MD08G1241400.v1.1

tRNA pseudouridine

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr08
Physical Location & Seq
Reverse (-)
30702689 .. 30706844
4156 bp
Loading structure...
UTR
Exon/CDS
Intron
MD08G1241400.v1.1.491

Sequence Viewer

Length: 1086 bp
ATGTCAGAAAATCTTAAGCACCCACTCGAACTAGATAGCATCAGTAGCTCCCAATTTCCCCAAAGGCCTCCAAAGGTCTCCAAAACCGCCGACGATCTCAGCGACGGCGATCAGGAATCACAGCAACCTCAACGGATGAGCCAACAGGCTCGAATCCAGCGGTATCTACTGGCAATCGAGTACATTGGTACTCGCTTTTCGGGCTCGCAGCAGCAGTCCAATTGCCGCACAGTTGTTGGAGTCCTTGAGGAGGCATTTCGTAAATTTATTGGCCAGCCGGTTTCAATTTTCTGTTCCAGTCGAACTGATGCAGGAGTTCATGCCTTGTCGAATGTTTGTCATGTAGATGTCAATCGCATAAGCAAAAGGAAGCCTGCTGAAGTGTTAGAACCCCATGAACCTTCAGTTGTCAAAAGAGCTGTGAATCATTTCTTACAGAAGAATGAAGGTGATGTAATGGTGATAGATGTTCAAAGTGTTCCAGCTGATTTTCATGCTCGATATAAAGCCCAAGAGCGCACGTATTTCTACCGTCTTCTGTTTGGACCAGAGCCTTTGCCAACCTTTGAAAAAGACCGCGCATGGCATGTACCCAACGAGCTGGATCTTTGTGCTATGCAGGAAGCATGCAAAGTTTTGGTTGGACATCATGATTTTAGTTCCTTTAGGGCAGCAGGTTGTCAGGCAAAATCGCCGATCAGAACGTTGGATGAACTTAATGTTTCTGAGGTAGTGTCAAGTCCTTATTTTCCATCAATAATGGAGAGGAAACAAAACAATTTAGTGGAGGAAGATCCTCATGCCCACGCTAACAAATCTGAGACTGGTACATCCTCTAGTTTCAATGGAGGACTAGGATTTGGCATGAGAAAAAAGCACCGTTGCTTTGTGGTAACCGCGCGAGCACGTTCTTTTCTGTACCACCAGGTTAGACTGCTTGTTGGTGTACTCAAATGCGTTGGCACCGGAGATTTAAGAATACCTGATGTTGAGAGGATCTTGAATGCAAAGACGGTGACTGCTGCTAGTCCCATGGCGCCTGCTTGTGGTCTGTACCTTGGACACGTGAAGTACGATTTGCCATGA
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

Protein Analysis

362

Amino Acids

40.38

Weight (kDa)

8.51

Isoelectric Point (pI)

51.15

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PseudoU_synth_1 PF01416 58 - 168 1.8e-08 tRNA pseudouridine synthase
PseudoU_synth_1 PF01416 209 - 359 1.8e-24 tRNA pseudouridine synthase
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Publication-ready

