MD01G1138500.v1.1

Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs)

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr01
OG0012533
Physical Location & Seq
Reverse (-)
24798526 .. 24799494
969 bp
Loading structure...
UTR
Exon/CDS
Intron
MD01G1138500.v1.1.491

Sequence Viewer

Length: 969 bp
ATGGCGAATCGATGGTGGGCTGGAAATGTTTCCATGGGGGGAGGAGGAGGAGTTCATGTGGACTCAATCTCCTCGACTCCGCCTTCTCTCCACCTCAGGAACACTGAGGAACAGCTTGACGACCAAAACAACACGACCACTCCCACCAACAGCAGCACCAGCCCTCACAAGCAGAACAAGAAACACCACGAAGACGACCGGGACAACAATGATCAGGAAGGCGACGATCAGGGCCCCAACACTGGTAGCGGCAGCCATGACAGCCTCGAGCCTGGAAGCAGCAACCGGAGGCCGCGTGGCCGGCCGCCCGGGTCGAAGAACAAGCCTAAACCCCCCATAGTCATCACCAAAGAGAGCCCCAACGCTCTCCGAAGCCATGTGTTGGAAATTAGTAGCGGCAGCGACATTGTGGACAGCATTGCCACCTTTGCCCAAAGGCGGCATAGAGGGGTTTCGGTTCTCAGCGGAAGTGGCATTGTCGCCAATGTCACTCTCCGACAACCAGCAGCACCAACTGGAGTGATCACATTGCACGGAAGGTTCGAGATACTATCGATGTCAGGAGCATTCCTGCCTTCCCCATCCCCACCTGGGGCGACAGGGCTGACCGTGTACTTGGCAGGCGGCCAGGGGCAGGTGGTGGGAGGCACCGTGATGGGAGCATTGGTGGCTTCCGGTCCAGTGATGGTTATAGCAGCTACCTTCACAAACGCGACATATGAGAGGCTGCCGCTTGAGGAGGAACAAGGTGGAGAAGAGGGAATGCAGTTGGAGCAACAGCAGCAGCAGCAATCAGGTGTGAATTCGGCAGGGACAGGAGCAAATTCAAATTCCCAAGGTTTGGGTGAGCATACTAGTGCAATGGCTGTTTACAATTTGCCTTCAAATTTACTTGCGAATGGTGGTCAGATCCCTCATGATATATTCTGGGGTCCTCCCCCTCCAAGACCTCCTCCTCCATCTTACTGA
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
DUF296

Protein Analysis

323

Amino Acids

33.7

Weight (kDa)

5.86

Isoelectric Point (pI)

56.52

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PCC PF03479 124 - 237 5.6e-24 Plants and Prokaryotes Conserved (PCC) domain
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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Orthologous Genes (Group: OG0012533)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G55560
fragaria_vesca FvH4_7g22970
malus_domestica MD01G1138500.v1.1 MD07G1202700.v1.1
prunus_persica Prupe.2G239000_v2.0.a1
pyrus_communis pycom01g15920 pycom07g18970
rosa_chinensis RchiOBHm_Chr1g0368171
rosa_laevigata RLG00000027233
rosa_multiflora Rmu_sc0006814.1_g000001 Rmu_sc0020763.1_g000001 Rmu_sc0035888.1_g000001
rosa_roxburghii Rroxscaffold_4G00288830
rosa_rugosa Rorug01G0339100
rosa_samantha Rh1AG346600 Rh1BG309200 Rh1CG324700 Rh1DG341100
rosa_wichuraiana Rw1G030810

