MD06G1003000.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
Chr06
OG0014937
Physical Location & Seq
Reverse (-)
330608 .. 331639
1032 bp
Loading structure...
UTR
Exon/CDS
Intron
MD06G1003000.v1.1.491

Sequence Viewer

Length: 1032 bp
ATGGCAGGGTACAATATAAATGAGTCAGCCTCGGTCTCTGCCGCCTCATCAGCCCCAACTTCAACTGCTTCTCCCTATGTCCACCCGCTCTTCAGGCCCCAACTCCACCTCCAACTCCAACAACTCCATCACCATCCTATTATTCCTCAACAACAACAACATCATCATCAACAAGAAGAACAAGATGATGATGATGACCAGGACGACGACCAAGACCACAATATTACTAAGATCGAATCTTCCGATACCGCCGCAACCAGTTCTGGTGGCGGTGGAGGCGGAGGTGGAACTGGTGGTTCCACCCGCCGTCCCAGAGGCCGTCCTGCAGGCTCCAAGAACAAACCCAAGCCTCCCATCATCGTCACACGCGACAGCCCCAACGCCCTCCGCTCCCACGTCCTTGAGGTCTCCGATGGGGCCGACATCATGGACAGCGTCTCCATCTACGCCAGGCGCAGGGGCAGAGGCGTCTGCGTGCTCAGCGGCAGCGGCACTGTCACCAACGTCACCCTGCGTCAGCCAGCTGCTCCTCCGGGAAGCGTGGTGACTCTTCACGGACGCTTCGAGTTACTATCGCTCTCCGGTACGGTGCTTCCCCCTCCGGCTCCTCCCGGTGCCGGCGGACTCTCCATATTCTTGTCCGGGGGGCAGGGACAAGTGGTGGGAGGAAACGTGGTGGGACCGCTGATGGCCTCCGGGCCTGTGGTTTTGATGGCTGCGTCTTTTGCAAATGCGGTGTTTGAGAGATTGCCATTGGATGATCCGGAAGAGGGAACTACTACTCCTACTGGTGGTGGTGGCGGAGGCAGCTTGCAAATCCATCAACCCACGGGGTCCCAATCTTCTGGGGTGTCTGGCGGTCTTGGTGATGGTACTGCTGGAAGTAGCGGCGGAGGTGGAGGTGGAGGTGGAGGTGCTGGGCTTTTTAATTTGGGAGGAAATATGGCGGCCAACTATCCCTTCCCGGGGAGTGACTTCTTCGGATGGGGTGGTGGAAGTGGAAGTGGAAGTACTCCGCGGCCTCCGTTTTAG
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

344

Amino Acids

34.32

Weight (kDa)

5.78

Isoelectric Point (pI)

61.68

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PCC PF03479 130 - 243 8.7e-22 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: OG0014937)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G20900 AT1G76500
fragaria_vesca FvH4_5g26230
malus_domestica MD06G1003000.v1.1
prunus_persica Prupe.5G004600_v2.0.a1
pyrus_communis pycom06g00310
rosa_chinensis RchiOBHm_Chr7g0216901
rosa_laevigata RLG00000002528
rosa_multiflora Rmu_sc0000854.1_g000020
rosa_roxburghii Rroxscaffold_3G00242760
rosa_rugosa Rorug07G0164300
rosa_samantha Rh7AG304600 Rh7BG296100 Rh7CG323000 Rh7DG304600
rosa_wichuraiana Rw7G025860