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 665
AccB1I GGYRCC 2 cut(s) 962, 1036
AccII CGCG 3 cut(s) 579, 899, 901
AciI CCGC 5 cut(s) 87, 160, 226, 577, 897
AclI AACGTT 1 cut(s) 704
AclWI GGATC 3 cut(s) 612, 788, 1004
AcoI YGGCCR 1 cut(s) 271
AcsI RAATTY 1 cut(s) 263
AcuI CTGAAG 2 cut(s) 387, 399
AcvI CACGTG 1 cut(s) 1066
AcyI GRCGYC 1 cut(s) 1037
AfaI GTAC 8 cut(s) 182, 190, 591, 829, 920, 948, 1055, 1073
AfiI CCNNNNNNNGG 2 cut(s) 250, 1046
AflII CTTAAG 1 cut(s) 14
AflIII ACRYGT 1 cut(s) 1063
AgsI TTSAA 5 cut(s) 285, 473, 569, 844, 1003
AjnI CCWGG 1 cut(s) 924
AluBI AGCT 4 cut(s) 48, 419, 485, 601
AluI AGCT 4 cut(s) 48, 419, 485, 601
Alw21I GWGCWC 1 cut(s) 907
Alw26I GTCTC 2 cut(s) 82, 815
AlwI GGATC 3 cut(s) 612, 788, 1004
AoxI GGCC 2 cut(s) 65, 271
ApeKI GCWGC 4 cut(s) 208, 211, 671, 1022
ApoI RAATTY 1 cut(s) 263
Asp700I GAANNNNTTC 1 cut(s) 428
AspLEI GCGC 4 cut(s) 519, 581, 901, 1039
AspS9I GGNCC 1 cut(s) 545
AsuHPI GGTGA 3 cut(s) 461, 472, 1027
AvaII GGWCC 1 cut(s) 545
BalI TGGCCA 1 cut(s) 273
BanI GGYRCC 2 cut(s) 962, 1036
BanII GRGCYC 1 cut(s) 206
BbrPI CACGTG 1 cut(s) 1066
BbsI GAAGAC 1 cut(s) 527
Bbv12I GWGCWC 1 cut(s) 907
BbvI GCAGC 4 cut(s) 220, 223, 683, 1009
BccI CCATC 1 cut(s) 760
BceAI ACGGC 1 cut(s) 121
BciT130I CCWGG 1 cut(s) 926
BcoDI GTCTC 2 cut(s) 82, 815
BfaI CTAG 4 cut(s) 32, 837, 854, 1026
BfoI RGCGCY 1 cut(s) 1040
BfrI CTTAAG 1 cut(s) 14
BfuAI ACCTGC 1 cut(s) 665
BisI GCNGC 5 cut(s) 209, 212, 226, 672, 1023
BlsI GCNGC 5 cut(s) 210, 213, 227, 673, 1024
Bme1390I CCNGG 1 cut(s) 926
Bme18I GGWCC 1 cut(s) 545
BmgT120I GGNCC 1 cut(s) 545
BmiI GGNNCC 2 cut(s) 964, 1038
BmrFI CCNGG 1 cut(s) 926
BmsI GCATC 2 cut(s) 48, 298
BpiI GAAGAC 1 cut(s) 527
BpuEI CTTGAG 1 cut(s) 266
BsaAI YACGTR 2 cut(s) 522, 1066
BsaBI GATNNNNATC 1 cut(s) 351
BsaHI GRCGYC 1 cut(s) 1037
BsaI GGTCTC 1 cut(s) 82
BsaJI CCNNGG 2 cut(s) 1032, 1057
BsaWI WCCGGW 1 cut(s) 965
Bsc4I CCNNNNNNNGG 2 cut(s) 250, 1046
Bse118I RCCGGY 1 cut(s) 277
Bse1I ACTGG 3 cut(s) 174, 297, 829
Bse8I GATNNNNATC 1 cut(s) 351
BseBI CCWGG 1 cut(s) 926
BseDI CCNNGG 2 cut(s) 1032, 1057
BseGI GGATG 3 cut(s) 141, 715, 830
BseJI GATNNNNATC 1 cut(s) 351
BseLI CCNNNNNNNGG 2 cut(s) 250, 1046
BseMII CTCAG 3 cut(s) 112, 717, 810
BseNI ACTGG 3 cut(s) 174, 297, 829
BseRI GAGGAG 1 cut(s) 263
BseXI GCAGC 4 cut(s) 220, 223, 683, 1009
Bsh1236I CGCG 3 cut(s) 579, 899, 901
BshFI GGCC 2 cut(s) 67, 273
BshNI GGYRCC 2 cut(s) 962, 1036
BsiHKAI GWGCWC 1 cut(s) 907
BsiSI CCGG 2 cut(s) 278, 966
BslFI GGGAC 1 cut(s) 1014
BslI CCNNNNNNNGG 2 cut(s) 250, 1046
