Rh2DG511900

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
Chr2D
OG0014578
Physical Location & Seq
Reverse (-)
73639073 .. 73639957
885 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh2DG511900.1

Sequence Viewer

Length: 885 bp
ATGGTACTATACTACTATATATACCACATTCTGAATGCAGCTCATGGTGATTCTCTGATCATTGCATACTGTGTGTATGAGAAAATGGCAGGAGGTGCGGATCTAACAGGACCTAATGTTGTGTCTAAAACTTCAGTCGACCGAAGCCAAGATGTGGATAAAGGTAATAATCACCACAGGCCTGGCATTGATGCATTGCTTATGGCACCAAAAATACCAAAGCCAGTGCAACCGGTTTCTTCAGCATCCGAGGGGGAGACAATCCGGCGACCTCGTGGAAGGCCTGCGGGTTCTAAAAACAAGCCAAAGCCACCTATCATTGTCACCCGCGATAGTGCTAATGCGCTTCGTGCGCATGCTATGGAAGTGAGTTCAGGCTGTGATGTGAGTGAAAGTTTAACCAACTTTGCAAGGAGGAAACAAAGAGGTATTTGCATACTGAGTGGAAGTGGTTGTGTAACCAATGTCACACTGCGGCAACCAGCTTCCTCCGGAGCCATTGTGACCCTCCACGGCCGTTTTGAGATTCTCTCATTGCTCGGATCAATCTTGCCTCCTCCAGCCCCTCCTGGGATTACAGGTCTAACTATCTACTTAGCTGGGGCTCAGGGGCAGGTTGTAGGTGGGGGTGTGGTAGGTGCACTCATTGCTTCGGGGCCTGTTGTGATCATGGCTGCATCGTTCATGAATGCAACTTTTGATCGTCTTCCACTGGATGAAGATGAAGTAGCTGCAGCTTTGCAAAACCAACAATACCAAAATGGTCGACACCACCACCTGGATATGTCAGATTTATATGGACTTCCACCAAATCTGCTCACTAATGGTAATGTGCCCCCTGAGGTTTACTCCTGGGCATCTGGCCGAACTATGTCAAAGACTTAA
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

294

Amino Acids

31.17

Weight (kDa)

8.86

Isoelectric Point (pI)

41.02

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PCC PF03479 117 - 229 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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Orthologous Genes (Group: OG0014578)

Species Orthologous Gene IDs
arabidopsis_thaliana AT2G42940
fragaria_vesca FvH4_6g38311
malus_domestica MD09G1151100.v1.1 MD17G1138700.v1.1
prunus_persica Prupe.3G173700_v2.0.a1
pyrus_communis pycom09g07090 pycom17g13180
rosa_chinensis RchiOBHm_Chr2g0151621
rosa_laevigata RLG00000020564
rosa_multiflora Rmu_sc0005287.1_g000005
rosa_roxburghii Rroxscaffold_2G00096310
rosa_rugosa Rorug02G0427300
rosa_samantha Rh2AG488200 Rh2BG500800 Rh2CG474700 Rh2DG511900
rosa_wichuraiana Rw2G040020

