Rh1AG346600

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
Chr1A
OG0012533
Physical Location & Seq
Reverse (-)
58230989 .. 58237900
6912 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh1AG346600.1

Sequence Viewer

Length: 942 bp
ATGGCGAATCGATGGTGGGCTGGAAATGTGGCGATGGGAGCTCATGACTCAATCACCGCCTCGACACCACCGTCTCTTCATCTTAGAAACTCTGAAGCCGAAGAGCACAACAACAACAACACACCCACCAACAGCAGCACCAGCAACCCAAACAACACTCCACCTCAGAAGCAGGACGACGACCAGGACAGCCGTGACAACGATCGAGAAGTTGACAATCAAGACCCTAGCTCCGGCGGCCCCGACAGCCTCGAGCCTGGCTCCAGCAACCGCCGGCCCAGAGGCCGTCCCCCCGGCTCGAAAAACAAGCCGAAACCGCCGATAATCATCACCAAAGAGTCTCCCAACGCTCTCCGGAGCCATGTCTTGGAAATCAGCAGCGGCAGCGACATCGTCGAGAGCATTGCCACCTTCGCACAGCGCAGGCACAGAGGAGTCTCCGTCTTAAGCGGCAGCGGCATTGTTTCTAACGTCACTCTCCGTCAGCCGGCCGCGCCGAGCGGGGTCATAACGCTCCACGGAAGGTTCGAGATTCTGTCCCTAAACGGTGCCTTTCTGCCTGCCCCGTCGCCGCCGGGGGCTAGTGGCCTGACCGTGTACTTGGGCGGCGGGCAGGGGCAGGTGGTTGGTGGGACTGTTGTTGGAGCTCTGTTGGCTTCCGGGCCGGTGATGATCATTGCGGCGACGTTCACTAATGCCACTTATGAGAGACTGCCGCTTGAGGATGAGAGCAATGAAGGGATGCAATTGCAACAGCAACAGCAGCAGCAATCCGGTGTGAATTCGGCGGGGACCGGAGGGAATTCGGGTTCTCAGGGCTTGAGTGATCAGCAGCAACAAGGGCCCATTTACGCTTTGCCTCCGACTTTGCTTCCAAATGGTCAGATGCCGCCTGATGTGTACTGGGGTCCTCCACCGCCTAGACCTCCGCCTGCTTACTGA
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

313

Amino Acids

32.84

Weight (kDa)

5.51

Isoelectric Point (pI)

