Rh1DG341100

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_samantha
Chr1D
OG0012533
Physical Location & Seq
Reverse (-)
56609046 .. 56610005
960 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh1DG341100.1

Sequence Viewer

Length: 960 bp
ATGGCGAATCGATGGTGGGCTGGAAATGTGGCGATGGGAGCTCACGACTCAATCACCGCCTCGACACCACCGTCTCTTCATCTTAGAAACTCTGAAGCCGAAGAGCACAACAACAACAACAACAACAACACACCCACCAACAGCAGCACCAGCAACCCAAACAACACTCCACCTCATAAGCAGGACGACGACCAGGACAGCCGTGACAACGATCGAGAAGTTGACAATCAAGACCCTAGCTCCGGCGGTCCCGACAGCCTCGAGCCTGGCTCCAGCAACCGCCGGCCCAGAGGCCGCCCCCCCGGCTCGAAAAACAAGCCGAAACCGCCGATAATCATCACCAAAGAGTCTCCCAACGCTCTCCGGAGCCATGTCTTGGAAATCAGCAGCGGCAGCGACATCGTCGAGAGCATTGCCACCTTCGCACAGCGCAGGCACAGAGGAGTCTCCGTCTTAAGCGGCAGCGGCATTGTTTCTAACGTCACTCTTCGTCAGCCGGCCGCGCCGAGCGGGGTCATAACGCTCCACGGAAGGTTCGAGATTCTGTCCCTAAACGGTGCGTTTCTGCCTGCCCCGTCGCCGCCGGGGGCTAGTGGCCTGACCGTGTACTTGGGCGGCGGCCAGGGGCAGGTGGTTGGTGGGACTGTTGTTGGAGCTCTCTTGGCTTCTGGGCCGGTGATGATCATTGCGGCGACGTTCACTAATGCCACTTATGAGAGACTGCCGCTTGAGGATGAGAGCAATGAAGGGATGCAATTGCAACAGCAACAGCAACAGCAGCAGCAGCAATCCGGTGTGAATTTGGCAGGGACCGGAGGGAATTCGGGTTCTCAGGGCTTGAGTGATCAGCAGCAACAAGTGCCCATTTACGCTTTGCCTCCGACTTTGCTTCCAAATGGTCAGATGCCGCCTGATGTGTACTGGGGTCCTCCACCGCCTAGACCTCCGCCTGCTTACTGA
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

319

Amino Acids

33.65

Weight (kDa)

5.63

Isoelectric Point (pI)

