#gap4db	FT term	SO term	SO ID	FT definition	SO definition
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# First part:
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# BaCh: from http://sequenceontology.org/resources/mapping/FT_SO.txt and added gap4 codes
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# added missing SO definitions for GenBank: C_region, J_segment, N_region,
#  S_region, V_region, V_segment, conflict, unsure
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# Added gap4db IDs which exist in FT or SO: Fgap for gap, FsoR for snoRNA
#
# Do NOT clean up tabs at end of lines which have some, these are needed!

F---	-	located_sequence_feature	SO:0000110	"-" 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;	A biological feature that can be attributed to a region of biological sequence.
F-10	-10_signal	minus_10_signal	SO:0000175	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];	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.
F-35	-35_signal	minus_35_signal	SO:0000176	a conserved hexamer about 35 bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA;	A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA.
F3_U	3'UTR	three_prime_UTR	SO:0000205	region at the 3' end of a mature transcript (following  the stop codon) that is not translated into a protein;	A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein.
F3_c	3'clip	three_prime_clip	SO:0000557	3'-most region of a precursor transcript that is clipped off during processing;	3'-most region of a precursor transcript that is clipped off during processing.
F5_U	5'UTR	five_prime_UTR	SO:0000204	region at the 5' end of a mature transcript (preceding  the initiation codon) that is not translated into a  protein;	A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein.
F5_c	5'clip	five_prime_clip	SO:0000555	5'-most region of a precursor transcript that is clipped off during processing;	5' most region of a precursor transcript that is clipped off during processing.
FCAA	CAAT_signal	CAAT_signal	SO:0000172	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; 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.
FCDS	CDS	CDS	SO:0000316	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.	A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon.
FCre	C_region	SO:0001834	SO:0001834	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	The constant region of an immunoglobulin polypeptide sequence. [SO:ke]
FD-l	D-loop	D_loop	SO:0000297	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	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.
FD-s	D_segment	D_gene	SO:0000458	Diversity segment of immunoglobulin heavy chain, and  T-cell receptor beta chain;  	germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment.
FGCs	GC_signal	GC_rich_region	SO:0000173	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;	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.
FJ-s	J_segment	J_gene_segment	SO:0000470	joining segment of immunoglobulin light and heavy  chains, and T-cell receptor alpha, beta, and gamma  chains;  	Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
FLTR	LTR	long_terminal_repeat	SO:0000286	long terminal repeat, a sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses;	A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses.
FN-r	N_region	N_region	SO:0001835	extra nucleotides inserted between rearranged  immunoglobulin segments.	Extra nucleotides inserted between rearranged immunoglobulin segments. [SO:ke]
FRBS	RBS	ribosome_entry_site	SO:0000139	ribosome binding site;	Region in mRNA where ribosome assembles.
FSTS	STS	STS	SO:0000331	sequence tagged site; 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;	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.
FS-r	S_region	S_region	SO:0001836	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;	The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell. [SO:ke]
FTAT	TATA_signal	TATA_box	SO:0000174	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];	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).
FV-r	V_region	V_region	SO:0001833	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;	The variable region of an immunoglobulin polypeptide sequence. [SO:ke]
FV-s	V_segment	V_gene_segment	SO:0000466	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;	Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR. [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
Fatt	attenuator	attenuator	SO:0000140	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	A sequence segment located between the promoter and a structural gene that causes partial termination of transcription.
Fcon	conflict	sequence_conflict	SO:0001085	independent determinations of the "same" sequence differ at this site or region; Or /compare=[accession-number.sequence-version]	Different sources report differing sequences. [EBIBS:GAR, UniProt:curation_manual]
Fenh	enhancer	enhancer	SO:0000165	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;	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.
Fexn	exon	exon	SO:0000147	region of genome that codes for portion of spliced mRNA,  rRNA and tRNA; may contain 5'UTR, all CDSs and 3' UTR; 	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).
Fgap	gap	gap	SO:0000730	gap in the sequence	A gap in the sequence of known length. THe unkown bases are filled in with N's.
Fgen	gene	gene	SO:0000704	region of biological interest identified as a gene  and for which a name has been assigned;	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
FiDN	iDNA	iDNA	SO:0000723	intervening DNA; DNA which is eliminated through any of several kinds of recombination;	Genomic sequence removed from the genome, as a normal event, by a process of recombination. 
Fint	intron	intron	SO:0000188	a segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it;	A segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it.
FmRN	mRNA	mRNA	SO:0000234	messenger RNA; includes 5'untranslated region (5'UTR), coding sequences (CDS, exon) and 3'untranslated region (3'UTR);	messenger RNA is the intermediate molecule between DNA and protein. It  includes UTR and coding sequences. It does not contain introns. 
Fmat	mat_peptide	mature_peptide	SO:0000419	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);	The coding sequence for the mature or final peptide or protein product following post-translational modification.
Fm-R	misc_RNA	transcript	SO:0000673	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);	An RNA synthesized on a DNA or RNA template by an RNA polymerase.
