Appendix IV: QUALIFIERS FOR MF FEATURE KEYS - ALPHABETICAL INDEX
* Feature key qualifiers - alphabetical index
* Qualifiers-Feature Keys Correlations
Last update 12NOV01 pc
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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 /A+T_rich
Definition A+T rich sequence
Value format none
Example /A+T_rich
Qualifier /altern_splice
Definition alternative splicing of introns
Value format none
Example /alter_splice
Qualifier attenuator
Definition
Value format
Example
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 indicated.
Qualifier clone_lib
Definition
Value format
Example
Qualifier /complete
Definition complete sequence of respective genome was obtained
Value format none
Example /complete
Qualifier /codon=
Definition codon which is translated differently from the given
genetic code.
Is used in combination with /translation
Value format (seq:codon-seq",aa:(amino_acid)
Example /codon=(seq:"ata",aa:Met)
Note Needs to be defined more precisely: codon_deviation?
translation_exception?
Qualifier /codon_altern=
Definition codon affected by base substitution, where the
sequence alternatives are represented through IUB
nucleotide code.
Is used in combination with /translation
Value format "text"
Example /codon=ATR
Qualifier /cons_splice
Definition differentiates between intron splice sites that conform to the
5'-GT ... AG-3' splice site consensus
Value format (5'site:, 3'site:)
Example /cons_splice=(5'site:YES, 3'site:NO)
Comment valid boolean values are yes and no; 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
Qualifier /codon_start=
Definition offset of the 1st complete codon, relative to the 1st
base of a coding feature.
Value format 1 or 2 or 3
Example /codon_start=2
Qualifier /copia
Definition copia retroelement of Drosophila
Value format none
Example /copia
Qualifier /copy_number
Definition copy number of genetic elements that occur in multiple
copies in a genome, e.g., duplicated tRNA genes
Value format integer
Example /copy_number=2
Comment replaces the previous syntax _1, _2
Qualifier /cultivar=
Definition variety of plant from which sequence was obtained.
Value format "text"
Example /cultivar="Taichung 65"
Comment used primarily in source feature key
Qualifier /cyanelle
Definition organelle type from which the sequence was obtained
Value format none
Example /cyanelle
Qualifier /deletion
Definition
Value format none
Example /deletion
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 /dispersed
Definition dispersed repeat element
Value format none
Example /dispersed
Qualifier /D-loop
Definition D-loop of animal mitochondrial DNA
Value format none
Example /D-loop
Comment D-loop is a feature in GenBank
Qualifier /DNAmodif
Definition DNA modification
Value format none
Example /DNAmodif
Qualifier /editing
Definition RNA editing site or region
Value format none
Example /editing
Qualifier elongator
Definition
Value format
Example
Qualifier endo
Definition
Value format
Example
Qualifier /first_aa
Definition Designates the 1st amino acid in a polypeptide, if it
is not a methionine.
Value format none
Example /first_aa=I
Qualifier /fragment_number=
Definition Fragment number of genes or genetic elements that
are not contiguous, e.g., rRNA genes in pieces
Value format integer
Example /fragment_number=2
Comment replaces the previous syntax _a, _b, etc.
Implementation in progress
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 protein gene that refers to a particular feature, e.g. RNA
Value format "text"
Example /gene="cox1"
Comment implementation in progress
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 /G+T_rich
Definition G+C rich sequence
Value format none
Example /G+C_rich
Qualifier /GIY-YIG=
Definition a group of conserved orfs (endonuclease or maturase)
Value format none
Example /GIY-YIG
Qualifier /group
Definition intron group
Value format 1[a,b,c..] or 2 or 3
Example /group=1a
Comment intron groups have been defined for organelles (I,II and III
and their subgroups Ia, Ib ...). Arabic rather than roman
digits are used here. The nomenclature for nuclear
encoded introns has still to be established.
Qualifier /halotype=
Definition haplotype of organism from which the sequence was obtained
Value format "text"
Example /haplotype="Dw3 B5 Cw1 A1"
Qualifier /hompos
Definition conserved insertion sites of introns or other insertion elements
Value format "text"
Example /hompos="225, E. coli"
Comment the example means that the insertion is after residue
225 of the corresponding sequence of E.coli.
[Rarely used: For a protein-coding gene, one may specify the
nucleotide position in a given codon.
E.g., for hompos="100-2, H.sapiens" as a qualifier of the
protein-coding gene atp6 means that an intron is inserted
at amino acid nr.225 of the human atp6 protein, and precisely
after the second nucleotide of the corresponding codon.]
