Rroxscaffold_2G00096310

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
GWHEROQ00000002
OG0014578
Physical Location & Seq
Forward (+)
17542338 .. 17543366
1029 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_2G00096310.1

Sequence Viewer

Length: 930 bp
ATGGGGAAGGCAATTAACATGAAGGAGAAATCAGTTGGGAGTTTGGCAGTGATTGTGACAATGGAGTTTGATAATTATGAGGTTGCTCATGGTGATTCTCTGATCATTGCACACTGCGTGTATGAGAAAATGGCAGGAGGTGCGGATCTAACAGGACCTAATGTTGTGTCTAAAACTGCAGTCGACCGAAGCCAAGATGCAGATAGAGGTAATAATCACCACAGGCCTGGCATTGATGCATTGCTTATGGCACCAAAAATACCAAAGCCAGTGCAGCCGGTTTCTTCAGCATCCGAAGGGGAGACAATCCGGCGACCTCGTGGCAGGCCGGCAGGTTCTAAAAACAAGCCAAAGCCACCTATCATTGTCACCCGTGATAGTGCTAATGCGCTTCGTGCGCATGCTATGGAAGTGAGTTCAGGCTGTGATGTGAGTGAAAGTTTAACCAACTTTGCAAGGAGGAAACAAAGAGGCATTTGCATACTGAGTGGTAGTGGTTGTGTAACCAATGTCACACTGCGGCAACCAGCTTCCTCCGGAGCCATTGTGACCCTCCACGGCCGTTTTGAGATTCTCTCATTGCTCGGATCAATCTTGCCTCCTCCAGCCCCTCCTGGGATTACAGGTCTAACTATCTACTTAGCTGGGGCTCAGGGGCAGGTTGTAGGTGGGAGTGTGGTAGGTGCACTCATTGCTTCGGGGCCTGTTGTGATCATGGCTGCATCGTTCATGAATGCAACGTTTGATCGTCTTCCACTGGATGAAGATGAAGTAGCTGCAGCTTTGCAAAACCAACAATACCAAAATGGTCGTCACCACCACCTGGATATGTCAGATTTTTATGGACTTCCACCAAATCTGCTCACTAATGGTAATGTGCCCCCTGAGGTTTACTCCTGGGCATCTGGCCGAACTATGTCAAAGACTTGA
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

309

Amino Acids

32.62

Weight (kDa)

8.66

Isoelectric Point (pI)

