Qualifier key

The qualifier keys that are used and recommended for DDBJ new submissions are as follows.
For further information of INSDC qualifier keys, read Feature Table Definition: 7.3.1 Qualifier List.

Feature/Qualifier Usage Matrix

The chart below explains recommended combinations of feature and qualifier keys for DDBJ submissions.

Feature/Qualifier usage matrix (November 9, 2016)

For more detail of available combinations of feature and qualifier keys in INSDC entries, read: Feature Table Definition: 7.2 Appendix II: Feature keys reference.

Definision of Qualifier key

alleleFeature Table Definition
Definition name of the allele for the given gene.
Value format <text>, excluding double quotation mark (")
Example adh1-1
altitudeFeature Table Definition
Definition geographical altitude of the location from which the sample was collected
Value format <text>, excluding double quotation mark (")
Example -256 m
330.12 m
Comment Values indicate altitudes above or below nominal sea level provided in metres
anticodonFeature Table Definition
Definition location of the anticodon of tRNA and the amino acid for which it codes
Value format for input: (pos:<location>,aa:<amino_acid>)
where location is the position of the anticodon and amino_acid is the abbreviation either for the abbreviation for Amino Acid Codes, or for Modified and unusual Amino Acids.
Example for input: (pos:34..36,aa:Phe)
(pos:join(5,495..496),aa:Leu)
(pos:complement(4156..4158),aa:Gln)
Value format for output: (pos:<location>,aa:<amino_acid>,seq:<nucleotides>)
Example for output: (pos:34..36,aa:Phe,seq:aaa)
(pos:join(5,495..496),aa:Leu,seq:tag)
(pos:complement(4156..4158),aa:Gln,seq:ttg)
artificial_locationFeature Table Definition
Definition indicates that location of the CDS or mRNA is modified to adjust for the presence of a frameshift or internal stop codon and not because of biological processing between the regions.
Value format "heterogeneous population sequenced" or "low-quality sequence region"
Comment expected to be used only for genome-scale annotation, either because a heterogeneous population was sequenced or because the feature is in a region of low-quality sequence.
bio_materialFeature Table Definition
Definition identifier for the biological material (living individual or strain) from which the nucleic acid sequence was obtained, with optional institution code and collection code for the place where it is currently stored.
Value format [<institution_code>:[<collection_code>:]]<material_id>
Example CGC:CB3912      <- Caenorhabditis stock centre
Comment the bio_material qualifier should be used to annotate the identifiers of material in biological collections that are not appropriate to annotate as either /specimen_voucher or /culture_collection; these include zoos and aquaria, stock centres, seed banks, germplasm repositories and DNA banks; material_id is mandatory, institution_code and collection_code are optional; institution code is mandatory where collection code is present.

You can find <institution_code> at
institution_code list (NCBI FTP site)
BioCollections
bound_moietyFeature Table Definition
Definition name of the molecule/complex that may bind to the given feature
Value format <text>, excluding double quotation mark (")
Example GAL4
cell_lineFeature Table Definition
Definition cell line from which the sequence was obtained
Value format <text>, excluding double quotation mark (")
Example MCF7
cell_typeFeature Table Definition
Definition cell type from which the sequence was obtained
Value format <text>, excluding double quotation mark (")
Example leukocyte
chromosomeFeature Table Definition
Definition chromosome (e.g. Chromosome number) from which the sequence was obtained
Value format <text>, excluding double quotation mark (")
Example 1
cloneFeature Table Definition
Definition clone from which the sequence was obtained
Value format <text>, excluding double quotation mark (")
Example lambda-hIL7.3
clone_libFeature Table Definition
Definition clone library from which the sequence was obtained
Value format <text>, excluding double quotation mark (")
Example lambda-hIL7
codon_startFeature Table Definition
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, 2 or 3
collected_byFeature Table Definition
Definition name of persons or institute who collected the specimen
Value format <text>, excluding double quotation mark (")
Example Dan Janzen
collection_dateFeature Table Definition
Definition The date on which the specimen was collected.
Date/time ranges are supported by providing two collection dates from among the supported value formats, delimited by a forward-slash character.
Collection times are supported by adding "T", then the hour and minute, after the date.
Collection times must be in Coordinated Universal Time (UTC), otherwise known as "Zulu Time" (Z).
Value format YYYY-MM-DDThh:mm:ssZ
YYYY-MM-DDThh:mmZ
YYYY-MM-DDThhZ
YYYY-MM-DD
YYYY-MM
YYYY