BsmAI GTCTC 2 cut(s) 82, 815
BsmFI GGGAC 1 cut(s) 1014
BsmI GAATGC 1 cut(s) 1009
BsnI GGCC 2 cut(s) 67, 273
Bso31I GGTCTC 1 cut(s) 82
Bsp1286I GDGCHC 2 cut(s) 206, 907
Bsp143I GATC 6 cut(s) 94, 109, 604, 696, 793, 996
Bsp19I CCATGG 1 cut(s) 1032
BspACI CCGC 5 cut(s) 87, 160, 226, 577, 897
BspANI GGCC 2 cut(s) 67, 273
BspCNI CTCAG 3 cut(s) 111, 718, 811
BspFNI CGCG 3 cut(s) 579, 899, 901
BspHI TCATGA 1 cut(s) 649
BspLI GGNNCC 2 cut(s) 964, 1038
BspMI ACCTGC 1 cut(s) 665
BspPI GGATC 3 cut(s) 612, 788, 1004
BspT107I GGYRCC 2 cut(s) 962, 1036
BspTI CTTAAG 1 cut(s) 14
BspTNI GGTCTC 1 cut(s) 82
BsrFI RCCGGY 1 cut(s) 277
BsrI ACTGG 3 cut(s) 174, 297, 829
BssAI RCCGGY 1 cut(s) 277
BssECI CCNNGG 2 cut(s) 1032, 1057
BssMI GATC 6 cut(s) 94, 109, 604, 696, 793, 996
BssNI GRCGYC 1 cut(s) 1037
BssT1I CCWWGG 2 cut(s) 1032, 1057
Bst2UI CCWGG 1 cut(s) 926
Bst4CI ACNGT 4 cut(s) 232, 533, 881, 1015
BstACI GRCGYC 1 cut(s) 1037
BstAFI CTTAAG 1 cut(s) 14
BstBAI YACGTR 2 cut(s) 522, 1066
BstC8I GCNNGC 6 cut(s) 206, 275, 375, 628, 903, 1041
BstDEI CTNAG 3 cut(s) 98, 726, 819
BstDSI CCRYGG 1 cut(s) 1032
BstEII GGTNACC 1 cut(s) 892
BstENI CCTNNNNNAGG 1 cut(s) 248
BstF5I GGATG 3 cut(s) 141, 715, 830
BstFNI CGCG 3 cut(s) 579, 899, 901
BstH2I RGCGCY 1 cut(s) 1040
BstHHI GCGC 4 cut(s) 519, 581, 901, 1039
BstKTI GATC 6 cut(s) 97, 112, 607, 699, 796, 999
BstMAI GTCTC 2 cut(s) 82, 815
BstMBI GATC 6 cut(s) 94, 109, 604, 696, 793, 996
BstMWI GCNNNNNNNGC 2 cut(s) 45, 201
BstNI CCWGG 1 cut(s) 926
BstNSI RCATGY 2 cut(s) 590, 630
BstPI GGTNACC 1 cut(s) 892
BstSCI CCNGG 1 cut(s) 924
BstUI CGCG 3 cut(s) 579, 899, 901
BstV1I GCAGC 4 cut(s) 220, 223, 683, 1009
BstV2I GAAGAC 1 cut(s) 527
BstX2I RGATCY 3 cut(s) 604, 793, 996
BstXI CCANNNNNNTGG 1 cut(s) 601
BstYI RGATCY 3 cut(s) 604, 793, 996
BsuRI GGCC 2 cut(s) 67, 273
BtgI CCRYGG 1 cut(s) 1032
BtsCI GGATG 3 cut(s) 141, 715, 830
BveI ACCTGC 1 cut(s) 665
Cac8I GCNNGC 6 cut(s) 206, 275, 375, 628, 903, 1041
CciI TCATGA 1 cut(s) 649
CfoI GCGC 4 cut(s) 519, 581, 901, 1039
Cfr10I RCCGGY 1 cut(s) 277
Cfr13I GGNCC 1 cut(s) 545
CsiI ACCWGGT 1 cut(s) 924
Csp6I GTAC 8 cut(s) 181, 189, 590, 828, 919, 947, 1054, 1072
CviQI GTAC 8 cut(s) 181, 189, 590, 828, 919, 947, 1054, 1072
DdeI CTNAG 3 cut(s) 98, 726, 819
DinI GGCGCC 1 cut(s) 1038
DpnI GATC 6 cut(s) 96, 111, 606, 698, 795, 998
DpnII GATC 6 cut(s) 94, 109, 604, 696, 793, 996
EaeI YGGCCR 1 cut(s) 271
Eco130I CCWWGG 2 cut(s) 1032, 1057
Eco147I AGGCCT 1 cut(s) 67
Eco24I GRGCYC 1 cut(s) 206
Eco31I GGTCTC 1 cut(s) 82
Eco47I GGWCC 1 cut(s) 545
