MD12G1206400.v1.1

synthase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr12
OG0009298
Physical Location & Seq
Forward (+)
28694100 .. 28696362
2263 bp
Loading structure...
UTR
Exon/CDS
Intron
MD12G1206400.v1.1.491

Sequence Viewer

Length: 1050 bp
ATGCCCTTCCCTCGTCCTCTCCTCTCTCCCCAACCCGCCATGGTATTGTACGCCCCCAAAGCCTACGTCTTTCTCAGCCGCCGCCGAGCCACCATGTCAGCCCAACACGACGCCGCAAATCCCAGTTCCCAAGCTGCGCTGCAAACCCCAGGGAACTACCCCGTGCCCCTCTCCCCGCCTCTTCCCGCCATCTCAAAGCACATAGAGCTAGCGAGAGCCATGTCCGCCTCTTCCAAATCCGGCCTCTTCTCCCTCTCGAGAAACGACGTCGTCTACGAGGACGAGTGGCTCATTGTGGTTAACAAGCCTCAGGGTGTTTACTGTGAGTCCGTGTTGGAATCGGTCCCTCAGCTTCTCTGTGACTCGGCCGAGTCAGTTGCAGAGACCCGAACAAAGCAGCCAGAGCTCCATCTTGCAAATCGACTTGATCGCGACACTAGTGGATTGATGATAATAACCAAGTCTCACAAAGTAGCGGCCAAGCTTGTAAAGGCATTTACAGATCACAAAGTTTCCAAAACATACATTGCACGCTGTGTTGGTTCAGCTCCGAAATGGGAAAGAATCACCCTCAAGTCAGGTCATGGTCGGTCTAAGTTTGGGGCATGGCGAGTGTATGCTGCTTCAGACGTAGGGCGGACACTTCCAGGTGGGTCAATGGTGAGAGACATGGAAACAGCGTTTGAAATTTTATCAAAAAATGGACAAGGGAGCTACAGAGAGCCATCTGAGTTTAAGAAAGATGAAGCGAATGTTGTAGTGGTTGAAGAGAAAGCTGTAATAGATGGAGACGCAAAGAAGGATGAGATTTTAGTAAGAGCCCGTCCTAGGAGTGGACGAACACATCAAATTCGCTTGCATTGCCAGTATCTTGGAATTTCCATAAGAGGGGATGTCAAGTATGAGGGTGTGTATGAGTGGAAAGGCACAACTTATGACGGCCATGAACTTCATGCGGAGAGCTTGTCTCTTGAGCACCCTGTTACTGGTCTTCCAGTAATGTTTCGGGCACCTGTACCTTCTTGGGCCAGCCAGGCGTTGCAGCACTAG

Protein Analysis

350

Amino Acids

38.6

Weight (kDa)

9.19

Isoelectric Point (pI)