60.38

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PCC PF03479 122 - 235 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) 619
AasI GACNNNNNNGTC 1 cut(s) 70
Acc36I ACCTGC 1 cut(s) 619
AccB7I CCANNNNNTGG 1 cut(s) 376
AccBSI CCGCTC 1 cut(s) 510
AccII CGCG 1 cut(s) 503
AccIII TCCGGA 1 cut(s) 363
AcoI YGGCCR 2 cut(s) 498, 619
AcsI RAATTY 2 cut(s) 799, 820
AcuI CTGAAG 1 cut(s) 114
AfaI GTAC 2 cut(s) 608, 920
AfiI CCNNNNNNNGG 3 cut(s) 242, 376, 628
AflII CTTAAG 1 cut(s) 454
AjnI CCWGG 3 cut(s) 192, 265, 621
AloI GAACNNNNNNTCC 2 cut(s) 811, 843
AluBI AGCT 3 cut(s) 41, 240, 656
AluI AGCT 3 cut(s) 41, 240, 656
Alw21I GWGCWC 3 cut(s) 43, 108, 658
Alw26I GTCTC 4 cut(s) 78, 354, 451, 712
Ama87I CYCGRG 1 cut(s) 260
Aor13HI TCCGGA 1 cut(s) 363
AoxI GGCC 6 cut(s) 284, 292, 498, 595, 619, 671
ApeKI GCWGC 8 cut(s) 144, 387, 393, 462, 778, 781, 784, 850
ApoI RAATTY 2 cut(s) 799, 820
AspLEI GCGC 2 cut(s) 432, 505
AspS9I GGNCC 5 cut(s) 248, 285, 671, 810, 926
AsuC2I CCSGG 2 cut(s) 303, 585
AsuHPI GGTGA 3 cut(s) 46, 331, 688
AvaI CYCGRG 1 cut(s) 260
AvaII GGWCC 3 cut(s) 248, 810, 926
BaeGI GKGCMC 1 cut(s) 864
BanII GRGCYC 2 cut(s) 43, 658
Bbv12I GWGCWC 3 cut(s) 43, 108, 658
BbvI GCAGC 8 cut(s) 156, 399, 405, 474, 790, 793, 796, 862
BccI CCATC 2 cut(s) 6, 28
BceAI ACGGC 1 cut(s) 186
BcgI CGANNNNNNTGC 4 cut(s) 382, 395, 416, 429
BciT130I CCWGG 3 cut(s) 194, 267, 623
BclI TGATCA 2 cut(s) 681, 844
BcnI CCSGG 2 cut(s) 303, 585
BcoDI GTCTC 4 cut(s) 78, 354, 451, 712
BfaI CTAG 3 cut(s) 237, 591, 939
BfrI CTTAAG 1 cut(s) 454
BfuAI ACCTGC 1 cut(s) 619
BglI GCCNNNNNGGC 1 cut(s) 303
Bme1390I CCNGG 5 cut(s) 194, 267, 303, 585, 623
Bme18I GGWCC 3 cut(s) 248, 810, 926
BmeT110I CYCGRG 1 cut(s) 260
BmgT120I GGNCC 5 cut(s) 248, 285, 671, 810, 926
BmiI GGNNCC 5 cut(s) 250, 271, 368, 811, 927
BmrFI CCNGG 5 cut(s) 194, 267, 303, 585, 623
BmrI ACTGGG 1 cut(s) 931
BmsI GCATC 2 cut(s) 741, 894
BmuI ACTGGG 1 cut(s) 931
BplI GAGNNNNNCTC 2 cut(s) 254, 286
BpmI CTGGAG 1 cut(s) 256
BpuEI CTTGAG 2 cut(s) 749, 859
BpuMI CCSGG 2 cut(s) 303, 585
Bsa29I ATCGAT 1 cut(s) 10
BsaBI GATNNNNATC 1 cut(s) 335
BsaJI CCNNGG 4 cut(s) 301, 526, 584, 622
BsaWI WCCGGW 3 cut(s) 363, 791, 812
BsaXI ACNNNNNCTCC 4 cut(s) 224, 254, 435, 465
Bsc4I CCNNNNNNNGG 3 cut(s) 242, 376, 628
Bse118I RCCGGY 3 cut(s) 282, 496, 673
Bse1I ACTGG 1 cut(s) 926
Bse3DI GCAATG 3 cut(s) 411, 684, 748
Bse8I GATNNNNATC 1 cut(s) 335
BseAI TCCGGA 1 cut(s) 363
BseBI CCWGG 3 cut(s) 194, 267, 623
BseCI ATCGAT 1 cut(s) 10
BseDI CCNNGG 4 cut(s) 301, 526, 584, 622
BseGI GGATG 2 cut(s) 739, 756
BseJI GATNNNNATC 1 cut(s) 335
BseLI CCNNNNNNNGG 3 cut(s) 242, 376, 628
