MD13G1232500.v1.1

tRNA pseudouridine synthase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr13
OG0006106
Physical Location & Seq
Forward (+)
23154493 .. 23159961
5469 bp
Loading structure...
UTR
Exon/CDS
Intron
MD13G1232500.v1.1.491

Sequence Viewer

Length: 1233 bp
ATGGAGAAGAAGGTTTTGGTTCACTACAACCACACCGATCCCTGCGCATTTGCACGCTGGACTACCAAAGAAAGCTTCCAGTTCATGGCCGCCCGGCCATGGCAACAGGTCATCGATTTTTACTCCGACGTGGTCACGGGCCGGAAGCCCCTGTCCGCCTTGTTGGGCAATGCTTGTTTGACTAGGAGTAATTTATGCAATAGGTTGGAGAGTGTTCCGCTGTCTCAAGATAAGGGTGGGAGGTGGGCTCGACTGACATTCAAGATTGTTGTTTCGTACCATGGCGGTTCGTTTGATGGGTGGCAGAGGCAGCCGGGACTCAATACTGTTCAAAGTTTGGTGGAAAAATCTCTGGGGAAATTTGTTGATGAGAGGAAAGCCAAGCAGCTGAGAGATAAAGGTTTACCATTAGAAGCGGCTGCTGTTGTTGCTGGGCGCACTGACAAAGGAGTGACTGCCCTTCATCAAGTTTGTTCTTTTTATACTTGGAATAAGGATGTTAAATCTCAAGATATTACAAATGCCATTAATAGTGCAGTACCAGGAAAACTCAGGGTTGTATCGGTTACGGAGGTATCACGGACCTTCCATCCAAATTTTACTGCCAAATGGAGACGCTATGTATATATATTTCCATTTAATGATGAAGAGGACATGGAGCAAAGTAATCAGAGTGGAGAGAATGCTCAAAACTTTAAGAGTACACAAAATCATCATGAGAATGAAAATGGGTGTTATCAATGCAGTGAGACAAATGCTGGAAATTTAATTATCAATGATAATGAAGACATTGGAATCGAGAAGAAACCTTGGAAATTCAGCGTAAGCAGGGTGAACCAACTTTTACAGAAACTAGAAGGAAAGTTATTATCATATAAGATGTTTGCACGTGATACCAAACCATCCAGAAATGTGGGTCCTCCAACAGAGTGTTTTGTCTTCCATGCTCGAGCTAAAGAATCCAAATTACCATGTTTAGAGCATGAAAGAGGAAGCAGGGTGATGTGTATTGAACTGGTTGCTAATCGATTCTTACGGAGGATGGTTCGGGTTCTTGTGGCAACTGCAATAAGGGAAGCAGCTGCAGGTGCAGATGAGGATGCATTGCTAAAGCTGATGGATGCTACATGCAGACGCGCCACTGCTCCACCGGCACCCCCTGATGGTTTATGTCTTGTTGATGTGGGTTATGAAGAATTTAATCCTCAAGATTGCCTTATCTCGAAGGAGTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
PseudoU_synth_1

Protein Analysis

411

Amino Acids

46.25

Weight (kDa)

8.82

Isoelectric Point (pI)

