Rw1G030810

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
rosa_wichuraiana
Chr1
OG0012533
Physical Location & Seq
Reverse (-)
58776081 .. 58777827
1747 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw1G030810.1

Sequence Viewer

Length: 894 bp
ATGGCGAATCGATGGTGGGCTGGAAATGTGGCGATGGGAGCTCATGACTCAATCACCGCCTCGACACCACCGTCTCTTCATCTTAGAAACTCTGAAGCCGAAGAGCACAACAACAACAACACACCCACCAACAGCAGCACCAGCAACCCAAACAACACTCCACCTCAGAAGCAGGACGACGACCAGGACAGCCGTGACAACGATCGAGAAGTTGACAATCAAGACCCTAGCTCCGGCGGCCCCGACAGCCTCGAGCCTGGCTCCAGCAACCGCCGGCCCAGAGGCCGTCCCCCCGGCTCGAAAAACAAGCCGAAACCGCCGATAATCATCACCAAAGAGTCTCCCAACGCTCTCCGGAGCCATGTCTTGGAAATCAGCAGCGGCAGCGACATCGTCGAGAGCATTGCCACCTTCGCACAGCGCAGGCACAGAGGAGTCTCCGTCTTAAGCGGCAGCGGCATTGTTTCTAACGTCACTCTCCGTCAGCCGGCCGCGCCGAGCGGGGTCATAACGCTCCACGGAAGGTTCGAGATTCTGTCCCTAAACGGTGCCTTTCTGCCTGCCCCGTCGCCGCCGGGGGCTAGTGGCCTGACCGTGTACTTGGGCGGCGGGCAGGGGCAGGTGGTTGGTGGGACTGTTGTTGGAGCTCTGTTGGCTTCCGGGCCGGTGATGATCATTGCGGCGACGTTCACTAATGCCACTTATGAGAGACTGCCGCTTGAGGATGAGAGCAATGAAGGGATGCAATTGCAACAGCAACAGCAGCAGCAGCAGCAGCAATCCGCAGCAACAAGGCCCATTTACGCTTTGCCTCCGACTTTGCTTCCAAATGGTCAGATGCCGCCTGATGTGTACTGGGGTCCTCCACCGCCTAGACCTCCGCCTGCTTACTGA
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

297

Amino Acids

31.51

Weight (kDa)

5.87

Isoelectric Point (pI)

