that
Office may choose not to follow those provisions for as long as that incompatibility continues.

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.2

ANNEX C
STANDARD FOR THE PRESENTATION
OF NUCLEOTIDE AND AMINO ACID SEQUENCE LISTINGS
IN INTERNATIONAL PATENT APPLICATIONS UNDER THE PCT
INTRODUCTION
1. This Standard has been elaborated so as to provide standardization of the presentation of
nucleotide and amino acid sequence listings in international patent applications. The Standard is
intended to allow the applicant to draw up a single sequence listing which is acceptable to all receiving
Offices, International Searching and Preliminary Examining Authorities for the purposes of the
international phase, and to all designated and elected Offices for the purposes of the national phase. It
is intended to enhance the accuracy and quality of presentations of nucleotide and amino acid
sequences given in international applications, to make for easier presentation and dissemination of
sequences for the benefit of applicants, the public and examiners, to facilitate searching of sequence
data and to allow the exchange of sequence data in electronic form and the introduction of sequence
data onto computerized databases.
DEFINITIONS
2.

For the purposes of this Standard:
(i) the expression “sequence listing” means a nucleotide and/or amino acid sequence listing
which gives a detailed disclosure of the nucleotide and/or amino acid sequences and other available
information;
(i-bis) the expression “sequence listing forming part of the international application” means a
sequence listing contained in the international application as filed (as referred to in paragraph 3) or a
sequence listing included in the international application by way of a correction under Rule 26, a
rectification under Rule 91 or an amendment under Article 34(2)(b) of the description in relation to
sequences contained in the international application as filed (as referred to in paragraph 3bis);
(i-ter) the expression “sequence listing not forming part of the international application”
means a sequence listing which does not form part of the international application but is furnished for
the purposes of the international search or international preliminary examination (as referred to in
paragraphs 4 and 4bis);
(ii) sequences which are included are any unbranched sequences of four or more amino
acids or unbranched sequences of ten or more nucleotides. Branched sequences, sequences with fewer
than four specifically defined nucleotides or amino acids as well as sequences comprising nucleotides
or amino acids other than those listed in Appendix 2, Tables 1, 2, 3 and 4, are specifically excluded
from this definition;
(iii) “nucleotides” embrace only those nucleotides that can be represented using the symbols
set forth in Appendix 2, Table 1. Modifications, for example, methylated bases, may be described as
set forth in Appendix 2, Table 2, but shall not be shown explicitly in the nucleotide sequence;
(iv) “amino acids” are those L-amino acids commonly found in naturally occurring proteins
and are listed in Appendix 2, Table 3. Those amino acid sequences containing at least one D-amino
acid are not intended to be embraced by this definition. Any amino acid sequence that contains posttranslationally modified amino acids may be described as the amino acid sequence that is initially
translated using the symbols shown in Appendix 2, Table 3, with the modified positions, for example,
hydroxylations or glycosylations, being described as set forth in Appendix 2, Table 4, but these
en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.3

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 2, Table 3, in conjunction with a
description elsewhere to describe, for example, abnormal linkages, cross-links (for example, disulfide
bridge) and end caps, non-peptidyl bonds, etc., is embraced by this definition;
(v) “sequence identifier” is a unique integer that corresponds to the SEQ ID NO assigned to
each sequence in the listing;
(vi) “numeric identifier” is a three-digit number which represents a specific data element;
(vii) “language-neutral vocabulary” is a controlled vocabulary used in the sequence listing
that represents scientific terms as prescribed by sequence database providers (including scientific
names, qualifiers and their controlled-vocabulary values, the symbols appearing in Appendix 2, Tables
1, 2, 3 and 4, and the feature keys appearing in Appendix 2, Tables 5 and 6);
(viii) “competent Authority” is the International Searching Authority that is to carry out the
international search and to establish the written opinion of the International Searching Authority on
the international application, or the International Preliminary Examining Authority that is to carry out
the international preliminary examination on the international application.
SEQUENCE LISTINGS
Sequence Listing Forming Part of the International Application
3.

