gap between two components of a CON record that is part of a genome assembly;
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
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 [1,2].
region of biological interest identified as a centromere and which has been experimentally characterized;
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.
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
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;
Enzyme Commission number for enzyme product of sequence
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, rRNA and tRNA; may contain 5'UTR, all CDSs and 3' UTR;
region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein;
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;
International Nucleotide Sequence Database Collaboration
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;
qualifiers required with the key; if there are no mandatory qualifiers, this field is omitted.
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);
messenger RNA; includes 5'untranslated region (5'UTR), coding sequences (CDS, exon) and 3'untranslated region (3'UTR);
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 [1,2,3,4];
a conserved hexamer about 35 bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA;
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 (unsure, old_sequence, variation, or modified_base);
region of biological interest which cannot be described by any other feature key; a new or rare feature;
any transcript or RNA product that cannot be defined by other RNA keys (prim_transcript, precursor_RNA, mRNA, 5'UTR, 3'UTR, exon, CDS, sig_peptide, transit_peptide, mat_peptide, intron, polyA_site, ncRNA, rRNA and tRNA);
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 or qualifiers of source key (/proviral);
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 nucleotide structure or conformation that cannot be described by other Structure keys (stem_loop and D-loop);
region of genome containing mobile elements;
the indicated nucleotide is a modified nucleotide and should be substituted for by the indicated molecule (given in the mod_base qualifier value)
extra nucleotides inserted between rearranged immunoglobulin segments.
a non-protein-coding gene, other than ribosomal RNA and transfer RNA, the functional molecule of which is the RNA transcript;
the presented sequence revises a previous version of the sequence at this location;
region containing polycistronic transcript including a cluster of genes that are under the control of the same regulatory sequences/promotor and in the same biological pathway
optional qualifiers associated with the key
origin of transfer; region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization
description of reaction conditions and components for PCR
PCR primers that were used to amplify the sequence. A single /PCR_primers qualifier should contain all the primers used for a single PCR reaction. If multiple forward or reverse primers are present in a single PCR reaction, multiple sets of fwd_name/fwd_seq or rev_name/rev_seq values will be present.
recognition region necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA [1];
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' untranslated region (5'UTR), coding sequences (CDS, exon), intervening sequences (intron) and 3' untranslated region (3'UTR);
primary (initial, unprocessed) transcript; includes 5' untranslated region (5'UTR), coding sequences (CDS, exon), intervening sequences (intron) and 3' untranslated region (3'UTR);
non-covalent primer binding site for initiation of replication, transcription, or reverse transcription; includes site(s) for synthetic e.g., PCR primer elements;
region on a DNA molecule involved in RNA polymerase binding to initiate transcription;
non-covalent protein binding site on nucleic acid;
region of genome containing repeating units;
origin of replication; starting site for duplication of nucleic acid to give two identical copies;
mature ribosomal RNA; RNA component of the ribonucleoprotein particle (ribosome) which assembles amino acids into proteins.
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;
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;
identifies the biological source of the specified span of the sequence; this key is mandatory; more than one source key per sequence is allowed; every entry/record will have, as a minimum, either a single source key spanning the entire sequence or multiple source keys, which together, span the entire sequence.
hairpin; a double-helical region formed by base-pairing between adjacent (inverted) complementary sequences in a single strand of RNA or DNA.
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;
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) [1,2];
region of biological interest identified as a telomere and which has been experimentally characterized;
sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription;
region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein;
transfer messenger RNA; tmRNA acts as a tRNA first, and then as an mRNA that encodes a peptide tag; the ribosome translates this mRNA region of tmRNA and attaches the encoded peptide tag to the C-terminus of the unfinished protein; this attached tag targets the protein for destruction or proteolysis;
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;
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;
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 composed of 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 (e.g., RFLPs, polymorphisms, etc.) which differ from the presented sequence at this location (and possibly others);
geographical altitude of the location from which the sample was collected
location of the anticodon of tRNA and the amino acid for which it codes
indicates that location of the CDS or mRNA is modified to adjust for the presence of a frameshift or internal stop codon and not because of biological processing between the regions.
identifier for the biological material from which the nucleic acid sequenced was obtained, with optional institution code and collection code for the place where it is currently stored.
name of the molecule/complex that may bind to the given feature
cell line from which the sequence was obtained
cell type from which the sequence was obtained
chromosome (e.g. Chromosome number) from which the sequence was obtained
reference to a citation listed in the entry reference field
clone from which the sequence was obtained
clone library from which the sequence was obtained
indicates the offset at which the first complete codon of a coding feature can be found, relative to the first base of that
name of persons or institute who collected the specimen
Reference details of an existing public INSD entry to which a comparison is made
locality of isolation of the sequenced organism indicated in terms of political names for nations, oceans or seas, followed by regions and localities
cultivar (cultivated variety) of plant from which sequence was obtained.
institution code and identifier for the culture from which the nucleic acid sequenced was obtained, with optional collection code.
database cross-reference: pointer to related information in another database.
if the sequence was obtained from an organism in a specific developmental stage, it is specified with this qualifier
a population within a given species displaying genetically based, phenotypic traits that reflect adaptation to a local habitat.
identifies sequences derived by direct molecular isolation from a bulk environmental DNA sample (by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods) with no reliable identification of the source organism. Environmental samples include clinical samples, gut contents, and other sequences from anonymous organisms that may be associated with a particular host. They do not include endosymbionts that can be reliably recovered from a particular host, organisms from a readily identifiable but uncultured field sample (e.g., many cyanobacteria), or phytoplasmas that can be reliably recovered from diseased plants (even though these cannot be grown in axenic culture).
