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#Sequence ontology for TEs.
#The first column: case sensitive, exact SO names used by the SO database: http://www.sequenceontology.org
#The second column: SO IDs used by the database.
#The third column and further: alias used in everywhere, which are used to make connections with the SO ID. 
#	Alias are commer separated with or without spaces. 
#All commented lines will be ignored.
#Author: Shujun Ou (shujun.ou.1@gmail.com) 07/02/2020
#Update: 03/15/2022
############################################################


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####### Warning #######
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# Everytime you add new SO entries to this file, you also need to update the EDTA/util/gff2bed.pl file, 
#  so that $type can be correctly recognized from Sequence Ontologies listed on the first column of this file.


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## Enhancement notes ##
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# These terms do not have their own SO terms and are put under a generic SO
# TIR/PiggyBac	SO:0000182	DNA_transposon
# TIR/Sola2	SO:0000182	DNA_transposon
# rDNA/45S	SO:0002360	rRNA_gene


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####### Contents ######
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#Sequence_Ontology	SO_ID	Alias
centromeric_repeat	SO:0001797	centromeric_repeat,Cent,Cent/CentC,CentC,CentM,Centro/tandem,Cent/centromeric_repeat
knob	SO:0002257	knob,knob/knob180,knob/TR-1
satellite_DNA	SO:0000005	satellite_DNA,Satellite/rice,satellite,minisatellite,microsatellite,Satellite/Satellite
telomeric_repeat	SO:0001496	telomeric_repeat,telomere,telomeric,telomere/telomere
subtelomere	SO:0001997	subtelomere,subtelomere/4-12-1
low_complexity	SO:0001004	low_complexity,Low_complexity,low_complexity_region,Simple_repeat
rDNA_intergenic_spacer_element	SO:0001860	rDNA_intergenic_spacer_element,rDNA/spacer,rDNA/IGS
2S_rRNA_gene	SO:0002336	2S_rRNA_gene,rRNA_2S_gene,cytosolic_rRNA_2S_gene,rDNA/2S,2S_rRNA
5S_rRNA_gene	SO:0002238	5S_rRNA_gene,cytosolic_rRNA_5S_gene,rDNA/5S,5S_rRNA
5_8S_rRNA_gene	SO:0002240	5_8S_rRNA_gene,cytosolic_rRNA_5_8S_gene,rDNA/5.8S,5.8S_rRNA,rDNA/5_8S,5_8S_rRNA
23S_rRNA_gene	SO:0002243	23S_rRNA_gene,rDNA/23S,23S_rRNA
25S_rRNA_gene	SO:0002242	25S_rRNA_gene,rDNA/25S,25S_rRNA
28S_rRNA_gene	SO:0002239	28S_rRNA_gene,rDNA/28S,28S_rRNA
18S_rRNA_gene	SO:0002236	18S_rRNA_gene,cytosolic_rRNA_18S_gene,rDNA/18S,18S_rRNA
16S_rRNA_gene	SO:0002237	16S_rRNA_gene,cytosolic_rRNA_16S_gene,rDNA/16S,16S_rRNA
rRNA_gene	SO:0002360	rRNA_gene,rDNA/45S
rRNA	SO:0000252	rRNA

#higher	order
repeat_region	SO:0000657	repeat_region,Unknown,unknown,unknown/unknown,NA/NA,Unknown/NA,Unknown/unknown,Unspecified,repeat/unknown,repeat/Unknown,Unknown/Unknown
retrotransposon	SO:0000180	Class_I,RNA_transposon,retrotransposon
DNA_transposon	SO:0000182	Class_II,DNA_transposon,DNA/unknown,TIR/PiggyBac,TIR/Sola2,DNA/Unknown

