RchiOBHm_Chr1g0368171

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_chinensis
1
OG0012533
Physical Location & Seq
Reverse (-)
58350998 .. 58354842
3845 bp
Loading structure...
UTR
Exon/CDS
Intron
N/A

Sequence Viewer

Length: 948 bp
ATGGCGAATCGATGGTGGGCTGGAAATGTTGCGATGGGAGCTCATGACTCAATCACCGCCTCGACACCACCGTCTCTTCATCTTAGAAACTCTGAAGCCGAAGAGCACAACAACAACAACAACACACCCACCAACAGCAGCACCAGCAACCCAAACAACACTCCACCTCAGAAGCAGGACGACGACCAGGACAGCCGTGACAACGATCGAGAAGTTGACAATCAAGACCCTAGCTCCGGCGGCCCCGACAGCCTCGAGCCTGGCTCCAGCAACCGCCGGCCCAGAGGCCGTCCCCCCGGCTCGAAAAACAAGCCGAAACCGCCGATAATCATCACCAAAGAGTCTCCCAACGCTCTCCGGAGCCATGTCTTGGAAATCAGCAGCGGCAGCGACATCGTCGAGAGCATTGCCACCTTCGCACAGCGCAGGCACAGAGGAGTCTCCGTCTTAAGCGGCAGCGGCATTGTTTCTAACGTCACTCTCCGTCAGCCGGCCGCGCCGAGCGGGGTCATAACGCTCCACGGAAGGTTCGAGATTCTGTCCCTAAACGGTGCGTTTCTGCCTGCCCCGTCGCCGCCGGGGGCTAGTGGCCTGACCGTGTACTTGGGCGGCGGGCAGGGGCAGGTGGTTGGTGGGACTGTTGTTGGAGCTCTGTTGGCTTCCGGGCCGGTGATGATCATTGCGGCGACGTTCACTAATGCCACTTATGAGAGACTGCCGCTTGAGGATGAGAGCAATGAAGGGATGCAATTGCAACAGCAACAGCAGCAGCAGCAATCCGGTGTGAATTCGGCAGGGACCGGAGGGAATTCGGGTTCTCAGGGCTTGAGTGATCAGCAGCAACAAGTGCCCATTTACGCTTTGCCTCCGACTTTGCTTCCAAATGGTCAGATGCCCCCTGATGTGTACTGGGGTCCTCCACCGCCTAGACCTCCGCCTGCTTACTGA
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

315

Amino Acids

33.13

Weight (kDa)

5.51

Isoelectric Point (pI)

