# Note: "SO: undefined" needs to be checked for a later SO definition

# 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
# New in 6.2 is alternate mandatory qualifiers, shown by m rather than M
# where e.g. /citation or /compare is used for a conflict

# Updated to EMBL/GenBank/DDBJ FTv6.5 by Peter Rice 30th May 2006
# Updated to EMBL/GenBank/DDBJ FTv8.0 by Peter Rice 12th March 2008

# "-" is a placeholder for no key; should be used when the need is
# merely to mark region in order to comment on it or to use it in
# another feature's location;

# Features in EMBL feature table with SO aliases
# ==============================================


# SO: A biological feature that can be
# attributed to a region of biological sequence.

misc_feature SO:0000110
	/allele
        /citation
        /db_xref                   
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
	/number
	/old_locus_tag
        /phenotype
        /product
        /pseudo
        /standard_name

# 1) region of DNA at which regulation of termination of transcription
# occurs, which controls the expression of some bacterial operons; 2)
# sequence segment located between the promoter and the first
# structural gene that causes partial termination of transcription

# SO: A sequence segment located between the promoter and a structural
# gene that causes partial termination of transcription.

attenuator SO:0000140
        /allele
        /citation
        /db_xref
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
	/old_locus_tag
	/operon
        /phenotype

# constant region of immunoglobulin light and heavy  chains, and T-cell
# receptor alpha, beta, and gamma  chains; includes one or more exons
# depending on the  particular chain

#org=prokaryotes
#mol=DNA

C_region SO:0000478
        /allele
        /citation
        /db_xref
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
	/old_locus_tag
        /product
        /pseudo
        /standard_name

# CAAT box; part of a conserved sequence located about 75 bp up-stream
# of the start point of eukaryotic transcription units which may be
# involved in RNA polymerase binding;

# SO: consensus=GG(C or T)CAATCT [1,2].  Part of a conserved sequence
# located about 75-bp upstream of the start point of eukaryotic
# transcription units which may be involved in RNA polymerase binding;
# consensus=GG(C|T)CAATCT.

#up=CDS
#org=eukaryotes

CAAT_signal SO:0000172
	/allele
        /citation
        /db_xref                     
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
	/old_locus_tag

# coding sequence; sequence of nucleotides that corresponds with the
# sequence of amino acids in a protein (location includes stop codon);
# feature includes amino acid conceptual translation.

# SO: A contiguous sequence which begins with, and includes, a start
# codon and ends with, and includes, a stop codon.

#org=eukaryotes,eukaryotic_viruses
#mol=DNA

CDS SO:0000316
	#  no mandatory /translation or /pseudo in FTv 6.5
	 /allele
         /citation
         /codon
         /codon_start
         /db_xref        
         /EC_number
         /exception
	 /experiment
         /function
         /gene
         /gene_synonym
	 /inference
         /label
	 /locus_tag
         /map
         /note
         /number
	 /old_locus_tag
	 /operon
         /product
         /protein_id
         /pseudo
	 /ribosomal_slippage
         /standard_name
         /translation
         /transl_except
         /transl_table
	 /trans_splicing

# independent determinations of the "same" sequence differ at this site
# or region;
#
# Or /compare=[accession-number.sequence-version]

conflict SO:0001085
       m/citation
       m/compare
        /allele   # New in 8.0
        /db_xref
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
	/old_locus_tag
# use /replace="" for a deletion
        /replace

# displacement loop; a region within mitochondrial DNA in which a
# short stretch of RNA is paired with one strand of DNA, displacing
# the original partner DNA strand in this region; also used to
# describe the displacement of a region of one strand of duplex DNA by
# a single stranded invader in the reaction catalyzed by RecA protein


# SO: Displacement loop; a region within mitochondrial DNA in which a
# short stretch of RNA is paired with one strand of DNA, displacing
# the original partner DNA strand in this region; also used to
# describe the displacement of a region of one strand of duplex DNA by
# a single stranded invader in the reaction catalyzed by RecA protein.