#TIR	DNA	transposons
terminal_inverted_repeat_element	SO:0000208	terminal_inverted_repeat_element,TIR/unknown,DNA/DTX,DTX,DNAauto/unknown,DNAnona/unknown,DNAauto/PILE,DNAnona/PILE,DNAauto/POLE,DNAnona/POLE,DNA/PILE,MITE/PILE,DNA/POLE,MITE/POLE,TIR/Unknown,DNAauto/Unknown,DNAnona/Unknown
MITE	SO:0000338	MITE,TIR/MITE,MITE/unknown,MITE/Unknown
CACTA_TIR_transposon	SO:0002285	CACTA_TIR_transposon,DNAauto/CACTA,DNAnona/CACTA,DNAauto/CACTG,DNAnona/CACTG,DNA/DTC,MITE/DTC,DTC,dSpm,CACTC,En-Spm,EnSpm,CMC-EnSpm,DNA/CACTA,DNA/CACTG,MITE/CACTA,MITE/CACTG,TIR/EnSpm_CACTA,DNA/EnSpm_CACTA,DNA/CMC-EnSpm
hAT_TIR_transposon	SO:0002279	hAT_TIR_transposon,DNAauto/hAT,DNAnona/hAT,MITE/DTA,DNA/DTA,DTA,hAT,Ac-Ds,Ac/Ds,hAT-Ac,DNA/hAT,MITE/hAT,TIR/hAT,DNA/hAT-Ac,DNA/hAT-Tag1
Mutator_TIR_transposon	SO:0002280	Mutator_TIR_transposon,DNAauto/MULE,DNAnona/MULE,DNAnona/MULEtir,MITE/DTM,DNA/DTM,DTM,Mutator,MuDR,DNA/MULE,DNA/MULEtir,MITE/MULE,MITE/MULEtir,MULEtir,TIR/MuDR_Mutator,DNA/Mutator,DNA/MuDR,DNA/MULE-MuDR
PIF_Harbinger_TIR_transposon	SO:0002284	PIF_Harbinger_TIR_transposon,DNAnona/Tourist,MITE/Tourist,MITE/DTH,DNA/DTH,DTH,PIF-Harbinger,PIF/Harbinger,Harbinger,Tourist,DNA/Tourist,TIR/PIF_Harbinger,DNA/Harbinger,DNA/PIF-Harbinger
Tc1_Mariner_TIR_transposon	SO:0002278	Tc1_Mariner_TIR_transposon,stowaway,Stowaway,DNA/DTT,MITE/Stow,MITE/DTT,DTT,Tc1-Mariner,Tc1_Mariner,Tc1_mariner,Tc1/Mariner,TcMar-Stowaway,DNAauto/MLE,DNAnona/MLE,DNA/MLE,MITE/MLE,TIR/Tc1_Mariner,DNA/Tc1-Mariner,DNA/TcMar-Pogo,DNA/Mariner,DNA/TcMar-Stowaway,DNA/TcMar-Mariner
P_TIR_transposon	SO:0001535	P_TIR_transposon,P-element,P_element,DNA/DTP
piggyBac_TIR_transposon	SO:0002283	piggyBac_TIR_transposon,PiggyBac,DNA/DTB,MITE/DTB
polinton	SO:0001170	polinton,maverick,Maverick
Transib_TIR_transposon	SO:0002282	Transib_TIR_transposon,transib,DNA/DTR,MITE/DTR
Merlin_TIR_transposon	SO:0002281	Merlin_TIR_transposon,Merlin,DNA/DTE,MITE/DTE,TIR/Merlin

#nonTIR	DNA	transposons
Crypton_YR_transposon	SO:0002277	Crypton_YR_transposon,Crypton,DNA/DYC,DYC
helitron	SO:0000544	helitron,DNAauto/Helitron,DNAnona/Helitron,DNA/Helitron,Helitron,RC/Helitron

