RLG00000027233

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_laevigata
Chr6
OG0012533
Physical Location & Seq
Forward (+)
9791159 .. 9792127
969 bp
Loading structure...
UTR
Exon/CDS
Intron
RLM00000027233

Sequence Viewer

Length: 969 bp
ATGGCGAATCGATGGTGGGCTGGAAATGTCGCGATGGGAGCTCACGACTCAATCACCGCCTCGACACCACCGTCTCTTCATCTTAGAAACTCTGAAGCCGAAGAGCACAACAACAACAACAACACACCCACCAACAGCAGCACCAGCAACCCAAACAACACTCCACCTCAGAAGCAGGACGACGAGCAGGACAGCCGTGACAACGATCTAGAAGTTGACAATCAAGACCCTAGCTCCGGCGGCCCCGACAGCCTCGAGCCTGGCTCCAGCAACCGGCGGCCCAGAGGCCGTCCCCCCGGCTCGAAAAACAAGCCGAAACCGCCGATAATCATCACCAAAGAGTCTCCCAACGCTCTCCGGAGCCATGTCTTGGAAATCAGCAGCGGCAGCGACATCGTCGAGAGCATTGCCACCTTCGCACAGCGGAGGCACAGAGGAGTCTCCGTCTTAAGCGGCAGCGGCATTGTTTCTAACGTCACTCTTCGTCAGCCGGCCGCGCCGAGCGGGGTCATAACGCTCCACGGAAGGTTCGAGATTCTGTCCCTAAACGGTGCGTTTCTGCCTGCCCCATCGCCGCCGGGGGCTAGTGGCCTGACCGTGTACTTGGGCGGCGGGCAGGGGCAGGTGGTTGGTGGGACTGTTGTTGGAGCTCTGTTGGCTTCCGGGCCGGTGATGATCATTGCGGCGACGTTCACTAATGCCACTTATGAGAGACTGCCGCTTGAGGATGAGAGCAATGAAGGGATGCTATTGCAACAGCAACAGCAACAGCAACAACAGCAGCAGCAATCCGGTGTGAATTCGGCAGGGACCGGAGGGAATTCGGGTTCTCAGGGCTTGAGTGATCAGCAGCAACAACAGCAACAAGTGCCCATTTACGCTTTGCCTCCGACTTTACTTCCAAATGGTCAGATGCCGCCTGATGTGTACTGGGGTCCTCCACCGCCTAGACCTCCGCCTGCTTACTGA
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

323

Amino Acids

33.98

Weight (kDa)

5.36

Isoelectric Point (pI)

63.83

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PCC PF03479 120 - 233 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
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

