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
Standard adopted by the PCIPI Executive Coordination Committee
at its twenty-second session on May 28, 1998

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, 1998, the national law and practice applicable by an Office is not compatible with the provisions of the first two
sentences of paragraph 3 of the “Standard for the Presentation of Nucleotide and Amino Acid Sequence Listings in
International Patent Applications Under the Patent Cooperation Treaty (PCT),” that Office may choose not to follow those
provisions for as long as that incompatibility continues.

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Ref.: Standards – ST.25

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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 part of the description of the application as filed or a document
filed subsequently to the application, which gives a detailed disclosure of the nucleotide and/or amino acid sequences
and other available information;
(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 post-translationally 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 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)
in the listing;
(vi)

“sequence identifier” is a unique integer that corresponds to the SEQ ID NO assigned to each sequence
“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 controlledvocabulary 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
on the international application, or the International Preliminary Examining Authority that is to carry out the international
preliminary examination on the international application, or the designated/elected Office before which the processing of
the international application has started.

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Ref.: Standards – ST.25

page: 3.25.3

SEQUENCE LISTING
3.
The sequence listing as defined in paragraph 2(i) shall, where it is filed together with the application, be placed at
the end of the application. This part shall be entitled “Sequence Listing,” begin on a new page and preferably have
independent page numbering. The sequence listing forms an integral part of the description; it is therefore
unnecessary, subject to paragraph 36, to describe the sequences elsewhere in the description.
4.
Where the sequence listing as defined in paragraph 2(i) is not contained in the application as filed but is a
separate document furnished subsequently to the filing of the application (see paragraph 37), it shall be entitled
“Sequence Listing” and shall have independent page numbering. The original numbering of the sequences (see
paragraph 5) in the application as filed shall be maintained in the subsequently furnished sequence listing.
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 non-coding 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).

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Ref.: Standards – ST.25

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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 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.

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Ref.: Standards – ST.25

page: 3.25.5

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 filed at the same
time as the application to which it pertains or at any time prior to the assignment of an application number, the following
data element shall be included in the sequence listing:
<130>

File reference

27.
In addition to the data elements identified in paragraph 25, above, when a sequence listing is filed in response to
a request from a competent Authority or at any time following the assignment of an application number, the following
data elements shall be included in the sequence listing:
<140>
<141>

Current patent application
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>
<151>

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Earlier patent application
Earlier application filing date

Date: November 1998

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Ref.: Standards – ST.25

page: 3.25.6

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.(1)
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 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.

36.
Where the sequence listing part of the description 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.”
SUBSEQUENTLY FURNISHED SEQUENCE LISTING
37.
Any sequence listing which is not contained in the application as filed but which is furnished subsequently shall
not go beyond the disclosure in the application as filed and shall be accompanied by a statement to that effect. This
means that a sequence listing furnished subsequently to the filing of the application shall contain only those sequences
that were disclosed in the application as filed.
38.
Any sequence listing not contained in the application as filed does not form part of the application. However, the
provisions of PCT Rules 13ter, 26.3 and 91 and PCT Article 34 would apply, so that it may be possible, subject to the
applicable provisions, for a sequence listing contained in the application as filed to be corrected under PCT Rules 13ter
or 26.3, rectified under PCT Rule 91 (in the case of an obvious error), or amended under PCT Article 34, or for a
sequence listing to be submitted under PCT Article 34 as an amendment to the application.

(1)

These tables contain extracts of the DDBJ/EMBL/GenBank Feature Table (nucleotide sequences) and the SWISS PROT
Feature Table (amino acid sequences).

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Ref.: Standards – ST.25

page: 3.25.7

COMPUTER READABLE FORM OF THE SEQUENCE LISTING
39.
A copy of the sequence listing shall also be submitted in computer readable form, in addition to the sequence
listing as contained in the application, whenever this is required by the competent Authority.
40.
Any sequence listing in computer readable form submitted in addition to the written sequence listing shall be
identical to the written sequence listing and shall be accompanied by a statement that “the information recorded in
computer readable form is identical to the written sequence listing.”
41.
The entire printable copy of the sequence listing shall be contained within one electronic file preferably on a
single diskette or any other electronic medium that is acceptable to the competent Authority. The file recorded on the
diskette or any other electronic medium that is acceptable to the competent Authority shall be encoded using IBM(2)
Code Page 437, IBM Code Page 932(3) or a compatible code page. 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.
42.
The computer readable form shall preferably be created by dedicated software such as PatentIn or other custom
computer programs; it may be created by any means, as long as the sequence listing on a submitted diskette or any
other electronic medium that is acceptable to the competent Authority is readable under a Personal Computer Operating
system that is acceptable to the competent Authority.
43.
File compression is acceptable when using diskette media, so long as the compressed file is in a self-extracting
format that will decompress on a Personal Computer Operating system that is acceptable to the competent Authority.
44.
The diskette or any other electronic medium that is acceptable to the competent Authority shall have a label
permanently affixed thereto on which has been hand-printed, in block capitals or typed, the name of the applicant, the
title of the invention, a reference number, the date on which the data were recorded, the computer operating system and
the name of the competent Authority.
45.
If the diskette or any other electronic medium that is acceptable to the competent Authority is submitted after the
date of filing of an application, the labels shall also include the filing date of the application and the application number.
46.
Any correction of the written sequence listing which is submitted under PCT Rules 13ter.1(a)(i) or 26.3, any
rectification of an obvious error in the written sequence listing which is submitted under PCT Rule 91, or any amendment
which includes a written sequence listing and which is submitted under PCT Article 34, shall be accompanied by a
computer readable form of the sequence listing including any such correction, rectification or amendment.