YYYY/YYYY
YYYY-MM-DD/YYYY-MM-DD
YYYY-MM/YYYY-MM
YYYY-MM-DDThh:mmZ/YYYY-MM-DDThh:mmZ

'YYYY' is a four-digit value representing the year.
'MM' is a two-digit value representing the month (01 to 12) .
'DD' is a two-digit value representing the day of the month (01 to 31) .
'hh' is a two-digit value representing the hour of the day (00 to 23).
'mm' is a two-digit value representing the minute of the hour (00 to 59).
'ss' is a two-digit value representing the second of the hour (00 to 59).
Example 2015-10-11T17:53:03Z
1952-10-21T11:43Z
1952-10-21T11Z
1952-10-21
1952-10
1952

1952/1953
1952-10-21/1953-02-15
1952-10/1953-02
1952-10-21T11:43Z/1952-10-21T17:43Z
Comment Collection dates that are specified to at least the month, day, and year (YYYY-MM-DD) are strongly encouraged.

Though INSDC still keep and accept old value formats that make use of 'Mmm' (month abbreviations), such as "21-Oct-1952", DDBJ no longer accepts new data submissions with old value formats of collection_date.
compareFeature Table Definition
Definition Reference details of an existing public INSD entry to which a comparison is made.
Value format <accession number>.<version>
Example AB123456.1
countryFeature Table Definition
Definition locality of isolation of the sequenced organism indicated in terms of political names for nations, oceans or seas, followed by regions and localities
Value format <country>[:<free-text for geographical name>]
Example Japan:Kanagawa, Hakone, Lake Ashi
Comment any <country> from the country list.
cultivarFeature Table Definition
Definition cultivar (cultivated variety) of plant from which sequence was obtained.
Value format <text>, excluding double quotation mark (")
Example Nipponbare
culture_collectionFeature Table Definition
Definition institution_code and identifier for the culture from which the nucleic acid sequence was obtained, with optional collection code.
Value format <institution_code>:[<collection_code>:]<culture_id>
Example ATCC:26370
Comment the culture_collection qualifier should be used to annotate live microbial and viral cultures, and cell lines that have been deposited in curated culture collections; microbial cultures in personal or laboratory collections should be annotated in strain qualifiers.
culture_id and institution_code are mandatory, collection_code is optional.