35.71

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PCC PF03479 132 - 244 2.1e-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) 399
Acc36I ACCTGC 2 cut(s) 323, 649
AccB1I GGYRCC 1 cut(s) 250
AccB7I CCANNNNNTGG 1 cut(s) 823
AccI GTMKAC 1 cut(s) 183
AccIII TCCGGA 1 cut(s) 536
AciI CCGC 2 cut(s) 143, 520
AclI AACGTT 1 cut(s) 740
AclWI GGATC 2 cut(s) 153, 595
AcoI YGGCCR 2 cut(s) 559, 907
AcuI CTGAAG 1 cut(s) 270
AdeI CACNNNGTG 1 cut(s) 118
AfiI CCNNNNNNNGG 2 cut(s) 615, 823
AjnI CCWGG 4 cut(s) 226, 613, 822, 896
AluBI AGCT 4 cut(s) 530, 644, 776, 782
AluI AGCT 4 cut(s) 530, 644, 776, 782
Alw21I GWGCWC 1 cut(s) 688
Alw26I GTCTC 1 cut(s) 296
Alw44I GTGCAC 1 cut(s) 684
AlwI GGATC 2 cut(s) 153, 595
Aor13HI TCCGGA 1 cut(s) 536
AoxI GGCC 5 cut(s) 224, 326, 559, 701, 907
ApaLI GTGCAC 1 cut(s) 684
ApeKI GCWGC 4 cut(s) 274, 719, 776, 779
ArsI GACNNNNNNTTYG 2 cut(s) 796, 828
AspLEI GCGC 2 cut(s) 391, 400
AspS9I GGNCC 2 cut(s) 155, 701
AsuHPI GGTGA 4 cut(s) 104, 209, 361, 806
AvaII GGWCC 1 cut(s) 155
AxyI CCTNAGG 1 cut(s) 885
BaeGI GKGCMC 2 cut(s) 688, 882
BanI GGYRCC 1 cut(s) 250
BanII GRGCYC 1 cut(s) 652
BauI CACGAG 1 cut(s) 318
BbsI GAAGAC 1 cut(s) 743
Bbv12I GWGCWC 1 cut(s) 688
BbvI GCAGC 4 cut(s) 286, 706, 763, 791
BceAI ACGGC 2 cut(s) 546, 574
BciT130I CCWGG 4 cut(s) 228, 615, 824, 898
BclI TGATCA 2 cut(s) 102, 711
BcoDI GTCTC 1 cut(s) 296
BfmI CTRYAG 2 cut(s) 177, 777
BfuAI ACCTGC 2 cut(s) 323, 649
BisI GCNGC 5 cut(s) 275, 521, 720, 777, 780
BlsI GCNGC 5 cut(s) 276, 522, 721, 778, 781
Bme1390I CCNGG 4 cut(s) 228, 615, 824, 898
Bme18I GGWCC 1 cut(s) 155
BmgT120I GGNCC 2 cut(s) 155, 701
BmiI GGNNCC 3 cut(s) 252, 541, 702
BmrFI CCNGG 4 cut(s) 228, 615, 824, 898
BmsI GCATC 5 cut(s) 187, 226, 299, 731, 911
BpiI GAAGAC 1 cut(s) 743
BplI GAGNNNNNCTC 4 cut(s) 560, 592, 878, 910
BpmI CTGGAG 1 cut(s) 588
Bpu10I CCTNAGC 1 cut(s) 651
BsaJI CCNNGG 3 cut(s) 556, 614, 897
BsaWI WCCGGW 1 cut(s) 536
BsaXI ACNNNNNCTCC 2 cut(s) 531, 561
Bsc4I CCNNNNNNNGG 2 cut(s) 615, 823
Bse118I RCCGGY 2 cut(s) 277, 328
Bse1I ACTGG 2 cut(s) 269, 762
Bse21I CCTNAGG 1 cut(s) 885
Bse3DI GCAATG 4 cut(s) 105, 239, 578, 690
BseAI TCCGGA 1 cut(s) 536
BseBI CCWGG 4 cut(s) 228, 615, 824, 898
BseDI CCNNGG 3 cut(s) 556, 614, 897
BseGI GGATG 2 cut(s) 290, 766
BseLI CCNNNNNNNGG 2 cut(s) 615, 823
BseMI GCAATG 4 cut(s) 105, 239, 578, 690
BseMII CTCAG 3 cut(s) 476, 665, 876