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc16I TGCGCA 1 cut(s) 354
Acc36I ACCTGC 1 cut(s) 604
AccB1I GGYRCC 1 cut(s) 205
AccB7I CCANNNNNTGG 2 cut(s) 154, 778
AccI GTMKAC 2 cut(s) 138, 766
AccII CGCG 1 cut(s) 330
AccIII TCCGGA 1 cut(s) 491
AciI CCGC 4 cut(s) 98, 287, 328, 475
AclWI GGATC 2 cut(s) 108, 550
AcoI YGGCCR 2 cut(s) 514, 862
AcuI CTGAAG 2 cut(s) 117, 225
AfaI GTAC 1 cut(s) 6
AfiI CCNNNNNNNGG 3 cut(s) 154, 570, 778
AgeI ACCGGT 1 cut(s) 232
AjnI CCWGG 4 cut(s) 181, 568, 777, 851
AluBI AGCT 5 cut(s) 41, 485, 599, 731, 737
AluI AGCT 5 cut(s) 41, 485, 599, 731, 737
Alw21I GWGCWC 1 cut(s) 643
Alw26I GTCTC 1 cut(s) 251
Alw44I GTGCAC 1 cut(s) 639
AlwI GGATC 2 cut(s) 108, 550
Aor13HI TCCGGA 1 cut(s) 491
AoxI GGCC 5 cut(s) 179, 281, 514, 656, 862
ApaLI GTGCAC 1 cut(s) 639
ApeKI GCWGC 4 cut(s) 38, 674, 731, 734
AsiGI ACCGGT 1 cut(s) 232
AspLEI GCGC 2 cut(s) 346, 355
AspS9I GGNCC 2 cut(s) 110, 656
AsuHPI GGTGA 3 cut(s) 59, 164, 316
AvaII GGWCC 1 cut(s) 110
AxyI CCTNAGG 1 cut(s) 840
BaeGI GKGCMC 2 cut(s) 643, 837
BanI GGYRCC 1 cut(s) 205
BanII GRGCYC 1 cut(s) 607
BauI CACGAG 1 cut(s) 273
BbsI GAAGAC 1 cut(s) 698
Bbv12I GWGCWC 1 cut(s) 643
BbvI GCAGC 4 cut(s) 50, 661, 718, 746
BceAI ACGGC 2 cut(s) 501, 529
BciT130I CCWGG 4 cut(s) 183, 570, 779, 853
BclI TGATCA 2 cut(s) 57, 666
BcoDI GTCTC 1 cut(s) 251
BfmI CTRYAG 1 cut(s) 732
BfuAI ACCTGC 1 cut(s) 604
BisI GCNGC 5 cut(s) 39, 476, 675, 732, 735
BlsI GCNGC 5 cut(s) 40, 477, 676, 733, 736
Bme1390I CCNGG 4 cut(s) 183, 570, 779, 853
Bme18I GGWCC 1 cut(s) 110
BmgT120I GGNCC 2 cut(s) 110, 656
BmiI GGNNCC 3 cut(s) 207, 496, 657
BmrFI CCNGG 4 cut(s) 183, 570, 779, 853
BmsI GCATC 4 cut(s) 181, 254, 686, 866
BpiI GAAGAC 1 cut(s) 698
BplI GAGNNNNNCTC 4 cut(s) 515, 547, 833, 865
BpmI CTGGAG 1 cut(s) 543
Bpu10I CCTNAGC 1 cut(s) 606
BsaJI CCNNGG 4 cut(s) 249, 511, 569, 852
BsaWI WCCGGW 2 cut(s) 232, 491
BsaXI ACNNNNNCTCC 2 cut(s) 486, 516
Bsc4I CCNNNNNNNGG 3 cut(s) 154, 570, 778
Bse118I RCCGGY 1 cut(s) 232
Bse1I ACTGG 2 cut(s) 224, 717
Bse21I CCTNAGG 1 cut(s) 840
Bse3DI GCAATG 4 cut(s) 60, 194, 533, 645
BseAI TCCGGA 1 cut(s) 491
BseBI CCWGG 4 cut(s) 183, 570, 779, 853
BseDI CCNNGG 4 cut(s) 249, 511, 569, 852
BseGI GGATG 2 cut(s) 245, 721
BseLI CCNNNNNNNGG 3 cut(s) 154, 570, 778
BseMI GCAATG 4 cut(s) 60, 194, 533, 645
BseMII CTCAG 3 cut(s) 431, 620, 831
