Rroxscaffold_5G00337070

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_roxburghii
GWHEROQ00000005
OG0004329
Physical Location & Seq
Reverse (-)
5104182 .. 5105806
1625 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_5G00337070.1

Sequence Viewer

Length: 696 bp
ATGGACCCGGCAGCCAATTCACCAGCAGCGCTAAACAAGCGAGAACTCGAGATTTCCATGAACGAAAACAGCGGCGGCAGAAGCAGTGGCGGTGGCAGAGACGACGACGAAGATAGAGATCAAGGAGAAGAGCCTAAAGAAGGGGCCGTCGAGATTGGATCTCGAAGGCCCCGAGGCCGACCGCCCGGATCCAAAAACAAACCCAAACCGCCCATCTTCGTGACCAGGGACAGCCCCAACTCCCTTAGAAGCCACATGATGGAAGTTGCCGGCGGTGCTGACGTGGCGGAGAGCGTGGCACAATTCGCACGGAGGCGTCAGAGAGGTGTTTGCGTGCTCAGCGGGAGTGGCTCAGTGGCCAACGTGACACTGAGACAACCCGCTGCCCCCGGGGCCGTTGTAGCACTCCATGGAAGGTTCGAGATCCTGTCCCTGAGCGGAGCGTTTCTTCCAGGACCTGCTCCGCCCGGGTCGACAGGCCTGACCGTCTACCTAGCAGGCGGTCAGGGTCAGGTTGTTGGGGGAAGCGTTGTTGGATCACTTGTTGCGGCTGGACCAGTTATGGTTGTGGCTGCTACTTTTGCTAATGCTACTTATGAGAGACTGCCTCTTGAGGAAGATGATGAGGCTGGAAGCGGTGGTGGTGGTGGAGGTCATGGAGCTTCTGGAAGCTCCCCCTACTGGAGTTGGAAGTAG
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

231

Amino Acids

23.5

Weight (kDa)

5.97

Isoelectric Point (pI)

