Feature Key assembly_gap Definition gap between two components of a genome or transcriptome assembly; Mandatory qualifiers /estimated_length=unknown or /gap_type="TYPE" /linkage_evidence="TYPE" (Note: Mandatory only if the /gap_type is "within scaffold" or "repeat within scaffold".If there are multiple types of linkage_evidence they will appear as multiple /linkage_evidence="TYPE" qualifiers. For all other types of assembly_gap features, use of the /linkage_evidence qualifier is invalid.) Mandatory qualifiers under assembly_gap feature for transcriptome shotgun assemblies (TSA): /estimated_length= /gap_type="within scaffold" and /linkage_evidence="TYPE" where TYPE can not be "unspecified"; Comment the location span of the assembly_gap feature for an unknown gap has to be specified by the submitter; the specified gap length has to be reasonable (less or = 1000) and will be indicated as "n"'s in sequence. However, the value for the estimated_length of assembly_gap features within a single (non-CON) transcriptome record must be an integer and can not be "unknown"; Feature Key C_region Definition 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 Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /product="text" /pseudo /pseudogene="TYPE" /standard_name="text" Parent Key CDS Organism scope eukaryotes Feature Key CDS Definition 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. Optional qualifiers /allele="text" /artificial_location="[artificial_location_value]" /citation=[number] /codon_start=<1 or 2 or 3> /db_xref=":" /EC_number="text" /exception="[exception_value]" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /number=unquoted text (single token) /old_locus_tag="text" (single token) /operon="text" /product="text" /protein_id="" /pseudo /pseudogene="TYPE" /ribosomal_slippage /standard_name="text" /translation="text" /transl_except=(pos:,aa:) /transl_table = /trans_splicing Comment /codon_start has valid value of 1 or 2 or 3, indicating the offset at which the first complete codon of a coding feature can be found, relative to the first base of that feature; /transl_table defines the genetic code table used if other than the universal genetic code table; genetic code exceptions outside the range of the specified tables is reported in /transl_except qualifier; /protein_id consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point; when the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; Feature Key centromere Definition region of biological interest identified as a centromere and which has been experimentally characterized; Optional qualifiers /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /inference="[CATEGORY:]TYPE[(same species)][:EVIDENCE_BASIS]" /note="text" /standard_name="text" Comment the centromere feature describes the interval of DNA that corresponds to a region where chromatids are held and a kinetochore is formed Feature Key D-loop Definition 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 Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) Molecule scope DNA Feature Key D_segment Definition Diversity segment of immunoglobulin heavy chain, and T-cell receptor beta chain; Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /product="text" /pseudo /pseudogene="TYPE" /standard_name="text" Parent Key CDS Organism scope eukaryotes Feature Key exon Definition region of genome that codes for portion of spliced mRNA, rRNA and tRNA; may contain 5'UTR, all CDSs and 3' UTR; Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /EC_number="text" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /number=unquoted text (single token) /old_locus_tag="text" (single token) /product="text" /pseudo /pseudogene="TYPE" /standard_name="text" /trans_splicing Feature Key gap Definition gap in the sequence Mandatory qualifiers /estimated_length=unknown or Optional qualifiers /experiment="[CATEGORY:]text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /map="text" /note="text" Comment the location span of the gap feature for an unknown gap is 100 bp, with the 100 bp indicated as 100 "n"'s in the sequence. Where estimated length is indicated by an integer, this is indicated by the same number of "n"'s in the sequence. No upper or lower limit is set on the size of the gap. Feature Key gene Definition region of biological interest identified as a gene and for which a name has been assigned; Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /operon="text" /product="text" /pseudo /pseudogene="TYPE" /phenotype="text" /standard_name="text" /trans_splicing Comment the gene feature describes the interval of DNA that corresponds to a genetic trait or phenotype; the feature is, by definition, not strictly bound to it's positions at the ends; it is meant to represent a region where the gene is located. Feature Key iDNA Definition intervening DNA; DNA which is eliminated through any of several kinds of recombination; Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /number=unquoted text (single token) /old_locus_tag="text" (single token) /standard_name="text" Molecule scope DNA Comment e.g., in the somatic processing of immunoglobulin genes. Feature Key intron Definition a segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it; Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /number=unquoted text (single token) /old_locus_tag="text" (single token) /pseudo /pseudogene="TYPE" /standard_name="text" /trans_splicing Feature Key J_segment Definition joining segment of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains; Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /product="text" /pseudo /pseudogene="TYPE" /standard_name="text" Parent Key CDS Organism scope eukaryotes Feature Key LTR Definition long terminal repeat, a sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses; Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /standard_name="text" Comment This Feature Key will be deprecated on 15-DEC-2015; please refer to Feature Key repeat_region and Qualifier Key /rpt_type. Feature Key mat_peptide Definition 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); Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /EC_number="text" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /product="text" /pseudo /pseudogene="TYPE" /standard_name="text" Feature Key misc_binding Definition 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); Mandatory qualifiers /bound_moiety="text" Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) Comment note that feature key regulatory with /regulatory_class="ribosome_binding_site" should be used for ribosome binding sites. Feature Key misc_difference Definition feature sequence is different from that presented in the entry and cannot be described by any other difference key (old_sequence, variation, or modified_base); Optional qualifiers /allele="text" /citation=[number] /clone="text" /compare=[accession-number.sequence-version] /db_xref=":" /experiment="[CATEGORY:]text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /phenotype="text" /replace="text" /standard_name="text" Comment the misc_difference feature key should be used to describe variability that arises as a result of genetic manipulation (e.g. site directed mutagenesis); use /replace="" to annotate deletion, e.g. misc_difference 412..433 /replace="" Feature Key misc_feature Definition region of biological interest which cannot be described by any other feature key; a new or rare feature; Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /number=unquoted text (single token) /old_locus_tag="text" (single token) /phenotype="text" /product="text" /pseudo /pseudogene="TYPE" /standard_name="text" Comment this key should not be used when the need is merely to mark a region in order to comment on it or to use it in another feature's location Feature Key misc_recomb Definition 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); Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /standard_name="text" Molecule scope DNA Feature Key misc_RNA Definition 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); Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /operon="text" /product="text" /pseudo /pseudogene="TYPE" /standard_name="text" /trans_splicing Feature Key misc_structure Definition any secondary or tertiary nucleotide structure or conformation that cannot be described by other Structure keys (stem_loop and D-loop); Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /standard_name="text" Feature Key mobile_element Definition region of genome containing mobile elements; Mandatory qualifiers /mobile_element_type=" [:]" Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /rpt_family="text" /rpt_type= /standard_name="text" Feature Key modified_base Definition the indicated nucleotide is a modified nucleotide and should be substituted for by the indicated molecule (given in the mod_base qualifier value) Mandatory qualifiers /mod_base= Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /frequency="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) Comment value is limited to the restricted vocabulary for modified base abbreviations; Feature Key mRNA Definition messenger RNA; includes 5'untranslated region (5'UTR), coding sequences (CDS, exon) and 3'untranslated region (3'UTR); Optional qualifiers /allele="text" /artificial_location="[artificial_location_value]" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /operon="text" /product="text" /pseudo /pseudogene="TYPE" /standard_name="text" /trans_splicing Feature Key ncRNA Definition a non-protein-coding gene, other than ribosomal RNA and transfer RNA, the functional molecule of which is the RNA transcript; Mandatory qualifiers /ncRNA_class="TYPE" Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /operon="text" /product="text" /pseudo /pseudogene="TYPE" /standard_name="text" /trans_splicing Example /ncRNA_class="miRNA" /ncRNA_class="siRNA" /ncRNA_class="scRNA" Comment the ncRNA feature is not used for ribosomal and transfer RNA annotation, for which the rRNA and tRNA feature keys should be used, respectively; Feature Key N_region Definition extra nucleotides inserted between rearranged immunoglobulin segments. Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /product="text" /pseudo /pseudogene="TYPE" /standard_name="text" Parent Key CDS Organism scope eukaryotes Feature Key old_sequence Definition the presented sequence revises a previous version of the sequence at this location; Mandatory qualifiers /citation=[number] Or /compare=[accession-number.sequence-version] Optional qualifiers /allele="text" /db_xref=":" /experiment="[CATEGORY:]text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /replace="text" Comment /replace="" is used to annotate deletion, e.g. old_sequence 12..15 /replace="" NOTE: This feature key is not valid in entries/records created from 15-Oct-2007. Feature Key operon Definition 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 Mandatory qualifiers /operon="text" Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /map="text" /note="text" /phenotype="text" /pseudo /pseudogene="TYPE" /standard_name="text" Feature