59.65

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PCC PF03479 120 - 233 1.2e-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) 613
AasI GACNNNNNNGTC 1 cut(s) 70
Acc36I ACCTGC 1 cut(s) 613
AccB7I CCANNNNNTGG 1 cut(s) 370
AccBSI CCGCTC 1 cut(s) 504
AccII CGCG 1 cut(s) 497
AccIII TCCGGA 1 cut(s) 357
AcoI YGGCCR 1 cut(s) 492
AcsI RAATTY 2 cut(s) 787, 808
AcuI CTGAAG 1 cut(s) 114
AfaI GTAC 2 cut(s) 602, 908
AfiI CCNNNNNNNGG 3 cut(s) 236, 370, 490
AflII CTTAAG 1 cut(s) 448
AjnI CCWGG 2 cut(s) 186, 259
AloI GAACNNNNNNTCC 2 cut(s) 799, 831
AluBI AGCT 3 cut(s) 41, 234, 650
AluI AGCT 3 cut(s) 41, 234, 650
Alw21I GWGCWC 3 cut(s) 43, 108, 652
Alw26I GTCTC 4 cut(s) 78, 348, 445, 706
Ama87I CYCGRG 1 cut(s) 254
Aor13HI TCCGGA 1 cut(s) 357
AoxI GGCC 6 cut(s) 241, 278, 286, 492, 589, 665
ApeKI GCWGC 8 cut(s) 138, 381, 387, 456, 766, 769, 772, 838
ApoI RAATTY 2 cut(s) 787, 808
AspLEI GCGC 2 cut(s) 426, 499
AspS9I GGNCC 5 cut(s) 242, 279, 665, 798, 914
AsuC2I CCSGG 3 cut(s) 297, 579, 664
AsuHPI GGTGA 3 cut(s) 46, 325, 682
AvaI CYCGRG 1 cut(s) 254
AvaII GGWCC 2 cut(s) 798, 914
BaeGI GKGCMC 1 cut(s) 852
BanII GRGCYC 2 cut(s) 43, 652
Bbv12I GWGCWC 3 cut(s) 43, 108, 652
BbvI GCAGC 8 cut(s) 150, 393, 399, 468, 778, 781, 784, 850
BccI CCATC 2 cut(s) 6, 28
BceAI ACGGC 2 cut(s) 180, 273
BcgI CGANNNNNNTGC 4 cut(s) 376, 389, 410, 423
BciT130I CCWGG 2 cut(s) 188, 261
BclI TGATCA 2 cut(s) 675, 832
BcnI CCSGG 3 cut(s) 297, 579, 664
BcoDI GTCTC 4 cut(s) 78, 348, 445, 706
BfaI CTAG 3 cut(s) 231, 585, 927
BfrI CTTAAG 1 cut(s) 448
BfuAI ACCTGC 1 cut(s) 613
Bme1390I CCNGG 5 cut(s) 188, 261, 297, 579, 664
Bme18I GGWCC 2 cut(s) 798, 914
BmeT110I CYCGRG 1 cut(s) 254
BmgT120I GGNCC 5 cut(s) 242, 279, 665, 798, 914
BmiI GGNNCC 5 cut(s) 244, 265, 362, 799, 915
BmrFI CCNGG 5 cut(s) 188, 261, 297, 579, 664
BmrI ACTGGG 1 cut(s) 919
BmsI GCATC 2 cut(s) 735, 882
BmuI ACTGGG 1 cut(s) 919
BplI GAGNNNNNCTC 2 cut(s) 248, 280
BpmI CTGGAG 1 cut(s) 250
BpuEI CTTGAG 2 cut(s) 743, 847
BpuMI CCSGG 3 cut(s) 297, 579, 664
Bsa29I ATCGAT 1 cut(s) 10
BsaBI GATNNNNATC 1 cut(s) 329
BsaJI CCNNGG 3 cut(s) 295, 520, 578
BsaWI WCCGGW 3 cut(s) 357, 779, 800
BsaXI ACNNNNNCTCC 4 cut(s) 218, 248, 429, 459
Bsc4I CCNNNNNNNGG 3 cut(s) 236, 370, 490
Bse118I RCCGGY 3 cut(s) 276, 490, 667
Bse1I ACTGG 1 cut(s) 914
Bse3DI GCAATG 3 cut(s) 405, 678, 742
Bse8I GATNNNNATC 1 cut(s) 329
BseAI TCCGGA 1 cut(s) 357
BseBI CCWGG 2 cut(s) 188, 261
BseCI ATCGAT 1 cut(s) 10
BseDI CCNNGG 3 cut(s) 295, 520, 578
BseGI GGATG 2 cut(s) 733, 750
BseJI GATNNNNATC 1 cut(s) 329
BseLI CCNNNNNNNGG 3 cut(s) 236, 370, 490