You can find <institution_code> at
institution_code list (NCBI FTP site)
BioCollections
db_xrefFeature Table Definition
Definition database cross-reference: pointer to related information in another database.
Value format
Value format
<database>:<identifier>, excluding double quotation mark (")
Example UniProtKB/Swiss-Prot:P28763
Comment In principle, the db_xref qualifier can not be entered in new submissions.
When you referred records in other database as evidence for annotation, use inference, not db_xref.
The controlled values of <database> are in the database list.
dev_stageFeature Table Definition
Definition if the sequence was obtained from an organism in a specific developmental stage, it is specified with this qualifier
Value format <text>, excluding double quotation mark (")
Example fourth instar larva
directionFeature Table Definition
Definition direction of DNA replication
Value format left, right, or both
Comment Where left indicates toward the 5' end of the entry sequence (as presented) and right indicates toward the 3' end.
EC_numberFeature Table Definition
Definition Enzyme Commission number for enzyme product of sequence
Value format <identifier>.<identifier>.<identifier>.<identifier>
Example 1.1.2.4
1.1.2.-
1.1.2.n
Comment The format represents a string of four numbers separated by full stops; up to three numbers starting from the end of the string can be replaced by dash "-" to indicate uncertain assignment. Symbol "n" can be used in the last position instead of a number where the EC number is awaiting assignment.
ecotypeFeature Table Definition
Definition a population within a given species displaying genetically based, phenotypic traits that reflect adaptation to a local habitat.
Value format <text>, excluding double quotation mark (")
Example Columbia
environmental_sampleFeature Table Definition
Definition identifies sequences derived by direct molecular isolation from a bulk environmental DNA sample (by PCR with or without subsequent cloning of the product, DGGE, or other anonymous methods) with no reliable identification of the source organism.
See also environmental samples in detail.
Value format no value.
Comment source feature keys containing the /environmental_sample qualifier should also contain the /isolation_source qualifier.
entries including /environmental_sample must not include the /strain qualifier
estimated_lengthFeature Table Definition
Definition estimated length of the gap in the sequence
Value format for input unknown or known
Example for input unknown
known
Value format for output unknown or <integer-number>
Example for output unknown
342
exceptionFeature Table Definition
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 one of followings;
  • RNA editing
  • reasons given in citation
  • rearrangement required for product
  • annotated by transcript or proteomic data
Comment An /inference qualifier should accompany any use of /exception="annotated by transcript or proteomic data", to provide support for the existence of the transcript/protein.
experimentFeature Table Definition
Definition a brief description of the nature of the experimental evidence that supports the feature identification or assignment.
Value format [CATEGORY:]<text>, excluding double quotation mark (")
CATEGORY is optional. if describing it, use either of followings;
  • COORDINATES
  • DESCRIPTION
  • EXISTENCE
Example COORDINATES: 5' and 3' RACE
Northern blot
heterologous expression system of Xenopus laevis oocytes.
Comment detailed experimental details should not be included, and would normally be found in the cited publications; value
"experimental evidence, no additional details recorded"
was used to replace instances of /evidence=EXPERIMENTAL in December 2005
focusFeature Table Definition
Definition identifies the source feature of primary biological interest for records that have multiple source features originating from different organisms and that are not transgenic.
Value format none
frequencyFeature Table Definition
Definition frequency of the occurrence of a feature
Value format <number of observed instances> in <total number of sequenced isolates>,
<number of observed instances>/<total number of sequenced isolates>, or <decimal fraction>
Example 1 in 12
23/108
.85
functionFeature Table Definition
Definition function attributed to a sequence
Value format <text>, excluding double quotation mark (")
Example essential for recognition of cofactor
gap_typeFeature Table Definition
Definition type of gap connecting components in records of a genome assembly, or the type of biological gap in a record that is part of a genome assembly
Value format one of the followings
  • between scaffolds
  • within scaffold
  • telomere
  • centromere
  • short arm
  • heterochromatin
  • repeat within scaffold
  • repeat between scaffolds
  • unknown
Comment This qualifier is used only for assembly_gap features and its values are controlled by the AGP Specification
geneFeature Table Definition
Definition symbol of the gene corresponding to a sequence region
Value format <text>, excluding double quotation mark (")
Example ilvE
Guidance for Submission: See also Gene nomenclature at DDBJ.
  • Please enter the abbreviation as gene symbol.
  • Even if there are multiple general abbreviations for the same gene, do not enter multiple abbreviations in 'gene'. Do not use needless symbolic letters as delimiter for multiple names. If you would like to describe more than two, please enter one of the most representative abbreviation in 'gene', and other(s) in gene_synonym qualifier.
gene_synonymFeature Table Definition
Definition symbol of the gene corresponding to a sequence region, synonym for the value used for gene or locus_tag qualifier
Value format <text>, excluding double quotation mark (")
Example ilvE
Guidance for Submission: See also Gene nomenclature at DDBJ.
  • Please enter the abbreviation as gene symbol.
  • Even if there are multiple general abbreviations for the same gene, do not enter multiple abbreviations in 'gene'. Do not use needless symbolic letters as delimiter for multiple names. If you would like to describe more than two, please enter one of the most representative abbreviation in 'gene', and other(s) in gene_synonym qualifier.
germlineFeature Table Definition
Definition the sequence presented in the entry has not undergone somatic rearrangement as part of an adaptive immune response; it is the unrearranged sequence that was inherited from the parental germline.
Value format none
Comment Do not use with rearranged qualifier.
haplogroupFeature Table Definition
Definition name for a group of similar haplotypes that share some sequence variation. Haplogroups are often used to track migration of population groups.
Value format <text>, excluding double quotation mark (")
Example H*
haplotypeFeature Table Definition
Definition name for a combination of alleles that are linked together on the same physical chromosome. In the absence of recombination, each haplotype is inherited as a unit, and may be used to track gene flow in populations.
Value format <text>, excluding double quotation mark (")
Example Dw3 B5 Cw1 A1
hostFeature Table Definition
Definition Natural (as opposed to laboratory) host to the organism from which sequenced molecule was obtained
Value format <text>, excluding double quotation mark (")
Example Homo sapiens
Homo sapiens 12 years old girl
identified_byFeature Table Definition
Definition name of the expert who identified the specimen taxonomically
Value format <text>, excluding double quotation mark (")
Example John Burns
inferenceFeature Table Definition
Definition a structured description of non-experimental evidence that supports the feature identification or assignment.
Value format [CATEGORY:]TYPE[ (same species)][:EVIDENCE_BASIS]
CATEGORY is optional. if describing it, use either of followings;
  • COORDINATES
  • DESCRIPTION
  • EXISTENCE

