DDBJ/EMBL/GenBank Feature Table
The 3 databases GenBank, DDBJ, and EMBL share a common definition named feature table format that devise a set of common standards for annotating nucleotide sequences. A copy of the table can be found hereafter; the most recent table can be found here.
The DDBJ/EMBL/GenBank
Feature Table:
Definition
Version 10.1 May 2012
DNA Data Bank of Japan, Mishima, Japan.
EMBL-Bank, 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
1 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 feature
2.2 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. Expression signal features
Indicate regions containing a signal that alters a biological function:
misc_signal location
3. Transcript features
Indicate products made by a region:
misc_RNA location
4. 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"
5. Repeat features
Indicate repetitive sequence elements:
repeat_region location
6. Recombination features
Indicate regions that have been either inserted or deleted by recombination:
misc_recomb location
7. Structure features
Indicate sequence for which there is secondary or tertiary structural
information:
misc_structure location
3.2.4 Feature key examples
Key Description
CDS Protein-coding sequence
RBS ribosome binding site
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. Sequences
3.3.3.1 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"
promoter <1..9
/gene="ubc42"
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 J00194
4 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 79
4.2 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 continuation
4.3 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 blanks
5 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"
promoter <1..9
/gene="ubc42"
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
polyA_signal 1310..1317
/gene="ubc42"
5.2 Bacterial operon
source 1..9430
/organism="Lactococcus sp."
/strain="MG1234"
/mol_type="genomic DNA"
operon 160..6865
/operon="gal"
-35_signal 160..165
/operon="gal"
-10_signal 179..184
/operon="gal"
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 join(complement(567..795),complement(21..349))
/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"
-35_signal 644..650
/gene="tRNA-Leu(UUR)"
tRNA 655..730
/gene="tRNA-Leu(UUR)"
/anticodon=(pos:678..680,aa:Leu)
/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 RBS 95..100
FT /gene="sod"
FT terminator 723..746
FT /gene="sod"
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"
RBS 95..100
/gene="sod"
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"
terminator 723..746
/gene="sod"
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"
RBS 95..100
/gene="sod"
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"
terminator 723..746
/gene="sod"
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 CON record that is
part of a genome assembly;
Mandatory qualifiers /estimated_length=unknown or <integer>
/gap_type="TYPE"
/linkage_evidence="TYPE" (Note: Mandatory only if the
/gap_type is "within scaffold" or "repeat within
scaffold".If there are multiple types of linkage_evidence
they will appear as multiple /linkage_evidence="TYPE"
qualifiers. For all other types of assembly_gap
features, use of the /linkage_evidence qualifier is
invalid.)
Comment the location span of the assembly_gap feature for an
unknown gap is 100 bp, with the 100 bp indicated as
100 "n"'s in sequence.
Feature Key attenuator
Definition 1) region of DNA at which regulation of termination of
transcription occurs, which controls the expression
of some bacterial operons;
2) sequence segment located between the promoter and the
first structural gene that causes partial termination
of transcription
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)
/operon="text"
/phenotype="text"
Organism scope prokaryotes
Molecule scope DNA
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"
/pseudogene="TYPE"
/standard_name="text"
Parent Key CDS
Organism scope eukaryotes
Feature Key CAAT_signal
Definition CAAT box; part of a conserved sequence located about 75
bp up-stream of the start point of eukaryotic
transcription units which may be involved in RNA
polymerase binding; consensus=GG(C or T)CAATCT [1,2].
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
Molecule scope DNA
References [1] Efstratiadis, A. et al. Cell 21, 653-668 (1980)
[2] Nevins, J.R. "The pathway of eukaryotic mRNA formation"
Ann Rev Biochem 52, 441-466 (1983)
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>"
/pseudogene="TYPE"
/ribosomal_slippage
/standard_name="text"
/translation="text"
/transl_except=(pos:<base_range>,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 (3+5 format
with 3 position letters and 5 numbers) plus a version
number after the decimal point; when the protein
sequence encoded by the CDS changes, only the version
number of the /protein_id value is incremented; the
stable part of the /protein_id remains unchanged and as
a result will permanently be associated with a given
protein;
Feature Key centromere
Definition region of biological interest identified as a centromere and
which has been experimentally characterized;
Optional qualifiers /citation=[number]
/db_xref="<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"
/pseudogene="TYPE"
/standard_name="text"
Parent Key CDS
Organism scope eukaryotes
Feature Key enhancer
Definition a cis-acting sequence that increases the utilization of
(some) eukaryotic promoters, and can function in either
orientation and in any location (upstream or downstream)
relative to the promoter;
Optional qualifiers /allele="text"
/bound_moiety="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"
Organism scope eukaryotes and eukaryotic viruses
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"
/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 GC_signal
Definition GC box; a conserved GC-rich region located upstream of
the start point of eukaryotic transcription units which
may occur in multiple copies or in either orientation;
consensus=GGGCGG;
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 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"
/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)
/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"
/pseudogene="TYPE"
/standard_name="text"
Parent Key CDS
Organism scope eukaryotes
Feature Key LTR
Definition long terminal repeat, a sequence directly repeated at
both ends of a defined sequence, of the sort typically
found in retroviruses;
Optional qualifiers /allele="text"
/citation=[number]
/db_xref="<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 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"
/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 the key RBS is 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 (unsure, 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"
/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)
/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"
/pseudogene="TYPE"
/standard_name="text"
/trans_splicing
Feature Key misc_signal
Definition any region containing a signal controlling or altering
gene function or expression that cannot be described by
other signal keys (promoter, CAAT_signal, TATA_signal,
-35_signal, -10_signal, GC_signal, RBS, polyA_signal,
enhancer, attenuator, terminator, and rep_origin).
