FT term SO term SO ID FT definition SO definition - located_sequence_feature SO:0000110 "-" is a placeholder for no key; should be used when the need is merely to mark region in order to comment on it or to use it in another feature's location; A biological feature that can be attributed to a region of biological sequence. -10_signal minus_10_signal SO:0000175 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 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 minus_35_signal SO:0000176 a conserved hexamer about 35 bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA; A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. 3'UTR three_prime_UTR SO:0000205 region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein; A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein. 3'clip three_prime_clip SO:0000557 3'-most region of a precursor transcript that is clipped off during processing; 3'-most region of a precursor transcript that is clipped off during processing. 5'UTR five_prime_UTR SO:0000204 region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein; A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein. 5'clip five_prime_clip SO:0000555 5'-most region of a precursor transcript that is clipped off during processing; 5' most region of a precursor transcript that is clipped off during processing. CAAT_signal CAAT_signal SO:0000172 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]. 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|T)CAATCT. CDS CDS SO:0000316 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. A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon. C_region undefined 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 D-loop D_loop SO:0000297 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 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 D_gene SO:0000458 Diversity segment of immunoglobulin heavy chain, and T-cell receptor beta chain; germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment. GC_signal GC_rich_region SO:0000173 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; 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. J_segment undefined joining segment of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains; LTR long_terminal_repeat SO:0000286 long terminal repeat, a sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses; A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses. N_region undefined extra nucleotides inserted between rearranged immunoglobulin segments. RBS ribosome_entry_site SO:0000139 ribosome binding site; Region in mRNA where ribosome assembles. STS STS SO:0000331 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; Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known. S_region undefined 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_signal TATA_box SO:0000174 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]; A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T). V_region undefined 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; V_segment undefined 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; attenuator attenuator SO:0000140 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 A sequence segment located between the promoter and a structural gene that causes partial termination of transcription. conflict undefined independent determinations of the "same" sequence differ at this site or region; Or /compare=[accession-number.sequence-version] enhancer enhancer SO:0000165 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; 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 exon SO:0000147 region of genome that codes for portion of spliced mRNA, rRNA and tRNA; may contain 5'UTR, all CDSs and 3' UTR; A region of the genome that codes for portion of spliced messenger RNA (SO:0000234); may contain 5'-untranslated region (SO:0000204), all open reading frames (SO:0000236) and 3'-untranslated region (SO:0000205). gap gap SO:0000730 gap in the sequence A gap in the sequence of known length. THe unkown bases are filled in with N's. gene gene SO:0000704 region of biological interest identified as a gene and for which a name has been assigned; A locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions iDNA iDNA SO:0000723 intervening DNA; DNA which is eliminated through any of several kinds of recombination; Genomic sequence removed from the genome, as a normal event, by a process of recombination. intron intron SO:0000188 a segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it; A segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it. mRNA mRNA SO:0000234 messenger RNA; includes 5'untranslated region (5'UTR), coding sequences (CDS, exon) and 3'untranslated region (3'UTR); messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns. mat_peptide mature_peptide SO:0000419 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); The coding sequence for the mature or final peptide or protein product following post-translational modification. misc_RNA transcript SO:0000673 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); An RNA synthesized on a DNA or RNA template by an RNA polymerase. misc_binding binding_site SO:0000409 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); A region on the surface of a molecule that may interact with another molecule. misc_difference sequence_difference SO:0000413 feature sequence is different from that presented in the entry and cannot be described by any other Difference key (conflict, unsure, old_sequence, variation, or modified_base); A region where the sequences differs from that of a specified sequence. misc_feature region SO:0000001 region of biological interest which cannot be described by any other feature key; a new or rare feature; Continous sequence. misc_recomb recombination_feature SO:0000298 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 (/insertion_seq, /transposon, /proviral); misc_signal regulatory_region SO:0005836 