49.4

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PseudoU_synth_2 PF00849 97 - 289 6.2e-25 RNA pseudouridylate synthase
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AatII GACGTC 1 cut(s) 270
AccB1I GGYRCC 1 cut(s) 1009
AccI GTMKAC 1 cut(s) 273
AccII CGCG 1 cut(s) 432
AcoI YGGCCR 3 cut(s) 366, 477, 940
AcsI RAATTY 3 cut(s) 687, 849, 876
AcuI CTGAAG 1 cut(s) 609
AcyI GRCGYC 2 cut(s) 111, 267
AdeI CACNNNGTG 1 cut(s) 536
AfaI GTAC 2 cut(s) 50, 1017
AfiI CCNNNNNNNGG 4 cut(s) 828, 833, 888, 986
AgsI TTSAA 2 cut(s) 686, 767
AhlI ACTAGT 1 cut(s) 437
AjnI CCWGG 3 cut(s) 148, 646, 1032
AluBI AGCT 9 cut(s) 134, 208, 352, 406, 484, 548, 714, 776, 963
AluI AGCT 9 cut(s) 134, 208, 352, 406, 484, 548, 714, 776, 963
Alw21I GWGCWC 2 cut(s) 408, 978
Alw26I GTCTC 5 cut(s) 377, 468, 660, 783, 972
Ama87I CYCGRG 1 cut(s) 256
AoxI GGCC 5 cut(s) 241, 366, 477, 940, 1026
ApeKI GCWGC 5 cut(s) 134, 139, 397, 620, 1042
ApoI RAATTY 3 cut(s) 687, 849, 876
ArsI GACNNNNNNTTYG 2 cut(s) 51, 83
AspA2I CCTAGG 1 cut(s) 827
AspLEI GCGC 1 cut(s) 139
AspS9I GGNCC 2 cut(s) 343, 1026
AsuHPI GGTGA 2 cut(s) 559, 673
AsuNHI GCTAGC 1 cut(s) 208
AvaI CYCGRG 1 cut(s) 256
AvaII GGWCC 1 cut(s) 343
AvrII CCTAGG 1 cut(s) 827
AxyI CCTNAGG 1 cut(s) 309
BaeGI GKGCMC 2 cut(s) 168, 1012
BanI GGYRCC 1 cut(s) 1009
BanII GRGCYC 2 cut(s) 408, 823
BbsI GAAGAC 1 cut(s) 983
Bbv12I GWGCWC 2 cut(s) 408, 978
BbvCI CCTCAGC 1 cut(s) 348
BbvI GCAGC 4 cut(s) 121, 126, 409, 607
BccI CCATC 4 cut(s) 197, 417, 733, 779
BceAI ACGGC 1 cut(s) 955
BcgI CGANNNNNNTGC 2 cut(s) 359, 393
BciT130I CCWGG 3 cut(s) 150, 648, 1034
BcoDI GTCTC 5 cut(s) 377, 468, 660, 783, 972
BcuI ACTAGT 1 cut(s) 437
BfaI CTAG 4 cut(s) 209, 438, 828, 1048
BfmI CTRYAG 1 cut(s) 715
BglI GCCNNNNNGGC 1 cut(s) 1034
BisI GCNGC 9 cut(s) 79, 82, 114, 135, 140, 398, 477, 621, 1043
BlnI CCTAGG 1 cut(s) 827
BlsI GCNGC 9 cut(s) 80, 83, 115, 136, 141, 399, 478, 622, 1044
Bme1390I CCNGG 3 cut(s) 150, 648, 1034
Bme18I GGWCC 1 cut(s) 343
BmeT110I CYCGRG 1 cut(s) 256
BmgT120I GGNCC 2 cut(s) 343, 1026
BmiI GGNNCC 2 cut(s) 345, 1011
BmrFI CCNGG 3 cut(s) 150, 648, 1034
BmrI ACTGGG 1 cut(s) 117
BmtI GCTAGC 1 cut(s) 212
BmuI ACTGGG 1 cut(s) 117
BpiI GAAGAC 1 cut(s) 983
BplI GAGNNNNNCTC 2 cut(s) 952, 984
Bpu10I CCTNAGC 1 cut(s) 348
BpuEI CTTGAG 2 cut(s) 557, 992
BsaHI GRCGYC 2 cut(s) 111, 267
BsaI GGTCTC 1 cut(s) 377
BsaJI CCNNGG 4 cut(s) 39, 148, 149, 827
BsaXI ACNNNNNCTCC 2 cut(s) 950, 980
Bsc4I CCNNNNNNNGG 4 cut(s) 828, 833, 888, 986
Bse1I ACTGG 4 cut(s) 123, 865, 991, 995
Bse21I CCTNAGG 1 cut(s) 309
Bse3DI GCAATG 2 cut(s) 525, 859
BseBI CCWGG 3 cut(s) 150, 648, 1034