58.98

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PCC PF03479 119 - 232 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) 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
AcsI RAATTY 2 cut(s) 781, 802
AcuI CTGAAG 1 cut(s) 114
AfaI GTAC 2 cut(s) 599, 902
AfiI CCNNNNNNNGG 3 cut(s) 233, 367, 487
AflII CTTAAG 1 cut(s) 445
AjnI CCWGG 2 cut(s) 183, 256
AloI GAACNNNNNNTCC 2 cut(s) 793, 825
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, 842
ApaI GGGCCC 1 cut(s) 846
ApeKI GCWGC 7 cut(s) 135, 378, 384, 453, 763, 766, 832
ApoI RAATTY 2 cut(s) 781, 802
AspLEI GCGC 2 cut(s) 423, 496
AspS9I GGNCC 7 cut(s) 239, 276, 662, 792, 842, 843, 908
AsuC2I CCSGG 3 cut(s) 294, 576, 661
AsuHPI GGTGA 3 cut(s) 46, 322, 679
AvaI CYCGRG 1 cut(s) 251
AvaII GGWCC 2 cut(s) 792, 908
BaeGI GKGCMC 1 cut(s) 846
BanI GGYRCC 1 cut(s) 548
BanII GRGCYC 3 cut(s) 43, 649, 846
Bbv12I GWGCWC 3 cut(s) 43, 108, 649
BbvI GCAGC 7 cut(s) 147, 390, 396, 465, 775, 778, 844
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 2 cut(s) 672, 826
BcnI CCSGG 3 cut(s) 294, 576, 661
BcoDI GTCTC 4 cut(s) 78, 345, 442, 703
BfaI CTAG 3 cut(s) 228, 582, 921
BfrI CTTAAG 1 cut(s) 445
BfuAI ACCTGC 1 cut(s) 610
Bme1390I CCNGG 5 cut(s) 185, 258, 294, 576, 661
Bme18I GGWCC 2 cut(s) 792, 908
BmeT110I CYCGRG 1 cut(s) 251
BmgT120I GGNCC 7 cut(s) 239, 276, 662, 792, 842, 843, 908
BmiI GGNNCC 7 cut(s) 241, 262, 359, 550, 793, 844, 909
BmrFI CCNGG 5 cut(s) 185, 258, 294, 576, 661
BmrI ACTGGG 1 cut(s) 913
BmsI GCATC 2 cut(s) 732, 876
BmuI ACTGGG 1 cut(s) 913
BplI GAGNNNNNCTC 2 cut(s) 245, 277
BpmI CTGGAG 1 cut(s) 247
BpuEI CTTGAG 2 cut(s) 740, 841
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 3 cut(s) 354, 773, 794
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) 908
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 2 cut(s) 179, 827
BseNI ACTGG 1 cut(s) 908
BseRI GAGGAG 1 cut(s) 447
BseSI GKGCMC 1 cut(s) 846
BseX3I CGGCCG 1 cut(s) 489
BseXI GCAGC 7 cut(s) 147, 390, 396, 465, 775, 778, 844
Bsh1236I CGCG 1 cut(s) 494
Bsh1285I CGRYCG 2 cut(s) 205, 492
BshFI GGCC 7 cut(s) 240, 277, 285, 491, 588, 664, 844
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
BslFI GGGAC 4 cut(s) 273, 523, 646, 805
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 4 cut(s) 273, 523, 646, 805
BsnI GGCC 7 cut(s) 240, 277, 285, 491, 588, 664, 844
BsoBI CYCGRG 1 cut(s) 251
Bsp120I GGGCCC 1 cut(s) 842
Bsp1286I GDGCHC 4 cut(s) 43, 108, 649, 846
Bsp13I TCCGGA 1 cut(s) 354
Bsp143I GATC 3 cut(s) 202, 672, 826
BspANI GGCC 7 cut(s) 240, 277, 285, 491, 588, 664, 844
BspCNI CTCAG 2 cut(s) 178, 826
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 7 cut(s) 241, 262, 359, 550, 793, 844, 909
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) 908
BssAI RCCGGY 3 cut(s) 273, 487, 664
BssECI CCNNGG 3 cut(s) 292, 517, 575
BssMI GATC 3 cut(s) 202, 672, 826
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, 933
BstDEI CTNAG 3 cut(s) 83, 165, 813
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 3 cut(s) 205, 675, 829
BstMAI GTCTC 4 cut(s) 78, 345, 442, 703
BstMBI GATC 3 cut(s) 202, 672, 826
BstMCI CGRYCG 2 cut(s) 205, 492
BstNI CCWGG 2 cut(s) 185, 258
BstSCI CCNGG 5 cut(s) 183, 256, 292, 574, 659
BstSLI GKGCMC 1 cut(s) 846
BstUI CGCG 1 cut(s) 494
BstV1I GCAGC 7 cut(s) 147, 390, 396, 465, 775, 778, 844
BstZI CGGCCG 1 cut(s) 489
Bsu15I ATCGAT 1 cut(s) 10
BsuRI GGCC 7 cut(s) 240, 277, 285, 491, 588, 664, 844
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, 933
CciI TCATGA 1 cut(s) 43
CfoI GCGC 2 cut(s) 423, 496
Cfr10I RCCGGY 3 cut(s) 273, 487, 664
Cfr13I GGNCC 7 cut(s) 239, 276, 662, 792, 842, 843, 908
ClaI ATCGAT 1 cut(s) 10
