MD11G1060800.v1.1

tRNA pseudouridine

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr11
OG0007446
Physical Location & Seq
Reverse (-)
5295322 .. 5298691
3370 bp
Loading structure...
UTR
Exon/CDS
Intron
MD11G1060800.v1.1.491

Sequence Viewer

Length: 1593 bp
ATGGCCGTCTCCTCACTGCGACACCCCTTCTCCCTCTGCCTCCCAAAGTTCCCATTTCGCACCTTCCATTTTTCAAAGCCAATTTTACCCCTCAGACTCAACCTTGTTTACTGCTGCTCCTCCTCCTCCCTCTGTACACCCGAACAAACATCAACCCGCTCCGGTCACAAATGGCAGCCCGTCCGAAAGAGGAAAGTGGTTCTCCGGGTCGGGTACGTCGGCACAGAGTACCGAGGCTTGCAAATGCAACGAGACGAAAATTCATTATCCACTATTGAGAAAGAGTTGGAAACTGCCATATATAACGCGGGCGGTATCCGTGAGAGCAATCTGGGGAACCTTAACAAGATTGCGTGGGCCAGGAGTAGCCGGACTGATAAAGGAGTTCACTCTTTAGCGACGATGATATCATTGAAAATGGAAATCCCAGAGAATGCATGGGTCGGAGACCCTTTTGGCATGGATCTTGTGAATCACATTAACTCTTATCTGCCTCGTAATATCAAAGTTTTCAGCATTTTGCCTGCGCAGAGGAGCTTTGATCCTAGAAAGGAGTGTAATCTCCGCATGTATTCATACCTCCTTCCTGCTGAAGTTATTGGAATCAAAAGTCATCTCAACGCAGATGAAATTGATTATCACATCTCAGACTTCAATAATATAATAAAAGCTTTTGAGGGAGAACATCCTTTTCATAATTATACTATACGATCTAAATACAGGTCGAAGTATCCTGCAAAACAATCACCCAAATATGGAAAAGTGTCGATAGCAGGTAGATCAACCAGAGAGGCAACAGCCTCTGAGTCTGAGTCTGAGTCTGAGGAAAGTGGCGGGGAAGAAAATTTTGATGAAACATATGCATCAGAATCAAATGCTGAGGAACTGAACCAAAATTCTTCGTTTTCTAGCAATAGTGAGGACAGCTTACTCGATGCTTGCAAGAAGCAGGGAGATGTTCTAAAGGTTCAAAGTGCTGGTTCGGTCATCCGTGCAAGATGGTTATTTGAACCTGATGAAAGAGATAGAATTGGTGCTTCTCATTTCAGAAAGATTTTTCAGTGCTCTTGTGGGAAGCTGGAGAAATCGCTTGGACATGATTATGTTGAAGTTTCCATATGGGGAGAGTCTTTCATGTTACATCAAATCCGCAAAATGGTTGGAACTGCTGTGGCTATAAAGCGCGAGTTACTCCCTAGAGATATTTTGACATTGTCACTGGCCAAGTTTTCCCGGATTGTCCTACCACTTGCCCCATCTGAAGTTTTGTTTTTAAGAGGGAACAGGTTTTCAATTAGAGTAAAAAATGTAACAAGGCCTGAAATGACGACAATGGTTGAATCAGAAGAAATAAATAAGGCGGTTGACGAGTTCTTCATATCTGTTATGTTGCCTCAAGTTACAAAGTTCTTAGATCCTTCAGGATATCCTTGGAATGAATGGGTTGAGAATTTGGATAGAAACACCGGCATTCCAGATGCAGAATTGGATGAAGTCAGGAACGCTTGGAAAGTGTGGAAGGAAAAGTTTGATGGTTTTGCATCAGTCCGAAACCAAAGAGACAAGGTAGATGCCGATGATTGCACTGGATAA

Protein Analysis

531

Amino Acids

60.31

Weight (kDa)

7.59

Isoelectric Point (pI)