A sequence listing which is contained in the international application as filed:
(i) shall be presented as a separate part of the description, be placed at the end of the
application, preferably be entitled “Sequence Listing”, begin on a new page and have independent
page numbering 34 ; preferably, the sequence listing shall not be reproduced in any other part of the
application; subject to paragraph 36, it is unnecessary to describe the sequences elsewhere in the
description;
(ii) shall present the sequences represented in the sequence listing and other available
information in the sequence listing in accordance with paragraphs 5 to 35;
(iii) if contained in an international application filed in electronic form, shall be in an
electronic document format and filed by a means of transmittal in accordance with paragraph 37.
3bis. Any correction under Rule 26, rectification under Rule 91 or amendment under Article 34(2)(b)
of the description submitted in relation to sequences contained in an international application filed in
electronic form shall be submitted in the form of a sequence listing in electronic form comprising the
entire listing with the relevant correction, rectification or amendment. Any such sequence listing:
(i) shall preferably be entitled “Sequence Listing – Correction”, “Sequence Listing –
Rectification” or “Sequence Listing – Amendment”, as the case may be, and have independent page
numbering34;
(ii) shall present the sequences represented in the sequence listing and other available
information in the sequence listing in accordance with paragraphs 5 to 35; where applicable, the
original numbering of the sequences in the international application as filed (as referred to in
paragraph 5) shall be maintained; otherwise, the sequences shall be numbered in accordance with
paragraph 5;
(iii) shall be in an electronic document format and filed by a means of transmittal in
accordance with paragraph 38.
34

Editor’s Note: No independent page numbering is required where the sequence listing is contained in an international
application filed in electronic form and is in the electronic document format referred to in paragraph 40.

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.4

Sequence Listing Not Forming Part of the International Application
4. A sequence listing furnished under Rule 13ter for the purposes of the international search or
international preliminary examination:
(i) shall preferably be entitled “Sequence Listing – Rule 13ter”;
(ii) shall present the sequences represented in the sequence listing and other available
information in the sequence listing in accordance with paragraphs 5 to 35; where applicable, the
original numbering of the sequences in the international application as filed (as referred to in
paragraph 5) shall be maintained; otherwise, the sequences shall be numbered in accordance with
paragraph 5;
(iii) if furnished on paper in accordance with Rule 13ter.1(b), shall have independent page
numbering;
(iv) if furnished in electronic form, shall be in an electronic document format and filed by a
means of transmittal in accordance with paragraph 39;
(v) if furnished in electronic form together with the international application, shall be
identical to the sequence listing as contained in the application and be accompanied by a statement that
“the information recorded in electronic form furnished under Rule 13ter is identical to the sequence
listing as contained in the international application”;
(vi) if furnished subsequently to the filing of the international application, shall not go
beyond the disclosure in the international application as filed and be accompanied by a statement to
that effect; any such sequence listing shall contain only those sequences that were disclosed in the
international application as filed.
4bis. Any correction under Rule 26, rectification under Rule 91 or amendment under Article 34(2)(b)
of the description submitted in relation to sequences contained in the international application as filed
shall be accompanied, for the purposes of the international search or international preliminary
examination, by a sequence listing in electronic form in an electronic document format in accordance
with paragraph 39, comprising the entire listing including any such correction, rectification or
amendment, whenever this is required by the competent authority, unless such listing in electronic
form is already available to that authority in a form and manner acceptable to it. Any such sequence
listing in electronic form:
(i) shall preferably be entitled “Sequence Listing – Correction – Rule 13ter”, “Sequence
Listing – Rectification – Rule 13ter” or “Sequence Listing – Amendment – Rule 13ter”,
as the case may be;
(ii) shall present the sequences represented in the sequence listing and other available
information in the sequence listing in accordance with paragraphs 5 to 35; where
applicable, the original numbering of the sequences in the international application as
filed (as referred to in paragraph 5) shall be maintained; otherwise, the sequences shall
be numbered in accordance with paragraph 5;
(iii) shall be filed by a means of transmittal in accordance with paragraph 39;
(iv) shall be identical to the sequence listing submitted under paragraph 3bis as a correction
under Rule 26, rectification under Rule 91 or amendment under Article 34(2)(b) of the
description and be accompanied by a statement that “the information recorded in
electronic form furnished under Rule 13ter is identical to the sequence listing furnished
as a correction under Rule 26 (or a rectification under Rule 91 or an amendment under
Article 34(2)(b), as the case may be) of the description in relation to sequences
contained in the international application as filed”.

