The DDBJ/ENA/GenBank Feature Table: Definition Version 10.9 November 2019 DNA Data Bank of Japan, Mishima, Japan. EMBL-EBI, European Nucleotide Archive, Cambridge, UK. GenBank, NCBI, Bethesda, MD, USA. 1 Introduction 2 Overview of the Feature Table format 2.1 Format Design 2.2 Key aspects of this feature table design 2.3 Feature Table Terminology 3 Feature table components and format 3.1 Naming conventions 3.2 Feature keys 3.2.1 Purpose 3.2.2 Format and conventions 3.2.3 Key groups and hierarchy 3.2.4 Feature key examples 3.3 Qualifiers 3.3.1 Purpose 3.3.2 Format and conventions 3.3.3 Qualifier values 3.3.4 Qualifier examples 3.4 Location 3.4.1 Purpose 3.4.2 Format and conventions 3.4.3 Location examples 4 Feature table Format 4.1 Format examples 4.2 Definition of line types 4.3 Data item positions 4.4 Use of blanks 5 Examples of sequence annotation 5.1 Eukaryotic gene 5.2 Bacterial operon 5.3 Artificial cloning vector (circular) 5.4 Plasmid 5.5 Repeat element 5.6 Immunoglobulin heavy chain 5.7 T-cell receptor 5.8 Transfer RNA 6 Limitations of this feature table design 7 Appendices 7.1 Appendix I EMBL, GenBank and DDBJ entries 7.1.1 EMBL Format 7.1.2 GenBank Format 7.1.3 DDBJ Format 7.2 Appendix II: Feature keys reference 7.3 Appendix III: Summary of qualifiers for feature keys 7.3.1 Qualifier List 7.4 Appendix IV: Controlled vocabularies 7.4.1 Nucleotide base codes (IUPAC) 7.4.2 Modified base abbreviations 7.4.3 Amino acid abbreviations 7.4.4 Modified and unusual Amino Acids 7.4.5 Genetic Code Tables 7.4.6 Country Names 7.4.7 Announces1 Introduction
Nucleic acid sequences provide the fundamental starting point for describing and understanding the structure, function, and development of genetically diverse organisms. The GenBank, EMBL, and DDBJ nucleic acid sequence data banks have from their inception used tables of sites and features to describe the roles and locations of higher order sequence domains and elements within the genome of an organism. In February, 1986, GenBank and EMBL began a collaborative effort (joined by DDBJ in 1987) to devise a common feature table format and common standards for annotation practice.2 Overview of the Feature Table format
The overall goal of the feature table design is to provide an extensive vocabulary for describing features in a flexible framework for manipulating them. The Feature Table documentation represents the shared rules that allow the three databases to exchange data on a daily basis. The range of features to be represented is diverse, including regions which: * perform a biological function, * affect or are the result of the expression of a biological function, * interact with other molecules, * affect replication of a sequence, * affect or are the result of recombination of different sequences, * are a recognizable repeated unit, * have secondary or tertiary structure, * exhibit variation, or have been revised or corrected.2.1 Format Design
The format design is based on a tabular approach and consists of the following items: Feature key - a single word or abbreviation indicating functional group Location - instructions for finding the feature Qualifiers - auxiliary information about a feature2.2 Key aspects of this feature table design
* Feature keys allow specific annotation of important sequence features. * Related features can be easily specified and retrieved. Feature keys are arranged hierarchically, allowing complex and compound features to be expressed. Both location operators and the feature keys show feature relationships even when the features are not contiguous. The hierarchy of feature keys allows broad categories of biological functionality, such as rRNAs, to be easily retrieved. * Generic feature keys provide a means for entering new or undefined features. A number of "generic" or miscellaneous feature keys have been added to permit annotation of features that cannot be adequately described by existing feature keys. These generic feature keys will serve as an intermediate step in the identification and addition of new feature keys. The syntax has been designed to allow the addition of new feature keys as they are required. * More complex locations (fuzzy and alternate ends, for example) can be specified. Each end point of a feature may be specified as a single point, an alternate set of possible end points, a base number beyond which the end point lies, or a region which contains the end point. * Features can be combined and manipulated in many different ways. The location field can contain operators or functional descriptors specifying what must be done to the sequence to reproduce the feature. For example, a series of exons may be "join"ed into a full coding sequence. * Standardized qualifiers provide precision and parsibility of descriptive details A combination of standardized qualifiers and their controlled-vocabulary values enable free-text descriptions to be avoided. * The nature of supporting evidence for a feature can be explicitly indicated. Features, such as open reading frames or sequences showing sequence similarity to consensus sequences, for which there is no direct experimental evidence can be annotated. Therefore, the feature table can incorporate contributions from researchers doing computational analysis of the sequence databases. However, all features that are supported by experimental data will be clearly marked as such. * The table syntax has been designed to be machine parsible. A consistent syntax allows machine extraction and manipulation of sequences coding for all features in the table.2.3 Feature Table Terminology
The format and wording in the feature table use common biological research terminology whenever possible. For example, an item in the feature table such as: Key Location/Qualifiers CDS 23..400 /product="alcohol dehydrogenase" /gene="adhI" might be read as: The feature CDS is a coding sequence beginning at base 23 and ending at base 400, has a product called 'alcohol dehydrogenase' and is coded for by a gene called "adhI". A more complex description: Key Location/Qualifiers CDS join(544..589,688..>1032) /product="T-cell receptor beta-chain" which might be read as: This feature, which is a partial coding sequence, is formed by joining elements indicated to form one contiguous sequence encoding a product called T- cell receptor beta-chain. The following sections contain detailed explanations of the feature table design showing conventions for each component of the feature table, examples of how the format might be implemented, a description of the exact column placement of all the data items and examples of complete sequence entries that have been annotated using the new format. The last section of this document describes known limitations of the current feature table design. Appendix I gives an example database entry for the DDBJ, GenBank and EMBL formats. Appendices II and III provide reference manuals for the feature table keys and qualifiers, respectively. Appendix IV includes controlled vocabularies such as nucleotide base codes, modified base abbreviations, genetic code tables etc. This document defines the syntax and vocabulary of the feature table. The syntax is sufficiently flexible to allow expression of a single biological entity in numerous ways. In such cases, the annotation staffs at the databases will propose conventions for standard means of denoting the entities. This feature table format is shared by GenBank, EMBL and DDBJ. Comments, corrections, and suggestions may be submitted to any of the database staffs. New format specifications will be added as needed.3 Feature table components and format
3.1 Naming conventions
Feature table components, including feature keys, qualifiers, accession numbers, database name abbreviations, and location operators, are all named following the same conventions. Component names may be no more than 20 characters long (Feature keys 15, Feature qualifiers 20) and must contain at least one letter. The following characters are permitted to occur in feature table component names: * Uppercase letters (A-Z) * Lowercase letters (a-z) Numbers (0-9) * Underscore (_) * Hyphen (-) * Single quotation mark or apostrophe (') * Asterisk (*)3.2 Feature keys
3.2.1 Purpose
Feature keys indicate (1) the biological nature of the annotated feature or (2) information about changes to or other versions of the sequence. The feature key permits a user to quickly find or retrieve similar features or features with related functions.3.2.2 Format and conventions
There is a defined list of allowable feature keys, which is shown in Appendix II. Each feature must contain a feature key.3.2.3 Key groups and hierarchy
The feature keys fall into families which are in some sense similar in function and which are annotated in a similar manner. A functional family may have a "generic" or miscellaneous key, which can be recognized by the 'misc.' prefix, that can used for instances not covered by the other defined keys of that group. The feature key groups are listed below with a short definition and an annotation example: 1. Difference and change features Indicate ways in which a sequence should be changed to produce a different "version": misc_difference location /replace="change_location" 2. Transcript features Indicate products made by a region: misc_RNA location 3. Binding features Indicate that a sequence or nucleotide is covalently, non-covalently, or otherwise bound to something else: misc_binding location /bound_moiety="bound molecule" 4. Repeat features Indicate repetitive sequence elements: repeat_region location 5. Recombination features Indicate regions that have been either inserted or deleted by recombination: misc_recomb location 6. Structure features Indicate sequence for which there is secondary or tertiary structural information: misc_structure location3.2.4 Feature key examples
Key Description CDS Protein-coding sequence rep_origin Origin of replication protein_bind Protein binding site on DNA tRNA mature transfer RNA See Appendix II for descriptions of all feature keys.3.3 Qualifiers
3.3.1 Purpose
Qualifiers provide a general mechanism for supplying information about features in addition to that conveyed by the key and location.3.3.2 Format and conventions
Qualifiers take the form of a slash (/) followed by the qualifier name and, if applicable, an equal sign (=) and a value. Each qualifier should have a single value; if multiple values are necessary, these should be represented by iterating the same qualifier, eg: Key Location/Qualifiers source 1..1000 /culture_collection="ATCC:11775" /culture_collection="CECT:515" If the location descriptor does not need a continuation line, the first qualifier begins a new line in the feature location column. If the location descriptor requires a continuation line, the first qualifier may follow immediately after the location. Any necessary continuation lines begin in the same column. See Section 4 for a complete description of data item positions.3.3.3 Qualifier values
Since qualifiers convey many different types of information, there are several value formats: 1. Free text 2. Controlled vocabulary or enumerated values 3. Citation or reference numbers 4. Sequences3.3.3.1 Free text
Most qualifier values will be a descriptive text phrase which must be enclosed in double quotation marks. When the text occupies more than one line, a single set of quotation marks is required at the beginning and at the end of the text. The text itself may be composed of any printable characters (ASCII values 32-126 decimal). If double quotation marks are used within a free text string, each set (") must be 'escaped' by placing a second double quotation mark immediately before it (""). For example: /note="This is an example of ""escaped"" quotation marks"3.3.3.2 Controlled vocabulary or enumerated values
Some qualifiers require values from a controlled vocabulary and are entered without quotation marks. For example, the '/direction' qualifier has only three values: 'left', 'right' or 'both'. Qualifier value controlled vocabularies, like feature table component names, must be treated as completely case insensitive: they may be entered and displayed in any combination of upper and lower case ('/direction=Left' '/direction=left' and '/ direction=LEFT' are all legal and all convey the same meaning). The database staffs reserve the right to regularize the case of qualifier values. Qualifier value controlled vocabularies will be maintained by the cooperating database staffs. Examples of controlled vocabularies can be found in Appendices IV and V. The database staff should be contacted for the current lists.3.3.3.3 Citation or reference numbers
