GERMANY
Patent Regulations
Patent Ordinance of 1 September 2003 (Federal Law Gazette I p. 1702),
last amended by Article 2 of the Ordinance of 17 December 2004 (Federal
Law Gazette I p. 3532)
TABLE OF CONTENTS
Part I General Provisions
Section 1 Scope of application
Section 2 German industrial standards, measuring units, symbols and signs
Part II Patent Applications; Patent Procedures
Section 3 Filing of the application
Section 4 Request for the grant of a patent
Section 5 Application documents
Section 6 Formal requirements for a written application
Section 7 Naming the inventor
Section 8 Omission of the mention of the inventor; change of the mention
of the inventor
Section 9 Patent claims
Section 10 Description
Section 11 Presentation of nucleotide and amino acid sequences
Section 12 Drawings
Section 13 Abstract
Section 14 German translations
Part III Other Formal Requirements
Section 15 Subsequently filed application documents; changes in
application documents
Section 16 Models and samples
Section 17 Official certification of signatures
Section 18 (deleted)
Part IV Supplementary Protection Certificates
Section 19 Filing of the application
Section 20 Supplementary protection certificates for medicinal products
Section 21 Supplementary protection certificates for plant protection
products
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Part V Final Provisions and Transitory Provisions
Section 22 Transitory provisions
Section 23 Entry into force; abrogation
Annex 1 (resp. Sec. 11(1), second sentence) Standards for the Filing of
Sequence Listings
Annex 2 (resp. Sec. 12) Standards for the Filing of Drawings
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Part I General Provisions
Section 1 Scope of application
In addition to the provisions of the Patent Law and the Ordinance
Concerning the German Patent and Trade Mark Office, the provisions of
this ordinance shall apply to procedures before the German Patent and
Trade Mark Office, prescribed in the Patent Law.
Section 2 German industrial standards, measuring units, symbols and signs
(1) German industrial standards, referred to in this ordinance, have been
published by Beuth-Verlag GmbH, Berlin and Cologne, and securely stored
in an archive at the German Patent and Trade Mark Office in Munich.
(2) Measuring units shall be indicated in accordance with the Law on
Measuring Units and the corresponding implementing regulations in the
respective applicable versions. For chemical formulae the signs and
symbols recognised in national or international practice in the field
in question shall be used.
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Part II Patent Applications; Patent Procedures
Section 3 Filing of the application
(1) The application (Sec. 34 Patent Law) and the abstract (Sec. 36 Patent
Law) shall be filed in writing with the German Patent and Trade Mark Office.
Section 12 of the Ordinance Concerning the German Patent and Trade Mark
Office shall apply for electronic filing.
(2) In the cases of Sections 8, 14 to 21 the electronic form shall be
excluded.
Section 4 Request for the grant of a patent
(1) The request for the grant of a patent (Sec. 34(3) No. 2 Patent Law)
or for the grant of a patent of addition (Sec. 16 Patent Law) shall be
filed on the form issued by the German Patent and Trade Mark Office or
as an electronic file in accordance with the format requirements published
by the German Patent and Trade Mark Office.
(2) The request shall contain:
1. the following information on the applicant:
a) if the applicant is a natural person, given name and the family name
or, if registration is sought under the trade name, the trade name as
recorded in the Commercial Register;
b) if the applicant is a legal entity or a partnership, the name of this
entity or partnership; the usual abbreviation of the legal form can be
used. If the legal entity or partnership is registered in a register,
the name shall be indicated in a form corresponding to that of the register
entry. In case of a partnership under the Civil Code, the name and address
of at least one partner entitled to act as representative shall also be
indicated;
it shall be made clear whether the patent is sought on behalf of one or
more than one individual or partnership, or for the applicant under the
trade name or under the civil name;
c) the residence or principal place of business and the address (street
and house number, postal code, town);
2. a short and precise title of the invention;
3. a statement that the grant of a patent or patent of addition is requested
for the invention;
4. if a representative has been appointed, his name and his address;
5. the signatures of all applicants or their representative;
6. if a patent of addition is sought, the file number of the parent patent
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application or the number of the parent patent shall also be given.