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.5

Where such sequence listing in electronic form and, where applicable, such statement is not available
to the competent authority, any such correction, rectification or amendment need only be taken into
account by that authority for the purposes of the international search or preliminary examination to the
extent that a meaningful search or preliminary examination can be carried out without such sequence
listing in electronic form.
PRESENTATION OF SEQUENCES
5. Each sequence shall be assigned a separate sequence identifier. The sequence identifiers shall
begin with 1 and increase sequentially by integers. If no sequence is present for a sequence identifier,
the code 000 should appear under numeric identifier <400>, beginning on the next line following the
SEQ ID NO. The response for numeric identifier <160> shall include the total number of SEQ ID
NOs, whether followed by a sequence or by the code 000.
6. In the description, claims or drawings of the application, the sequences represented in the
sequence listing shall be referred to by the sequence identifier and preceded by “SEQ ID NO:”.
7. Nucleotide and amino acid sequences should be represented by at least one of the following three
possibilities:
(i) a pure nucleotide sequence;
(ii) a pure amino acid sequence;
(iii) a nucleotide sequence together with its corresponding amino acid sequence.
For those sequences disclosed in the format specified in option (iii), above, the amino acid sequence
must be disclosed separately in the sequence listing as a pure amino acid sequence with a separate
integer sequence identifier.
Nucleotide Sequences
Symbols to Be Used
8. A nucleotide sequence shall be presented only by a single strand, in the 5’-end to 3’-end direction
from left to right. The terms 3’ and 5’ shall not be represented in the sequence.
9. The bases of a nucleotide sequence shall be represented using the one-letter code for nucleotide
sequence characters. Only lower case letters in conformity with the list given in Appendix 2, Table 1,
shall be used.
10. Modified bases shall be represented as the corresponding unmodified bases or as “n” in the
sequence itself if the modified base is one of those listed in Appendix 2, Table 2, and the modification
shall be further described in the feature section of the sequence listing, using the codes given in
Appendix 2, Table 2. These codes may be used in the description or the feature section of the
sequence listing but not in the sequence itself (see also paragraph 32). The symbol “n” is the
equivalent of only one unknown or modified nucleotide.
Format to Be Used
11. A nucleotide sequence shall be listed with a maximum of 60 bases per line, with a space between
each group of 10 bases.
12. The bases of 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, should be grouped together and separated from adjacent groups by a space.
13. The bases of the coding parts of a nucleotide sequence shall be listed as triplets (codons).
en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.6

14. The enumeration of the nucleotide shall start at the first base of the sequence with number 1. It
shall be continuous through the whole sequence in the direction 5’ to 3’. It shall be marked 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. The enumeration method for nucleotide sequences set forth above remains
applicable to nucleotide sequences that are circular in configuration, with the exception that the
designation of the first nucleotide of the sequence may be made at the option of the applicant.
15. A nucleotide sequence that is made up of one or more non-contiguous segments of a larger
sequence or of segments from different sequences shall be numbered as a separate sequence, with a
separate sequence identifier. A sequence with a gap or gaps shall be numbered as a plurality of
separate sequences with separate sequence identifiers, with the number of separate sequences being
equal in number to the number of continuous strings of sequence data.
Amino Acid Sequences
Symbols to Be Used
16. The amino acids in a protein or peptide sequence shall be listed in the amino to carboxy direction
from left to right. The amino and carboxy groups shall not be represented in the sequence.
17. The amino acids shall be represented using the three-letter code with the first letter as a capital
and shall conform to the list given in Appendix 2, Table 3. An amino acid sequence that contains a
blank or internal terminator symbols (for example, “Ter” or “*” or “.”) may not be represented as a
single amino acid sequence, but shall be presented as separate amino acid sequences (see
paragraph 22).
18. Modified and unusual amino acids shall be represented as the corresponding unmodified amino
acids or as “Xaa” in the sequence itself if the modified amino acid is one of those listed in Appendix 2,
Table 4, and the modification shall be further described in the feature section of the sequence listing,
using the codes given in Appendix 2, Table 4. These codes may be used in the description or the
feature section of the sequence listing but not in the sequence itself (see also paragraph 32). The
symbol “Xaa” is the equivalent of only one unknown or modified amino acid.
Format to Be Used
19. 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.
20. Amino acids corresponding to the codons in the coding parts of a nucleotide sequence shall be
placed immediately under the corresponding codons. Where a codon is split by an intron, the amino
acid symbol should be given below the portion of the codon containing two nucleotides.
21. The enumeration of amino acids shall start at the first amino acid of the sequence, with number 1.
Optionally, the amino acids preceding the mature protein, for example pre-sequences, pro-sequences,
pre-pro-sequences and signal sequences, when present, may have negative numbers, counting
backwards starting with the amino acid next to number 1. Zero (0) is not used when the numbering of
amino acids uses negative numbers to distinguish the mature protein. It shall be marked under the
sequence every five amino acids. The enumeration method for amino acid sequences set forth above
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.
22. An amino acid sequence that is made up of one or more non-contiguous segments of a larger
sequence or of segments from different sequences shall be numbered as a separate sequence, with a
separate sequence identifier. A sequence with a gap or gaps shall be numbered as a plurality of
en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.7