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 1 cut(s) 614
AccBSI CCGCTC 2 cut(s) 88, 390
AccII CGCG 2 cut(s) 369, 1018
AccIII TCCGGA 1 cut(s) 763
AclWI GGATC 1 cut(s) 755
AcoI YGGCCR 1 cut(s) 948
AcuI CTGAAG 1 cut(s) 76
AcyI GRCGYC 1 cut(s) 468
AfaI GTAC 4 cut(s) 11, 586, 874, 1012
AfiI CCNNNNNNNGG 6 cut(s) 456, 617, 770, 791, 965, 966
AgsI TTSAA 1 cut(s) 63
AjiI CACGTC 1 cut(s) 397
AjnI CCWGG 2 cut(s) 198, 449
AjuI GAANNNNNNNTTGG 2 cut(s) 944, 976
AloI GAACNNNNNNTCC 2 cut(s) 766, 798
AluBI AGCT 2 cut(s) 524, 810
AluI AGCT 2 cut(s) 524, 810
Alw21I GWGCWC 1 cut(s) 480
Alw26I GTCTC 3 cut(s) 40, 412, 442
AlwI GGATC 1 cut(s) 755
Ama87I CYCGRG 1 cut(s) 964
Aor13HI TCCGGA 1 cut(s) 763
AoxI GGCC 7 cut(s) 95, 316, 417, 690, 698, 948, 1019
ApeKI GCWGC 4 cut(s) 486, 524, 716, 807
AspLEI GCGC 1 cut(s) 456
AspS9I GGNCC 5 cut(s) 96, 417, 680, 698, 834
AsuC2I CCSGG 6 cut(s) 534, 612, 643, 697, 965, 966
AsuHPI GGTGA 5 cut(s) 122, 490, 499, 556, 878
AvaI CYCGRG 1 cut(s) 964
AvaII GGWCC 2 cut(s) 680, 834
BanI GGYRCC 1 cut(s) 614
BarI GAAGNNNNNNTAC 2 cut(s) 994, 1026
Bbv12I GWGCWC 1 cut(s) 480
BbvI GCAGC 4 cut(s) 498, 511, 703, 819
BceAI ACGGC 2 cut(s) 291, 303
BciT130I CCWGG 2 cut(s) 200, 451
BcnI CCSGG 6 cut(s) 534, 612, 643, 697, 965, 966
BcoDI GTCTC 3 cut(s) 40, 412, 442
BfmI CTRYAG 1 cut(s) 324
BlpI GCTNAGC 1 cut(s) 479
BmcAI AGTACT 1 cut(s) 1012
Bme1390I CCNGG 8 cut(s) 200, 451, 534, 612, 643, 697, 965, 966
Bme18I GGWCC 2 cut(s) 680, 834
BmeT110I CYCGRG 1 cut(s) 964
BmgBI CACGTC 1 cut(s) 397
BmgT120I GGNCC 5 cut(s) 96, 417, 680, 698, 834
BmiI GGNNCC 9 cut(s) 98, 298, 331, 418, 606, 616, 681, 835, 836
BmrFI CCNGG 8 cut(s) 200, 451, 534, 612, 643, 697, 965, 966
BplI GAGNNNNNCTC 2 cut(s) 14, 46
Bpu1102I GCTNAGC 1 cut(s) 479
BpuEI CTTGAG 1 cut(s) 422
BpuMI CCSGG 6 cut(s) 534, 612, 643, 697, 965, 966
BsaHI GRCGYC 1 cut(s) 468
BsaI GGTCTC 2 cut(s) 40, 412
BsaJI CCNNGG 6 cut(s) 30, 642, 828, 964, 965, 1016
BsaWI WCCGGW 2 cut(s) 581, 763
Bsc4I CCNNNNNNNGG 6 cut(s) 456, 617, 770, 791, 965, 966
Bse118I RCCGGY 1 cut(s) 617
Bse1I ACTGG 3 cut(s) 258, 295, 793
BseAI TCCGGA 1 cut(s) 763
BseBI CCWGG 2 cut(s) 200, 451
BseDI CCNNGG 6 cut(s) 30, 642, 828, 964, 965, 1016
BseGI GGATG 3 cut(s) 133, 763, 989
BseLI CCNNNNNNNGG 6 cut(s) 456, 617, 770, 791, 965, 966
BseMII CTCAG 1 cut(s) 493
BseNI ACTGG 3 cut(s) 258, 295, 793
BseRI GAGGAG 2 cut(s) 519, 597
BseXI GCAGC 4 cut(s) 498, 511, 703, 819
BseYI CCCAGC 1 cut(s) 917