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"
/phenotype="text"
/standard_name="text"
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"
/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"
/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"
/pseudogene="TYPE"
/standard_name="text"
Parent Key CDS
Organism scope eukaryotes
Feature Key old_sequence
Definition the presented sequence revises a previous version of the
sequence at this location;
Mandatory qualifiers /citation=[number]
Or
/compare=[accession-number.sequence-version]
Optional qualifiers /allele="text"
/db_xref="<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
containing genes that encode enzymes that are
in the same metabolic pathway and regulatory sequences
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"
/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_signal
Definition recognition region necessary for endonuclease cleavage
of an RNA transcript that is followed by polyadenylation;
consensus=AATAAA [1];
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
References [1] Proudfoot, N. and Brownlee, G.G. Nature 263, 211-214
(1976)
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 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; includes 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 promoter
Definition region on a DNA molecule involved in RNA polymerase
binding to initiate transcription;
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"
/pseudogene="TYPE"
/standard_name="text"
Molecule scope DNA
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 RBS is used for ribosome binding sites.
Feature Key RBS
Definition ribosome binding site;
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"
References [1] Shine, J. and Dalgarno, L. Proc Natl Acad Sci USA
71, 1342-1346 (1974)
[2] Gold, L. et al. Ann Rev Microb 35, 365-403 (1981)
Comment in prokaryotes, known as the Shine-Dalgarno sequence: is
located 5 to 9 bases upstream of the initiation codon;
consensus GGAGGT [1,2].
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"
/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"
/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"
/pseudogene="TYPE"
/standard_name="text"
Parent Key misc_signal
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"
/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 /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
/frequency="text"
/germline
/haplogroup="text"
/haplotype="text"
/host="text"
/identified_by="text"
/isolate="text"
/isolation_source="text"
/lab_host="text"
/lat_lon="text"
/macronuclear
/map="text"
/mating_type="text"
/note="text"
/organelle=<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"
/sub_species="text"
/sub_strain="text"
/tissue_lib="text"
/tissue_type="text"
/transgenic
/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 IV /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
Parent key misc_binding
Comment STS location to include primer(s) in primer_bind key or
primers.
Feature Key TATA_signal
Definition TATA box; Goldberg-Hogness box; a conserved AT-rich
septamer found about 25 bp before the start point of
each eukaryotic RNA polymerase II transcript unit which
may be involved in positioning the enzyme for correct
initiation; consensus=TATA(A or T)A(A or T) [1,2];
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
Molecule scope DNA
References [1] Efstratiadis, A. et al. Cell 21, 653-668 (1980)
[2] Corden, J., et al. "Promoter sequences of
eukaryotic protein-encoding genes" Science 209,
1406-1414 (1980)
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 terminator
Definition sequence of DNA located either at the end of the
transcript that causes RNA polymerase to terminate
transcription;
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)
/operon="text"
/standard_name="text"
Molecule scope DNA
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"
/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"
/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>)
/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"
/pseudogene="TYPE"
/standard_name="text"
/trans_splicing
Feature Key unsure
Definition author is unsure of exact sequence in this region;
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"
/pseudogene="TYPE"
/standard_name="text"
Parent Key CDS
Organism scope eukaryotes
Feature Key V_segment
Definition variable segment of immunoglobulin light and heavy
chains, and T-cell receptor alpha, beta, and gamma
chains; codes for most of the variable region (V_region)
and the last few amino acids of the leader peptide;
Optional qualifiers /allele="text"
/citation=[number]
/db_xref="<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"
/pseudogene="TYPE"
/standard_name="text"
Parent Key CDS
Organism scope eukaryotes
Feature Key variation
Definition a related strain contains stable mutations from the same
gene (e.g., RFLPs, polymorphisms, etc.) which differ
from the presented sequence at this location (and
possibly others);
Optional qualifiers /allele="text"
/citation=[number]
/compare=[accession-number.sequence-version]