40.33

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PseudoU_synth_1 PF01416 332 - 398 3.2e-08 tRNA pseudouridine synthase
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AarI CACCTGC 1 cut(s) 1076
Acc16I TGCGCA 1 cut(s) 46
Acc36I ACCTGC 1 cut(s) 1076
AccB1I GGYRCC 1 cut(s) 1153
AccB7I CCANNNNNTGG 1 cut(s) 85
AccII CGCG 1 cut(s) 1137
AciI CCGC 5 cut(s) 90, 156, 218, 285, 416
AclWI GGATC 1 cut(s) 32
AcoI YGGCCR 2 cut(s) 87, 95
AcsI RAATTY 5 cut(s) 359, 595, 763, 815, 1196
AcvI CACGTG 1 cut(s) 890
AfaI GTAC 3 cut(s) 278, 540, 703
AfiI CCNNNNNNNGG 3 cut(s) 85, 99, 1163
AgsI TTSAA 3 cut(s) 262, 332, 1013
AjiI CACGTC 1 cut(s) 130
AjnI CCWGG 1 cut(s) 541
AjuI GAANNNNNNNTTGG 3 cut(s) 31, 59, 91
AluBI AGCT 5 cut(s) 75, 388, 953, 1082, 1114
AluI AGCT 5 cut(s) 75, 388, 953, 1082, 1114
Alw26I GTCTC 3 cut(s) 228, 607, 743
AlwI GGATC 1 cut(s) 32
Ama87I CYCGRG 1 cut(s) 948
AoxI GGCC 3 cut(s) 87, 95, 139
ApeKI GCWGC 5 cut(s) 310, 385, 419, 1079, 1082
ApoI RAATTY 5 cut(s) 359, 595, 763, 815, 1196
AseI ATTAAT 1 cut(s) 528
AspLEI GCGC 3 cut(s) 47, 438, 1139
AspS9I GGNCC 3 cut(s) 139, 582, 917
AsuC2I CCSGG 2 cut(s) 94, 315
AsuHPI GGTGA 2 cut(s) 844, 1012
AvaI CYCGRG 1 cut(s) 948
AvaII GGWCC 2 cut(s) 582, 917
BaeI ACNNNNGTAYC 2 cut(s) 558, 591
BanI GGYRCC 1 cut(s) 1153
BanII GRGCYC 1 cut(s) 250
BbrPI CACGTG 1 cut(s) 890
BbsI GAAGAC 2 cut(s) 792, 931
BbvI GCAGC 5 cut(s) 322, 397, 406, 1069, 1091
BccI CCATC 6 cut(s) 290, 597, 910, 1036, 1111, 1157
BciT130I CCWGG 1 cut(s) 543
BcnI CCSGG 2 cut(s) 94, 315
BcoDI GTCTC 3 cut(s) 228, 607, 743
BfaI CTAG 2 cut(s) 183, 854
BfmI CTRYAG 1 cut(s) 1083
BfuAI ACCTGC 1 cut(s) 1076
BisI GCNGC 7 cut(s) 90, 311, 386, 417, 420, 1080, 1083
BlsI GCNGC 7 cut(s) 91, 312, 387, 418, 421, 1081, 1084
Bme1390I CCNGG 3 cut(s) 94, 315, 543
Bme18I GGWCC 2 cut(s) 582, 917
BmeT110I CYCGRG 1 cut(s) 948
BmgBI CACGTC 1 cut(s) 130
BmgT120I GGNCC 3 cut(s) 139, 582, 917
BmiI GGNNCC 2 cut(s) 918, 1155
BmrFI CCNGG 3 cut(s) 94, 315, 543
BmsI GCATC 2 cut(s) 1090, 1111
BpiI GAAGAC 2 cut(s) 792, 931
BplI GAGNNNNNCTC 2 cut(s) 232, 264
BpuEI CTTGAG 3 cut(s) 210, 492, 1191
BpuMI CCSGG 2 cut(s) 94, 315
Bsa29I ATCGAT 2 cut(s) 114, 1027
