# Updated to EMBL/GenBank/DDBJ FTv5.0 by Peter Rice 17th Jan 2003
# Updated to EMBL/GenBank/DDBJ FTv6.2 by Peter Rice 27th Jan 2005

note QTEXT

# should be identical for all features related to one gene
# and must differ from /gene
allele QTEXT

anticodon SPECIAL
#      (pos:<base_range>,aa:<amino_acid>)

# multiple values allowed for promoter and enhancer features
# single value for misc_binding, oriT and protein_bind features
bound_moiety QTEXT

cell_line QTEXT

cell_type QTEXT

chromosome QTEXT

# removed in FTv3.0 Jan 2001
# chloroplast VOID

# removed in FTv3.0 Jan 2001
# chromoplast VOID

citation SPECIAL
# value [number]
# # brackets are historical from use for multiple citations
# now represented by multiple /citation qualifiers

clone QTEXT

clone_lib QTEXT

codon SPECIAL
#       (seq:"ttt",aa:Leu)
# seq is 3 bases - use join() location for ribosomal slippage
# use aa:OTHER for amino acids not on approved list

codon_start  LIMITED 1,2,3

# new in FT 6.0
# multiple occurrences allowed
# value is accnumber.version with no quotes
compare SPECIAL

cons_splice SPECIAL
# (5'site:YES,3'site:NO)
# ABSENT also allowed if beyond end e.g.  (5'site:NO,3'site:ABSENT)

collected_by QTEXT

collection_date QSPECIAL
# "DD-Mmm-YYYY", "Mmm-YYYY" or "YYYY"

country QTEXT
# Value country country:region or country:region,locality

# artificially selected plants or fungi - see also /variety
cultivar QTEXT

# removed in FTv3.0 Jan 2001
# cyanelle VOID

db_xref QSPECIAL
#      "<database>:<identifier>"
# the complete list of allowed database types is kept by NCBI at
# http://www.ncbi.nlm.nih.gov/projects/collab/ 

dev_stage QTEXT

direction  LIMITED left,right,both
# for oriT features BOTH is incorrect

EC_number QTEXT
# EC number value

ecotype QTEXT

environmental_sample VOID
# when used expect /isolation_source

estimated_length SPECIAL
# gap length: unknown or integer
# unknown gaps are 100 "n"s in the sequence
# gap size is unlimited

# Removed in FTv6.5, replaced by /experiment and /inference
#evidence LIMITED experimental,not_experimental

exception QTEXT

experiment QTEXT

#source feature of biological interest - defines the translation table
# and which organism to put in the taxonomy of the entry
# use for one of multiple source features
# do not use for transgenic (multiple source) entries
focus VOID

frequency QTEXT
# represents fraction of population e.g. ".85"

function QTEXT

gene QTEXT

germline VOID

haplotype QTEXT

identified_by QTEXT

# a structured description of non-experimental evidence that supports
# the feature identification or assignment.
#
# TYPE[ (same species)][:EVIDENCE_BASIS]" where TYPE is one of the following:
#  "non-experimental evidence, no additional details recorded"
#       "similar to sequence"
#            "similar to AA sequence"
#            "similar to DNA sequence"
#            "similar to RNA sequence"
#                "similar to RNA sequence, mRNA"
#                "similar to RNA sequence, EST"
#                "similar to RNA sequence, other RNA"
#       "profile"
#            "nucleotide motif"
#            "protein motif"
#            "ab initio prediction"
#  where the optional text "(same species)" is included when the inference comes 
#  from the same species as the entry.
#  where the optional "EVIDENCE_BASIS" is either a reference to a database entry 
#  (including accession and version) or an algorithm (including version) , eg 
#  'INSD:AACN010222672.1', 'InterPro:IPR001900', 'ProDom:PD000600', 
#  'Genscan:2.0', etc.

inference QSPECIAL

# replaced by mobile_element in Dec 2006
insertion_seq QTEXT

isolate QTEXT

isolation_source QTEXT

# removed in FTv3.0 Jan 2001
# kinetoplast VOID  

label TEXT

lab_host QTEXT

#degrees latitude and longitude in format "d[d.dd] N|S d[dd.dd] W|E"
# (see the examples)
# /lat_lon="47.94 N 28.12 W" /lat_lon="45.01 S 4.12 E" 

lat_lon QSPECIAL

# new in FTv5.0 - to mark features for tracking purposes
# Use in any features if /gene is valid - must be unique in the entry
# Only allows a single word from January 2005
# but old entries may have multiple values

locus_tag QWORD

map QTEXT

macronuclear VOID

# removed in FTv3.0 Jan 2001
# mitochondrion VOID  

mobile_element QSPECIAL

mod_base TEXT
# There is a controlled vocabulary in appendix 7.5.2 of
# http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
# others should have OTHER with /note="name of base"