/db_xref="<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 region at the 3' end of a mature transcript (following
the 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 region at the 5' end of a mature transcript (preceding
the 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_splicing
Feature Key -10_signal
Definition Pribnow box; a conserved region about 10 bp upstream of
the start point of bacterial transcription units which
may be involved in binding RNA polymerase;
consensus=TAtAaT [1,2,3,4];
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)
/operon="text"
/standard_name="text"
Organism scope prokaryotes
Molecule scope DNA
References [1] Schaller, H., Gray, C., and Hermann, K. Proc Natl
Acad Sci USA 72, 737-741 (1974)
[2] Pribnow, D. Proc Natl Acad Sci USA 72, 784-788 (1974)
[3] Hawley, D.K. and McClure, W.R. "Compilation and
analysis of Escherichia coli promoter DNA sequences"
Nucl Acid Res 11, 2237-2255 (1983)
[4] Rosenberg, M. and Court, D. "Regulatory sequences
involved in the promotion and termination of RNA
transcription" Ann Rev Genet 13, 319-353 (1979)
Feature Key -35_signal
Definition a conserved hexamer about 35 bp upstream of the start
point of bacterial transcription units; consensus=TTGACa
or TGTTGACA;
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)
/operon="text"
/standard_name="text"
Organism scope prokaryotes
Molecule scope DNA
References [1] Takanami, M., et al. Nature 260, 297-302 (1976)
[2] Moran, C.P., Jr., et al. Molec Gen Genet 186,
339-346 (1982)
[3] Maniatis, T., et al. Cell 5, 109-113 (1975)
7.3 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 /anticodon=
Definition location of the anticodon of tRNA and the amino acid for which
it codes
Value format (pos:<location>,aa:<amino_acid>) where location is the position
of the anticodon and amino_acid is the abbreviation for the
amino acid encoded
Example /anticodon=(pos:34..36,aa:Phe)
/anticodon=(pos:join(5,495..496),aa:Leu)
/anticodon=(pos:complement(4156..4158),aa:Gln)
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 Multiple /bound_moiety qualifiers are legal on "promoter"
and "enhancer" features. 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 the person who collected the specimen
Value format "text"
Example /collected_by="Dan Janzen"
Qualifier /collection_date=
Definition date that the specimen was collected
Value format "DD-Mmm-YYYY", "Mmm-YYYY" or "YYYY"
Example /collection_date="21-Oct-1952"
/collection_date="Oct-1952"
/collection_date="1952"
Comment full date format DD-Mmm-YYYY is preferred; where day and/or month
of collection is not known either "Mmm-YYYY" or "YYYY" can be used;
three-letter month abbreviation can be one of the following: Jan,
Feb, Mar, Apr, May, Jun, Jul, Aug, Sep, Oct, Nov, Dec.
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/country
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.
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"
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.
Symbol "n" 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; 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"
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 2.0:
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/agp/AGP_Specification.shtml
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 taxonomist who identified the specimen
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;
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"or "repeat within scaffold";
Value format "paired-ends", "align genus", "align xgenus", "align trnscpt", "within clone",
"clone contig", "map", "strobe", "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 2.0:
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/agp/AGP_Specification.shtml
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 /proteid_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 /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
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 (http://www.insdc.org/rna_vocab.html); on
15-Oct-2008, the following terms were valid:
"antisense_RNA"
"autocatalytically_spliced_intron"
"ribozyme"
"hammerhead_ribozyme"
"RNase_P_RNA"
"RNase_MRP_RNA"
"telomerase_RNA"
"guide_RNA"
"rasiRNA"
"scRNA"
"siRNA"
"miRNA"
"piRNA"
"snoRNA"
"snRNA"
"SRP_RNA"
"vault_RNA"
"Y_RNA"
"other"
ncRNA classes not yet in the INSDC /ncRNA_class controlled
vocabulary can be annotated by entering
'/ncRNA_class="other"' with '/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"
Comment currently valid only on Prokaryota-specific features
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
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 a variation that characterizes a particular
sub-population within a given species. The variation could be
in the genotype or the phenotype.
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 (3+5 format
with 3 position letters and 5 numbers) plus a version number
after the decimal point.
Value format <identifier>
Example /protein_id="AAA12345.1"
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 not to be used for new submissions from 15-APR-2012; After
15-APR-2012 a new qualifier /pseudogene will become valid.