The citation or published reference number (as enumerated in the entry 'REFERENCE' or 'RN' data item) should be enclosed in square brackets (e.g., [3]) to distinguish it from other numbers.3.3.3.4 Sequences
Literal sequence of nucleotide bases e.g., join(12..45,"atgcatt",988..1050) in location descriptors has become illegal starting from implementation of version 2.1 of the Feature Table Definition Document (December 15, 1998)3.3.4 Qualifier examples
Key Location/Qualifiers source 1..1509 /organism="Mus musculus" /strain="CD1" /mol_type="genomic DNA" regulatory <1..9 /gene="ubc42" /regulatory_class="promoter" mRNA join(10..567,789..1320) /gene="ubc42" CDS join(54..567,789..1254) /gene="ubc42" /product="ubiquitin conjugating enzyme" /function="cell division control"3.4 Location
3.4.1 Purpose
The location indicates the region of the presented sequence which corresponds to a feature.3.4.2 Format and conventions
The location contains at least one sequence location descriptor and may contain one or more operators with one or more sequence location descriptors. Base numbers refer to the numbering in the entry. This numbering designates the first base (5' end) of the presented sequence as base 1. Base locations beyond the range of the presented sequence may not be used in location descriptors, the only exception being location in a remote entry (see 3.4.2.1, e). Location operators and descriptors are discussed in more detail below.3.4.2.1 Location descriptors
The location descriptor can be one of the following: (a) a single base number (b) a site between two indicated adjoining bases (c) a single base chosen from within a specified range of bases (not allowed for new entries) (d) the base numbers delimiting a sequence span (e) a remote entry identifier followed by a local location descriptor (i.e., a-d) A site between two adjoining nucleotides, such as endonucleolytic cleavage site, is indicated by listing the two points separated by a carat (^). The permitted formats for this descriptor are n^n+1 (for example 55^56), or, for circular molecules, n^1, where "n" is the full length of the molecule, ie 1000^1 for circular molecule with length 1000. A single base chosen from a range of bases is indicated by the first base number and the last base number of the range separated by a single period (e.g., '12.21' indicates a single base taken from between the indicated points). From October 2006 the usage of this descriptor is restricted : it is illegal to use "a single base from a range" (c) either on its own or in combination with the "sequence span" (d) descriptor for newly created entries. The existing entries where such descriptors exist are going to be retrofitted. Sequence spans are indicated by the starting base number and the ending base number separated by two periods (e.g., '34..456'). The '<' and '>' symbols may be used with the starting and ending base numbers to indicate that an end point is beyond the specified base number. The starting and ending base positions can be represented as distinct base numbers ('34..456') or a site between two indicated adjoining bases. A location in a remote entry (not the entry to which the feature table belongs) can be specified by giving the accession-number and sequence version of the remote entry, followed by a colon ":", followed by a location descriptor which applies to that entry's sequence (i.e. J12345.1:1..15, see also examples below)3.4.2.2 Operators
The location operator is a prefix that specifies what must be done to the indicated sequence to find or construct the location corresponding to the feature. A list of operators is given below with their definitions and most common format. complement(location) Find the complement of the presented sequence in the span specified by " location" (i.e., read the complement of the presented strand in its 5'-to-3' direction) join(location,location, ... location) The indicated elements should be joined (placed end-to-end) to form one contiguous sequence order(location,location, ... location) The elements can be found in the specified order (5' to 3' direction), but nothing is implied about the reasonableness about joining them Note : location operator "complement" can be used in combination with either " join" or "order" within the same location; combinations of "join" and "order" within the same location (nested operators) are illegal.3.4.3 Location examples
The following is a list of common location descriptors with their meanings: Location Description 467 Points to a single base in the presented sequence 340..565 Points to a continuous range of bases bounded by and including the starting and ending bases <345..500 Indicates that the exact lower boundary point of a feature is unknown. The location begins at some base previous to the first base specified (which need not be contained in the presented sequence) and continues to and includes the ending base <1..888 The feature starts before the first sequenced base and continues to and includes base 888 1..>888 The feature starts at the first sequenced base and continues beyond base 888 102.110 Indicates that the exact location is unknown but that it is one of the bases between bases 102 and 110, inclusive 123^124 Points to a site between bases 123 and 124 join(12..78,134..202) Regions 12 to 78 and 134 to 202 should be joined to form one contiguous sequence complement(34..126) Start at the base complementary to 126 and finish at the base complementary to base 34 (the feature is on the strand complementary to the presented strand) complement(join(2691..4571,4918..5163)) Joins regions 2691 to 4571 and 4918 to 5163, then complements the joined segments (the feature is on the strand complementary to the presented strand) join(complement(4918..5163),complement(2691..4571)) Complements regions 4918 to 5163 and 2691 to 4571, then joins the complemented segments (the feature is on the strand complementary to the presented strand) J00194.1:100..202 Points to bases 100 to 202, inclusive, in the entry (in this database) with primary accession number 'J00194' join(1..100,J00194.1:100..202) Joins region 1..100 of the existing entry with the region 100..202 of remote entry J001944 Feature table Format
The examples below show the preferred sequence annotations for a number of commonly occurring sequence types. These examples may not be appropriate in all cases but should be used as a guide whenever possible. This section describes the columnar format used to write this feature table in "flat-file" form for distributions of the database.4.1 Format examples
Feature table format example (EMBL): FT source 1..1859 FT /db_xref="taxon:3899" FT /organism="Trifolium repens" FT /tissue_type="leaves" FT /clone_lib="lambda gt10" FT /clone="TRE361" FT /mol_type="genomic DNA" FT CDS 14..1495 FT /db_xref="MENDEL:11000" FT /db_xref="UniProtKB/Swiss-Prot:P26204" FT /note="non-cyanogenic" FT /EC_number="3.2.1.21" FT /product="beta-glucosidase" FT /protein_id="CAA40058.1" FT /translation="MDFIVAIFALFVISSFTITSTNAVEASTLLDIGNLSR....... ---------+---------+---------+---------+---------+---------+---------+--------- 1 10 20 30 40 50 60 70 79 Feature table format example (GenBank): source 1..8959 /organism="Homo sapiens" /db_xref="taxon:9606" /mol_type="genomic DNA" gene 212..8668 /gene="NF1" CDS 212..8668 /gene="NF1" /note="putative" /codon_start=1 /product="GAP-related protein" /protein_id="AAA59924.1" /translation="MAAHRPVEWVQAVVSRFDEQLPIKTGQQNTHTKVSTE....... ---------+---------+---------+---------+---------+---------+---------+--------- 1 10 20 30 40 50 60 70 79 Feature table format example (DDBJ): source 1..2136 /clone="pK28" /organism="Rattus norvegicus" /strain="Sprague-Dawley" /tissue_type="kidney" /mol_type="genomic DNA" mRNA 19..2128 CDS 31..1212 /codon_start=1 /function="Dual specificity protein tyrosine/threonine kinase" /product="MAP kinase kinase" /protein_id="BAA02603.1" /translation="MPKKKPTPIQLNPAPDGSAVNGTSSAETNLEALQKKL....... ---------+---------+---------+---------+---------+---------+---------+--------- 1 10 20 30 40 50 60 70 794.2 Definition of line types
The feature table consists of a header line, which contains the column titles for the table, and the individual feature entries. Each feature entry is composed of a feature descriptor line and qualifier and continuation lines, if needed. The feature descriptor line contains the feature's name, key, and location. If the location cannot be contained on the first line of the feature descriptor, it is continued on a continuation line immediately following the descriptor line. If the feature requires further attributes, feature qualifier lines immediately follow the corresponding feature descriptor line (or its continuation). Qualifier information that cannot be contained on one line continues on the following continuation lines as necessary. Thus, there are 4 types of feature table lines: Line type Content #/entry #/feature --------- ------- ------- --------- Header Column titles 1* N/A Feature descriptor Key and location 1 to many* 1 Feature qualifiers Qualifiers and values N/A 0 to many Continuation lines Feature descriptor or 0 to many 0 to many qualifier continuation4.3 Data item positions
The position of the data items within the feature descriptor line is as follows: column position data item --------------- --------- 1-5 blank 6-20 feature key 21 blank 22-80 location Data on the qualifier and continuation lines begins in column position 22 (the first 21 columns contain blanks). The EMBL format for all lines differs from the GenBank / DDBJ formats that it includes a line type abbreviation in columns 1 and 2.4.4 Use of blanks
Blanks (spaces) may, in general, be used within the feature location and qualifier values to make the construction more readable. The following rules should be observed: * Names of feature table components may not contain blanks (see Section 3.1) * Operator names may not be separated from the following open parenthesis (the beginning of the operand list) by blanks. * Qualifiers may not be separated from the preceding slash or the following equals sign (if one) by blanks5 Examples of sequence annotation
The examples below show the preferred sequence annotations for a number of commonly occurring sequence types. These examples may not be appropriate in all cases but should be used as a guide whenever possible.5.1 Eukaryotic gene
source 1..1509 /organism="Mus musculus" /strain="CD1" /mol_type="genomic DNA" regulatory <1..9 /gene="ubc42" /regulatory_class="promoter" mRNA join(10..567,789..1320) /gene="ubc42" CDS join(54..567,789..1254) /gene="ubc42" /product="ubiquitin conjugating enzyme" /function="cell division control" /translation="MVSSFLLAEYKNLIVNPSEHFKISVNEDNLTEGPPDTLY QKIDTVLLSVISLLNEPNPDSPANVDAAKSYRKYLYKEDLESYPMEKSLDECS AEDIEYFKNVPVNVLPVPSDDYEDEEMEDGTYILTYDDEDEEEDEEMDDE" exon 10..567 /gene="ubc42" /number=1 intron 568..788 /gene="ubc42" /number=1 exon 789..1320 /gene="ubc42" /number=2 regulatory 1310..1317 /regulatory_class="polyA_signal_sequence" /gene="ubc42"5.2 Bacterial operon
source 1..9430 /organism="Lactococcus sp." /strain="MG1234" /mol_type="genomic DNA" operon 160..6865 /operon="gal" regulatory 160..165 /operon="gal" /regulatory_class="minus_35_signal" regulatory 179..184 /operon="gal" /regulatory_class="minus_10_signal" CDS 405..1934 /operon="gal" /gene="galA" /product="galactose permease" /function="galactose transporter" CDS 2003..3001 /operon="gal" /gene="galM" /product="aldose 1-epimerase" /EC_number="5.1.3.3" /function="mutarotase" CDS 3235..4537 /operon="gal" /gene="galK" /product="galactokinase" /EC_number="2.7.1.6" mRNA 189..6865 /operon="gal"5.3 Artificial cloning vector (circular)