50.56

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PseudoU_synth_1 PF01416 346 - 425 4.2e-06 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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc16I TGCGCA 1 cut(s) 528
Acc36I ACCTGC 1 cut(s) 764
AccBSI CCGCTC 1 cut(s) 159
AccII CGCG 2 cut(s) 308, 1185
AciI CCGC 7 cut(s) 157, 308, 312, 565, 834, 1150, 1361
AclWI GGATC 3 cut(s) 471, 536, 1409
AcoI YGGCCR 2 cut(s) 3, 1221
AcsI RAATTY 4 cut(s) 259, 844, 895, 1450
AcuI CTGAAG 3 cut(s) 612, 1281, 1404
AfaI GTAC 3 cut(s) 136, 215, 230
AfiI CCNNNNNNNGG 2 cut(s) 755, 1156
AgsI TTSAA 8 cut(s) 75, 415, 655, 971, 1010, 1109, 1293, 1340
AjnI CCWGG 1 cut(s) 359
AluBI AGCT 4 cut(s) 537, 671, 927, 1078
AluI AGCT 4 cut(s) 537, 671, 927, 1078
Alw21I GWGCWC 1 cut(s) 1067
Alw26I GTCTC 4 cut(s) 13, 246, 441, 1554
AlwI GGATC 3 cut(s) 471, 536, 1409
AlwNI CAGNNNCTG 1 cut(s) 803
AoxI GGCC 4 cut(s) 3, 357, 1221, 1316
ApeKI GCWGC 2 cut(s) 114, 175
ApoI RAATTY 4 cut(s) 259, 844, 895, 1450
AspLEI GCGC 2 cut(s) 529, 1185
AspS9I GGNCC 1 cut(s) 357
AsuC2I CCSGG 2 cut(s) 206, 1234
AsuHPI GGTGA 1 cut(s) 738
BalI TGGCCA 1 cut(s) 1223
Bbv12I GWGCWC 1 cut(s) 1067
BbvCI CCTCAGC 1 cut(s) 879
BbvI GCAGC 2 cut(s) 101, 187
BccI CCATC 3 cut(s) 993, 1264, 1526
BciT130I CCWGG 1 cut(s) 361
BciVI GTATCC 2 cut(s) 326, 741
BcnI CCSGG 2 cut(s) 206, 1234
BcoDI GTCTC 4 cut(s) 13, 246, 441, 1554
BfaI CTAG 3 cut(s) 546, 909, 1197
BfuAI ACCTGC 1 cut(s) 764
BfuI GTATCC 2 cut(s) 326, 741
BisI GCNGC 2 cut(s) 115, 176
BlsI GCNGC 2 cut(s) 116, 177
Bme1390I CCNGG 3 cut(s) 206, 361, 1234
BmgT120I GGNCC 1 cut(s) 357
BmiI GGNNCC 1 cut(s) 338
BmrFI CCNGG 3 cut(s) 206, 361, 1234
BmsI GCATC 5 cut(s) 872, 925, 1468, 1550, 1561
BpmI CTGGAG 1 cut(s) 1100
Bpu10I CCTNAGC 1 cut(s) 879
BpuEI CTTGAG 1 cut(s) 1380
BpuMI CCSGG 2 cut(s) 206, 1234
BsaI GGTCTC 1 cut(s) 441
BsaJI CCNNGG 2 cut(s) 232, 1430
BsaWI WCCGGW 1 cut(s) 161
BsaXI ACNNNNNCTCC 4 cut(s) 14, 44, 101, 131
Bsc4I CCNNNNNNNGG 2 cut(s) 755, 1156
Bse118I RCCGGY 1 cut(s) 1466
Bse1I ACTGG 2 cut(s) 1224, 1591
BseBI CCWGG 1 cut(s) 361
BseDI CCNNGG 2 cut(s) 232, 1430
BseGI GGATG 3 cut(s) 685, 987, 1495
BseLI CCNNNNNNNGG 2 cut(s) 755, 1156
BseMII CTCAG 7 cut(s) 106, 660, 795, 801, 807, 813, 870
BseNI ACTGG 2 cut(s) 1224, 1591
BseRI GAGGAG 4 cut(s) 109, 112, 115, 547
