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2422 Nucleotide and/or Amino Acid Sequence Disclosures in Patent Applications - 2400 Biotechnology
2422 Nucleotide and/or Amino Acid Sequence Disclosures in Patent Applications
37 CFR 1.821 Nucleotide and/or amino acid sequence disclosures in patent applications.
(a) Nucleotide and/or amino acid sequences as used in §§ 1.821 through 1.825 are interpreted to mean an unbranched sequence of four or more amino acids or an unbranched sequence of ten or more nucleotides. Branched sequences are specifically excluded from this definition. Sequences with fewer than four specifically defined nucleotides or amino acids are specifically excluded from this section. "Specifically defined" means those amino acids other than "Xaa" and those nucleotide bases other than "n" defined in accordance with the World Intellectual Property Organization (WIPO) Handbook on Industrial Property Information and Documentation, Standard ST.25: Standard for the Presentation of Nucleotide and Amino Acid Sequence Listings in Patent Applications (1998), including Tables 1 through 6 in Appendix 2, herein incorporated by reference. (Hereinafter "WIPO
Standard ST.25 (1998)""). This incorporation by reference was approved by the Director of the Federal Register in accordance with 5 U.S.C. 552(a) and 1 CFR part 51. Copies of WIPO Standard ST.25 (1998) may be obtained from the World Intellectual Property Organization; 34 chemin des Colombettes; 1211 Geneva 20 Switzerland. Copies of ST.25 may be inspected at the Patent Search Room; Crystal Plaza 3, Lobby Level; 2021 South Clark Place; Arlington, VA 22202. Copies may also be inspected at the Office of the Federal Register, 800 North Capitol Street, NW, Suite 700, Washington, DC. Nucleotides and amino acids are further defined as follows:
(1) Nucleotides: Nucleotides are intended to embrace only those nucleotides that can be represented using the symbols set forth in WIPO Standard ST.25 (1998), Appendix 2, Table 1. Modifications, e.g., methylated bases, may be described as set forth in WIPO Standard ST.25 (1998), Appendix 2, Table 2, but shall not be shown explicitly in the nucleotide sequence.
(2) Amino acids: Amino acids are those L-amino acids commonly found in naturally occurring proteins and are listed in WIPO Standard ST.25 (1998), Appendix 2, Table 3. Those amino acid sequences containing D-amino acids 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 WIPO Standard ST.25 (1998), Appendix 2, Table 3 with the modified positions; e.g., hydroxylations or glycosylations, being described as set forth in WIPO Standard ST.25 (1998), Appendix 2, Table 4, but these modifications shall not be shown explicitly in the amino acid sequence. Any peptide or protein that can be expressed as a sequence using the symbols in WIPO Standard ST.25 (1998), Appendix 2, Table 3 in conjunction with a description in the Feature section
to describe, for example, modified linkages, cross links and end caps, non-peptidyl bonds, etc., is embraced by this definition.
(b) Patent applications which contain disclosures of nucleotide and/or amino acid sequences, in accordance with the definition in paragraph (a) of this section, shall, with regard to the manner in which the nucleotide and/or amino acid sequences are presented and described, conform exclusively to the requirements of §§ 1.821 through 1.825.
(c) Patent applications which contain disclosures of nucleotide and/or amino acid sequences must contain, as a separate part of the disclosure, a paper copy disclosing the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of §§ 1.822 and 1.823. This paper copy is hereinafter referred to as the "Sequence Listing." Each sequence disclosed must appear separately in the "Sequence Listing." Each sequence set forth in the "Sequence Listing" 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" shall be used in place of the sequence. The response for the numeric identifier <160> shall include the total
number of SEQ ID NOs, whether followed by a sequence or by the code "000."
(d) Where the description or claims of a patent application discuss a sequence that is set forth in the "Sequence Listing" in accordance with paragraph (c) of this section, reference must be made to the sequence by use of the sequence identifier, preceded by "SEQ ID NO:" in the text of the description or claims, even if the sequence is also embedded in the text of the description or claims of the patent application.
(e) A copy of the "Sequence Listing" referred to in paragraph (c) of this section must also be submitted in computer readable form in accordance with the requirements of § 1.824. The computer readable form is a copy of the "Sequence Listing" and will not necessarily be retained as a part of the patent application file. If the computer readable form of a new application is to be identical with the computer readable form of another application of the applicant on file in the Patent and Trademark Office, reference may be made to the other application and computer readable form in lieu of filing a duplicate computer readable form in the new application if the computer readable form in the other application was compliant with all of the requirements of these rules. The new application shall be accompanied by a letter making such reference to the other application and computer readable form, both of
which shall be completely identified. In the new application, applicant must also request the use of the compliant computer readable "Sequence Listing" that is already on file for the other application and must state that the paper copy of the "Sequence Listing" in the new application is identical to the computer readable copy filed for the other application.