Eco57I CTGAAG 2 cut(s) 387, 399
Eco72I CACGTG 1 cut(s) 1066
Eco91I GGTNACC 1 cut(s) 892
EcoNI CCTNNNNNAGG 1 cut(s) 248
EcoO65I GGTNACC 1 cut(s) 892
EcoRII CCWGG 1 cut(s) 924
EcoT14I CCWWGG 2 cut(s) 1032, 1057
EcoT38I GRGCYC 1 cut(s) 206
EgeI GGCGCC 1 cut(s) 1038
EheI GGCGCC 1 cut(s) 1038
ErhI CCWWGG 2 cut(s) 1032, 1057
FaqI GGGAC 1 cut(s) 1014
Fnu4HI GCNGC 5 cut(s) 209, 212, 226, 672, 1023
FokI GGATG 3 cut(s) 148, 722, 817
FriOI GRGCYC 1 cut(s) 206
Fsp4HI GCNGC 5 cut(s) 209, 212, 226, 672, 1023
FspBI CTAG 4 cut(s) 32, 837, 854, 1026
GlaI GCGC 4 cut(s) 518, 580, 900, 1038
GluI GCNGC 5 cut(s) 209, 212, 226, 672, 1023
HaeII RGCGCY 1 cut(s) 1040
HaeIII GGCC 2 cut(s) 67, 273
HapII CCGG 2 cut(s) 278, 966
HhaI GCGC 4 cut(s) 519, 581, 901, 1039
Hin1I GRCGYC 1 cut(s) 1037
Hin6I GCGC 4 cut(s) 517, 579, 899, 1037
HinP1I GCGC 4 cut(s) 517, 579, 899, 1037
HinfI GANTC 4 cut(s) 116, 153, 240, 424
HpaII CCGG 2 cut(s) 278, 966
HphI GGTGA 3 cut(s) 461, 472, 1027
Hpy166II GTNNAC 1 cut(s) 947
Hpy188I TCNGA 4 cut(s) 7, 701, 727, 820
Hpy188III TCNNGA 3 cut(s) 113, 650, 1000
Hpy8I GTNNAC 1 cut(s) 947
Hpy99I CGWCG 2 cut(s) 95, 107
HpyAV CCTTC 2 cut(s) 411, 440
HpyCH4III ACNGT 4 cut(s) 232, 533, 881, 1015
HpyCH4IV ACGT 4 cut(s) 521, 704, 907, 1065
HpyCH4V TGCA 4 cut(s) 311, 619, 630, 1007
HpyF10VI GCNNNNNNNGC 2 cut(s) 45, 201
HpyF3I CTNAG 3 cut(s) 98, 726, 819
HpySE526I ACGT 4 cut(s) 521, 704, 907, 1065
Hsp92I GRCGYC 1 cut(s) 1037
HspAI GCGC 4 cut(s) 517, 579, 899, 1037
KasI GGCGCC 1 cut(s) 1036
Kzo9I GATC 6 cut(s) 94, 109, 604, 696, 793, 996
LmnI GCTCC 1 cut(s) 53
Lsp1109I GCAGC 4 cut(s) 220, 223, 683, 1009
LweI GCATC 2 cut(s) 48, 298
MabI ACCWGGT 1 cut(s) 924
MaeI CTAG 4 cut(s) 32, 837, 854, 1026
MaeII ACGT 4 cut(s) 521, 704, 907, 1065
MaeIII GTNAC 2 cut(s) 892, 1015
MalI GATC 6 cut(s) 96, 111, 606, 698, 795, 998
MboI GATC 6 cut(s) 94, 109, 604, 696, 793, 996
MboII GAAGA 3 cut(s) 451, 527, 803
MfeI CAATTG 1 cut(s) 220
MflI RGATCY 3 cut(s) 604, 793, 996
MhlI GDGCHC 2 cut(s) 206, 907
MlsI TGGCCA 1 cut(s) 273
MluCI AATT 5 cut(s) 53, 220, 263, 285, 778
MluNI TGGCCA 1 cut(s) 273
Mly113I GGCGCC 1 cut(s) 1037
MlyI GAGTC 1 cut(s) 249
MmeI TCCRAC 3 cut(s) 217, 622, 687
Mox20I TGGCCA 1 cut(s) 273
MroXI GAANNNNTTC 1 cut(s) 428
MscI TGGCCA 1 cut(s) 273
MseI TTAA 3 cut(s) 15, 717, 974
MslI CAYNNNNRTG 1 cut(s) 345
Msp20I TGGCCA 1 cut(s) 273
MspA1I CMGCKG 2 cut(s) 160, 485
MspCI CTTAAG 1 cut(s) 14
MspI CCGG 2 cut(s) 278, 966
MspR9I CCNGG 1 cut(s) 926
MunI CAATTG 1 cut(s) 220
Mva1269I GAATGC 1 cut(s) 1009