estimated length of the gap in the sequence
indicates that the coding region cannot be translated using standard biological rules
annotated by transcript or proteomic data
a brief description of the nature of the experimental evidence that supports the feature identification or assignment.
identifies the source feature of primary biological interest for records that have multiple source features originating from different organisms and that are not transgenic.
frequency of the occurrence of a feature
type of gap connecting components in records of a genome assembly, or the type of biological gap in a record that is part of a genome assembly;
symbol of the gene corresponding to a sequence region
synonymous, replaced, obsolete or former gene symbol
the sequence presented in the entry has not undergone somatic rearrangement as part of an adaptive immune response; it is the unrearranged sequence that was inherited from the parental germline
name for a group of similar haplotypes that share some sequence variation. Haplogroups are often used to track migration of population groups.
name for a combination of alleles that are linked together on the same physical chromosome. In the absence of recombination, each haplotype is inherited as a unit, and may be used to track gene flow in populations.
natural (as opposed to laboratory) host to the organism from which sequenced molecule was obtained
name of the expert who identified the specimen taxonomically
a structured description of non-experimental evidence that supports the feature identification or assignment.
individual isolate from which the sequence was obtained
describes the physical, environmental and/or local geographical source of the biological sample from which the sequence was derived
scientific name of the laboratory host used to propagate the source organism from which the sequenced molecule was obtained
geographical coordinates of the location where the specimen was collected
type of evidence establishing linkage across an assembly_gap. Only allowed to be used with assembly_gap features that have a /gap_type value of "within scaffold" or "repeat within scaffold";
a submitter-supplied, systematic, stable identifier for a gene and its associated features, used for tracking purposes
if the sequence shown is DNA and from an organism which undergoes chromosomal differentiation between macronuclear and micronuclear stages, this qualifier is used to denote that the sequence is from macronuclear DNA.
mating type of the organism from which the sequence was obtained; mating type is used for prokaryotes, and for eukaryotes that undergo meiosis without sexually dimorphic gametes
type and name or identifier of the mobile element which is described by the parent feature
abbreviation for a modified nucleotide base
a structured description of the classification of the non-coding RNA described by the ncRNA parent key
a number to indicate the order of genetic elements (e.g., exons or introns) in the 5' to 3' direction
feature tag assigned for tracking purposes
name of the group of contiguous genes transcribed into a single transcript to which that feature belongs.
type of membrane-bound intracellular structure from which the sequence was obtained
scientific name of the organism that provided the sequenced genetic material.
differentiates between complete regions and partial ones
not to be used for new entries from 15-DEC-2001; use '<' and '>' signs in the location descriptors to indicate that the sequence is partial.
phenotype conferred by the feature, where phenotype is defined as a physical, biochemical or behavioural characteristic or set of characteristics
name of naturally occurring plasmid from which the sequence was obtained, where plasmid is defined as an independently replicating genetic unit that cannot be described by /chromosome or /segment
name of subpopulation or phenotype of the sample from which the sequence was derived
name of the product associated with the feature, e.g. the mRNA of an mRNA feature, the polypeptide of a CDS, the mature peptide of a mat_peptide, etc.
protein identifier, issued by International collaborators. this qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point.
this qualifier is used to flag sequence obtained from a virus or phage that is integrated into the genome of another organism
indicates that this feature is a non-functional version of the element named by the feature key
indicates that this feature is a pseudogene of the element named by the feature key
the sequence presented in the entry has undergone somatic rearrangement as part of an adaptive immune response; it is not the unrearranged sequence that was inherited from the parental germline
indicates that the sequence identified a feature's intervals is replaced by the sequence shown in "text"; if no sequence is contained within the qualifier, this indicates a deletion.
during protein translation, certain sequences can program ribosomes to change to an alternative reading frame by a mechanism known as ribosomal slippage
type of repeated sequence; "Alu" or "Kpn", for example
identifier for a satellite DNA marker, compose of many tandem repeats (identical or related) of a short basic repeated unit;
name of viral or phage segment sequenced
serological variety of a species characterized by its antigenic properties
serological variety of a species (usually a prokaryote) characterized by its antigenic properties
sex of the organism from which the sequence was obtained; sex is used for eukaryotic organisms that undergo meiosis and have sexually dimorphic gametes
identifier for the specimen from which the nucleic acid sequenced was obtained
sub-clone from which sequence was obtained
name of sub-species of organism from which sequence was obtained
name or identifier of a genetically or otherwise modified strain from which sequence was obtained, derived from a parental strain (which should be annotated in the /strain qualifier).sub_strain from which sequence was obtained
base location encoding the polypeptide for proteolysis tag of tmRNA and its termination codon;
tissue library from which sequence was obtained
tissue type from which the sequence was obtained
indicates that exons from two RNA molecules are ligated in intermolecular reaction to form mature RNA
identifies the source feature of the organism which was the recipient of transgenic DNA.
translational exception: single codon the translation of which does not conform to genetic code defined by /organism or /transl_table.
definition of genetic code table used if other than universal genetic code table. Tables used are described in appendix IV.
automatically generated one-letter abbreviated amino acid sequence derived from either the universal genetic code or the table as specified in /transl_table and as determined by an exception in the /transl_except qualifier
variety (= varietas, a formal Linnaean rank) of organism from which sequence was derived.