# mRNA (incl. EST)
# other RNA (incl. synthetic)
# other DNA (incl. synthetic)
# unassigned DNA (incl. unknown)
# unassigned RNA (incl. unknown)
mol_type QLIMITED genomic DNA,genomic RNA,mRNA,tRNA,rRNA,snoRNA,snRNA,scRNA,pre-RNA,other RNA,other DNA,unassigned DNA,unassigned RNA
# FT 6.2 was pre-mRNA in FT 5.0

#alphanumeric e.g. 4, 6B, XIIb for order of genetic elements
number TEXT

# Only allows a single word from January 2005
# but old entries may have multiple values
# expect to find /locus_tag with the current locus name
# locus_tag is to mark features for tracking purposes
old_locus_tag QWORD

operon QTEXT

organelle QLIMITED mitochondrion,nucleomorph,plastid,mitochondrion:kinetoplast,plastid:chloroplast,plastid:apicoplast,plastid:chromoplast,plastid:cyanelle,platid:leucoplast,plastid:proplastid
# FT 6.2 was plastid:protoplastid in FT5.0

organism QTEXT

# obsolete from 15-Dec-01, but used in old entries
partial VOID

PCR_conditions QTEXT

# /PCR_primers="[fwd_name: XXX, ]fwd_seq: xxxxx,
# [rev_name: YYY, ]rev_seq: yyyyy" 
#
# Example: /PCR_primers="fwd_name: CO1P1, fwd_seq: ttgattttttggtcayccwgaagt,
# rev_name: CO1R4, rev_seq: ccwvytardcctarraartgttg" 
# /PCR_primers="fwd_seq: tgtgtgtgtgactgaca, rev_seq: tagcgatacggtcaatgc" 
#
# fwd_seq and rev_seq are both mandatory; fwd_name and rev_name are both
# optional. Both sequences should be presented in 5'>3' order. The
# sequences should be given in the IUPAC degenerate-base alphabet.

# New in FTv6.5
PCR_primers QSPECIAL

phenotype QTEXT

plasmid QTEXT

pop_variant QTEXT

product QTEXT

protein_id QSPECIAL
#   "AAA12345.1"

proviral VOID

pseudo VOID

rearranged VOID

replace QSPECIAL
#      "ACGT"
#      "" for a deletion

# during protein translation, certain sequences can program ribosomes
# to change to an alternative reading frame by a mechanism known as
# ribosomal slippage
#
# a join operator,e.g.: [join(486..1784,1787..4810)] should be used in
# the CDS spans to indicate the location of ribosomal_slippage 

ribosomal_slippage VOID

rpt_family QTEXT

rpt_type LIMITED TANDEM,INVERTED,FLANKING,TERMINAL,DIRECT,DISPERSED,OTHER

rpt_unit SPECIAL
#    202..245
#FT6.2: or "sequence"

rpt_unit_range SPECIAL
# base range 202..245

rpt_unit_seq QSPECIAL
# sequence perhaps with repeats /rpt_unit_seq="aagggc" or
# /rpt_unit_seq="ag(5)tg(8)"

# new in FTv5.0 for viral segments
segment QTEXT

# obsolete in FT 6.2
# sequenced_mol QLIMITED cDNA,cDNA to genomic RNA,cDNA to mRNA,cDNA to other RNA,cDNA to rRNA,DNA,mRNA,RNA,rRNA,scRNA,snRNA,tRNA

serotype QTEXT

serovar QTEXT

sex QTEXT
#       male,female, hermaphrodite, ...

specific_host QTEXT

specimen_voucher QTEXT

standard_name QTEXT

strain QTEXT

sub_clone TEXT

sub_species TEXT

sub_strain TEXT

tissue_lib QTEXT

tissue_type QTEXT

# transgenic is supposed to be only in extra source keys for an entry
# identifies the recipient source, used in taxonomy
# entries with /transgenic should not have /focus
transgenic VOID

translation QSPECIAL
# X used for exceptions
# mandatory for CDS unless /pseudo is present

transl_except SPECIAL
#  (pos:213..215,aa:Trp)

# FTv3.0 has no definition for 17, 18, 19, 20
# FTv6.2 has no definition for 7, 8
transl_table LIMITED 1,2,3,4,5,6,9,10,11,12,13,14,15,16,21,22,23
# 1 is universal genetic code

transposon QTEXT

# indicates that exons from two RNA molecules are ligated in
# intermolecular reaction to form mature RNA

trans_splicing VOID

#removed in FTv6.5 - not listed for any feature key
# usedin TEXT

# plant and fungal varieties only
variety QTEXT

virion VOID