BseMI GCAATG 3 cut(s) 411, 684, 748
BseMII CTCAG 1 cut(s) 845
BseNI ACTGG 1 cut(s) 926
BseRI GAGGAG 1 cut(s) 456
BseSI GKGCMC 1 cut(s) 864
BseX3I CGGCCG 1 cut(s) 498
BseXI GCAGC 8 cut(s) 156, 399, 405, 474, 790, 793, 796, 862
Bsh1236I CGCG 1 cut(s) 503
Bsh1285I CGRYCG 2 cut(s) 214, 501
BshFI GGCC 6 cut(s) 286, 294, 500, 597, 621, 673
BshVI ATCGAT 1 cut(s) 10
BsiEI CGRYCG 2 cut(s) 214, 501
BsiHKAI GWGCWC 3 cut(s) 43, 108, 658
BsiHKCI CYCGRG 1 cut(s) 260
BsiSI CCGG 9 cut(s) 243, 283, 303, 364, 497, 584, 674, 792, 813
BslFI GGGAC 4 cut(s) 234, 532, 655, 823
BslI CCNNNNNNNGG 3 cut(s) 242, 376, 628
BsmAI GTCTC 4 cut(s) 78, 354, 451, 712
BsmBI CGTCTC 1 cut(s) 78
BsmFI GGGAC 4 cut(s) 234, 532, 655, 823
BsnI GGCC 6 cut(s) 286, 294, 500, 597, 621, 673
BsoBI CYCGRG 1 cut(s) 260
Bsp1286I GDGCHC 4 cut(s) 43, 108, 658, 864
Bsp13I TCCGGA 1 cut(s) 363
Bsp143I GATC 3 cut(s) 211, 681, 844
BspANI GGCC 6 cut(s) 286, 294, 500, 597, 621, 673
BspCNI CTCAG 1 cut(s) 844
BspDI ATCGAT 1 cut(s) 10
BspEI TCCGGA 1 cut(s) 363
BspFNI CGCG 1 cut(s) 503
BspLI GGNNCC 5 cut(s) 250, 271, 368, 811, 927
BspMI ACCTGC 1 cut(s) 619
BspQI GCTCTTC 1 cut(s) 96
BspTI CTTAAG 1 cut(s) 454
BsrBI CCGCTC 1 cut(s) 510
BsrDI GCAATG 3 cut(s) 411, 684, 748
BsrFI RCCGGY 3 cut(s) 282, 496, 673
BsrI ACTGG 1 cut(s) 926
BssAI RCCGGY 3 cut(s) 282, 496, 673
BssECI CCNNGG 4 cut(s) 301, 526, 584, 622
BssMI GATC 3 cut(s) 211, 681, 844
Bst2UI CCWGG 3 cut(s) 194, 267, 623
Bst4CI ACNGT 4 cut(s) 72, 557, 604, 646
Bst6I CTCTTC 3 cut(s) 81, 96, 492
BstAFI CTTAAG 1 cut(s) 454
BstAPI GCANNNNNTGC 1 cut(s) 859
BstC8I GCNNGC 5 cut(s) 284, 434, 498, 570, 951
BstDEI CTNAG 2 cut(s) 83, 831
BstDSI CCRYGG 1 cut(s) 526
BstF5I GGATG 2 cut(s) 739, 756
BstFNI CGCG 1 cut(s) 503
BstHHI GCGC 2 cut(s) 432, 505
BstKTI GATC 3 cut(s) 214, 684, 847
BstMAI GTCTC 4 cut(s) 78, 354, 451, 712
BstMBI GATC 3 cut(s) 211, 681, 844
BstMCI CGRYCG 2 cut(s) 214, 501
BstNI CCWGG 3 cut(s) 194, 267, 623
BstSCI CCNGG 5 cut(s) 192, 265, 301, 583, 621
BstSLI GKGCMC 1 cut(s) 864
BstUI CGCG 1 cut(s) 503
BstV1I GCAGC 8 cut(s) 156, 399, 405, 474, 790, 793, 796, 862
BstZI CGGCCG 1 cut(s) 498
Bsu15I ATCGAT 1 cut(s) 10
BsuRI GGCC 6 cut(s) 286, 294, 500, 597, 621, 673
BsuTUI ATCGAT 1 cut(s) 10
BtgI CCRYGG 1 cut(s) 526
BtgZI GCGATG 1 cut(s) 47
BtsCI GGATG 2 cut(s) 739, 756
BveI ACCTGC 1 cut(s) 619
Cac8I GCNNGC 5 cut(s) 284, 434, 498, 570, 951
CfoI GCGC 2 cut(s) 432, 505
Cfr10I RCCGGY 3 cut(s) 282, 496, 673
Cfr13I GGNCC 5 cut(s) 248, 285, 671, 810, 926
ClaI ATCGAT 1 cut(s) 10
Csp6I GTAC 2 cut(s) 607, 919
CviAII CATG 1 cut(s) 371
CviQI GTAC 2 cut(s) 607, 919
DdeI CTNAG 2 cut(s) 83, 831
