Patent Biological Sequence Listings Data Dictionary

This numeric identifier is followed by the applicant name. This may include an individual and/or a company.

Note: If the applicant name is written in characters other than those of the Latin alphabet, the value will be a translation or transliteration.

This numeric identifier is followed by the title of the invention.

This numeric identifier is followed by the physical file reference to the application.

Note: This numeric identifier appears if the sequence listing was furnished at any time prior to the assignment of an application number.

This numeric identifier is followed by the patent application's number.

Note: This numeric identifier appears if the sequence listing was furnished following the assignment of an application number.

This numeric identifier is followed by the filing date of the application.

Note: This numeric identifier appears if the sequence listing was furnished following the assignment of an application number.

This numeric identifier is followed by the application number of an earlier application when a sequence listing is filed relating to an application which claims the priority of an earlier application.

This numeric identifier is followed by the date of filing of an earlier application when a sequence listing is filed relating to an application which claims the priority of an earlier application.

This numeric identifier is followed by the number of sequences (<400>) found in the document.

This numeric identifier is followed by the software used in the creation of sequence listings for inclusions in patent applications.

This numeric identifier is followed by the sequence identification number related to the following sequence (<400>).

This numeric identifier is followed by the length of the sequence (i.e. number of base pairs or amino acids).

This numeric identifier is followed by the type of molecule sequenced. The type can be DNA, RNA or PRT.

Note: If a nucleotide sequence contains both DNA and RNA fragments, the value following this numeric identifier will be DNA.

This numeric identifier is followed by the Genus Species/scientific name of the molecule sequenced. This value may also be "Artificial Sequence" or "Unknown".

This numeric identifier is always blank, but is followed by other numeric identifiers having a description of points of biological significance in the sequence.

Note: This numeric identifier is used when "n" or "Xaa" or a modified base or modified/unusual L-amino acid is used in the sequence or if the organism (numeric identifier <213>) is "Artificial Sequence" or "Unknown".

This numeric identifier is followed by the feature key representing points of biological significance in the sequence. These feature keys and their definition can be found in Appendix E and Appendix F.

Note: This numeric identifier is used when "n" or "Xaa" or a modified base or modified/unusual L-amino acid is used in the sequence.

This numeric identifier is followed by the location of the points of biological significance in the sequence as per the length of the sequence.

Note: This numeric identifier is used when "n" or "Xaa" or a modified base or modified/unusual L-amino acid is used in the sequence.

This numeric identifier is followed by the description of points of biological significance in the sequence.

Note: This numeric identifier is used when "n" or "Xaa" or a modified base or modified/unusual L-amino acid is used in the sequence or if the organism (numeric identifier <213>) is "Artificial Sequence" or "Unknown".

This numeric identifier is always blank but is followed by publication information.

This numeric identifier is followed by the name of the author of the publication in which the sequence listing can be found.

This numeric identifier is followed by the title of publication in the journal in which the sequence listing can be found.

This numeric identifier is followed by the title of the journal in which the sequence listing can be found.

This numeric identifier is followed by the volume of the journal in which the sequence listing can be found.

This numeric identifier is followed by the issue of the journal in which the sequence listing can be found.

This numeric identifier is followed by the range of pages of the journal in which the sequence listing can be found.

This numeric identifier is followed by the date of publication of the journal in which the sequence listing can be found.

Accession number assigned by database including database name.

Date of entry in database

Document number, for patent-type citations only.

Document filing date, for patent-type citations only.

Document publication date; for patent-type citations only.

Sequence ID numbers (SEQ ID NOS) referred to in the cited publication.

Met Ser Arg Asp Arg Phe Arg Ser Arg Gly Gly Gly Gly Gly Gly Phe

1 5 10 15

His Arg Arg Gly Gly Gly Gly Gly Arg Gly Gly Leu His Asp Phe Arg

20 25 30

Ser Pro Pro Pro Gly Met Gly Leu Asn Gln Asn Arg Gly Pro Met Gly

35 40 45

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)

(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

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 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

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

independent determinations of the "same" sequence differ at this site or region

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

diversity segment of immunoglobulin heavy chain, and T-cell receptor beta chain

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

region of genome that codes for portion of spliced mRNA; may contain 5'UTR, all CDSs, and 3'UTR

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

region of biological interest identified as a gene and for which a name has been assigned

intervening DNA; DNA which is eliminated through any of several kinds of recombination

a segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it

joining segment of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains

long terminal repeat, a sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses

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)

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)

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)

region of biological interest which cannot be described by any other feature key; a new or rare feature

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)

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)

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)

any secondary or tertiary structure or conformation that cannot be described by other Structure keys (stem_loop and D-loop)

the indicated nucleotide is a modified nucleotide and should be substituted for by the indicated molecule (given in the mod_base qualifier value)

messenger RNA; includes 5' untranslated region (5'UTR), coding sequences (CDS, exon) and 3' untranslated region (3'UTR)

a related strain has an abrupt, inheritable change in the sequence at this location

extra nucleotides inserted between rearranged immunoglobulin segments

the presented sequence revises a previous version of the sequence at this location

recognition region necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA

site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation

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)

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)

non-covalent primer binding site for initiation of replication, transcription, or reverse transcription; includes site(s) for synthetic, for example, PCR primer elements

region on a DNA molecule involved in RNA polymerase binding to initiate transcription

non-covalent protein binding site on nucleic acid

ribosome binding site

region of genome containing repeating units

single repeat element

origin of replication; starting site for duplication of nucleic acid to give two identical copies

mature ribosomal RNA; the RNA component of the ribonucleoprotein particle (ribosome) which assembles amino acids into proteins

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

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

small cytoplasmic RNA; any one of several small cytoplasmic RNA molecules present in the cytoplasm and (sometimes) nucleus of a eukaryote

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

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

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

hairpin; a double-helical region formed by base-pairing between adjacent (inverted) complementary sequences in a single strand of RNA or DNA

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 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)

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 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

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

author is unsure of exact sequence in this 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

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

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'-most region of a precursor transcript that is clipped off during processing

region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein

5'-most region of a precursor transcript that is clipped off during processing

region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein

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

a conserved hexamer about 35 bp upstream of the start point of bacterial transcription units; consensus=TTGACa [ ] or TGTTGACA [ ]