62.06

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PCC PF03479 119 - 232 1e-23 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) 610
AasI GACNNNNNNGTC 1 cut(s) 70
Acc36I ACCTGC 1 cut(s) 610
AccB1I GGYRCC 1 cut(s) 548
AccB7I CCANNNNNTGG 1 cut(s) 367
AccBSI CCGCTC 1 cut(s) 501
AccII CGCG 1 cut(s) 494
AccIII TCCGGA 1 cut(s) 354
AcoI YGGCCR 1 cut(s) 489
AcuI CTGAAG 1 cut(s) 114
AfaI GTAC 2 cut(s) 599, 854
AfiI CCNNNNNNNGG 3 cut(s) 233, 367, 487
AflII CTTAAG 1 cut(s) 445
AjnI CCWGG 2 cut(s) 183, 256
AluBI AGCT 3 cut(s) 41, 231, 647
AluI AGCT 3 cut(s) 41, 231, 647
Alw21I GWGCWC 3 cut(s) 43, 108, 649
Alw26I GTCTC 4 cut(s) 78, 345, 442, 703
Ama87I CYCGRG 1 cut(s) 251
Aor13HI TCCGGA 1 cut(s) 354
AoxI GGCC 7 cut(s) 238, 275, 283, 489, 586, 662, 794
AspLEI GCGC 2 cut(s) 423, 496
AspS9I GGNCC 5 cut(s) 239, 276, 662, 795, 860
AsuC2I CCSGG 3 cut(s) 294, 576, 661
AsuHPI GGTGA 3 cut(s) 46, 322, 679
AvaI CYCGRG 1 cut(s) 251
AvaII GGWCC 1 cut(s) 860
BanI GGYRCC 1 cut(s) 548
BanII GRGCYC 2 cut(s) 43, 649
Bbv12I GWGCWC 3 cut(s) 43, 108, 649
BccI CCATC 2 cut(s) 6, 28
BceAI ACGGC 2 cut(s) 177, 270
BcgI CGANNNNNNTGC 4 cut(s) 373, 386, 407, 420
BciT130I CCWGG 2 cut(s) 185, 258
BclI TGATCA 1 cut(s) 672
BcnI CCSGG 3 cut(s) 294, 576, 661
BcoDI GTCTC 4 cut(s) 78, 345, 442, 703
BfaI CTAG 3 cut(s) 228, 582, 873
BfrI CTTAAG 1 cut(s) 445
BfuAI ACCTGC 1 cut(s) 610
Bme1390I CCNGG 5 cut(s) 185, 258, 294, 576, 661
Bme18I GGWCC 1 cut(s) 860
BmeT110I CYCGRG 1 cut(s) 251
BmgT120I GGNCC 5 cut(s) 239, 276, 662, 795, 860
BmiI GGNNCC 5 cut(s) 241, 262, 359, 550, 861
BmrFI CCNGG 5 cut(s) 185, 258, 294, 576, 661
BmrI ACTGGG 1 cut(s) 865
BmsI GCATC 2 cut(s) 732, 828
BmuI ACTGGG 1 cut(s) 865
BplI GAGNNNNNCTC 2 cut(s) 245, 277
BpmI CTGGAG 1 cut(s) 247
BpuEI CTTGAG 1 cut(s) 740
BpuMI CCSGG 3 cut(s) 294, 576, 661
Bsa29I ATCGAT 1 cut(s) 10
BsaBI GATNNNNATC 1 cut(s) 326
BsaJI CCNNGG 3 cut(s) 292, 517, 575
BsaWI WCCGGW 1 cut(s) 354
BsaXI ACNNNNNCTCC 4 cut(s) 215, 245, 426, 456
Bsc4I CCNNNNNNNGG 3 cut(s) 233, 367, 487
Bse118I RCCGGY 3 cut(s) 273, 487, 664
Bse1I ACTGG 1 cut(s) 860
Bse3DI GCAATG 3 cut(s) 402, 675, 739
Bse8I GATNNNNATC 1 cut(s) 326
BseAI TCCGGA 1 cut(s) 354
BseBI CCWGG 2 cut(s) 185, 258
BseCI ATCGAT 1 cut(s) 10
BseDI CCNNGG 3 cut(s) 292, 517, 575
BseGI GGATG 2 cut(s) 730, 747
BseJI GATNNNNATC 1 cut(s) 326
BseLI CCNNNNNNNGG 3 cut(s) 233, 367, 487
BseMI GCAATG 3 cut(s) 402, 675, 739
BseMII CTCAG 1 cut(s) 179
BseNI ACTGG 1 cut(s) 860
BseRI GAGGAG 1 cut(s) 447