BseXI GCAGC 2 cut(s) 101, 187
Bsh1236I CGCG 2 cut(s) 308, 1185
BshFI GGCC 4 cut(s) 5, 359, 1223, 1318
BsiHKAI GWGCWC 1 cut(s) 1067
BsiSI CCGG 5 cut(s) 162, 205, 370, 1234, 1467
BslI CCNNNNNNNGG 2 cut(s) 755, 1156
BsmAI GTCTC 4 cut(s) 13, 246, 441, 1554
BsmBI CGTCTC 2 cut(s) 13, 246
BsmI GAATGC 2 cut(s) 439, 1470
BsnI GGCC 4 cut(s) 5, 359, 1223, 1318
Bso31I GGTCTC 1 cut(s) 441
Bsp1286I GDGCHC 1 cut(s) 1067
Bsp1407I TGTACA 1 cut(s) 134
Bsp143I GATC 5 cut(s) 463, 541, 710, 779, 1414
BspACI CCGC 7 cut(s) 157, 308, 312, 565, 834, 1150, 1361
BspANI GGCC 4 cut(s) 5, 359, 1223, 1318
BspCNI CTCAG 7 cut(s) 105, 659, 796, 802, 808, 814, 871
BspFNI CGCG 2 cut(s) 308, 1185
BspLI GGNNCC 1 cut(s) 338
BspMI ACCTGC 1 cut(s) 764
BspPI GGATC 3 cut(s) 471, 536, 1409
BspTNI GGTCTC 1 cut(s) 441
BsrBI CCGCTC 1 cut(s) 159
BsrFI RCCGGY 1 cut(s) 1466
BsrGI TGTACA 1 cut(s) 134
BsrI ACTGG 2 cut(s) 1224, 1591
BssAI RCCGGY 1 cut(s) 1466
BssECI CCNNGG 2 cut(s) 232, 1430
BssMI GATC 5 cut(s) 463, 541, 710, 779, 1414
BssT1I CCWWGG 1 cut(s) 1430
Bst2UI CCWGG 1 cut(s) 361
BstAUI TGTACA 1 cut(s) 134
BstC8I GCNNGC 4 cut(s) 239, 310, 525, 940
BstDEI CTNAG 8 cut(s) 92, 646, 804, 810, 816, 822, 879, 1411
BstF5I GGATG 3 cut(s) 685, 987, 1495
BstFNI CGCG 2 cut(s) 308, 1185
BstHHI GCGC 2 cut(s) 529, 1185
BstKTI GATC 5 cut(s) 466, 544, 713, 782, 1417
BstMAI GTCTC 4 cut(s) 13, 246, 441, 1554
BstMBI GATC 5 cut(s) 463, 541, 710, 779, 1414
BstNI CCWGG 1 cut(s) 361
BstNSI RCATGY 1 cut(s) 571
BstSCI CCNGG 3 cut(s) 204, 359, 1232
BstUI CGCG 2 cut(s) 308, 1185
BstV1I GCAGC 2 cut(s) 101, 187
BstX2I RGATCY 2 cut(s) 463, 1414
BstYI RGATCY 2 cut(s) 463, 1414
BsuI GTATCC 2 cut(s) 326, 741
BsuRI GGCC 4 cut(s) 5, 359, 1223, 1318
BtsCI GGATG 3 cut(s) 685, 987, 1495
BtsI GCAGTG 1 cut(s) 14
BtsIMutI CAGTG 4 cut(s) 14, 1067, 1217, 1584
BveI ACCTGC 1 cut(s) 764
Cac8I GCNNGC 4 cut(s) 239, 310, 525, 940
CaiI CAGNNNCTG 1 cut(s) 803
CfoI GCGC 2 cut(s) 529, 1185
Cfr10I RCCGGY 1 cut(s) 1466
Cfr13I GGNCC 1 cut(s) 357
Csp6I GTAC 3 cut(s) 135, 214, 229
CviAII CATG 5 cut(s) 438, 460, 568, 1097, 1135
CviQI GTAC 3 cut(s) 135, 214, 229
DdeI CTNAG 8 cut(s) 92, 646, 804, 810, 816, 822, 879, 1411
DpnI GATC 5 cut(s) 465, 543, 712, 781, 1416
DpnII GATC 5 cut(s) 463, 541, 710, 779, 1414
EaeI YGGCCR 2 cut(s) 3, 1221
Eco130I CCWWGG 1 cut(s) 1430