MvaI CCWGG 1 cut(s) 926
MvnI CGCG 3 cut(s) 579, 899, 901
MwoI GCNNNNNNNGC 2 cut(s) 45, 201
NarI GGCGCC 1 cut(s) 1037
NcoI CCATGG 1 cut(s) 1032
NdeII GATC 6 cut(s) 94, 109, 604, 696, 793, 996
NlaIV GGNNCC 2 cut(s) 964, 1038
NmuCI GTSAC 1 cut(s) 1015
NspI RCATGY 2 cut(s) 590, 630
PaeI GCATGC 1 cut(s) 630
PagI TCATGA 1 cut(s) 649
PceI AGGCCT 1 cut(s) 67
PcsI WCGNNNNNNNCGW 2 cut(s) 99, 1071
PctI GAATGC 1 cut(s) 1009
PdmI GAANNNNTTC 1 cut(s) 428
PfeI GAWTC 3 cut(s) 116, 153, 424
PkrI GCNGC 5 cut(s) 210, 213, 227, 673, 1024
PleI GAGTC 1 cut(s) 248
PluTI GGCGCC 1 cut(s) 1040
PmaCI CACGTG 1 cut(s) 1066
PmlI CACGTG 1 cut(s) 1066
PpsI GAGTC 1 cut(s) 248
Ppu21I YACGTR 2 cut(s) 522, 1066
Psp1406I AACGTT 1 cut(s) 704
Psp6I CCWGG 1 cut(s) 924
PspCI CACGTG 1 cut(s) 1066
PspEI GGTNACC 1 cut(s) 892
PspGI CCWGG 1 cut(s) 924
PspN4I GGNNCC 2 cut(s) 964, 1038
PspPI GGNCC 1 cut(s) 545
PsuI RGATCY 3 cut(s) 604, 793, 996
PvuII CAGCTG 1 cut(s) 485
RsaI GTAC 8 cut(s) 182, 190, 591, 829, 920, 948, 1055, 1073
RsaNI GTAC 8 cut(s) 181, 189, 590, 828, 919, 947, 1054, 1072
RseI CAYNNNNRTG 1 cut(s) 345
SaqAI TTAA 3 cut(s) 15, 717, 974
SatI GCNGC 5 cut(s) 209, 212, 226, 672, 1023
Sau3AI GATC 6 cut(s) 94, 109, 604, 696, 793, 996
Sau96I GGNCC 1 cut(s) 545
SchI GAGTC 1 cut(s) 249
ScrFI CCNGG 1 cut(s) 926
SduI GDGCHC 2 cut(s) 206, 907
SexAI ACCWGGT 1 cut(s) 924
SfaNI GCATC 2 cut(s) 48, 298
SfoI GGCGCC 1 cut(s) 1038
SinI GGWCC 1 cut(s) 545
SmiMI CAYNNNNRTG 1 cut(s) 345
SmlI CTYRAG 2 cut(s) 14, 245
SmoI CTYRAG 2 cut(s) 14, 245
SphI GCATGC 1 cut(s) 630
Sse9I AATT 5 cut(s) 53, 220, 263, 285, 778
SseBI AGGCCT 1 cut(s) 67
SsiI CCGC 5 cut(s) 87, 160, 226, 577, 897
SspDI GGCGCC 1 cut(s) 1036
SspMI CTAG 4 cut(s) 32, 837, 854, 1026
StuI AGGCCT 1 cut(s) 67
StyD4I CCNGG 1 cut(s) 924
StyI CCWWGG 2 cut(s) 1032, 1057
TaaI ACNGT 4 cut(s) 232, 533, 881, 1015
TaiI ACGT 4 cut(s) 524, 707, 910, 1068
TaqI TCGA 6 cut(s) 27, 151, 177, 301, 329, 499
TasI AATT 5 cut(s) 53, 220, 263, 285, 778
TatI WGTACW 2 cut(s) 180, 946
TauI GCSGC 1 cut(s) 228
TfiI GAWTC 3 cut(s) 116, 153, 424
Tru1I TTAA 3 cut(s) 15, 717, 974
Tru9I TTAA 3 cut(s) 15, 717, 974
TseFI GTSAC 1 cut(s) 1015
TseI GCWGC 4 cut(s) 208, 211, 671, 1022
Tsp45I GTSAC 1 cut(s) 1015
TspDTI ATGAA 5 cut(s) 308, 411, 459, 482, 726
TspGWI ACGGA 1 cut(s) 148
Vha464I CTTAAG 1 cut(s) 14
VpaK11BI GGWCC 1 cut(s) 545
XagI CCTNNNNNAGG 1 cut(s) 248
XapI RAATTY 1 cut(s) 263
XceI RCATGY 2 cut(s) 590, 630
XmnI GAANNNNTTC 1 cut(s) 428
XspI CTAG 4 cut(s) 32, 837, 854, 1026
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.