BseMI GCAATG 3 cut(s) 405, 678, 742
BseMII CTCAG 2 cut(s) 182, 833
BseNI ACTGG 1 cut(s) 914
BseRI GAGGAG 1 cut(s) 450
BseSI GKGCMC 1 cut(s) 852
BseX3I CGGCCG 1 cut(s) 492
BseXI GCAGC 8 cut(s) 150, 393, 399, 468, 778, 781, 784, 850
Bsh1236I CGCG 1 cut(s) 497
Bsh1285I CGRYCG 2 cut(s) 208, 495
BshFI GGCC 6 cut(s) 243, 280, 288, 494, 591, 667
BshVI ATCGAT 1 cut(s) 10
BsiEI CGRYCG 2 cut(s) 208, 495
BsiHKAI GWGCWC 3 cut(s) 43, 108, 652
BsiHKCI CYCGRG 1 cut(s) 254
BslFI GGGAC 4 cut(s) 276, 526, 649, 811
BslI CCNNNNNNNGG 3 cut(s) 236, 370, 490
BsmAI GTCTC 4 cut(s) 78, 348, 445, 706
BsmBI CGTCTC 1 cut(s) 78
BsmFI GGGAC 4 cut(s) 276, 526, 649, 811
BsnI GGCC 6 cut(s) 243, 280, 288, 494, 591, 667
BsoBI CYCGRG 1 cut(s) 254
Bsp1286I GDGCHC 4 cut(s) 43, 108, 652, 852
Bsp13I TCCGGA 1 cut(s) 357
Bsp143I GATC 3 cut(s) 205, 675, 832
BspANI GGCC 6 cut(s) 243, 280, 288, 494, 591, 667
BspCNI CTCAG 2 cut(s) 181, 832
BspDI ATCGAT 1 cut(s) 10
BspEI TCCGGA 1 cut(s) 357
BspFNI CGCG 1 cut(s) 497
BspHI TCATGA 1 cut(s) 43
BspLI GGNNCC 5 cut(s) 244, 265, 362, 799, 915
BspMI ACCTGC 1 cut(s) 613
BspQI GCTCTTC 1 cut(s) 96
BspTI CTTAAG 1 cut(s) 448
BsrBI CCGCTC 1 cut(s) 504
BsrDI GCAATG 3 cut(s) 405, 678, 742
BsrFI RCCGGY 3 cut(s) 276, 490, 667
BsrI ACTGG 1 cut(s) 914
BssAI RCCGGY 3 cut(s) 276, 490, 667
BssECI CCNNGG 3 cut(s) 295, 520, 578
BssMI GATC 3 cut(s) 205, 675, 832
Bst2UI CCWGG 2 cut(s) 188, 261
Bst4CI ACNGT 4 cut(s) 72, 551, 598, 640
Bst6I CTCTTC 2 cut(s) 81, 96
BstAFI CTTAAG 1 cut(s) 448
BstAPI GCANNNNNTGC 1 cut(s) 847
BstC8I GCNNGC 6 cut(s) 278, 428, 492, 564, 614, 939
BstDEI CTNAG 3 cut(s) 83, 168, 819
BstDSI CCRYGG 1 cut(s) 520
BstF5I GGATG 2 cut(s) 733, 750
BstFNI CGCG 1 cut(s) 497
BstHHI GCGC 2 cut(s) 426, 499
BstKTI GATC 3 cut(s) 208, 678, 835
BstMAI GTCTC 4 cut(s) 78, 348, 445, 706
BstMBI GATC 3 cut(s) 205, 675, 832
BstMCI CGRYCG 2 cut(s) 208, 495
BstNI CCWGG 2 cut(s) 188, 261
BstSCI CCNGG 5 cut(s) 186, 259, 295, 577, 662
BstSLI GKGCMC 1 cut(s) 852
BstUI CGCG 1 cut(s) 497
BstV1I GCAGC 8 cut(s) 150, 393, 399, 468, 778, 781, 784, 850
BstZI CGGCCG 1 cut(s) 492
Bsu15I ATCGAT 1 cut(s) 10
BsuRI GGCC 6 cut(s) 243, 280, 288, 494, 591, 667
BsuTUI ATCGAT 1 cut(s) 10
BtgI CCRYGG 1 cut(s) 520
BtgZI GCGATG 1 cut(s) 47
BtsCI GGATG 2 cut(s) 733, 750
BveI ACCTGC 1 cut(s) 613
Cac8I GCNNGC 6 cut(s) 278, 428, 492, 564, 614, 939
CciI TCATGA 1 cut(s) 43
CfoI GCGC 2 cut(s) 426, 499
Cfr10I RCCGGY 3 cut(s) 276, 490, 667
Cfr13I GGNCC 5 cut(s) 242, 279, 665, 798, 914
ClaI ATCGAT 1 cut(s) 10
Csp6I GTAC 2 cut(s) 601, 907
CviAII CATG 2 cut(s) 44, 365
CviQI GTAC 2 cut(s) 601, 907