D-loop SO:0000297
	/allele
        /citation
        /db_xref
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
	/old_locus_tag

# Diversity segment of immunoglobulin heavy chain, and  T-cell receptor
# beta chain;

# SO: germline genomic DNA including D-region with 5' UTR and 3' UTR, also
# designated as D-segment.

#mol=DNA

D_segment SO:0000458
	/allele
        /citation
        /db_xref
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
	/old_locus_tag
        /product
        /pseudo
        /standard_name

# a cis-acting sequence that increases the utilization of (some)
# eukaryotic promoters, and can function in either orientation and in
# any location (upstream or downstream) relative to the promoter;

# SO: A cis-acting sequence that increases the utilization of (some)
# eukaryotic promoters, and can function in either orientation and in
# any location (upstream or downstream) relative to the promoter.

#up=CDS
#org=eukaryotes

enhancer SO:0000165
	/allele
	/bound_moiety
        /citation
        /db_xref        
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
	/old_locus_tag
        /standard_name

# region of genome that codes for portion of spliced mRNA, rRNA and
# tRNA; may contain 5'UTR, all CDSs and 3' UTR;

# SO: A region of the genome that codes for portion of spliced
# messenger RNA (SO:0000234); may contain 5'-untranslated region
# (SO:0000204), all open reading frames (SO:0000236) and
# 3'-untranslated region (SO:0000205).

#org=eukaryotes,eukaryotic_viruses

exon SO:0000147
	/allele
        /citation
        /db_xref                    
        /EC_number
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
        /number
	/old_locus_tag
        /product
        /pseudo
        /standard_name

# gap in the sequence

# SO: A gap in the sequence of known length. The unkown bases are
# filled in with N's.

# New in 6.2
gap SO:0000730
	M/estimated_length
	/experiment
	/inference
	/map
	/note

# GC box; a conserved GC-rich region located upstream of the start
# point of eukaryotic transcription units which may occur in multiple
# copies or in either orientation; consensus=GGGCGG;

# SO: A conserved GC-rich region located upstream of the start point
# of eukaryotic transcription units which may occur in multiple copies
# or in either orientation; consensus=GGGCGG.

GC_signal SO:0000173
	/allele
        /citation
        /db_xref                    
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
	/old_locus_tag

# region of biological interest identified as a gene and for which a
# name has been assigned;

# SO: A locatable region of genomic sequence, corresponding to a unit
# of inheritance, which is associated with regulatory regions,
# transcribed regions and/or other functional sequence regions

#org=eukaryotes,eukaryotic_viruses

gene SO:0000704
        /allele
        /citation
        /db_xref
	/experiment
        /function
	# gene added as genbank has several entries
        /gene 
        /gene_synonym
	/inference 
        /label
	/locus_tag
        /map
        /note
	/old_locus_tag
	/operon
        /product
        /pseudo
        /phenotype
        /standard_name
	/trans_splicing

# DNA which is eliminated through any of several kinds of recombination;

# SO: Genomic sequence removed from the genome, as a normal event, by
# a process of recombination.

iDNA SO:0000723
	/allele
        /citation
        /db_xref                    
	/experiment
        /function
	/gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
        /number
 	/old_locus_tag
        /standard_name

# a segment of DNA that is transcribed, but removed from within the
# transcript by splicing together the sequences (exons) on either side
# of it;

# SO: A segment of DNA that is transcribed, but removed from within
# the transcript by splicing together the sequences (exons) on either
# side of it.

#mol=DNA

intron SO:0000188
	/allele
        /citation
	# /cons_splice is used only when one of the intron's splice
        # sites does not match the GT...AG consensus
        /cons_splice
        /db_xref                    
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
        /number
 	/old_locus_tag
	/pseudo
        /standard_name

# joining segment of immunoglobulin light and heavy  chains, and T-cell
# receptor alpha, beta, and gamma  chains;

J_segment SO:0000470
	/allele
        /citation
        /db_xref
	/experiment
        /gene
        /gene_synonym
	/inference
	/locus_tag
        /map
        /note
 	/old_locus_tag
        /product
        /pseudo
        /standard_name

# long terminal repeat, a sequence directly repeated at both ends of a
# defined sequence, of the sort typically found in retroviruses;

# SO: A sequence directly repeated at both ends of a defined sequence,
# of the sort typically found in retroviruses.

#up=CDS
#org=eukaryotes

LTR SO:0000286
	/allele
        /citation
        /db_xref                    
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
        /standard_name

# mature peptide or protein coding sequence; coding sequence for the
# mature or final peptide or protein product following
# post-translational modification; the location does not include the
# stop codon (unlike the corresponding CDS);