(3) If the residence or principle place of business of the applicant is
not in Germany, the applicant shall also indicate the country in addition
to the town when indicating the address under subsection (2) No. 1 item
c). Furthermore, the applicant may also indicate the district, county
or state where he has his residence or principle place of business or
to whose legal order he is subject to.
(4) If the German Patent and Trade Mark Office has assigned an applicant’s
number to the applicant, this number should be indicated in the
application.
(5) If the German Patent and Trade Mark Office has assigned a
representative’s number or the number of a general power of attorney to
the representative, this number should be indicated.
(6) In the event of employees signing the request on behalf of their
employer who files an application, the authority to sign shall be proved
to the satisfaction of the office; reference shall be made to any
employee’s authority to sign, deposited with the German Patent and Trade
Mark Office, indicating the identification number communicated for this
purpose.
Section 5 Application documents
(1) The documents making up the application and the abstract shall not
contain any pictorial representation in the text matter. It may contain
chemical and mathematical formulae as well as tables. Fancy names, trade
marks or other designations which are not suited to clearly indicate the
nature of an object, shall not be used. If, in exceptional cases, an
indication can only be clearly denoted by using a trade mark, the said
designation shall make it clear that it is a trade mark.
(2) Technical terms and designations as well as reference signs shall
be used uniformly throughout the application unless the use of different
terms is adequate. With respect to technical terms and designations, the
same applies to applications of addition in relation to the parent
application.
Section 6 Formal requirements for a written application
(1) The documents making up the application shall be so presented as to
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admit of electronic data input. Extensive application documents
consisting of more than 300 pages shall also be furnished on two data
carriers each containing the application documents in machine-readable
form. The standards prescribed in annex 1 (resp. Sec. 11(1), second
sentence) No. 41 shall apply mutatis mutandis to the data carriers. A
declaration shall be attached to the data carriers, stating that the
information stored on the data carriers corresponds to the application
documents.
(2) The patent claims, the description, the drawings as well as the text
and the drawings of the abstract shall be filed on separate sheets in
three copies. The size of the sheets shall be A4 according to DIN 476
(German industrial standard) and be used in upright position. For the
drawings, the sheets may, if appropriate, be used sideways; in this case,
the top of the figures shall be presented at the left side of the sheet
in an upright position. This shall apply mutatis mutandis to the
representation of chemical and mathematical formulae and tables. All
sheets shall be free from creases, tears and folds. The paper of the sheets
shall be non-transparent, pliable, strong, smooth, matt and durable.
(3) Only one side of the sheets shall be typed or printed or contain
drawings. The sheets shall be connected in such a way that they can be
easily separated and joined together again. Each of the documents making
up the application (request form, patent claims, description, drawings)
and the abstract (text matter, drawings) shall commence on a new sheet.
The sheets of the description shall be numbered in consecutive Arabic
numerals. These numbers shall be placed below the top margin of the sheet,
in the middle. The lines and paragraphs should not be numbered nor any
other numbering be applied.
(4) The margins of the sheets containing the request, the patent claims,
the description and the abstract must be blank. The minimum margins shall
be as follows:
top 2.0 cm
left side 2.5 cm
right side 2.0 cm
bottom 2.0 cm
The minimum margins may contain the name, the trade name or other
designation of the applicant as well as the file number of the application.
(5) The request, the patent claims, the description and the abstract shall
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be typed or printed, using single-column formatting. The right margin
should not be justified. The letters of the type used shall be clearly
separated and must not touch. Graphic symbols and characters and chemical
or mathematical formulae may, if necessary, be written by hand or drawn.
The typing shall be 1 1/2 spaced. The text matter shall be in characters,
the capital letters of which are not less than 0.21 cm high (the minimum
font size shall be 10 point) and shall be in dark, indelible colour. The
typeface shall have sharp outlines and be high-contrast. Each sheet shall
be reasonably free from erasures, alterations, overwriting and
interlineations. If appropriate, non-compliance with this rule may be
authorised. The text shall not be underlined, italicised, bolted;
character spacing shall not be expanded.
(6) The documents making up an application shall clearly show to which
application they pertain.
Section 7 Naming the inventor
(1) The applicant shall indicate the inventor on the form issued by the
German Patent and Trade Mark Office or on an electronic file pursuant
to the formatting requirements published by the German Patent and Trade
Mark Office.
