Paragraph 11 – Representation of a nucleotide sequence Cross-referenced examples Example 3(g)-4: Nucleic Acid Analogues Example 7(a)-1: Branched nucleotide sequence Paragraph 11(a) – Double-stranded nucleotide sequence - complementary Example 11(a)-1: Double-stranded nucleotide sequence – same lengths Paragraph 11(b) – Double-stranded nucleotide sequence – not fully complementary Example 11(b)-1: Double-stranded nucleotide sequence – different lengths Example 11(b)-2: Double-stranded nucleotide sequence – no base-pairing segment Paragraph 13 – Representation of nucleotides Cross-referenced examples Example 3(k)-2: Ambiguity symbol “n” used in both a conventional and nonconventional manner Example 7(a)-1: Branched nucleotide sequence Example 14-1: The symbol “t” represents uracil in RNA Example 91-1: Representation of enumerated variants Paragraph 14 – Symbol “t” construed as uracil in RNA Example 14-1: The symbol “t” represents uracil in RNA Cross-referenced examples Example 55-1: Combined DNA/RNA Molecule Paragraph 15 – The most restrictive nucleotide ambiguity symbol should be used examples Example 3(g)-1: Nucleotide sequence interrupted by a C3 spacer Example 3(g)-2: Nucleotide sequence with residue alternatives, including a C3 spacer Example 3(k)-4: Ambiguity symbols other than “n” are “specifically defined” Example 93(b)-1: Representation of individual variant sequences with multiple interdependent variations Paragraph 16 – Representation of a modified amino acid Cross-referenced examples Example 3(g)-1: Nucleotide sequence interrupted by a C3 spacer Example 3(g)-4: Nucleic Acid Analogues Paragraph 17 – Annotation of a modified amino acid examples Example 3(g)-1: Nucleotide sequence interrupted by a C3 spacer Example 3(g)-3: Abasic site ...
Example 37-2: Sequence with regions of an unknown number of “X” residues must not be represented as a single sequence Paragraph 41 – Reserved characters examples Example 87-2: Feature location extends beyond the disclosed sequence Paragraph 54 – The element INSDSeq_moltype Cross-referenced examples Example 14-1: The symbol “t” represents uracil in RNA Paragraph 55 – A nucleotide sequence that contains both DNA and RNA segments Example 55-1: Combined DNA/RNA Molecule……………………………………………………………………………………. Paragraph 56 – Example illustrating a nucleotide sequence that contains both DNA and RNA segments examples Example 55-1: Combined DNA/RNA Molecule Paragraph 57 – The element INSDSeq_sequence Cross-referenced examples Example 28-1: Encoding nucleotide sequence and encoded amino acid sequence Example 90-1: Amino acid sequence encoded by a coding sequence with introns Paragraph 65 – Location descriptor Cross-referenced examples Example 3(g)-4: Nucleic Acid Analogues Example 87-2: Feature location extends beyond the disclosed sequence Paragraph 66 – Location descriptor syntax Cross-referenced examples Example 3(g)-4: Nucleic Acid Analogues Example 29-1: Most restrictive ambiguity symbol for an “other” amino acid Example 87-2: Feature location extends beyond the disclosed sequence Paragraph 67 – Location operator Cross-referenced examples Example 7(b)-4: Cyclic peptide containing a branched acid sequence Paragraph 68 – Join and location operators examples Example 7(b)-4: Cyclic peptide containing a branched amino acid sequence
Paragraph 3(c) – Definition of “enumeration of its residues” Example 3(c)-1: Enumeration of amino acids by chemical structure Question 1: Does ST.26 require inclusion of the sequence(s)? YES The enumerated peptide, illustrated as a structure, contains at four specifically defined amino acids. Therefore, the sequence must be included in a sequence listing. Question 3: How should the sequence(s) be represented in the sequence listing? The sequence may be represented as: VAFXGK (SEQ ID NO: 2) wherein “X” represents an modified amino acid: , which requires a feature key “SITE” together with the qualifier “NOTE”. The