BseDI CCNNGG 4 cut(s) 39, 148, 149, 827
BseGI GGATG 2 cut(s) 808, 898
BseLI CCNNNNNNNGG 4 cut(s) 828, 833, 888, 986
BseMI GCAATG 2 cut(s) 525, 859
BseMII CTCAG 4 cut(s) 88, 323, 362, 720
BseNI ACTGG 4 cut(s) 123, 865, 991, 995
BseRI GAGGAG 1 cut(s) 11
BseSI GKGCMC 2 cut(s) 168, 1012
BseX3I CGGCCG 1 cut(s) 366
BseXI GCAGC 4 cut(s) 121, 126, 409, 607
Bsh1236I CGCG 1 cut(s) 432
Bsh1285I CGRYCG 1 cut(s) 369
BshFI GGCC 5 cut(s) 243, 368, 479, 942, 1028
BshNI GGYRCC 1 cut(s) 1009
BsiEI CGRYCG 1 cut(s) 369
BsiHKAI GWGCWC 2 cut(s) 408, 978
BsiHKCI CYCGRG 1 cut(s) 256
BsiSI CCGG 1 cut(s) 240
BslFI GGGAC 1 cut(s) 329
BslI CCNNNNNNNGG 4 cut(s) 828, 833, 888, 986
BsmAI GTCTC 5 cut(s) 377, 468, 660, 783, 972
BsmBI CGTCTC 1 cut(s) 783
BsmFI GGGAC 1 cut(s) 329
BsnI GGCC 5 cut(s) 243, 368, 479, 942, 1028
Bso31I GGTCTC 1 cut(s) 377
BsoBI CYCGRG 1 cut(s) 256
Bsp1286I GDGCHC 5 cut(s) 168, 408, 823, 978, 1012
Bsp143I GATC 2 cut(s) 427, 502
Bsp19I CCATGG 1 cut(s) 39
Bsp68I TCGCGA 1 cut(s) 432
BspANI GGCC 5 cut(s) 243, 368, 479, 942, 1028
BspCNI CTCAG 4 cut(s) 87, 322, 361, 721
BspFNI CGCG 1 cut(s) 432
BspLI GGNNCC 2 cut(s) 345, 1011
BspOI GCTAGC 1 cut(s) 212
BspT107I GGYRCC 1 cut(s) 1009
BspTNI GGTCTC 1 cut(s) 377
BsrDI GCAATG 2 cut(s) 525, 859
BsrI ACTGG 4 cut(s) 123, 865, 991, 995
BssECI CCNNGG 4 cut(s) 39, 148, 149, 827
BssMI GATC 2 cut(s) 427, 502
BssNI GRCGYC 2 cut(s) 111, 267
BssT1I CCWWGG 2 cut(s) 39, 827
Bst2UI CCWGG 3 cut(s) 150, 648, 1034
Bst4CI ACNGT 1 cut(s) 323
Bst6I CTCTTC 4 cut(s) 186, 235, 251, 762
BstACI GRCGYC 2 cut(s) 111, 267
BstC8I GCNNGC 4 cut(s) 210, 532, 857, 1030
BstDEI CTNAG 5 cut(s) 74, 309, 348, 594, 729
BstDSI CCRYGG 1 cut(s) 39
BstF5I GGATG 2 cut(s) 808, 898
BstFNI CGCG 1 cut(s) 432
BstHHI GCGC 1 cut(s) 139
BstKTI GATC 2 cut(s) 430, 505
BstMAI GTCTC 5 cut(s) 377, 468, 660, 783, 972
BstMBI GATC 2 cut(s) 427, 502
BstMCI CGRYCG 1 cut(s) 369
BstMWI GCNNNNNNNGC 6 cut(s) 59, 205, 224, 403, 861, 1034
BstNI CCWGG 3 cut(s) 150, 648, 1034
BstSCI CCNGG 3 cut(s) 148, 646, 1032
BstSFI CTRYAG 1 cut(s) 715
BstSLI GKGCMC 2 cut(s) 168, 1012
BstUI CGCG 1 cut(s) 432
BstV1I GCAGC 4 cut(s) 121, 126, 409, 607
BstV2I GAAGAC 1 cut(s) 983
BstXI CCANNNNNNTGG 1 cut(s) 872
BstZI CGGCCG 1 cut(s) 366
Bsu36I CCTNAGG 1 cut(s) 309
BsuRI GGCC 5 cut(s) 243, 368, 479, 942, 1028
BtgI CCRYGG 1 cut(s) 39
BtsCI GGATG 2 cut(s) 808, 898
BtuMI TCGCGA 1 cut(s) 432
Cac8I GCNNGC 4 cut(s) 210, 532, 857, 1030
CfoI GCGC 1 cut(s) 139
Cfr13I GGNCC 2 cut(s) 343, 1026
CseI GACGC 2 cut(s) 119, 800
Csp6I GTAC 2 cut(s) 49, 1016
CviAII CATG 8 cut(s) 40, 94, 220, 584, 606, 670, 944, 953
CviQI GTAC 2 cut(s) 49, 1016
