-
Notifications
You must be signed in to change notification settings - Fork 73
/
TE_Sequence_Ontology.txt
145 lines (131 loc) · 13.2 KB
/
TE_Sequence_Ontology.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
############################################################
#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 ([email protected]) 07/02/2020
#Updates:
# 12/21/2023
# 05/03/2023
# 04/21/2023
############################################################
#######################
####### Warning #######
#######################
# Everytime you add new SO entries to this file (new line), you also need to update the EDTA/bin/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
rRNA_5_external_transcribed_sequence SO:0002360 rRNA_5_external_transcribed_sequence,rDNA/5_ETS
rRNA_3_external_transcribed_sequence SO:0002360 rRNA_3_external_transcribed_sequence,rDNA/3_ETS
rRNA_internal_transcribed_spacer1 SO:0002360 rRNA_internal_transcribed_spacer1,rDNA/ITS1,rRNA/ITS1
rRNA_internal_transcribed_spacer2 SO:0002360 rRNA_internal_transcribed_spacer2,rDNA/ITS2,rRNA/ITS2
Sola_TIR_transposon SO:0000182 TIR/Sola2,Sola_TIR_transposon,TIR/Sola3,DNA/Sola,DNA/Sola1,DNA/Sola2,DNA/Sola3,DNA/Sola_1,DNA/Sola_2,DNA/Sola-1,DNA/Sola-2,DNA/Sola-3
PILE_TIR_transposon SO:0000182 PILE_TIR_transposon,DNAauto/PILE,DNAnona/PILE,DNA/PILE,MITE/PILE,TIR/PILE
POLE_TIR_transposon SO:0000182 POLE_TIR_transposon,DNAauto/POLE,DNAnona/POLE,DNA/POLE,MITE/POLE,TIR/POLE
Ginger_TIR_transposon SO:0000182 Ginger_TIR_transposon,TIR/Ginger,TIR/Ginger1,DNA/Ginger,DNA/Ginger1
Kolobok_TIR_transposon SO:0000182 Kolobok_TIR_transposon,TIR/Kolobok,TIR/tvBac,DNA/Kolobok,DNA/Kolobok-T2,DNA/Kolobok_T2,DNA/Kolobok-H,DNA/Kolobok_H,DNA/Kolobok-Hydra,DNA/Kolobok_Hydra,DNA/Kolobok
Dada_TIR_transposon SO:0000182 Dada_TIR_transposon,DNA/Dada
IS3EU_TIR_transposon SO:0000182 IS3EU_TIR_transposon,DNA/IS3EU
Zator_TIR_transposon SO:0000182 Zator_TIR_transposon,DNA/Zator
Zisupton_TIR_transposon SO:0000182 Zisupton_TIR_transposon,DNA/Zisupton,DNA/Zisupton-hAT-hybrid,DNA/Zisupton-hAT_hybrid
Alu_SINE_retrotransposon SO:0000206 Alu_SINE_retrotransposon,SINE/Alu
B2_SINE_retrotransposon SO:0000206 B2_SINE_retrotransposon,SINE/B2
B4_SINE_retrotransposon SO:0000206 B4_SINE_retrotransposon,SINE/B4
ID_SINE_retrotransposon SO:0000206 ID_SINE_retrotransposon,SINE/ID
MIR_SINE_retrotransposon SO:0000206 MIR_SINE_retrotransposon,SINE/MIR
CR1_LINE_retrotransposon SO:0000194 CR1_LINE_retrotransposon,LINE/CR1,LINE/CR1?,LINE/CR1-Zenon,LINE/CR1_Zenon
L2_LINE_retrotransposon SO:0000194 L2_LINE_retrotransposon,LINE/L2,LINE/L2A,LINE/L2B,LINE/L2-Hydra,LINE/L2_Hydra
R1_LINE_retrotransposon SO:0000194 R1_LINE_retrotransposon,LINE/R1,LINE/R1_LOA,LINE/R1-LOA,LINE/LOA
R4_LINE_retrotransposon SO:0000194 R4_LINE_retrotransposon,LINE/R4,LINE/Dong-R4,LINE/Dong_R4
Crack_LINE_retrotransposon SO:0000194 Crack_LINE_retrotransposon,LINE/Crack
Vingi_LINE_retrotransposon SO:0000194 Vingi_LINE_retrotransposon,LINE/Vingi
Tx1_LINE_retrotransposon SO:0000194 Tx1_LINE_retrotransposon,LINE/Tx1
Tad1_LINE_retrotransposon SO:0000194 Tad1_LINE_retrotransposon,LINE/Tad1,LINE/Tad1?
