| 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 upstream 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 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 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 [ ]. |