55.93

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PCC PF03479 83 - 195 1.2e-24 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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 466
AccB7I CCANNNNNTGG 1 cut(s) 259
AccBSI CCGCTC 1 cut(s) 438
AccI GTMKAC 2 cut(s) 473, 489
AclWI GGATC 5 cut(s) 166, 183, 196, 418, 544
AcoI YGGCCR 1 cut(s) 357
AcyI GRCGYC 1 cut(s) 316
AfeI AGCGCT 1 cut(s) 30
AfiI CCNNNNNNNGG 3 cut(s) 140, 259, 681
AjiI CACGTC 1 cut(s) 283
AjnI CCWGG 2 cut(s) 224, 451
AluBI AGCT 2 cut(s) 662, 672
AluI AGCT 2 cut(s) 662, 672
Alw21I GWGCWC 1 cut(s) 339
Alw26I GTCTC 3 cut(s) 93, 367, 595
AlwI GGATC 5 cut(s) 166, 183, 196, 418, 544
AlwNI CAGNNNCTG 1 cut(s) 458
Ama87I CYCGRG 4 cut(s) 47, 171, 389, 467
Aor51HI AGCGCT 1 cut(s) 30
AoxI GGCC 6 cut(s) 144, 167, 175, 357, 393, 478
ApeKI GCWGC 4 cut(s) 11, 26, 383, 572
AspLEI GCGC 1 cut(s) 31
AspS9I GGNCC 6 cut(s) 4, 144, 168, 393, 455, 554
AsuC2I CCSGG 6 cut(s) 8, 186, 390, 391, 468, 469
AsuHPI GGTGA 1 cut(s) 12
AvaI CYCGRG 4 cut(s) 47, 171, 389, 467
AvaII GGWCC 3 cut(s) 4, 455, 554
BalI TGGCCA 1 cut(s) 359
BamHI GGATCC 1 cut(s) 188
Bbv12I GWGCWC 1 cut(s) 339
BbvI GCAGC 4 cut(s) 23, 38, 370, 559
BccI CCATC 2 cut(s) 221, 253
BceAI ACGGC 2 cut(s) 131, 380
BciT130I CCWGG 2 cut(s) 226, 453
BcnI CCSGG 6 cut(s) 8, 186, 390, 391, 468, 469
BcoDI GTCTC 3 cut(s) 93, 367, 595
BfaI CTAG 1 cut(s) 494
BfoI RGCGCY 1 cut(s) 32
BfuAI ACCTGC 1 cut(s) 466
BglI GCCNNNNNGGC 1 cut(s) 392
BisI GCNGC 7 cut(s) 12, 27, 73, 76, 384, 549, 573
BlpI GCTNAGC 1 cut(s) 338
BlsI GCNGC 7 cut(s) 13, 28, 74, 77, 385, 550, 574
Bme1390I CCNGG 8 cut(s) 8, 186, 226, 390, 391, 453, 468, 469
Bme18I GGWCC 3 cut(s) 4, 455, 554
BmeT110I CYCGRG 4 cut(s) 47, 171, 389, 467
BmgBI CACGTC 1 cut(s) 283
BmgT120I GGNCC 6 cut(s) 4, 144, 168, 393, 455, 554
BmiI GGNNCC 5 cut(s) 6, 145, 170, 190, 394
BmrFI CCNGG 8 cut(s) 8, 186, 226, 390, 391, 453, 468, 469
BplI GAGNNNNNCTC 2 cut(s) 592, 624
Bpu10I CCTNAGC 1 cut(s) 434
Bpu1102I GCTNAGC 1 cut(s) 338
BpuEI CTTGAG 1 cut(s) 632
BpuMI CCSGG 6 cut(s) 8, 186, 390, 391, 468, 469
BsaBI GATNNNNATC 1 cut(s) 117
BsaHI GRCGYC 1 cut(s) 316
BsaJI CCNNGG 7 cut(s) 172, 225, 388, 389, 390, 409, 467
Bsc4I CCNNNNNNNGG 3 cut(s) 140, 259, 681
Bse118I RCCGGY 1 cut(s) 269
Bse1I ACTGG 2 cut(s) 557, 686
Bse8I GATNNNNATC 1 cut(s) 117
BseBI CCWGG 2 cut(s) 226, 453
BseDI CCNNGG 7 cut(s) 172, 225, 388, 389, 390, 409, 467
BseJI GATNNNNATC 1 cut(s) 117