source 1..5300 /organism="Cloning vector pABC" /lab_host="Escherichia coli" /mol_type="other DNA" /focus source 1..5138 /organism="Escherichia coli" /mol_type="other DNA" /strain="K12" source 5139..5247 /organism="Aequorea victoria" /mol_type="other DNA" /dev_stage="adult" source 5248..5300 /organism="Escherichia coli" /mol_type="other DNA" /strain="K12" CDS join(complement(1..799),complement(5080..5120)) /gene="mob1" /product="mobilization protein 1" CDS complement(1697..2512) /gene="Km" /product="kanamycin resistance protein" CDS 3037..3711 /gene="rep1" /product="replication protein 1" CDS complement(4170..4829) /gene="Cm" /product="chloramphenicol resistance protein" CDS 5139..5247 /gene="GFP" /product="green fluorescent protein"5.4 Plasmid
source 1..2245 /organism="Escherichia coli" /plasmid="Plasmid XYZ" /strain="K12" /mol_type="genomic DNA" rep_origin 6 /direction=LEFT /note="ori" CDS complement(join(21..349,567..795)) /gene="trbC" /product="transfer protein C" CDS 803..1344 /gene="traN" /product="transfer protein N" CDS 1559..1985 /gene="incA" /product="incompatability protein A" CDS join(2004..2195,3..20) /gene="finP" /product="fertility inhibition protein P"5.5 Repeat element
source 1..1011 /organism="Homo sapiens" /clone="pha281u/1DO" /mol_type="genomic DNA" repeat_region 80..401 /rpt_type=DISPERSED /rpt_family="Alu-J"5.6 Immunoglobulin heavy chain
source 1..321 /organism="Mus musculus " /strain="BALB/c2 /cell_line="hybridoma 1A4" /rearranged /mol_type="mRNA" CDS <1..>321 /codon_start=1 /gene="VFM1-DFL16.1-JH4" /product="immunoglobulin heavy chain" V_region 1..277 /gene="VFM1" /product="immunoglobulin heavy chain variable region"5.7 T-cell receptor
source 1..402 /organism="Homo sapiens" /sex="male" /cell_type="CD4+ T-lymphocyte" /rearranged /clone="TCR1A.12" /mol_type="mRNA" sig_peptide 1..54 /gene="TCR1A" CDS 1..402 /gene="TCR1A" /product="T-cell receptor alpha chain" mat_peptide 55..399 /gene="TCR1A" /product="T-cell receptor alpha chain" V_region 55..327 /gene="TCR1A" J_segment 328..393 /gene="TCR1A" C_region 394..399 /gene="TCR1A"5.8 Transfer RNA
source 1..2345 /organism="Yersinia sp." /strain="IP134" /mol_type="genomic DNA" regulatory 644..650 /gene="tRNA-Leu(UUR)" /regulatory_class="minus_35_signal" tRNA 655..730 /gene="tRNA-Leu(UUR)" /anticodon=(pos:678..680,aa:Leu,seq:taa) /product="transfer RNA-Leu(UUR)"6 Limitations of this feature table design
During the development of the feature table design numerous choices between simplicity and representational power had to be made. In order to create a design which was capable of representing the most common features of biological significance, a certain degree of complexity in the syntax was guaranteed. However, to limit that level of complexity, certain limitations of the design syntax have been accepted.7 Appendices
7.1 Appendix I EMBL, GenBank and DDBJ entries
7.1.1 EMBL Format
ID X64011; SV 1; linear; genomic DNA; STD; PRO; 756 BP. XX AC X64011; S78972; XX SV X64011.1 XX DT 28-APR-1992 (Rel. 31, Created) DT 30-JUN-1993 (Rel. 36, Last updated, Version 6) XX DE Listeria ivanovii sod gene for superoxide dismutase XX KW sod gene; superoxide dismutase. XX OS Listeria ivanovii OC Bacteria; Firmicutes; Bacillus/Clostridium group; OC Bacillus/Staphylococcus group; Listeria. XX RN [1] RX MEDLINE; 92140371. RA Haas A., Goebel W.; RT "Cloning of a superoxide dismutase gene from Listeria ivanovii by RT functional complementation in Escherichia coli and characterization of the RT gene product."; RL Mol. Gen. Genet. 231:313-322(1992). XX RN [2] RP 1-756 RA Kreft J.; RT ; RL Submitted (21-APR-1992) to the EMBL/GenBank/DDBJ databases. RL J. Kreft, Institut f. Mikrobiologie, Universitaet Wuerzburg, Biozentrum Am RL Hubland, 8700 Wuerzburg, FRG XX FH Key Location/Qualifiers FH FT source 1..756 FT /db_xref="taxon:1638" FT /organism="Listeria ivanovii" FT /strain="ATCC 19119" FT /mol_type="genomic DNA" FT regulatory 95..100 FT /gene="sod" FT /regulatory_class="ribosome_binding_site" FT regulatory 723..746 FT /gene="sod" FT /regulatory_class="terminator" FT CDS 109..717 FT /transl_table=11 FT /gene="sod" FT /EC_number="1.15.1.1" FT /db_xref="GOA:P28763" FT /db_xref="HSSP:P00448" FT /db_xref="InterPro:IPR001189" FT /db_xref="UniProtKB/Swiss-Prot:P28763" FT /product="superoxide dismutase" FT /protein_id="CAA45406.1" FT /translation="MTYELPKLPYTYDALEPNFDKETMEIHYTKHHNIYVTKLNEAVSG FT HAELASKPGEELVANLDSVPEEIRGAVRNHGGGHANHTLFWSSLSPNGGGAPTGNLKAA FT IESEFGTFDEFKEKFNAAAAARFGSGWAWLVVNNGKLEIVSTANQDSPLSEGKTPVLGL FT DVWEHAYYLKFQNRRPEYIDTFWNVINWDERNKRFDAAK" XX SQ Sequence 756 BP; 247 A; 136 C; 151 G; 222 T; 0 other; cgttatttaa ggtgttacat agttctatgg aaatagggtc tatacctttc gccttacaat 60 gtaatttctt .......... 120 //7.1.2 GenBank Format
LOCUS LISOD 756 bp DNA linear BCT 30-JUN-1993 DEFINITION Listeria ivanovii sod gene for superoxide dismutase. ACCESSION X64011 S78972 VERSION X64011.1 GI:44010 KEYWORDS sod gene; superoxide dismutase. SOURCE Listeria ivanovii ORGANISM Listeria ivanovii Bacteria; Firmicutes; Bacillales; Listeriaceae; Listeria. REFERENCE 1 (bases 1 to 756) AUTHORS Haas,A. and Goebel,W. TITLE Cloning of a superoxide dismutase gene from Listeria ivanovii by functional complementation in Escherichia coli and characterization of the gene product JOURNAL Mol. Gen. Genet. 231 (2), 313-322 (1992) MEDLINE 92140371 REFERENCE 2 (bases 1 to 756) AUTHORS Kreft,J. TITLE Direct Submission JOURNAL Submitted (21-APR-1992) J. Kreft, Institut f. Mikrobiologie, Universitaet Wuerzburg, Biozentrum Am Hubland, 8700 Wuerzburg, FRG FEATURES Location/Qualifiers source 1..756 /organism="Listeria ivanovii" /strain="ATCC 19119" /db_xref="taxon:1638" /mol_type="genomic DNA" regulatory 95..100 /gene="sod" /regulatory_class="ribosome_binding_site" gene 95..746 /gene="sod" CDS 109..717 /gene="sod" /EC_number="1.15.1.1" /codon_start=1 /transl_table=11 /product="superoxide dismutase" /db_xref="GI:44011" /db_xref="GOA:P28763" /db_xref="InterPro:IPR001189" /db_xref="UniProtKB/Swiss-Prot:P28763" /protein_id="CAA45406.1" /translation="MTYELPKLPYTYDALEPNFDKETMEIHYTKHHNIYVTKLNEAVS GHAELASKPGEELVANLDSVPEEIRGAVRNHGGGHANHTLFWSSLSPNGGGAPTGNLK AAIESEFGTFDEFKEKFNAAAAARFGSGWAWLVVNNGKLEIVSTANQDSPLSEGKTPV LGLDVWEHAYYLKFQNRRPEYIDTFWNVINWDERNKRFDAAK" regulatory 723..746 /gene="sod" /regulatory_class="terminator" ORIGIN 1 cgttatttaa ggtgttacat agttctatgg aaatagggtc tatacctttc gccttacaat 61 gtaatttctt .......... //7.1.3 DDBJ Format
LOCUS LISOD 756 bp DNA linear BCT 30-JUN-1993 DEFINITION Listeria ivanovii sod gene for superoxide dismutase. ACCESSION X64011 S78972 VERSION X64011.1 GI:44010 KEYWORDS sod gene; superoxide dismutase. SOURCE Listeria ivanovii ORGANISM Listeria ivanovii Bacteria; Firmicutes; Bacillales; Listeriaceae; Listeria. REFERENCE 1 (bases 1 to 756) AUTHORS Haas,A. and Goebel,W. TITLE Cloning of a superoxide dismutase gene from Listeria ivanovii by functional complementation in Escherichia coli and characterization of the gene product JOURNAL Mol. Gen. Genet. 231 (2), 313-322 (1992) MEDLINE 92140371 REFERENCE 2 (bases 1 to 756) AUTHORS Kreft,J. TITLE Direct Submission JOURNAL Submitted (21-APR-1992) J. Kreft, Institut f. Mikrobiologie, Universitaet Wuerzburg, Biozentrum Am Hubland, 8700 Wuerzburg, FRG FEATURES Location/Qualifiers source 1..756 /organism="Listeria ivanovii" /strain="ATCC 19119" /db_xref="taxon:1638" /mol_type="genomic DNA" regulatory 95..100 /gene="sod" /regulatory_class="ribosome_binding_site" gene 95..746 /gene="sod" CDS 109..717 /gene="sod" /EC_number="1.15.1.1" /codon_start=1 /transl_table=11 /product="superoxide dismutase" /db_xref="GOA:P28763" /db_xref="HSSP:P00448" /db_xref="InterPro:IPR001189" /db_xref="UniProtKB/Swiss-Prot:P28763" /protein_id="CAA45406.1" /translation="MTYELPKLPYTYDALEPNFDKETMEIHYTKHHNIYVTKLNEAVS GHAELASKPGEELVANLDSVPEEIRGAVRNHGGGHANHTLFWSSLSPNGGGAPTGNLK AAIESEFGTFDEFKEKFNAAAAARFGSGWAWLVVNNGKLEIVSTANQDSPLSEGKTPV LGLDVWEHAYYLKFQNRRPEYIDTFWNVINWDERNKRFDAAK" regulatory 723..746 /gene="sod" /regulatory_class="terminator" BASE COUNT 247 a 136 c 151 g 222 t ORIGIN 1 cgttatttaa ggtgttacat agttctatgg aaatagggtc tatacctttc gccttacaat 61 gtaatttctt .......... //7.2 Appendix II: Feature keys reference
The following has been organized according to the following format: Feature Key the feature key name Definition the definition of the key Mandatory qualifiers qualifiers required with the key; if there are no mandatory qualifiers, this field is omitted. Optional qualifiers optional qualifiers associated with the key Organism scope valid organisms for the key; if the scope is any organism, this field is omitted. Molecule scope valid molecule types; if the scope is any molecule type, this field is omitted. References citations of published reports, usually supporting the feature consensus sequence Comment comments and clarifications Abbreviations: accnum an entry primary accession number <amino_acid> abbreviation for amino acid <base_range> location descriptor for a simple range of bases <bool> Boolean truth value. Valid values are yes and no <integer> unsigned integer value <location> general feature location descriptor <modified_base> abbreviation for modified nucleotide base [number] integer representing number of citation in entry's reference list <repeat_type> value indicating the organization of a repeated sequence. "text" any text or character string. Since the string is delimited by double quotes, double quotes may only appear as part of the string if they appear in pairs. For example, the sentence: The "label" qualifier is no longer legal. would be formatted thus: "The ""label"" qualifier is no longer legal." Feature Key assembly_gap Definition gap between two components of a genome or transcriptome assembly; Mandatory qualifiers /estimated_length=unknown or <integer> /gap_type="TYPE" /linkage_evidence="TYPE" (Note: Mandatory only if the /gap_type is "within scaffold", "repeat within scaffold" or "contamination". 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=<integer> /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="<database>:<identifier>" /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 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="<database>:<identifier>" /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="<identifier>" /pseudo /pseudogene="TYPE" /ribosomal_slippage /standard_name="text" /translation="text" /transl_except=(pos:<location>,aa:<amino_acid>) /transl_table =<integer> /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 (from the end of 2018 new accessions may be extended to a 3+7 accession format with 3 position letters and 7 numbers; existing data before the end of 2018 uses a 3+5 format) 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="<database>:<identifier>" /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="<database>:<identifier>" /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="<database>:<identifier>" /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 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="<database>:<identifier>" /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 <integer> 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="<database>:<identifier>" /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="<database>:<identifier>" /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="<database>:<identifier>" /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="<database>:<identifier>" /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 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="<database>:<identifier>" /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="<database>:<identifier>" /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="<database>:<identifier>" /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="<database>:<identifier>" /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="<database>:<identifier>" /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) /recombination_class="TYPE" /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="<database>:<identifier>" /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="<database>:<identifier>" /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="<mobile_element_type> [:<mobile_element_name>]" Optional qualifiers /allele="text" /citation=[number] /db_xref="<database>:<identifier>" /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=<repeat_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=<modified_base> Optional qualifiers /allele="text" /citation=[number] /db_xref="<database>:<identifier>" /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="<database>:<identifier>" /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="<database>:<identifier>" /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="<database>:<identifier>" /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 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="<database>:<identifier>" /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/promoter and in the same biological pathway Mandatory qualifiers /operon="text" Optional qualifiers /allele="text" /citation=[number] /db_xref="<database>:<identifier>" /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="<database>:<identifier>" /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=<repeat_type> /rpt_unit_range=<base_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="<database>:<identifier>" /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="<database>:<identifier>" /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="<database>:<identifier>" /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="<database>:<identifier>" /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 propeptide Definition propeptide coding sequence; coding sequence for the domain of a proprotein that is cleaved to form the mature protein product. Optional qualifiers /allele="text" /citation=[number] /db_xref="<database>:<identifier>" /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 protein_bind Definition non-covalent protein binding site on nucleic acid; Mandatory qualifiers /bound_moiety="text" Optional qualifiers /allele="text" /citation=[number] /db_xref="<database>:<identifier>" /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, translation, replication or chromatin structure; Mandatory qualifiers /regulatory_class="TYPE" Optional qualifiers /allele="text" /bound_moiety="text" /citation=[number] /db_xref="<database>:<identifier>" /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="<database>:<identifier>" /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=<repeat_type> /rpt_unit_range=<base_range> /rpt_unit_seq="text" /satellite="<satellite_type>[:<class>][ <identifier>]" /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="<database>:<identifier>" /direction=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" /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="<database>:<identifier>" /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="<database>:<identifier>" /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="<database>:<identifier>" /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="[<institution-code>:[<collection-code>:]]<material_id>" /cell_line="text" /cell_type="text" /chromosome="text" /citation=[number] /clone="text" /clone_lib="text" /collected_by="text" /collection_date="text" /country="<country_value>[:<region>][, <locality>]" /cultivar="text" /culture_collection="<institution-code>:[<collection-code>:]<culture_id>" /db_xref="<database>:<identifier>" /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" /metagenome_source="text" /note="text" /organelle=<organelle_value> /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="[<institution-code>:[<collection-code>:]]<specimen_id>" /strain="text" /sub_clone="text" /submitter_seqid="text" /sub_species="text" /sub_strain="text" /tissue_lib="text" /tissue_type="text" /transgenic /type_material="<type-of-type> of <organism name>" /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 <organelle_value> 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="<database>:<identifier>" /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="<database>:<identifier>" /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 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="<database>:<identifier>" /experiment="[CATEGORY:]text"/note="text" /inference="[CATEGORY:]TYPE[(same species)][:EVIDENCE_BASIS]" /note="text" /rpt_type=<repeat_type> /rpt_unit_range=<base_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="<database>:<identifier>" /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=<base_range> 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="<database>:<identifier>" /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:<location>,aa:<amino_acid>,seq:<text>) /citation=[number] /db_xref="<database>:<identifier>" /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="<database>:<identifier>" /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="<database>:<identifier>" /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 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="<database>:<identifier>" /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 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="<database>:<identifier>" /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="<database>:<identifier>" /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="<database>:<identifier>" /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_splicing7.3 Appendix III: Summary of qualifiers for feature keys
7.3.1 Qualifier List
The following is a list of available qualifiers for feature keys and their usage. The information is arranged as follows: Qualifier name of qualifier; qualifier requires a value if followed by an equal sign Definition definition of the qualifier Value format format of value, if required Example example of qualifier with value Comment comments, questions and clarifications Qualifier /allele= Definition name of the allele for the given gene Value format "text" Example /allele="adh1-1" Comment all gene-related features (exon, CDS etc) for a given gene should share the same /allele qualifier value; the /allele qualifier value must, by definition, be different from the /gene qualifier value; when used with the variation feature key, the allele qualifier value should be that of the variant. Qualifier /altitude= Definition geographical altitude of the location from which the sample was collected Value format "text" Example /altitude="-256 m" /altitude="330.12 m" Comment Values indicate altitudes above or below nominal sea level provided in metres Qualifier /anticodon= Definition location of the anticodon of tRNA and the amino acid for which it codes Value format (pos:<location>,aa:<amino_acid>,seq:<text>) where location is the position of the anticodon and amino_acid is the abbreviation for the amino acid encoded and seq is the sequence of the anticodon Example /anticodon=(pos:34..36,aa:Phe,seq:aaa) /anticodon=(pos:join(5,495..496),aa:Leu,seq:taa) /anticodon=(pos:complement(4156..4158),aa:Gln,seq:ttg) Qualifier /artificial_location Definition 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. Value format "heterogeneous population sequenced", "low-quality sequence region" Example /artificial_location="heterogeneous population sequenced" /artificial_location="low-quality sequence region" Comment expected to be used only for genome-scale annotation. Qualifier /bio_material= Definition 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. Value format "[<institution-code>:[<collection-code>:]]<material_id>" Example /bio_material="CGC:CB3912" <- Caenorhabditis stock centre Comment the bio_material qualifier should be used to annotate the identifiers of material in biological collections that are not appropriate to annotate as either /specimen_voucher or /culture_collection; these include zoos and aquaria, stock centres, seed banks, germplasm repositories and DNA banks; material_id is mandatory, institution_code and collection_code are optional; institution code is mandatory where collection code is present; institution code and collection code are taken from a controlled vocabulary maintained by the INSDC. Qualifier /bound_moiety= Definition name of the molecule/complex that may bind to the given feature Value format "text" Example /bound_moiety="GAL4" Comment A single /bound_moiety qualifier is legal on the "misc_binding", "oriT" and "protein_bind" features. Qualifier /cell_line= Definition cell line from which the sequence was obtained Value format "text" Example /cell_line="MCF7" Qualifier /cell_type= Definition cell type from which the sequence was obtained Value format "text" Example /cell_type="leukocyte" Qualifier /chromosome= Definition chromosome (e.g. Chromosome number) from which the sequence was obtained Value format "text" Example /chromosome="1" Qualifier /citation= Definition reference to a citation listed in the entry reference field Value format [integer-number] where integer-number is the number of the reference as enumerated in the reference field Example /citation=[3] Comment used to indicate the citation providing the claim of and/or evidence for a feature; brackets are used for conformity. Qualifier /clone= Definition clone from which the sequence was obtained Value format "text" Example /clone="lambda-hIL7.3" Comment not more than one clone should be specified for a given source feature; to indicate that the sequence was obtained from multiple clones, multiple source features should be given. Qualifier /clone_lib= Definition clone library from which the sequence was obtained Value format "text" Example /clone_lib="lambda-hIL7" Qualifier /codon_start= Definition indicates the offset at which the first complete codon of a coding feature can be found, relative to the first base of that feature. Value format 1 or 2 or 3 Example /codon_start=2 Qualifier /collected_by= Definition name of persons or institute who collected the specimen Value format "text" Example /collected_by="Dan Janzen" Qualifier /collection_date= Definition The date on which the specimen was collected. Date/time ranges are supported by providing two collection dates from among the supported value formats, delimited by a forward-slash character. Collection times are supported by adding "T", then the hour and minute and seconds, after the date. Collection times must be in Coordinated Universal Time (UTC), otherwise known as "Zulu Time" (Z). Value format "DD-Mmm-YYYY", "Mmm-YYYY", "YYYY" "YYYY-MM-DDThh:mmZ", "YYYY-MM-DDThh:mm:ssZ", "YYYY-MM-DDThhZ", "YYYY-MM-DD", or "YYYY-MM" Example /collection_date="21-Oct-1952" /collection_date="Oct-1952" /collection_date="1952" /collection_date="1952-10-21T11:43Z" /collection_date="1952-10-21T11Z" /collection_date="1952-10-21" /collection_date="1952-10" /collection_date="21-Oct-1952/15-Feb-1953" /collection_date="Oct-1952/Feb-1953" /collection_date="1952/1953" /collection_date="1952-10-21/1953-02-15" /collection_date="1952-10/1953-02" /collection_date="1952-10-21T11:43Z/1952-10-21T17:43Z" /collection_date="2015-10-11T17:53:03Z" Comment 'Mmm' represents a three-letter month abbreviation, and can be one of the following: Jan, Feb, Mar, Apr, May, Jun, Jul, Aug, Sep, Oct, Nov, Dec 'YYYY' is a four-digit value representing the year. 'MM' is a two-digit value representing the month. 'DD' is a two-digit value representing the day of the month. 