qualifier “NOTE” provides the complete, unabbreviated name of the modified tryptophan in position 4 of the enumerated peptide, e.g., “6-amino-7-(1H-indol-3-yl)-5-oxoheptanoic acid”. Further, additional feature keys “SITE” and qualifier “NOTE” are required to indicate the acetylation of the and the methylation of the C-terminus. Alternatively, the sequence may be represented as: VAFW (SEQ ID NO: 3) A feature key “SITE” and qualifier “NOTE” are required to indicate modification of tryptophan in position 4 of the enumerated peptide with the value: “C-terminus linked via a glutaraldehyde bridge to dipeptide GK”. Further, an additional feature key “SITE” at location 1 and qualifier “NOTE” is required to indicate the acetylation of the Relevant ST.26 paragraphs: Paragraphs 3(c), 7(b), 29, 30, and 31 terminus
Example 3(k)-4: Ambiguity symbols other than “n” are “specifically defined” A patent application describes the following sequence: 5’ NNG KNG KNG KAG VCR 3’ wherein N, K, V, and R are IUPAC-IUB ambiguity codes Question 1: Does ST.26 require inclusion of the sequence(s)? YES IUPAC-IUB ambiguity codes correspond to the list of nucleotide symbols defined in Annex I, Section 1, Table 1. According to paragraph 3(k), a “specifically defined” nucleotide is any nucleotide other than those represented by the symbol “n” listed in Annex I, Section 1, Table 1. Therefore, “K”, “V”, and “R” are “specifically defined” nucleotides. The sequence has eleven enumerated and “specifically defined” nucleotides and is required by ST.26 paragraph 7(a) to be included in a sequence listing. Question 3: How should the sequence(s) be represented in the sequence listing? The sequence must be included in a sequence listing as: nngkngkngkagvcr (SEQ ID NO: 16) Relevant ST.26 paragraphs: Paragraphs 3(k), 7(a) and 15
Question 3: How should the sequence(s) be represented in the sequence listing? Peptides 1-6 must be represented with separate sequence identifiers: RISL (SEQ ID NO: 26) LLKK (SEQ ID NO: 27) IPACTA (SEQ ID NO: 28) FRAGGK (SEQ ID NO: 29) HQYFA (SEQ ID NO: 30) ATFGKKKA (SEQ ID NO: 31) The cross linkage is preferably noted using the feature key “SITE” and the mandatory qualifier “NOTE” with the value e.g., “This sequence is one part of a branched peptideamino acid sequence”. According to ST.26 paragraph 29, SEQ ID NOs 27, 29, and 31, must include an annotation for each lysine to indicate that it is a modified amino acid, using the feature key “SITE” together with the qualifier “NOTE” describing that the side chain of the lysine is linked via an amide linkage to another sequence. Preferably, each of SEQ ID Nos 26, 28 and 30 should include an annotation to indicate that the C-terminal amino acid is linked to another sequence, using the feature key “SITE” together with the qualifier “NOTE”. Relevant ST.26 paragraphs: Paragraphs 7(b), 8, 26, 29, 30, and 31
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<INSDFeature_location>1..216</INSDFeature_location> <INSDFeature_quals> <INSDQualifier> <INSDQualifier_name>organism</INSDQualifier_name> <INSDQualifier_value>Homo sapiens</INSDQualifier_value> </INSDQualifier> <INSDQualifier> <INSDQualifier_name>mol_type</INSDQualifier_name> <INSDQualifier_value>genomic DNA</INSDQualifier_value> </INSDQualifier> </INSDFeature_quals> </INSDFeature> <INSDFeature> <INSDFeature_key>CDS</INSDFeature_key> <INSDFeature_location>&lt;1..&gt;216</INSDFeature_location> <INSDFeature_quals> <INSDQualifier> <INSDQualifier_name>protein_id</INSDQualifier_name> <INSDQualifier_value>94</INSDQualifier_value> </INSDQualifier> <INSDQualifier> <INSDQualifier_name>translation</INSDQualifier_name> </INSDQualifier> </INSDFeature_quals> </INSDFeature> </INSDSeq_feature-table> </INSDSeq> </SequenceData> <SequenceData sequenceIDNumber="94"> <INSDSeq> <INSDSeq_length>72</INSDSeq_length> <INSDSeq_moltype>AA</INSDSeq_moltype> <INSDSeq_division>PAT</INSDSeq_division> <INSDSeq_feature-table>