BseLI CCNNNNNNNGG 3 cut(s) 140, 259, 681
BseMII CTCAG 4 cut(s) 352, 362, 366, 425
BseNI ACTGG 2 cut(s) 557, 686
BseXI GCAGC 4 cut(s) 23, 38, 370, 559
Bsh1285I CGRYCG 1 cut(s) 182
BshFI GGCC 6 cut(s) 146, 169, 177, 359, 395, 480
BsiEI CGRYCG 1 cut(s) 182
BsiHKAI GWGCWC 1 cut(s) 339
BsiHKCI CYCGRG 4 cut(s) 47, 171, 389, 467
BsiSI CCGG 5 cut(s) 8, 186, 270, 390, 468
BslFI GGGAC 2 cut(s) 242, 415
BslI CCNNNNNNNGG 3 cut(s) 140, 259, 681
BsmAI GTCTC 3 cut(s) 93, 367, 595
BsmBI CGTCTC 1 cut(s) 93
BsmFI GGGAC 2 cut(s) 242, 415
BsnI GGCC 6 cut(s) 146, 169, 177, 359, 395, 480
BsoBI CYCGRG 4 cut(s) 47, 171, 389, 467
Bsp1286I GDGCHC 1 cut(s) 339
Bsp143I GATC 5 cut(s) 118, 158, 188, 423, 536
Bsp1720I GCTNAGC 1 cut(s) 338
Bsp19I CCATGG 1 cut(s) 409
BspANI GGCC 6 cut(s) 146, 169, 177, 359, 395, 480
BspCNI CTCAG 4 cut(s) 351, 363, 365, 426
BspLI GGNNCC 5 cut(s) 6, 145, 170, 190, 394
BspMI ACCTGC 1 cut(s) 466
BspPI GGATC 5 cut(s) 166, 183, 196, 418, 544
BspQI GCTCTTC 1 cut(s) 123
BsrBI CCGCTC 1 cut(s) 438
BsrFI RCCGGY 1 cut(s) 269
BsrI ACTGG 2 cut(s) 557, 686
BssAI RCCGGY 1 cut(s) 269
BssECI CCNNGG 7 cut(s) 172, 225, 388, 389, 390, 409, 467
BssMI GATC 5 cut(s) 118, 158, 188, 423, 536
BssNI GRCGYC 1 cut(s) 316
BssT1I CCWWGG 1 cut(s) 409
Bst2UI CCWGG 2 cut(s) 226, 453
Bst4CI ACNGT 1 cut(s) 487
Bst6I CTCTTC 1 cut(s) 123
BstACI GRCGYC 1 cut(s) 316
BstC8I GCNNGC 3 cut(s) 271, 335, 499
BstDEI CTNAG 5 cut(s) 245, 338, 352, 371, 434
BstDSI CCRYGG 1 cut(s) 409
BstENI CCTNNNNNAGG 1 cut(s) 138
BstH2I RGCGCY 1 cut(s) 32
BstHHI GCGC 1 cut(s) 31
BstKTI GATC 5 cut(s) 121, 161, 191, 426, 539
BstMAI GTCTC 3 cut(s) 93, 367, 595
BstMBI GATC 5 cut(s) 118, 158, 188, 423, 536
BstMCI CGRYCG 1 cut(s) 182
BstNI CCWGG 2 cut(s) 226, 453
BstSCI CCNGG 8 cut(s) 6, 184, 224, 388, 389, 451, 466, 467
BstV1I GCAGC 4 cut(s) 23, 38, 370, 559
BstX2I RGATCY 3 cut(s) 158, 188, 423
BstYI RGATCY 3 cut(s) 158, 188, 423
BsuRI GGCC 6 cut(s) 146, 169, 177, 359, 395, 480
BtgI CCRYGG 1 cut(s) 409
BtrI CACGTC 1 cut(s) 283
BtsI GCAGTG 1 cut(s) 91
BtsIMutI CAGTG 3 cut(s) 91, 360, 368
BveI ACCTGC 1 cut(s) 466
Cac8I GCNNGC 3 cut(s) 271, 335, 499
CaiI CAGNNNCTG 1 cut(s) 458
CfoI GCGC 1 cut(s) 31
Cfr10I RCCGGY 1 cut(s) 269
Cfr13I GGNCC 6 cut(s) 4, 144, 168, 393, 455, 554
Cfr9I CCCGGG 2 cut(s) 389, 467
CseI GACGC 1 cut(s) 305
CviAII CATG 4 cut(s) 58, 256, 410, 656
DdeI CTNAG 5 cut(s) 245, 338, 352, 371, 434
DpnI GATC 5 cut(s) 120, 160, 190, 425, 538