(f) In addition to the paper copy required by paragraph (c) of this section and the computer readable form required by paragraph (e) of this section, a statement that the content of the paper and computer readable copies are the same must be submitted with the computer readable form, e.g., a statement that "the information recorded in computer readable form is identical to the written sequence listing."
(g) If any of the requirements of paragraphs (b) through (f) of this section are not satisfied at the time of filing under 35 U.S.C. 111(a) or at the time of entering the national stage under 35 U.S.C. 371, applicant will be notified and given a period of time within which to comply with such requirements in order to prevent abandonment of the application. Any submission in reply to a requirement under this paragraph must be accompanied by a statement that the submission includes no new matter.
(h) If any of the requirements of paragraphs (b) through (f) of this section are not satisfied at the time of filing an international application under the Patent Cooperation Treaty (PCT), which application is to be searched by the United States International Searching Authority or examined by the United States International Preliminary Examining Authority, applicant will be sent a notice necessitating compliance with the requirements within a prescribed time period. Any submission in reply to a requirement under this paragraph must be accompanied by a statement that the submission does not include matter which goes beyond the disclosure in the international application as filed. If applicant fails to timely provide the required computer readable form, the United States International Searching Authority shall search only to the extent that a meaningful search can be performed without the computer readable form and the United States International
Preliminary Examining Authority shall examine only to the extent that a meaningful examination can be performed without the computer readable form.
37 CFR 1.821 incorporates by reference the World Intellectual Property Organization (WIPO) Handbook on Industrial Property Information and Documentation, Standard ST.25 (1998), including Tables 1 through 6 of Appendix 2. Copies may be obtained from the World Intellectual Property Organization; 34 chemin des Colombettes; 1211 Geneva 20 Switzerland. Copies may be inspected at the Patent Search Room; Crystal Plaza 3, Lobby Level; 2021 South Clark Place; Arlington, VA 22202. Copies may also be inspected at the Office of the Federal Register, 800 North Capitol Street, NW, Suite 700, Washington, DC 20408. These tables are reproduced below.
WIPO Standard ST.25 (1998), Appendix 2, Table 1, provides that the bases of a nucleotide sequence should be represented using the following one-letter code for nucleotide sequence characters:
Table 1: List of Nucleotides
Symbol
|
Meaning
|
Origin of designation |
a |
a |
adenine |
g |
g |
guanine |
c |
c |
cytosine |
t |
t |
thymine |
u |
u |
uracil |
r |
g or a |
purine |
y |
t/u or c |
pyrimidine |
m |
a or c |
amino |
k |
g or t/u |
keto |
s |
g or c |
strong interactions 3H-bonds |
w |
a or t/u |
weak interactions 2H-bonds |
b |
g or c or t/u |
not a |
d |
a or g or t/u |
not c |
h |
a or c or t/u |
not g |
v |
a or g or c |
not t, not u |
n |
a or g or c or t/u, unknown, or other |
any |
WIPO Standard ST.25 (1998), Appendix 2, Table 2, provides that modified bases may be represented as the corresponding unmodified bases in the sequence itself, if the modified base is one of those listed below and the modification is further described in the Feature section of the Sequence Listing. The codes from the list below may be used in the description (i.e., the specification and drawing, or in the Sequence Listing) but these codes may not be used in the sequence itself.
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-yl)N-methylcarbamoyl)threonine |
mv |
uridine-5-oxyacetic acid-methylester |
o5u |
uridine-5-oxyacetic acid |
osyw |
wybutoxosine |
p |
pseudouridine |
q |
queuosine |
s2t |
5-methyl-2-thiouridine |
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 |
WIPO Standard ST.25 (1998), Appendix 2, Table 3, provides that the amino acids should be represented using the following three-letter code with the first letter as a capital.
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 |
WIPO Standard ST.25 (1998), Appendix 2, Table 4, provides that modified and unusual amino acids may be represented as the corresponding unmodified amino acids in the sequence itself if the modified or unusual amino acid is one of those listed below and the modification is further described in the Feature section of the Sequence Listing. The codes from the list below may be used in the description (i.e., the specification and drawings, or in Sequence Listing) but these codes may not be used in the sequence itself.