Bsh1236I CGCG 2 cut(s) 369, 1018
BshFI GGCC 7 cut(s) 97, 318, 419, 692, 700, 950, 1021
BshNI GGYRCC 1 cut(s) 614
BsiHKAI GWGCWC 1 cut(s) 480
BsiHKCI CYCGRG 1 cut(s) 964
BsiSI CCGG 9 cut(s) 533, 582, 602, 612, 618, 642, 696, 764, 965
BslFI GGGAC 4 cut(s) 294, 666, 693, 820
BslI CCNNNNNNNGG 6 cut(s) 456, 617, 770, 791, 965, 966
BsmAI GTCTC 3 cut(s) 40, 412, 442
BsmBI CGTCTC 1 cut(s) 442
BsmFI GGGAC 4 cut(s) 294, 666, 693, 820
BsnI GGCC 7 cut(s) 97, 318, 419, 692, 700, 950, 1021
Bso31I GGTCTC 2 cut(s) 40, 412
BsoBI CYCGRG 1 cut(s) 964
Bsp1286I GDGCHC 1 cut(s) 480
Bsp13I TCCGGA 1 cut(s) 763
Bsp143I GATC 2 cut(s) 231, 760
Bsp1720I GCTNAGC 1 cut(s) 479
BspANI GGCC 7 cut(s) 97, 318, 419, 692, 700, 950, 1021
BspCNI CTCAG 1 cut(s) 492
BspEI TCCGGA 1 cut(s) 763
BspFNI CGCG 2 cut(s) 369, 1018
BspLI GGNNCC 9 cut(s) 98, 298, 331, 418, 606, 616, 681, 835, 836
BspMAI CTGCAG 1 cut(s) 328
BspPI GGATC 1 cut(s) 755
BspQI GCTCTTC 1 cut(s) 95
BspT107I GGYRCC 1 cut(s) 614
BspTNI GGTCTC 2 cut(s) 40, 412
BsrBI CCGCTC 2 cut(s) 88, 390
BsrFI RCCGGY 1 cut(s) 617
BsrI ACTGG 3 cut(s) 258, 295, 793
BssAI RCCGGY 1 cut(s) 617
BssECI CCNNGG 6 cut(s) 30, 642, 828, 964, 965, 1016
BssMI GATC 2 cut(s) 231, 760
BssNI GRCGYC 1 cut(s) 468
Bst2UI CCWGG 2 cut(s) 200, 451
Bst4CI ACNGT 2 cut(s) 496, 589
Bst6I CTCTTC 3 cut(s) 95, 555, 762
BstACI GRCGYC 1 cut(s) 468
BstC8I GCNNGC 5 cut(s) 328, 476, 522, 619, 812
BstDEI CTNAG 2 cut(s) 228, 479
BstDSI CCRYGG 2 cut(s) 828, 1016
BstF5I GGATG 3 cut(s) 133, 763, 989
BstFNI CGCG 2 cut(s) 369, 1018
BstHHI GCGC 1 cut(s) 456
BstKTI GATC 2 cut(s) 234, 763
BstMAI GTCTC 3 cut(s) 40, 412, 442
BstMBI GATC 2 cut(s) 231, 760
BstMWI GCNNNNNNNGC 7 cut(s) 50, 94, 276, 480, 489, 725, 807
BstNI CCWGG 2 cut(s) 200, 451
BstSCI CCNGG 8 cut(s) 198, 449, 532, 610, 641, 695, 963, 964
BstSFI CTRYAG 1 cut(s) 324
BstUI CGCG 2 cut(s) 369, 1018
BstV1I GCAGC 4 cut(s) 498, 511, 703, 819
BstXI CCANNNNNNTGG 1 cut(s) 845
BsuRI GGCC 7 cut(s) 97, 318, 419, 692, 700, 950, 1021
BtgI CCRYGG 2 cut(s) 828, 1016
BtrI CACGTC 1 cut(s) 397
BtsCI GGATG 3 cut(s) 133, 763, 989
BtsIMutI CAGTG 1 cut(s) 492
Cac8I GCNNGC 5 cut(s) 328, 476, 522, 619, 812
CfoI GCGC 1 cut(s) 456
Cfr10I RCCGGY 1 cut(s) 617
Cfr13I GGNCC 5 cut(s) 96, 417, 680, 698, 834
Cfr42I CCGCGG 1 cut(s) 1019
Cfr9I CCCGGG 1 cut(s) 964
CseI GACGC 5 cut(s) 424, 457, 503, 567, 708
Csp6I GTAC 4 cut(s) 10, 585, 873, 1011
CviAII CATG 1 cut(s) 427
CviQI GTAC 4 cut(s) 10, 585, 873, 1011