# SO: The coding sequence for the mature or final peptide or protein
# product following post-translational modification.

mat_peptide SO:0000419
	/allele
        /citation
        /db_xref                    
        /EC_number
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
        /product
        /pseudo
        /standard_name

# site in nucleic acid which covalently or non-covalently binds
# another moiety that cannot be described by any other binding key
# (primer_bind or protein_bind);

# SO: A region on the surface of a molecule that may interact with
# another molecule.

misc_binding SO:0000409
       M/bound_moiety
        /allele
        /citation
        /db_xref                    
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag

# feature sequence is different from that presented in the entry and
# cannot be described by any other Difference key (conflict, unsure,
# old_sequence, variation, or modified_base);

# SO: A region where the sequences differs from that of a specified
# sequence.

misc_difference SO:0000413
	/allele
        /citation
        /clone
	/compare
        /db_xref
	/experiment                   
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map                    
        /note
 	/old_locus_tag
	/phenotype
        /replace  
        /standard_name

# site of any generalized, site-specific or replicative recombination
# event where there is a breakage and reunion of duplex DNA that
# cannot be described by other recombination keys or qualifiers of
# source key (/insertion_seq, /transposon, /proviral);

# SO: undefined general term that includes iDNA
# sequence_rearrangement_feature haplotype_block and
# recombination_hotspot

misc_recomb SO:0000298
	/allele
        /citation
        /db_xref                     
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
	# No longer mandatory /organism from FTv5.0
	# If omitted, assume only the SOURCE organism is involved
        /organism
        /standard_name

# any transcript or RNA product that cannot be defined by other RNA
# keys (prim_transcript, precursor_RNA, mRNA, 5'clip, 3'clip, 5'UTR,
# 3'UTR, exon, CDS, sig_peptide, transit_peptide, mat_peptide, intron,
# polyA_site, rRNA, tRNA, scRNA, and snRNA);

# SO: An RNA synthesized on a DNA or RNA template by an RNA
# polymerase.

#mol=DNA

misc_RNA SO:0000673
	/allele
        /citation
        /db_xref                    
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
	/operon
        /product
	/pseudo
        /standard_name
	/trans_splicing

# any region containing a signal controlling or altering gene function
# or expression that cannot be described by other signal keys
# (promoter, CAAT_signal, TATA_signal, -35_signal, -10_signal,
# GC_signal, RBS, polyA_signal, enhancer, attenuator, terminator, and
# rep_origin).

# SO: A DNA sequence that controls the expression of a gene.

misc_signal SO:0005836
	/allele
        /citation
        /db_xref                 
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
	/operon
        /phenotype
        /standard_name

# any secondary or tertiary nucleotide structure or conformation that
# cannot be described by other Structure keys (stem_loop and D-loop);

# SO: A folded sequence.

misc_structure SO:0000002
	/allele
        /citation
        /db_xref                  
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
        /standard_name

# the indicated nucleotide is a modified nucleotide and should be
# substituted for by the indicated molecule (given in the mod_base
# qualifier value)

# SO: A modified nucleotide, i.e. a nucleotide other than A, T, C. G
# or (in RNA) U.

modified_base SO:0000305
       M/mod_base
        /allele
        /citation
        /db_xref                     
	/experiment
        /frequency
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
	/old_locus_tag

# messenger RNA; includes 5'untranslated region (5'UTR), coding
# sequences (CDS, exon) and 3'untranslated region (3'UTR);

# SO: messenger RNA is the intermediate molecule between DNA and
# protein. It includes UTR and coding sequences. It does not contain
# introns.

mRNA SO:0000234
	/allele
        /citation
        /db_xref                     
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
	/operon
        /product
        /pseudo
        /standard_name
	/trans_splicing

# An RNA transcript that does not encode for a protein rather the RNA
# molecule is the gene product
# A ncRNA is a processed_transcript, so it may not contain parts such
# as transcribed_spacer_regions that are removed in the act of
# processing.
# the ncRNA feature is not used for ribosomal and transfer
# RNA annotation, for which the rRNA and tRNA feature keys
# should be used, respectively; 
# New in FT 7.0

ncRNA SO:0000655
       m/ncRNA_class
	/allele
        /citation
        /db_xref
	/experiment
	/function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
	/operon
        /product
        /pseudo
        /standard_name
	/trans_splicing