separate sequences with separate sequence identifiers, with the number of separate sequences being
equal in number to the number of continuous strings of sequence data.
OTHER AVAILABLE INFORMATION IN THE SEQUENCE LISTING
23. The order of the items of information in the sequence listings shall follow the order in which
those items are listed in the list of numeric identifiers of data elements as defined in Appendix 1.
24. Only numeric identifiers of data elements as defined in Appendix 1 shall be used for the
presentation of the items of information in the sequence listing. The corresponding numeric identifier
descriptions shall not be used. The provided information shall follow immediately after the numeric
identifier while only those numeric identifiers for which information is given need appear on the
sequence listing. Two exceptions to this requirement are numeric identifiers <220> and <300>, which
serve as headers for “Feature” and “Publication Information,” respectively, and are associated with
information in numeric identifiers <221> to <223> and <301> to <313>, respectively. When feature
and publication information is provided in the sequence listing under those numeric identifiers,
numeric identifiers <220> and <300>, respectively, should be included, but left blank. Generally, a
blank line shall be inserted between numeric identifiers when the digit in the first or second position of
the numeric identifier changes. An exception to this general rule is that no blank line should appear
preceding numeric identifier <310>. Additionally, a blank line shall precede any repeated numeric
identifier.
Mandatory Data Elements
25. The sequence listing shall include, in addition to and immediately preceding the actual nucleotide
and/or amino acid sequence, the following items of information defined in Appendix 1 (mandatory
data elements):
<110>

Applicant name

<120>

Title of invention

<160>

Number of SEQ ID NOs

<210>

SEQ ID NO: x

<211>

Length

<212>

Type

<213>

Organism

<400>

Sequence

Where the name of the applicant (numeric identifier <110>) is written in characters other than
those of the Latin alphabet, it shall also be indicated in characters of the Latin alphabet either as a
mere transliteration or through translation into English.
The data elements, except those under numeric identifiers <110>, <120> and <160>, shall be
repeated for each sequence included in the sequence listing. Only the data elements under numeric
identifiers <210> and <400> are mandatory if no sequence is present for a sequence identifier (see
paragraph 5, above, and SEQ ID NO: 4 in the example depicted in Appendix 3 of this Standard).
26. In addition to the data elements identified in paragraph 25, above, when a sequence listing is
furnished at any time prior to the assignment of an application number, the following data element
shall be included in the sequence listing:

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

<130>

page: 3.25.8

File reference

27. In addition to the data elements identified in paragraph 25, above, when a sequence listing is
furnished at any time following the assignment of an application number, the following data elements
shall be included in the sequence listing:
<140>

Current patent application

<141>

Current filing date

28. In addition to the data elements identified in paragraph 25, above, when a sequence listing is filed
relating to an application which claims the priority of an earlier application, the following data
elements shall be included in the sequence listing:
<150>

Earlier patent application

<151>

Earlier application filing date

29. If “n” or “Xaa” or a modified base or modified/unusual L-amino acid is used in the sequence, the
following data elements are mandatory:
<220>

Feature

<221>

Name/key

<222>

Location

<223>

Other information

30. If the organism (numeric identifier <213>) is “Artificial Sequence” or “Unknown,” the following
data elements are mandatory:
<220>