BseX3I CGGCCG 1 cut(s) 489
Bsh1236I CGCG 1 cut(s) 494
Bsh1285I CGRYCG 2 cut(s) 205, 492
BshFI GGCC 7 cut(s) 240, 277, 285, 491, 588, 664, 796
BshNI GGYRCC 1 cut(s) 548
BshVI ATCGAT 1 cut(s) 10
BsiEI CGRYCG 2 cut(s) 205, 492
BsiHKAI GWGCWC 3 cut(s) 43, 108, 649
BsiHKCI CYCGRG 1 cut(s) 251
BsiSI CCGG 8 cut(s) 234, 274, 294, 355, 488, 575, 660, 665
BslFI GGGAC 3 cut(s) 273, 523, 646
BslI CCNNNNNNNGG 3 cut(s) 233, 367, 487
BsmAI GTCTC 4 cut(s) 78, 345, 442, 703
BsmBI CGTCTC 1 cut(s) 78
BsmFI GGGAC 3 cut(s) 273, 523, 646
BsnI GGCC 7 cut(s) 240, 277, 285, 491, 588, 664, 796
BsoBI CYCGRG 1 cut(s) 251
Bsp1286I GDGCHC 3 cut(s) 43, 108, 649
Bsp13I TCCGGA 1 cut(s) 354
Bsp143I GATC 2 cut(s) 202, 672
BspANI GGCC 7 cut(s) 240, 277, 285, 491, 588, 664, 796
BspCNI CTCAG 1 cut(s) 178
BspDI ATCGAT 1 cut(s) 10
BspEI TCCGGA 1 cut(s) 354
BspFNI CGCG 1 cut(s) 494
BspHI TCATGA 1 cut(s) 43
BspLI GGNNCC 5 cut(s) 241, 262, 359, 550, 861
BspMI ACCTGC 1 cut(s) 610
BspQI GCTCTTC 1 cut(s) 96
BspT107I GGYRCC 1 cut(s) 548
BspTI CTTAAG 1 cut(s) 445
BsrBI CCGCTC 1 cut(s) 501
BsrDI GCAATG 3 cut(s) 402, 675, 739
BsrFI RCCGGY 3 cut(s) 273, 487, 664
BsrI ACTGG 1 cut(s) 860
BssAI RCCGGY 3 cut(s) 273, 487, 664
BssECI CCNNGG 3 cut(s) 292, 517, 575
BssMI GATC 2 cut(s) 202, 672
Bst2UI CCWGG 2 cut(s) 185, 258
Bst4CI ACNGT 4 cut(s) 72, 548, 595, 637
Bst6I CTCTTC 2 cut(s) 81, 96
BstAFI CTTAAG 1 cut(s) 445
BstC8I GCNNGC 6 cut(s) 275, 425, 489, 561, 611, 885
BstDEI CTNAG 2 cut(s) 83, 165
BstDSI CCRYGG 1 cut(s) 517
BstF5I GGATG 2 cut(s) 730, 747
BstFNI CGCG 1 cut(s) 494
BstHHI GCGC 2 cut(s) 423, 496
BstKTI GATC 2 cut(s) 205, 675
BstMAI GTCTC 4 cut(s) 78, 345, 442, 703
BstMBI GATC 2 cut(s) 202, 672
BstMCI CGRYCG 2 cut(s) 205, 492
BstNI CCWGG 2 cut(s) 185, 258
BstSCI CCNGG 5 cut(s) 183, 256, 292, 574, 659
BstUI CGCG 1 cut(s) 494
BstZI CGGCCG 1 cut(s) 489
Bsu15I ATCGAT 1 cut(s) 10
BsuRI GGCC 7 cut(s) 240, 277, 285, 491, 588, 664, 796
BsuTUI ATCGAT 1 cut(s) 10
BtgI CCRYGG 1 cut(s) 517
BtgZI GCGATG 1 cut(s) 47
BtsCI GGATG 2 cut(s) 730, 747
BveI ACCTGC 1 cut(s) 610
Cac8I GCNNGC 6 cut(s) 275, 425, 489, 561, 611, 885
CciI TCATGA 1 cut(s) 43
CfoI GCGC 2 cut(s) 423, 496
Cfr10I RCCGGY 3 cut(s) 273, 487, 664
Cfr13I GGNCC 5 cut(s) 239, 276, 662, 795, 860
ClaI ATCGAT 1 cut(s) 10
Csp6I GTAC 2 cut(s) 598, 853
CviAII CATG 2 cut(s) 44, 362
CviQI GTAC 2 cut(s) 598, 853
DdeI CTNAG 2 cut(s) 83, 165
DpnI GATC 2 cut(s) 204, 674
DpnII GATC 2 cut(s) 202, 672
DrdI GACNNNNNNGTC 1 cut(s) 70