BseNI ACTGG 2 cut(s) 224, 717
BseRI GAGGAG 1 cut(s) 546
BseSI GKGCMC 2 cut(s) 643, 837
BseX3I CGGCCG 1 cut(s) 514
BseXI GCAGC 4 cut(s) 50, 661, 718, 746
BseYI CCCAGC 1 cut(s) 599
Bsh1236I CGCG 1 cut(s) 330
Bsh1285I CGRYCG 2 cut(s) 142, 517
BshFI GGCC 5 cut(s) 181, 283, 516, 658, 864
BshNI GGYRCC 1 cut(s) 205
BshTI ACCGGT 1 cut(s) 232
BsiEI CGRYCG 2 cut(s) 142, 517
BsiHKAI GWGCWC 1 cut(s) 643
BsiSI CCGG 3 cut(s) 233, 265, 492
BslI CCNNNNNNNGG 3 cut(s) 154, 570, 778
BsmAI GTCTC 1 cut(s) 251
BsmI GAATGC 2 cut(s) 40, 694
BsnI GGCC 5 cut(s) 181, 283, 516, 658, 864
Bsp1286I GDGCHC 3 cut(s) 607, 643, 837
Bsp13I TCCGGA 1 cut(s) 491
Bsp143I GATC 5 cut(s) 57, 100, 542, 666, 700
BspACI CCGC 4 cut(s) 98, 287, 328, 475
BspANI GGCC 5 cut(s) 181, 283, 516, 658, 864
BspCNI CTCAG 3 cut(s) 432, 619, 832
BspEI TCCGGA 1 cut(s) 491
BspFNI CGCG 1 cut(s) 330
BspHI TCATGA 1 cut(s) 684
BspLI GGNNCC 3 cut(s) 207, 496, 657
BspMAI CTGCAG 1 cut(s) 736
BspMI ACCTGC 1 cut(s) 604
BspPI GGATC 2 cut(s) 108, 550
BspT107I GGYRCC 1 cut(s) 205
BsrDI GCAATG 4 cut(s) 60, 194, 533, 645
BsrFI RCCGGY 1 cut(s) 232
BsrI ACTGG 2 cut(s) 224, 717
BssAI RCCGGY 1 cut(s) 232
BssECI CCNNGG 4 cut(s) 249, 511, 569, 852
BssMI GATC 5 cut(s) 57, 100, 542, 666, 700
BssSI CACGAG 1 cut(s) 273
Bst2BI CACGAG 1 cut(s) 273
Bst2UI CCWGG 4 cut(s) 183, 570, 779, 853
Bst4CI ACNGT 1 cut(s) 71
BstAPI GCANNNNNTGC 2 cut(s) 95, 647
BstC8I GCNNGC 2 cut(s) 285, 357
BstDEI CTNAG 4 cut(s) 440, 595, 606, 840
BstDSI CCRYGG 1 cut(s) 511
BstF5I GGATG 2 cut(s) 245, 721
BstFNI CGCG 1 cut(s) 330
BstHHI GCGC 2 cut(s) 346, 355
BstKTI GATC 5 cut(s) 60, 103, 545, 669, 703
BstMAI GTCTC 1 cut(s) 251
BstMBI GATC 5 cut(s) 57, 100, 542, 666, 700
BstMCI CGRYCG 2 cut(s) 142, 517
BstMWI GCNNNNNNNGC 4 cut(s) 95, 350, 352, 647
BstNI CCWGG 4 cut(s) 183, 570, 779, 853
BstNSI RCATGY 1 cut(s) 359
BstSCI CCNGG 4 cut(s) 181, 568, 777, 851
BstSFI CTRYAG 1 cut(s) 732
BstSLI GKGCMC 2 cut(s) 643, 837
BstUI CGCG 1 cut(s) 330
BstV1I GCAGC 4 cut(s) 50, 661, 718, 746
BstV2I GAAGAC 1 cut(s) 698
BstX2I RGATCY 1 cut(s) 100
BstXI CCANNNNNNTGG 1 cut(s) 182
BstYI RGATCY 1 cut(s) 100
BstZI CGGCCG 1 cut(s) 514
Bsu36I CCTNAGG 1 cut(s) 840
BsuRI GGCC 5 cut(s) 181, 283, 516, 658, 864
BtgI CCRYGG 1 cut(s) 511
BtsCI GGATG 2 cut(s) 245, 721
BtsI GCAGTG 1 cut(s) 470
BtsIMutI CAGTG 3 cut(s) 231, 470, 710
BveI ACCTGC 1 cut(s) 604