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) 613
AasI GACNNNNNNGTC 1 cut(s) 70
Acc36I ACCTGC 1 cut(s) 613
AccB7I CCANNNNNTGG 1 cut(s) 370
AccBSI CCGCTC 1 cut(s) 504
AccII CGCG 2 cut(s) 32, 497
AccIII TCCGGA 1 cut(s) 357
AcoI YGGCCR 1 cut(s) 492
AcsI RAATTY 2 cut(s) 799, 820
AcuI CTGAAG 1 cut(s) 114
AfaI GTAC 2 cut(s) 602, 929
AfiI CCNNNNNNNGG 3 cut(s) 236, 273, 370
AflII CTTAAG 1 cut(s) 448
AjnI CCWGG 1 cut(s) 259
AloI GAACNNNNNNTCC 2 cut(s) 811, 843
AluBI AGCT 3 cut(s) 41, 234, 650
AluI AGCT 3 cut(s) 41, 234, 650
Alw21I GWGCWC 3 cut(s) 43, 108, 652
Alw26I GTCTC 4 cut(s) 78, 348, 445, 706
Ama87I CYCGRG 1 cut(s) 254
Aor13HI TCCGGA 1 cut(s) 357
AoxI GGCC 6 cut(s) 241, 278, 286, 492, 589, 665
ApeKI GCWGC 7 cut(s) 138, 381, 387, 456, 781, 784, 850
ApoI RAATTY 2 cut(s) 799, 820
AspLEI GCGC 1 cut(s) 499
AspS9I GGNCC 5 cut(s) 242, 279, 665, 810, 935
AsuC2I CCSGG 3 cut(s) 297, 579, 664
AsuHPI GGTGA 3 cut(s) 46, 325, 682
AvaI CYCGRG 1 cut(s) 254
AvaII GGWCC 2 cut(s) 810, 935
BaeGI GKGCMC 1 cut(s) 873
BanII GRGCYC 2 cut(s) 43, 652
Bbv12I GWGCWC 3 cut(s) 43, 108, 652
BbvI GCAGC 7 cut(s) 150, 393, 399, 468, 793, 796, 862
BccI CCATC 3 cut(s) 6, 28, 577
BceAI ACGGC 2 cut(s) 180, 273
BcgI CGANNNNNNTGC 4 cut(s) 376, 389, 410, 423
BciT130I CCWGG 1 cut(s) 261
BclI TGATCA 2 cut(s) 675, 844
BcnI CCSGG 3 cut(s) 297, 579, 664
BcoDI GTCTC 4 cut(s) 78, 348, 445, 706
BfaI CTAG 4 cut(s) 209, 231, 585, 948
BfrI CTTAAG 1 cut(s) 448
BfuAI ACCTGC 1 cut(s) 613
Bme1390I CCNGG 4 cut(s) 261, 297, 579, 664
Bme18I GGWCC 2 cut(s) 810, 935
BmeT110I CYCGRG 1 cut(s) 254
BmgT120I GGNCC 5 cut(s) 242, 279, 665, 810, 935
BmiI GGNNCC 5 cut(s) 244, 265, 362, 811, 936
BmrFI CCNGG 4 cut(s) 261, 297, 579, 664
BmrI ACTGGG 1 cut(s) 940
BmsI GCATC 2 cut(s) 735, 903
BmuI ACTGGG 1 cut(s) 940
BplI GAGNNNNNCTC 2 cut(s) 248, 280
BpmI CTGGAG 1 cut(s) 250
BpuEI CTTGAG 2 cut(s) 743, 859
BpuMI CCSGG 3 cut(s) 297, 579, 664
Bsa29I ATCGAT 1 cut(s) 10
BsaBI GATNNNNATC 1 cut(s) 329
BsaJI CCNNGG 3 cut(s) 295, 520, 578
BsaWI WCCGGW 3 cut(s) 357, 791, 812
BsaXI ACNNNNNCTCC 4 cut(s) 218, 248, 429, 459
Bsc4I CCNNNNNNNGG 3 cut(s) 236, 273, 370
Bse118I RCCGGY 3 cut(s) 273, 490, 667
Bse1I ACTGG 1 cut(s) 935
Bse3DI GCAATG 3 cut(s) 405, 678, 742
Bse8I GATNNNNATC 1 cut(s) 329
BseAI TCCGGA 1 cut(s) 357
BseBI CCWGG 1 cut(s) 261
BseCI ATCGAT 1 cut(s) 10
BseDI CCNNGG 3 cut(s) 295, 520, 578
BseGI GGATG 2 cut(s) 733, 750
BseJI GATNNNNATC 1 cut(s) 329
BseLI CCNNNNNNNGG 3 cut(s) 236, 273, 370
BseMI GCAATG 3 cut(s) 405, 678, 742
BseMII CTCAG 2 cut(s) 182, 845
BseNI ACTGG 1 cut(s) 935
BseRI GAGGAG 1 cut(s) 450
BseSI GKGCMC 1 cut(s) 873
BseX3I CGGCCG 1 cut(s) 492
BseXI GCAGC 7 cut(s) 150, 393, 399, 468, 793, 796, 862
Bsh1236I CGCG 2 cut(s) 32, 497
Bsh1285I CGRYCG 1 cut(s) 495
BshFI GGCC 6 cut(s) 243, 280, 288, 494, 591, 667
BshVI ATCGAT 1 cut(s) 10
BsiEI CGRYCG 1 cut(s) 495
BsiHKAI GWGCWC 3 cut(s) 43, 108, 652
BsiHKCI CYCGRG 1 cut(s) 254
BslFI GGGAC 4 cut(s) 276, 526, 649, 823
BslI CCNNNNNNNGG 3 cut(s) 236, 273, 370
BsmAI GTCTC 4 cut(s) 78, 348, 445, 706
BsmBI CGTCTC 1 cut(s) 78
BsmFI GGGAC 4 cut(s) 276, 526, 649, 823
