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| DDBJ/EMBL/GenBank |
Feature Table Definition |
- DNA Data Bank of Japan, Mishima, Japan.
- EMBL Nucleotide Sequence Database, Cambridge, UK.
- GenBank, NCBI, Bethesda, MD, USA.
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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
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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 keyword 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.
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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 allow to
avoid the free-text descriptions
-
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 new 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 corresponds to the 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
the indicated elements to form one contiguous sequence encoding a product
called T-cell receptor beta-chain.
The following sections contain detailed explanations of the new feature
table design showing conventions for each component of the new 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 both the EMBL, GenBank and DDBJ formats. Appendix
II describes the format in Backus-Naur-Form (BNF). Appendices III
and
IV provide reference manuals for the feature
table keys and qualifiers, respectively.
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.
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3 Feature table components and format
3.1 Naming conventions
Feature table components, including feature keys, qualifiers, accession
numbers, database name abbreviations, feature labels, 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. While case should not be
regarded as significant in comparing feature labels ('Prot1' and 'pROT1'
are the same), the databanks will preserve the case of labels as originally
annotated. The following characters are permitted to occur in feature table
component names:
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Upper-case letters (A-Z)
-
Lower-case letters (a-z)
-
Numbers (0-9)
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Underscore (_)
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Hyphen (-)
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Single quotation mark or apostrophe (')
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Asterisk (*)
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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
III. Each feature must contain a feature key. Features created solely as
location references should use a single hyphen "-" as their feature key.
Users may define their own feature keys for local use but user-defined
keys' names should begin with an asterisk (*) and follow the naming conventions
described in section 3.1. The data banks will, in the future, create new
feature keys as necessary. However, key names beginning with an asterisk
will be reserved for local use.
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:
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Difference and change features.
Indicate ways in which a sequence should be changed to produce a different
"version":
misc_difference location
/replace="change_location"
Expression signal features.
Indicate regions containing a signal that alters a biological function:
misc_signal location
Transcript features.
Indicate products made by a region:
misc_RNA location
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"
Repeat features.
Indicate repetitive sequence elements:
repeat_region location
Recombination features.
Indicate regions that have been either inserted or deleted by recombination:
misc_recomb location
Structure features.
Indicate sequence for which there is secondary or tertiary structural
information:
misc_structure location
In addition to the functional groupings shown above, the feature keys can
also be arranged in a hierarchical tree based on the degree of specificity
or level of detail known about a feature. This hierarchy is shown in outline
form in
Appendix III where the most general
level is the 'misc_feature' key and other keys are arranged in increasing
level of detail. By using more general keys, features can be annotated
even if their biological functions are insufficiently well characterized
to assign them more specific keys.
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 III for descriptions of all
feature keys.
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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
CDS 1..1000
/codon=(seq:"cug",aa:Ser)
/codon=(seq:"tga",aa:Trp)
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:
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Free text
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Controlled vocabulary or enumerated values
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Citation or reference numbers
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Sequences
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Feature labels
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 are 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 in the interest of
readability, unlike the case of feature labels where the databases will
maintain the case as originally entered (see
Section
3.4.2). 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"
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"
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3.4 Feature labels
The /label= qualifier takes as its value a feature label. Feature labels
follow the same naming conventions as other feature table components (e.g.,
keys and qualifiers). While feature labels are optional, attaching a label
to a feature allows it to be referred to unambiguously. For example, the
feature label can be used to refer unambiguously to a coding region that
exists in a different entry to the exons of which it is comprised.
3.4.1 Purpose
The feature label identifies a feature item within an entry and, when combined
with the entry's primary accession number and the name of the database
from which it came, is a permanent internationally unique tag for that
feature. There are, however, certain situations in which a "permanent"
feature may "disappear" from the distributed version of the database and
others in which it may be desirable to change a feature's label.
3.4.2 Format and conventions
Each feature in a feature table may have a label which must be unique within
that entry, but which may be the same as feature labels used in other entries.
A feature can be given any label. However, labels containing meaningful
abbreviations will be much more easily remembered than non-descriptive
labels. Because letter case is not significant, two features within one
entry cannot have labels that differ only in case: '16S_rRNA' and '16s_rRNA'
could not both be used in the same entry.
The full feature name syntax is as follows:
Database name::primary accession number:feature label
References to a feature should use as much of the full feature name as
required to unambiguously identify the feature.
3.4.3 Examples of feature labels
Feature label Description
adhI adhI gene coding for alcohol dehydrogenase
tfp35 tail fiber protein 35
3'-ltr 3' long terminal repeat
a1col_x51 prepro-alpha-1-collagen, exon 51
refnum reference to numbering in a citation
X10045:diff1 first conflict for the sequence of entry X10045
GB::K10675:catexA feature with label catexA in entry K10675
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3.5 Location
3.5.1 Purpose
The location indicates the region of the presented sequence which corresponds
to a feature.
3.5.2 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, which
is not necessarily the same as the numbering scheme used in the published
report cited, 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. Location operators and descriptors
are discussed in more detail below.
3.5.2.1 Location descriptors
The location descriptor can be one of the following:
(a) a single base number
(b) a site between two indicated base numbers
(c) a single base chosen from within a specified range of bases
(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 points (nucleotides), such as endonucleolytic cleavage
site, is indicated by listing the two points separated by a carat (^).
A single base chosen from a range or span 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).
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 (and does not include) the specified base number.
The starting and ending base positions can be represented as distinct base
numbers ('34..456') or as alternatives specified by an operator. A single
point chosen from a range of points uses the 'x.y' format described above.
A location in a remote entry (not the entry to which the feature table
belongs) can be specified by giving the remote entry (accession-number)
followed by a location descriptor which applies to that entry's sequence.
3.5.2.2 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 allowable operators is given below with their definitions
and most common format.