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). A DNA sequence that controls the expression of a gene. misc_structure sequence_secondary_structure SO:0000002 any secondary or tertiary nucleotide structure or conformation that cannot be described by other Structure keys (stem_loop and D-loop); A folded sequence. modified_base modified_base_site SO:0000305 the indicated nucleotide is a modified nucleotide and should be substituted for by the indicated molecule (given in the mod_base qualifier value) A modified nucleotide, i.e. a nucleotide other than A, T, C. G or (in RNA) U. old_sequence undefined the presented sequence revises a previous version of the sequence at this location; Or /compare=[accession-number.sequence-version] operon operon SO:0000178 region containing polycistronic transcript containing genes that encode enzymes that are in the same metabolic pathway and regulatory sequences A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region. oriT origin_of_transfer SO:0000724 origin of transfer; region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization A region of a DNA molecule whre transfer is initiated during the process of conjugation or mobilization. polyA_signal polyA_signal_sequence SO:0000551 recognition region necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA [1]; The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA. polyA_site polyA_site SO:0000553 site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation; The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. precursor_RNA primary_transcript SO:0000185 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); The primary (initial, unprocessed) transcript; includes five_prime_clip (SO:0000555), five_prime_untranslated_region (SO:0000204), open reading frames (SO:0000236), introns (SO:0000188) and three_prime_ untranslated_region (three_prime_UTR), and three_prime_clip (SO:0000557). prim_transcript primary_transcript SO:0000185 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); The primary (initial, unprocessed) transcript; includes five_prime_clip (SO:0000555), five_prime_untranslated_region (SO:0000204), open reading frames (SO:0000236), introns (SO:0000188) and three_prime_ untranslated_region (three_prime_UTR), and three_prime_clip (SO:0000557). primer_bind primer_binding_site SO:0005850 non-covalent primer binding site for initiation of replication, transcription, or reverse transcription; includes site(s) for synthetic e.g., PCR primer elements; Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription. promoter promoter SO:0000167 region on a DNA molecule involved in RNA polymerase binding to initiate transcription; The region on a DNA molecule involved in RNA polymerase binding to initiate transcription. protein_bind protein_binding_site SO:0000410 non-covalent protein binding site on nucleic acid; A region of a molecule that binds to a protein. rRNA rRNA SO:0000252 mature ribosomal RNA ; RNA component of the ribonucleoprotein particle (ribosome) which assembles amino acids into proteins. RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity. repeat_region repeat_region SO:0000657 region of genome containing repeating units; A region of sequence containing one or more repeat units. repeat_unit repeat_unit SO:0000726 single repeat element; A single repeat element. satellite satellite_DNA SO:0000005 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; The 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 scRNA SO:0000013 small cytoplasmic RNA; any one of several small cytoplasmic RNA molecules present in the cytoplasm and (sometimes) nucleus of a eukaryote; Any one of several small cytoplasmic RNA moleculespresent in the cytoplasm and sometimes nucleus of a eukaryote. sig_peptide signal_peptide SO:0000418 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; The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence. snRNA snRNA SO:0000274 small nuclear RNA molecules involved in pre-mRNA splicing and processing Small non-coding RNA in the nucleoplasm. snoRNA snoRNA SO:0000275 small nucleolar RNA molecules mostly involved in rRNA modification and processing; Small nucleolar RNAs (snoRNAs) are involved in the processing and modification of rRNA in the nucleolus. There are two main classes of snoRNAs: the box C/D class, and the box H/ACA class. U3 snoRNA is a member of the box C/D class. Indeed, the box C/D element is a subset of the six short sequence elements found in all U3 snoRNAs, namely boxes A, A', B, C, C', and D. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA. source databank_entry SO:2000061 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. /mol_type="genomic DNA", "genomic RNA", "mRNA", "tRNA", "rRNA", "snoRNA", "snRNA", "scRNA", "pre-RNA", "other RNA", "other DNA", "unassigned DNA", "unassigned RNA" The sequence referred to by an entry in a databank such as Genbank or SwissProt. stem_loop stem_loop SO:0000313 hairpin; a double-helical region formed by base-pairing between adjacent (inverted) complementary sequences in a single strand of RNA or DNA. A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences. tRNA tRNA SO:0000253 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; Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. tRNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). tRNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position. terminator terminator SO:0000141 sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription; The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription. transit_peptide transit_peptide SO:0000725 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; The 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. unsure undefined author is unsure of exact sequence in this region; variation sequence_variant SO:0000109 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); A region of sequence where variation has been observed.