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AarI CACCTGC 1 cut(s) 625
Acc36I ACCTGC 1 cut(s) 625
AccB1I GGYRCC 1 cut(s) 647
AccB7I CCANNNNNTGG 2 cut(s) 382, 841
AccII CGCG 2 cut(s) 295, 713
AciI CCGC 9 cut(s) 80, 249, 293, 305, 396, 439, 465, 624, 731
AclWI GGATC 1 cut(s) 904
AcoI YGGCCR 3 cut(s) 298, 302, 625
AcsI RAATTY 4 cut(s) 802, 823, 829, 886
AfaI GTAC 1 cut(s) 614
AfiI CCNNNNNNNGG 7 cut(s) 242, 382, 438, 591, 592, 634, 841
AgsI TTSAA 2 cut(s) 828, 885
AhlI ACTAGT 1 cut(s) 854
AjnI CCWGG 3 cut(s) 271, 589, 627
AloI GAACNNNNNNTCC 2 cut(s) 36, 68
AluBI AGCT 2 cut(s) 115, 698
AluI AGCT 2 cut(s) 115, 698
AlwI GGATC 1 cut(s) 904
Ama87I CYCGRG 2 cut(s) 266, 308
AoxI GGCC 5 cut(s) 232, 290, 298, 302, 625
ApaI GGGCCC 1 cut(s) 236
ApoI RAATTY 4 cut(s) 802, 823, 829, 886
Asp700I GAANNNNTTC 1 cut(s) 28
AspS9I GGNCC 4 cut(s) 232, 233, 677, 932
AsuC2I CCSGG 3 cut(s) 200, 309, 310
AsuHPI GGTGA 2 cut(s) 337, 857
AvaI CYCGRG 2 cut(s) 266, 308
AvaII GGWCC 2 cut(s) 677, 932
AxyI CCTNAGG 1 cut(s) 95
BaeGI GKGCMC 1 cut(s) 236
BanI GGYRCC 1 cut(s) 647
BanII GRGCYC 2 cut(s) 236, 359
BbsI GAAGAC 1 cut(s) 198
BccI CCATC 5 cut(s) 6, 589, 649, 679, 967
BciT130I CCWGG 3 cut(s) 273, 591, 629
BclI TGATCA 2 cut(s) 211, 522
BcnI CCSGG 3 cut(s) 200, 309, 310
BcuI ACTAGT 1 cut(s) 854
BfaI CTAG 1 cut(s) 855
BfuAI ACCTGC 1 cut(s) 625
Bme1390I CCNGG 6 cut(s) 200, 273, 309, 310, 591, 629
Bme18I GGWCC 2 cut(s) 677, 932
BmeT110I CYCGRG 2 cut(s) 266, 308
BmgT120I GGNCC 4 cut(s) 232, 233, 677, 932
BmiI GGNNCC 4 cut(s) 234, 235, 649, 933
BmrFI CCNGG 6 cut(s) 200, 273, 309, 310, 591, 629
BpiI GAAGAC 1 cut(s) 198
BpmI CTGGAG 1 cut(s) 537
BpuEI CTTGAG 1 cut(s) 755
BpuMI CCSGG 3 cut(s) 200, 309, 310
Bsa29I ATCGAT 2 cut(s) 10, 554
BsaJI CCNNGG 5 cut(s) 33, 308, 590, 628, 835
BsaWI WCCGGW 2 cut(s) 285, 674
Bsc4I CCNNNNNNNGG 7 cut(s) 242, 382, 438, 591, 592, 634, 841
Bse118I RCCGGY 1 cut(s) 300
Bse1I ACTGG 3 cut(s) 247, 520, 680
Bse21I CCTNAGG 1 cut(s) 95
Bse3DI GCAATG 3 cut(s) 417, 527, 867
BseBI CCWGG 3 cut(s) 273, 591, 629
BseCI ATCGAT 2 cut(s) 10, 554
BseDI CCNNGG 5 cut(s) 33, 308, 590, 628, 835
BseGI GGATG 1 cut(s) 581
BseLI CCNNNNNNNGG 7 cut(s) 242, 382, 438, 591, 592, 634, 841
BseMI GCAATG 3 cut(s) 417, 527, 867
BseMII CTCAG 3 cut(s) 96, 109, 475
BseNI ACTGG 3 cut(s) 247, 520, 680
BseRI GAGGAG 7 cut(s) 57, 60, 61, 63, 752, 942, 945
BseSI GKGCMC 1 cut(s) 236
BseX3I CGGCCG 1 cut(s) 302