DpnII GATC 5 cut(s) 118, 158, 188, 423, 536
EaeI YGGCCR 1 cut(s) 357
Eam1104I CTCTTC 1 cut(s) 123
EarI CTCTTC 1 cut(s) 123
EciI GGCGGA 2 cut(s) 302, 453
Eco130I CCWWGG 1 cut(s) 409
Eco147I AGGCCT 1 cut(s) 480
Eco47I GGWCC 3 cut(s) 4, 455, 554
Eco47III AGCGCT 1 cut(s) 30
Eco88I CYCGRG 4 cut(s) 47, 171, 389, 467
EcoNI CCTNNNNNAGG 1 cut(s) 138
EcoO109I RGGNCCY 2 cut(s) 168, 455
EcoRII CCWGG 2 cut(s) 224, 451
EcoT14I CCWWGG 1 cut(s) 409
ErhI CCWWGG 1 cut(s) 409
Esp3I CGTCTC 1 cut(s) 93
FaeI CATG 4 cut(s) 61, 259, 413, 659
FaiI YATR 6 cut(s) 59, 257, 411, 563, 597, 657
FaqI GGGAC 2 cut(s) 242, 415
FatI CATG 4 cut(s) 57, 255, 409, 655
FauI CCCGC 2 cut(s) 335, 388
FblI GTMKAC 2 cut(s) 473, 489
Fnu4HI GCNGC 7 cut(s) 12, 27, 73, 76, 384, 549, 573
Fsp4HI GCNGC 7 cut(s) 12, 27, 73, 76, 384, 549, 573
FspBI CTAG 1 cut(s) 494
GlaI GCGC 1 cut(s) 30
GluI GCNGC 7 cut(s) 12, 27, 73, 76, 384, 549, 573
HaeII RGCGCY 1 cut(s) 32
HaeIII GGCC 6 cut(s) 146, 169, 177, 359, 395, 480
HapII CCGG 5 cut(s) 8, 186, 270, 390, 468
HgaI GACGC 1 cut(s) 305
HhaI GCGC 1 cut(s) 31
Hin1I GRCGYC 1 cut(s) 316
Hin1II CATG 4 cut(s) 61, 259, 413, 659
Hin6I GCGC 1 cut(s) 29
HinP1I GCGC 1 cut(s) 29
HincII GTYRAC 1 cut(s) 474
HindII GTYRAC 1 cut(s) 474
HpaII CCGG 5 cut(s) 8, 186, 270, 390, 468
HphI GGTGA 1 cut(s) 12
Hpy166II GTNNAC 2 cut(s) 474, 490
Hpy188I TCNGA 1 cut(s) 321
Hpy188III TCNNGA 7 cut(s) 49, 151, 162, 220, 421, 611, 666
Hpy8I GTNNAC 2 cut(s) 474, 490
Hpy99I CGWCG 3 cut(s) 107, 110, 152
HpyAV CCTTC 3 cut(s) 134, 159, 408
HpyCH4III ACNGT 1 cut(s) 487
HpyCH4IV ACGT 2 cut(s) 282, 363
HpyF3I CTNAG 5 cut(s) 245, 338, 352, 371, 434
HpySE526I ACGT 2 cut(s) 282, 363
Hsp92I GRCGYC 1 cut(s) 316
Hsp92II CATG 4 cut(s) 61, 259, 413, 659
HspAI GCGC 1 cut(s) 29
KroI GCCGGC 1 cut(s) 269
KroNI GCCGGC 1 cut(s) 271
Kzo9I GATC 5 cut(s) 118, 158, 188, 423, 536
LguI GCTCTTC 1 cut(s) 123
LmnI GCTCC 4 cut(s) 440, 466, 659, 677
Lsp1109I GCAGC 4 cut(s) 23, 38, 370, 559
MaeI CTAG 1 cut(s) 494
MaeII ACGT 2 cut(s) 282, 363
MaeIII GTNAC 2 cut(s) 220, 364
MalI GATC 5 cut(s) 120, 160, 190, 425, 538
MbiI CCGCTC 1 cut(s) 438
MboI GATC 5 cut(s) 118, 158, 188, 423, 536
MboII GAAGA 5 cut(s) 122, 140, 208, 440, 629
MflI RGATCY 3 cut(s) 158, 188, 423
MhlI GDGCHC 1 cut(s) 339
MlsI TGGCCA 1 cut(s) 359
MluCI AATT 2 cut(s) 16, 302
MluNI TGGCCA 1 cut(s) 359
MmeI TCCRAC 2 cut(s) 514, 668
MnlI CCTC 7 cut(s) 167, 306, 317, 607, 618, 619, 644
Mox20I TGGCCA 1 cut(s) 359
MroNI GCCGGC 1 cut(s) 269