# extra nucleotides inserted between rearranged immunoglobulin
# segments.


N_region SO:0000563
	/allele
        /citation
        /db_xref
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
        /product
        /pseudo
        /standard_name

# the presented sequence revises a previous version of the sequence at
# this location;
#
# Or /compare=[accession-number.sequence-version]

#up=CDS
#org=eukaryotes

old_sequence  SO:0001082
       m/citation
       m/compare
        /allele
        /db_xref
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
	#use /replace="" to annotate a deletion
        /replace

# region containing polycistronic transcript containing genes that
# encode enzymes that are in the same metabolic pathway and regulatory
# sequences

# SO: A group of contiguous genes transcribed as a single
# (polycistronic) mRNA from a single regulatory region.

# New in FT 6.2
operon SO:0000178
	M/operon
	 /allele
	 /citation
	 /db_xref
	 /experiment
	 /function
	 /inference
	 /label
	 /map
	 /note
	 /phenotype
	 /pseudo
	 /standard_name

# origin of transfer; region of a DNA molecule where transfer is
# initiated during the process of conjugation or mobilization

# SO: A region of a DNA molecule whre transfer is initiated during the
# process of conjugation or mobilization.

# New in FT 6.2
oriT SO:0000724
	/allele
	/bound_moiety
	/citation
	/db_xref
	# Only /direction=LEFT or RIGHT are valid
	/direction
	/experiment
	/gene
        /gene_synonym
	/inference
	/label
	/locus_tag
	/map
	/note
	/old_locus_tag
	/rpt_family
	/rpt_type
	/rpt_unit_range
	/rpt_unit_seq
	/standard_name

# recognition region necessary for endonuclease cleavage of an RNA
# transcript that is followed by polyadenylation; consensus=AATAAA
# [1];

# SO: The recognition sequence necessary for endonuclease cleavage of
# an RNA transcript that is followed by polyadenylation;
# consensus=AATAAA.

#mol=DNA

polyA_signal SO:0000551
	/allele
        /citation
        /db_xref                    
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag

# site on an RNA transcript to which will be added adenine residues by
# post-transcriptional polyadenylation;

# SO: The site on an RNA transcript to which will be added adenine
# residues by post-transcriptional polyadenylation.

#org=eukaryotes,eukaryotic_viruses

polyA_site SO:0000553
	/allele
        /citation
        /db_xref                    
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag

# any RNA species that is not yet the mature RNA product; may include
# 5' clipped region (5'clip), 5' untranslated region (5'UTR), coding
# sequences (CDS, exon), intervening sequences (intron), 3'
# untranslated region (3'UTR), and 3' clipped region (3'clip);

# SO: The primary (initial, unprocessed) transcript; includes
# five_prime_clip (SO:0000555), five_prime_untranslated_region
# (SO:0000204), open reading frames (SO:0000236), introns (SO:0000188)
# and three_prime_ untranslated_region (three_prime_UTR), and
# three_prime_clip (SO:0000557).  precursor_RNA SO:0000185 /allele
# /citation /db_xref /evidence /function /gene /label /locus_tag /map
# /note /old_locus_tag /operon # removed in FTv5.0 for new entries -
# use <> in location instead # /partial # added in FTv3.0 Jan 2001
# /product /standard_name /usedin

#org=eukaryotes,eukaryotic_viruses

precursor_RNA SO:0000835
	/allele
        /citation
        /db_xref
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
	/operon
        /product        
        /standard_name
	/trans_splicing

#SO: The primary (initial, unprocessed) transcript; includes
# five_prime_clip (SO:0000555), five_prime_untranslated_region
# (SO:0000204), open reading frames (SO:0000236), introns (SO:0000188)
# and three_prime_ untranslated_region (three_prime_UTR), and
# three_prime_clip (SO:0000557)

prim_transcript SO:0000185
	/allele
        /citation
        /db_xref                    
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
	/operon
        /standard_name

# non-covalent primer binding site for initiation of replication,
# transcription, or reverse transcription; includes site(s) for
# synthetic e.g., PCR primer elements;

# SO: Non-covalent primer binding
# site for initiation of replication, transcription, or reverse
# transcription.

primer_bind SO:0005850
	/allele
        /citation
        /db_xref                    
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
        /PCR_conditions
        /standard_name