'hh' is a two-digit value representing the hour of the day (00 to 23) 'mm' is a two-digit value representing the minute of the hour (00 to 59) 'ss' is a two-digit value representing the second of the hour (00 to 59) Within a date range, value formats that make use of 'Mmm' (month abbreviations) cannot be combined with value formats that make use of 'MM' (two-digit month number) Collection dates that are specified to at least the month, day, and year (DD-Mmm-YYYY or YYYY-MM-DD) are strongly encouraged. If the day and/or month of the collection date are not known, Mmm-YYYY or YYYY-MM or YYYY may be used. Within a collection date range, the first date (possibly including time) must be prior to the second date (possibly including time). Within a collection date range for which the day, month, and year are identical, the first time value must be prior to the second time value. Qualifier /compare= Definition Reference details of an existing public INSD entry to which a comparison is made Value format [accession-number.sequence-version] Example /compare=AJ634337.1 Comment This qualifier may be used on the following features: misc_difference, unsure, old_sequence and variation. The feature "old_sequence" must have either a /citation or a /compare qualifier. Multiple /compare qualifiers with different contents are allowed within a single feature. This qualifier is not intended for large-scale annotation of variations, such as SNPs. Qualifier /country= Definition locality of isolation of the sequenced organism indicated in terms of political names for nations, oceans or seas, followed by regions and localities Value format "<country_value>[:<region>][, <locality>]" where country_value is any value from the controlled vocabulary at http://www.insdc.org/documents/country-qualifier-vocabulary Example /country="Canada:Vancouver" /country="France:Cote d'Azur, Antibes" /country="Atlantic Ocean:Charlie Gibbs Fracture Zone" Comment Intended to provide a reference to the site where the source organism was isolated or sampled. Regions and localities should be indicated where possible. Note that the physical geography of the isolation or sampling site should be represented in /isolation_source. Qualifier /cultivar= Definition cultivar (cultivated variety) of plant from which sequence was obtained. Value format "text" Example /cultivar="Nipponbare" /cultivar="Tenuifolius" /cultivar="Candy Cane" /cultivar="IR36" Comment 'cultivar' is applied solely to products of artificial selection; use the variety qualifier for natural, named plant and fungal varieties; Qualifier /culture_collection= Definition institution code and identifier for the culture from which the nucleic acid sequenced was obtained, with optional collection code. Value format "<institution-code>:[<collection-code>:]<culture_id>" Example /culture_collection="ATCC:26370" Comment the /culture_collection qualifier should be used to annotate live microbial and viral cultures, and cell lines that have been deposited in curated culture collections; microbial cultures in personal or laboratory collections should be annotated in strain qualifiers; annotation with a culture_collection qualifier implies that the sequence was obtained from a sample retrieved (by the submitter or a collaborator) from the indicated culture collection, or that the sequence was obtained from a sample that was deposited (by the submitter or a collaborator) in the indicated culture collection; annotation with more than one culture_collection qualifier indicates that the sequence was obtained from a sample that was deposited (by the submitter or a collaborator) in more than one culture collection. culture_id and institution_code are mandatory, collection_code is optional; institution code and collection code are taken from a controlled vocabulary maintained by the INSDC. http://www.insdc.org/controlled-vocabulary-culturecollection-qualifier Qualifier /db_xref= Definition database cross-reference: pointer to related information in another database. Value format "<database:identifier>" where database is the name of the database containing related information, and identifier is the internal identifier of the related information according to the naming conventions of the cross-referenced database. Example /db_xref="UniProtKB/Swiss-Prot:P28763" Comment the complete list of allowed database types is kept at http://www.insdc.org/db_xref.html Qualifier /dev_stage= Definition if the sequence was obtained from an organism in a specific developmental stage, it is specified with this qualifier Value format "text" Example /dev_stage="fourth instar larva" Qualifier /direction= Definition direction of DNA replication Value format left, right, or both where left indicates toward the 5' end of the entry sequence (as presented) and right indicates toward the 3' end Example /direction=LEFT Qualifier /EC_number= Definition Enzyme Commission number for enzyme product of sequence Value format "text" Example /EC_number="1.1.2.4" /EC_number="1.1.2.-" /EC_number="1.1.2.n" /EC_number="1.1.2.n1" Comment valid values for EC numbers are defined in the list prepared by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) (published in Enzyme Nomenclature 1992, Academic Press, San Diego, or a more recent revision thereof). The format represents a string of four numbers separated by full stops; up to three numbers starting from the end of the string can be replaced by dash "." to indicate uncertain assignment. Symbols including an "n", e.g. "n", "n1" and so on, can be used in the last position instead of a number where the EC number is awaiting assignment. Please note that such incomplete EC numbers are not approved by NC-IUBMB. Qualifier /ecotype= Definition a population within a given species displaying genetically based, phenotypic traits that reflect adaptation to a local habitat. Value Format "text" Example /ecotype="Columbia" Comment an example of such a population is one that has adapted hairier than normal leaves as a response to an especially sunny habitat. 'Ecotype' is often applied to standard genetic stocks of Arabidopsis thaliana, but it can be applied to any sessile organism. Qualifier /environmental_sample Definition 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). Value format none Example /environmental_sample Comment used only with the source feature key; source feature keys containing the /environmental_sample qualifier should also contain the /isolation_source qualifier. entries including /environmental_sample must not include the /strain qualifier Qualifier /estimated_length= Definition estimated length of the gap in the sequence Value format unknown or <integer> Example /estimated_length=unknown /estimated_length=342 Qualifier /exception= Definition indicates that the coding region cannot be translated using standard biological rules Value format "RNA editing", "reasons given in citation", "rearrangement required for product", "annotated by transcript or proteomic data" Example /exception="RNA editing" /exception="reasons given in citation" /exception="rearrangement required for product" /exception="annotated by transcript or proteomic data" Comment only to be used to describe biological mechanisms such as RNA editing; where the exception cannot easily be described a published citation must be referred to; protein translation of /exception CDS will be different from the according conceptual translation; - An /inference qualifier should accompany any use of /exception="annotated by transcript or proteomic data", to provide support for the existence of the transcript/protein. - must not be used where transl_except would be adequate, e.g. in case of stop codon completion use: /transl_except=(pos:6883,aa:TERM) /note="TAA stop codon is completed by addition of 3' A residues to mRNA". - must not be used for ribosomal slippage, instead use join operator, e.g.: CDS join(486..1784,1787..4810) /note="ribosomal slip on tttt sequence at 1784..1787" Qualifier /experiment= Definition a brief description of the nature of the experimental evidence that supports the feature identification or assignment. Value format "[CATEGORY:]text" where CATEGORY is one of the following: "COORDINATES" support for the annotated coordinates "DESCRIPTION" support for a broad concept of function such as that based on phenotype, genetic approach, biochemical function, pathway information, etc. "EXISTENCE" support for the known or inferred existence of the product where text is free text (see examples) Example /experiment="5' RACE" /experiment="Northern blot [DOI: 12.3456/FT.789.1.234-567.2010]" /experiment="heterologous expression system of Xenopus laevis oocytes [PMID: 12345678, 10101010, 987654]" /experiment="COORDINATES: 5' and 3' RACE" Comment detailed experimental details should not be included, and would normally be found in the cited publications; PMID, DOI and any experimental database ID is allowed to be used in /experiment qualifier; value "experimental evidence, no additional details recorded" was used to replace instances of /evidence=EXPERIMENTAL in December 2005 Qualifier /focus Definition identifies the source feature of primary biological interest for records that have multiple source features originating from different organisms and that are not transgenic. Value format none Example /focus Comment the source feature carrying the /focus qualifier identifies the main organism of the entry, this determines: a) the name displayed in the organism lines, b) if no translation table is specified, the translation table, c) the DDBJ/EMBL/GenBank taxonomic division in which the entry will appear; only one source feature with /focus is allowed in an entry; the /focus and /transgenic qualifiers are mutually exclusive in an entry. Qualifier /frequency= Definition frequency of the occurrence of a feature Value format text representing the proportion of a population carrying the feature expressed as a fraction Example /frequency="23/108" /frequency="1 in 12" /frequency=".85" Qualifier /function= Definition function attributed to a sequence Value format "text" Example function="essential for recognition of cofactor" Comment /function is used when the gene name and/or product name do not convey the function attributable to a sequence. Qualifier /gap_type= Definition 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; Value format "between scaffolds", "within scaffold", "telomere", "centromere", "short arm", "heterochromatin", "repeat within scaffold", "repeat between scaffolds", "contamination", "unknown" Example /gap_type="between scaffolds" /gap_type="within scaffold" Comment This qualifier is used only for assembly_gap features and its values are controlled by the AGP Specification version 2.1: https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/ Please also visit: http://www.insdc.org/controlled-vocabulary-gaptype-qualifier Qualifier /gene= Definition symbol of the gene corresponding to a sequence region Value format "text" Example /gene="ilvE" Qualifier /gene_synonym= Definition synonymous, replaced, obsolete or former gene symbol Value format "text" Example /gene_synonym="Hox-3.3" in a feature where /gene="Hoxc6" Comment used where it is helpful to indicate a gene symbol synonym; when used, a primary gene symbol must always be indicated in /gene or a /locus_tag must be used. Qualifier /germline Definition 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 Value format none Example /germline Comment /germline should not be used to indicate that the source of the sequence is a gamete or germ cell; /germline and /rearranged cannot be used in the same source feature; /germline and /rearranged should only be used for molecules that can undergo somatic rearrangements as part of an adaptive immune response; these are the T-cell receptor (TCR) and immunoglobulin loci in the jawed vertebrates, and the unrelated variable lymphocyte receptor (VLR) locus in the jawless fish (lampreys and hagfish); /germline and /rearranged should not be used outside of the Craniata (taxid=89593) Qualifier /haplogroup= Definition name for a group of similar haplotypes that share some sequence variation. Haplogroups are often used to track migration of population groups Value format "text" Example /haplogroup="H*" Qualifier /haplotype= Definition 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. Value format "text" Example /haplotype="Dw3 B5 Cw1 A1" Qualifier /host= Definition natural (as opposed to laboratory) host to the organism from which sequenced molecule was obtained Value format "text" Example /host="Homo sapiens" /host="Homo sapiens 12 year old girl" /host="Rhizobium NGR234" Qualifier /identified_by= Definition name of the expert who identified the specimen taxonomically Value format "text" Example /identified_by="John Burns" Qualifier /inference= Definition a structured description of non-experimental evidence that supports the feature identification or assignment. Value format "[CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]" where CATEGORY is one of the following: "COORDINATES" support for the annotated coordinates "DESCRIPTION" support for a broad concept of function such as that based on phenotype, genetic approach, biochemical function, pathway information, etc. "EXISTENCE" support for the known or inferred existence of the product where TYPE is one of the following: "non-experimental evidence, no additional details recorded" "similar to sequence" "similar to AA sequence" "similar to DNA sequence" "similar to RNA sequence" "similar to RNA sequence, mRNA" "similar to RNA sequence, EST" "similar to RNA sequence, other RNA" "profile" "nucleotide motif" "protein motif" "ab initio prediction" "alignment" where the optional text "(same species)" is included when the inference comes from the same species as