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complement(location)
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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)
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join(location,location, ... location)
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The indicated elements should be joined (placed end-to-end) to form one
contiguous sequence
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order(location,location, ... location)
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The elements can be found in the specified order (5' to 3' direction),
but nothing is implied about the reasonableness about joining them
3.5.3 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 con-
tinues to and includes the ending base
<1..888 The feature starts before the first sequenced base and
continues to and includes base 888
(102.110) Indicates that the exact location is unknown but that
it is one of the bases between bases 102 and 110, in-
clusive
(23.45)..600 Specifies that the starting point is one of the bases be-
tween bases 23 and 45, inclusive, and the end point is
base 600
(122.133)..(204.221) The feature starts at a base between 122 and 133, in-
clusive, and ends at a base between 204 and 221, in-
clusive
123^124 Points to a site between bases 123 and 124
145^177 Points to a site between two adjacent bases anywhere
between bases 145 and 177
join(12..78,134..202) Regions 12 to 78 and 134 to 202 should be joined to form
one contiguous sequence
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)
complement(34..(122.126)) Start at one of the bases complementary to those
between 122 and 126 on the presented strand and finish
at the base complementary to base 34 (the feature is
on the strand complementary to the presented strand)
J00194:100..202 Points to bases 100 to 202, inclusive, in the entry (in
this database) with primary accession number 'J00194'
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4 Feature table format
This section describes the columnar format used to write this feature table
in "flat file" form for distributions of the databases.
4.1 Format examples
Feature table format example (EMBL):
source 1..1859
/db_xref="taxon:3899"
/organism="Trifolium repens"
/tissue_type="leaves"
/clone_lib="lambda gt10"
/clone="TRE361"
CDS 14..1495
/db_xref="MENDEL:11000"
/db_xref="SWISS-PROT:P26204"
/note="non-cyanogenic"
/EC_number="3.2.1.21"
/product="beta-glucosidase"
/protein_id="CAA40058.1"
/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"
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"
/sequenced_mol="cDNA to mRNA"
/strain="Sprague-Dawley"
/tissue_type="kidney"
mRNA 19..2128
CDS 31..1212
/codon_start=1
/evidence=not_experimental
/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
Additional examples of the feature table format can be found in
Section
5 and
Appendix I in this document.
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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 that described above in 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
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5 Examples of sequence annotation
Note that the examples given below are only samples of one way a sequence
may be annotated and other ways may also be acceptable.
5.1 Eukaryotic gene
source 1..1509
/organism="Mus musculus"
/strain="CD1"
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"
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5.2 Bacterial Operon
source 1..9430
/organism="Lactococcus sp."
/strain="MG1234"
-35_signal 160..165
/gene="galA"
/evidence=EXPERIMENTAL
-10_signal 179..184
/gene="galA"
/evidence=EXPERIMENTAL
CDS 405..1934
/gene="galA"
/product="galactose permease"
/function="galactose transporter"
/evidence=EXPERIMENTAL
CDS 2003..3001
/gene="galM"
/product="aldose 1-epimerase"
/EC_number="5.1.3.3"
/function="mutarotase"
CDS 3235..4537
/gene="galK"
/product="galactokinase"
/EC_number="2.7.1.6"
/evidence=EXPERIMENTAL
misc_RNA 189..6865
/gene="galAMK"
/evidence=EXPERIMENTAL
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5.3 Artificial cloning vector (circular)
source 1..5300
/organism="Cloning vector pABC"
/lab_host="Escherichia coli"
/focus
source 1..5138
/organism="Escherichia coli"
/strain="K12"
source 5139..5247
/organism="Aequorea victoria"
/dev_stage="adult"
source 5248..5300
/organism="Escherichia coli"
/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"
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5.4 Plasmid
source 1..2245
/organism="Escherichia coli"
/plasmid="Plasmid Z"
/strain="K12"
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"
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5.5 Repeat element
source 1..1011
/organism="Homo sapiens"
/clone="pha281u/1DO"
repeat_region 80..401
/rpt_type=DISPERSED
/rpt_family="Alu-J"
/rpt_unit=80..401
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5.6 Immunoglobulin heavy chain
source 1..348
/organism="Homo sapiens"
/cell_type="B-lymphocyte"
/rearranged
CDS <1..>336
/codon_start=1
/gene="IGHV1"
/product="immunoglobulin heavy chain variable region"
V_region <1..>336
/gene="IGHV1"
/product="immunoglobulin heavy chain variable region"
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5.7 T-cell receptor
source 1..402
/organism="Homo sapiens"
/sex="male"
/cell_type="CD4+ T-lymphocyte"
/rearranged
/clone="TCR1A.12"
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..>402
/gene="TCR1A"
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5.8 Transfer RNA
source 1..2345
/organism="Yersinia sp."
/strain="IP134"
-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)"
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6 Known limitations of this feature table design
During the development of this 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.
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7. Appendices
7.1 Appendix I EMBL,GenBank and DDBJ entries
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7.1.1 EMBL format
ID LISOD standard; DNA; 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
DR SWISS-PROT; P28763; SODM_LISIV.