Qualifier /inframe
Definition intron orf in frame with upstream exon (CDS)
Value format none
Example /inframe
Comment usually in combination with /first_aa=
Qualifier initiator
Definition
Value format
Example
Qualifier /insertion=
Definition insert following bases
Value format "text"
Example /insertion="AGCTGAGTGAGTGAC"
Qualifier /intronic
Definition defines that a genetic element is located within an intron
Value format none
Example /intronic
Qualifier /inversion/
Definition site of inversion
Value format "text"
Example /inversion
Qualifier /isolate=
Definition individual isolate from which the sequence was obtained
Value format "text"
Example /isolate="Patient #152"
Qualifier /join
Definition join the pieces of a genetic element, e.g.,for translation
Value format none
Example /join
Qualifier /kinetoplast
Definition organelle type from which the sequence was obtained
Value format none
Example /kinetoplast
Qualifier /label=
Definition a label used to permanently tag a feature
Value format feature_label. feature labels follow the naming conventtions
for all feature table objects
(see Sections 3.1 and 3.4)
Example /label=Alb1_exon1
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 /LAGLIDADG
Definition a group of conserved orfs (endonuclease or maturase)
Value format none
Example /LAGLIDADG
Qualifier /LTR
Definition long terminal repeat, used in a general sense
Value format none
Example /LTR
Commment LTR is a feature in GenBank
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 /missence
Definition translation of a codon that is affected by base substitution
results in another amino acid.
Value format none
Example /missense
Qualifier /mitochondrion
Definition organelle type from which the sequence was obtained
Value format none
Example /mitochondrion
Qualifier /mutation
Definition
Value format none
Example /mutation
Qualifier /mod_base
Definition abbreviation for a modified base
Value format modified base
Example /mod_base=m5c
Qualifier /mRNA
Definition specifies that an RNA belongs to the type messenger RNA
Value format none
Comment should be accompanied by a /gene qualifier to indicate
which protein gene the mRNA codes for (implementation
in progress)
Qualifier /nonsence
Definition translation of a codon that is affected by base substitution
results in a stop codon.
Value format none
Example /nonsense
Qualifier /note=
Definition any comment or additional information
Value format "text"
Example /note="This qualifier is equivalent to a commebase"
Qualifier /nuclear
Definition organelle type from which the sequence was obtained
Value format none
Example /nuclear
Qualifier /nucleomorph
Definition organelle type from which the sequence was obtained
Value format none
Example /nucleomorph
Qualifier /OMEGA
Definition a group of conserved orfs (endonuclease or maturase)
Value format none
Example /OMEGA
Qualifier /organism=
Definition The scientific name of the organism that provided the
sequenced genetic material.
Value format "text"
Example /organism="Homo sapiens"
Comment Both EMBL and GenBank will continue with their existing OS
and ORGANISM linetypes respectively. 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 /organization=
Definition organization of repeat units
Value format "text"
Syntax rules: (i) repeat units are named according to their length,
names are enclosed in brackets, and are separated
by commas, e.g.:
/organization="(rep34a),(rep34b),(rep35)"
(ii) the number following a repeat unit name (in brackets)
indicates the number of adjacent tandem repeats, e.g., in
the following expression rep34 a an rep34b occure once,
but rep35 occurs four times in a row:
/organization="(rep34a),(rep34b),(rep35)4"
(iii) The number of units can be given
by a precise (e.g., 3), a relative (>4) or a
range value (2-4):
/organization="(rep34a)>4,(rep34b)<100,(rep35)2-4"
(iv) when various repeats units are separated by stretches
of unique sequence, these unique regions are marked with
an extra komma in the expression:
/organization="(rep34a),,(rep34b),(rep35)4"
(v) repeat units occuring on the opposite strand
(inverse/complement) are preceded by a minus sign:
/organization="(rep34a),(rep35),(-rep34a)"
Example /organization="text"
Qualifier /ORI
Definition replication origin
Value format none
Example /ORI
Qualifier /partial
Definition differentiates between complete regions and partial ones
Value format none
Example /partial
Comment when the 5'end is missing, the start annotation obtains
the additional qualifier /nostart
the qualifier /nostop. This applies to protein-coding
genes and indicates that start or stop codons are absent.