 
where TYPE is one of the following
  • similar to sequence
  • similar to AA sequence
  • similar to DNA sequence
  • similar to RNA sequence
  • similar to RNA sequence, mRNA
  • similar to RNA sequence, EST
  • similar to RNA sequence, other RNA
  • profile
  • nucleotide motif
  • protein motif
  • ab initio prediction
  • alignment
Example similar to DNA sequence:INSD:AY411252.1
similar to RNA sequence, mRNA:RefSeq:NM_000041.2
similar to DNA sequence (same species):INSD:AACN010222672.1
profile:tRNAscan:2.1
protein motif:InterPro:IPR001900
ab initio prediction:Genscan:2.0
alignment:Splign:1.26p:RefSeq:NM_000041.2,INSD:BC003557.1
Comment where the optional text "(same species)" is included when the inference comes from the same species as the entry.
where the optional "EVIDENCE_BASIS" is either a reference to a database entry (including accession and version) or an algorithm (including version)
Recommendations for vocabulary in INSDC /inference qualifiers.
* /inference="non-experimental evidence, no additional details recorded" was used to replace instances of /evidence=NOT_EXPERIMENTAL in December 2005
isolateFeature Table Definition
Definition individual isolate from which the sequence was obtained
Value format <text>, excluding double quotation mark (")
Example SI-152
DGGE: C12
isolation_sourceFeature Table Definition
Definition describes the physical, environmental and/or local geographical source of the biological sample from which the sequence was derived
Value format <text>, excluding double quotation mark (")
Example rumen isolates from standard Pelleted ration-fed steer #67
lab_hostFeature Table Definition
Definition scientific name of the laboratory host used to propagate the source organism from which the sequenced molecule was obtained
Value format <text>, excluding double quotation mark (")
Example Gallus gallus
Gallus gallus embryo
Escherichia coli strain DH5 alpha
Homo sapiens HeLa cells
lat_lonFeature Table Definition
Definition geographical coordinates of the location where the sequenced sample was collected
Value format d[d.dddd] <N or S> d[dd.dddd] <W or E>
Example 47.94 N 28.12 W
45.0123 S 4.1234 E
Comment Please describe the figure below the decimal point by not minute and second but the decimal.
linkage_evidenceFeature Table Definition
Definition type of evidence establishing linkage across an assembly_gap. Only allowed to be used with assembly_gap features that have a /gap_type value of "within scaffold" or "repeat within scaffold"
Value format one of the followings
  • paired-ends
  • pcr
  • align genus
  • align xgenus
  • align trnscpt
  • within clone
  • clone contig
  • map
  • strobe
  • unspecified
Comment This qualifier is used only for assembly_gap features and its values are controlled by the AGP Specification
locus_tagFeature Table Definition
Definition a submitter-supplied (mainly genome project), systematic, stable identifier for a gene and its associated features, used for tracking purpose
Value format <text>, excluding double quotation mark (")
Example ABC_0022
A1C_00001
Comment identical /locus_tag values may be used within an entry/record, but only if the identical /locus_tag values are associated with the same gene; in all other circumstances the /locus_tag value must be unique within that entry/record.
INSDC requires prior registrations of the prefix for values of /locus_tag to keep uniqueness of the /locus_tag value through the database
macronuclearFeature Table Definition
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
mapFeature Table Definition
Definition genomic map position of feature
Value format <text>, excluding double quotation mark (")
Example 8q12-13
mating_typeFeature Table Definition
Definition mating type of the organism from which the sequence was obtained. mating type is used for prokaryotes, and for eukaryotes that undergo meiosis without sexually dimorphic gametes (cf. sex).
Value format <text>, excluding double quotation mark (")
Example MAT-1
plus
-
odd
even
mobile_element_typeFeature Table Definition
Definition type and name or identifier of the mobile element which is described by the parent feature
Value format <mobile_element_type> [:<mobile_element_name>] where mobile_element_type is one of the following;
  • transposon
  • retrotransposon
  • integron
  • insertion sequence
  • non-LTR retrotransposon
  • SINE
  • MITE
  • LINE
  • other
Example transposon:Tnp9
mod_baseFeature Table Definition
Definition abbreviation for a modified nucleotide base
Value format modified_base where modified_base is the abbreviation for Modified Base Abbreviation.
Example m2g
mol_typeFeature Table Definition
Definition describes the in vivo, synthetic or hypothetical molecule represented in sequence corresponding to the parent feature
Value format limited to followings;
genomic DNA, genomic RNA, mRNA, tRNA, rRNA, transcribed RNA,
other RNA, other DNA ,viral cRNA, unassigned DNA, unassigned RNA
Comment all values refer to the in vivo or synthetic molecule for primary entries and the hypothetical molecule in Third Party Annotation entries;
  • The value "genomic DNA" does not imply that the molecule is nuclear (e.g. organelle and plasmid DNAs should be described by using "genomic DNA").
  • For ribosomal RNA genes (rDNA), select "genomic DNA".
  • For cDNA sequence, template of mRNA, select "mRNA".