BseNI ACTGG 2 cut(s) 269, 762
BseRI GAGGAG 1 cut(s) 591
BseSI GKGCMC 2 cut(s) 688, 882
BseX3I CGGCCG 1 cut(s) 559
BseXI GCAGC 4 cut(s) 286, 706, 763, 791
BseYI CCCAGC 1 cut(s) 644
BsgI GTGCAG 1 cut(s) 293
Bsh1285I CGRYCG 2 cut(s) 187, 562
BshFI GGCC 5 cut(s) 226, 328, 561, 703, 909
BshNI GGYRCC 1 cut(s) 250
BsiEI CGRYCG 2 cut(s) 187, 562
BsiHKAI GWGCWC 1 cut(s) 688
BsiSI CCGG 4 cut(s) 278, 310, 329, 537
BslI CCNNNNNNNGG 2 cut(s) 615, 823
BsmAI GTCTC 1 cut(s) 296
BsmI GAATGC 1 cut(s) 739
BsnI GGCC 5 cut(s) 226, 328, 561, 703, 909
Bsp1286I GDGCHC 3 cut(s) 652, 688, 882
Bsp13I TCCGGA 1 cut(s) 536
Bsp143I GATC 5 cut(s) 102, 145, 587, 711, 745
BspACI CCGC 2 cut(s) 143, 520
BspANI GGCC 5 cut(s) 226, 328, 561, 703, 909
BspCNI CTCAG 3 cut(s) 477, 664, 877
BspEI TCCGGA 1 cut(s) 536
BspHI TCATGA 1 cut(s) 729
BspLI GGNNCC 3 cut(s) 252, 541, 702
BspMAI CTGCAG 2 cut(s) 181, 781
BspMI ACCTGC 2 cut(s) 323, 649
BspPI GGATC 2 cut(s) 153, 595
BspT107I GGYRCC 1 cut(s) 250
BsrDI GCAATG 4 cut(s) 105, 239, 578, 690
BsrFI RCCGGY 2 cut(s) 277, 328
BsrI ACTGG 2 cut(s) 269, 762
BssAI RCCGGY 2 cut(s) 277, 328
BssECI CCNNGG 3 cut(s) 556, 614, 897
BssMI GATC 5 cut(s) 102, 145, 587, 711, 745
BssSI CACGAG 1 cut(s) 318
Bst2BI CACGAG 1 cut(s) 318
Bst2UI CCWGG 4 cut(s) 228, 615, 824, 898
BstAPI GCANNNNNTGC 2 cut(s) 140, 692
BstC8I GCNNGC 3 cut(s) 326, 330, 402
BstDEI CTNAG 4 cut(s) 485, 640, 651, 885
BstDSI CCRYGG 1 cut(s) 556
BstF5I GGATG 2 cut(s) 290, 766
BstHHI GCGC 2 cut(s) 391, 400
BstKTI GATC 5 cut(s) 105, 148, 590, 714, 748
BstMAI GTCTC 1 cut(s) 296
BstMBI GATC 5 cut(s) 102, 145, 587, 711, 745
BstMCI CGRYCG 2 cut(s) 187, 562
BstMWI GCNNNNNNNGC 5 cut(s) 140, 274, 395, 397, 692
BstNI CCWGG 4 cut(s) 228, 615, 824, 898
BstNSI RCATGY 1 cut(s) 404
BstSCI CCNGG 4 cut(s) 226, 613, 822, 896
BstSFI CTRYAG 2 cut(s) 177, 777
BstSLI GKGCMC 2 cut(s) 688, 882
BstV1I GCAGC 4 cut(s) 286, 706, 763, 791
BstV2I GAAGAC 1 cut(s) 743
BstX2I RGATCY 1 cut(s) 145
BstXI CCANNNNNNTGG 1 cut(s) 227
BstYI RGATCY 1 cut(s) 145
BstZI CGGCCG 1 cut(s) 559
Bsu36I CCTNAGG 1 cut(s) 885
BsuRI GGCC 5 cut(s) 226, 328, 561, 703, 909
BtgI CCRYGG 1 cut(s) 556
BtsCI GGATG 2 cut(s) 290, 766
BtsI GCAGTG 3 cut(s) 54, 112, 515
BtsIMutI CAGTG 5 cut(s) 54, 112, 276, 515, 755
BveI ACCTGC 2 cut(s) 323, 649
Cac8I GCNNGC 3 cut(s) 326, 330, 402
CciI TCATGA 1 cut(s) 729
CfoI GCGC 2 cut(s) 391, 400
Cfr10I RCCGGY 2 cut(s) 277, 328