DseDI GACNNNNNNGTC 1 cut(s) 70
EaeI YGGCCR 1 cut(s) 489
EagI CGGCCG 1 cut(s) 489
Eam1104I CTCTTC 2 cut(s) 81, 96
EarI CTCTTC 2 cut(s) 81, 96
EciI GGCGGA 1 cut(s) 870
Ecl136II GAGCTC 2 cut(s) 41, 647
EclXI CGGCCG 1 cut(s) 489
Eco24I GRGCYC 2 cut(s) 43, 649
Eco47I GGWCC 1 cut(s) 860
Eco52I CGGCCG 1 cut(s) 489
Eco53kI GAGCTC 2 cut(s) 41, 647
Eco57I CTGAAG 1 cut(s) 114
Eco88I CYCGRG 1 cut(s) 251
EcoICRI GAGCTC 2 cut(s) 41, 647
EcoO109I RGGNCCY 1 cut(s) 860
EcoRII CCWGG 2 cut(s) 183, 256
EcoT38I GRGCYC 2 cut(s) 43, 649
Esp3I CGTCTC 1 cut(s) 78
FaeI CATG 2 cut(s) 47, 365
FaiI YATR 4 cut(s) 45, 363, 509, 705
FaqI GGGAC 3 cut(s) 273, 523, 646
FatI CATG 2 cut(s) 43, 361
FauI CCCGC 2 cut(s) 494, 602
FbaI TGATCA 1 cut(s) 672
FokI GGATG 2 cut(s) 737, 754
FriOI GRGCYC 2 cut(s) 43, 649
FspBI CTAG 3 cut(s) 228, 582, 873
GlaI GCGC 2 cut(s) 422, 495
GsuI CTGGAG 1 cut(s) 247
HaeIII GGCC 7 cut(s) 240, 277, 285, 491, 588, 664, 796
HapII CCGG 8 cut(s) 234, 274, 294, 355, 488, 575, 660, 665
HhaI GCGC 2 cut(s) 423, 496
Hin1II CATG 2 cut(s) 47, 365
Hin6I GCGC 2 cut(s) 421, 494
HinP1I GCGC 2 cut(s) 421, 494
HincII GTYRAC 1 cut(s) 214
HindII GTYRAC 1 cut(s) 214
HinfI GANTC 5 cut(s) 7, 47, 338, 435, 532
HpaII CCGG 8 cut(s) 234, 274, 294, 355, 488, 575, 660, 665
HphI GGTGA 3 cut(s) 46, 322, 679
Hpy166II GTNNAC 4 cut(s) 214, 598, 690, 853
Hpy188I TCNGA 4 cut(s) 94, 168, 816, 837
Hpy188III TCNNGA 6 cut(s) 44, 206, 221, 355, 397, 529
Hpy8I GTNNAC 4 cut(s) 214, 598, 690, 853
Hpy99I CGWCG 4 cut(s) 182, 398, 571, 688
HpyAV CCTTC 3 cut(s) 421, 516, 731
HpyCH4III ACNGT 4 cut(s) 72, 548, 595, 637
HpyCH4IV ACGT 2 cut(s) 471, 686
HpyCH4V TGCA 2 cut(s) 745, 751
HpyF3I CTNAG 2 cut(s) 83, 165
HpySE526I ACGT 2 cut(s) 471, 686
Hsp92II CATG 2 cut(s) 47, 365
HspAI GCGC 2 cut(s) 421, 494
Kpn2I TCCGGA 1 cut(s) 354
KroI GCCGGC 2 cut(s) 273, 487
KroNI GCCGGC 2 cut(s) 275, 489
Ksp22I TGATCA 1 cut(s) 672
Kzo9I GATC 2 cut(s) 202, 672
LguI GCTCTTC 1 cut(s) 96
LmnI GCTCC 6 cut(s) 38, 236, 266, 357, 519, 644
LweI GCATC 2 cut(s) 732, 828
MaeI CTAG 3 cut(s) 228, 582, 873
MaeII ACGT 2 cut(s) 471, 686
MaeIII GTNAC 2 cut(s) 194, 472
MalI GATC 2 cut(s) 204, 674
MbiI CCGCTC 1 cut(s) 501
MboI GATC 2 cut(s) 202, 672
MboII GAAGA 2 cut(s) 68, 113
MfeI CAATTG 1 cut(s) 746
MhlI GDGCHC 3 cut(s) 43, 108, 649
MluCI AATT 1 cut(s) 746
MlyI GAGTC 3 cut(s) 41, 347, 444
MmeI TCCRAC 2 cut(s) 622, 839
MnlI CCTC 9 cut(s) 70, 174, 260, 275, 425, 715, 822, 873, 888
MroI TCCGGA 1 cut(s) 354
MroNI GCCGGC 2 cut(s) 273, 487