DdeI CTNAG 2 cut(s) 228, 479
DpnI GATC 2 cut(s) 233, 762
DpnII GATC 2 cut(s) 231, 760
EaeI YGGCCR 1 cut(s) 948
Eam1104I CTCTTC 3 cut(s) 95, 555, 762
EarI CTCTTC 3 cut(s) 95, 555, 762
EciI GGCGGA 4 cut(s) 294, 636, 816, 906
Eco31I GGTCTC 2 cut(s) 40, 412
Eco47I GGWCC 2 cut(s) 680, 834
Eco57I CTGAAG 1 cut(s) 76
Eco88I CYCGRG 1 cut(s) 964
EcoO109I RGGNCCY 2 cut(s) 96, 834
EcoRII CCWGG 2 cut(s) 198, 449
Esp3I CGTCTC 1 cut(s) 442
FaeI CATG 1 cut(s) 430
FaiI YATR 5 cut(s) 17, 78, 428, 632, 944
FaqI GGGAC 4 cut(s) 294, 666, 693, 820
FatI CATG 1 cut(s) 426
FauI CCCGC 2 cut(s) 93, 311
FokI GGATG 3 cut(s) 120, 770, 996
GlaI GCGC 1 cut(s) 455
GsaI CCCAGC 1 cut(s) 921
HaeIII GGCC 7 cut(s) 97, 318, 419, 692, 700, 950, 1021
HapII CCGG 9 cut(s) 533, 582, 602, 612, 618, 642, 696, 764, 965
HgaI GACGC 5 cut(s) 424, 457, 503, 567, 708
HhaI GCGC 1 cut(s) 456
Hin1I GRCGYC 1 cut(s) 468
Hin1II CATG 1 cut(s) 430
Hin6I GCGC 1 cut(s) 454
HinP1I GCGC 1 cut(s) 454
HinfI GANTC 4 cut(s) 23, 236, 547, 624
HpaII CCGG 9 cut(s) 533, 582, 602, 612, 618, 642, 696, 764, 965
HphI GGTGA 5 cut(s) 122, 490, 499, 556, 878
Hpy166II GTNNAC 1 cut(s) 82
Hpy188I TCNGA 3 cut(s) 244, 412, 983
Hpy188III TCNNGA 1 cut(s) 764
Hpy8I GTNNAC 1 cut(s) 82
Hpy99I CGWCG 1 cut(s) 209
HpyAV CCTTC 1 cut(s) 970
HpyCH4III ACNGT 2 cut(s) 496, 589
HpyCH4IV ACGT 3 cut(s) 396, 504, 672
HpyCH4V TGCA 3 cut(s) 326, 728, 814
HpyF10VI GCNNNNNNNGC 7 cut(s) 50, 94, 276, 480, 489, 725, 807
HpyF3I CTNAG 2 cut(s) 228, 479
HpySE526I ACGT 3 cut(s) 396, 504, 672
Hsp92I GRCGYC 1 cut(s) 468
Hsp92II CATG 1 cut(s) 430
HspAI GCGC 1 cut(s) 454
KflI GGGWCCC 1 cut(s) 834
Kpn2I TCCGGA 1 cut(s) 763
KroI GCCGGC 1 cut(s) 617
KroNI GCCGGC 1 cut(s) 619
KspI CCGCGG 1 cut(s) 1019
Kzo9I GATC 2 cut(s) 231, 760
LguI GCTCTTC 1 cut(s) 95
LmnI GCTCC 4 cut(s) 335, 395, 532, 610
Lsp1109I GCAGC 4 cut(s) 498, 511, 703, 819
MaeII ACGT 3 cut(s) 396, 504, 672
MaeIII GTNAC 6 cut(s) 361, 496, 505, 544, 567, 971
MalI GATC 2 cut(s) 233, 762
MbiI CCGCTC 2 cut(s) 88, 390
MboI GATC 2 cut(s) 231, 760
MboII GAAGA 7 cut(s) 82, 188, 231, 542, 779, 834, 970
MhlI GDGCHC 1 cut(s) 480
MluCI AATT 1 cut(s) 928
MlyI GAGTC 3 cut(s) 32, 541, 618
MmeI TCCRAC 2 cut(s) 136, 142
MroI TCCGGA 1 cut(s) 763
MroNI GCCGGC 1 cut(s) 617
MseI TTAA 1 cut(s) 927
MspA1I CMGCKG 5 cut(s) 483, 489, 524, 685, 1018
MspI CCGG 9 cut(s) 533, 582, 602, 612, 618, 642, 696, 764, 965
MspR9I CCNGG 8 cut(s) 200, 451, 534, 612, 643, 697, 965, 966