XX
FH Key Location/Qualifiers
FH
FT source 1..756
FT /db_xref="taxon:1638"
FT /organism="Listeria ivanovii"
FT /strain="ATCC 19119"
FT RBS 95..100
FT /gene="sod"
FT terminator 723..746
FT /gene="sod"
FT CDS 109..717
FT /db_xref="SWISS-PROT:P28763"
FT /transl_table=11
FT /gene="sod"
FT /EC_number="1.15.1.1"
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 ttcacataaa taataaacaa tccgaggagg aatttttaat gacttacgaa 120
ttaccaaaat taccttatac ttatgatgct ttggagccga attttgataa agaaacaatg 180
gaaattcact atacaaagca ccacaatatt tatgtaacaa aactaaatga agcagtctca 240
ggacacgcag aacttgcaag taaacctggg gaagaattag ttgctaatct agatagcgtt 300
cctgaagaaa ttcgtggcgc agtacgtaac cacggtggtg gacatgctaa ccatacttta 360
ttctggtcta gtcttagccc aaatggtggt ggtgctccaa ctggtaactt aaaagcagca 420
atcgaaagcg aattcggcac atttgatgaa ttcaaagaaa aattcaatgc ggcagctgcg 480
gctcgttttg gttcaggatg ggcatggcta gtagtgaaca atggtaaact agaaattgtt 540
tccactgcta accaagattc tccacttagc gaaggtaaaa ctccagttct tggcttagat 600
gtttgggaac atgcttatta tcttaaattc caaaaccgtc gtcctgaata cattgacaca 660
ttttggaatg taattaactg ggatgaacga aataaacgct ttgacgcagc aaaataatta 720
tcgaaaggct cacttaggtg ggtcttttta tttcta 756
//
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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; Bacillus/Clostridium group; Bacillaceae;
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"
gene 95..746
/gene="sod"
RBS 95..100
/gene="sod"
CDS 109..717
/gene="sod"
/EC_number="1.15.1.1"
/codon_start=1
/transl_table=11
/product="superoxide dismutase"
/protein_id="CAA45406.1"
/db_xref="SWISS-PROT:P28763"
/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 ttcacataaa taataaacaa tccgaggagg aatttttaat gacttacgaa
121 ttaccaaaat taccttatac ttatgatgct ttggagccga attttgataa agaaacaatg
181 gaaattcact atacaaagca ccacaatatt tatgtaacaa aactaaatga agcagtctca
241 ggacacgcag aacttgcaag taaacctggg gaagaattag ttgctaatct agatagcgtt
301 cctgaagaaa ttcgtggcgc agtacgtaac cacggtggtg gacatgctaa ccatacttta
361 ttctggtcta gtcttagccc aaatggtggt ggtgctccaa ctggtaactt aaaagcagca
421 atcgaaagcg aattcggcac atttgatgaa ttcaaagaaa aattcaatgc ggcagctgcg
481 gctcgttttg gttcaggatg ggcatggcta gtagtgaaca atggtaaact agaaattgtt
541 tccactgcta accaagattc tccacttagc gaaggtaaaa ctccagttct tggcttagat
601 gtttgggaac atgcttatta tcttaaattc caaaaccgtc gtcctgaata cattgacaca
661 ttttggaatg taattaactg ggatgaacga aataaacgct ttgacgcagc aaaataatta
721 tcgaaaggct cacttaggtg ggtcttttta tttcta
//
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|
7.1.3 DDBJ Format
LOCUS LISOD 756 bp DNA linear BCT 30-JUN-1993
DEFINITION L.ivanovii sod gene for superoxide dismutase.
ACCESSION X64011 S78972
VERSION X64011.1
KEYWORDS sod gene; superoxide dismutase.
SOURCE Listeria ivanovii.
ORGANISM Listeria ivanovii
Bacteria; Firmicutes; Bacillus/Clostridium group; Bacillales;
Listeriaceae; Listeria.
REFERENCE 1
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, 313-322(1992).
MEDLINE 92140371
REFERENCE 2 (bases 1 to 756)
AUTHORS Kreft,J.
JOURNAL Submitted (21-APR-1992) to the EMBL/GenBank/DDBJ databases. J.
Kreft, Institut f. Mikrobiologie, Universitaet Wuerzburg, Biozentrum
Am Hubland, 8700 Wuerzburg, FRG
FEATURES Location/Qualifiers
source 1..756
/db_xref="taxon:1638"
/organism="Listeria ivanovii"
/strain="ATCC 19119"
RBS 95..100
/gene="sod"
terminator 723..746
/gene="sod"
CDS 109..717
/db_xref="SWISS-PROT:P28763"
/transl_table=11
/gene="sod"
/EC_number="1.15.1.1"
/product="superoxide dismutase"
/protein_id="CAA45406.1"
/translation="MTYELPKLPYTYDALEPNFDKETMEIHYTKHHNIYVTKLNEAVSG
HAELASKPGEELVANLDSVPEEIRGAVRNHGGGHANHTLFWSSLSPNGGGAPTGNLKAA
IESEFGTFDEFKEKFNAAAAARFGSGWAWLVVNNGKLEIVSTANQDSPLSEGKTPVLGL
DVWEHAYYLKFQNRRPEYIDTFWNVINWDERNKRFDAAK"
BASE COUNT 247 a 136 c 151 g 222 t
ORIGIN
1 cgttatttaa ggtgttacat agttctatgg aaatagggtc tatacctttc gccttacaat
61 gtaatttctt ttcacataaa taataaacaa tccgaggagg aatttttaat gacttacgaa
121 ttaccaaaat taccttatac ttatgatgct ttggagccga attttgataa agaaacaatg
181 gaaattcact atacaaagca ccacaatatt tatgtaacaa aactaaatga agcagtctca
241 ggacacgcag aacttgcaag taaacctggg gaagaattag ttgctaatct agatagcgtt
301 cctgaagaaa ttcgtggcgc agtacgtaac cacggtggtg gacatgctaa ccatacttta
361 ttctggtcta gtcttagccc aaatggtggt ggtgctccaa ctggtaactt aaaagcagca
421 atcgaaagcg aattcggcac atttgatgaa ttcaaagaaa aattcaatgc ggcagctgcg
481 gctcgttttg gttcaggatg ggcatggcta gtagtgaaca atggtaaact agaaattgtt
541 tccactgcta accaagattc tccacttagc gaaggtaaaa ctccagttct tggcttagat
601 gtttgggaac atgcttatta tcttaaattc caaaaccgtc gtcctgaata cattgacaca
661 ttttggaatg taattaactg ggatgaacga aataaacgct ttgacgcagc aaaataatta
721 tcgaaaggct cacttaggtg ggtcttttta tttcta
//
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|
Appendix II Feature table: Backus-Naur form
Feature table is a mandatory part of an entry. Full entry syntax is
specified elsewhere.
feature_table ::= <feature_table_header><feature_table_body> feature_table_header
::= FH Key Location/Qualifiers | FEATURES Location/Qualifiers
feature_table_body ::= <feature> | <feature_table_body><feature>
At least one feature is required.