DdeI CTNAG 3 cut(s) 83, 168, 819
DpnI GATC 3 cut(s) 207, 677, 834
DpnII GATC 3 cut(s) 205, 675, 832
DrdI GACNNNNNNGTC 1 cut(s) 70
DseDI GACNNNNNNGTC 1 cut(s) 70
EaeI YGGCCR 1 cut(s) 492
EagI CGGCCG 1 cut(s) 492
Eam1104I CTCTTC 2 cut(s) 81, 96
EarI CTCTTC 2 cut(s) 81, 96
EciI GGCGGA 1 cut(s) 924
Ecl136II GAGCTC 2 cut(s) 41, 650
EclXI CGGCCG 1 cut(s) 492
Eco24I GRGCYC 2 cut(s) 43, 652
Eco47I GGWCC 2 cut(s) 798, 914
Eco52I CGGCCG 1 cut(s) 492
Eco53kI GAGCTC 2 cut(s) 41, 650
Eco57I CTGAAG 1 cut(s) 114
Eco88I CYCGRG 1 cut(s) 254
EcoICRI GAGCTC 2 cut(s) 41, 650
EcoO109I RGGNCCY 1 cut(s) 914
EcoRI GAATTC 2 cut(s) 787, 808
EcoRII CCWGG 2 cut(s) 186, 259
EcoT38I GRGCYC 2 cut(s) 43, 652
Esp3I CGTCTC 1 cut(s) 78
FaeI CATG 2 cut(s) 47, 368
FaiI YATR 4 cut(s) 45, 366, 512, 708
FaqI GGGAC 4 cut(s) 276, 526, 649, 811
FatI CATG 2 cut(s) 43, 364
FauI CCCGC 2 cut(s) 497, 605
FbaI TGATCA 2 cut(s) 675, 832
FokI GGATG 2 cut(s) 740, 757
FriOI GRGCYC 2 cut(s) 43, 652
FspBI CTAG 3 cut(s) 231, 585, 927
GlaI GCGC 2 cut(s) 425, 498
GsuI CTGGAG 1 cut(s) 250
HaeIII GGCC 6 cut(s) 243, 280, 288, 494, 591, 667
HhaI GCGC 2 cut(s) 426, 499
Hin1II CATG 2 cut(s) 47, 368
Hin6I GCGC 2 cut(s) 424, 497
HinP1I GCGC 2 cut(s) 424, 497
HincII GTYRAC 1 cut(s) 217
HindII GTYRAC 1 cut(s) 217
HinfI GANTC 5 cut(s) 7, 47, 341, 438, 535
HphI GGTGA 3 cut(s) 46, 325, 682
Hpy166II GTNNAC 4 cut(s) 217, 601, 693, 907
Hpy188I TCNGA 4 cut(s) 94, 171, 870, 891
Hpy188III TCNNGA 6 cut(s) 44, 209, 224, 358, 400, 532
Hpy8I GTNNAC 4 cut(s) 217, 601, 693, 907
Hpy99I CGWCG 4 cut(s) 185, 401, 574, 691
HpyAV CCTTC 3 cut(s) 424, 519, 734
HpyCH4III ACNGT 4 cut(s) 72, 551, 598, 640
HpyCH4IV ACGT 2 cut(s) 474, 689
HpyCH4V TGCA 2 cut(s) 748, 754
HpyF3I CTNAG 3 cut(s) 83, 168, 819
HpySE526I ACGT 2 cut(s) 474, 689
Hsp92II CATG 2 cut(s) 47, 368
HspAI GCGC 2 cut(s) 424, 497
Kpn2I TCCGGA 1 cut(s) 357
KroI GCCGGC 2 cut(s) 276, 490
KroNI GCCGGC 2 cut(s) 278, 492
Ksp22I TGATCA 2 cut(s) 675, 832
Kzo9I GATC 3 cut(s) 205, 675, 832
LguI GCTCTTC 1 cut(s) 96
LmnI GCTCC 6 cut(s) 38, 239, 269, 360, 522, 647
Lsp1109I GCAGC 8 cut(s) 150, 393, 399, 468, 778, 781, 784, 850
LweI GCATC 2 cut(s) 735, 882
MaeI CTAG 3 cut(s) 231, 585, 927
MaeII ACGT 2 cut(s) 474, 689
MaeIII GTNAC 2 cut(s) 197, 475
MalI GATC 3 cut(s) 207, 677, 834
MbiI CCGCTC 1 cut(s) 504
MboI GATC 3 cut(s) 205, 675, 832
MboII GAAGA 2 cut(s) 68, 113
MfeI CAATTG 1 cut(s) 749
MhlI GDGCHC 4 cut(s) 43, 108, 652, 852
MluCI AATT 3 cut(s) 749, 787, 808
MlyI GAGTC 3 cut(s) 41, 350, 447
MmeI TCCRAC 2 cut(s) 625, 893
MroI TCCGGA 1 cut(s) 357
MroNI GCCGGC 2 cut(s) 276, 490
MseI TTAA 1 cut(s) 449