Bsh1236I CGCG 2 cut(s) 295, 713
Bsh1285I CGRYCG 2 cut(s) 199, 305
BshFI GGCC 5 cut(s) 234, 292, 300, 304, 627
BshNI GGYRCC 1 cut(s) 647
BshVI ATCGAT 2 cut(s) 10, 554
BsiEI CGRYCG 2 cut(s) 199, 305
BsiHKCI CYCGRG 2 cut(s) 266, 308
BsiSI CCGG 5 cut(s) 199, 286, 301, 309, 675
BslFI GGGAC 2 cut(s) 215, 826
BslI CCNNNNNNNGG 7 cut(s) 242, 382, 438, 591, 592, 634, 841
BsmFI GGGAC 2 cut(s) 215, 826
BsmI GAATGC 2 cut(s) 566, 768
BsnI GGCC 5 cut(s) 234, 292, 300, 304, 627
BsoBI CYCGRG 2 cut(s) 266, 308
Bsp120I GGGCCC 1 cut(s) 232
Bsp1286I GDGCHC 2 cut(s) 236, 359
Bsp143I GATC 4 cut(s) 211, 226, 522, 909
Bsp19I CCATGG 1 cut(s) 33
BspACI CCGC 9 cut(s) 80, 249, 293, 305, 396, 439, 465, 624, 731
BspANI GGCC 5 cut(s) 234, 292, 300, 304, 627
BspCNI CTCAG 3 cut(s) 97, 108, 474
BspDI ATCGAT 2 cut(s) 10, 554
BspFNI CGCG 2 cut(s) 295, 713
BspHI TCATGA 1 cut(s) 916
BspLI GGNNCC 4 cut(s) 234, 235, 649, 933
BspMI ACCTGC 1 cut(s) 625
BspPI GGATC 1 cut(s) 904
BspT107I GGYRCC 1 cut(s) 647
BsrDI GCAATG 3 cut(s) 417, 527, 867
BsrFI RCCGGY 1 cut(s) 300
BsrI ACTGG 3 cut(s) 247, 520, 680
BssAI RCCGGY 1 cut(s) 300
BssECI CCNNGG 5 cut(s) 33, 308, 590, 628, 835
BssMI GATC 4 cut(s) 211, 226, 522, 909
BssT1I CCWWGG 2 cut(s) 33, 835
Bst2UI CCWGG 3 cut(s) 273, 591, 629
Bst4CI ACNGT 2 cut(s) 610, 652
Bst6I CTCTTC 1 cut(s) 750
BstC8I GCNNGC 2 cut(s) 302, 622
BstDEI CTNAG 3 cut(s) 95, 105, 461
BstDSI CCRYGG 1 cut(s) 33
BstF5I GGATG 1 cut(s) 581
BstFNI CGCG 2 cut(s) 295, 713
BstKTI GATC 4 cut(s) 214, 229, 525, 912
BstMBI GATC 4 cut(s) 211, 226, 522, 909
BstMCI CGRYCG 2 cut(s) 199, 305
BstMWI GCNNNNNNNGC 9 cut(s) 159, 261, 301, 428, 471, 668, 772, 781, 787
BstNI CCWGG 3 cut(s) 273, 591, 629
BstSCI CCNGG 6 cut(s) 198, 271, 307, 308, 589, 627
BstSLI GKGCMC 1 cut(s) 236
BstUI CGCG 2 cut(s) 295, 713
BstV2I GAAGAC 1 cut(s) 198
BstX2I RGATCY 1 cut(s) 909
BstYI RGATCY 1 cut(s) 909
BstZI CGGCCG 1 cut(s) 302
Bsu15I ATCGAT 2 cut(s) 10, 554
Bsu36I CCTNAGG 1 cut(s) 95
BsuRI GGCC 5 cut(s) 234, 292, 300, 304, 627
BsuTUI ATCGAT 2 cut(s) 10, 554
BtgI CCRYGG 1 cut(s) 33
BtsCI GGATG 1 cut(s) 581
BtsIMutI CAGTG 3 cut(s) 102, 240, 687
BveI ACCTGC 1 cut(s) 625
Cac8I GCNNGC 2 cut(s) 302, 622
CciI TCATGA 1 cut(s) 916
Cfr10I RCCGGY 1 cut(s) 300
Cfr13I GGNCC 4 cut(s) 232, 233, 677, 932
Cfr9I CCCGGG 1 cut(s) 308
ClaI ATCGAT 2 cut(s) 10, 554
Csp6I GTAC 1 cut(s) 613
CviAII CATG 5 cut(s) 34, 56, 257, 377, 917
CviQI GTAC 1 cut(s) 613
DdeI CTNAG 3 cut(s) 95, 105, 461