Table 4: List of Modified and Unusual Amino Acids
Symbol |
Meaning |
Aad |
2-Aminoadipic acid |
bAad |
3-Aminoadipic acid |
bAla |
beta-Alanine, beta-Aminopropionic acid |
Abu |
2-Aminobutyric acid |
4Abu |
4-Aminobutyric acid, piperidinic acid |
Acp |
6-Aminocaproic acid |
Ahe |
2-Aminoheptanoic acid |
Aib |
2-Aminoisobutyric acid |
bAib |
3-Aminoisobutyric acid |
Apm |
2-Aminopimelic acid |
Dbu |
2,4-Diaminobutyric acid |
Des |
Desmosine |
Dpm |
2,2' -Diaminopimelic acid |
Dpr |
2,3-Diaminopropionic acid |
EtGly |
N-Ethylglycine |
EtAsn |
N-Ethylasparagine |
Hyl |
Hydroxylysine |
aHyl |
allo-Hydroxylysine |
3Hyp |
3-Hydroxyproline |
4Hyp |
4-Hydroxyproline |
Ide |
Isodesmosine |
aIle |
allo-Isoleucine |
MeGly |
N-Methylglycine, sarcosine |
MeIle |
N-Methylisoleucine |
MeLys |
6-N-Methyllysine |
MeVal |
N-Methylvaline |
Nva |
Norvaline |
Nle |
Norleucine |
Orn |
Ornithine |
WIPO Standard ST.25 (1998), Appendix 2, Table 5, provides for feature keys related to DNA sequences.
Table 5: List of Feature Keys Related to Nucleotide Sequences
Key |
Description |
allele |
a related individual or strain contains stable, alternative forms of the same gene which differs from the presented sequence at this location (and perhaps others) |
attenuator |
(1) region of DNA at which regulation of termination of transcription occurs, which controls the expression of some bacterial operons; (2) sequence segment located between the promoter and the first structural gene that causes partial termination of transcription |
C_region |
constant region of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains; includes one or more exons depending on the particular chain |
CAAT_signal |
CAAT box; part of a conserved sequence located about 75 bp up-stream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG (C or T) CAATCT |
CDS |
coding sequence; sequence of nucleotides that corresponds with the sequence of amino acids in a protein (location includes stop codon); feature includes amino acid conceptual translation |
conflict |
independent determinations of the "same" sequence differ at this site or region |
D-loop |
displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein |
D-segment |
diversity segment of immunoglobulin heavy chain, and T-cell receptor beta chain |
enhancer |
a cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter |
exon |
region of genome that codes for portion of spliced mRNA; may contain 5'UTR, all CDSs, and 3'UTR |
GC_signal |
GC box; a conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG |
gene |
region of biological interest identified as a gene and for which a name has been assigned |
iDNA |
intervening DNA; DNA which is eliminated through any of several kinds of recombination |
intron |
a segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it |
J_segment |
joining segment of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains |
LTR |
long terminal repeat, a sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses |
mat_peptide |
mature peptide or protein coding sequence; coding sequence for the mature or final peptide or protein product following post-translational modification; the location does not include the stop codon (unlike the corresponding CDS) |
misc_binding |
site in nucleic acid which covalently or non-covalently binds another moiety that cannot be described by any other Binding key (primer_bind or protein_bind) |
misc_difference |
feature sequence is different from that presented in the entry and cannot be described by any other Difference key (conflict, unsure, old_sequence, mutation, variation, allele, or modified_base) |
misc_feature |
region of biological interest which cannot be described by any other feature key; a new or rare feature |
misc_recomb |
site of any generalized, site-specific or replicative recombination event where there is a breakage and reunion of duplex DNA that cannot be described by other recombination keys (iDNA and virion) or qualifiers of source key (/insertion_seq, /transposon, /proviral) |
misc_RNA |
any transcript or RNA product that cannot be defined by other RNA keys (prim_transcript, precursor_RNA, mRNA, 5'clip, 3'clip, 5'UTR, 3'UTR, exon, CDS, sig_peptide, transit_peptide, mat_peptide, intron, polyA_site, rRNA, tRNA, scRNA, and snRNA) |
misc_signal |
any region containing a signal controlling or altering gene function or expression that cannot be described by other Signal keys (promoter, CAAT_signal, TATA_signal, -35_signal, -10_signal, GC_signal, RBS, polyA_signal, enhancer, attenuator, terminator, and rep_origin) |
misc_structure |
any secondary or tertiary structure or conformation that cannot be described by other Structure keys (stem_loop and D-loop) |
modified_base |
the indicated nucleotide is a modified nucleotide and should be substituted for by the indicated molecule (given in the mod_base qualifier value) |
mRNA |
messenger RNA; includes 5' untranslated region (5'UTR), coding sequences (CDS, exon) and 3' untranslated region (3'UTR) |
mutation |
a related strain has an abrupt, inheritable change in the sequence at this location |