DdeI CTNAG 5 cut(s) 74, 309, 348, 594, 729
DpnI GATC 2 cut(s) 429, 504
DpnII GATC 2 cut(s) 427, 502
DraIII CACNNNGTG 1 cut(s) 536
EaeI YGGCCR 3 cut(s) 366, 477, 940
EagI CGGCCG 1 cut(s) 366
Eam1104I CTCTTC 4 cut(s) 186, 235, 251, 762
EarI CTCTTC 4 cut(s) 186, 235, 251, 762
EciI GGCGGA 2 cut(s) 214, 652
Ecl136II GAGCTC 1 cut(s) 406
EclXI CGGCCG 1 cut(s) 366
Eco130I CCWWGG 2 cut(s) 39, 827
Eco24I GRGCYC 2 cut(s) 408, 823
Eco31I GGTCTC 1 cut(s) 377
Eco47I GGWCC 1 cut(s) 343
Eco52I CGGCCG 1 cut(s) 366
Eco53kI GAGCTC 1 cut(s) 406
Eco57I CTGAAG 1 cut(s) 609
Eco81I CCTNAGG 1 cut(s) 309
Eco88I CYCGRG 1 cut(s) 256
EcoICRI GAGCTC 1 cut(s) 406
EcoRII CCWGG 3 cut(s) 148, 646, 1032
EcoT14I CCWWGG 2 cut(s) 39, 827
EcoT38I GRGCYC 2 cut(s) 408, 823
ErhI CCWWGG 2 cut(s) 39, 827
Esp3I CGTCTC 1 cut(s) 783
FaeI CATG 8 cut(s) 43, 97, 223, 587, 609, 673, 947, 956
FaqI GGGAC 1 cut(s) 329
FatI CATG 8 cut(s) 39, 93, 219, 583, 605, 669, 943, 952
FauI CCCGC 3 cut(s) 43, 183, 193
FblI GTMKAC 1 cut(s) 273
Fnu4HI GCNGC 9 cut(s) 79, 82, 114, 135, 140, 398, 477, 621, 1043
FokI GGATG 2 cut(s) 815, 905
FriOI GRGCYC 2 cut(s) 408, 823
Fsp4HI GCNGC 9 cut(s) 79, 82, 114, 135, 140, 398, 477, 621, 1043
FspBI CTAG 4 cut(s) 209, 438, 828, 1048
GlaI GCGC 1 cut(s) 138
GluI GCNGC 9 cut(s) 79, 82, 114, 135, 140, 398, 477, 621, 1043
HaeIII GGCC 5 cut(s) 243, 368, 479, 942, 1028
HapII CCGG 1 cut(s) 240
HgaI GACGC 2 cut(s) 119, 800
HhaI GCGC 1 cut(s) 139
Hin1I GRCGYC 2 cut(s) 111, 267
Hin1II CATG 8 cut(s) 43, 97, 223, 587, 609, 673, 947, 956
Hin6I GCGC 1 cut(s) 137
HinP1I GCGC 1 cut(s) 137
HincII GTYRAC 1 cut(s) 301
HindII GTYRAC 1 cut(s) 301
HindIII AAGCTT 1 cut(s) 482
HinfI GANTC 5 cut(s) 326, 338, 362, 371, 564
HpaI GTTAAC 1 cut(s) 301
HpaII CCGG 1 cut(s) 240
HphI GGTGA 2 cut(s) 559, 673
Hpy166II GTNNAC 4 cut(s) 274, 301, 319, 836
Hpy188I TCNGA 3 cut(s) 552, 628, 730
Hpy188III TCNNGA 4 cut(s) 256, 258, 431, 971
Hpy8I GTNNAC 4 cut(s) 274, 301, 319, 836
Hpy99I CGWCG 3 cut(s) 113, 269, 272
HpyAV CCTTC 3 cut(s) 16, 793, 1029
HpyCH4III ACNGT 1 cut(s) 323
HpyCH4IV ACGT 3 cut(s) 66, 267, 630
HpyCH4V TGCA 6 cut(s) 142, 380, 416, 530, 859, 1042
HpyF10VI GCNNNNNNNGC 6 cut(s) 59, 205, 224, 403, 861, 1034
HpyF3I CTNAG 5 cut(s) 74, 309, 348, 594, 729
HpySE526I ACGT 3 cut(s) 66, 267, 630
Hsp92I GRCGYC 2 cut(s) 111, 267
Hsp92II CATG 8 cut(s) 43, 97, 223, 587, 609, 673, 947, 956
HspAI GCGC 1 cut(s) 137
KspAI GTTAAC 1 cut(s) 301
Kzo9I GATC 2 cut(s) 427, 502
LmnI GCTCC 3 cut(s) 411, 553, 711
Lsp1109I GCAGC 4 cut(s) 121, 126, 409, 607
MaeI CTAG 4 cut(s) 209, 438, 828, 1048
MaeII ACGT 3 cut(s) 66, 267, 630
MaeIII GTNAC 2 cut(s) 359, 982