(2) This indication must contain:
1. the given name and family name, residence and the address (street and
house number, postal code, town, postal district, if any) of the inventor;
2. the affirmation of the applicant that to his knowledge no other person
has contributed to the invention (Sec. 37(1) Patent Law);
3. if the applicant is not the inventor or not the sole inventor, a
statement by the applicant on how he acquired the right to the patent
(Sec. 37(1), second sentence, Patent Law);
4. the title of the invention and the official file number, if already
known;
5. the signature of the applicant or his representative; if the patent
grant has been requested by several persons, each person or their
representative shall sign the declaration.
Section 8 Omission of the mention of the inventor; change of the mention
of the inventor
(1) The request by the inventor not to be mentioned as inventor, the
withdrawal of this request (Sec. 63(1), third and fourth sentences, Patent
Law) and the requests for correction or subsequent mention of the inventor
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(Sec. 63(2) Patent Law) shall be filed in writing. The documents shall
be signed by the inventor and shall contain the title of the invention
and the official file number.
(2) The consent to the correction or subsequent mention of the inventor
(Sec. 63(2) Patent Law) by the applicant or patentee and the person wrongly
mentioned shall be given in writing.
Section 9 Patent claims
(1) Patent claims shall contain what is to be protected by the patent
(Sec. 34(3) No. 3 of the Patent Law) and shall be drafted in one piece
or shall be divided into generic part and characterising portion
(two-piece). In both cases the version may be arranged according to
features.
(2) If the two-piece claim formulation is chosen, the known features of
the invention comprised in the state of the art shall be included in the
generic part; the characterising portion shall include the features of
the invention for which protection is sought in connection with the
features of the generic part. The characterising portion shall be preceded
by such words as “characterised in that” or “characterised by” or any
other expressions to this effect.
(3) If patent claims are arranged according to features or groups of
features, the said arrangement shall be set off by starting a new line
for each feature or group of features. The features or groups of features
shall be preceded by subdivision signs clearly set off against the text
matter.
(4) The essential features of the invention shall be indicated in the
first patent claim (principal claim).
(5) An application may contain several independent patent claims provided
the principle of unity of the invention is respected (Sec. 34(5) of the
Patent Law). Subsection (4) shall apply mutatis mutandis. Independent
claims may contain a reference to at least one of the preceding patent
claims.
(6) Any principal or independent patent claim, respectively, may be
followed by one or more dependent claims concerning particular
embodiments of the invention. Dependent claims shall contain a reference
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to at least one of the preceding patent claims. They shall be grouped
together to the extent and in the most appropriate way possible.
(7) If there are several patent claims, they shall be numbered
consecutively in Arabic numerals.
(8) Claims shall not, except where absolutely necessary, rely, in respect
of the technical features of the invention, on references to the
description or drawings. In particular, they shall not rely on such
references as: “as described in part ... of the description”, or “as
illustrated in figure ... of the drawings”.
(9) If the patent application contains drawings, the features mentioned
in the claims shall preferably be followed by reference signs, if the
intelligibility of the claim can thereby be increased.
(10) For electronic filing, an electronic file pursuant to the formatting
requirements published by the German Patent and Trade Mark Office shall
be used.
Section 10 Description
(1) The description according to Section 34(3) No. 4 of the Patent Law
shall first state the title of the invention as appearing in the request.
(2) Additionally, it shall:
1. specify the technical field to which the invention relates unless it
follows from the claims or the indications concerning the state of the
art;
2. indicate the state of the art known to the applicant which may be taken
into account for the understanding of the invention and its protectability
by indicating the sources known to the applicant;
3. describe the problem underlying the invention unless it follows from
the indicated solution or the indications made with regard to No. 6, in
particular, if it is indispensable for the understanding of the invention
or for specifying its contents more closely;
4. indicate the invention for which protection is sought in the patent
claims;
5. when it is not obvious from the description or the nature of the
invention, indicate at least one way in which the invention is capable
of exploitation in industry;
6. state any advantageous effects of the invention with reference to the
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background art;
7. describe in detail at least one way of carrying out the invention
claimed, using, where appropriate, examples or drawings, indicating the
respective reference signs.
(3) The description shall not include any indications obviously not
necessary in order to explain the invention. Repetitions of claims or
parts of claims may be replaced by corresponding references.