DpnI GATC 4 cut(s) 213, 228, 524, 911
DpnII GATC 4 cut(s) 211, 226, 522, 909
EaeI YGGCCR 3 cut(s) 298, 302, 625
EagI CGGCCG 1 cut(s) 302
Eam1104I CTCTTC 1 cut(s) 750
EarI CTCTTC 1 cut(s) 750
EciI GGCGGA 1 cut(s) 69
EclXI CGGCCG 1 cut(s) 302
Eco130I CCWWGG 2 cut(s) 33, 835
Eco24I GRGCYC 2 cut(s) 236, 359
Eco47I GGWCC 2 cut(s) 677, 932
Eco52I CGGCCG 1 cut(s) 302
Eco81I CCTNAGG 1 cut(s) 95
Eco88I CYCGRG 2 cut(s) 266, 308
EcoO109I RGGNCCY 3 cut(s) 232, 233, 932
EcoRI GAATTC 1 cut(s) 802
EcoRII CCWGG 3 cut(s) 271, 589, 627
EcoT14I CCWWGG 2 cut(s) 33, 835
EcoT38I GRGCYC 2 cut(s) 236, 359
ErhI CCWWGG 2 cut(s) 33, 835
FaeI CATG 5 cut(s) 37, 59, 260, 380, 920
FaqI GGGAC 2 cut(s) 215, 826
FatI CATG 5 cut(s) 33, 55, 256, 376, 916
FauNDI CATATG 1 cut(s) 718
FbaI TGATCA 2 cut(s) 211, 522
FokI GGATG 1 cut(s) 568
FriOI GRGCYC 2 cut(s) 236, 359
FseI GGCCGGCC 1 cut(s) 304
FspBI CTAG 1 cut(s) 855
GsuI CTGGAG 1 cut(s) 537
HaeIII GGCC 5 cut(s) 234, 292, 300, 304, 627
HapII CCGG 5 cut(s) 199, 286, 301, 309, 675
Hin1II CATG 5 cut(s) 37, 59, 260, 380, 920
HinfI GANTC 3 cut(s) 7, 62, 76
HpaII CCGG 5 cut(s) 199, 286, 301, 309, 675
HphI GGTGA 2 cut(s) 337, 857
Hpy166II GTNNAC 4 cut(s) 61, 412, 613, 871
Hpy188I TCNGA 3 cut(s) 371, 497, 909
Hpy188III TCNNGA 5 cut(s) 97, 215, 544, 561, 917
Hpy8I GTNNAC 4 cut(s) 61, 412, 613, 871
Hpy99I CGWCG 1 cut(s) 227
HpyAV CCTTC 6 cut(s) 93, 212, 531, 585, 712, 891
HpyCH4III ACNGT 2 cut(s) 610, 652
HpyCH4V TGCA 3 cut(s) 532, 766, 860
HpyF10VI GCNNNNNNNGC 9 cut(s) 159, 261, 301, 428, 471, 668, 772, 781, 787
HpyF3I CTNAG 3 cut(s) 95, 105, 461
Hsp92II CATG 5 cut(s) 37, 59, 260, 380, 920
KroI GCCGGC 1 cut(s) 300
KroNI GCCGGC 1 cut(s) 302
Ksp22I TGATCA 2 cut(s) 211, 522
Kzo9I GATC 4 cut(s) 211, 226, 522, 909
LmnI GCTCC 4 cut(s) 563, 659, 772, 818
MaeI CTAG 1 cut(s) 855
MaeIII GTNAC 1 cut(s) 487
MalI GATC 4 cut(s) 213, 228, 524, 911
MboI GATC 4 cut(s) 211, 226, 522, 909
MboII GAAGA 3 cut(s) 203, 328, 767
MflI RGATCY 1 cut(s) 909
MhlI GDGCHC 2 cut(s) 236, 359
MluCI AATT 6 cut(s) 387, 802, 823, 829, 874, 886
MlyI GAGTC 2 cut(s) 56, 70
MmeI TCCRAC 3 cut(s) 363, 520, 750
MroNI GCCGGC 1 cut(s) 300
MroXI GAANNNNTTC 1 cut(s) 28
MslI CAYNNNNRTG 2 cut(s) 653, 855
MspA1I CMGCKG 1 cut(s) 465
MspI CCGG 5 cut(s) 199, 286, 301, 309, 675
MspR9I CCNGG 6 cut(s) 200, 273, 309, 310, 591, 629
Mva1269I GAATGC 2 cut(s) 566, 768
MvaI CCWGG 3 cut(s) 273, 591, 629
MvnI CGCG 2 cut(s) 295, 713