# region on a DNA molecule involved in RNA polymerase binding to
# initiate transcription;

# SO: The region on a DNA molecule involved in RNA polymerase binding
# to initiate transcription.

promoter SO:0000167
	/allele
	/bound_moiety
        /citation
        /db_xref                   
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
	/operon
        /phenotype
        /pseudo
        /standard_name

# non-covalent protein binding site on nucleic acid;

# SO: A region of a molecule that binds to a protein.

#mol=DNA

# Use RBS instead for ribosome binding sites

protein_bind SO:0000410
       M/bound_moiety
        /allele
        /citation
        /db_xref                   
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
	/operon
        /standard_name

# ribosome binding site;

# SO: Region in mRNA where ribosome assembles

RBS SO:0000139
	/allele
        /citation
        /db_xref                     
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
        /standard_name

# region of genome containing repeating units;

# SO: A region of sequence containing one or more repeat units.

repeat_region SO:0000657 SO:0000705
	/allele
        /citation
        /db_xref                     
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
	/mobile_element
        /note
 	/old_locus_tag
        /rpt_family
        /rpt_type
	/rpt_unit_range
	/rpt_unit_seq
	/satellite
        /standard_name

# single repeat element;

# SO: A single repeat element.
# removed in FTv8.0
#repeat_unit SO:0000726
#	/allele
#       /citation
#       /db_xref                     
#	/experiment
#       /function
#       /gene
#       /gene_synonym
#	/inference
#       /label
#	/locus_tag
#       /map
#       /note
# 	/old_locus_tag
#       /rpt_family
#       /rpt_type
#	/rpt_unit_range
#	/rpt_unit_seq


# SO: regulatory_region, equivalent to EMBL/GB misc_signal

rep_origin SO:0000296
	/allele
        /citation
        /db_xref               
        /direction
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
        /standard_name

# mature ribosomal RNA ; RNA component of the ribonucleoprotein
# particle (ribosome) which assembles amino acids into proteins.

# SO: RNA that comprises part of a ribosome, and that can provide both
# structural scaffolding and catalytic activity.

rRNA SO:0000252
	/allele
        /citation
        /db_xref                  
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
	# use /product for rRNA sizes
        /product
        /pseudo
        /standard_name

# switch region of immunoglobulin heavy chains; involved in the
# rearrangement of heavy chain DNA leading to the expression of a
# different immunoglobulin class from the same B-cell;

S_region SO:0000301_S_region
	/allele
        /citation
        /db_xref
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
        /product
        /pseudo
        /standard_name

# many tandem repeats (identical or related) of a short basic
# repeating unit; many have a base composition or other property
# different from the genome average that allows them to be separated
# from the bulk (main band) genomic DNA;

# SO: The many tandem repeats (identical or related) of a short basic
# repeating unit; many have a base composition or other property
# different from the genome average that allows them to be separated
# from the bulk (main band) genomic DNA.

#up=misc_signal
#org=eukaryotes

# Removed FTv8.0
#satellite SO:0000005
#	/allele
#       /citation
#       /db_xref        
#	/experiment
#       /gene
#       /gene_synonym
#	/inference
#       /label
#	/locus_tag
#       /map
#       /note
# 	/old_locus_tag
#       /rpt_type
#       /rpt_family
#	/rpt_unit_range
#	/rpt_unit_seq
#       /standard_name

# small cytoplasmic RNA; any one of several small cytoplasmic RNA
# molecules present in the cytoplasm and (sometimes) nucleus of a
# eukaryote;

# SO: Any one of several small cytoplasmic RNA moleculespresent in the
# cytoplasm and sometimes nucleus of a eukaryote.

#mol=DNA

# removed FTv8.0
#scRNA SO:0000013
#	/allele
#       /citation
#       /db_xref        
#	/experiment
#       /function
#       /gene
#       /gene_synonym
#	/inference
#       /label
#	/locus_tag
#       /map
#       /note
# 	/old_locus_tag
#       /product
#       /pseudo
#       /standard_name

# signal peptide coding sequence; coding sequence for an N-terminal
# domain of a secreted protein; this domain is involved in attaching
# nascent polypeptide to the membrane leader sequence;

# SO: The sequence for an N-terminal domain of a secreted protein;
# this domain is involved in attaching nascent polypeptide to the
# membrane leader sequence.