feature ::= <feature_key><feature_details>
Key is required, location required, qualifier list optional
feature_key ::= <symbol> | -
feature_details ::= <location><qualifier_list> | <location>
There exists a table of legal keys. "-" is a placeholder for no key.
location ::= <absolute_location> | <feature_name> |
<functional_operator>(<location_list>)
absolute_location ::= <local_location> | <path> : <local_location>
path ::= <database> :: <primary_accession> | <primary_accession>
feature_name ::= <path>:<feature_label> | <feature_label>
feature_label :== <symbol>
local_location ::= <base_position> | <between_position> | <base_range>
location_list ::= <location> | <location_list>,<location>
functional_operator ::= <symbol>
base_position ::= <integer> | <low_base_bound> | <high_base_bound> |
<two_base_bound>
low_base_bound ::= > <integer>
high_base_bound ::= < <integer>
two_base_bound ::= <base_position>.<base_position>
between_position ::= <base_position>^<base_position>
base_range ::= <base_position>..<base_position>
database ::= <symbol>
primary_accession ::= <symbol>
sequence_character ::= a | b | c | d | g | h | k | m | n | r | s | t | u | v | w | y
qualifier_list ::= <qualifier> | <qualifier_list><qualifier>
qualifier ::= /<qualifier_name> | /<qualifier_name>=<value>
qualifier_name ::= <symbol>
value ::= <simple_value> | (<value_list>) | (<tagged_value_list>)
simple_value ::= <integer> | <location> | <reference_number> | "<text_string>" |
<symbol>
value_list ::= <value> | <value_list>,<value>
tagged_value_list ::= <tagged_value> | <tagged_value_list>,<tagged_value>
tagged_value ::= <tag>:<value>
tag ::= <symbol>
reference_number ::= [ <unsigned_integer> ]
symbol ::= <letter> | <symbol><symbol_character> | <symbol_character><symbol>
text_string ::= <string_character>| <text_string><string_character>
unsigned_integer ::= <digit> | <unsigned_integer><digit>
integer ::= <unsigned_integer> | - <unsigned_integer>
string_character ::= <letter> | <digit> | <punctuation> | ""
symbol_character ::= <up_case_letter> | <low_case_letter> |<digit> | _ | - | ' | *
letter ::= <up_case_letter> | <low_case_letter>
up_case_letter ::= A | B| ... | Z
low_case_letter ::= a | b | ... | z
digit ::= 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
punctuation ::= <space> | ! | # | $ | % | & | ' | ( | ) | * | + | , |
- | . | / | : | ; | < | = | > | ? | @ | [ | \ | ] | ^ | _ | ` | { |
<bar> | } | ~
bar ::= |
space ::= ascii 32
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Appendix III: Feature keys reference
Feature key reference manual
The following manual 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
<evidence_value> value indicating the nature of supporting evidence.
feature_label the feature label (follows naming conventions for all
feature table components)
<integer> unsigned integer value
<location> general feature location descriptor
<modified_base> abbreviation for modified nucleoside base
[number] integer representing number of citation in entry's
reference list
<repeat_type> value indicating the organization of a repeated
sequence. Currently valid values are tandem,
inverted, flanking, terminal, direct, dispersed,
and other
"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 feature label "ops-tata" is used with the
"promoter" feature key
would be formatted thus:
"The feature label""ops-tata" " is used with the
" "promoter" " feature key"
|
|
Feature key relationship tree
|
Feature key definitions - alphabetical
|
Feature Key attenuator
Organism scope prokaryotes
Molecule scope DNA
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/phenotype="text"
/usedin=accnum:feature_label
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/product="text"
/pseudo
/standard_name="text"
/usedin=accnum:feature_label
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/usedin=accnum:feature_label
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"
/citation=[number]
/codon=(seq:"text",aa:<amino_acid>)
/codon_start=<1 or 2 or 3>
/db_xref="<database>:<identifier>"
/EC_number="text"
/evidence=<evidence_value>
/exception="text"
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/number=unquoted text (single token)
/product="text"
/protein_id="<identifier>"
/pseudo
/standard_name="text"
/translation="text"
/transl_except=(pos:<base_range>,aa:<amino_acid>)
/transl_table =<integer>
/usedin=accnum:feature_label
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;
/codon is used to specify unusual genetic codes,
including rare-usage start codons, organellar codes, etc.;
/codon is used to describe a single codon exception to
the code defined as the "normal" code for the organism;
it implies that the translation it specifies is used
throughout the feature;
/codon specifies that a specific codon specified by
"seq" codes for the amino acid or stop codon specified
by "aa";
/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;
/transl_except is used to specify a single codon the
translation of which does not conform to the genetic
code defined by the "normal" code for organism or by the
/codon qualifiers given for the feature;
/transl_table defines genetic code table used if other
than universal genetic code table; genetic code
exception outside the range of the specified tables are
reported in /codon or /transl_except qualifiers.
|
|
Feature Key conflict
Definition independent determinations of the "same" sequence differ
at this site or region
Mandatory qualifiers /citation=[number]
Optional qualifiers /db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/label=feature_label
/map="text"
/note="text"
/gene="text"
/locus_tag="text" (single token)
/replace="text"
/usedin=accnum:feature_label
|
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/usedin=accnum:feature_label
Molecule scope DNA
|
|
Feature Key D_segment
Definition Diversity segment of immunoglobulin heavy chain, and
T-cell receptor beta chain.
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label\
/locus_tag="text" (single token)
/map="text"
/note="text"
/product="text"
/pseudo
/standard_name="text"
/usedin=accnum:feature_label
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/standard_name="text"
/usedin=accnum:feature_label
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"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/number=unquoted text (single token)
/product="text"
/pseudo
/standard_name="text"
/usedin=accnum:feature_label
|
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/usedin=accnum:feature_label
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>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/product="text"
/pseudo
/phenotype="text"
/standard_name="text"
/usedin=accnum:feature_label
Commentm the gene feature key 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.