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:
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 /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 organization of repeated sequence
Value format tandem, inverted, flanking, terminal, direct, dispersed, and other
Example /rpt_type=INVERTED
Comment the values are case-insensitive, i.e. both "INVERTED" and "inverted"
are valid;
Definitions of the values:
tandem, a repeat that exists adjacent to another in the same
orientation;
inverted, a repeat which occurs as part of as set (normally a part)
organized in the reverse orientation;
flanking, a repeat lying outside the sequence for which it has
functional significance (eg. transposon insertion target sites);
terminal, a repeat at the ends of and within the sequence for which
it has functional significance (eg. transposon LTRs);
direct, a repeat that exists not always adjacent but is in the same
orientation;
dispersed, a repeat that is found dispersed throughout the genome;
other, a repeat exhibiting important attributes that cannot be
described by other values.
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.
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;
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 /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
exceptions in the /transl_except and /codon qualifiers
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" 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 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 /codon or /transl_except qualifiers.
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 /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 V: 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 Names
7.4.1 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 t
7.4.2 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
d dihydrouridine
fm 2'-O-methylpseudouridine
gal q beta,D-galactosylqueosine
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
m5c 5-methylcytidine
m6a N6-methyladenosine
m7g 7-methylguanosine
mam5u 5-methylaminomethyluridine
mam5s2u 5-methoxyaminomethyl-2-thiouridine
man q beta,D-mannosylqueosine
mcm5s2u 5-methoxycarbonylmethyl-2-thiouridine
mcm5u 5-methoxycarbonylmethyluridine
mo5u 5-methoxyuridine
ms2i6a 2-methylthio-N6-isopentenyladenosine
ms2t6a N-((9-beta-D-ribofuranosyl-2-methyltiopurine-6-yl)car
bamoyl)threonine
mt6a N-((9-beta-D-ribofuranosylpurine-6-yl)N-methyl-carbam
oyl)threonine
mv uridine-5-oxyacetic acid-methylester
o5u uridine-5-oxyacetic acid (v)
osyw wybutoxosine
p pseudouridine
q queosine
s2c 2-thiocytidine
s2t 5-methyl-2-thiouridine
s2u 2-thiouridine
s4u 4-thiouridine
t 5-methyluridine
t6a N-((9-beta-D-ribofuranosylpurine-6-yl)carbamoyl)threo
nine
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 codon
7.4.4 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 http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
Genetic Code [1]
Standard Code (transl_table=1)
AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = ---M---------------M---------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Genetic Code [2]
Vertebrate Mitochondrial Code (transl_table=2)
AAs = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG
Starts = --------------------------------MMMM---------------M------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Genetic Code [3]
Yeast Mitochondrial Code (transl_table=3)
AAs = FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = ----------------------------------MM----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Genetic Code [4]
Mold, Protozoan, Coelenterate Mitochondrial Code & Mycoplasma/Spiroplasma
Code (transl_table=4)
AAs = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = --MM---------------M------------MMMM---------------M------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Genetic Code [5]
Invertebrate Mitochondrial Code (transl_table=5)
AAs = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG
Starts = ---M----------------------------MMMM---------------M------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Genetic Code [6]
Ciliate, Dasycladacean and Hexamita Nuclear Code (transl_table=6)
AAs = FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Genetic Code [9]
Echinoderm and Flatworm Mitochondrial Code (transl_table=9)
AAs = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
Starts = -----------------------------------M---------------M------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Genetic Code [10]
Euplotid Nuclear Code (transl_table=10)
AAs = FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Genetic Code [11]
Bacterial, Archaeal and Plant Plastid Code (transl_table=11)
AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = ---M---------------M------------MMMM---------------M------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Genetic Code [12]
Alternative Yeast Nuclear Code (transl_table=12)
AAs = FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = -------------------M---------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Genetic Code [13]
Ascidian Mitochondrial Code (transl_table=13)
AAs = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG
Starts = ---M------------------------------MM---------------M------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Genetic Code [14]
Alternative Flatworm Mitochondrial Code (transl_table=14)
AAs = FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Genetic Code [15]
Blepharisma Nuclear Code (transl_table=15)
AAs = FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Genetic Code [16]
Chlorophycean Mitochondrial Code (transl_table=16)
AAs = FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Genetic Code [21]
Trematode Mitochondrial Code (transl_table=21)
AAs = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG
Starts = -----------------------------------M---------------M------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Genetic Code [22]
Scenedesmus obliquus mitochondrial
AAs = FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Genetic Code [23]
Thraustochytrium Mitochondrial Code (transl_table=23)
AAs = FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = --------------------------------M--M---------------M------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Genetic Code [24]
Pterobranchia mitochondrial code (transl_table=24)
AAs = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG
Starts = ---M---------------M---------------M---------------M------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
7.4.6 Country Names
Authority International Nucleotide Sequence Database Collaboration
Contact INSDC member databases
Scope /country qualifier
URL http://www.insdc.org/country