sig_peptide SO:0000418
	/allele
        /citation
        /db_xref        
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
        /product
        /pseudo
        /standard_name

# small nucleolar RNA molecules mostly involved in rRNA modification
# and processing;

# SO: Small nucleolar RNAs (snoRNAs) are involved in the processing
# and modification of rRNA in the nucleolus. There are two main
# classes of snoRNAs: the box C/D class, and the box H/ACA class. U3
# snoRNA is a member of the box C/D class. Indeed, the box C/D element
# is a subset of the six short sequence elements found in all U3
# snoRNAs, namely boxes A, A', B, C, C', and D. The U3 snoRNA
# secondary structure is characterised by a small 5' domain (with
# boxes A and A'), and a larger 3' domain (with boxes B, C, C', and
# D), the two domains being linked by a single-stranded hinge. Boxes B
# and C form the B/C motif, which appears to be exclusive to U3
# snoRNAs, and boxes C' and D form the C'/D motif. The latter is
# functionally similar to the C/D motifs found in other snoRNAs. The
# 5' domain and the hinge region act as a pre-rRNA-binding domain. The
# 3' domain has conserved protein-binding sites. Both the box B/C and
# box C'/D motifs are sufficient for nuclear retention of U3
# snoRNA. The box C'/D motif is also necessary for nucleolar
# localization, stability and hypermethylation of U3 snoRNA. Both box
# B/C and C'/D motifs are involved in specific protein interactions
# and are necessary for the rRNA processing functions of U3 snoRNA.

# replaced by ncrna FTv7.0
#snoRNA SO:0000275
#	/allele
#       /citation
#       /db_xref        
#	/experiment
#       /function
#       /gene
#       /gene_synonym
#	/inference
#       /label
#	/locus_tag
#       /map
#       /note
# 	/old_locus_tag
#       /product
#       /pseudo
#       /standard_name

# small nuclear RNA molecules involved in pre-mRNA splicing and
# processing

# SO: Small non-coding RNA in the nucleoplasm.

# replaced by ncrna FTv7.0
#snRNA SO:0000274
#	/allele
#       /citation
#       /db_xref        
#	/experiment
#       /function
#       /gene
#       /gene_synonym
#	/inference
#       /label
#	/locus_tag
#       /map
#       /note
# 	/old_locus_tag
#       /product
#       /pseudo
#       /standard_name

#identifies the biological source of the specified span of the
#sequence; this key is mandatory; more than one source key per
#sequence is allowed; every entry/record will have, as a minimum,
#either a single source key spanning the entire sequence or multiple
#source keys which together span the entire
#sequence. /mol_type="genomic DNA", "genomic RNA", "mRNA", "tRNA",
#"rRNA", "snoRNA", "snRNA", "scRNA", "pre-RNA", "other RNA", "other
#DNA", "unassigned DNA", "unassigned RNA"

# SO: The sequence referred to by an entry in a databank such as
# Genbank or SwissProt.

source SO:2000061
       M/organism
	# New in FTv5.0
	# mandatory from 01-July-2003
       M/mol_type
         /bio_material
        /cell_line
        /cell_type
        /chromosome
        /citation
        /clone
        /clone_lib
	/collected_by
	/collection_date
        /country
        /cultivar
	/culture_collection                # new in FTv7.0
        /db_xref                    
        /dev_stage
	/ecotype
	# /environmental_sample and /isolation_source should appear together
	/environmental_sample
        /focus
        /frequency
        /germline
        /haplotype
	/host			# new in FTv8.0
	/identified_by
        /isolate
	# /environmental_sample and /isolation_source should appear together
	/isolation_source
	/lab_host
        /label
	/lat_lon
        /macronuclear
        /map
	/mating_type		# New in FTv8.0
        /note
        /organelle
	/PCR_primers
        /plasmid
        /pop_variant
        /proviral
        /rearranged
	/segment
        /serotype
	/serovar
        /sex
        /specimen_voucher
        # /specific_host	# removed in FTv8.0
        /strain
        /sub_clone
        /sub_species
        /sub_strain
        /tissue_lib
        /tissue_type
	# transgenic is supposed to be only in extra source keys for an entry
	/transgenic
        /variety
        # /virion		# removed in FTv8.0

# hairpin; a double-helical region formed by base-pairing between
# adjacent (inverted) complementary sequences in a single strand of
# RNA or DNA.