Feature

<223>

Other information

Optional Data Elements
31. All data elements defined in Appendix 1, not mentioned in paragraphs 25 to 30, above, are
optional (optional data elements).
Presentation of Features
32. When features of sequences are presented (that is, numeric identifier <220>), they shall be
described by the “feature keys” set out in Appendix 2, Tables 5 and 6. 35
Free Text
33. “Free text” is a wording describing characteristics of the sequence under numeric identifier <223>
(Other information) which does not use language-neutral vocabulary as referred to in paragraph 2(vii).
34. The use of free text shall be limited to a few short terms indispensable for the understanding of
the sequence. It shall not exceed four lines with a maximum of 65 characters per line for each given
35

Editor’s Note: These tables contain extracts from the DDBJ/EMBL/GenBank Feature Table (nucleotide sequences) and
the SWISS PROT Feature Table (amino acid sequences).

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.9

data element, when written in English. Any further information shall be included in the main part of
the description in the language thereof.
35. Any free text should preferably be in the English language.
REPETITION OF FREE TEXT IN MAIN PART OF DESCRIPTION
36. Where the sequence listing forming part of the international application contains free text, any
such free text shall be repeated in the main part of the description in the language thereof. It is
recommended that the free text in the language of the main part of the description be put in a specific
section of the description called “Sequence Listing Free Text”.
SEQUENCE LISTINGS IN ELECTRONIC FORM
37. Any sequence listing referred to in paragraph 3 contained in an international application filed in
electronic form shall be in an electronic document format and be filed by a means of transmittal that
has been specified by the receiving Office for the purposes of filing of international applications in
electronic form, provided that any such sequence listing shall preferably be in the electronic document
format specified in paragraph 40 and be filed, if possible, by a means of transmittal which has been
specified by both the receiving Office and the competent authority. 36 , 37

36

37

Editor’s Note: Where a sequence listing in electronic form complying with this Standard is not available to the
competent authority in a form and manner acceptable to it (that is, in particular, where it is not available to it in the
electronic document format specified in paragraph 40), the competent authority may invite the applicant to furnish to it
such a sequence listing in electronic form (see Rule 13ter).
Editor’s Note: Irrespective of the electronic document format of the sequence listing, the spatial relationship
(e.g., columns and rows) of the data elements included in the sequence listing and the format of the actual nucleotide
and/or amino acid sequences, as specified in this Annex, shall be maintained.

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.10

38. Any sequence listing in electronic form referred to in paragraph 3bis shall be in an electronic
document format that has been specified by the receiving Office (in the case of a correction) or by the
competent authority (in the case of a rectification or an amendment) for the purposes of filing of
international applications in electronic form, provided that any such listing shall preferably be in the
electronic document format specified in paragraph 40. Any such listing shall be filed by a means of
transmittal which has been specified by the receiving Office or the competent authority, as applicable,
for the purposes of this paragraph; if possible, it shall preferably be filed by a means of transmittal
which has been specified by both the receiving Office and the competent authority. 38
39. Any sequence listing in electronic form referred to in paragraphs 4 and 4bis furnished for the
purposes of the international search or international preliminary examination shall be in the electronic
document format specified in paragraph 40 and be filed by a means of transmittal which has been
specified by the competent authority for the purposes of this paragraph.
40. For the purposes of the international search and international preliminary examination, any
sequence listing in electronic form shall be contained within one electronic file encoded using IBM 39
Code Page 437, IBM Code Page 932 40 or a compatible code page to represent the sequence listing as
set out in paragraphs 5 to 36 with no other codes included. A compatible code page, as would be
required for, for example, Japanese, Chinese, Cyrillic, Arabic, Greek or Hebrew characters, is one that
assigns the Roman alphabet and numerals to the same hexadecimal positions as do the specified code
pages.
41. Any sequence listing in the electronic document format specified in paragraph 40 shall preferably
be created by dedicated software such as PatentIn.
PROCEDURE BEFORE DESIGNATED AND ELECTED OFFICES
42. For the purposes of the procedure before a designated or elected Office before which the
processing of an international application which contains the disclosure of one or more nucleotide
and/or amino acid sequences has started (see Rule 13ter.3):
(i) any reference to the receiving Office or the competent authority shall be construed as a
reference to the designated or elected Office concerned;
(ii) any reference to a sequence listing which is included in the international application by
way of a correction under Rule 26, a rectification under Rule 91 or an amendment under
Article 34(2)(b) of the description in relation to sequences contained in the application as filed shall be
construed to also include any sequence listing included in the application, under the national law
applied by the designated or elected Office concerned, by way of a correction (of a formality defect),
rectification (of an obvious mistake) or amendment of the description in relation to sequences
contained in the application as filed;