MspA1I CMGCKG 2 cut(s) 384, 459
MspCI CTTAAG 1 cut(s) 448
MspR9I CCNGG 5 cut(s) 188, 261, 297, 579, 664
MunI CAATTG 1 cut(s) 749
MvaI CCWGG 2 cut(s) 188, 261
MvnI CGCG 1 cut(s) 497
NaeI GCCGGC 2 cut(s) 278, 492
NciI CCSGG 3 cut(s) 297, 579, 664
NdeII GATC 3 cut(s) 205, 675, 832
NgoMIV GCCGGC 2 cut(s) 276, 490
NlaIII CATG 2 cut(s) 47, 368
NlaIV GGNNCC 5 cut(s) 244, 265, 362, 799, 915
NmeAIII GCCGAG 1 cut(s) 525
NmuCI GTSAC 2 cut(s) 197, 475
PaeR7I CTCGAG 1 cut(s) 254
PagI TCATGA 1 cut(s) 43
PaqCI CACCTGC 1 cut(s) 613
PciSI GCTCTTC 1 cut(s) 96
PcsI WCGNNNNNNNCGW 2 cut(s) 68, 528
PdiI GCCGGC 2 cut(s) 278, 492
PfeI GAWTC 2 cut(s) 7, 535
PflFI GACNNNGTC 1 cut(s) 395
PflMI CCANNNNNTGG 1 cut(s) 370
Ple19I CGATCG 1 cut(s) 208
PleI GAGTC 3 cut(s) 41, 349, 446
PpsI GAGTC 3 cut(s) 41, 349, 446
PpuMI RGGWCCY 1 cut(s) 914
Psp124BI GAGCTC 2 cut(s) 43, 652
Psp5II RGGWCCY 1 cut(s) 914
Psp6I CCWGG 2 cut(s) 186, 259
PspGI CCWGG 2 cut(s) 186, 259
PspN4I GGNNCC 5 cut(s) 244, 265, 362, 799, 915
PspPI GGNCC 5 cut(s) 242, 279, 665, 798, 914
PspPPI RGGWCCY 1 cut(s) 914
PspXI VCTCGAGB 1 cut(s) 254
PsyI GACNNNGTC 1 cut(s) 395
PvuI CGATCG 1 cut(s) 208
RsaI GTAC 2 cut(s) 602, 908
RsaNI GTAC 2 cut(s) 601, 907
SacI GAGCTC 2 cut(s) 43, 652
SapI GCTCTTC 1 cut(s) 96
SaqAI TTAA 1 cut(s) 449
Sau3AI GATC 3 cut(s) 205, 675, 832
Sau96I GGNCC 5 cut(s) 242, 279, 665, 798, 914
SchI GAGTC 3 cut(s) 41, 350, 447
ScrFI CCNGG 5 cut(s) 188, 261, 297, 579, 664
SduI GDGCHC 4 cut(s) 43, 108, 652, 852
SfaNI GCATC 2 cut(s) 735, 882
Sfr274I CTCGAG 1 cut(s) 254
SinI GGWCC 2 cut(s) 798, 914
SlaI CTCGAG 1 cut(s) 254
SmlI CTYRAG 4 cut(s) 254, 448, 722, 826
SmoI CTYRAG 4 cut(s) 254, 448, 722, 826
Sse9I AATT 3 cut(s) 749, 787, 808
SspMI CTAG 3 cut(s) 231, 585, 927
SstI GAGCTC 2 cut(s) 43, 652
StyD4I CCNGG 5 cut(s) 186, 259, 295, 577, 662
TaaI ACNGT 4 cut(s) 72, 551, 598, 640
TaiI ACGT 2 cut(s) 477, 692
TaqI TCGA 7 cut(s) 10, 62, 208, 255, 302, 399, 531
TasI AATT 3 cut(s) 749, 787, 808
TatI WGTACW 2 cut(s) 600, 906
TauI GCSGC 9 cut(s) 243, 387, 456, 462, 497, 577, 612, 686, 721
TfiI GAWTC 2 cut(s) 7, 535
Tru1I TTAA 1 cut(s) 449
Tru9I TTAA 1 cut(s) 449
TseFI GTSAC 2 cut(s) 197, 475
TseI GCWGC 8 cut(s) 138, 381, 387, 456, 766, 769, 772, 838
Tsp45I GTSAC 2 cut(s) 197, 475
TspDTI ATGAA 2 cut(s) 68, 753
TspGWI ACGGA 3 cut(s) 433, 473, 537
Tth111I GACNNNGTC 1 cut(s) 395
Van91I CCANNNNNTGG 1 cut(s) 370
Vha464I CTTAAG 1 cut(s) 448
VpaK11BI GGWCC 2 cut(s) 798, 914
XapI RAATTY 2 cut(s) 787, 808
XhoI CTCGAG 1 cut(s) 254
XspI CTAG 3 cut(s) 231, 585, 927
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.