[Appendices 1 to 3 follow]

(2)
(3)

IBM is a registered trademark of International Business Machine Corporation, United States of America.
The specified code pages are de facto standards for personal computers.

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Ref.: Standards – ST.25

page: 3.25.8

APPENDICES
Appendix 1:

Numeric Identifiers

Appendix 2:

Nucleotide and Amino Acid Symbols and Feature Table

Appendix 3:

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Table 1:

List of Nucleotides

Table 2:

List of Modified Nucleotides

Table 3:

List of Amino Acids

Table 4:

List of Modified and Unusual Amino Acids

Table 5:

List of Feature Keys Related to Nucleotide Sequences

Table 6:

List of Feature Keys Related to Protein Sequences

Specimen Sequence Listing

Date: November 1998

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Ref.: Standards – ST.25

page: 3.25.9

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

<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)

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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

Date: November 1998

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page: 3.25.10
Appendix 1, page 2

Numeric
Identifier

Numeric Identifier
Description

Mandatory (M) or
Optional (O)

<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)

<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

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Comment

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page: 3.25.11
Appendix 1, page 3

Numeric
Identifier

Numeric Identifier
Description

Mandatory (M) or
Optional (O)

Comment

<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

<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)

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page: 3.25.12
Appendix 1, page 4

Numeric
Identifier

Numeric Identifier
Description

Mandatory (M) or
Optional (O)

Comment

<310>

Document number

O

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

<311>

Filing date

O

document filing date, for patent-type
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 patenttype 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)

[Appendix 2 follows]

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page: 3.25.13

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: November 1998

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

page: 3.25.14
Appendix 2, page 2

Table 2: List of Modified Nucleotides
Symbol
ac4c
chm5u
cm
cmnm5s2u
cmnm5u
d
fm
gal q
gm
i
i6a
m1a
m1f
m1g
m1i
m22g
m2a
m2g
m3c
m5c
m6a
m7g
mam5u
mam5s2u
man q
mcm5s2u
mcm5u
mo5u
ms2i6a
ms2t6a
mt6a
mv
o5u
osyw
p
q
s2c
s2t
s2u
s4u
t
t6a
tm
um
yw
x
en / 03-25-01

Meaning
4-acetylcytidine
5-(carboxyhydroxymethyl)uridine
2’-O-methylcytidine
5-carboxymethylaminomethyl-2-thiouridine
5-carboxymethylaminomethyluridine
dihydrouridine
2’-O-methylpseudouridine
beta, D-galactosylqueuosine
2’-O-methylguanosine
inosine
N6-isopentenyladenosine
1-methyladenosine
1-methylpseudouridine
1-methylguanosine
1-methylinosine
2,2-dimethylguanosine
2-methyladenosine
2-methylguanosine
3-methylcytidine
5-methylcytidine
N6-methyladenosine
7-methylguanosine
5-methylaminomethyluridine
5-methoxyaminomethyl-2-thiouridine
beta, D-mannosylqueuosine
5-methoxycarbonylmethyl-2-thiouridine
5-methoxycarbonylmethyluridine
5-methoxyuridine
2-methylthio-N6-isopentenyladenosine
N-((9-beta-D-ribofuranosyl-2-methylthiopurine-6-yl)carbamoyl)threonine
N-((9-beta-D-ribofuranosylpurine-6-yl)N-methylcarbamoyl)threonine
uridine-5-oxyacetic acid-methylester
uridine-5-oxyacetic acid
wybutoxosine
pseudouridine
queuosine
2-thiocytidine
5-methyl-2-thiouridine
2-thiouridine
4-thiouridine
5-methyluridine
N-((9-beta-D-ribofuranosylpurine-6-yl)-carbamoyl)threonine
2’-O-methyl-5-methyluridine
2’-O-methyluridine
wybutosine
3-(3-amino-3-carboxy-propyl)uridine, (acp3)u
Date: November 1998

