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Patent Regulation (Patent Ordinance of September 1, 2003, as amended by Article 2 of the Ordinance of December 17, 2004), Germany

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Details Details Year of Version 2004 Dates Entry into force: October 15, 2003 Issued: September 1, 2003 Type of Text Implementing Rules/Regulations Subject Matter Patents (Inventions) Subject Matter (secondary) IP Regulatory Body Notes The English translation of the Patent Regulation is reproduced with the permission of the Japan Patent Office (JPO) from the following URL http://www.jpo.go.jp/shiryou_e/s_sonota_e/fips_e/pdf/germany_e/e_tokkyo_kisoku.pdf. (Retrieved on June 12, 2012).

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Main text(s) Main text(s) English Patent Regulation (Patent Ordinance of September 1, 2003, as amended by Article 2 of the Ordinance of December 17, 2004)        
 Patent Regulations

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

1

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

2

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.

3

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

4

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

5

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

6

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

7

(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

8

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

9

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,

10

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

11

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.

12

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

13

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)

14

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).

15

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.

16

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

17

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

18

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

19

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

20

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


Legislation Is superseded by (2 text(s)) Is superseded by (2 text(s))
No data available.

WIPO Lex No. DE152