Cfr13I GGNCC 2 cut(s) 155, 701
CviAII CATG 5 cut(s) 19, 89, 401, 715, 730
DdeI CTNAG 4 cut(s) 485, 640, 651, 885
DpnI GATC 5 cut(s) 104, 147, 589, 713, 747
DpnII GATC 5 cut(s) 102, 145, 587, 711, 745
DraIII CACNNNGTG 1 cut(s) 118
EaeI YGGCCR 2 cut(s) 559, 907
EagI CGGCCG 1 cut(s) 559
EclXI CGGCCG 1 cut(s) 559
Eco147I AGGCCT 1 cut(s) 226
Eco24I GRGCYC 1 cut(s) 652
Eco47I GGWCC 1 cut(s) 155
Eco52I CGGCCG 1 cut(s) 559
Eco57I CTGAAG 1 cut(s) 270
Eco81I CCTNAGG 1 cut(s) 885
EcoO109I RGGNCCY 2 cut(s) 155, 701
EcoRII CCWGG 4 cut(s) 226, 613, 822, 896
EcoT22I ATGCAT 1 cut(s) 241
EcoT38I GRGCYC 1 cut(s) 652
FaeI CATG 5 cut(s) 22, 92, 404, 718, 733
FatI CATG 5 cut(s) 18, 88, 400, 714, 729
FbaI TGATCA 2 cut(s) 102, 711
FblI GTMKAC 1 cut(s) 183
Fnu4HI GCNGC 5 cut(s) 275, 521, 720, 777, 780
FokI GGATG 2 cut(s) 277, 773
FriOI GRGCYC 1 cut(s) 652
Fsp4HI GCNGC 5 cut(s) 275, 521, 720, 777, 780
FspAI RTGCGCAY 1 cut(s) 399
FspI TGCGCA 1 cut(s) 399
GlaI GCGC 2 cut(s) 390, 399
GluI GCNGC 5 cut(s) 275, 521, 720, 777, 780
GsaI CCCAGC 1 cut(s) 648
GsuI CTGGAG 1 cut(s) 588
HaeIII GGCC 5 cut(s) 226, 328, 561, 703, 909
HapII CCGG 4 cut(s) 278, 310, 329, 537
HhaI GCGC 2 cut(s) 391, 400
Hin1II CATG 5 cut(s) 22, 92, 404, 718, 733
Hin6I GCGC 2 cut(s) 389, 398
HinP1I GCGC 2 cut(s) 389, 398
HincII GTYRAC 1 cut(s) 184
HindII GTYRAC 1 cut(s) 184
HinfI GANTC 2 cut(s) 95, 571
HpaII CCGG 4 cut(s) 278, 310, 329, 537
HphI GGTGA 4 cut(s) 104, 209, 361, 806
Hpy166II GTNNAC 3 cut(s) 184, 686, 892
Hpy188I TCNGA 4 cut(s) 102, 295, 587, 835
Hpy188III TCNNGA 2 cut(s) 537, 730
Hpy8I GTNNAC 3 cut(s) 184, 686, 892
HpyAV CCTTC 2 cut(s) 16, 290
HpyCH4IV ACGT 1 cut(s) 740
HpyF10VI GCNNNNNNNGC 5 cut(s) 140, 274, 395, 397, 692
HpyF3I CTNAG 4 cut(s) 485, 640, 651, 885
HpySE526I ACGT 1 cut(s) 740
Hsp92II CATG 5 cut(s) 22, 92, 404, 718, 733
HspAI GCGC 2 cut(s) 389, 398
Kpn2I TCCGGA 1 cut(s) 536
KroI GCCGGC 1 cut(s) 328
KroNI GCCGGC 1 cut(s) 330
Ksp22I TGATCA 2 cut(s) 102, 711
Kzo9I GATC 5 cut(s) 102, 145, 587, 711, 745
LmnI GCTCC 1 cut(s) 539
Lsp1109I GCAGC 4 cut(s) 286, 706, 763, 791
LweI GCATC 5 cut(s) 187, 226, 299, 731, 911
MaeII ACGT 1 cut(s) 740
MaeIII GTNAC 6 cut(s) 55, 367, 502, 511, 547, 812
MalI GATC 5 cut(s) 104, 147, 589, 713, 747
MboI GATC 5 cut(s) 102, 145, 587, 711, 745
MboII GAAGA 3 cut(s) 276, 743, 776
MflI RGATCY 1 cut(s) 145
MhlI GDGCHC 3 cut(s) 652, 688, 882
MluCI AATT 2 cut(s) 12, 73