#LTR	retrotransposons
LTR_retrotransposon	SO:0000186	LTR_retrotransposon,LTR/unknown,LTR/Solo,LTR/Unknown,LTR/solo
Retrovirus_LTR_retrotransposon	SO:0002267	Retrovirus_LTR_retrotransposon,LTR/retrovirus,retrovirus,LTR/RLR,RLR
TRIM	SO:0002261	TRIM,LTR/TRIM
LARD	SO:0002260	LARD,LTR/LARD
Copia_LTR_retrotransposon	SO:0002264	Copia_LTR_retrotransposon,LTR/Copia,LTR/RLC,RLC,Copia,Ty1,LTR/Ty1
Gypsy_LTR_retrotransposon	SO:0002265	Gypsy_LTR_retrotransposon,LTR/Gypsy,LTR/RLG,RLG,Gypsy,Ty3,LTR/CRM,LTR/Ty3
Bel_Pao_LTR_retrotransposon	SO:0002266	Bel_Pao_LTR_retrotransposon,LTR/Bel-Pao,LTR/RLB,Bel-Pao,Bel/Pao
Endogenous_Retrovirus_LTR_retrotransposon	SO:0002268	Endogenous_Retrovirus_LTR_retrotransposon,LTR/HERV,HERV,LTR/ERV,LTR/RLE,RLE

#nonLTR	retrotransposons
non_LTR_retrotransposon	SO:0000189	Evirus/ERTBV-A,Evirus/ERTBV-B,Evirus/ERTBV-C,Evirus/ERTBV,pararetrovirus,non_LTR_retrotransposon,non_LTR,nonLTR/unknown,nonLTR/Unknown,pararetrovirus/NA,DNAvirus/ERTBV-C,Evirus/ERTBV,DNAvirus/ERTBV-A,DNAvirus/ERTBV-B
LINE_element	SO:0000194	LINE_element,LINE/unknown,LINE,LINE/Unknown
R2_LINE_retrotransposon	SO:0002269	R2_LINE_retrotransposon,LINE/R2,LINE/RIR,nonLTR/RIR,RIR
Jockey_LINE_retrotransposon	SO:0002271	Jockey_LINE_retrotransposon,LINE/Jockey,LINE/RIJ,nonLTR/RIJ,RIJ
L1_LINE_retrotransposon	SO:0002272	L1_LINE_retrotransposon,LINE/L1,LINE/RIL,nonLTR/RIL,RIL,LINE-1
I_LINE_retrotransposon	SO:0002273	I_LINE_retrotransposon,LINE/I,LINE/RII,nonLTR/RII
RTE_LINE_retrotransposon	SO:0002270	RTE_LINE_retrotransposon,LINE/RTE,LINE/RIT,nonLTR/RIT,RIT
SINE_element	SO:0000206	SINE_element,SINE/unknown,SINE,SINE/Unknown
tRNA_SINE_retrotransposon	SO:0002274	tRNA_SINE_retrotransposon,SINE/tRNA,SINE/RST,nonLTR/RST,RST,tRNA
5S_SINE_retrotransposon	SO:0002276	5S_SINE_retrotransposon,SINE/5S,SINE/RSS,nonLTR/RSS,RSS
7SL_SINE_retrotransposon	SO:0002275	7SL_SINE_retrotransposon,SINE/7SL,SINE/RSL,nonLTR/RSL,RSL
YR_retrotransposon	SO:0002286	YR_retrotransposon,YR/unknown,YR/Unknown
Ngaro_YR_retrotransposon	SO:0002288	Ngaro_YR_retrotransposon,YR/Ngaro,YR/RYN,Ngaro,RYN
DIRS_YR_retrotransposon	SO:0002287	DIRS_YR_retrotransposonYR/DIRS,YR/RYD,DIRS,RYD
Viper_YR_retrotransposon	SO:0002289	Viper_YR_retrotransposon,YR/Viper,YR/RYV,Viper,RYV
Penelope_retrotransposon	SO:0002290	Penelope_retrotransposon,Penelope,nonLTR/RPP,RPP

#parts
terminal_inverted_repeat	SO:0000481	terminal_inverted_repeat,TIR
target_site_duplication	SO:0000434	target_site_duplication,TSD
primer_binding_site	SO:0005850	primer_binding_site,PBS
long_terminal_repeat	SO:0000286	long_terminal_repeat,LTR
U_box	SO:0001788	U_box
RR_tract	SO:0000435	poly_purine_tract,RR_tract