Fm-b	misc_binding	binding_site	SO:0000409	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);	A region on the surface of a molecule that may interact with another molecule.
Fm-d	misc_difference	sequence_difference	SO:0000413	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);	A region where the sequences differs from that of a specified sequence.
Fm-f	misc_feature	region	SO:0000001	region of biological interest which cannot be described by any other feature key; a new or rare feature;	Continous sequence.
Fm-r	misc_recomb	recombination_feature	SO:0000298	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);	
Fm-S	misc_signal	regulatory_region	SO:0005836	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).	A DNA sequence that controls the expression of a gene.
Fm-s	misc_structure	sequence_secondary_structure	SO:0000002	any secondary or tertiary nucleotide structure or  conformation that cannot be described by other Structure keys (stem_loop and D-loop);	A folded sequence.
Fmod	modified_base	modified_base_site	SO:0000305	the indicated nucleotide is a modified nucleotide and should be substituted for by the indicated molecule (given in the mod_base qualifier value)	A modified nucleotide, i.e. a nucleotide other than A, T, C. G or (in RNA) U.
Fmut	old_sequence			the presented sequence revises a previous version of the sequence at this location; Or /compare=[accession-number.sequence-version]	
Fold	operon	operon	SO:0000178	region containing polycistronic transcript containing genes that encode enzymes that are  in the same metabolic pathway and regulatory sequences 	A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region.
Frpo	rep_origin	origin_of_replication	SO:0000296	The origin of replication;	starting site for duplication of a nucleic acid molecule to give two identical copies.
	oriT	origin_of_transfer	SO:0000724	origin of transfer; region of a DNA molecule where  transfer is initiated during the process of conjugation  or mobilization	A region of a DNA molecule whre transfer is initiated during the process of conjugation or mobilization.
FpAS	polyA_signal	polyA_signal_sequence	SO:0000551	recognition region necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA [1];	The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA.
FpAs	polyA_site	polyA_site	SO:0000553	site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation;	The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation.
FpRN	precursor_RNA	primary_transcript	SO:0000185	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);	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).
Fp_t	prim_transcript	primary_transcript	SO:0000185	primary (initial, unprocessed) transcript;  includes 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);	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).
Fp_b	primer_bind	primer_binding_site	SO:0005850	non-covalent primer binding site for initiation of replication, transcription, or reverse transcription; includes site(s) for synthetic e.g., PCR primer elements;	Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription.  
Fpro	promoter	promoter	SO:0000167	region on a DNA molecule involved in RNA polymerase binding to initiate transcription;	The region on a DNA molecule involved in RNA polymerase binding to initiate transcription.
Fprt	protein_bind	protein_binding_site	SO:0000410	non-covalent protein binding site on nucleic acid;	A region of a molecule that binds to a protein.
FrRN	rRNA	rRNA	SO:0000252	mature ribosomal RNA ; RNA component of the ribonucleoprotein particle (ribosome) which assembles amino acids into proteins.	RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity.
Frpr	repeat_region	repeat_region	SO:0000657	region of genome containing repeating units;	A region of sequence containing one or more repeat units.
Frpu	repeat_unit	repeat_unit	SO:0000726	single repeat element;	A single repeat element.
Fsat	satellite	satellite_DNA	SO:0000005	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;	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.
FscR	scRNA	scRNA	SO:0000013	small cytoplasmic RNA; any one of several small cytoplasmic RNA molecules present in the cytoplasm and (sometimes) nucleus of a eukaryote; 	Any one of several small cytoplasmic RNA moleculespresent in the cytoplasm and sometimes nucleus of a eukaryote. 
Fsig	sig_peptide	signal_peptide	SO:0000418	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;	The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence.
FsnR	snRNA	snRNA	SO:0000274	small nuclear RNA molecules involved in pre-mRNA  splicing and processing  	Small non-coding RNA in the nucleoplasm.
FsoR	snoRNA	snoRNA	SO:0000275	small nucleolar RNA molecules mostly involved in  rRNA modification and processing;  	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.
Fsrc	source	databank_entry	SO:2000061	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"	The sequence referred to by an entry in a databank such as Genbank or SwissProt.
Fstm	stem_loop	stem_loop	SO:0000313	hairpin; a double-helical region formed by base-pairing between adjacent (inverted) complementary sequences in a single strand of RNA or DNA. 	A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences.
FtRN	tRNA	tRNA	SO:0000253	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;	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.
Fter	terminator	terminator	SO:0000141	sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate  transcription;	The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription.
Ft-p	transit_peptide	transit_peptide	SO:0000725	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;	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. 
F???	unsure	sequence_uncertainty	SO:0001086	author is unsure of exact sequence in this region;	Describes the positions in a sequence where the authors are unsure about the sequence assignment. [EBIBS:GAR, UniProt:curation_manual]
Fvar	variation	sequence_variant	SO:0000109	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);	A region of sequence where variation has been observed.


# Second part
#
# BaCh: added some gap4/SO translations used previously

Fctg		contig	   		     
Fmel		mobile_element			
FncR		ncRNA			
Fpgn		pseudogene			
Fpxn		pseudogenic_exon			
Fprg		pseudogenic_region			
FptR		pseudotRNA			
Freg		region			
Frrg		regulatory_region			
FtmR		tmRNA			
Fptr		processed_transcript			
COMM		remark			