38

39
40

Editor’s Note: Where a replacement sequence listing in electronic form including any correction, rectification or
amendment is not available to the competent authority in a form and manner acceptable to it (that is, in particular, where
it is not available to it in the electronic document format specified in paragraph 40), any such correction, rectification or
amendment need only be taken into account by that authority for the purposes of the international search or preliminary
examination to the extent that a meaningful search or preliminary examination can be carried out without the
replacement sequence listing (see paragraph 4bis, above). See also Editor’s Note 38, which equally applies to any
replacement sequence listing in electronic form referred to in paragraph 3bis.
Editor’s Note: IBM is a registered trademark of International Business Machine Corporation, United States of America.
Editor’s Note: The specified code pages are de facto standards for personal computers.

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.11

(iii) any reference to a sequence listing furnished for the purposes of international search or
international preliminary examination shall be construed to also include any such listing furnished to
the designated or elected Office concerned for the purposes of national search or examination by that
Office;
(iv) the designated or elected Office concerned may invite the applicant to furnish to it,
within a time limit which shall be reasonable under the circumstances, for the purposes of national
search and/or examination, a sequence listing in electronic form complying with this Standard, unless
such listing in electronic form is already available to that Office in a form and manner acceptable to it.
Appendices
Appendix 1: Numeric Identifiers
Appendix 2: Nucleotide and Amino Acid Symbols and Feature Table
Table 1:
Table 2:
Table 3:
Table 4:
Table 5:
Table 6:

List of Nucleotides
List of Modified Nucleotides
List of Amino Acids
List of Modified and Unusual Amino Acids
List of Feature Keys Related to Nucleotide Sequences
List of Feature Keys Related to Protein Sequences

Appendix 3: Specimen Sequence Listing
[Appendices 1 to 3 to Annex C follow]

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.12

Annex C, Appendix 1
Numeric Identifiers
Only numeric identifiers as defined below may be used in sequence listings submitted in
applications. The text of the data element headings given below shall not be included in the
sequence listings.
Numeric identifiers of mandatory data elements, that is, data elements which must be included in
all sequence listings (see paragraph 25 of this Standard: items 110, 120, 160, 210, 211, 212, 213
and 400) and numeric identifiers of data elements which must be included in circumstances
specified in this Standard (see paragraphs 26, 27, 28, 29 and 30 of this Standard: items 130, 140,
141, 150 and 151, and 220 to 223) are marked by the symbol “M.”
Numeric identifiers of optional data elements (see paragraph 31 of this Standard) are marked by
the symbol “O.”

Numeric
Identifier

Numeric Identifier
Description

Mandatory (M) or
Optional (O)

Comment

<110>

Applicant name

M

where the name of the applicant is
written in characters other than
those of the Latin alphabet, the
same shall also be indicated in
characters of the Latin alphabet
either as a mere transliteration or
through translation into English

<120>

Title of invention

M

<130>

File reference

M,
in the circumstances
specified in
paragraph 26 of
this Standard

see paragraph 26 of this Standard

<140>

Current patent application

M,
in the circumstances
specified in
paragraph 27 of
this Standard

see paragraph 27 of this Standard;
the current patent application shall
be identified, in the following
order, by the two-letter code
indicated in accordance with WIPO
Standard ST.3 and the application
number (in the format used by the
industrial property Office with
which the current patent application
is filed) or, for an international
application, by the international
application number

<141>

Current filing date

M,
in the circumstances
specified in
paragraph 27 of
this Standard

see paragraph 27 of this Standard;
the date shall be indicated in
accordance with WIPO Standard
ST.2 (CCYY MM DD)

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.13

[Annex C, Appendix 1, continued]
Numeric
Identifier

Numeric Identifier
Description

Mandatory (M) or
Optional (O)

Comment

<150>

Earlier patent application

M,
in the circumstances
specified in
paragraph 28 of
this Standard

see paragraph 28 of this Standard;
the earlier patent application shall
be identified, in the following
order, by the two-letter code
indicated in accordance with WIPO
Standard ST.3 and the application
number (in the format used by the
industrial property Office with
which the earlier patent application
was filed) or, for an international
application, by the international
application number