BsaAI YACGTR 1 cut(s) 890
BsaJI CCNNGG 3 cut(s) 98, 280, 809
Bsc4I CCNNNNNNNGG 3 cut(s) 85, 99, 1163
Bse118I RCCGGY 1 cut(s) 1150
Bse1I ACTGG 2 cut(s) 79, 1020
Bse3DI GCAATG 2 cut(s) 175, 1103
BseBI CCWGG 1 cut(s) 543
BseCI ATCGAT 2 cut(s) 114, 1027
BseDI CCNNGG 3 cut(s) 98, 280, 809
BseGI GGATG 6 cut(s) 502, 589, 902, 1047, 1105, 1126
BseLI CCNNNNNNNGG 3 cut(s) 85, 99, 1163
BseMI GCAATG 2 cut(s) 175, 1103
BseMII CTCAG 2 cut(s) 380, 565
BseNI ACTGG 2 cut(s) 79, 1020
BseXI GCAGC 5 cut(s) 322, 397, 406, 1069, 1091
BseYI CCCAGC 1 cut(s) 431
BsgI GTGCAG 2 cut(s) 555, 1110
Bsh1236I CGCG 1 cut(s) 1137
BshFI GGCC 3 cut(s) 89, 97, 141
BshNI GGYRCC 1 cut(s) 1153
BshVI ATCGAT 2 cut(s) 114, 1027
BsiHKCI CYCGRG 1 cut(s) 948
BsiSI CCGG 4 cut(s) 94, 142, 314, 1151
BslFI GGGAC 1 cut(s) 330
BslI CCNNNNNNNGG 3 cut(s) 85, 99, 1163
BsmAI GTCTC 3 cut(s) 228, 607, 743
BsmBI CGTCTC 1 cut(s) 607
BsmFI GGGAC 1 cut(s) 330
BsmI GAATGC 1 cut(s) 688
BsnI GGCC 3 cut(s) 89, 97, 141
BsoBI CYCGRG 1 cut(s) 948
Bsp1286I GDGCHC 1 cut(s) 250
Bsp143I GATC 1 cut(s) 37
Bsp19I CCATGG 2 cut(s) 98, 280
BspACI CCGC 5 cut(s) 90, 156, 218, 285, 416
BspANI GGCC 3 cut(s) 89, 97, 141
BspCNI CTCAG 2 cut(s) 381, 564
BspDI ATCGAT 2 cut(s) 114, 1027
BspFNI CGCG 1 cut(s) 1137
BspHI TCATGA 1 cut(s) 715
BspLI GGNNCC 2 cut(s) 918, 1155
BspMAI CTGCAG 1 cut(s) 1087
BspMI ACCTGC 1 cut(s) 1076
BspPI GGATC 1 cut(s) 32
BspT107I GGYRCC 1 cut(s) 1153
BsrDI GCAATG 2 cut(s) 175, 1103
BsrFI RCCGGY 1 cut(s) 1150
BsrI ACTGG 2 cut(s) 79, 1020
BssAI RCCGGY 1 cut(s) 1150
BssECI CCNNGG 3 cut(s) 98, 280, 809
BssMI GATC 1 cut(s) 37
BssT1I CCWWGG 3 cut(s) 98, 280, 809
Bst2UI CCWGG 1 cut(s) 543
Bst4CI ACNGT 1 cut(s) 328
Bst6I CTCTTC 1 cut(s) 642
BstBAI YACGTR 1 cut(s) 890
BstC8I GCNNGC 1 cut(s) 55
BstDEI CTNAG 2 cut(s) 389, 551
BstDSI CCRYGG 2 cut(s) 98, 280
BstF5I GGATG 6 cut(s) 502, 589, 902, 1047, 1105, 1126
BstFNI CGCG 1 cut(s) 1137
BstHHI GCGC 3 cut(s) 47, 438, 1139
BstKTI GATC 1 cut(s) 40
BstMAI GTCTC 3 cut(s) 228, 607, 743
BstMBI GATC 1 cut(s) 37
BstMWI GCNNNNNNNGC 4 cut(s) 310, 428, 1088, 1151
BstNI CCWGG 1 cut(s) 543
BstNSI RCATGY 1 cut(s) 1131
BstSCI CCNGG 3 cut(s) 92, 313, 541