  • For cDNA sequence, template of premature RNA, select "transcribed RNA".
  • "other RNA" and "other DNA" should be applied to synthetic molecules.
  • In general, select "genomic RNA" for RNA viruses.
  • For ssRNA negative-strand virus, select "viral cRNA", in principal.
    "viral cRNA" is a plus-strand copy of a minus strand RNA genome which serves as a template to make viral progeny genomes.
    For genomic sequence data derived from ssRNA negative-strand viruses, in principle, DDBJ uniformly uses following values for mol_type qualifier;
Protein-coding sequences exist in positive orientation: viral cRNA Protein-coding sequences exist in complementary orientation: genomic RNA
ncRNA_classFeature Table Definition
Definition the classification of the non-protein-coding RNA (ncRNA)
Value format <TYPE>
Example miRNA
siRNA
Comment Controlled vocabulary for ncRNA classes is valid for <TYPE>. /ncRNA_class="other" with /product="<name of novel ncRNA_class>" or /note="<brief explanation of novel ncRNA_class>"
noteFeature Table Definition
Definition any comment or additional information
Value format <text>, excluding double quotation mark (")
numberFeature Table Definition
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 5a
old_locus_tagFeature Table Definition
Definition feature tag assigned for tracking purposes
Value format <text>, excluding double quotation mark (")
Example RSc0382
operonFeature Table Definition
Definition name of the group of contiguous genes transcribed into a single transcript to which that feature belongs.
Value format <text>, excluding double quotation mark (")
Example lac
organelleFeature Table Definition
Definition type of membrane-bound intracellular structure from which the sequence was obtained
Value format limited to followings
  • mitochondrion
  • mitochondrion:kinetoplast
  • hydrogenosome
  • plastid:chloroplast
  • plastid:apicoplast
  • plastid:chromoplast
  • plastid:cyanelle
  • plastid:leucoplast
  • plastid:proplastid
  • plastid
  • chromatophore
  • nucleomorph
organism
Definition The scientific name of the organism that provided the sequenced genetic material.
Value format <text>, excluding double quotation mark (")
Example Homo sapiens
Comment For further information of this Qualifier key read Organism Qualifier
PCR_conditionsFeature Table Definition
Definition description of reaction conditions and components for PCR
Value format <text>, excluding double quotation mark (")
Example Initial denaturation:94degC,1.5min
PCR_primersFeature Table Definition
Definition A single /PCR_primers qualifier should contain all the primers used for a single PCR reaction. If multiple forward or reverse primers are present in a single PCR reaction, multiple sets of fwd_name/fwd_seq or rev_name/rev_seq values will be present.
Value format [fwd_name: XXX1, ]fwd_seq: xxxxx1,[fwd_name: XXX2, ]fwd_seq: xxxxx2, [rev_name: YYY1, ]rev_seq: yyyyy1, [rev_name: YYY2, ]rev_seq: yyyyy2
Example 1
fwd_name: CO1P1, fwd_seq: ttgattttttggtcayccwgaagt, rev_name: CO1R4, rev_seq: ccwvytardcctarraartgttg
Example 2
fwd_seq: tgtgtgtgtgactgaca, rev_seq: tagcgatacggtcaatgc
Example 3
fwd_name: hoge1, fwd_seq: cgkgtgtatcttact, rev_name: hoge2, rev_seq: cggtgtatcttact
Example 4
fwd_name: CO1P1, fwd_seq: ttgattttttggtcayccwgaagt, fwd_name: CO1P2, fwd_seq: gatacacaggtcayccwgaagt, rev_name: CO1R4, rev_seq: ccwvytardcctarraartgttg"
Comment fwd_seq and rev_seq are both mandatory; fwd_name and rev_name are both optional.
Both sequences should be presented in 5' to 3' order.
The sequences should be given in the IUPAC degenerate-base alphabet, except for the modified bases; those must be enclosed within angle brackets < >
plasmidFeature Table Definition
Definition name of naturally occurring plasmid from which the sequence was obtained. Must not be used for description of cloning vector.
Value format <text>, excluding double quotation mark (")
Example C-589
productFeature Table Definition
Definition name of the product associated with the feature, e.g. the mRNA of an mRNA feature, the polypeptide of a CDS, the mature peptide of a mat_peptide, etc.
Value format <text>, excluding double quotation mark (")
Example trypsinogen (when qualifier appears in CDS feature)
trypsin (when qualifier appears in mat_peptide feature)
XYZ neural-specific transcript (when qualifier appears in mRNA feature)
Guidance for Submission: See also Gene nomenclature at DDBJ.
  • In principle, please enter a general name, not abbreviation.
  • Do not include the organism name.
  • Even if there are multiple general names for the same product, do not enter multiple names in 'product'. Do not use needless symbolic letters as delimiter for multiple names. If you would like to describe more than two names, please enter one of the most representative name in 'product', and other(s) in 'note' qualifier.
  • If the name and function are not known, we recommend to describe as "hypothetical protein".
protein_idFeature Table Definition
Definition Protein Identifier for CDS feature, issued by INSDC.
Value format <identifier>.<version>
Example BAA12345.1
Comment 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.
When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented.
The stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein.
This qualifier is valid only on CDS features which translate into a valid protein.