<151>

Earlier application filing
date

M,
in the circumstances
specified in
paragraph 28 of
this Standard

see paragraph 28 of this Standard;
the date shall be indicated in
accordance with WIPO Standard
ST.2 (CCYY MM DD)

<160>

Number of SEQ ID NOs

M

<170>

Software

O

<210>

Information for
SEQ ID NO: x

M

response shall be an integer
representing the SEQ ID NO shown

<211>

Length

M

sequence length expressed in
number of base pairs or amino
acids

<212>

Type

M

type of molecule sequenced in SEQ
ID NO: x, either DNA, RNA or
PRT; if a nucleotide sequence
contains both DNA and RNA
fragments, the value shall be
“DNA”; in addition, the combined
DNA/RNA molecule shall be
further described in the <220> to
<223> feature section

<213>

Organism

M

Genus Species (that is, scientific
name) or “Artificial Sequence” or
“Unknown”

<220>

Feature

M,
in the circumstances
specified in
paragraph 29 and 30
of this Standard

leave blank; see paragraphs 29 and
30 of this Standard; description of
points of biological significance in
the sequence in SEQ ID NO: x)
(may be repeated depending on the
number of features indicated)

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.14

[Annex C, Appendix 1, continued]
<221>

Name/key

M,
in the circumstances
specified in
paragraph 29 of
this Standard

see paragraph 29 of this Standard;
only those keys as described in
Table 5 or 6 of Appendix 2 shall be
used

<222>

Location

M,
in the circumstances
specified in
paragraph 29 of
this Standard

see paragraph 29 of this Standard;
– from (number of first
base/amino acid in the feature)
– to (number of last base/amino
acid in the feature)
– base pairs (numbers refer to
positions of base pairs in a
nucleotide sequence)
– amino acids (numbers refer to
positions of amino acid residues
in an amino acid sequence)
– whether feature is located on the
complementary strand to that
filed in the sequence listing

<223>

Other information:

M,
in the circumstances
specified in
paragraphs 29 and 30
of this Standard

see paragraphs 29 and 30 of this
Standard; any other relevant
information, using language neutral
vocabulary, or free text (preferably
in English); any free text is to be
repeated in the main part of the
description in the language thereof
(see paragraph 36 of this Standard);
where any modified base or
modified/unusual L-amino acid
appearing in Appendix 2, Tables 2
and 4, is in the sequence, the
symbol associated with that base or
amino acid from Appendix 2,
Tables 2 and 4, should be used

<300>

Publication information

O

leave blank; repeat section for each
relevant publication

<301>

Authors

O

<302>

Title

O

title of publication

<303>

Journal

O

journal name in which data
published

<304>

Volume

O

journal volume in which data
published

<305>

Issue

O

journal issue number in which data
published

<306>

Pages

O

journal page numbers on which
data published

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.15

[Annex C, Appendix 1, continued]
<307>

Date

O

journal date on which data
published; if possible, the date
shall be indicated in accordance
with WIPO Standard ST.2 (CCYY
MM DD)

<308>

Database accession number

O

accession number assigned by
database including database name

<309>

Database entry date

O

date of entry in database; the date
shall be indicated in accordance
with WIPO Standard ST.2 (CCYY
MM DD)

<310>

Document number

O

document number, for patent type
citations only; the full document
shall specify, in the following
order, the two-letter code indicated
in accordance with WIPO Standard
ST.3, the publication number
indicated in accordance with WIPO
Standard ST.6, and the kind-ofdocument code indicated in
accordance with WIPO Standard
ST.16

<311>

Filing date

O

document filing date, for patenttype citations only; the date shall
be indicated in accordance with
WIPO Standard ST.2 (CCYY MM
DD)

<312>

Publication date

O

document publication date; for
patent-type citations only; the date
shall be indicated in accordance
with WIPO Standard ST.2 (CCYY
MM DD)

<313>

Relevant residues in
SEQ ID NO: x: from to

O

<400>

Sequence

M

SEQ ID NO: x should follow the
numeric identifier and should
appear on the line preceding the
sequence (see Appendix 3)

[Annex C, Appendix 2, follows]