Cac8I GCNNGC 2 cut(s) 285, 357
CciI TCATGA 1 cut(s) 684
CfoI GCGC 2 cut(s) 346, 355
Cfr10I RCCGGY 1 cut(s) 232
Cfr13I GGNCC 2 cut(s) 110, 656
Csp6I GTAC 1 cut(s) 5
CspAI ACCGGT 1 cut(s) 232
CviAII CATG 4 cut(s) 44, 356, 670, 685
CviQI GTAC 1 cut(s) 5
DdeI CTNAG 4 cut(s) 440, 595, 606, 840
DpnI GATC 5 cut(s) 59, 102, 544, 668, 702
DpnII GATC 5 cut(s) 57, 100, 542, 666, 700
EaeI YGGCCR 2 cut(s) 514, 862
EagI CGGCCG 1 cut(s) 514
EclXI CGGCCG 1 cut(s) 514
Eco147I AGGCCT 2 cut(s) 181, 283
Eco24I GRGCYC 1 cut(s) 607
Eco47I GGWCC 1 cut(s) 110
Eco52I CGGCCG 1 cut(s) 514
Eco57I CTGAAG 2 cut(s) 117, 225
Eco81I CCTNAGG 1 cut(s) 840
EcoO109I RGGNCCY 2 cut(s) 110, 656
EcoRII CCWGG 4 cut(s) 181, 568, 777, 851
EcoT22I ATGCAT 1 cut(s) 196
EcoT38I GRGCYC 1 cut(s) 607
FaeI CATG 4 cut(s) 47, 359, 673, 688
FatI CATG 4 cut(s) 43, 355, 669, 684
FauI CCCGC 2 cut(s) 280, 335
FbaI TGATCA 2 cut(s) 57, 666
FblI GTMKAC 2 cut(s) 138, 766
Fnu4HI GCNGC 5 cut(s) 39, 476, 675, 732, 735
FokI GGATG 2 cut(s) 232, 728
FriOI GRGCYC 1 cut(s) 607
Fsp4HI GCNGC 5 cut(s) 39, 476, 675, 732, 735
FspAI RTGCGCAY 1 cut(s) 354
FspI TGCGCA 1 cut(s) 354
GlaI GCGC 2 cut(s) 345, 354
GluI GCNGC 5 cut(s) 39, 476, 675, 732, 735
GsaI CCCAGC 1 cut(s) 603
GsuI CTGGAG 1 cut(s) 543
HaeIII GGCC 5 cut(s) 181, 283, 516, 658, 864
HapII CCGG 3 cut(s) 233, 265, 492
HhaI GCGC 2 cut(s) 346, 355
Hin1II CATG 4 cut(s) 47, 359, 673, 688
Hin6I GCGC 2 cut(s) 344, 353
HinP1I GCGC 2 cut(s) 344, 353
HincII GTYRAC 2 cut(s) 139, 767
HindII GTYRAC 2 cut(s) 139, 767
HinfI GANTC 2 cut(s) 50, 526
HpaII CCGG 3 cut(s) 233, 265, 492
HphI GGTGA 3 cut(s) 59, 164, 316
Hpy166II GTNNAC 4 cut(s) 139, 641, 767, 847
Hpy188I TCNGA 5 cut(s) 33, 57, 250, 542, 790
Hpy188III TCNNGA 2 cut(s) 492, 685
Hpy8I GTNNAC 4 cut(s) 139, 641, 767, 847
HpyAV CCTTC 1 cut(s) 273
HpyCH4III ACNGT 1 cut(s) 71
HpyF10VI GCNNNNNNNGC 4 cut(s) 95, 350, 352, 647
HpyF3I CTNAG 4 cut(s) 440, 595, 606, 840
Hsp92II CATG 4 cut(s) 47, 359, 673, 688
HspAI GCGC 2 cut(s) 344, 353
Kpn2I TCCGGA 1 cut(s) 491
Ksp22I TGATCA 2 cut(s) 57, 666
Kzo9I GATC 5 cut(s) 57, 100, 542, 666, 700
LmnI GCTCC 1 cut(s) 494
Lsp1109I GCAGC 4 cut(s) 50, 661, 718, 746
LweI GCATC 4 cut(s) 181, 254, 686, 866
MaeIII GTNAC 4 cut(s) 322, 457, 466, 502
MalI GATC 5 cut(s) 59, 102, 544, 668, 702
MboI GATC 5 cut(s) 57, 100, 542, 666, 700