proviralFeature Table Definition
Definition this qualifier is used to flag sequence obtained from a virus or phage that is integrated into the genome of another organism
Value format none
pseudoFeature Table Definition
Definition indicates that this feature is a non-functional version of the element named by the feature key. When pseudo qualifier is shown, CDS feature does not have translation.
Value format none
Comment Do not use for new submission. If necessary, describe pseudogene.
pseudogeneFeature Table Definition
Definition indicates that this feature is considered a pseudogene of the element named by the feature key. When pseudogene qualifier is shown, CDS feature does not have translation.
Value format "TYPE"
where TYPE is one of the following:
  • processed
  • unprocessed
  • unitary
  • allelic
  • unknown
Comment See Controlled vocabulary for /pseudogene qualifier for TYPE, in detail.
rearrangedFeature Table Definition
Definition the sequence presented in the entry has undergone somatic rearrangement as part of an adaptive immune response; it is not the unrearranged sequence that was inherited from the parental germline.
Value format none
Comment Do not use with germline qualifier.
regulatory_classFeature Table Definition
Definition a structured description of the classification of transcriptional, translational, replicational and chromatin structure related regulatory elements in a sequence
Value format TYPE
where TYPE is one of the following:
  • attenuator
  • CAAT_signal
  • DNase_I_hypersensitive_site
  • enhancer
  • enhancer_blocking_element
  • GC_signal
  • imprinting_control_region
  • insulator
  • locus_control_region
  • matrix_attachment_region
  • minus_35_signal
  • minus_10_signal
  • polyA_signal_sequence
  • promoter
  • recoding_stimulatory_region
  • replication_regulatory_region
  • response_element
  • ribosome_binding_site
  • riboswitch
  • silencer
  • TATA_box
  • terminator
  • transcriptional_cis_regulatory_region
  • other
Comment See Controlled vocabulary for /regulatory_class for TYPE, in detail.
replaceFeature Table Definition
Definition indicates that the sequence identified a feature's intervals is replaced by the sequence shown in "text"
Value format <text>, excluding double quotation mark (")
Example a
ribosomal_slippageFeature Table Definition
Definition during protein translation, certain sequences can program ribosomes to change to an alternative reading frame by a mechanism known as ribosomal slippage
Value format none
Comment a join operator, e.g.: [join(486..1784,1784..4810)] should be used in the CDS spans to indicate the location of ribosomal_slippage
rpt_familyFeature Table Definition
Definition type of repeated sequence
Value format <text>, excluding double quotation mark (")
Example Alu
Kpn
rpt_typeFeature Table Definition
Definition organization of repeated sequence
Value format limited to followings;
  • tandem
  • inverted
  • flanking
  • terminal
  • direct
  • dispersed
  • nested
  • long_terminal_repeat
  • non_ltr_retrotransposon_polymeric_tract
  • x_element_combinatorial_repeat
  • y_prime_element
  • telomeric_repeat
  • centromeric_repeat
  • other
Comment See Controlled vocabulary for /rpt_type qualifier, in detail.
rpt_unit_seqFeature Table Definition
Definition identity of a repeat sequence
Value format text; limited to following letters; acgtmrwsykvhdbn0123456798()
Example aagggc
ag(5)tg(8)
(aaaga)6(aaaa)1(aaaga)12
satelliteFeature Table Definition
Definition identifier for satellite DNA marker; many tandem repeats (identical or related) of a short basic repeating unit
Value format <satellite_type>[:<class>][ <identifier>]
Example satellite: S1a
satellite: alpha
satellite: gamma III
microsatellite: DC130
Comment
<satellite_type> is mandatory. Please select from either of followings; 
  • satellite
  • microsatellite
  • minisatellite
segmentFeature Table Definition
Definition name of viral or phage segment from which sequence was obtained.
Value format <text>, excluding double quotation mark (")
Example 6
serotypeFeature Table Definition
Definition variety of a species (usually bacteria or virus) characterized by its antigenic properties
Value format <text>, excluding double quotation mark (")
Example B1
serovarFeature Table Definition
Definition serological variety of a species (usually a prokaryote) characterized by its antigenic properties
Value format <text>, excluding double quotation mark (")
Example O157:H7
sexFeature Table Definition
Definition sex of the organism from which the sequence was obtained. sex is used for eukaryotic organisms that undergo meiosis and have sexually dimorphic gametes (cf. mating_type).
Value format <text>, excluding double quotation mark (")
Example female
male
hermaphrodite
monoecious
dioecious
specimen_voucherFeature Table Definition
Definition identifier for the specimen (a part or an individual of a typical animal or plant) from which the sequence was obtained
Value format [<institution_code>:[<collection_code>:]]<specimen_id>
Example UAM:Mamm:52179
AMCC:101706
USNM:field series 8798
personal:Dan Janzen:99-SRNP-2003
Comment the /specimen_voucher qualifier is intended to annotate a reference to the physical specimen that remains after the sequence has been obtained; <collection_code>is optional.