BstSFI CTRYAG 1 cut(s) 1083
BstUI CGCG 1 cut(s) 1137
BstV1I GCAGC 5 cut(s) 322, 397, 406, 1069, 1091
BstV2I GAAGAC 2 cut(s) 792, 931
BstXI CCANNNNNNTGG 1 cut(s) 913
Bsu15I ATCGAT 2 cut(s) 114, 1027
BsuRI GGCC 3 cut(s) 89, 97, 141
BsuTUI ATCGAT 2 cut(s) 114, 1027
BtgI CCRYGG 2 cut(s) 98, 280
BtrI CACGTC 1 cut(s) 130
BtsCI GGATG 6 cut(s) 502, 589, 902, 1047, 1105, 1126
BtsI GCAGTG 2 cut(s) 751, 1140
BtsIMutI CAGTG 3 cut(s) 438, 751, 1140
BveI ACCTGC 1 cut(s) 1076
Cac8I GCNNGC 1 cut(s) 55
CciI TCATGA 1 cut(s) 715
CfoI GCGC 3 cut(s) 47, 438, 1139
Cfr10I RCCGGY 1 cut(s) 1150
Cfr13I GGNCC 3 cut(s) 139, 582, 917
ClaI ATCGAT 2 cut(s) 114, 1027
CseI GACGC 2 cut(s) 624, 1143
Csp6I GTAC 3 cut(s) 277, 539, 702
CviAII CATG 9 cut(s) 85, 99, 281, 655, 716, 944, 972, 983, 1128
CviQI GTAC 3 cut(s) 277, 539, 702
DdeI CTNAG 2 cut(s) 389, 551
DpnI GATC 1 cut(s) 39
DpnII GATC 1 cut(s) 37
EaeI YGGCCR 2 cut(s) 87, 95
Eam1104I CTCTTC 1 cut(s) 642
EarI CTCTTC 1 cut(s) 642
EciI GGCGGA 1 cut(s) 145
Eco130I CCWWGG 3 cut(s) 98, 280, 809
Eco24I GRGCYC 1 cut(s) 250
Eco47I GGWCC 2 cut(s) 582, 917
Eco72I CACGTG 1 cut(s) 890
Eco88I CYCGRG 1 cut(s) 948
EcoO109I RGGNCCY 1 cut(s) 917
EcoRII CCWGG 1 cut(s) 541
EcoT14I CCWWGG 3 cut(s) 98, 280, 809
EcoT22I ATGCAT 1 cut(s) 1105
EcoT38I GRGCYC 1 cut(s) 250
ErhI CCWWGG 3 cut(s) 98, 280, 809
Esp3I CGTCTC 1 cut(s) 607
FaeI CATG 9 cut(s) 88, 102, 284, 658, 719, 947, 975, 986, 1131
FalI AAGNNNNNCTT 2 cut(s) 1200, 1232
FaqI GGGAC 1 cut(s) 330
FatI CATG 9 cut(s) 84, 98, 280, 654, 715, 943, 971, 982, 1127
Fnu4HI GCNGC 7 cut(s) 90, 311, 386, 417, 420, 1080, 1083
FokI GGATG 6 cut(s) 509, 576, 889, 1054, 1112, 1133
FriOI GRGCYC 1 cut(s) 250
Fsp4HI GCNGC 7 cut(s) 90, 311, 386, 417, 420, 1080, 1083
FspBI CTAG 2 cut(s) 183, 854
FspI TGCGCA 1 cut(s) 46
GlaI GCGC 3 cut(s) 46, 437, 1138
GluI GCNGC 7 cut(s) 90, 311, 386, 417, 420, 1080, 1083
GsaI CCCAGC 1 cut(s) 435
HaeIII GGCC 3 cut(s) 89, 97, 141
HapII CCGG 4 cut(s) 94, 142, 314, 1151
HgaI GACGC 2 cut(s) 624, 1143
HhaI GCGC 3 cut(s) 47, 438, 1139
Hin1II CATG 9 cut(s) 88, 102, 284, 658, 719, 947, 975, 986, 1131
Hin6I GCGC 3 cut(s) 45, 436, 1137