MseI TTAA 1 cut(s) 446
MspA1I CMGCKG 2 cut(s) 381, 456
MspCI CTTAAG 1 cut(s) 445
MspI CCGG 8 cut(s) 234, 274, 294, 355, 488, 575, 660, 665
MspR9I CCNGG 5 cut(s) 185, 258, 294, 576, 661
MunI CAATTG 1 cut(s) 746
MvaI CCWGG 2 cut(s) 185, 258
MvnI CGCG 1 cut(s) 494
NaeI GCCGGC 2 cut(s) 275, 489
NciI CCSGG 3 cut(s) 294, 576, 661
NdeII GATC 2 cut(s) 202, 672
NgoMIV GCCGGC 2 cut(s) 273, 487
NlaIII CATG 2 cut(s) 47, 365
NlaIV GGNNCC 5 cut(s) 241, 262, 359, 550, 861
NmeAIII GCCGAG 1 cut(s) 522
NmuCI GTSAC 2 cut(s) 194, 472
PaeR7I CTCGAG 1 cut(s) 251
PagI TCATGA 1 cut(s) 43
PaqCI CACCTGC 1 cut(s) 610
PciSI GCTCTTC 1 cut(s) 96
PcsI WCGNNNNNNNCGW 2 cut(s) 68, 525
PdiI GCCGGC 2 cut(s) 275, 489
PfeI GAWTC 2 cut(s) 7, 532
PflFI GACNNNGTC 1 cut(s) 392
PflMI CCANNNNNTGG 1 cut(s) 367
Ple19I CGATCG 1 cut(s) 205
PleI GAGTC 3 cut(s) 41, 346, 443
PpsI GAGTC 3 cut(s) 41, 346, 443
PpuMI RGGWCCY 1 cut(s) 860
Psp124BI GAGCTC 2 cut(s) 43, 649
Psp5II RGGWCCY 1 cut(s) 860
Psp6I CCWGG 2 cut(s) 183, 256
PspGI CCWGG 2 cut(s) 183, 256
PspN4I GGNNCC 5 cut(s) 241, 262, 359, 550, 861
PspPI GGNCC 5 cut(s) 239, 276, 662, 795, 860
PspPPI RGGWCCY 1 cut(s) 860
PspXI VCTCGAGB 1 cut(s) 251
PsyI GACNNNGTC 1 cut(s) 392
PvuI CGATCG 1 cut(s) 205
RsaI GTAC 2 cut(s) 599, 854
RsaNI GTAC 2 cut(s) 598, 853
SacI GAGCTC 2 cut(s) 43, 649
SapI GCTCTTC 1 cut(s) 96
SaqAI TTAA 1 cut(s) 446
Sau3AI GATC 2 cut(s) 202, 672
Sau96I GGNCC 5 cut(s) 239, 276, 662, 795, 860
SchI GAGTC 3 cut(s) 41, 347, 444
ScrFI CCNGG 5 cut(s) 185, 258, 294, 576, 661
SduI GDGCHC 3 cut(s) 43, 108, 649
SfaNI GCATC 2 cut(s) 732, 828
Sfr274I CTCGAG 1 cut(s) 251
SinI GGWCC 1 cut(s) 860
SlaI CTCGAG 1 cut(s) 251
SmlI CTYRAG 3 cut(s) 251, 445, 719
SmoI CTYRAG 3 cut(s) 251, 445, 719
Sse9I AATT 1 cut(s) 746
SspMI CTAG 3 cut(s) 228, 582, 873
SstI GAGCTC 2 cut(s) 43, 649
StyD4I CCNGG 5 cut(s) 183, 256, 292, 574, 659
TaaI ACNGT 4 cut(s) 72, 548, 595, 637
TaiI ACGT 2 cut(s) 474, 689
TaqI TCGA 7 cut(s) 10, 62, 205, 252, 299, 396, 528
TasI AATT 1 cut(s) 746
TatI WGTACW 2 cut(s) 597, 852
TfiI GAWTC 2 cut(s) 7, 532
Tru1I TTAA 1 cut(s) 446
Tru9I TTAA 1 cut(s) 446
TseFI GTSAC 2 cut(s) 194, 472
Tsp45I GTSAC 2 cut(s) 194, 472
TspDTI ATGAA 2 cut(s) 68, 750
TspGWI ACGGA 3 cut(s) 430, 470, 534
Tth111I GACNNNGTC 1 cut(s) 392
Van91I CCANNNNNTGG 1 cut(s) 367
Vha464I CTTAAG 1 cut(s) 445
VpaK11BI GGWCC 1 cut(s) 860
XhoI CTCGAG 1 cut(s) 251
XspI CTAG 3 cut(s) 228, 582, 873
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.