(4) For electronic filing, an electronic file pursuant to the formatting
requirements published by the German Patent and Trade Mark Office shall
be used.
Section 11 Presentation of nucleotide and amino acid sequences
(1) If structural formulae in form of nucleotide or amino acid sequences
are indicated and hence disclosed in concrete terms in the patent
application, a corresponding sequence listing shall be filed as annex
to the application, separately from the description and the claims. The
sequence listing shall comply with the standards for the filing of
sequence listings prescribed in annex 1.
(2) If the patent application is filed in writing, two data carriers each
containing the sequence listing in machine readable form shall be
submitted in addition to the written application documents. The data
carriers shall be clearly marked as data carriers for a sequence listing
and comply with the standards mentioned in subsection (1). The data
carriers shall be accompanied by a statement that the information recorded
on the data carriers is identical to the written sequence listing.
(3) If the sequence listing on the data carrier filed in the application
is corrected subsequently, the applicant shall submit a statement that
the corrected sequence listing does not include matter which goes beyond
the content of the application as filed. Subsections (1) and (2) shall
apply mutatis mutandis to the correction.
(4) In case of an application derived from an international patent
application under the Patent Cooperation Treaty in respect of which the
German Patent and Trade Mark Office is a designated or an elected office
(Art. III Sec. 4(1), Sec. 6(1) of the Law on International Patent Treaties
of 21 June 1976, Federal Law Gazette 1976 II p. 649), the rules of the
Regulations under the Patent Cooperation Treaty shall apply directly,
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insofar as they concern the standard for filing sequence listings.
(5) Electronic filing of the application by e-mail is possible only if
the application with the sequence listing does not exceed the file size
admissible for the transmission process.
Section 12 Drawings
Drawings furnished shall comply with the standards contained in annex
2.
Section 13 Abstract
(1) The abstract according to Section 36 of the Patent Law shall preferably
not consist of more than 1,500 characters.
(2) The abstract may also indicate the chemical formula which best
characterises the invention.
(3) Section 9(8) shall apply mutatis mutandis.
(4) For electronic filing, an electronic file pursuant to the formatting
requirements published by the German Patent and Trade Mark Office shall
be used.
Section 14 German translations
(1) German translations of documents forming part of the documentation
relating to the application shall be certified by an attorney-at-law or
patent attorney or be done by an officially authorised translator. The
translator’s signature shall be officially certified (Article 129 of the
Civil Code) and it shall also be certified that he is officially authorised
for such purposes.
(2) German translations of
1. priority documents submitted under the revised Paris Convention for
the Protection of Industrial Property (Federal Law Gazette 1970 II p.
391), or
2. copies of earlier applications (Sec. 41(1), first sentence, Patent
Law)
shall only be furnished upon invitation by the German Patent and Trade
Mark Office.
(3) German translations of documents
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1. not forming part of the documentation relating to the application and
2. filed in English, French, Italian or Spanish,
shall be subsequently furnished only upon invitation by the German Patent
and Trade Mark Office.
(4) If foreign-language documents not forming part of the documentation
relating to the application are filed in languages not mentioned in
subsection (3) No. 2, German translations shall be filed subsequently
within one month after receipt of the documents.
(5) The translation under subsection (3) or (4) shall be certified by
an attorney-at-law or patent attorney or done by an officially authorised
translator. If the translation is not filed in due time, the
foreign-language document is deemed to have been received on the date
of receipt of the translation.
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Part III Other Formal Requirements
Section 15 Subsequently filed application documents; changes in
application documents
(1) Any document filed after communication of the official file number
shall indicate the complete file number. If the application documents
are altered in the course of the procedure, the applicant shall submit
clean copies incorporating any changes. Two clean copies shall be filed.
Sec. 6(1) and Sec. 11(2) shall apply mutatis mutandis.
(2) If the applicant subsequently furnishes further copies of the
application documents, the documents shall be accompanied by a
declaration stating that the subsequently furnished documents correspond
to the documents as originally filed.
(3) Insofar as the changes have not been proposed by the German Patent
and Trade Mark Office, the applicant shall state in detail where the
features of the invention described in the new documents are disclosed
in the originally filed documents. In addition, the changes effected shall
be marked either in a copy of the changed documents, by separate
explanations, or in the clean copies. If the changes are marked in the
clean copies, they shall be in bold lettering.