Csp6I GTAC 2 cut(s) 598, 901
CviAII CATG 2 cut(s) 44, 362
CviQI GTAC 2 cut(s) 598, 901
DdeI CTNAG 3 cut(s) 83, 165, 813
DpnI GATC 3 cut(s) 204, 674, 828
DpnII GATC 3 cut(s) 202, 672, 826
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) 918
Ecl136II GAGCTC 2 cut(s) 41, 647
EclXI CGGCCG 1 cut(s) 489
Eco24I GRGCYC 3 cut(s) 43, 649, 846
Eco47I GGWCC 2 cut(s) 792, 908
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 2 cut(s) 842, 908
EcoRI GAATTC 2 cut(s) 781, 802
EcoRII CCWGG 2 cut(s) 183, 256
EcoT38I GRGCYC 3 cut(s) 43, 649, 846
Esp3I CGTCTC 1 cut(s) 78
FaeI CATG 2 cut(s) 47, 365
FaiI YATR 4 cut(s) 45, 363, 509, 705
FaqI GGGAC 4 cut(s) 273, 523, 646, 805
FatI CATG 2 cut(s) 43, 361
FauI CCCGC 3 cut(s) 494, 602, 781
FbaI TGATCA 2 cut(s) 672, 826
FokI GGATG 2 cut(s) 737, 754
FriOI GRGCYC 3 cut(s) 43, 649, 846
FspBI CTAG 3 cut(s) 228, 582, 921
GlaI GCGC 2 cut(s) 422, 495
GsuI CTGGAG 1 cut(s) 247
HaeIII GGCC 7 cut(s) 240, 277, 285, 491, 588, 664, 844
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
HphI GGTGA 3 cut(s) 46, 322, 679
Hpy166II GTNNAC 4 cut(s) 214, 598, 690, 901
Hpy188I TCNGA 4 cut(s) 94, 168, 864, 885
Hpy188III TCNNGA 6 cut(s) 44, 206, 221, 355, 397, 529
Hpy8I GTNNAC 4 cut(s) 214, 598, 690, 901
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 3 cut(s) 83, 165, 813
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 2 cut(s) 672, 826
Kzo9I GATC 3 cut(s) 202, 672, 826
LguI GCTCTTC 1 cut(s) 96
LmnI GCTCC 6 cut(s) 38, 236, 266, 357, 519, 644
Lsp1109I GCAGC 7 cut(s) 147, 390, 396, 465, 775, 778, 844
LweI GCATC 2 cut(s) 732, 876
MaeI CTAG 3 cut(s) 228, 582, 921
MaeII ACGT 2 cut(s) 471, 686
MaeIII GTNAC 2 cut(s) 194, 472
MalI GATC 3 cut(s) 204, 674, 828
MbiI CCGCTC 1 cut(s) 501
MboI GATC 3 cut(s) 202, 672, 826
MboII GAAGA 2 cut(s) 68, 113
MfeI CAATTG 1 cut(s) 746
MhlI GDGCHC 4 cut(s) 43, 108, 649, 846
MluCI AATT 3 cut(s) 746, 781, 802
MlyI GAGTC 3 cut(s) 41, 347, 444
MmeI TCCRAC 2 cut(s) 622, 887
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
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 3 cut(s) 202, 672, 826
NgoMIV GCCGGC 2 cut(s) 273, 487
NlaIII CATG 2 cut(s) 47, 365
NlaIV GGNNCC 7 cut(s) 241, 262, 359, 550, 793, 844, 909
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) 908
Psp124BI GAGCTC 2 cut(s) 43, 649
Psp5II RGGWCCY 1 cut(s) 908
Psp6I CCWGG 2 cut(s) 183, 256
PspGI CCWGG 2 cut(s) 183, 256
PspN4I GGNNCC 7 cut(s) 241, 262, 359, 550, 793, 844, 909
PspOMI GGGCCC 1 cut(s) 842
PspPI GGNCC 7 cut(s) 239, 276, 662, 792, 842, 843, 908
PspPPI RGGWCCY 1 cut(s) 908
PspXI VCTCGAGB 1 cut(s) 251
PsyI GACNNNGTC 1 cut(s) 392
PvuI CGATCG 1 cut(s) 205
RsaI GTAC 2 cut(s) 599, 902
RsaNI GTAC 2 cut(s) 598, 901
SacI GAGCTC 2 cut(s) 43, 649
SapI GCTCTTC 1 cut(s) 96
SaqAI TTAA 1 cut(s) 446
Sau3AI GATC 3 cut(s) 202, 672, 826
Sau96I GGNCC 7 cut(s) 239, 276, 662, 792, 842, 843, 908
SchI GAGTC 3 cut(s) 41, 347, 444
ScrFI CCNGG 5 cut(s) 185, 258, 294, 576, 661
SduI GDGCHC 4 cut(s) 43, 108, 649, 846
SfaNI GCATC 2 cut(s) 732, 876
Sfr274I CTCGAG 1 cut(s) 251
SinI GGWCC 2 cut(s) 792, 908
SlaI CTCGAG 1 cut(s) 251
SmlI CTYRAG 4 cut(s) 251, 445, 719, 820
SmoI CTYRAG 4 cut(s) 251, 445, 719, 820
Sse9I AATT 3 cut(s) 746, 781, 802
SspMI CTAG 3 cut(s) 228, 582, 921
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 3 cut(s) 746, 781, 802
TatI WGTACW 2 cut(s) 597, 900
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
TseI GCWGC 7 cut(s) 135, 378, 384, 453, 763, 766, 832
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 2 cut(s) 792, 908
XapI RAATTY 2 cut(s) 781, 802
XhoI CTCGAG 1 cut(s) 251
XspI CTAG 3 cut(s) 228, 582, 921
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.