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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