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.16

Annex C, Appendix 2
Nucleotide and Amino Acid Symbols and Feature Table
Table 1: List of Nucleotides
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

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.17

[Annex C, Appendix 2, continued]
Table 2: 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

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.18

[Annex C, Appendix 2, continued]
Symbol

Meaning

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

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.19

[Annex C, Appendix 2, continued]
Table 3: 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

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.20

[Annex C, Appendix 2, continued]
Table 4: 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

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.21

[Annex C, Appendix 2, continued]
Table 5: 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 up-stream 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

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.22

[Annex C, Appendix 2, continued]
Key

Description

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 posttranscriptional 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)

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.23

[Annex C, Appendix 2, continued]
Key

Description

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 permissable

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

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.24

[Annex C, Appendix 2, continued]
Key

Description

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 [ ]

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.25

[Annex C, Appendix 2, continued]
Table 6: 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 alphacarboxyl 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

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.26

[Annex C, Appendix 2, continued]
Key

Description

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

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.27

[Annex C, Appendix 2, continued]
Key

Description

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

[Annex C, Appendix 3, follows]

en / 03-25-01

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.28

Annex C, Appendix 3
Specimen Sequence Listing
<110>

Smith, John;

<120>

Example of a Sequence Listing

<130>

01-00001

<140>
<141>

PCT/EP98/00001
1998-12-31

<150>
<151>

US 08/999,999
1997-10-15

<160>

4

<170>

PatentIn version 2.0

<210>
<211>
<212>
<213>

1
389
DNA
Paramecium sp.

<220>
<221>
<222>

CDS
(279)...(389)

<300>
<301>
<302>

Smithgene Inc.

Doe, Richard
Isolation and Characterization of a Gene Encoding a Protease
from Paramecium sp.

<303>
<304>
<305>
<306>
<307>
<308>
<309>

Journal of Genes
1
4
1-7
1988-06-31
123456
1988-06-31

<400>

1

agctgtagtc

attcctgtgt

cctcttctct

ctgggcttct

Caccctgcta

atcagatctc

60

agggagagtg

tcttgaccct

cctctgcctt

tgcagcttca

Caggcaggca

ggcaggcagc

120

tgatgtggca

attgctggca

gtgccacagg

cttttcagcc

Aggcttaggg

tgggttccgc

180

cgcggcgcgg

cggcccctct

cgcgctcctc

tcgcgcctct

Ctctcgctct

cctctcgctc

240

ggacctgatt

aggtgagcag

gaggaggggg

cagttagc

atg
Met
1

Gtt
Val

tca
Ser

atg
Met

ttc
Phe
5

agc
Ser

296

caa
Gln

344

ttg
Leu

tct
Ser

ttc
Phe

aaa
Lys
10

tgg
Trp

cct
Pro

gga
Gly

ttt
Phe

tgt
Cys
15

ttg
Leu

ttt
Phe

Gtt
Val

tgt
Cys

ttg
Leu
20

ttc
Phe

tgt
Cys

ccc
Pro

aaa
Lys
25

gtc
Val

ctc
Leu

ccc
Pro

tgt
Cys

cac
His
30

tca
Ser

tca
Ser

ctg
Leu

Cag
Gln

ccg
Pro
35

aat
Asn

ctt
Leu

en / 03-25-01

389

Date: December 2009

HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION
Ref.: Standards – ST.25

page: 3.25.29

[Annex C, Appendix 3, continued]
<210>
<211>
<212>
<213>

2
37
PRT
Paramecium sp.

<400>
Met Val
1

2
Ser

Phe

Val

Leu

Gln

<210>
<211>
<212>
<213>
<220>
<223>
<400>
Met Val
1

Met

Phe
5

Ser

Leu

Ser

Phe

Lys
10

Trp

Pro

Gly

Phe

Cys
15

Leu

Cys

Leu
20

Phe

Gln

Cys

Pro

Lys
25

Val

Leu

Pro

Cys

His
30

Ser

Ser

Pro
35

Asn

Leu

3
11
PRT
Artificial Sequence
Designed peptide based on size and polarity to act as a linker
between the alpha and beta chains of Protein XYZ.
3
Asn

<210>

4

<400>

4

Leu

Glu
5

Pro

Met

His

Thr

Glu
10

Ile

000

[End of Appendix 3 and of Standard]

en / 03-25-01

Date: December 2009