Rex_LINE_retrotransposon SO:0000194 Rex_LINE_retrotransposon,LINE/Rex-Babar,LINE/Rex,LINE/Rex_Babar
Proto2_LINE_retrotransposon SO:0000194 Proto2_LINE_retrotransposon,LINE/Proto2
ERTBV_retrotransposon SO:0000189 ERTBV_retrotransposon,DNAvirus/ERTBV-A,Evirus/ERTBV-A,DNAvirus/ERTBV-B,Evirus/ERTBV-B,DNAvirus/ERTBV-C,Evirus/ERTBV-C,Evirus/ERTBV,Evirus/Unknown,Evirus/unknown
pararetrovirus SO:0000189 pararetrovirus,pararetrovirus/NA,pararetrovirus/Unknown,pararetrovirus/unknown,LTR/Caulimovirus
#######################
####### 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,Satellite/Y-chromosome,Satellite,Satellite/Y_chromosome,SAT,MSAT
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,Simple_repeat/NA
chloroplast_DNA SO:0001033 chloroplast_DNA,chloroplast/chloroplast
mitochondrial_DNA SO:0001032 mitochondrial_DNA,mitochondrion/mitochondrion
## higher order
repeat_region SO:0000657 repeat_region
repeat_fragment SO:0001050 repeat_fragment,Unknown,unknown,unknown/unknown,NA/NA,Unknown/NA,Unknown/unknown,Unspecified,repeat/unknown,repeat/Unknown,Unknown/Unknown,unknown/NA
retrotransposon SO:0000180 Class_I,RNA_transposon,retrotransposon,Retroposon,Retroposon/L1_dep
DNA_transposon SO:0000182 Class_II,DNA_transposon,DNA/unknown,DNA/Unknown,DNA,DNA/NA
snRNA SO:0000274 snRNA,snRNA/NA
scRNA SO:0000013 scRNA
## rDNA and NOR
rRNA_gene SO:0002360 rRNA_gene,rDNA/45S,rRNA
rDNA_intergenic_spacer_element SO:0001860 rDNA_intergenic_spacer_element,rDNA/spacer,rDNA/IGS
cytosolic_2S_rRNA SO:0002337 cytosolic_2S_rRNA,rDNA/2s_rRNA,rDNA/2S,2S_rRNA,2s_rRNA,rDNA/2s
cytosolic_5S_rRNA SO:0000652 cytosolic_5S_rRNA,rDNA/5s_rRNA,rDNA/5S,5S_rRNA,5s_rRNA,rDNA/5s
cytosolic_5_8S_rRNA SO:0000375 cytosolic_5_8S_rRNA,rDNA/5.8s_rRNA,rDNA/5.8S_rRNA,5.8s_rRNA,5_8s_rRNA,5_8S_rRNA_gene,rDNA/5.8S,rDNA/5.8s,5.8S_rRNA,rDNA/5_8S,5_8S_rRNA
cytosolic_16S_rRNA SO:0001000 cytosolic_16S_rRNA,rDNA/16s_rRNA,rDNA/16S_rRNA,rDNA/16S,rDNA/16s,16S_rRNA,16s_rRNA
cytosolic_18S_rRNA SO:0000407 cytosolic_18S_rRNA,rDNA/18s_rRNA,rDNA/18S_rRNA,18s_rRNA,rDNA/18S,rDNA/18s,18S_rRNA
cytosolic_23S_rRNA SO:0001001 cytosolic_23S_rRNA,rDNA/23s_rRNA,rDNA/23S_rRNA,rDNA/23S,rDNA/23s,23S_rRNA,23s_rRNA
cytosolic_25S_rRNA SO:0001002 cytosolic_25S_rRNA,rDNA/25s_rRNA,rDNA/25S_rRNA,25S_rRNA,rDNA/25S,rDNA/25s,25s_rRNA
cytosolic_28S_rRNA SO:0000653 cytosolic_28S_rRNA,rDNA/28s_rRNA,rDNA/28S_rRNA,rDNA/28S,rDNA/28s,28S_rRNA,28s_rRNA
## TIR DNA transposons
terminal_inverted_repeat_element SO:0000208 terminal_inverted_repeat_element,TIR/unknown,DNA/DTX,DTX,DNAauto/unknown,DNAnona/unknown,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,DNA/CMC_Chapaev_3,DNA/CMC_EnSpm,DNA/CMC-Chapaever,DNA/CMC-Chapaev-3,DNA/CMC-EnSpmo,DNA/CMC-Miragen
