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TE_Sequence_Ontology.txt
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TE_Sequence_Ontology.txt
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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
############################################################
#######################
####### Warning #######
#######################
# 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.
#######################
## Enhancement notes ##
#######################
# 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
#######################
####### Contents ######
#######################
#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
retrotransposon SO:0000180 Class_I,RNA_transposon,retrotransposon
DNA_transposon SO:0000182 Class_II,DNA_transposon,DNA/unknown,TIR/PiggyBac,TIR/Sola2
#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
MITE SO:0000338 MITE,TIR/MITE,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
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
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
#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
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
Gypsy_LTR_retrotransposon SO:0002265 Gypsy_LTR_retrotransposon,LTR/Gypsy,LTR/RLG,RLG,Gypsy,Ty3,LTR/CRM
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
LINE_element SO:0000194 LINE_element,LINE/unknown,LINE
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
tRNA_SINE_retrotransposon SO:0002274 tRNA_SINE_retrotransposon,SINE/tRNA,SINE/RST,nonLTR/RST,RST
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
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