the entry. where the optional "EVIDENCE_BASIS" is either a reference to a database entry (including accession and version) or an algorithm (including version) , eg 'INSD:AACN010222672.1', 'InterPro:IPR001900', 'ProDom:PD000600', 'Genscan:2.0', etc. and is structured "[ALGORITHM][:EVIDENCE_DBREF[,EVIDENCE_DBREF]*[,...]]" Example /inference="COORDINATES:profile:tRNAscan:2.1" /inference="similar to DNA sequence:INSD:AY411252.1" /inference="similar to RNA sequence, mRNA:RefSeq:NM_000041.2" /inference="similar to DNA sequence (same species):INSD:AACN010222672.1" /inference="protein motif:InterPro:IPR001900" /inference="ab initio prediction:Genscan:2.0" /inference="alignment:Splign:1.0" /inference="alignment:Splign:1.26p:RefSeq:NM_000041.2,INSD:BC003557.1" Comment /inference="non-experimental evidence, no additional details recorded" was used to replace instances of /evidence=NOT_EXPERIMENTAL in December 2005; any database ID can be used in /inference= qualifier; recommentations for choice of resource acronym for[EVIDENCE_BASIS] are provided in the /inference qualifier vocabulary recommendation document (http://www.insdc.org/inference.html); Qualifier /isolate= Definition individual isolate from which the sequence was obtained Value format "text" Example /isolate="Patient #152" /isolate="DGGE band PSBAC-13" Qualifier /isolation_source= Definition describes the physical, environmental and/or local geographical source of the biological sample from which the sequence was derived Value format "text" Examples /isolation_source="rumen isolates from standard Pelleted ration-fed steer #67" /isolation_source="permanent Antarctic sea ice" /isolation_source="denitrifying activated sludge from carbon_limited continuous reactor" Comment used only with the source feature key; source feature keys containing an /environmental_sample qualifier should also contain an /isolation_source qualifier; the /country qualifier should be used to describe the country and major geographical sub-region. Qualifier /lab_host= Definition scientific name of the laboratory host used to propagate the source organism from which the sequenced molecule was obtained Value format "text" Example /lab_host="Gallus gallus" /lab_host="Gallus gallus embryo" /lab_host="Escherichia coli strain DH5 alpha" /lab_host="Homo sapiens HeLa cells" Comment the full binomial scientific name of the host organism should be used when known; extra conditional information relating to the host may also be included Qualifier /lat_lon= Definition geographical coordinates of the location where the specimen was collected Value format "text" Example /lat_lon="47.94 N 28.12 W" /lat_lon="45.0123 S 4.1234 E" Comment degrees latitude and longitude in format "d[d.dddd] N|S d[dd.dddd] W|E" (see the examples) Qualifier /linkage_evidence= Definition 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", "repeat within scaffold" or "contamination"; Please note if /gap-type="contamination", /linkage_evidence must be used and the value of /linkage_evidence must be "unspecified". Value format "pcr", "paired-ends", "align genus", "align xgenus", "align trnscpt", "within clone", "clone contig", "map", "strobe", "proximity ligation", "unspecified" Example /linkage_evidence="paired-ends" /linkage_evidence="within clone" Comment This qualifier is used only for assembly_gap features and its values are controlled by the AGP Specification version 2.1: https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/ Please also visit: http://www.insdc.org/controlled-vocabulary-linkageevidence-qualifier Qualifier /locus_tag= Definition a submitter-supplied, systematic, stable identifier for a gene and its associated features, used for tracking purposes Value Format "text"(single token) but not "<1-5 letters><5-9 digit integer>[.<integer>]" Example /locus_tag="ABC_0022" /locus_tag="A1C_00001" Comment /locus_tag can be used with any feature that /gene can be used with; identical /locus_tag values may be used within an entry/record, but only if the identical /locus_tag values are associated with the same gene; in all other circumstances the /locus_tag value must be unique within that entry/record. Multiple /locus_tag values are not allowed within one feature for entries created after 15-OCT-2004. If a /locus_tag needs to be re-assigned the /old_locus_tag qualifier should be used to store the old value. The /locus_tag value should not be in a format which resembles INSD accession numbers, accession.version, or /protein_id identifiers. Qualifier /macronuclear Definition 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. Value format none Example /macronuclear Qualifier /map= Definition genomic map position of feature Value format "text" Example /map="8q12-q13" Qualifier /mating_type= Definition 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 Value format "text" Examples /mating_type="MAT-1" /mating_type="plus" /mating_type="-" /mating_type="odd" /mating_type="even" Comment /mating_type="male" and /mating_type="female" are valid in the prokaryotes, but not in the eukaryotes; for more information, see the entry for /sex. Qualifier /metagenome_source Definition sequences from a Metagenome Assembled Genome (MAG), i.e a single-taxon assembly drawn from a binned metagenome, are specified with this qualifier to indicate that the assembly is derived from a metagenomic source, rather than from an isolated organism. Where this qualifier is present it must contain the word "metagenome" and must exist in the NCBI taxonomy database: https://www.ncbi.nlm.nih.gov/Taxonomy/ Value format "text" Examples /metagenome_source="human gut metagenome" /metagenome_source="soil metagenome" Comment the qualifier /metagenome_source is mandatory when a single-taxon sequence is derived from a metagenome; sequences with a /metagenome_source require also an /environmental_sample qualifier. Qualifier /mobile_element_type= Definition type and name or identifier of the mobile element which is described by the parent feature Value format "<mobile_element_type>[:<mobile_element_name>]" where mobile_element_type is one of the following: "transposon", "retrotransposon", "integron", "insertion sequence", "non-LTR retrotransposon", "SINE", "MITE", "LINE", "other". Example /mobile_element_type="transposon:Tnp9" Comment /mobile_element_type is legal on mobile_element feature key only. Mobile element should be used to represent both elements which are currently mobile, and those which were mobile in the past. Value "other" requires a mobile_element_name. Qualifier /mod_base= Definition abbreviation for a modified nucleotide base Value format modified_base Example /mod_base=m5c Comment modified nucleotides not found in the restricted vocabulary list can be annotated by entering '/mod_base=OTHER' with '/note="name of modified base"' Qualifier /mol_type= Definition in vivo molecule type of sequence Value format "genomic DNA", "genomic RNA", "mRNA", "tRNA", "rRNA", "other RNA", "other DNA", "transcribed RNA", "viral cRNA", "unassigned DNA", "unassigned RNA" Example /mol_type="genomic DNA" Comment all values refer to the in vivo or synthetic molecule for primary entries and the hypothetical molecule in Third Party Annotation entries; the value "genomic DNA" does not imply that the molecule is nuclear (e.g. organelle and plasmid DNA should be described using "genomic DNA"); ribosomal RNA genes should be described using "genomic DNA"; "rRNA" should only be used if the ribosomal RNA molecule itself has been sequenced; /mol_type is mandatory on every source feature key; all /mol_type values within one entry/record must be the same; values "other RNA" and "other DNA" should be applied to synthetic molecules, values "unassigned DNA", "unassigned RNA" should be applied where in vivo molecule is unknown Please also visit: http://www.insdc.org/controlled-vocabulary-moltype-qualifier Qualifier /ncRNA_class= Definition a structured description of the classification of the non-coding RNA described by the ncRNA parent key Value format "TYPE" Example /ncRNA_class="miRNA" /ncRNA_class="siRNA" /ncRNA_class="scRNA" Comment TYPE is a term taken from the INSDC controlled vocabulary for ncRNA classes. For a complete list of supported values, please see: http://www.insdc.org/documents/ncrna-vocabulary; ncRNA classes not yet in the INSDC /ncRNA_class controlled vocabulary can be annotated by entering '/ncRNA_class="other"' with either '/product="[name of the product]"' OR '/note="[brief explanation of novel ncRNA_class]"'; Qualifier /note= Definition any comment or additional information Value format "text" Example /note="This qualifier is equivalent to a comment." Qualifier /number= Definition a number to indicate the order of genetic elements (e.g., exons or introns) in the 5' to 3' direction Value format unquoted text (single token) Example /number=4 /number=6B Comment text limited to integers, letters or combination of integers and/or letters represented as an unquoted single token (e.g. 5a, XIIb); any additional terms should be included in /standard_name. Example: /number=2A /standard_name="long" Qualifier /old_locus_tag= Definition feature tag assigned for tracking purposes Value Format "text" (single token) Example /old_locus_tag="RSc0382" /locus_tag="YPO0002" Comment /old_locus_tag can be used with any feature where /gene is valid and where a /locus_tag qualifier is present. Identical /old_locus_tag values may be used within an entry/record, but only if the identical /old_locus_tag values are associated with the same gene; in all other circumstances the /old_locus_tag value must be unique within that entry/record. Multiple/old_locus_tag qualifiers with distinct values are allowed within a single feature; /old_locus_tag and /locus_tag values must not be identical within a single feature. Qualifier /operon= Definition name of the group of contiguous genes transcribed into a single transcript to which that feature belongs. Value format "text" Example /operon="lac" Qualifier /organelle= Definition type of membrane-bound intracellular structure from which the sequence was obtained Value format chromatophore, hydrogenosome, mitochondrion, nucleomorph, plastid, mitochondrion:kinetoplast, plastid:chloroplast, plastid:apicoplast, plastid:chromoplast, plastid:cyanelle, plastid:leucoplast, plastid:proplastid Examples /organelle="chromatophore" /organelle="hydrogenosome" /organelle="mitochondrion" /organelle="nucleomorph" /organelle="plastid" /organelle="mitochondrion:kinetoplast" /organelle="plastid:chloroplast" /organelle="plastid:apicoplast" /organelle="plastid:chromoplast" /organelle="plastid:cyanelle" /organelle="plastid:leucoplast" /organelle="plastid:proplastid" Comments modifier text limited to values from controlled list Please also visit: http://www.insdc.org/controlled-vocabulary-organelle-qualifier Qualifier /organism= Definition scientific name of the organism that provided the sequenced genetic material. Value format "text" Example /organism="Homo sapiens" Comment the organism name which appears on the OS or ORGANISM line will match the value of the /organism qualifier of the source key in the simplest case of a one-source sequence. Qualifier /partial Definition differentiates between complete regions and partial ones Value format none Example /partial Comment 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. Qualifier /PCR_conditions= Definition description of reaction conditions and components for PCR Value format "text" Example /PCR_conditions="Initial denaturation:94degC,1.5min" Comment used with primer_bind key Qualifier /PCR_primers= Definition 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. Value format /PCR_primers="[fwd_name: XXX1, ]fwd_seq: xxxxx1,[fwd_name: XXX2,] fwd_seq: xxxxx2, [rev_name: YYY1, ]rev_seq: yyyyy1, [rev_name: YYY2, ]rev_seq: yyyyy2" Example /PCR_primers="fwd_name: CO1P1, fwd_seq: ttgattttttggtcayccwgaagt, rev_name: CO1R4, rev_seq: ccwvytardcctarraartgttg" /PCR_primers=" fwd_name: hoge1, fwd_seq: cgkgtgtatcttact, rev_name: hoge2, rev_seq: cg<i>gtgtatcttact" /PCR_primers="fwd_name: CO1P1, fwd_seq: ttgattttttggtcayccwgaagt, fwd_name: CO1P2, fwd_seq: gatacacaggtcayccwgaagt, rev_name: CO1R4, rev_seq: ccwvytardcctarraartgttg" Comment fwd_seq and rev_seq are both mandatory; fwd_name and rev_name are both optional. Both sequences should be presented