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,DNA/hAT-Blackjack,DNA/hAT-Charlie,DNA/hAT-hAT5,DNA/hAT-hAT6,DNA/hAT-hobo,DNA/hAT-Tip100,DNA/hAT_Ac,DNA/hAT_Blackjack,DNA/hAT_Charlie,DNA/hAT_hAT5,DNA/hAT_hAT6,DNA/hAT_hobo,DNA/hAT_Pegasus,DNA/hAT_Tag1,DNA/hAT_Tip100,DNA/hAT-hATm,DNA/hAT-AcTigger,DNA/hAT_AcTigger,DNA/hAT-hAT1,DNA/hAT_hAT1,DNA/hAT-hATm-hAT-hybrid,DNA/hAT-hATm-hAT_hybrid,DNA/hAT-hATw,DNA/hAT_hATw,DNA/hAT-hATx,DNA/hAT_hATx,DNA/hAT-Pegasus,DNA/hAT-Restless,DNA/hAT_Restless,DNA/hAT-Tag11,DNA/hAT_Tag11,DNA/hAT-Tip100?,DNA/hAT_Tip100?,DNA/hAT-Tol2,DNA/hAT_Tol2
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,DNA/MULE-NOF,DNA/MULE_MuDR,DNA/MULE_NOF,DNA/MuLE-NOF?,DNA/MuLE_NOF?,DNA/MuLE-MuDR,DNA/MuLE_MuDR,DNA/MuLE-F,DNA/MuLE_F,DNA/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,DNA/PIF,DNA/PIF-ISL2EU,DNA/PIF_ISL2EU,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,DNA/TcMar,DNA/TcMar-Fot1,DNA/TcMar-ISRm11,DNA/TcMar-Tc1,DNA/TcMar-Tigger,DNA/TcMar_Fot1,DNA/TcMar_ISRm11,DNA/TcMar_Mariner,DNA/TcMar_Tc1,DNA/TcMar_Tc2,DNA/TcMar_Tigger,DNA/TcMar_Pogo,DNA/Tc1_Mariner,DNA/TcMar_Stowaway,DNA/TcMareSL,DNA/TcMar-Ant1,DNA/TcMar_Ant1,DNA/TcMar-Gizmo,DNA/TcMar_Gizmo,DNA/TcMar-IS630,DNA/TcMar_IS630,DNA/TcMar-IS885,DNA/TcMar_IS885,DNA/TcMar-m44,DNA/TcMar_m44,DNA/TcMar-Mogwai,DNA/TcMar_Mogwai,DNA/TcMar-Sagan,DNA/TcMar_Sagan,DNA/TcMar-Tc2,DNA/TcMar-Tc4,DNA/TcMar_Tc4,Mariner/Tc1
P_TIR_transposon SO:0001535 P_TIR_transposon,P-element,P_element,DNA/DTP,TIR/P,DNA/P
piggyBac_TIR_transposon SO:0002283 piggyBac_TIR_transposon,PiggyBac,DNA/DTB,MITE/DTB,TIR/PiggyBac,TIR/piggyBac,piggyBac,DNA/PiggyBac,DNA/PiggyBacen,DNA/piggyBac
polinton SO:0001170 polinton,maverick,Maverick,DNA/Maverick,TIR/Maverick,Polinton
Transib_TIR_transposon SO:0002282 Transib_TIR_transposon,transib,DNA/DTR,MITE/DTR,DNA/CMC-Transib,DNA/CMC-Transibway,DNA/Transib
Merlin_TIR_transposon SO:0002281 Merlin_TIR_transposon,Merlin,DNA/DTE,MITE/DTE,TIR/Merlin,DNA/Merlin,DNA/Merlin1
terminal_inverted_repeat SO:0000481 terminal_inverted_repeat,TIR
## nonTIR DNA transposons
Crypton_YR_transposon SO:0002277 Crypton_YR_transposon,Crypton,DNA/DYC,DYC,DNA/Crypton,DNA/Crypton-A,DNA/Crypton-H,DNA/Crypton-V,DNA/Crypton_A,DNA/Crypton_H,DNA/Crypton_V,DNA/CryptonA,DNA/CryptonF,DNA/CryptonI,DNA/CryptonS,DNA/CryptonV
helitron SO:0000544 helitron,DNAauto/Helitron,DNAnona/Helitron,DNA/Helitron,Helitron,RC/Helitron,Unknown/Helitron-2,nonDNA/Helitron
## LTR retrotransposons
LTR_retrotransposon SO:0000186 LTR_retrotransposon,LTR/unknown,LTR/Solo,LTR/Unknown,LTR/solo,LTR,LTR/NA
Retrovirus_LTR_retrotransposon SO:0002267 Retrovirus_LTR_retrotransposon,LTR/retrovirus,retrovirus,LTR/RLR,RLR,LTR/Retrovirus
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,LTR/Copia?