N_region |
extra nucleotides inserted between rearranged immunoglobulin segments |
old_sequence |
the presented sequence revises a previous version of the sequence at this location |
polyA_signal |
recognition region necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA |
polyA_site |
site on an RNA transcript to which will be added adenine residues by 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 |
scRNA |
small cytoplasmic RNA; any one of several small cytoplasmic RNA molecules present in the cytoplasm and (sometimes) nucleus of a eukaryote |
sig_peptide |
signal peptide coding sequence; coding sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane; leader sequence |
snRNA |
small nuclear RNA; any one of many small RNA species confined to the nucleus; several of the snRNAs are involved in splicing or other RNA processing reactions |
source |
identifies the biological source of the specified span of the sequence; this key is mandatory; every entry will have, as a minimum, a single source key spanning the entire sequence; more than one source key per sequence is permissable |
stem_loop |
hairpin; a double-helical region formed by base-pairing between adjacent (inverted) complementary sequences in a single strand of RNA or DNA |
STS |
Sequence Tagged Site; short, single-copy DNA sequence that characterizes a mapping landmark on the genome and can be detected by PCR; a region of the genome can be mapped by determining the order of a series of STSs |
TATA_signal |
TATA box; Goldberg-Hogness box; a conserved AT-rich septamer found about 25 bp before the start point of each eukaryotic RNA polymerase II transcript unit which may be involved in positioning the enzyme for correct initiation; consensus=TATA(A or T)A(A or T) |
terminator |
sequence of DNA located either at the end of the transcript or adjacent to a promoter region that causes RNA polymerase to terminate transcription; may also be site of binding of repressor protein |
transit_peptide |
transit peptide coding sequence; coding sequence for an N-terminal domain of a nuclear-encoded organellar protein; this domain is involved in post-translational import of the protein into the organelle |
tRNA |
mature transfer RNA, a small RNA molecule (75-85 bases long) that mediates the translation of a nucleic acid sequence into an amino acid sequence |
unsure |
author is unsure of exact sequence in this region |
V_region |
variable region of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains; codes for the variable amino terminal portion; can be made up from V_segments, D_segments, N_regions, and J_segments |
V_segment |
variable segment of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains; codes for most of the variable region (V_region) and the last few amino acids of the leader peptide |
variation |
a related strain contains stable mutations from the same gene (for example, RFLPs, polymorphisms, etc.) which differ from the presented sequence at this location (and possibly others) |
3'clip |
3'-most region of a precursor transcript that is clipped off during processing |
3'UTR |
region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein |
5'clip |
5'-most region of a precursor transcript that is clipped off during processing |
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 [ ] |
WIPO Standard ST.25 (1998), Appendix 2, Table 6 provides for feature keys related to protein sequences .
Table 6: List of Feature Keys Related to Protein Sequences
Key |
Description |
CONFLICT |
different papers report differing sequences |
VARIANT |
authors report that sequence variants exist |
VARSPLIC |
description of sequence variants produced by alternative splicing |
MUTAGEN |
site which has been experimentally altered |
MOD_RES |
post-translational modification of a residue |
ACETYLATION |
N-terminal or other |
AMIDATION |
generally at the C-terminal of a mature active peptide |
BLOCKED |
undetermined N- or C-terminal blocking group |
FORMYLATION |
of the N-terminal methionine |
GAMMA-CARBOXYGLUTAMIC ACID HYDROXYLATION |
of asparagine, aspartic acid, proline or lysine |
METHYLATION |
generally of lysine or arginine |
PHOSPHORYLATION |
of serine, threonine, tyrosine, aspartic acid or histidine |
PYRROLIDONE CARBOXYLIC ACID |
N-terminal glutamate which has formed an internal cyclic lactam |
SULFATATION |
generally of tyrosine |
LIPID |
covalent binding of a lipidic moiety |
MYRISTATE |
myristate group attached through an amide bond to the N-terminal glycine residue of the mature form of a protein or to an internal lysine residue |
PALMITATE |
palmitate group attached through a thioether bond to a cysteine residue or through an ester bond to a serine or threonine residue |
FARNESYL |
farnesyl group attached through a thioether bond to a cysteine residue |
GERANYL-GERANYL |
geranyl-geranyl group attached through a thioether bond to a cysteine residue |
GPI-ANCHOR |
glycosyl-phosphatidylinositol (GPI) group linked to the alpha-carboxyl group of the C-terminal residue of the mature form of a protein |