(4) Insofar as the changes have been proposed by the German Patent and
Trade Mark Office and have been accepted by the applicant without further
changes, the applicant shall attach a declaration to the clean copies
mentioned in subsection (1), second and third sentences; this declaration
shall state that the clean copies do not contain any other changes than
the changes proposed by the German Patent and Trade Mark Office.
Section 16 Models and samples
(1) Models and samples shall only be supplied if the German Patent and
Trade Mark Office invites the applicant to do so. They shall bear durable
labels indicating the contents and the application to which they relate.
If necessary, clear reference shall be made to the patent claim and the
description.
(2) Fragile models and samples shall be submitted in sturdy containers
clearly so marked. Small articles hall be fastened on stiff paper.
(3) Samples of chemical materials shall be submitted in durable and firmly
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closed containers. If they are poisonous, corrosive or inflammable or
have other dangerous characteristics, they shall bear an indication to
this effect.
(4) Dyeing and tanning samples as well as other flat samples shall be
firmly fixed on stiff paper (size A4 according to DIN 476). They shall
be accompanied by a precise description of the process of manufacture
or use.
Section 17 Official certification of signatures
Upon invitation by the German Patent and Trade Mark Office the signatures
mentioned in Section 7(2) No. 5 and in Section 8 shall be officially
certified (Section 129 of the Civil Code).
Section 18 (deleted)
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Part IV Supplementary Protection Certificates
Section 19 Filing of the application
(1) The request for the grant of a supplementary protection certificate
(Sec. 49a Patent Law) shall be furnished on the form issued by the German
Patent and Trade Mark Office. Section 4(2) Nos. 1, 4 and 5, and Section
14(1), (3) to (5) shall apply mutatis mutandis.
(2) The request shall be accompanied by information setting forth the
protection afforded by the parent patent.
Section 20 Supplementary protection certificates for medicinal products
The request for the grant of a supplementary protection certificate for
medicinal products shall contain the information and documents specified
in Article 8 of the Council Regulation (EEC) No. 1768/92 of 18 June 1992
concerning the creation of a supplementary protection certificate for
medicinal products (OJ EC No. L 182 p. 1).
Section 21 Supplementary protection certificates for plant protection
products
The request for the grant of a supplementary protection certificate for
plant protection products shall contain the information and documents
specified in Article 8 of the Council Regulation (EC) No. 1610/96 of 23
July 1996 concerning the creation of a supplementary protection
certificate for plant protection products (OJ EC No. L 198 p. 30).
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Part V Final Provisions and Transitory Provisions
Section 22 Transitory provisions
For patent applications, the naming of the inventor and requests for the
grant of a supplementary protection certificate filed before the entry
into force of the amendments to this ordinance, the provisions heretofore
in force shall remain applicable in the version applicable until that
date.
Section 23 Entry into force; abrogation
This ordinance shall enter into force on 15 October 2003. At the same
date,
1. the Order Concerning Patent Applications of 29 May 1981 (Federal Law
Gazette I p. 521), last amended by the ordinance of 1 January 2002 (Federal
Law Gazette I p. 32), and
2. the order concerning the naming of the inventor of 29 May 1981 (Federal
Law Gazette I p. 525)
shall be abrogated.
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Annex 1 (resp. Sec. 11(1), second sentence) Standards for the Filing of
Sequence Listings
Definitions
1. For the purposes of this Standard the following definitions shall be
applicable:
(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 paragraph 48, 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 paragraph 48, table 1.
Modifications, for example, methylated bases, may be described as set
forth in paragraph 48, 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 paragraph 48, 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
paragraph 48, table 3, with the modified positions, for example,
hydroxylations or glycosylations, being described as set forth in
paragraph 48, 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 paragraph 48, 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
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sequence database providers (including scientific names, qualifiers and
their controlled-vocabulary values, the symbols appearing in paragraph
48, tables 1, 2, 3 and 4, and the feature keys appearing in paragraph
48, 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.
Sequence Listing
2. The sequence listing as defined in paragraph 1(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” or
“Sequenzprotokoll” 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 35, to
describe the sequences elsewhere in the description.