MwoI GCNNNNNNNGC 9 cut(s) 159, 261, 301, 428, 471, 668, 772, 781, 787
NaeI GCCGGC 1 cut(s) 302
NciI CCSGG 3 cut(s) 200, 309, 310
NcoI CCATGG 1 cut(s) 33
NdeI CATATG 1 cut(s) 718
NdeII GATC 4 cut(s) 211, 226, 522, 909
NgoMIV GCCGGC 1 cut(s) 300
NlaIII CATG 5 cut(s) 37, 59, 260, 380, 920
NlaIV GGNNCC 4 cut(s) 234, 235, 649, 933
NmuCI GTSAC 1 cut(s) 487
PaeR7I CTCGAG 1 cut(s) 266
PagI TCATGA 1 cut(s) 916
PaqCI CACCTGC 1 cut(s) 625
PcsI WCGNNNNNNNCGW 1 cut(s) 540
PctI GAATGC 2 cut(s) 566, 768
PdiI GCCGGC 1 cut(s) 302
PdmI GAANNNNTTC 1 cut(s) 28
PfeI GAWTC 1 cut(s) 7
PflMI CCANNNNNTGG 2 cut(s) 382, 841
PleI GAGTC 2 cut(s) 56, 70
PpsI GAGTC 2 cut(s) 56, 70
PpuMI RGGWCCY 1 cut(s) 932
Psp5II RGGWCCY 1 cut(s) 932
Psp6I CCWGG 3 cut(s) 271, 589, 627
PspGI CCWGG 3 cut(s) 271, 589, 627
PspN4I GGNNCC 4 cut(s) 234, 235, 649, 933
PspOMI GGGCCC 1 cut(s) 232
PspPI GGNCC 4 cut(s) 232, 233, 677, 932
PspPPI RGGWCCY 1 cut(s) 932
PspXI VCTCGAGB 1 cut(s) 266
PsuI RGATCY 1 cut(s) 909
RigI GGCCGGCC 1 cut(s) 304
RsaI GTAC 1 cut(s) 614
RsaNI GTAC 1 cut(s) 613
RseI CAYNNNNRTG 2 cut(s) 653, 855
Sau3AI GATC 4 cut(s) 211, 226, 522, 909
Sau96I GGNCC 4 cut(s) 232, 233, 677, 932
SchI GAGTC 2 cut(s) 56, 70
ScrFI CCNGG 6 cut(s) 200, 273, 309, 310, 591, 629
SduI GDGCHC 2 cut(s) 236, 359
Sfr274I CTCGAG 1 cut(s) 266
SinI GGWCC 2 cut(s) 677, 932
SlaI CTCGAG 1 cut(s) 266
SmaI CCCGGG 1 cut(s) 310
SmiMI CAYNNNNRTG 2 cut(s) 653, 855
SmlI CTYRAG 2 cut(s) 266, 734
SmoI CTYRAG 2 cut(s) 266, 734
SpeI ACTAGT 1 cut(s) 854
Sse9I AATT 6 cut(s) 387, 802, 823, 829, 874, 886
SsiI CCGC 9 cut(s) 80, 249, 293, 305, 396, 439, 465, 624, 731
SspMI CTAG 1 cut(s) 855
StyD4I CCNGG 6 cut(s) 198, 271, 307, 308, 589, 627
StyI CCWWGG 2 cut(s) 33, 835
TaaI ACNGT 2 cut(s) 610, 652
TaqI TCGA 6 cut(s) 10, 74, 267, 314, 543, 554
TasI AATT 6 cut(s) 387, 802, 823, 829, 874, 886
TatI WGTACW 1 cut(s) 612
TauI GCSGC 7 cut(s) 252, 295, 307, 399, 442, 627, 733
TfiI GAWTC 1 cut(s) 7
TscAI CASTG 3 cut(s) 109, 247, 687
TseFI GTSAC 1 cut(s) 487
Tsp45I GTSAC 1 cut(s) 487
TspDTI ATGAA 1 cut(s) 44
TspGWI ACGGA 1 cut(s) 549
TspMI CCCGGG 1 cut(s) 308
TspRI CASTG 3 cut(s) 109, 247, 687
Van91I CCANNNNNTGG 2 cut(s) 382, 841
VpaK11BI GGWCC 2 cut(s) 677, 932
XapI RAATTY 4 cut(s) 802, 823, 829, 886
XhoI CTCGAG 1 cut(s) 266
XmaI CCCGGG 1 cut(s) 308
XmnI GAANNNNTTC 1 cut(s) 28
XspI CTAG 1 cut(s) 855
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.