Key oriT Definition origin of transfer; region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization Optional qualifiers /allele="text" /bound_moiety="text" /citation=[number] /db_xref=":" /direction=value /experiment="[CATEGORY:]text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /rpt_family="text" /rpt_type= /rpt_unit_range= /rpt_unit_seq="text" /standard_name="text" Molecule Scope DNA Comment rep_origin should be used for origins of replication; /direction has legal values RIGHT, LEFT and BOTH, however only RIGHT and LEFT are valid when used in conjunction with the oriT feature; origins of transfer can be present in the chromosome; plasmids can contain multiple origins of transfer Feature Key polyA_site Definition site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation; Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) Organism scope eukaryotes and eukaryotic viruses Feature Key precursor_RNA Definition any RNA species that is not yet the mature RNA product; may include ncRNA, rRNA, tRNA, 5' untranslated region (5'UTR), coding sequences (CDS, exon), intervening sequences (intron) and 3' untranslated region (3'UTR); Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /operon="text" /product="text" /standard_name="text" /trans_splicing Comment used for RNA which may be the result of post-transcriptional processing; if the RNA in question is known not to have been processed, use the prim_transcript key. Feature Key prim_transcript Definition primary (initial, unprocessed) transcript; may include ncRNA, rRNA, tRNA, 5' untranslated region (5'UTR), coding sequences (CDS, exon), intervening sequences (intron) and 3' untranslated region (3'UTR); Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /operon="text" /standard_name="text" Feature Key primer_bind Definition non-covalent primer binding site for initiation of replication, transcription, or reverse transcription; includes site(s) for synthetic e.g., PCR primer elements; Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /standard_name="text" /PCR_conditions="text" Comment used to annotate the site on a given sequence to which a primer molecule binds - not intended to represent the sequence of the primer molecule itself; PCR components and reaction times may be stored under the "/PCR_conditions" qualifier; since PCR reactions most often involve pairs of primers, a single primer_bind key may use the order() operator with two locations, or a pair of primer_bind keys may be used. Feature Key protein_bind Definition non-covalent protein binding site on nucleic acid; Mandatory qualifiers /bound_moiety="text" Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /operon="text" /standard_name="text" Comment note that feature key regulatory with /regulatory_class="ribosome_binding_site" should be used for ribosome binding sites. Feature Key regulatory Definition any region of sequence that functions in the regulation of transcription or translation; Mandatory qualifiers /regulatory_class="TYPE" Optional qualifiers /allele="text" /bound_moiety="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /operon="text" /phenotype="text" /pseudo /pseudogene="TYPE" /standard_name="text" Comment This feature has replaced the following Feature Keys on 15-DEC-2014: enhancer, promoter, CAAT_signal, TATA_signal, -35_signal, -10_signal, RBS, GC_signal, polyA_signal, attenuator, terminator, misc_signal. Feature Key repeat_region Definition region of genome containing repeating units; Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /rpt_family="text" /rpt_type= /rpt_unit_range= /rpt_unit_seq="text" /satellite="[:][ ]" /standard_name="text" Feature Key rep_origin Definition origin of replication; starting site for duplication of nucleic acid to give two identical copies; Optional Qualifiers /allele="text" /citation=[number] /db_xref=":" /direction=value /experiment="[CATEGORY:]text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /standard_name="text" Comment /direction has valid values: RIGHT, LEFT, or BOTH. Feature Key rRNA Definition mature ribosomal RNA; RNA component of the ribonucleoprotein particle (ribosome) which assembles amino acids into proteins. Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /operon="text" /product="text" /pseudo /pseudogene="TYPE" /standard_name="text" Comment rRNA sizes should be annotated with the /product qualifier. Feature Key S_region Definition 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; Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /product="text" /pseudo /pseudogene="TYPE" /standard_name="text" Organism scope eukaryotes Feature Key sig_peptide Definition 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; Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /product="text" /pseudo /pseudogene="TYPE" /standard_name="text" Feature Key source Definition 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. Mandatory qualifiers /organism="text" /mol_type="genomic DNA", "genomic RNA", "mRNA", "tRNA", "rRNA", "other RNA", "other DNA", "transcribed RNA", "viral cRNA", "unassigned DNA", "unassigned RNA" Optional qualifiers /altitude="text" /bio_material="[:[:]]" /cell_line="text" /cell_type="text" /chromosome="text" /citation=[number] /clone="text" /clone_lib="text" /collected_by="text" /collection_date="text" /country="[:][, ]" /cultivar="text" /culture_collection=":[:]" /db_xref=":" /dev_stage="text" /ecotype="text" /environmental_sample /focus /germline /haplogroup="text" /haplotype="text" /host="text" /identified_by="text" /isolate="text" /isolation_source="text" /lab_host="text" /lat_lon="text" /macronuclear /map="text" /mating_type="text" /note="text" /organelle= /PCR_primers="[fwd_name: XXX, ]fwd_seq: xxxxx, [rev_name: YYY, ]rev_seq: yyyyy" /plasmid="text" /pop_variant="text" /proviral /rearranged /segment="text" /serotype="text" /serovar="text" /sex="text" /specimen_voucher="[:[:]]" /strain="text" /sub_clone="text" /sub_species="text" /sub_strain="text" /tissue_lib="text" /tissue_type="text" /transgenic /type_material=" of " /variety="text" Molecule scope any Comment transgenic sequences must have at least two source feature keys; in a transgenic sequence the source feature key describing the organism that is the recipient of the DNA must span the entire sequence; see Appendix III /organelle for a list of Feature Key stem_loop Definition hairpin; a double-helical region formed by base-pairing between adjacent (inverted) complementary sequences in a single strand of RNA or DNA. Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /operon="text" /standard_name="text" Feature Key STS Definition 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; Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /standard_name="text" Molecule scope DNA Parent key misc_binding Comment STS location to include primer(s) in primer_bind key or primers. Feature Key telomere Definition region of biological interest identified as a telomere and which has been experimentally characterized; Optional qualifiers /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text"/note="text" /inference="[CATEGORY:]TYPE[(same species)][:EVIDENCE_BASIS]" /note="text" /rpt_type= /rpt_unit_range= /rpt_unit_seq="text" /standard_name="text" Comment the telomere feature describes the interval of DNA that corresponds to a specific structure at the end of the linear eukaryotic chromosome which is required for the integrity and maintenance of the end; this region is unique compared to the rest of the chromosome and represent the physical end of the chromosome; Feature Key tmRNA Definition 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; Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /product="text" /pseudo /pseudogene="TYPE" /standard_name="text" /tag_peptide= Feature Key transit_peptide Definition 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; Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /product="text" /pseudo /pseudogene="TYPE" /standard_name="text" Feature Key tRNA Definition 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; Optional qualifiers /allele="text" /anticodon=(pos:,aa:,seq:) /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /operon="text" /product="text" /pseudo /pseudogene="TYPE" /standard_name="text" /trans_splicing Feature Key unsure Definition a small region of sequenced bases, generally 10 or fewer in its length, which could not be confidently identified. Such a region might contain called bases (A, T, G, or C), or a mixture of called-bases and uncalled-bases ('N'). The unsure feature should not be used when annotating gaps in genome assemblies. Please refer to assembly_gap feature for gaps within the sequence of an assembled genome. For annotation of gaps in other sequences than assembled genomes use the gap feature. Optional qualifiers /allele="text" /citation=[number] /compare=[accession-number.sequence-version] /db_xref=":" /experiment="[CATEGORY:]text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /replace="text" Comment use /replace="" to annotate deletion, e.g. unsure 11..15 /replace="" Feature Key V_region Definition 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; Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /product="text" /pseudo /pseudogene="TYPE" /standard_name="text" Parent Key CDS Organism scope eukaryotes Feature Key V_segment Definition 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; Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /product="text" /pseudo /pseudogene="TYPE" /standard_name="text" Parent Key CDS Organism scope eukaryotes Feature Key variation Definition 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); Optional qualifiers /allele="text" /citation=[number] /compare=[accession-number.sequence-version] /db_xref=":" /experiment="[CATEGORY:]text" /frequency="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /phenotype="text" /product="text" /replace="text" /standard_name="text" Comment used to describe alleles, RFLP's,and other naturally occurring mutations and polymorphisms; variability arising as a result of genetic manipulation (e.g. site directed mutagenesis) should be described with the misc_difference feature; use /replace="" to annotate deletion, e.g. variation 4..5 /replace="" Feature Key 3'UTR Definition 1) region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein; 2) region at the 3' end of an RNA virus (following the last stop codon) that is not translated into a protein; Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /standard_name="text" /trans_splicing Feature Key 5'UTR Definition 1) region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein; 2) region at the 5' end of an RNA virus genome (preceding the first initiation codon) that is not translated into a protein; Optional qualifiers /allele="text" /citation=[number] /db_xref=":" /experiment="[CATEGORY:]text" /function="text" /gene="text" /gene_synonym="text" /inference="[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" /locus_tag="text" (single token) /map="text" /note="text" /old_locus_tag="text" (single token) /standard_name="text" /trans_splicing