3. Where the sequence listing as defined in paragraph 1(i) is not contained
in the application as filed but is a separate document furnished
subsequently to the filing of the application (see paragraph 36), it shall
be entitled “Sequence Listing” or “Sequenzprotokoll” and shall have
independent page numbering. The original numbering of the sequences (see
paragraph 4) in the application as filed shall be maintained in the
subsequently furnished sequence listing.
4. 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.
5. 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:”.
6. 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
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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
7. 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.
8. 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 paragraph 48, table 1, shall
be used.
9. 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 paragraph 48, table 2, and the modification shall be
further described in the feature section of the sequence listing, using
the codes given in paragraph 48, 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 31). The symbol “n” is the
equivalent of only one unknown or modified nucleotide.
Format to be used
10. A nucleotide sequence shall be listed with a maximum of 60 bases per
line, with a space between each group of 10 bases.
11. 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.
12. The bases of the coding parts of a nucleotide sequence shall be listed
as triplets (codons).
13. 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
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the option of the applicant.
14. 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
15. 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.
16. 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
paragraph 48, 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 21).
17. 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 paragraph 48, table
4, and the modification shall be further described in the feature section
of the sequence listing, using the codes given in paragraph 48, 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
31). The symbol “Xaa” is the equivalent of only one unknown or modified
amino acid.
Format to be used
18. 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.
19. 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.
20. 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
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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.
21. 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
22. 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 paragraph 47.
23. Only numeric identifiers of data elements as defined in paragraph
47 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
24. The sequence listing shall include, in addition to and immediately
preceding the actual nucleotide and/or amino acid sequence, the following
21
items of information defined in paragraph 47 (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 4, above, and SEQ ID NO: 4 in the example depicted in the end
of this Standard).
25. In addition to the data elements identified in paragraph 24, 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> Reference number 26. In addition to the data elements identified in paragraph 24, 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> Current patent application <141> Current filing date 27. In addition to the data elements identified in paragraph 24, 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 28. 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 29. If the organism (numeric identifier <213>) is “Artificial Sequence”
or “Unknown,” the following data elements are mandatory:
22
<220> Feature <223> Other information
Optional Data Elements
30. All data elements defined in paragraph 47, not mentioned in paragraphs
24 to 29, above, are optional (optional data elements).
Presentation of Features
31. When features of sequences are presented (that is, numeric identifier
<220>), they shall be described by the “feature keys” set out in paragraph
48, tables 5 and 6.
Free Text
32. “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 1(vii).
33. The use of free text should be limited to a few short terms
indispensable for the understanding of the sequence. It should not exceed
four lines with a maximum of 65 characters per line for each given data
element. Any further information shall be included in the main part of
the description in the language thereof.
34. Any free text may be in the German or the English language.
35. 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
36. Any sequence listing which is not contained in the application as
filed but which is furnished subsequently shall not go beyond the
disclosure of the sequences indicated in the application. The
subsequently furnished sequence listing shall be accompanied by a
statement confirming that fact. This means that a sequence listing
furnished subsequently to the filing of the application shall contain
only those sequences that have been contained in the application as filed.
37. Any sequence listing not contained in the application as filed does
not form part of the disclosure of the invention. It is possible for a
sequence listing contained in the application as filed to be corrected
under Sec. 11(3) by remedying the defects.
23
Computer Readable Form of the Sequence Listing
38. A copy of the sequence listing contained in the application shall
also be submitted in computer readable form.
39. 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.”
40. 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 German Patent and Trade Mark
Office. The file shall be encoded using IBM Code Page 437, IBM Code Page
932 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.
41. The following media types and formats shall be acceptable for
machine-readable sequence listings: Physical Medium Type Format CD-R 120 mm Recordable Disk ISO 9660 DVD-R 120 mm DVD-Recordable
Disk (4.7 GB) complying with ISO 9660 or OSTA UDF (1.02 or higher)
DVD+R 120 mm DVD-Recordable Disk (4.7 GB)
complying with ISO 9660 or OSTA UDF (1.02 or higher)
42. The computer readable version may be created by any means. However,
it shall correspond to the formats indicated by the German Patent and
Trade Mark Office. It should preferably be created by dedicated special
software such as PatentIn.