MalI GATC 2 cut(s) 429, 504
MboI GATC 2 cut(s) 427, 502
MboII GAAGA 5 cut(s) 173, 222, 238, 779, 983
MhlI GDGCHC 5 cut(s) 168, 408, 823, 978, 1012
MluCI AATT 3 cut(s) 687, 849, 876
MlyI GAGTC 3 cut(s) 335, 356, 380
MmeI TCCRAC 1 cut(s) 315
MseI TTAA 2 cut(s) 300, 735
MspI CCGG 1 cut(s) 240
MspR9I CCNGG 3 cut(s) 150, 648, 1034
MvaI CCWGG 3 cut(s) 150, 648, 1034
MvnI CGCG 1 cut(s) 432
MwoI GCNNNNNNNGC 6 cut(s) 59, 205, 224, 403, 861, 1034
NcoI CCATGG 1 cut(s) 39
NdeII GATC 2 cut(s) 427, 502
NheI GCTAGC 1 cut(s) 208
NlaIII CATG 8 cut(s) 43, 97, 223, 587, 609, 673, 947, 956
NlaIV GGNNCC 2 cut(s) 345, 1011
NmeAIII GCCGAG 3 cut(s) 110, 344, 394
NmuCI GTSAC 1 cut(s) 359
NruI TCGCGA 1 cut(s) 432
PaeR7I CTCGAG 1 cut(s) 256
PasI CCCWGGG 1 cut(s) 149
PcsI WCGNNNNNNNCGW 1 cut(s) 273
PfeI GAWTC 2 cut(s) 338, 564
PflFI GACNNNGTC 1 cut(s) 269
PkrI GCNGC 9 cut(s) 80, 83, 115, 136, 141, 399, 478, 622, 1044
PleI GAGTC 3 cut(s) 334, 356, 379
PpsI GAGTC 3 cut(s) 334, 356, 379
Psp124BI GAGCTC 1 cut(s) 408
Psp6I CCWGG 3 cut(s) 148, 646, 1032
PspGI CCWGG 3 cut(s) 148, 646, 1032
PspN4I GGNNCC 2 cut(s) 345, 1011
PspPI GGNCC 2 cut(s) 343, 1026
PsyI GACNNNGTC 1 cut(s) 269
RruI TCGCGA 1 cut(s) 432
RsaI GTAC 2 cut(s) 50, 1017
RsaNI GTAC 2 cut(s) 49, 1016
SacI GAGCTC 1 cut(s) 408
SaqAI TTAA 2 cut(s) 300, 735
SatI GCNGC 9 cut(s) 79, 82, 114, 135, 140, 398, 477, 621, 1043
Sau3AI GATC 2 cut(s) 427, 502
Sau96I GGNCC 2 cut(s) 343, 1026
SchI GAGTC 3 cut(s) 335, 356, 380
ScrFI CCNGG 3 cut(s) 150, 648, 1034
SduI GDGCHC 5 cut(s) 168, 408, 823, 978, 1012
SfcI CTRYAG 1 cut(s) 715
Sfr274I CTCGAG 1 cut(s) 256
SinI GGWCC 1 cut(s) 343
SlaI CTCGAG 1 cut(s) 256
SmlI CTYRAG 3 cut(s) 256, 572, 971
SmoI CTYRAG 3 cut(s) 256, 572, 971
SpeI ACTAGT 1 cut(s) 437
Sse9I AATT 3 cut(s) 687, 849, 876
SspMI CTAG 4 cut(s) 209, 438, 828, 1048
SstI GAGCTC 1 cut(s) 408
StyD4I CCNGG 3 cut(s) 148, 646, 1032
StyI CCWWGG 2 cut(s) 39, 827
TaaI ACNGT 1 cut(s) 323
TaiI ACGT 3 cut(s) 69, 270, 633
TaqI TCGA 2 cut(s) 257, 421
TaqII GACCGA 2 cut(s) 331, 579
TasI AATT 3 cut(s) 687, 849, 876
TauI GCSGC 4 cut(s) 81, 84, 116, 479
TfiI GAWTC 2 cut(s) 338, 564
Tru1I TTAA 2 cut(s) 300, 735
Tru9I TTAA 2 cut(s) 300, 735
TseFI GTSAC 1 cut(s) 359
TseI GCWGC 5 cut(s) 134, 139, 397, 620, 1042
Tsp45I GTSAC 1 cut(s) 359
TspDTI ATGAA 3 cut(s) 759, 941, 960
TspGWI ACGGA 1 cut(s) 319
Tth111I GACNNNGTC 1 cut(s) 269
VpaK11BI GGWCC 1 cut(s) 343
XapI RAATTY 3 cut(s) 687, 849, 876
XhoI CTCGAG 1 cut(s) 256
XmaJI CCTAGG 1 cut(s) 827
XmiI GTMKAC 1 cut(s) 273
XspI CTAG 4 cut(s) 209, 438, 828, 1048
ZraI GACGTC 1 cut(s) 268
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.