DpnI GATC 3 cut(s) 213, 683, 846
DpnII GATC 3 cut(s) 211, 681, 844
DrdI GACNNNNNNGTC 1 cut(s) 70
DseDI GACNNNNNNGTC 1 cut(s) 70
EaeI YGGCCR 2 cut(s) 498, 619
EagI CGGCCG 1 cut(s) 498
Eam1104I CTCTTC 3 cut(s) 81, 96, 492
EarI CTCTTC 3 cut(s) 81, 96, 492
EciI GGCGGA 1 cut(s) 936
Ecl136II GAGCTC 2 cut(s) 41, 656
EclXI CGGCCG 1 cut(s) 498
Eco24I GRGCYC 2 cut(s) 43, 658
Eco47I GGWCC 3 cut(s) 248, 810, 926
Eco52I CGGCCG 1 cut(s) 498
Eco53kI GAGCTC 2 cut(s) 41, 656
Eco57I CTGAAG 1 cut(s) 114
Eco88I CYCGRG 1 cut(s) 260
EcoICRI GAGCTC 2 cut(s) 41, 656
EcoO109I RGGNCCY 1 cut(s) 926
EcoRI GAATTC 1 cut(s) 820
EcoRII CCWGG 3 cut(s) 192, 265, 621
EcoT38I GRGCYC 2 cut(s) 43, 658
Esp3I CGTCTC 1 cut(s) 78
FaeI CATG 1 cut(s) 374
FaiI YATR 4 cut(s) 177, 372, 518, 714
FaqI GGGAC 4 cut(s) 234, 532, 655, 823
FatI CATG 1 cut(s) 370
FauI CCCGC 1 cut(s) 503
FbaI TGATCA 2 cut(s) 681, 844
FokI GGATG 2 cut(s) 746, 763
FriOI GRGCYC 2 cut(s) 43, 658
FspBI CTAG 3 cut(s) 237, 591, 939
GlaI GCGC 2 cut(s) 431, 504
GsuI CTGGAG 1 cut(s) 256
HaeIII GGCC 6 cut(s) 286, 294, 500, 597, 621, 673
HapII CCGG 9 cut(s) 243, 283, 303, 364, 497, 584, 674, 792, 813
HhaI GCGC 2 cut(s) 432, 505
Hin1II CATG 1 cut(s) 374
Hin6I GCGC 2 cut(s) 430, 503
HinP1I GCGC 2 cut(s) 430, 503
HincII GTYRAC 1 cut(s) 223
HindII GTYRAC 1 cut(s) 223
HinfI GANTC 5 cut(s) 7, 47, 347, 444, 541
HpaII CCGG 9 cut(s) 243, 283, 303, 364, 497, 584, 674, 792, 813
HphI GGTGA 3 cut(s) 46, 331, 688
Hpy166II GTNNAC 4 cut(s) 223, 607, 699, 919
Hpy188I TCNGA 3 cut(s) 94, 882, 903
Hpy188III TCNNGA 7 cut(s) 44, 215, 230, 251, 364, 406, 538
Hpy8I GTNNAC 4 cut(s) 223, 607, 699, 919
Hpy99I CGWCG 4 cut(s) 191, 407, 580, 697
HpyAV CCTTC 3 cut(s) 430, 525, 740
HpyCH4III ACNGT 4 cut(s) 72, 557, 604, 646
HpyCH4IV ACGT 2 cut(s) 480, 695
HpyCH4V TGCA 2 cut(s) 754, 760
HpyF3I CTNAG 2 cut(s) 83, 831
HpySE526I ACGT 2 cut(s) 480, 695
Hsp92II CATG 1 cut(s) 374
HspAI GCGC 2 cut(s) 430, 503
Kpn2I TCCGGA 1 cut(s) 363
KroI GCCGGC 2 cut(s) 282, 496
KroNI GCCGGC 2 cut(s) 284, 498
Ksp22I TGATCA 2 cut(s) 681, 844
Kzo9I GATC 3 cut(s) 211, 681, 844
LguI GCTCTTC 1 cut(s) 96
LmnI GCTCC 6 cut(s) 38, 245, 275, 366, 528, 653
Lsp1109I GCAGC 8 cut(s) 156, 399, 405, 474, 790, 793, 796, 862
LweI GCATC 2 cut(s) 741, 894
MaeI CTAG 3 cut(s) 237, 591, 939
MaeII ACGT 2 cut(s) 480, 695
MaeIII GTNAC 2 cut(s) 203, 481
MalI GATC 3 cut(s) 213, 683, 846
MbiI CCGCTC 1 cut(s) 510
MboI GATC 3 cut(s) 211, 681, 844
MboII GAAGA 3 cut(s) 68, 113, 479
MfeI CAATTG 1 cut(s) 755
MhlI GDGCHC 4 cut(s) 43, 108, 658, 864
MluCI AATT 3 cut(s) 755, 799, 820
MlyI GAGTC 3 cut(s) 41, 356, 453
MmeI TCCRAC 2 cut(s) 631, 905
MroI TCCGGA 1 cut(s) 363