# SO: A double-helical region of nucleic acid formed by base-pairing between
# adjacent (inverted) complementary sequences.

stem_loop SO:0000313
	/allele
        /citation
        /db_xref                     
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
	/operon
        /standard_name

# short, single-copy DNA sequence that characterizes a mapping
# landmark on the genome and can be detected by PCR; a region of the
# genome can be mapped by determining the order of a series of STSs;

# SO: Short (typically a few hundred base pairs) DNA sequence that has
# a single occurrence in a genome and whose location and base sequence
# are known.

STS SO:0000331
# Location to include the primer(s) annotated usually in primer_bind feature
	/allele
        /citation
        /db_xref
	/experiment
        /gene
        /gene_synonym
	/inference
        /label      
	/locus_tag
        /map
        /note
 	/old_locus_tag
        /standard_name

# TATA box; Goldberg-Hogness box; a conserved AT-rich septamer found
# about 25 bp before the start point of each eukaryotic RNA polymerase
# II transcript unit which may be involved in positioning the enzyme
# for correct initiation; consensus=TATA(A or T)A(A or T) [1,2];

# SO: A conserved AT-rich septamer found about 25-bp before the start
# point of many eukaryotic RNA polymerase II transcript units; may be
# involved in positioning the enzyme for correct initiation;
# consensus=TATA(A|T)A(A|T).

#mol=DNA
#up=misc_binding

TATA_signal SO:0000174
	/allele
        /citation
        /db_xref        
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag

# sequence of DNA located either at the end of the transcript that
# causes RNA polymerase to terminate  transcription;

# SO: The sequence of DNA located either at the end of the transcript that
# causes RNA polymerase to terminate transcription.

#org=eukaryotes,eukaryotic_viruses
#mol=DNA

terminator SO:0000141
	/allele
        /citation
        /db_xref                     
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
	/old_locus_tag
	/operon
        /standard_name

# New in Fv7.0

# transfer messenger RNA; tmRNA acts as a tRNA first, and then as an
# mRNA that encodes a peptide tag; the ribosome translates this mRNA
# region of tmRNA and attaches the encoded peptide tag to the
# C-terminus of the unfinished protein; this attached tag targets the
# protein for destruction or proteolysis;

tmRNA SO:0000584
	/allele
        /citation
        /db_xref                     
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
	/old_locus_tag
	/product
	/pseudo
	/standard_name
	/tag_peptide

# transit peptide coding sequence; coding sequence for an N-terminal
# domain of a nuclear-encoded organellar protein; this domain is
# involved in post-translational import of the protein into the
# organelle;

# SO: The coding sequence for an N-terminal domain of a
# nuclear-encoded organellar protein: this domain is involved in post
# translational import of the protein into the organelle.

#mol=DNA

transit_peptide SO:0000725
	/allele
        /citation
        /db_xref                     
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
        /product
        /pseudo
        /standard_name

# mature transfer RNA, a small RNA molecule (75-85 bases long) that
# mediates the translation of a nucleic acid sequence into an amino
# acid sequence;

# SO: Transfer RNA (tRNA) molecules are approximately 80 nucleotides
# in length. Their secondary structure includes four short
# double-helical elements and three loops (D, anti-codon, and T
# loops). Further hydrogen bonds mediate the characteristic L-shaped
# molecular structure. tRNAs have two regions of fundamental
# functional importance: the anti-codon, which is responsible for
# specific mRNA codon recognition, and the 3' end, to which the tRNA's
# corresponding amino acid is attached (by aminoacyl-tRNA
# synthetases). tRNAs cope with the degeneracy of the genetic code in
# two manners: having more than one tRNA (with a specific anti-codon)
# for a particular amino acid; and 'wobble' base-pairing,
# i.e. permitting non-standard base-pairing at the 3rd anti-codon
# position.

tRNA SO:0000253
	/allele
        /anticodon
        /citation
        /db_xref                     
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
        /product
        /pseudo
        /standard_name
	/trans_splicing		# New in FTv6.5

# author is unsure of exact sequence in this region;

unsure  SO:0001086
	/allele
        /citation
	/compare
        /db_xref                     
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
        /replace