Gypsy_LTR_retrotransposon SO:0002265 Gypsy_LTR_retrotransposon,LTR/Gypsy,LTR/RLG,RLG,Gypsy,Ty3,LTR/CRM,LTR/Ty3,LTR/Gypsy?,LTR/Gypsy-Cigr,LTR/Gypsy_Cigr,LTR/Gypsy-Troyka,LTR/Gypsy_Troyka
Bel_Pao_LTR_retrotransposon SO:0002266 Bel_Pao_LTR_retrotransposon,LTR/Bel-Pao,LTR/RLB,Bel-Pao,Bel/Pao,LTR/BEL,LTR/Pao,LTR/Bel_Pao
Endogenous_Retrovirus_LTR_retrotransposon SO:0002268 Endogenous_Retrovirus_LTR_retrotransposon,LTR/HERV,HERV,LTR/ERV,LTR/RLE,RLE,LTR/ERV1,LTR/ERV2,LTR/ERV3,LTR/ERV4,LTR/ERV-Foamy,LTR/ERVK,LTR/ERVL,LTR/ERV-MaLR,LTR/ERV_Foamy,LTR/ERVL_MaLR,LTR/ERVL-MaLR,Endogenous_Retrovirus,LTR/Foamy,LTR/ERV-Lenti,LTR/ERV_Lenti,LTR/Lenti
RR_tract SO:0000435 poly_purine_tract,RR_tract
primer_binding_site SO:0005850 primer_binding_site,PBS
long_terminal_repeat SO:0000286 long_terminal_repeat
## nonLTR retrotransposons
non_LTR_retrotransposon SO:0000189 non_LTR_retrotransposon,non_LTR,nonLTR/unknown,nonLTR/Unknown
LINE_element SO:0000194 LINE_element,LINE/unknown,LINE,LINE/Unknown,LINE/NA
R2_LINE_retrotransposon SO:0002269 R2_LINE_retrotransposon,LINE/R2,LINE/RIR,nonLTR/RIR,RIR,LINE/R2-Hero,LINE/R2-NeSL,LINE/R2_Hero,LINE/R2_NeSL,LINE/R2-Dualen,LINE/R2_Dualen
Jockey_LINE_retrotransposon SO:0002271 Jockey_LINE_retrotransposon,LINE/Jockey,LINE/RIJ,nonLTR/RIJ,RIJ,LINE/I-Jockey
L1_LINE_retrotransposon SO:0002272 L1_LINE_retrotransposon,LINE/L1,LINE/RIL,nonLTR/RIL,RIL,LINE-1,LINE/L1-Tx1,LINE/L1_Tx1,LINE/L1?
I_LINE_retrotransposon SO:0002273 I_LINE_retrotransposon,LINE/I,LINE/RII,nonLTR/RII,LINE/I-Nimb,LINE/I_Nimb
RTE_LINE_retrotransposon SO:0002270 RTE_LINE_retrotransposon,LINE/RTE,LINE/RIT,nonLTR/RIT,RIT,LINE/RTEX,LINE/RTE-X,LINE/RTE-BovB,LINE/RTE_BovB,LINE/RTE_X,LINE/RTE-RTE,LINE/RTE_RTE
SINE_element SO:0000206 SINE_element,SINE/unknown,SINE,SINE/Unknown,SINE?,SINE?/NA,SINE/U,SINE/NA
tRNA_SINE_retrotransposon SO:0002274 tRNA_SINE_retrotransposon,SINE/tRNA,SINE/RST,nonLTR/RST,RST,tRNA,SINE2/tRNA,SINE/tRNA-Core-RTE,SINE/tRNA-V-CR1,tRNA,SINE/tRNA_CR1,SINE/tRNA_RTE,SINE/tRNA_V_RTE,SINE/tRNA-V-RTE,SINE/tRNA-CR1,SINE/tRNA_Core_RTE,SINE/tRNA_V_CR1,SINE/tRNA-RTE,tRNA/NA
5S_SINE_retrotransposon SO:0002276 5S_SINE_retrotransposon,SINE/5S,SINE/RSS,nonLTR/RSS,RSS,SINE3/5S,SINE/5S-Deu-L2,SINE/5S_Deu_L2
7SL_SINE_retrotransposon SO:0002275 7SL_SINE_retrotransposon,SINE/7SL,SINE/RSL,nonLTR/RSL,RSL,SINE1/7SL
YR_retrotransposon SO:0002286 YR_retrotransposon,YR/unknown,YR/Unknown
Ngaro_YR_retrotransposon SO:0002288 Ngaro_YR_retrotransposon,YR/Ngaro,YR/RYN,Ngaro,RYN,LTR/Ngaro
DIRS_YR_retrotransposon SO:0002287 DIRS_YR_retrotransposonYR/DIRS,YR/RYD,DIRS,RYD,LTR/DIRS,DIRS/NA,LTR/DIRS?
Viper_YR_retrotransposon SO:0002289 Viper_YR_retrotransposon,YR/Viper,YR/RYV,Viper,RYV
Penelope_retrotransposon SO:0002290 Penelope_retrotransposon,Penelope,nonLTR/RPP,RPP,nonLTR/Penelope,Penelope/NA,LINE/Penelope
## parts
target_site_duplication SO:0000434 target_site_duplication,TSD
U_box SO:0001788 U_box