MroNI GCCGGC 2 cut(s) 282, 496
MseI TTAA 1 cut(s) 455
MspA1I CMGCKG 2 cut(s) 390, 465
MspCI CTTAAG 1 cut(s) 454
MspI CCGG 9 cut(s) 243, 283, 303, 364, 497, 584, 674, 792, 813
MspR9I CCNGG 5 cut(s) 194, 267, 303, 585, 623
MunI CAATTG 1 cut(s) 755
MvaI CCWGG 3 cut(s) 194, 267, 623
MvnI CGCG 1 cut(s) 503
NaeI GCCGGC 2 cut(s) 284, 498
NciI CCSGG 2 cut(s) 303, 585
NdeII GATC 3 cut(s) 211, 681, 844
NgoMIV GCCGGC 2 cut(s) 282, 496
NlaIII CATG 1 cut(s) 374
NlaIV GGNNCC 5 cut(s) 250, 271, 368, 811, 927
NmeAIII GCCGAG 1 cut(s) 531
NmuCI GTSAC 2 cut(s) 203, 481
PaeR7I CTCGAG 1 cut(s) 260
PaqCI CACCTGC 1 cut(s) 619
PciSI GCTCTTC 1 cut(s) 96
PcsI WCGNNNNNNNCGW 2 cut(s) 68, 534
PdiI GCCGGC 2 cut(s) 284, 498
PfeI GAWTC 2 cut(s) 7, 541
PflFI GACNNNGTC 1 cut(s) 401
PflMI CCANNNNNTGG 1 cut(s) 376
Ple19I CGATCG 1 cut(s) 214
PleI GAGTC 3 cut(s) 41, 355, 452
PpsI GAGTC 3 cut(s) 41, 355, 452
PpuMI RGGWCCY 1 cut(s) 926
Psp124BI GAGCTC 2 cut(s) 43, 658
Psp5II RGGWCCY 1 cut(s) 926
Psp6I CCWGG 3 cut(s) 192, 265, 621
PspGI CCWGG 3 cut(s) 192, 265, 621
PspN4I GGNNCC 5 cut(s) 250, 271, 368, 811, 927
PspPI GGNCC 5 cut(s) 248, 285, 671, 810, 926
PspPPI RGGWCCY 1 cut(s) 926
PspXI VCTCGAGB 1 cut(s) 260
PsyI GACNNNGTC 1 cut(s) 401
PvuI CGATCG 1 cut(s) 214
RsaI GTAC 2 cut(s) 608, 920
RsaNI GTAC 2 cut(s) 607, 919
SacI GAGCTC 2 cut(s) 43, 658
SapI GCTCTTC 1 cut(s) 96
SaqAI TTAA 1 cut(s) 455
Sau3AI GATC 3 cut(s) 211, 681, 844
Sau96I GGNCC 5 cut(s) 248, 285, 671, 810, 926
SchI GAGTC 3 cut(s) 41, 356, 453
ScrFI CCNGG 5 cut(s) 194, 267, 303, 585, 623
SduI GDGCHC 4 cut(s) 43, 108, 658, 864
SfaNI GCATC 2 cut(s) 741, 894
Sfr274I CTCGAG 1 cut(s) 260
SinI GGWCC 3 cut(s) 248, 810, 926
SlaI CTCGAG 1 cut(s) 260
SmlI CTYRAG 4 cut(s) 260, 454, 728, 838
SmoI CTYRAG 4 cut(s) 260, 454, 728, 838
Sse9I AATT 3 cut(s) 755, 799, 820
SspMI CTAG 3 cut(s) 237, 591, 939
SstI GAGCTC 2 cut(s) 43, 658
StyD4I CCNGG 5 cut(s) 192, 265, 301, 583, 621
TaaI ACNGT 4 cut(s) 72, 557, 604, 646
TaiI ACGT 2 cut(s) 483, 698
TaqI TCGA 7 cut(s) 10, 62, 214, 261, 308, 405, 537
TasI AATT 3 cut(s) 755, 799, 820
TatI WGTACW 2 cut(s) 606, 918
TfiI GAWTC 2 cut(s) 7, 541
Tru1I TTAA 1 cut(s) 455
Tru9I TTAA 1 cut(s) 455
TseFI GTSAC 2 cut(s) 203, 481
TseI GCWGC 8 cut(s) 144, 387, 393, 462, 778, 781, 784, 850
Tsp45I GTSAC 2 cut(s) 203, 481
TspDTI ATGAA 2 cut(s) 68, 759
TspGWI ACGGA 2 cut(s) 439, 543
Tth111I GACNNNGTC 1 cut(s) 401
Van91I CCANNNNNTGG 1 cut(s) 376
Vha464I CTTAAG 1 cut(s) 454
VpaK11BI GGWCC 3 cut(s) 248, 810, 926
XapI RAATTY 2 cut(s) 799, 820
XhoI CTCGAG 1 cut(s) 260
XspI CTAG 3 cut(s) 237, 591, 939
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.