43. File compression is acceptable when using physical data carriers,
so long as the compressed file is in a self-extracting format that will
decompress on an operating system (MS Windows) that is acceptable to the
German Patent and Trade Mark Office. Likewise files relating as regards
their contents may be compressed in a non-self-extracting format, if the
archive file exists in ZIP format in the version of 13 July 1998 and neither
contains other ZIP archives nor a directory structure.
44. The physical data carrier 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.
45. If the physical data carrier 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. Corrections or amendments
24
relating to the sequence listing shall be submitted in writing and in
machine-readable form.
46. Any correction of the printed version of the sequence listing which
is submitted under PCT Rules 13ter 1(a)(i) or 26.3, any rectification
of an obvious error in the printed version which is submitted, based on
PCT Rule 91, or any addition which was integrated into the printed version
of the sequence listing under PCT Article 34, shall additionally be
submitted in an enhanced version of the sequence listing in a
machine-readable form including any such additions.
47. 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 24 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 25, 26, 27, 28 and 29 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 30 of this
Standard) are marked by the symbol “O”. Admissible Numeric Identifiers
Numeric Numeric Mandatory Comment Identifier Identifier
Description (M) or
Optional (O)
<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> Reference number
M, In the circumsta nces specified in paragraph 25 of this Standard
see paragraph 25 of this Standard
<140> Current patent application
M, In the circumsta nces
see paragraph 26 of this Standard; the current patent application shall be identified, in the following order, by the two-letter
25
specified code indicated in accordance with in WIPO Standard ST.3 and the paragraph application number (in the format 26 of this used by the industrial property Standard 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 circumsta nces specified in paragraph 26 of this Standard
see paragraph 26 of this Standard; the date shall be indicated in accordance with WIPO Standard ST.2 (CCYY MM DD)
<150> Earlier patent application
M, In the circumsta nces specified in paragraph 27 of this Standard
see paragraph 27 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 circumsta nces 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)
<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 bases 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
26
<220> to <223> feature section <213> Organism M Genus Species (that is, scientific
name) or “Artificial Sequence” or “Unknown”
<220> Feature M, In the circumsta nces specified in paragraph s 28 and 29 of this Standard
leave blank; see paragraphs 28 and 29 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 circumsta nces specified in paragraph 28 of this Standard
see paragraph 28 of this Standard; only those keys as described in table 5 or 6 of paragraph 48 shall be used
<222> Location M, In the circumsta nces specified in paragraph 28 of this Standard
see paragraph 28 of this Standard; - from (number of first base/amino acid in the feature) - to (number of last base/amino acid in the feature) - bases (numbers refer to positions of bases 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 circumsta nces specified in paragraph s 28 and 29 of this Standard
see paragraphs 28 and 29 of this Standard; any other relevant information, using language neutral vocabulary, or free text (in German or English); any free text is to be repeated in the main part of the description in the language thereof (see paragraph 35 of this Standard); where any modified base or modified/unusual L-amino acid appearing in paragraph 48, tables 2 and 4, is in the sequence, the symbol associated with that base or amino acid from paragraph 48, tables 2 and 4, should be used
<300> Publication information
O leave blank; repeat section for each relevant publication
<301> Authors O
27
<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)
<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-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 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 example)
48. Nucleotide and amino acid symbols and feature table Table 1
List of Nucleotides Symbol Meaning Origin of Designation a a adenine
28
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
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 Mt6a N-((9-beta-D-ribofuranosylpurine-6-yn( �-
methylcarbamoyl)threonine
29
Mv uridine-5-oxyacetic acid-methylester o5u uridine-5-oxyacetic acid(v) 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
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
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
30
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
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
31
a region of duplex DNA by a single stranded nucleic acid 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, coding nucleic acid 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
LTR long, directly repeating sequence 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
32
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 post-transcriptional 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 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
33
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 permissible
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
34
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
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
35
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
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
36
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
Example:
<110> Smith, John; Smithgene Inc.
<120> Example for a sequence listing
<130> 01 - 00001
<140> PCT/EP98 / 00001
<141> 1998-12-31
<150> US 08 / 999,999
<151> 1997-10-15
<160> 4
<170> PatentIn Version 2.0
<210> 1
<211> 389
<212> DNA
<213> Paramecium sp.