HinP1I GCGC 3 cut(s) 45, 436, 1137
HindIII AAGCTT 1 cut(s) 73
HinfI GANTC 4 cut(s) 318, 795, 959, 1029
HpaII CCGG 4 cut(s) 94, 142, 314, 1151
HphI GGTGA 2 cut(s) 844, 1012
Hpy166II GTNNAC 4 cut(s) 22, 404, 704, 835
Hpy188I TCNGA 2 cut(s) 127, 672
Hpy188III TCNNGA 8 cut(s) 227, 262, 509, 716, 799, 906, 1208, 1222
Hpy8I GTNNAC 4 cut(s) 22, 404, 704, 835
Hpy99I CGWCG 1 cut(s) 131
HpyAV CCTTC 5 cut(s) 4, 470, 595, 851, 1219
HpyCH4III ACNGT 1 cut(s) 328
HpyCH4IV ACGT 2 cut(s) 129, 889
HpyF10VI GCNNNNNNNGC 4 cut(s) 310, 428, 1088, 1151
HpyF3I CTNAG 2 cut(s) 389, 551
HpySE526I ACGT 2 cut(s) 129, 889
Hsp92II CATG 9 cut(s) 88, 102, 284, 658, 719, 947, 975, 986, 1131
HspAI GCGC 3 cut(s) 45, 436, 1137
Kzo9I GATC 1 cut(s) 37
LmnI GCTCC 2 cut(s) 658, 1150
Lsp1109I GCAGC 5 cut(s) 322, 397, 406, 1069, 1091
LweI GCATC 2 cut(s) 1090, 1111
MaeI CTAG 2 cut(s) 183, 854
MaeII ACGT 2 cut(s) 129, 889
MaeIII GTNAC 3 cut(s) 133, 451, 565
MalI GATC 1 cut(s) 39
MboI GATC 1 cut(s) 37
MboII GAAGA 6 cut(s) 19, 659, 797, 814, 931, 1205
MhlI GDGCHC 1 cut(s) 250
MluCI AATT 8 cut(s) 190, 359, 595, 763, 768, 815, 965, 1196
MlyI GAGTC 1 cut(s) 312
MmeI TCCRAC 3 cut(s) 150, 186, 947
Mph1103I ATGCAT 1 cut(s) 1105
MseI TTAA 6 cut(s) 501, 528, 639, 696, 767, 1200
MslI CAYNNNNRTG 1 cut(s) 720
MspA1I CMGCKG 3 cut(s) 220, 388, 1082
MspI CCGG 4 cut(s) 94, 142, 314, 1151
MspR9I CCNGG 3 cut(s) 94, 315, 543
Mva1269I GAATGC 1 cut(s) 688
MvaI CCWGG 1 cut(s) 543
MvnI CGCG 1 cut(s) 1137
MwoI GCNNNNNNNGC 4 cut(s) 310, 428, 1088, 1151
NciI CCSGG 2 cut(s) 94, 315
NcoI CCATGG 2 cut(s) 98, 280
NdeII GATC 1 cut(s) 37
NlaIII CATG 9 cut(s) 88, 102, 284, 658, 719, 947, 975, 986, 1131
NlaIV GGNNCC 2 cut(s) 918, 1155
NmuCI GTSAC 2 cut(s) 133, 451
NsbI TGCGCA 1 cut(s) 46
NsiI ATGCAT 1 cut(s) 1105
NspI RCATGY 1 cut(s) 1131
PaeR7I CTCGAG 1 cut(s) 948
PagI TCATGA 1 cut(s) 715
PaqCI CACCTGC 1 cut(s) 1076
PctI GAATGC 1 cut(s) 688
PfeI GAWTC 3 cut(s) 795, 959, 1029
PflFI GACNNNGTC 1 cut(s) 131
PflMI CCANNNNNTGG 1 cut(s) 85
PkrI GCNGC 7 cut(s) 91, 312, 387, 418, 421, 1081, 1084
PleI GAGTC 1 cut(s) 312
PmaCI CACGTG 1 cut(s) 890
PmlI CACGTG 1 cut(s) 890
PpsI GAGTC 1 cut(s) 312
Ppu21I YACGTR 1 cut(s) 890