Eco147I AGGCCT 1 cut(s) 1318
Eco31I GGTCTC 1 cut(s) 441
Eco32I GATATC 2 cut(s) 408, 1427
Eco57I CTGAAG 3 cut(s) 612, 1281, 1404
EcoRII CCWGG 1 cut(s) 359
EcoRV GATATC 2 cut(s) 408, 1427
EcoT14I CCWWGG 1 cut(s) 1430
EcoT22I ATGCAT 2 cut(s) 439, 865
ErhI CCWWGG 1 cut(s) 1430
Esp3I CGTCTC 2 cut(s) 13, 246
FaeI CATG 5 cut(s) 441, 463, 571, 1100, 1138
FatI CATG 5 cut(s) 437, 459, 567, 1096, 1134
FauI CCCGC 3 cut(s) 164, 301, 827
FauNDI CATATG 2 cut(s) 859, 1118
Fnu4HI GCNGC 2 cut(s) 115, 176
FokI GGATG 3 cut(s) 672, 974, 1502
Fsp4HI GCNGC 2 cut(s) 115, 176
FspBI CTAG 3 cut(s) 546, 909, 1197
FspI TGCGCA 1 cut(s) 528
GlaI GCGC 2 cut(s) 528, 1184
GluI GCNGC 2 cut(s) 115, 176
GsuI CTGGAG 1 cut(s) 1100
HaeIII GGCC 4 cut(s) 5, 359, 1223, 1318
HapII CCGG 5 cut(s) 162, 205, 370, 1234, 1467
HhaI GCGC 2 cut(s) 529, 1185
Hin1II CATG 5 cut(s) 441, 463, 571, 1100, 1138
Hin6I GCGC 2 cut(s) 527, 1183
HinP1I GCGC 2 cut(s) 527, 1183
HincII GTYRAC 1 cut(s) 1366
HindII GTYRAC 1 cut(s) 1366
HindIII AAGCTT 1 cut(s) 669
HinfI GANTC 9 cut(s) 96, 472, 603, 806, 812, 818, 869, 1127, 1340
HpaII CCGG 5 cut(s) 162, 205, 370, 1234, 1467
HphI GGTGA 1 cut(s) 738
Hpy166II GTNNAC 4 cut(s) 109, 137, 388, 1366
Hpy188III TCNNGA 3 cut(s) 1422, 1475, 1498
Hpy8I GTNNAC 4 cut(s) 109, 137, 388, 1366
Hpy99I CGWCG 2 cut(s) 221, 403
HpyAV CCTTC 5 cut(s) 37, 73, 593, 1428, 1513
HpyCH4IV ACGT 1 cut(s) 216
HpyF3I CTNAG 8 cut(s) 92, 646, 804, 810, 816, 822, 879, 1411
HpySE526I ACGT 1 cut(s) 216
Hsp92II CATG 5 cut(s) 441, 463, 571, 1100, 1138
HspAI GCGC 2 cut(s) 527, 1183
Kzo9I GATC 5 cut(s) 463, 541, 710, 779, 1414
LmnI GCTCC 3 cut(s) 122, 164, 534
Lsp1109I GCAGC 2 cut(s) 101, 187
LweI GCATC 5 cut(s) 872, 925, 1468, 1550, 1561
MaeI CTAG 3 cut(s) 546, 909, 1197
MaeII ACGT 1 cut(s) 216
MaeIII GTNAC 6 cut(s) 164, 1137, 1188, 1215, 1309, 1399
MalI GATC 5 cut(s) 465, 543, 712, 781, 1416
MbiI CCGCTC 1 cut(s) 159
MboI GATC 5 cut(s) 463, 541, 710, 779, 1414
MboII GAAGA 4 cut(s) 851, 891, 1358, 1366
MflI RGATCY 2 cut(s) 463, 1414
MhlI GDGCHC 1 cut(s) 1067
MlsI TGGCCA 1 cut(s) 1223
MluNI TGGCCA 1 cut(s) 1223
MlyI GAGTC 5 cut(s) 90, 815, 821, 827, 1136
MmeI TCCRAC 3 cut(s) 267, 424, 1141
Mox20I TGGCCA 1 cut(s) 1223
Mph1103I ATGCAT 2 cut(s) 439, 865
MscI TGGCCA 1 cut(s) 1223
MseI TTAA 3 cut(s) 342, 480, 1274
MslI CAYNNNNRTG 1 cut(s) 1101