<220>
<221> CDS
<222> (279) ... (389)
<300>
<301> Doe, Richard
<302> Isolation and Characterization of a Gene Encoding a Protease from
Paramecium sp.
<303> Journal of Genes
<304> 1
<305> 4
<306> 1-7
<307> 1988-06-31
<308> 123456
<309> 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 gtt tca atg ttc agc 296
Met Val Ser Met Phe Ser 1 5
ttg tct ttc aaa tgg cct gga ttt tgt ttg ttt gtt tgt ttg ttc caa 344
37
Leu Ser Phe Lys Trp Pro Gly Phe Cys Leu Phe Val Cys Leu Phe Gln 10 15 20
tgt ccc aaa gtc ctc ccc tgt cac tca tca ctg cag ccg aat ctt 389 Cys Pro Lys Val Leu Pro Cys His Ser Ser Leu Gln Pro Asn Leu
25 30 35
38
Annex 2 (resp. Sec. 12) Standards for the Filing of Drawings
A. Paper filing
1. The drawings shall be on sheets with the following minimum margins:
top 2.5 cm
left side 2.5 cm
right side 1.5 cm
bottom 1.0 cm
The area used for drawings may not exceed 26.2 cm x 17 cm; the area used
for the drawing of the abstract may be 8.1 cm x 9.4 cm when presented
in an upright position, or 17.4 cm x 4.5 cm when presented sideways.
2. Drawings shall be executed with sufficient contrast in durable, black,
sufficiently dense and dark, uniformly thick and clearly delineated lines
and strokes without colourings.
3. For illustrating the invention, in addition to views and sectional
views, perspectives and exploded views may be used. Cross-sections shall
be indicated by hatching which should not impede the clear reading of
the reference signs and leading lines.
4. The scale of the drawings and the distinctness of their graphical
execution shall be such that all details can be distinguished without
difficulty, after electronic data capture (scanning), in a linear
reduction in size to two-thirds. If, as an exception, the scale is given
on a drawing, it shall be represented graphically.
5. The lines in the drawings shall be drawn with the aid of drafting
instruments rather than freehand. The numbers and letters used in the
drawings shall not be less than 0.32 cm of height. For the lettering of
drawings, the Latin and, where customary, the Greek alphabets shall be
used.
6. The same sheet of drawings may contain several figures. The different
figures shall be arranged without wasting space while remaining clearly
separated from one another, preferably in an upright position, and shall
be numbered consecutively in Arabic numerals. Drawings concerning the
state of the art are admissible if the understanding of the invention
is thereby facilitated; however, they shall be clearly marked as “Stand
der Technik” (state of the art). Where figures on two or more sheets form
in effect a single complete figure, the figures on the several sheets
shall be so arranged that the complete figure can be assembled without
concealing any part of the partial figures. All elements of a figure shall
be in the same scale, except where the use of different scales is
indispensable for the clarity of the figure.
7. Reference signs not mentioned in the description and claims shall not
39
appear in the drawings, and vice versa. The same shall apply mutatis
mutandis to the abstract and its drawing.
8. The drawings shall not contain text matter, except, when absolutely
indispensable, a single word or words such as “water”, “steam”, “open”,
“closed”, “section on AB”, and, in the case of electric circuits and block
schematic or flow sheet diagrams, a few short catchwords indispensable
for understanding.
B. Electronic filing
9. The following image file formats are admissible for the electronic
filing of patent applications with the German Patent and Trade Mark
Office: Image File
Format
Compression Colour Depth Description
TIFF no compression or LZW or Fax group 4
1 bit/p or (black and white)
maximum size: A4 and resolution: 300*300 dpi corresponding to 2480*3508 pixels (width*height)
TIFF no compression or LZW or Fax group 4
8 bit/p grayscale (256 shades of grey)
maximum size: A4 and resolution: 150*150 dpi corresponding to 1240*1754 pixels (width*height)
JPEG individual compression
24 bit/p maximum size: A4 and resolution: 150*150 dpi accepts shades of grey only
PDF no compression black and white admissible only
the following typefaces (fonts) are allowed: - Times (serif font, proportional) - Helvetica (without serifs, proportional) - Courier - Symbol (symbols) Colour graphics not admissible Use restrictions possible for PDF files at file level by means of cryptographic means (encryption, deactivation of printing options) are not admissible
40