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|
Feature Key iDNA
Definition intervening DNA; DNA which is eliminated through any of
several kinds of recombination
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/label=feature_label
/gene="text"
/locus_tag="text" (single token)
/map="text"
/note="text"
/number=unquoted text (single token)
/standard_name="text"
/usedin=accnum:feature_label
Molecule scope DNA
Comment e.g., in the somatic processing of immunoglobulin genes.
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|
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]
/cons_splice=(5'site:<bool>,3'site:<bool>)
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/number=unquoted text (single token)
/standard_name="text"
/usedin=accnum:feature_label
Comment cons_splice is used only when one of the intron's splice
sites does not match the GT...AG consensus.
|
|
Feature Key J_segment
Definition Joining segment of immunoglobulin light and heavy
chains, and T-cell receptor alpha, beta, and gamma
chains.
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/locus_tag="text" (single token)
/map="text"
/note="text"
/product="text"
/pseudo
/standard_name="text"
/usedin=accnum:feature_label
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/standard_name="text"
/usedin=accnum:feature_label
|
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 /citation=[number]
/db_xref="<database>:<identifier>"
/EC_number="text"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/product="text"
/pseudo
/standard_name="text"
/usedin=accnum:feature_label
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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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/usedin=accnum:feature_label
Comment note that the key RBS is used for ribosome binding site
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Feature Key misc_difference
Definition feature sequence is different from that presented in the
entry and cannot be described by any other difference
key (conflict, unsure, old_sequence, variation or
modified_base).
Optional qualifiers /citation=[number]
/clone="text"
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/phenotype="text"
/replace="text"
/standard_name="text"
/usedin=accnum:feature_label
Comment used to describe variability that arises as a result of
genetic manipulation (e.g. site directed mutagenesis).
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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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/number=unquoted text (single token)
/phenotype="text"
/product="text"
/pseudo
/standard_name="text"
/usedin=accnum:feature_label
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; use the '-' pseudo-key instead.
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|
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
(/insertion_seq, /transposon, /proviral);
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/organism="text"
/standard_name="text"
/usedin=accnum:feature_label
Molecule scope DNA
Comment if no /organism is provided with misc_recomb,
this suggests that only one organism (same as in SOURCE)
is involved in the recombination event
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|
Feature Key misc_RNA
Definition any transcript or RNA product that cannot be defined by
other RNA keys (prim_transcript, precursor_RNA, mRNA,
5'clip, 3'clip, 5'UTR, 3'UTR, exon, CDS, sig_peptide,
transit_peptide, mat_peptide, intron, polyA_site, rRNA,
tRNA, scRNA, and snRNA)
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/product="text"
/standard_name="text"
/usedin=accnum:feature_label
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|
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/phenotype="text"
/standard_name="text"
/usedin=accnum:feature_label
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|
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/standard_name="text"
/usedin=accnum:feature_label
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|
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/frequency="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/usedin=accnum:feature_label
Comment value is limited to the restricted to the restrictewd
vocabulary for modified base abbreviations.
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|
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"
/citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/product="text"
/pseudo
/standard_name="text"
/usedin=accnum:feature_label
Feature Key N_region
Definition extra nucleotides inserted between rearranged
immmunoglobulin segments.
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/product="text"
/pseudo
/standard_name="text"
/usedin=accnum:feature_label
Parent Key CDS
Organism scope eukaryotes
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Feature Key old_sequence
Definition the presented sequence revises a previous version of the
sequence at this location.
Mandatory qualifiers /citation=[number]
Optional qualifiers /db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/replace="text"
/usedin=accnum:feature_label
|
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/usedin=accnum:feature_label
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/usedin=accnum:feature_label
Organism scope eukaryotes and eukaryotic viruses
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|
Feature Key precursor_RNA
Definition any RNA species that is not yet the mature RNA product;
may include 5' clipped region (5'clip), 5' untranslated
region (5'UTR), coding sequences (CDS, exon),
intervening sequences (intron), 3' untranslated region
(3'UTR), and 3' clipped region (3'clip).
Optional qualifiers /allele="text"
/citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/product="text"
/standard_name="text"
/usedin=accnum:feature_label
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.
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|
Feature Key prim_transcript
Definition primary (initial, unprocessed) transcript; includes 5'
clipped region (5'clip), 5' untranslated region (5'UTR),
coding sequences (CDS, exon), intervening sequences
(intron), 3' untranslated region (3'UTR), and 3' clipped
region (3'clip).
Optional qualifiers /allele="text"
/citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/standard_name="text"
/usedin=accnum:feature_label
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|
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/standard_name="text"
/PCR_conditions="text"
/usedin=accnum:feature_label
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.
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|
Feature Key promoter
Definition region on a DNA molecule involved in RNA polymerase
binding to initiate transcription.
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/function="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/phenotype="text"
/pseudo
/standard_name="text"
/usedin=accnum:feature_label
Molecule scope DNA
|
Feature Key protein_bind
Definition non-covalent protein binding site on nucleic acid.
Mandatory qualifiers /bound_moiety="text"
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/standard_name="text"
/usedin=accnum:feature_label
Comment note that RBS is used for ribosome binding sites
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|
Feature Key RBS
Definition ribosome binding site
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/standard_name="text"
/usedin=accnum:feature_label
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].
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Feature Key repeat_region
Definition region of genome containing repeating units.
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/insertion_seq="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/rpt_family="text"
/rpt_type=<repeat_type>
/rpt_unit=<feature_label> or <base_range>
/standard_name="text"
/transposon="text"
/usedin=accnum:feature_label
|
Feature Key repeat_unit
Definition single repeat element
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/rpt_family="text"
/rpt_type=<repeat_type>
/rpt_unit=<feature_label> or <base_range>
/usedin=accnum:feature_label
Comment preferred usage is to annotate the /rpt_family and
rpt_type qualifiers on the repeat_region, not on the
repeat_unit(s).
|
Feature Key rep_origin
Definition origin of replication; starting site for duplication of
nucleic acid to give two identical copies.
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/direction=value
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/standard_name="text"
/usedin=accnum:feature_label
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/product="text"
/pseudo
/standard_name="text"
/usedin=accnum:feature_label
Comment rRNA sizes should be annotated with the /product
qualifier.