Mph1103I ATGCAT 1 cut(s) 241
MroI TCCGGA 1 cut(s) 536
MroNI GCCGGC 1 cut(s) 328
MseI TTAA 2 cut(s) 15, 443
MspI CCGG 4 cut(s) 278, 310, 329, 537
MspR9I CCNGG 4 cut(s) 228, 615, 824, 898
Mva1269I GAATGC 1 cut(s) 739
MvaI CCWGG 4 cut(s) 228, 615, 824, 898
MwoI GCNNNNNNNGC 5 cut(s) 140, 274, 395, 397, 692
NaeI GCCGGC 1 cut(s) 330
NdeII GATC 5 cut(s) 102, 145, 587, 711, 745
NgoMIV GCCGGC 1 cut(s) 328
NlaIII CATG 5 cut(s) 22, 92, 404, 718, 733
NlaIV GGNNCC 3 cut(s) 252, 541, 702
NmuCI GTSAC 5 cut(s) 55, 367, 511, 547, 812
NsbI TGCGCA 1 cut(s) 399
NsiI ATGCAT 1 cut(s) 241
NspI RCATGY 1 cut(s) 404
PaeI GCATGC 1 cut(s) 404
PagI TCATGA 1 cut(s) 729
PceI AGGCCT 1 cut(s) 226
PctI GAATGC 1 cut(s) 739
PdiI GCCGGC 1 cut(s) 330
PfeI GAWTC 2 cut(s) 95, 571
PflMI CCANNNNNTGG 1 cut(s) 823
PkrI GCNGC 5 cut(s) 276, 522, 721, 778, 781
PpuMI RGGWCCY 1 cut(s) 155
Psp1406I AACGTT 1 cut(s) 740
Psp5II RGGWCCY 1 cut(s) 155
Psp6I CCWGG 4 cut(s) 226, 613, 822, 896
PspFI CCCAGC 1 cut(s) 644
PspGI CCWGG 4 cut(s) 226, 613, 822, 896
PspN4I GGNNCC 3 cut(s) 252, 541, 702
PspPI GGNCC 2 cut(s) 155, 701
PspPPI RGGWCCY 1 cut(s) 155
PstI CTGCAG 2 cut(s) 181, 781
PsuI RGATCY 1 cut(s) 145
SalI GTCGAC 1 cut(s) 182
SaqAI TTAA 2 cut(s) 15, 443
SatI GCNGC 5 cut(s) 275, 521, 720, 777, 780
Sau3AI GATC 5 cut(s) 102, 145, 587, 711, 745
Sau96I GGNCC 2 cut(s) 155, 701
ScrFI CCNGG 4 cut(s) 228, 615, 824, 898
SduI GDGCHC 3 cut(s) 652, 688, 882
SfaNI GCATC 5 cut(s) 187, 226, 299, 731, 911
SfcI CTRYAG 2 cut(s) 177, 777
SinI GGWCC 1 cut(s) 155
SphI GCATGC 1 cut(s) 404
Sse9I AATT 2 cut(s) 12, 73
SseBI AGGCCT 1 cut(s) 226
SsiI CCGC 2 cut(s) 143, 520
StuI AGGCCT 1 cut(s) 226
StyD4I CCNGG 4 cut(s) 226, 613, 822, 896
TaiI ACGT 1 cut(s) 743
TaqI TCGA 1 cut(s) 183
TaqII GACCGA 1 cut(s) 201
TasI AATT 2 cut(s) 12, 73
TauI GCSGC 1 cut(s) 523
TfiI GAWTC 2 cut(s) 95, 571
Tru1I TTAA 2 cut(s) 15, 443
Tru9I TTAA 2 cut(s) 15, 443
TscAI CASTG 5 cut(s) 54, 119, 276, 522, 762
TseFI GTSAC 5 cut(s) 55, 367, 511, 547, 812
TseI GCWGC 4 cut(s) 274, 719, 776, 779
Tsp45I GTSAC 5 cut(s) 55, 367, 511, 547, 812
TspDTI ATGAA 5 cut(s) 35, 718, 746, 777, 783
TspRI CASTG 5 cut(s) 54, 119, 276, 522, 762
Van91I CCANNNNNTGG 1 cut(s) 823
VneI GTGCAC 1 cut(s) 684
VpaK11BI GGWCC 1 cut(s) 155
XceI RCATGY 1 cut(s) 404
XmiI GTMKAC 1 cut(s) 183
Zsp2I ATGCAT 1 cut(s) 241
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.