MboII GAAGA 3 cut(s) 231, 698, 731
MflI RGATCY 1 cut(s) 100
MhlI GDGCHC 3 cut(s) 607, 643, 837
Mph1103I ATGCAT 1 cut(s) 196
MroI TCCGGA 1 cut(s) 491
MseI TTAA 2 cut(s) 398, 883
MspI CCGG 3 cut(s) 233, 265, 492
MspR9I CCNGG 4 cut(s) 183, 570, 779, 853
Mva1269I GAATGC 2 cut(s) 40, 694
MvaI CCWGG 4 cut(s) 183, 570, 779, 853
MvnI CGCG 1 cut(s) 330
MwoI GCNNNNNNNGC 4 cut(s) 95, 350, 352, 647
NdeII GATC 5 cut(s) 57, 100, 542, 666, 700
NlaIII CATG 4 cut(s) 47, 359, 673, 688
NlaIV GGNNCC 3 cut(s) 207, 496, 657
NmuCI GTSAC 3 cut(s) 322, 466, 502
NsbI TGCGCA 1 cut(s) 354
NsiI ATGCAT 1 cut(s) 196
NspI RCATGY 1 cut(s) 359
PaeI GCATGC 1 cut(s) 359
PagI TCATGA 1 cut(s) 684
PceI AGGCCT 2 cut(s) 181, 283
PctI GAATGC 2 cut(s) 40, 694
PfeI GAWTC 2 cut(s) 50, 526
PflMI CCANNNNNTGG 2 cut(s) 154, 778
PinAI ACCGGT 1 cut(s) 232
PkrI GCNGC 5 cut(s) 40, 477, 676, 733, 736
PpuMI RGGWCCY 1 cut(s) 110
Psp5II RGGWCCY 1 cut(s) 110
Psp6I CCWGG 4 cut(s) 181, 568, 777, 851
PspFI CCCAGC 1 cut(s) 599
PspGI CCWGG 4 cut(s) 181, 568, 777, 851
PspN4I GGNNCC 3 cut(s) 207, 496, 657
PspPI GGNCC 2 cut(s) 110, 656
PspPPI RGGWCCY 1 cut(s) 110
PstI CTGCAG 1 cut(s) 736
PsuI RGATCY 1 cut(s) 100
RsaI GTAC 1 cut(s) 6
RsaNI GTAC 1 cut(s) 5
SalI GTCGAC 2 cut(s) 137, 765
SaqAI TTAA 2 cut(s) 398, 883
SatI GCNGC 5 cut(s) 39, 476, 675, 732, 735
Sau3AI GATC 5 cut(s) 57, 100, 542, 666, 700
Sau96I GGNCC 2 cut(s) 110, 656
ScrFI CCNGG 4 cut(s) 183, 570, 779, 853
SduI GDGCHC 3 cut(s) 607, 643, 837
SfaNI GCATC 4 cut(s) 181, 254, 686, 866
SfcI CTRYAG 1 cut(s) 732
SinI GGWCC 1 cut(s) 110
SphI GCATGC 1 cut(s) 359
SseBI AGGCCT 2 cut(s) 181, 283
SsiI CCGC 4 cut(s) 98, 287, 328, 475
StuI AGGCCT 2 cut(s) 181, 283
StyD4I CCNGG 4 cut(s) 181, 568, 777, 851
TaaI ACNGT 1 cut(s) 71
TaqI TCGA 2 cut(s) 138, 766
TaqII GACCGA 1 cut(s) 156
TauI GCSGC 1 cut(s) 478
TfiI GAWTC 2 cut(s) 50, 526
Tru1I TTAA 2 cut(s) 398, 883
Tru9I TTAA 2 cut(s) 398, 883
TscAI CASTG 3 cut(s) 231, 477, 717
TseFI GTSAC 3 cut(s) 322, 466, 502
TseI GCWGC 4 cut(s) 38, 674, 731, 734
Tsp45I GTSAC 3 cut(s) 322, 466, 502
TspDTI ATGAA 4 cut(s) 673, 701, 732, 738
TspRI CASTG 3 cut(s) 231, 477, 717
Van91I CCANNNNNTGG 2 cut(s) 154, 778
VneI GTGCAC 1 cut(s) 639
VpaK11BI GGWCC 1 cut(s) 110
XceI RCATGY 1 cut(s) 359
XmiI GTMKAC 2 cut(s) 138, 766
Zsp2I ATGCAT 1 cut(s) 196
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.