Msp20I TGGCCA 1 cut(s) 1223
MspI CCGG 5 cut(s) 162, 205, 370, 1234, 1467
MspR9I CCNGG 3 cut(s) 206, 361, 1234
Mva1269I GAATGC 2 cut(s) 439, 1470
MvaI CCWGG 1 cut(s) 361
MvnI CGCG 2 cut(s) 308, 1185
NciI CCSGG 2 cut(s) 206, 1234
NdeI CATATG 2 cut(s) 859, 1118
NdeII GATC 5 cut(s) 463, 541, 710, 779, 1414
NlaIII CATG 5 cut(s) 441, 463, 571, 1100, 1138
NlaIV GGNNCC 1 cut(s) 338
NmuCI GTSAC 2 cut(s) 164, 1215
NsbI TGCGCA 1 cut(s) 528
NsiI ATGCAT 2 cut(s) 439, 865
NspI RCATGY 1 cut(s) 571
PceI AGGCCT 1 cut(s) 1318
PctI GAATGC 2 cut(s) 439, 1470
PfeI GAWTC 4 cut(s) 472, 603, 869, 1340
PflFI GACNNNGTC 1 cut(s) 1213
PfoI TCCNGGA 1 cut(s) 1232
PkrI GCNGC 2 cut(s) 116, 177
PleI GAGTC 5 cut(s) 90, 814, 820, 826, 1135
PpsI GAGTC 5 cut(s) 90, 814, 820, 826, 1135
Psp6I CCWGG 1 cut(s) 359
PspGI CCWGG 1 cut(s) 359
PspN4I GGNNCC 1 cut(s) 338
PspPI GGNCC 1 cut(s) 357
PstNI CAGNNNCTG 1 cut(s) 803
PsuI RGATCY 2 cut(s) 463, 1414
PsyI GACNNNGTC 1 cut(s) 1213
RsaI GTAC 3 cut(s) 136, 215, 230
RsaNI GTAC 3 cut(s) 135, 214, 229
RseI CAYNNNNRTG 1 cut(s) 1101
SaqAI TTAA 3 cut(s) 342, 480, 1274
SatI GCNGC 2 cut(s) 115, 176
Sau3AI GATC 5 cut(s) 463, 541, 710, 779, 1414
Sau96I GGNCC 1 cut(s) 357
SchI GAGTC 5 cut(s) 90, 815, 821, 827, 1136
ScrFI CCNGG 3 cut(s) 206, 361, 1234
SduI GDGCHC 1 cut(s) 1067
SfaNI GCATC 5 cut(s) 872, 925, 1468, 1550, 1561
SmiMI CAYNNNNRTG 1 cut(s) 1101
SmlI CTYRAG 1 cut(s) 1395
SmoI CTYRAG 1 cut(s) 1395
SseBI AGGCCT 1 cut(s) 1318
SsiI CCGC 7 cut(s) 157, 308, 312, 565, 834, 1150, 1361
SspMI CTAG 3 cut(s) 546, 909, 1197
StuI AGGCCT 1 cut(s) 1318
StyD4I CCNGG 3 cut(s) 204, 359, 1232
StyI CCWWGG 1 cut(s) 1430
TaiI ACGT 1 cut(s) 219
TaqI TCGA 3 cut(s) 725, 767, 933
TaqII GACCGA 1 cut(s) 973
TatI WGTACW 1 cut(s) 134
TfiI GAWTC 4 cut(s) 472, 603, 869, 1340
Tru1I TTAA 3 cut(s) 342, 480, 1274
Tru9I TTAA 3 cut(s) 342, 480, 1274
TscAI CASTG 4 cut(s) 21, 1067, 1224, 1591
TseFI GTSAC 2 cut(s) 164, 1215
TseI GCWGC 2 cut(s) 114, 175
Tsp45I GTSAC 2 cut(s) 164, 1215
TspGWI ACGGA 2 cut(s) 308, 980
TspRI CASTG 4 cut(s) 21, 1067, 1224, 1591
Tth111I GACNNNGTC 1 cut(s) 1213
XapI RAATTY 4 cut(s) 259, 844, 895, 1450
XceI RCATGY 1 cut(s) 571
XcmI CCANNNNNNNNNTGG 1 cut(s) 435
XspI CTAG 3 cut(s) 546, 909, 1197
Zsp2I ATGCAT 2 cut(s) 439, 865
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.