Qualifier polyA_site
Definition
Value format
Example
Qualifier polyA_signal
Definition
Value format
Example
Qualifier /polymorph
Definition polymorphic site
Value format none
Example /polymorph
Qualifier /pop_variant
Definition population variant from which the sequence was obtained
Value format "text"
Example /pop_variant="population variant name"
Qualifier /phenotype=
Definition phenotype conferred by the feature
Value format "text"
Example /phenotype="erythromycin resistance"
Qualifier /plasmid=
Definition name of plasmid from which sequence was obtained
Value format "text"
Example /plasmid="C-589"
Qualifier /plastid
Definition organelle type from which the sequence was obtained
Value format none
Example /plastid
Qualifier /polymorph
Definition polymorphic site
Value format none
Example /polymorph
Qualifier precursor_RNA
Definition
Value format
Example
Qualifier primary_transcript
Definition
Value format
Example
Qualifier /product
Definition name of a product encoded by a sequence
Value format "text"
Example /product="catalase"
Qualifier /promoter
Definition
Value format none
Example /promoter
Commment promoter is a feature in GenBank
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 /putative
Definition indicates that the identiy of this feature is not proven
experimentally
Value format none
Example /putative
Comment is the substitute of /evidence=non_experimental
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 /RBS
Definition ribosome binding site
Value format none
Example /RBS
Commment RBS is a feature in GenBank
Qualifier REPinit
Definition
Value format
Example
Qualifier /recomb
Definition recombination site
Value format none
Example /recomb
Qualifier /repetitive
Definition repetitive sequence element
Value format none
Example /repetitive
Qualifier /repeat_region
Definition a sequence region that contains repeats
Value format none
Example /repeat_region
Qualifier /repeat_element
Definition repeat element of a repetitive sequence
Value format none
Example /repeat_element
Qualifier /rev_trans
Definition a group of conserved intron orfs (reverse transcriptase or
maturase)
Value format none
Example /rev_trans
Qualifier /retro
Definition retrotransposon
Value format none
Example /retro
Qualifier RNA-3`
Definition
Value format
Example
Qualifier RNA-5`
Definition
Value format
Example
Qualifier /RNAproc
Definition RNA processing site
Value format none
Example /RNAproc
Qualifier /RNAinit
Definition initiation of transcription
Value format none
Example /RNAinit
Qualifier /RNAmodif
Definition RNA modification
Value format none
Example /RNAmodif
Qualifier /RNAterm
Definition termination of transcription
Value format none
Example /RNAterm
Qualifier /repeat_unit
Definition repeat element of a repetitive sequence
Value format text
Example /rpt_unit=
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 /sex=
Definition sex of the organism from which the sequence was obtained
Value format "text"
Example /sex="female"
Qualifier /shape=
Definition shape of the genome, circular, linear
Value format "text"
Example /shape="circular"
Qualifier /silent
Definition translation of a codon that is affected by base substitution
where all alternative codon sequences specify the same
amino acid.
Value format none
Example /silent
Qualifier /specific_host=
Definition natural host from which the sequence was obtained
Value format "text"
Example /specific_host="Rhizobium NGR234"
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 /stem_loop
Definition
Value format none
Example /stem_loop
Comment stem-loop is a feature in GenBank
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="japonica"
Qualifier /sub_strain=
Definition sub_strain from which the sequence was obtained
Value format "text"
Example /sub_strain="abis"
Qualifier /substitution
Definition substitute following base with one or more alternatives
Value format "text"
Example /substitution="A==>G,C,T"
Comment used for polymorphism, mutations, editing, RNA and DNA
modifications
Qualifier /synonym
Definition synonyms for gene names, etc.
Value format "text"
Example /synonym=urfa(S.pombe mt)[2]
Comment synonym gene names can be specified with the species name and
source (in brackets) and a reference number
Qualifier /tandem
Definition tandem arrangement of repeat_elements
Value format none
Example /tandem
Qualifier /telomere
Definition telomer
Value format none
Example /telomere
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 /transl_altern=
Definition alternative translations of a codon that is
affected by base substitution.
Value format UPAC 1-letter amino acid abbreviation
Example /translation=M,I
Comment Is used in combination with /codon_altern
Qualifier /transl_except=
Definition individual codon whose translation does not conform with
the given genetic code.
Value format ,
Example /translat_except=ATA,M (UPAC 1-letter amino acid code)
Comment Is used in combination with /Sig. In the Genbank feature
definitions, its value format is
(pos:base_range,aa:)
note This qualifier conceptually overlaps with /codon
Qualifier /translate_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 ; 1=non-universal table 1;2=non-universal table 2;...
Example /transl_table=4
Comment Genetic code exceptions outside range of specified tables are
reported in /codon or /transl_except qualifiers
Qualifier /trans_splice
Definition trans splicing of introns
Value format none
Example /trans_splice
Qualifier transposon
Definition
Value format
Example
Qualifier /tRNA-editing
Definition post-transcriptional editing of tRNA
Value format none
Comment evidently used in context of tRNA genes
Qualifier /twintron
Definition an intron inserted into an intron
Value format none
Example /twintron
Qualifier /TY
Definition TY retroelement of yeast
Value format none
Example /TY
Qualifier /variety=
Definition variety from which sequence was obtained
Value format "text"
Example /variety="Bright Yellow 4"
Comment Used primarily in Source feature key
Qualifier /ymf
Definition temporary gene name for conserved organellar orfs.
Names are administered by CPGN nomenclature commission.
Value format "text"
Example /ymf52
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