MscI TGGCCA 1 cut(s) 359
MslI CAYNNNNRTG 1 cut(s) 218
Msp20I TGGCCA 1 cut(s) 359
MspA1I CMGCKG 3 cut(s) 72, 342, 383
MspI CCGG 5 cut(s) 8, 186, 270, 390, 468
MspR9I CCNGG 8 cut(s) 8, 186, 226, 390, 391, 453, 468, 469
MvaI CCWGG 2 cut(s) 226, 453
NaeI GCCGGC 1 cut(s) 271
NciI CCSGG 6 cut(s) 8, 186, 390, 391, 468, 469
NcoI CCATGG 1 cut(s) 409
NdeII GATC 5 cut(s) 118, 158, 188, 423, 536
NgoMIV GCCGGC 1 cut(s) 269
NlaIII CATG 4 cut(s) 61, 259, 413, 659
NlaIV GGNNCC 5 cut(s) 6, 145, 170, 190, 394
NmuCI GTSAC 2 cut(s) 220, 364
PaeR7I CTCGAG 1 cut(s) 47
PceI AGGCCT 1 cut(s) 480
PciSI GCTCTTC 1 cut(s) 123
PcsI WCGNNNNNNNCGW 1 cut(s) 169
PdiI GCCGGC 1 cut(s) 271
PflMI CCANNNNNTGG 1 cut(s) 259
PfoI TCCNGGA 1 cut(s) 451
PkrI GCNGC 7 cut(s) 13, 28, 74, 77, 385, 550, 574
PpuMI RGGWCCY 1 cut(s) 455
Psp5II RGGWCCY 1 cut(s) 455
Psp6I CCWGG 2 cut(s) 224, 451
PspGI CCWGG 2 cut(s) 224, 451
PspN4I GGNNCC 5 cut(s) 6, 145, 170, 190, 394
PspPI GGNCC 6 cut(s) 4, 144, 168, 393, 455, 554
PspPPI RGGWCCY 1 cut(s) 455
PstNI CAGNNNCTG 1 cut(s) 458
PsuI RGATCY 3 cut(s) 158, 188, 423
RseI CAYNNNNRTG 1 cut(s) 218
SalI GTCGAC 1 cut(s) 472
SapI GCTCTTC 1 cut(s) 123
SatI GCNGC 7 cut(s) 12, 27, 73, 76, 384, 549, 573
Sau3AI GATC 5 cut(s) 118, 158, 188, 423, 536
Sau96I GGNCC 6 cut(s) 4, 144, 168, 393, 455, 554
ScrFI CCNGG 8 cut(s) 8, 186, 226, 390, 391, 453, 468, 469
SduI GDGCHC 1 cut(s) 339
Sfr274I CTCGAG 1 cut(s) 47
SinI GGWCC 3 cut(s) 4, 455, 554
SlaI CTCGAG 1 cut(s) 47
SmaI CCCGGG 2 cut(s) 391, 469
SmiMI CAYNNNNRTG 1 cut(s) 218
SmlI CTYRAG 2 cut(s) 47, 611
SmoI CTYRAG 2 cut(s) 47, 611
Sse9I AATT 2 cut(s) 16, 302
SseBI AGGCCT 1 cut(s) 480
SspMI CTAG 1 cut(s) 494
StuI AGGCCT 1 cut(s) 480
StyD4I CCNGG 8 cut(s) 6, 184, 224, 388, 389, 451, 466, 467
StyI CCWWGG 1 cut(s) 409
TaaI ACNGT 1 cut(s) 487
TaiI ACGT 2 cut(s) 285, 366
TaqI TCGA 5 cut(s) 48, 150, 163, 420, 473
TasI AATT 2 cut(s) 16, 302
TauI GCSGC 3 cut(s) 75, 78, 551
TscAI CASTG 3 cut(s) 91, 360, 375
TseFI GTSAC 2 cut(s) 220, 364
TseI GCWGC 4 cut(s) 11, 26, 383, 572
Tsp45I GTSAC 2 cut(s) 220, 364
TspDTI ATGAA 1 cut(s) 74
TspGWI ACGGA 1 cut(s) 325
TspMI CCCGGG 2 cut(s) 389, 467
TspRI CASTG 3 cut(s) 91, 360, 375
Van91I CCANNNNNTGG 1 cut(s) 259
VpaK11BI GGWCC 3 cut(s) 4, 455, 554
XagI CCTNNNNNAGG 1 cut(s) 138
XhoI CTCGAG 1 cut(s) 47
XmaI CCCGGG 2 cut(s) 389, 467
XmiI GTMKAC 2 cut(s) 473, 489
XspI CTAG 1 cut(s) 494
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.