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

page: 3.25.15
Appendix 2, page 3

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: November 1998

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

page: 3.25.16
Appendix 2, page 4

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: November 1998

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

page: 3.25.17
Appendix 2, page 5

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: November 1998

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

page: 3.25.18
Appendix 2, page 6

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)

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

en / 03-25-01

Date: November 1998

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

page: 3.25.19
Appendix 2, page 7

Key

Description

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

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

en / 03-25-01

Date: November 1998

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

page: 3.25.20
Appendix 2, page 8

Key

Description

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: November 1998

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

page: 3.25.21
Appendix 2, page 9

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 alpha-carboxyl
group of the C-terminal residue of the mature form of a protein

N-ACYL DIGLYCERIDE

N-terminal cysteine of the mature form of a prokaryotic lipoprotein
with an amide-linked fatty acid and a glyceryl group to which two fatty
acids are linked by ester linkages

DISULFID

disulfide bond; the ‘FROM’ and ‘TO’ endpoints represent the two
residues which are linked by an intra-chain disulfide bond; if the
‘FROM’ and ‘TO’ endpoints are identical, the disulfide bond is an
interchain one and the description field indicates the nature of the
cross-link

THIOLEST

thiolester bond; the ‘FROM’ and ‘TO’ endpoints represent the two
residues which are linked by the thiolester bond

THIOETH

thioether bond; the ‘FROM’ and ‘TO’ endpoints represent the two
residues which are linked by the thioether bond

CARBOHYD

glycosylation site; the nature of the carbohydrate (if known) is given
in the description field

METAL

binding site for a metal ion; the description field indicates the nature
of the metal

en / 03-25-01

Date: November 1998

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

page: 3.25.22
Appendix 2, page 10

Key

Description

BINDING

binding site for any chemical group (co-enzyme, prosthetic group,
etc.); the chemical nature of the group is given in the description
field

SIGNAL

extent of a signal sequence (prepeptide)

TRANSIT

extent of a transit peptide (mitochondrial, chloroplastic, or for a
microbody)

PROPEP

extent of a propeptide

CHAIN

extent of a polypeptide chain in the mature protein

PEPTIDE

extent of a released active peptide

DOMAIN

extent of a domain of interest on the sequence; the nature of that
domain is given in the description field

CA_BIND

extent of a calcium-binding region

DNA_BIND

extent of a DNA-binding region

NP_BIND

extent of a nucleotide phosphate binding region; the nature of the
nucleotide phosphate is indicated in the description field

TRANSMEM

extent of a transmembrane region

ZN_FING

extent of a zinc finger region

SIMILAR

extent of a similarity with another protein sequence; precise
information, relative to that sequence is given in the description field

REPEAT

extent of an internal sequence repetition

HELIX

secondary structure: Helices, for example, Alpha-helix, 3(10) helix,
or Pi-helix

STRAND

secondary structure: Beta-strand, for example, Hydrogen bonded
beta-strand, or Residue in an isolated beta-bridge

TURN

secondary structure Turns, for example, H-bonded turn (3-turn,
4-turn or 5-turn)

ACT_SITE

amino acid(s) involved in the activity of an enzyme

SITE

any other interesting site on the sequence

INIT_MET

the sequence is known to start with an initiator methionine

NON_TER

the residue at an extremity of the sequence is not the terminal
residue; if applied to position 1, this signifies that the first position is
not the N-terminus of the complete molecule; if applied to the last
position, it signifies that this position is not the C-terminus of the
complete molecule; there is no description field for this key

NON_CONS

non consecutive residues; indicates that two residues in a sequence
are not consecutive and that there are a number of unsequenced
residues between them

UNSURE

uncertainties in the sequence; used to describe region(s) of a
sequence for which the authors are unsure about the sequence
assignment

[Appendix 3 follows]

en / 03-25-01

Date: November 1998

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

page: 3.25.23

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.

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

Doe, Richard
Isolation and Characterization of a Gene Encoding a Protease
from Paramecium sp.
Journal of Genes
1
4
1-7
1988-06-31
123456
1988-06-31

<400>
agctgtagtc

1
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

en / 03-25-01

Date: November 1998

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

page: 3.25.24
Appendix 3, page 1

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

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

389

2
37
PRT
Paramecium sp.

<400>
Met Val
1

2
Ser Met

Phe

Val

Cys

Leu

Gln

Pro
35

<210>
<211>
<212>
<213>
<220>
<223>
<400>
Met Val
1
<210>
<400>
000

Phe
5

Ser

Leu

Ser

Phe

Lys
10

Trp

Pro

Gly

Phe

Cys
15

Leu

Leu
20

Phe

Gln

Cys

Pro

Lys
25

Val

Leu

Pro

Cys

His
30

Ser

Ser

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 Leu

Glu
5

Pro

Met

His

Thr

Glu
10

Ile

4
4

[End of Appendix 3 and of Standard]

en / 03-25-01

Date: November 1998