in 5'>3' order. The sequences should be given in the IUPAC degenerate-base alphabet, except for the modified bases; those must be enclosed within angle brackets <> Qualifier /phenotype= Definition phenotype conferred by the feature, where phenotype is defined as a physical, biochemical or behavioural characteristic or set of characteristics Value format "text" Example /phenotype="erythromycin resistance" Qualifier /plasmid= Definition 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 Value format "text" Example /plasmid="C-589" Qualifier /pop_variant= Definition name of subpopulation or phenotype of the sample from which the sequence was derived Value format "text" Example /pop_variant="pop1" /pop_variant="Bear Paw" Qualifier /product= Definition 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. Value format "text" Example /product="trypsinogen" (when qualifier appears in CDS feature) /product="trypsin" (when qualifier appears in mat_peptide feature) /product="XYZ neural-specific transcript" (when qualifier appears in mRNA feature) Qualifier /protein_id= Definition protein identifier, issued by International collaborators. this qualifier consists of a stable ID portion (accessioned data before the end of 2018 uses a 3+5 format; from the end of 2018 new accessions may be extended to a 3+7 accession format with 3 position letters and 7 numbers) plus a version number after the decimal point. Value format <identifier> Example /protein_id="AAA12345.1" /protein_id="AAA1234567.1" Comment 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; this qualifier is valid only on CDS features which translate into a valid protein. Qualifier /proviral Definition this qualifier is used to flag sequence obtained from a virus or phage that is integrated into the genome of another organism Value format none Example /proviral Qualifier /pseudo Definition indicates that this feature is a non-functional version of the element named by the feature key Value format none Example /pseudo Comment The qualifier /pseudo should be used to describe non-functional genes that are not formally described as pseudogenes, e.g. CDS has no translation due to other reasons than pseudogenisation events. Other reasons may include sequencing or assembly errors. In order to annotate pseudogenes the qualifier /pseudogene= must be used indicating the TYPE which can be taken from the INSDC controlled vocabulary for pseudogenes. Qualifier /pseudogene= Definition indicates that this feature is a pseudogene of the element named by the feature key Value format "TYPE" where TYPE is one of the following: processed, unprocessed, unitary, allelic, unknown Example /pseudogene="processed" /pseudogene="unprocessed" /pseudogene="unitary" /pseudogene="allelic" /pseudogene="unknown" Comment TYPE is a term taken from the INSDC controlled vocabulary for pseudogenes (http://www.insdc.org/documents/pseudogene-qualifier-vocabulary): processed: the pseudogene has arisen by reverse transcription of a mRNA into cDNA, followed by reintegration into the genome. Therefore, it has lost any intron/exon structure, and it might have a pseudo-polyA-tail. unprocessed: the pseudogene has arisen from a copy of the parent gene by duplication followed by accumulation of random mutations. The changes, compared to their functional homolog, include insertions, deletions, premature stop codons, frameshifts and a higher proportion of non-synonymous versus synonymous substitutions. unitary: the pseudogene has no parent. It is the original gene, which is functional is some species but disrupted in some way (indels, mutation, recombination) in another species or strain. allelic: a (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes. unknown: the submitter does not know the method of pseudogenisation. Qualifier /rearranged Definition 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 Value format none Example /rearranged Comment /rearranged should not be used to annotate chromosome rearrangements that are not involved in an adaptive immune response; /germline and /rearranged cannot be used in the same source feature; /germline and /rearranged should only be used for molecules that can undergo somatic rearrangements as part of an adaptive immune response; these are the T-cell receptor (TCR) and immunoglobulin loci in the jawed vertebrates, and the unrelated variable lymphocyte receptor (VLR) locus in the jawless fish (lampreys and hagfish); /germline and /rearranged should not be used outside of the Craniata (taxid=89593) Qualifier /recombination_class Definition a structured description of the classification of recombination hotspot region within a sequence Value format "TYPE" Example /recombination_class="meiotic" /recombination_class="chromosome_breakpoint" Comment TYPE is a term taken from the INSDC controlled vocabulary for recombination classes (http://www.insdc.org/controlled-vocabulary-recombination-class); in DEC 2017, the following terms were valid: "meiotic" "mitotic" "non_allelic_homologous" "chromosome_breakpoint" "other" recombination classes not yet in the INSDC /recombination_class controlled vocabulary can be annotated by entering /recombination_class="other" with /note="[brief explanation of novel /recombination_class]"; Qualifier /regulatory_class Definition a structured description of the classification of transcriptional, translational, replicational and chromatin structure related regulatory elements in a sequence Value format "TYPE" Example /regulatory_class="promoter" /regulatory_class="enhancer" /regulatory_class="ribosome_binding_site" Comment TYPE is a term taken from the INSDC controlled vocabulary for regulatory classes. For a complete list of supported values, please see: http://www.insdc.org/controlled-vocabulary-regulatoryclass; regulatory classes not yet in the INSDC /regulatory_class controlled vocabulary can be annotated by entering /regulatory_class="other" with /note="[brief explanation of novel regulatory_class]"; Qualifier /replace= Definition 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. Value format "text" Example /replace="a" /replace="" Qualifier /ribosomal_slippage Definition during protein translation, certain sequences can program ribosomes to change to an alternative reading frame by a mechanism known as ribosomal slippage Value format none Example /ribosomal_slippage Comment a join operator,e.g.: [join(486..1784,1787..4810)] should be used in the CDS spans to indicate the location of ribosomal_slippage Qualifier /rpt_family= Definition type of repeated sequence; "Alu" or "Kpn", for example Value format "text" Example /rpt_family="Alu" Qualifier /rpt_type= Definition structure and distribution of repeated sequence Value format tandem, direct, inverted, flanking, nested, dispersed, terminal, long_terminal_repeat, non_ltr_retrotransposon_polymeric_tract, centromeric_repeat, telomeric_repeat, x_element_combinatorial_repeat, y_prime_element and other Example /rpt_type=INVERTED Comment the values are case-insensitive, i.e. both "INVERTED" and "inverted" are valid; For the most current list of allowed values and their definitions please visit: http://www.insdc.org/controlled-vocabulary-rpttype-qualifier Qualifier /rpt_unit_range= Definition identity of a repeat range Value format <base_range> Example /rpt_unit_range=202..245 Comment used to indicate the base range of the sequence that constitutes a repeated sequence specified by the feature keys oriT and repeat_region; qualifiers /rpt_unit_range and /rpt_unit_seq replaced qualifier /rpt_unit in December 2005 Qualifier /rpt_unit_seq= Definition identity of a repeat sequence Value format "text" Example /rpt_unit_seq="aagggc" /rpt_unit_seq="ag(5)tg(8)" /rpt_unit_seq="(AAAGA)6(AAAA)1(AAAGA)12" Comment used to indicate the literal sequence that constitutes a repeated sequence specified by the feature keys oriT and repeat_region; qualifiers /rpt_unit_range and /rpt_unit_seq replaced qualifier /rpt_unit in December 2005 Qualifier /satellite= Definition identifier for a satellite DNA marker, compose of many tandem repeats (identical or related) of a short basic repeated unit; Value format "<satellite_type>[:<class>][ <identifier>]" where satellite_type is one of the following "satellite", "microsatellite", "minisatellite" Example /satellite="satellite: S1a" /satellite="satellite: alpha" /satellite="satellite: gamma III" /satellite="microsatellite: DC130" Comment many satellites have base composition or other properties that differ from those of the rest of the genome that allows them to be identified. Please also visit: http://www.insdc.org/controlled-vocabulary-satellite-qualifier Qualifier /segment= Definition name of viral or phage segment sequenced Value format "text" Example /segment="6" Qualifier /serotype= Definition serological variety of a species characterized by its antigenic properties Value format "text" Example /serotype="B1" Comment used only with the source feature key; the Bacteriological Code recommends the use of the term 'serovar' instead of 'serotype' for the prokaryotes; see the International Code of Nomenclature of Bacteria (1990 Revision) Appendix 10.B "Infraspecific Terms". Qualifier /serovar= Definition serological variety of a species (usually a prokaryote) characterized by its antigenic properties Value format "text" Example /serovar="O157:H7" Comment used only with the source feature key; the Bacteriological Code recommends the use of the term 'serovar' instead of 'serotype' for prokaryotes; see the International Code of Nomenclature of Bacteria (1990 Revision) Appendix 10.B "Infraspecific Terms". Qualifier /sex= Definition sex of the organism from which the sequence was obtained; sex is used for eukaryotic organisms that undergo meiosis and have sexually dimorphic gametes Value format "text" Examples /sex="female" /sex="male" /sex="hermaphrodite" /sex="unisexual" /sex="bisexual" /sex="asexual" /sex="monoecious" [or monecious] /sex="dioecious" [or diecious] Comment /sex should be used (instead of /mating_type) in the Metazoa, Embryophyta, Rhodophyta & Phaeophyceae; /mating_type should be used (instead of /sex) in the Bacteria, Archaea & Fungi; neither /sex nor /mating_type should be used in the viruses; outside of the taxa listed above, /mating_type should be used unless the value of the qualifier is taken from the vocabulary given in the examples above Qualifier /specimen_voucher= Definition identifier for the specimen from which the nucleic acid sequenced was obtained Value format /specimen_voucher="[<institution-code>:[<collection-code>:]]<specimen_id>" Example /specimen_voucher="UAM:Mamm:52179" /specimen_voucher="AMCC:101706" /specimen_voucher="USNM:field series 8798" /specimen_voucher="personal:Dan Janzen:99-SRNP-2003" /specimen_voucher="99-SRNP-2003" Comment the /specimen_voucher qualifier is intended to annotate a reference to the physical specimen that remains after the sequence has been obtained; if the specimen was destroyed in the process of sequencing, electronic images (e-vouchers) are an adequate substitute for a physical voucher specimen; ideally the specimens will be deposited in a curated museum, herbarium, or frozen tissue collection, but often they will remain in a personal or laboratory collection for some time before they are deposited in a curated collection; there are three forms of specimen_voucher qualifiers; if the text of the qualifier includes one or more colons it is a 'structured voucher'; structured vouchers include institution-codes (and optional collection-codes) taken from a controlled vocabulary maintained by the INSDC that denotes the museum or herbarium collection where the specimen resides; Please also visit: http://www.insdc.org/controlled-vocabulary-specimenvoucher-qualifier Qualifier /standard_name= Definition accepted standard name for this feature Value format "text" Example /standard_name="dotted" Comment use /standard_name to give full gene name, but use /gene to give gene symbol (in the above example /gene="Dt"). Qualifier /strain= Definition strain from which sequence was obtained Value format "text" Example /strain="BALB/c" Comment entries including /strain must not include the /environmental_sample qualifier Qualifier /sub_clone= Definition sub-clone from which sequence was obtained Value format "text" Example /sub_clone="lambda-hIL7.20g" Comment the comments on /clone apply to /sub_clone Qualifier /submitter_seqid= Definition identifier attributed to each sequence within an assembly. This identifier is appropriate for WGS, TSA, TLS and CON records. The submitter_seqid should be unique within the context of a single set of assembled sequences. Value format "text" Example /submitter_seqid="NODE_1" Comment The length of the value should be limited to <51 characters. Spaces, greater than (>), left/right square brackets ([ ]) and vertical bar (|) in addition to double quotation marks (") can not be used for the value of /submitter_seqid qualifier. Qualifier /sub_species= Definition name of sub-species of organism from which sequence was obtained Value format "text" Example /sub_species="lactis" Qualifier /sub_strain= Definition 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 Value format "text" Example /sub_strain="abis" Comment if the parental strain is not given, this should be annotated in the strain qualifier instead of sub_strain. Either: /strain="K-12" /sub_strain="MG1655" or: /strain="MG1655" Qualifier /tag_peptide= Definition base location encoding the polypeptide for proteolysis tag of tmRNA and its termination codon; Value format <base_range> Example /tag_peptide=90..122 Comment it is recommended that the amino acid sequence corresponding to the /tag_peptide be annotated by describing a 5' partial CDS feature; e.g. CDS <90..122; Qualifier /tissue_lib= Definition tissue library from which sequence was obtained Value format "text" Example /tissue_lib="tissue library 772" Qualifier /tissue_type= Definition tissue type from which the sequence was obtained Value format "text" Example /tissue_type="liver" Qualifier /transgenic Definition identifies the source feature of the organism which was the recipient of transgenic DNA. Value format none Example /transgenic Comment transgenic sequences must have at least two source feature keys; the source feature key having the /transgenic qualifier must span the whole sequence; the source feature carrying the /transgenic qualifier identifies the main organism of the entry, this determines: a) the name displayed in the organism lines, b) if no translation table is specified, the translation table; only one source feature with /transgenic is allowed in an entry; the /focus and /transgenic qualifiers are mutually exclusive in an entry. Qualifier /translation= Definition 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 Value format IUPAC one-letter amino acid abbreviation, "X" is to be used for AA exceptions. Example /translation="MASTFPPWYRGCASTPSLKGLIMCTW" Comment to be used with CDS feature only; this is a mandatory qualifier in the CDS feature key except where /pseudogene="TYPE" or /pseudo is shown; see /transl_table for definition and location of genetic code tables. Qualifier /transl_except= Definition translational exception: single codon the translation of which does not conform to genetic code defined by /organism or /transl_table. Value format (pos:<location>,aa:<amino_acid>) where amino_acid is the amino acid coded by the codon at the base_range position Example /transl_except=(pos:213..215,aa:Trp) /transl_except=(pos:1017,aa:TERM) /transl_except=(pos:2000..2001,aa:TERM) /transl_except=(pos:X22222:15..17,aa:Ala) Comment if the amino acid is not on the restricted vocabulary list use e.g., '/transl_except=(pos:213..215,aa:OTHER)' with '/note="name of unusual amino acid"'; for modified amino-acid selenocysteine use three letter code 'Sec' (one letter code 'U' in amino-acid sequence) /transl_except=(pos:1002..1004,aa:Sec); for partial termination codons where TAA stop codon is completed by the addition of 3' A residues to the mRNA either a single base_position or a base_range is used, e.g. if partial stop codon is a single base: /transl_except=(pos:1017,aa:TERM) if partial stop codon consists of two bases: /transl_except=(pos:2000..2001,aa:TERM) with '/note='stop codon completed by the addition of 3' A residues to the mRNA'. Qualifier /transl_table= Definition definition of genetic code table used if other than universal genetic code table. Tables used are described at the specified URLs in appendix IV. Value format <integer> 1=universal table 1;2=non-universal table 2;... Example /transl_table=4 Comment genetic code exceptions outside range of specified tables are reported in /transl_except qualifier. Qualifier /trans_splicing Definition indicates that exons from two RNA molecules are ligated in intermolecular reaction to form mature RNA Value format none Example /trans_splicing Comment should be used on features such as CDS, mRNA and other features that are produced as a result of a trans-splicing event. This qualifier should be used only when the splice event is indicated in the "join" operator, eg join(complement(69611..69724),139856..140087) Qualifier /type_material= Definition indicates that the organism from which this sequence was obtained is a nomenclatural type of the species (or subspecies) corresponding with the /organism identified in the sequence entry Value format "<type-of-type> of <organism name>" where type-of-type is one of the following: type strain, neotype strain, holotype, paratype, neotype, allotype, hapanotype, syntype, lectotype, paralectotype, isotype, epitype, isosyntype, ex-type, reference strain, type material; Example /type_material="type strain of Escherichia coli" /type_material="holotype of Cercopitheus lomamiensis" /type_material="paratype of Cercopitheus lomamiensis" Comment <type-of-type> is taken from the INSDC controlled vocabularly for /type_material at: http://www.insdc.org/controlled-vocabulary-typematerial-qualifer <organism name> should be listed as the scientific name (or as a synonym) at the species (or subspecies) node in the taxonomy database. INSDC will automatically populate this qualifier from the NCBI taxonomy database to flag sequences of form type in the INSDC databases (ENA/GenBank/DDBJ). Qualifier /variety= Definition variety (= varietas, a formal Linnaean rank) of organism from which sequence was derived. Value format "text" Example /variety="insularis" Comment use the cultivar qualifier for cultivated plant varieties, i.e., products of artificial selection; varieties other than plant and fungal variatas should be annotated via /note, e.g. /note="breed:Cukorova"7.4 Appendix IV: Controlled vocabularies
This appendix contains information on the restricted vocabulary fields used in the Feature Table. The information contained in this appendix is subject to change, please contact the database staff for the most recent information concerning controlled vocabularies. This appendix is organized as follows: Authority The organization with authority to define the vocabulary Reference Publications of (or about) the vocabulary Contact Name of database staff responsible for maintaining the database copy of the vocabulary Scope Feature Table qualifiers which take members of this vocabulary as values Listing A listing of the current vocabulary with definitions or explanations This appendix includes reference lists for the following controlled vocabulary fields: - Nucleotide base codes (IUPAC) - Modified base abbreviations - Amino acid abbreviations - Modified and unusual Amino Acids - Genetic Code Tables - Country Names7.4.1 Nucleotide base codes (IUPAC)
Authority Nomenclature Committee of the International Union of Biochemistry Reference Cornish-Bowden, A. Nucl Acid Res 13, 3021-3030 (1985) Contact EMBL-EBI Scope Location descriptors Listing Symbol Meaning ------ ------- a a; adenine c c; cytosine g g; guanine t t; thymine in DNA; uracil in RNA m a or c r a or g w a or t s c or g y c or t k g or t v a or c or g; not t h a or c or t; not g d a or g or t; not c b c or g or t; not a n a or c or g or t7.4.2 Modified base abbreviations
Authority Sprinzl, M. and Gauss, D.H. Reference Sprinzl, M. and Gauss, D.H. Nucl Acid Res 10, r1 (1982). (note that in Cornish_Bowden, A. Nucl Acid Res 13, 3021-3030 (1985) the IUPAC-IUB declined to recommend a set of abbreviations for modified nucleotides) Contact NCBI Scope /mod_base Abbreviation Modified base description ------------ ------------------------- ac4c 4-acetylcytidine chm5u 5-(carboxyhydroxylmethyl)uridine cm 2'-O-methylcytidine cmnm5s2u 5-carboxymethylaminomethyl-2-thiouridine cmnm5u 5-carboxymethylaminomethyluridine dhu dihydrouridine fm 2'-O-methylpseudouridine gal q beta-D-galactosylqueuosine gm 2'-O-methylguanosine i inosine i6a N6-isopentenyladenosine m1a 1-methyladenosine m1f 1-methylpseudouridine m1g 1-methylguanosine m1i 1-methylinosine m22g 2,2-dimethylguanosine m2a 2-methyladenosine m2g 2-methylguanosine m3c 3-methylcytidine m4c N4-methylcytosine m5c 5-methylcytidine m6a N6-methyladenosine m7g 7-methylguanosine mam5u 5-methylaminomethyluridine mam5s2u 5-methylaminomethyl-2-thiouridine man q beta-D-mannosylqueuosine mcm5s2u 5-methoxycarbonylmethyl-2-thiouridine mcm5u 5-methoxycarbonylmethyluridine mo5u 5-methoxyuridine ms2i6a 2-methylthio-N6-isopentenyladenosine ms2t6a N-((9-beta-D-ribofurnosyl-2-methylthiopurin-6-yl)carbamoyl)threonine mt6a N-((9-beta-D-ribofuranosylpurine-6-yl)N-methyl-carbamoyl)threonine mv uridine-5-oxoacetic acid methylester o5u uridine-5-oxyacetic acid (v) osyw wybutoxosine p pseudouridine q queuosine s2c 2-thiocytidine s2t 5-methyl-2-thiouridine s2u 2-thiouridine s4u 4-thiouridine m5u 5-methyluridine t6a N-((9-beta-D-ribofuranosylpurine-6-yl)carbamoyl)threonine tm 2'-O-methyl-5-methyluridine um 2'-O-methyluridine yw wybutosine x 3-(3-amino-3-carboxypropyl)uridine, (acp3)u OTHER (requires /note= qualifier)7.4.3 Amino acid abbreviations
Authority IUPAC-IUB Joint Commission on Biochemical Nomenclature. Reference IUPAC-IUB Joint Commission on Biochemical Nomenclature. Nomenclature and Symbolism for Amino Acids and Peptides. Eur. J. Biochem. 138:9-37(1984). IUPAC-IUBMB JCBN Newsletter, 1999 http://www.chem.qmul.ac.uk/iubmb/newsletter/1999/item3.html Scope /anticodon, /transl_except Contact EMBL-EBI Listing (note that the abbreviations are legal values for amino acids, not the full names) Abbreviation Amino acid name ------------ --------------- Ala A Alanine Arg R Arginine Asn N Asparagine Asp D Aspartic acid (Aspartate) Cys C Cysteine Gln Q Glutamine Glu E Glutamic acid (Glutamate) Gly G Glycine His H Histidine Ile I Isoleucine Leu L Leucine Lys K Lysine Met M Methionine Phe F Phenylalanine Pro P Proline Pyl O Pyrrolysine Ser S Serine Sec U Selenocysteine Thr T Threonine Trp W Tryptophan Tyr Y Tyrosine Val V Valine Asx B Aspartic acid or Asparagine Glx Z Glutamine or Glutamic acid. Xaa X Any amino acid. Xle J Leucine or Isoleucine TERM termination codon7.4.4 Modified and unusual Amino Acids
Abbreviation Amino acid ------------ --------- Aad 2-Aminoadipic acid bAad 3-Aminoadipic acid bAla beta-Alanine, beta-Aminoproprionic acid Abu 2-Aminobutyric acid 4Abu 4-Aminobutyric acid, piperidinic acid Acp 6-Aminocaproic acid Ahe 2-Aminoheptanoic acid Aib 2-Aminoisobutyric acid bAib 3-Aminoisobutyric acid Apm 2-Aminopimelic acid Dbu 2,4-Diaminobutyric acid Des Desmosine Dpm 2,2'-Diaminopimelic acid Dpr 2,3-Diaminoproprionic acid EtGly N-Ethylglycine EtAsn N-Ethylasparagine Hyl Hydroxylysine aHyl allo-Hydroxylysine 3Hyp 3-Hydroxyproline 4Hyp 4-Hydroxyproline Ide Isodesmosine aIle allo-Isoleucine MeGly N-Methylglycine, sarcosine MeIle N-Methylisoleucine MeLys 6-N-Methyllysine MeVal N-Methylvaline Nva Norvaline Nle Norleucine Orn Ornithine OTHER (requires /note=)7.4.5 Genetic Code Tables
Authority International Nucleotide Sequence Database Collaboration Contact NCBI Scope /transl_table qualifier URL https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c URL http://www.insdc.org/genetic-code-tables7.4.6 Country Names
Authority International Nucleotide Sequence Database Collaboration Contact INSDC member databases Scope /country qualifier URL http://www.insdc.org/country7.4.7 Announces
Additional controlled vocabulary terms for qualifier values might be added outside of the cycle of the Feature Table document release. See also www.insdc.org with controlled vocabularies in the Feature Table document. From December 2016 a complete list of the genetic codes will also be maintained outside of the cycle of the Feature Table document release at: http://www.insdc.org/genetic-code-tables