You can find <institution_code> at
institution_code list (NCBI FTP site)
BioCollections
strainFeature Table Definition
Definition strain from which the sequence was obtained
Value format <text>, excluding double quotation mark (")
Example BALB/c
submitter_seqidFeature Table Definition
Definition unique identifier within whole of the set version for WGS, TSA, TLS and CON
Value format <text>, excluding double quotation ("), pipe (|), equal (=) marks and space
Example contig53
scaffold25
sub_cloneFeature Table Definition
Definition sub-clone from which the sequence was obtained
Value format <text>, excluding double quotation mark (")
Example lambda-hIL7.20g
sub_speciesFeature Table Definition
Definition subspecies name of organism from which the sequence was obtained
Value format <text>, excluding double quotation mark (")
Example troglodytes
sub_strainFeature Table Definition
Definition sub_strain from which sequence was obtained. name or identifier of a genetically or otherwise modified strain from which sequence was obtained, derived from a parental strain (which should be annotated in the /strain qualifier). 
Value format <text>, excluding double quotation mark (")
Example abis
Comment If the parental strain is not given, this should be annotated in the strain qualifier instead of sub_strain. 
  • In general: /strain="K-12", /sub_strain="MG1655"
  • not given parental: /strain="MG1655"
tag_peptideFeature Table Definition
Definition base location encoding the polypeptide for proteolysis tag of tmRNA and its termination codon
Value format <base_range>
Example 90..122
tissue_typeFeature Table Definition
Definition tissue type from which the sequence was obtained
Value format <text>, excluding double quotation mark (")
Example liver
trans_splicingFeature Table Definition
Definition indicates that exons from two RNA molecules are ligated in intermolecular reaction to form mature RNA
Value format none
Comment should be used on features such as CDS, mRNA and other features that are produced as a result of a trans-splicing event. This qualifier should be used only when the splice event is indicated in the join operator eg join(complement(69611..69724),139856..140087)
transgenicFeature Table Definition
Definition identifies the source feature of the organism which was the recipient of transgenic DNA 
Value format no value
transl_exceptFeature Table Definition
Definition translational exception: single codon the translation of which does not conform to genetic code indicated by transl_table
Value format (pos:location,aa:<amino_acid>)
where amino_acid is the amino acid coded by the codon at the base_range position. Amino acids are limited to the abbreviation either for Amino Acid Codes, or for Modified and Unusual Amino Acids.
Example 1 For exceptional translation at the specific position;
/transl_except=(pos:213..215,aa:Sec)