MvaI CCWGG 2 cut(s) 200, 451
MvnI CGCG 2 cut(s) 369, 1018
MwoI GCNNNNNNNGC 7 cut(s) 50, 94, 276, 480, 489, 725, 807
NaeI GCCGGC 1 cut(s) 619
NciI CCSGG 6 cut(s) 534, 612, 643, 697, 965, 966
NdeII GATC 2 cut(s) 231, 760
NgoMIV GCCGGC 1 cut(s) 617
NlaIII CATG 1 cut(s) 430
NlaIV GGNNCC 9 cut(s) 98, 298, 331, 418, 606, 616, 681, 835, 836
NmuCI GTSAC 5 cut(s) 361, 496, 505, 544, 971
PciSI GCTCTTC 1 cut(s) 95
PcsI WCGNNNNNNNCGW 3 cut(s) 240, 366, 561
PdiI GCCGGC 1 cut(s) 619
PfeI GAWTC 1 cut(s) 236
PflFI GACNNNGTC 1 cut(s) 434
PfoI TCCNGGA 1 cut(s) 532
PleI GAGTC 3 cut(s) 31, 541, 618
PpsI GAGTC 3 cut(s) 31, 541, 618
PpuMI RGGWCCY 1 cut(s) 834
Psp5II RGGWCCY 1 cut(s) 834
Psp6I CCWGG 2 cut(s) 198, 449
PspFI CCCAGC 1 cut(s) 917
PspGI CCWGG 2 cut(s) 198, 449
PspN4I GGNNCC 9 cut(s) 98, 298, 331, 418, 606, 616, 681, 835, 836
PspPI GGNCC 5 cut(s) 96, 417, 680, 698, 834
PspPPI RGGWCCY 1 cut(s) 834
PstI CTGCAG 1 cut(s) 328
PsyI GACNNNGTC 1 cut(s) 434
PvuII CAGCTG 1 cut(s) 524
RsaI GTAC 4 cut(s) 11, 586, 874, 1012
RsaNI GTAC 4 cut(s) 10, 585, 873, 1011
SacII CCGCGG 1 cut(s) 1019
SapI GCTCTTC 1 cut(s) 95
SaqAI TTAA 1 cut(s) 927
Sau3AI GATC 2 cut(s) 231, 760
Sau96I GGNCC 5 cut(s) 96, 417, 680, 698, 834
SbfI CCTGCAGG 1 cut(s) 328
ScaI AGTACT 1 cut(s) 1012
SchI GAGTC 3 cut(s) 32, 541, 618
ScrFI CCNGG 8 cut(s) 200, 451, 534, 612, 643, 697, 965, 966
SdaI CCTGCAGG 1 cut(s) 328
SduI GDGCHC 1 cut(s) 480
SfcI CTRYAG 1 cut(s) 324
Sfr303I CCGCGG 1 cut(s) 1019
SgrBI CCGCGG 1 cut(s) 1019
SinI GGWCC 2 cut(s) 680, 834
SmaI CCCGGG 1 cut(s) 966
SmlI CTYRAG 1 cut(s) 401
SmoI CTYRAG 1 cut(s) 401
Sse8387I CCTGCAGG 1 cut(s) 328
Sse9I AATT 1 cut(s) 928
SspI AATATT 1 cut(s) 223
StyD4I CCNGG 8 cut(s) 198, 449, 532, 610, 641, 695, 963, 964
TaaI ACNGT 2 cut(s) 496, 589
TaiI ACGT 3 cut(s) 399, 507, 675
TaqI TCGA 2 cut(s) 234, 564
TaqII GACCGA 1 cut(s) 22
TasI AATT 1 cut(s) 928
TatI WGTACW 1 cut(s) 1010
TauI GCSGC 7 cut(s) 44, 254, 486, 492, 891, 950, 1021
TfiI GAWTC 1 cut(s) 236
Tru1I TTAA 1 cut(s) 927
Tru9I TTAA 1 cut(s) 927
TscAI CASTG 1 cut(s) 499
TseFI GTSAC 5 cut(s) 361, 496, 505, 544, 971
TseI GCWGC 4 cut(s) 486, 524, 716, 807
Tsp45I GTSAC 5 cut(s) 361, 496, 505, 544, 971
TspGWI ACGGA 2 cut(s) 570, 1014
TspMI CCCGGG 1 cut(s) 964
TspRI CASTG 1 cut(s) 499
Tth111I GACNNNGTC 1 cut(s) 434
VpaK11BI GGWCC 2 cut(s) 680, 834
XmaI CCCGGG 1 cut(s) 964
ZrmI AGTACT 1 cut(s) 1012
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.