N-ACYL DIGLYCERIDE |
N-terminal cysteine of the mature form of a prokaryotic lipoprotein with an amide-linked fatty acid and a glyceryl group to which two fatty acids are linked by ester linkages |
DISULFID |
disulfide bond; the `FROM' and `TO' endpoints represent the two residues which are linked by an intra-chain disulfide bond; if the `FROM' and `TO' endpoints are identical, the disulfide bond is an interchain one and the description field indicates the nature of the cross-link |
THIOLEST |
thiolester bond; the `FROM' and `TO' endpoints represent the two residues which are linked by the thiolester bond |
THIOETH |
thioether bond; the `FROM' and `TO' endpoints represent the two residues which are linked by the thioether bond |
CARBOHYD |
glycosylation site; the nature of the carbohydrate (if known) is given in the description field |
METAL |
binding site for a metal ion; the description field indicates the nature of the metal |
BINDING |
binding site for any chemical group (co-enzyme, prosthetic group, etc.); the chemical nature of the group is given in the description field |
SIGNAL |
extent of a signal sequence (prepeptide) |
TRANSIT |
extent of a transit peptide (mitochondrial, chloroplastic, or for a microbody) |
PROPEP |
extent of a propeptide |
CHAIN |
extent of a polypeptide chain in the mature protein |
PEPTIDE |
extent of a released active peptide |
DOMAIN |
extent of a domain of interest on the sequence; the nature of that domain is given in the description field |
CA_BIND |
extent of a calcium-binding region |
DNA_BIND |
extent of a DNA-binding region |
NP_BIND |
extent of a nucleotide phosphate binding region; the nature of the nucleotide phosphate is indicated in the description field |
TRANSMEM |
extent of a transmembrane region |
ZN_FING |
extent of a zinc finger region |
SIMILAR |
extent of a similarity with another protein sequence; precise information, relative to that sequence is given in the description field |
REPEAT |
extent of an internal sequence repetition |
HELIX |
secondary structure: Helices, for example, Alpha-helix, 3(10) helix, or Pi-helix |
STRAND |
secondary structure: Beta-strand, for example, Hydrogen bonded beta-strand, or Residue in an isolated beta-bridge |
TURN |
secondary structure: Turns, for example, H-bonded turn (3-turn, 4-turn, or 5-turn) |
ACT_SITE |
amino acid(s) involved in the activity of an enzyme |
SITE |
any other interesting site on the sequence |
INIT_MET |
the sequence is known to start with an initiator methionine |
NON_TER |
the residue at an extremity of the sequence is not the terminal residue; if applied to position 1, this signifies that the first position is not the N-terminus of the complete molecule; if applied to the last position, it signifies that this position is not the C-terminus of the complete molecule; there is no description field for this key |
NON_CONS |
non consecutive residues; indicates that two residues in a sequence are not consecutive and that there are a number of unsequenced residues between them |
UNSURE |
uncertainties in the sequence; used to describe region(s) of a sequence for which the authors are unsure about the sequence assignment |
FILING INTERNATIONALLY
The revisions to 37 CFR 1.821 through 1.825 are the result of an effort to harmonize the PTO, PCT, EPO and JPO Sequence Listing requirements to the extent possible. The requirements of WIPO Standard ST.25 are substantially identical to the requirements of 37 CFR 1.821 through 1.825. PatentIn Version 3.1 software, now available (see MPEP § 2430), generates sequence listings that meet all of the requirements of WIPO Standard ST.25 (1998). The requirements of 37 CFR 1.821 through 1.825, however, are less stringent than the requirements of WIPO Standard ST.25 (1998). Thus, applicants who wish to file in countries which adhere to WIPO Standard ST.25 (1998) should consider the following when not using PatentIn Version 3.1:
(A) The WIPO Standard ST.25 (1998) does not permit submissions using a Macintosh computer;
(B) The WIPO Standard ST.25 (1998) does not accept the range of media permitted by 37 CFR 1.821 through 1.825;
(C) The answers in fields <221> and <222> must use selections from Tables 5 and 6 of WIPO Standard ST.25 (1998) to comply with that standard. The terms from these Tables are considered language neutral vocabulary;
(D) Any free text in numeric identifier <223> of a Sequence Listing will not be translated and thus must also appear in the specification of applications filed under WIPO Standard ST.25 (1998) for compliance;
(E) A CRF filed after the filing of an application under the PCT is not considered to be part of the disclosure and will not be published in the pamphlet;
(F) Paragraph 39 of WIPO Standard ST.25 (1998) requires the specific wording "the information recorded on the form is identical to the written sequence listing"; and
(G) WIPO Standard ST.25 (1998), paragraph 24, requires spaces between specified numeric identifiers in the Sequence Listing.
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