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|
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/product="text"
/pseudo
/standard_name="text"
/usedin=accnum:feature_label
Parent Key misc_signal
Organism scope eukaryotes
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|
Feature Key satellite
Definition many tandem repeats (identical or related) of a short
basic repeating unit; many have a base composition or
other property different from the genome average that
allows them to be separated from the bulk (main band)
genomic DNA.
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/rpt_type=<repeat_type>
/rpt_family="text"
/rpt_unit=<feature_label> or <base_range>
/standard_name="text"
/usedin=accnum:feature_label
Molecule scope DNA
Comment use the satellite key to identify the entire region of
satellite sequence within an entry; use repeat_unit to
identify individual repeated units (one is generally
sufficient) of the satellite.
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|
Feature Key scRNA
Definition small cytoplasmic RNA; any one of several small
cytoplasmic RNA molecules present in the cytoplasm and
(sometimes) nucleus of a eukaryote.
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/product="text"
/pseudo
/standard_name="text"
/usedin=accnum:feature_label
|
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/product="text"
/pseudo
/standard_name="text"
/usedin=accnum:feature_label
|
Feature Key snRNA
Definition small nuclear RNA molecules involved in pre-mRNA splicing
and processing.
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/partial
/product="text"
/pseudo
/standard_name="text"
/usedin=accnum:feature_label
|
Feature Key snoRNA
Definition small nucleolar RNA molecules mostly involved in
rRNA modification and processing.
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/partial
/product="text"
/pseudo
/standard_name="text"
/usedin=accnum:feature_label
|
|
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 permissible;
every entry will have, as a minimum, a single
source key spanning the entire sequence or
multiple source keys together spanning the entire
sequence.
Mandatory qualifiers /organism="text"
Optional qualifiers /cell_line="text"
/cell_type="text"
/chromosome="text"
/citation=[number]
/clone="text"
/clone_lib="text"
/country="any country from
http://www.ncbi.nlm.nih.gov/projects/collab/country.html
/cultivar="text"
/db_xref="<database>:<identifier>"
/dev_stage="text"
/environmental_sample
/focus="text"
/frequency="text"
/germline
/haplotype="text"
/lab_host="text"
/isolate="text"
/isolation_source="text"
/label=feature_label
/macronuclear
/map="text"
/mol_type="text"
/note="text"
/organelle=<organelle_value>
/plasmid="text"
/pop_variant="text"
/proviral
/rearranged
/segment="text"
/sequenced_mol="text"
/serotype="text"
/serovar="text"
/sex="text"
/specimen_voucher="text"
/specific_host="text"
/strain="text"
/sub_clone="text"
/sub_species="text"
/sub_strain="text"
/tissue_lib="text"
/tissue_type="text"
/transgenic
/usedin=accnum:feature_label
/variety="text"
/virion
Molecule scope any
Comment multiple qualifiers (e.g., /clone=) may occur;
see Appendix IV for allowed values of /organelle;
transgenic sequences must at least have two source
feature keys; the source feature key describing
the organism of the recipient DNA must span the
whole sequence;
/mol_type will become mandatory from 01-JUL-2003.
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|
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/standard_name="text"
/usedin=accnum:feature_label
|
|
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 /citation=[number]
/db_xref="<database>:<identifier
/evidence=<evidence_value>
/standard_name="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/usedin=accnum:feature_label
/note="text"
/map="text"
Molecule scope DNA
Parent key misc_binding
Comment STS location to include primer(s) in primer_bind key or
primers.
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|
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 unitwhich
may be involved in positioning the enzyme for correct
initiation; consensus=TATA(A or T)A(A or T) [1,2].
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/usedin=accnum:feature_label
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)
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|
Feature Key terminator
Definition sequence of DNA located either at the end of the
transcript that causes RNA polymerase to terminate
transcription.
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/standard_name="text"
/usedin=accnum:feature_label
Molecule scope DNA
|
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/product="text"
/pseudo
/standard_name="text"
/usedin=accnum:feature_label
|
|
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 /anticodon=(pos:<base_range>,aa:<amino_acid>)
/citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/product="text"
/pseudo
/standard_name="text"
/usedin=accnum:feature_label
|
Feature Key unsure
Definition author is unsure of exact sequence in this region.
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/replace="text"
/usedin=accnum:feature_label
|
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/product="text"
/pseudo
/standard_name="text"
/usedin=accnum:feature_label
Parent Key CDS
Organism scope eukaryotes
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|
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/product="text"
/pseudo
/standard_name="text"
/usedin=accnum:feature_label
Parent Key CDS
Organism scope eukaryotes
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|
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]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/frequency="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/phenotype="text"
/product="text"
/replace="text"
/standard_name="text"
/usedin=accnum:feature_label
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=""
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|
Feature Key 3'clip
Definition 3'-most region of a precursor transcript that is clipped
off during processing.
Optional qualifiers /allele="text"
/citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/standard_name="text"
/usedin=accnum:feature_label
|
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>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/standard_name="text"
/usedin=accnum:feature_label
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Feature Key 5'clip
Definition 5'-most region of a precursor transcript that is clipped
off during processing.
Optional qualifiers /allele="text"
/citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/partial
/standard_name="text"
/usedin=accnum:feature_label
|
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>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/partial
/standard_name="text"
/usedin=accnum:feature_label
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|
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/standard_name="text"
/usedin=accnum:feature_label
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 /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/standard_name="text"
/usedin=accnum:feature_label
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)
|
|
Feature Key -
Definition "-" is a placeholder for no key;
should be used when the need is merely to mark region in order to
comment on it or to use it in another feature's location.