The codon at base 213 to 215 is exceptionally translated to selenocysteine(one letter code 'U' in amino-acid sequence)
Example 2 For partial termination codons;
/transl_except=(pos:1017,aa:TERM)
/transl_except=(pos:2000..2001,aa:TERM)
TAA stop codon, either a single base T at base 1017, or two bases TA at base 2000 to 2001, are completed by the addition of 3' A residues to the mRNA.
Example 3 If the amino acid is not on the restricted vocabulary list use;
/transl_except=(pos:213..215,aa:OTHER)

/note="name of unusual amino acid"
The codon at the position at base 213 to 215 is exceptionally translated to the amino acid defined in the /note qualifier (one letter code 'X' in amino-acid sequence).
transl_tableFeature Table Definition
Definition definition of genetic code table used if other than universal genetic code table.
Value format <integer> (1 - 6, 9 - 14, 16, 21 - 31)
Example 11
Comment Nucleotide sequence of CDS is automatically translated to one-letter abbreviated amino acid sequence.
Genetic code exceptions should be reported in /transl_except or /exception.

See the genetic code list.
When /transl_table is not specified, standard code (/transl_table=1) is used for translation automatically.
Input method for Nucleotide Sequence Submission System
If the organism name is not found in the taxonomy database, please enter 'genetic code' for source feature. Then the value is reflected to transl_table qualifier of each CDS feature.
for MSS
Please specify the appropriate genetic code corresponds to the organism and organelle.
translationFeature Table Definition
Definition In usual, 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 qualifiers. So, it is not required for submitter to describe except using exception qualifier.
Value format IUPAC one-letter amino acid abbreviation as shown in Amino Acid Codes,"X" is to be used for AA exceptions.
Example MERRYCHRISTMASANDHAPPYNEWYEAR
Comment When pseudo or pseudogene qualifier is shown, CDS does not have /translation.
varietyFeature Table Definition
Definition variety (= varietas, a formal Linnaean rank) of organism from which sequence was derived.
Value format <text>, excluding double quotation mark (")
Example insularis