PpuMI RGGWCCY 1 cut(s) 917
PshBI ATTAAT 1 cut(s) 528
Psp5II RGGWCCY 1 cut(s) 917
Psp6I CCWGG 1 cut(s) 541
PspCI CACGTG 1 cut(s) 890
PspFI CCCAGC 1 cut(s) 431
PspGI CCWGG 1 cut(s) 541
PspN4I GGNNCC 2 cut(s) 918, 1155
PspPI GGNCC 3 cut(s) 139, 582, 917
PspPPI RGGWCCY 1 cut(s) 917
PspXI VCTCGAGB 1 cut(s) 948
PstI CTGCAG 1 cut(s) 1087
PsyI GACNNNGTC 1 cut(s) 131
PvuII CAGCTG 2 cut(s) 388, 1082
RsaI GTAC 3 cut(s) 278, 540, 703
RsaNI GTAC 3 cut(s) 277, 539, 702
RseI CAYNNNNRTG 1 cut(s) 720
SaqAI TTAA 6 cut(s) 501, 528, 639, 696, 767, 1200
SatI GCNGC 7 cut(s) 90, 311, 386, 417, 420, 1080, 1083
Sau3AI GATC 1 cut(s) 37
Sau96I GGNCC 3 cut(s) 139, 582, 917
SchI GAGTC 1 cut(s) 312
ScrFI CCNGG 3 cut(s) 94, 315, 543
SduI GDGCHC 1 cut(s) 250
SfaNI GCATC 2 cut(s) 1090, 1111
SfcI CTRYAG 1 cut(s) 1083
Sfr274I CTCGAG 1 cut(s) 948
SinI GGWCC 2 cut(s) 582, 917
SlaI CTCGAG 1 cut(s) 948
SmiMI CAYNNNNRTG 1 cut(s) 720
SmlI CTYRAG 4 cut(s) 225, 507, 948, 1206
SmoI CTYRAG 4 cut(s) 225, 507, 948, 1206
Sse9I AATT 8 cut(s) 190, 359, 595, 763, 768, 815, 965, 1196
SsiI CCGC 5 cut(s) 90, 156, 218, 285, 416
SspMI CTAG 2 cut(s) 183, 854
StyD4I CCNGG 3 cut(s) 92, 313, 541
StyI CCWWGG 3 cut(s) 98, 280, 809
TaaI ACNGT 1 cut(s) 328
TaiI ACGT 2 cut(s) 132, 892
TaqI TCGA 6 cut(s) 114, 250, 798, 949, 1027, 1223
TasI AATT 8 cut(s) 190, 359, 595, 763, 768, 815, 965, 1196
TatI WGTACW 1 cut(s) 701
TauI GCSGC 2 cut(s) 92, 419
TfiI GAWTC 3 cut(s) 795, 959, 1029
Tru1I TTAA 6 cut(s) 501, 528, 639, 696, 767, 1200
Tru9I TTAA 6 cut(s) 501, 528, 639, 696, 767, 1200
TscAI CASTG 3 cut(s) 445, 751, 1147
TseFI GTSAC 2 cut(s) 133, 451
TseI GCWGC 5 cut(s) 310, 385, 419, 1079, 1082
Tsp45I GTSAC 2 cut(s) 133, 451
TspDTI ATGAA 7 cut(s) 73, 452, 660, 738, 798, 999, 1206
TspGWI ACGGA 3 cut(s) 584, 595, 1051
TspRI CASTG 3 cut(s) 445, 751, 1147
Tth111I GACNNNGTC 1 cut(s) 131
Van91I CCANNNNNTGG 1 cut(s) 85
VpaK11BI GGWCC 2 cut(s) 582, 917
VspI ATTAAT 1 cut(s) 528
XapI RAATTY 5 cut(s) 359, 595, 763, 815, 1196
XceI RCATGY 1 cut(s) 1131
XhoI CTCGAG 1 cut(s) 948
XspI CTAG 2 cut(s) 183, 854
Zsp2I ATGCAT 1 cut(s) 1105
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.