Optional qualifiers /citation=[number]
/db_xref="<database>:<identifier>"
/evidence=<evidence_value>
/function="text"
/gene="text"
/label=feature_label
/locus_tag="text" (single token)
/map="text"
/note="text"
/number=unquoted text (single token)
/phenotype="text"
/product="text"
/pseudo
/standard_name="text"
/usedin=accnum:feature_label
Comment Example: - 1..17
/usedin="X55079:GAA_CDS"
|
Appendix IV: Summary of qualifiers for feature
keys
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
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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=(pos: ,aa: )
Definition location of the anticodon of tRNA and the amino acid for which
it codes
Value format pos:<base_range>,aa:<amino_acid> where base_range
is the position of the anticodon and amino_acid is the
abbreviation for the amino acid encoded
Example /anticodon=(pos:34..36,aa:Phe)
Qualifier /bound_moiety=
Definition moiety bound
Value format "text"
Example /bound_moiety="repressor"
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=
Definition specifies a codon which is different from any found in the
reference genetic code
Value format (seq:"codon-sequence",aa:<amino_acid>) where
codon-sequence is the bases of the codon and amino_acid is
either the abbreviation for the translated amino acid, or for
modified/ unusual amino_acids from section 7.5
or it can be the word OTHER
Example /codon=(seq:"ttt", aa:Leu)
Comment amino acids not on the controlled vocabulary list can be
indicated by using "aa:OTHER" as the amino acid designation
and giving the name of the residue in a /note
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 /cons_splice=
Definition differentiates between intron splice sites that conform
to the 5'-GT ... AG-3' splice site consensus
Value format (5'site:<value>, 3'site:<value>), where <value>
can be 'YES', 'NO' or 'ABSENT'
Example /cons_splice=(5'site:YES, 3'site:NO)
/cons_splice=(5'site:ABSENT, 3'site:NO)
Comment since the vast majority of splice sites conform to the
consensus, this qualifier should be used only when one does
not and the sequence has been checked; 'ABSENT' can be used
when one of the termini is not part of the sequence and
information on splice site is not available.
Qualifier /country=
Definition Country of origin for DNA sample, intended for epidemiological
or population studies
Value format: "any country from http://www.ncbi.nlm.nih.gov/projects/collab/country.html"
Example: "Canada"
Comment: /country should be a single token taken from the country list
/country can also have the following format: country:sub_region,
such as: /country="Canada:Vancouver".
Qualifier /cultivar=
Definition cultivar (cultivated variety) of plant or fungus 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 /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="SWISS-PROT:P12345"
Comment the complete list of allowed database types is kept on
NCBI's public WWW server, at URL:
http://www.ncbi.nlm.nih.gov/projects/collab/
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"
Comment valid values for EC numbers are defined in the list prepared
by the IUPAC-IUB Commission on Biochemical Enzyme Nomenclature
(published in Enzyme Nomenclature 1984. New York: Academic
Press (1984) or a more recent revision thereof)
Qualifier /environmental_sample=
Definition identifies sequences derived by direct molecular
isolation (PCR, DGGE, or other anonymous methods) from
an environmental sample with no reliable identification
of the source organism
Value format none
Example /environmental_sample
Comment used only with the source feature key; source features keys
containing the /environmental_sample qualifier should
also contain the /isolation_source qualifier
Qualifier /evidence=
Definition value indicating the nature of supporting evidence,
distinguishing between experimentally determined and
theoretically derived data
Value format experimental, not_experimental
Example /evidence=experimental
Comment experimental indicates that the feature identification or
assignment is supported by direct experimental evidence.
not_experimental indicates that the data for the feature are
derived (eg promoter as identified by consensus match)
Qualifier /exception=
Definition indicates that the amino acid or RNA sequence will not
translate or agree with the DNA sequence according to
standard biological rules
Value format "text"
Example /exception="RNA editing"
/exception="reasons given in citation"
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;
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 /focus
Definition defines the source feature of primary biological interest for
records that have multiple source features originating from
different organisms
Value format none
Example /focus
Comment the /focus qualifier identifies the organism which is
displayed in the organism line and determines the
DDBJ/EMBL/GenBank taxonomic division the entry will appear in;
if no translation table is specified, the organism with /focus
will define the translation table; within an entry with several
source features, only one will exist with /focus on it;
multi-source entries with a /transgenic source feature
should not have a /focus qualifier.
Qualifier /frequency=
Definition frequency of the occurrence of a feature
Value format text representing the fraction of population carrying the
variation expressed as a decimal fraction
Example /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 /gene=
Definition symbol of the gene corresponding to a sequence region
Value format "text"
Example /gene="ilvE"
Comment see O'Brien, S.J., ed., Genetic Maps 1987, Cold Spring Harbor
or a recent revision.
Qualifier /germline
Definition if the sequence shown is DNA and a member of the immunoglobulin
family, this qualifier is used to denote that the sequence is
from unrearranged DNA.
Value format none
Example /germline
Qualifier /haplotype=
Definition haplotype of organism from which the sequence was obtained
Value format "text"
Example /haplotype="Dw3 B5 Cw1 A1"
Qualifier /insertion_seq=
Definition insertion sequence element from which the sequence was obtained
Value format "text"
Example /insertion_seq="IS-11"
Comment /insertion_seq is legal on repeat_region feature key;
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 /isolate=
Definition individual isolate from which the sequence was obtained
Value format "text"
Example /isolate="Patient #152"
Qualifier /label=
Definition a label used to permanently tag a feature
Value format feature_label
(see Sections 3.1 and 3.4)
Example /label=Alb1_exon1
Comment feature labels follow the naming conventions for all feature
table objects (see Sections 3.1 and 3.4)
Qualifier /lab_host=
Definition laboratory host used to propagate the organism from which the
sequence was obtained
Value format "text"
Example /lab_host="chicken embryos"
Qualifier: /locus_tag
Definition: feature tag assigned for tracking purposes
Value Format: "text"(single token)
Example: /locus_tag="RSc0382"
/locus_tag="YPO0002"
Comment: /locus_tag can be used with any feature where /gene
is valid; /locus_tag value must be unique within that entry;
Qualifier /map=
Definition genomic map position of feature
Value format "text"
Example /map="8q12-13"
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 /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
Value format "text"
Example /mol_type="genomic DNA",
Comment text limited to "genomic DNA", "genomic RNA", "mRNA" (incl. EST),
"tRNA", "rRNA", "snoRNA", "snRNA", "scRNA", "pre-mRNA",
"other RNA" (incl. synthetic), "other DNA" (incl. synthetic),
"unassigned DNA" (incl. unknown), "unassigned RNA" (incl.
unknown);
/mol_type will become a mandatory qualifier to the SOURCE
feature key from 01-JUL-2003.