# variable region of immunoglobulin light and heavy chains, and T-cell
# receptor alpha, beta, and gamma chains; codes for the variable amino
# terminal portion; can be composed of V_segments, D_segments,
# N_regions, and J_segments;

V_region SO:0000938
	/allele
        /citation
        /db_xref
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
        /product
        /pseudo
        /standard_name

# variable segment of immunoglobulin light and heavy chains, and
# T-cell receptor alpha, beta, and gamma chains; codes for most of the
# variable region (V_region) and the last few amino acids of the
# leader peptide;

#up=CDS
#org=eukaryotes

V_segment  SO:0000466
	/allele
        /citation
        /db_xref
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
        /product
        /pseudo
        /standard_name

# a related strain contains stable mutations from the same gene (e.g.,
# RFLPs, polymorphisms, etc.) which differ from the presented sequence
# at this location (and possibly others);

# SO: A region of sequence where variation has been observed.

#up=CDS
#org=eukaryotes
# was variation SO:0000109 but this is now obsoleted in SO

variation SO:0001060 SO:0000109
        /allele
        /citation
	/compare
        /db_xref
        /experiment
        /frequency
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
	/phenotype
        /product
	# Use /replace="" for deletion
        /replace
        /standard_name

# 3'-most region of a precursor transcript that is clipped off during
# processing;

# SO: 3'-most region of a precursor transcript that is clipped off
# during processing.

# Removed in FTv7.0

#3'clip SO:0000557
#	/allele
#       /citation
#       /db_xref                   
#	/experiment
#       /function
#       /gene
#       /gene_synonym
#	/inference
#       /label
#	/locus_tag
#       /map
#       /note
# 	/old_locus_tag
#       /standard_name

# region at the 3' end of a mature transcript (following the stop
# codon) that is not translated into a protein;

# SO: A region at the 3' end of a mature transcript (following the
# stop codon) that is not translated into a protein.


3'UTR SO:0000205
	/allele
        /citation
        /db_xref                   
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
        /standard_name
	/trans_splicing

# 5'-most region of a precursor transcript that is clipped off during
# processing;

# SO: 5' most region of a precursor transcript that is clipped off
# during processing.

# Removed in FTv7.0
#5'clip SO:0000555
#	/allele
#       /citation
#       /db_xref                   
#	/experiment
#       /function
#       /gene
#       /gene_synonym
#	/inference
#       /label
#	/locus_tag
#       /map
#       /note
# 	/old_locus_tag
#       /standard_name

# region at the 5' end of a mature transcript (preceding the
# initiation codon) that is not translated into a protein;

# SO: A region at the 5' end of a mature transcript (preceding the
# initiation codon) that is not translated into a protein.

5'UTR SO:0000204
	/allele
        /citation
        /db_xref                   
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
        /standard_name
	/trans_splicing

# Pribnow box; a conserved region about 10 bp upstream of the start
# point of bacterial transcription units which may be involved in
# binding RNA polymerase; consensus=TAtAaT [1,2,3,4];

# SO: A conserved region about 10-bp upstream of the start point of
# bacterial transcription units which may be involved in binding RNA
# polymerase; consensus=TAtAaT.

-10_signal SO:0000175
	/allele
        /citation
        /db_xref                   
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
	/operon
        /standard_name

# a conserved hexamer about 35 bp upstream of the start point of
# bacterial transcription units; consensus=TTGACa or TGTTGACA;

# SO: A conserved hexamer about 35-bp upstream of the start point of
# bacterial transcription units; consensus=TTGACa or TGTTGACA.

#org=prokaryotes
#mol=DNA

-35_signal SO:0000176
	/allele
        /citation
        /db_xref                   
	/experiment
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
 	/old_locus_tag
	/operon
        /standard_name

# "-" is a placeholder for no key; should be used when the need is
# merely to mark region in order to comment on it or to use it in
# another feature's location;
# Otherwise, use misc_feature

# SO: A biological feature that can be
# attributed to a region of biological sequence.

#org=prokaryotes
#mol=DNA

- SO:0000001
	/allele
        /citation
        /db_xref
	/experiment
        /function
        /gene
        /gene_synonym
	/inference
        /label
	/locus_tag
        /map
        /note
        /number
 	/old_locus_tag
        /phenotype
        /product
        /pseudo
        /standard_name
