| 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 [ ] |