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 /organelle=
Definition type of membrane-bound intracellular structure from which the
sequence was obtained
Value format mitochondrion, nucleomorph, plastid, mitochondrion:kinetoplast,
plastid:chloroplast, plastid:apicoplast, plastid:chromoplast,
plastid:cyanelle, plastid:leucoplast, plastid:proplastid,
Example /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"
Comment 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
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 /phenotype=
Definition phenotype conferred by the feature
Value format "text"
Example /phenotype="erythromycin resistance"
Qualifier /pop_variant=
Definition population variant from which the sequence was obtained
Value format "text"
Example /pop_variant="population variant name"
Qualifier /plasmid=
Definition name of plasmid from which sequence was obtained
Value format "text"
Example /plasmid="C-589"
Qualifier /product=
Definition name of a product encoded by a sequence
Value format "text"
Example /product="catalase"
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 feature keys which translate
into a valid protein.
Qualifier /proviral
Definition if the sequence shown is viral and integrated into another
organism's genome, this qualifier is used to denote that
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
Qualifier /rearranged
Definition if the sequence shown is DNA and a member of the immunoglobulin
family, this qualifier is used to denote that the sequence is
from rearranged DNA
Value format none
Example /rearranged
Qualifier /replace=
Definition indicates that the sequence identified by 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 /rpt_family=
Definition type of repeated sequence; "Alu" or "Kpn", for example
Value format "text"
Example /rpt_family="Alu"
Comment preferred usage is to qualify the repeat_region instead of any
of the constituent repeat_units
Qualifier /rpt_type=
Definition organization of repeated sequence
Value format tandem, inverted, flanking, terminal, direct, dispersed, and
other
Example /rpt_type=INVERTED
Comment preferred usage is to qualify the repeat_region instead of any
of the constituent repeat_units. definitions of these values
will be added in a future release of this document. see
Singer, M. Int Rev Cytol 76, 67-112 (1982); Cell 26, 293-95
(1981); Hardman, N. Biochem J 234, 1-11 (1986)
Qualifier /rpt_unit=
Definition identity of repeat unit which constitutes a repeat_region
Value format <feature_label> or <base_range>
Example /rpt_unit=Alu_rpt1
/rpt_unit=202..245
Comment used to indicate feature which defines (or base range of) the
repeat unit of which a repeat region is made
Qualifier /segment=
Definition name of viral or phage segment sequenced
Value format "text"
Example /segment="6"
Qualifier /sequenced_mol=
Definition molecule from which the sequence was obtained
Value format "text"
Example /sequenced_mol="cDNA to mRNA"
Comment text limited to "cDNA", "cDNA to genomic RNA", "cDNA to mRNA",
"cDNA to other RNA", "cDNA to rRNA", "DNA", "mRNA", "RNA",
"rRNA", "scRNA", "snRNA", "tRNA".
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
Value format "text"
Example /sex="female"
Qualifier /specific_host=
Definition natural host from which the sequence was obtained
Value format "text"
Example /specific_host="Rhizobium NGR234"
Qualifier /specimen_voucher=
Definition an identifier of the individual or collection of the source
organism and the place where it is currently stored, usually
an institution
Value format "text"
Example /specimen_voucher="Smith s. n. 4-IV-1995 (U. S. Natl.
Herbarium)"
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 the sequence was obtained
Value format "text"
Example /strain="BALB/c"
Qualifier /sub_clone=
Definition sub-clone from which the 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 sub-species name of organism from which the sequence was
obtained
Value format "text"
Example /sub_species="lactis"
Qualifier /sub_strain=
Definition sub_strain from which the sequence was obtained
Value format "text"
Example /sub_strain="abis"
Qualifier /tissue_lib=
Definition tissue library from which the 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 at least have two source
feature keys; the source feature key describing the
organism of the recipient DNA must span the whole
sequence; the /transgenic qualifier identifies the
organism which is displayed in the organism line and
determines that the entry will appear in the
DDBJ/EMBL/GenBank Synthetic Construct division;
multi-source entries including a /transgenic source
feature should not have a /focus qualifier.
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 key only; this is a mandatory qualifier
to the CDS feature key except for /pseudo CDSs;
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 and /codon=
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)
Qualifier /transl_table=
Definition definition of genetic code table used if other than universal
genetic code table. Tables used are described in appendix V,
section 7.5.5.
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 /transposon=
Definition transposable element from which the sequence was obtained
Value format "text"
Example /transposon="Tn9"
Comment /transposon is legal on repeat_region feature key;
Qualifier /usedin=
Definition indicates that the feature is used in a compound feature in
another entry
Value format Accession-number:feature-name or
Database_name::Acc_number:feature_label
Example /usedin=X10087:proteinx
Comment database_name is an abbreviation for the name of the database
in which the entry for the accession number can be found.
Qualifier /variety
Definition variety (= varietas, a formal Linnaean rank) of organism
from which sequence was derived.
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"
Qualifier /virion
Definition viral genomic sequence as it is encapsidated (distinguished from its
proviral form integrated in a host cell's chromosome)
Value format none
Example /virion
|
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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:
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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
Scope Location descriptors, /codon
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
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
Listing
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)
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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).
Scope /anticodon, /codon, /transl_except
Contact EMBL
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
Ser S Serine
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.
TERM termination codon
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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
Sec Selenocysteine
OTHER (requires /note=)
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Genetic Code Tables
Authority International Sequence Databank Collaboration
Contact NCBI
Scope /transl_table qualifier
URL http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c
Genetic Code [1]
The 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 = -----------------------------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
Genetic Code [4]
Mold, Protozoan, Coelenterate Mitochondrial Code and the 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----------------------------
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 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----------------------------
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
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