BsnI GGCC 6 cut(s) 243, 280, 288, 494, 591, 667
BsoBI CYCGRG 1 cut(s) 254
Bsp1286I GDGCHC 4 cut(s) 43, 108, 652, 873
Bsp13I TCCGGA 1 cut(s) 357
Bsp143I GATC 3 cut(s) 205, 675, 844
Bsp68I TCGCGA 1 cut(s) 32
BspANI GGCC 6 cut(s) 243, 280, 288, 494, 591, 667
BspCNI CTCAG 2 cut(s) 181, 844
BspDI ATCGAT 1 cut(s) 10
BspEI TCCGGA 1 cut(s) 357
BspFNI CGCG 2 cut(s) 32, 497
BspLI GGNNCC 5 cut(s) 244, 265, 362, 811, 936
BspMI ACCTGC 1 cut(s) 613
BspQI GCTCTTC 1 cut(s) 96
BspTI CTTAAG 1 cut(s) 448
BsrBI CCGCTC 1 cut(s) 504
BsrDI GCAATG 3 cut(s) 405, 678, 742
BsrFI RCCGGY 3 cut(s) 273, 490, 667
BsrI ACTGG 1 cut(s) 935
BssAI RCCGGY 3 cut(s) 273, 490, 667
BssECI CCNNGG 3 cut(s) 295, 520, 578
BssMI GATC 3 cut(s) 205, 675, 844
Bst2UI CCWGG 1 cut(s) 261
Bst4CI ACNGT 4 cut(s) 72, 551, 598, 640
Bst6I CTCTTC 3 cut(s) 81, 96, 486
BstAFI CTTAAG 1 cut(s) 448
BstAPI GCANNNNNTGC 1 cut(s) 868
BstC8I GCNNGC 4 cut(s) 492, 564, 614, 960
BstDEI CTNAG 3 cut(s) 83, 168, 831
BstDSI CCRYGG 1 cut(s) 520
BstF5I GGATG 2 cut(s) 733, 750
BstFNI CGCG 2 cut(s) 32, 497
BstHHI GCGC 1 cut(s) 499
BstKTI GATC 3 cut(s) 208, 678, 847
BstMAI GTCTC 4 cut(s) 78, 348, 445, 706
BstMBI GATC 3 cut(s) 205, 675, 844
BstMCI CGRYCG 1 cut(s) 495
BstNI CCWGG 1 cut(s) 261
BstSCI CCNGG 4 cut(s) 259, 295, 577, 662
BstSLI GKGCMC 1 cut(s) 873
BstUI CGCG 2 cut(s) 32, 497
BstV1I GCAGC 7 cut(s) 150, 393, 399, 468, 793, 796, 862
BstZI CGGCCG 1 cut(s) 492
Bsu15I ATCGAT 1 cut(s) 10
BsuRI GGCC 6 cut(s) 243, 280, 288, 494, 591, 667
BsuTUI ATCGAT 1 cut(s) 10
BtgI CCRYGG 1 cut(s) 520
BtgZI GCGATG 2 cut(s) 47, 555
BtsCI GGATG 2 cut(s) 733, 750
BtuMI TCGCGA 1 cut(s) 32
BveI ACCTGC 1 cut(s) 613
Cac8I GCNNGC 4 cut(s) 492, 564, 614, 960
CfoI GCGC 1 cut(s) 499
Cfr10I RCCGGY 3 cut(s) 273, 490, 667
Cfr13I GGNCC 5 cut(s) 242, 279, 665, 810, 935
ClaI ATCGAT 1 cut(s) 10
Csp6I GTAC 2 cut(s) 601, 928
CviAII CATG 1 cut(s) 365
CviQI GTAC 2 cut(s) 601, 928
DdeI CTNAG 3 cut(s) 83, 168, 831
DpnI GATC 3 cut(s) 207, 677, 846
DpnII GATC 3 cut(s) 205, 675, 844
DrdI GACNNNNNNGTC 1 cut(s) 70
DseDI GACNNNNNNGTC 1 cut(s) 70
EaeI YGGCCR 1 cut(s) 492
EagI CGGCCG 1 cut(s) 492
Eam1104I CTCTTC 3 cut(s) 81, 96, 486
EarI CTCTTC 3 cut(s) 81, 96, 486
EciI GGCGGA 1 cut(s) 945
Ecl136II GAGCTC 2 cut(s) 41, 650
EclXI CGGCCG 1 cut(s) 492
Eco24I GRGCYC 2 cut(s) 43, 652
Eco47I GGWCC 2 cut(s) 810, 935
Eco52I CGGCCG 1 cut(s) 492
Eco53kI GAGCTC 2 cut(s) 41, 650
Eco57I CTGAAG 1 cut(s) 114
Eco88I CYCGRG 1 cut(s) 254
EcoICRI GAGCTC 2 cut(s) 41, 650
EcoO109I RGGNCCY 1 cut(s) 935
EcoRI GAATTC 2 cut(s) 799, 820
EcoRII CCWGG 1 cut(s) 259
EcoT38I GRGCYC 2 cut(s) 43, 652
Esp3I CGTCTC 1 cut(s) 78
FaeI CATG 1 cut(s) 368
FaiI YATR 3 cut(s) 366, 512, 708
FaqI GGGAC 4 cut(s) 276, 526, 649, 823
FatI CATG 1 cut(s) 364
FauI CCCGC 2 cut(s) 497, 605
FbaI TGATCA 2 cut(s) 675, 844
FokI GGATG 2 cut(s) 740, 757
FriOI GRGCYC 2 cut(s) 43, 652
FspBI CTAG 4 cut(s) 209, 231, 585, 948
GlaI GCGC 1 cut(s) 498
GsuI CTGGAG 1 cut(s) 250
HaeIII GGCC 6 cut(s) 243, 280, 288, 494, 591, 667
HhaI GCGC 1 cut(s) 499
Hin1II CATG 1 cut(s) 368
Hin6I GCGC 1 cut(s) 497
HinP1I GCGC 1 cut(s) 497
HincII GTYRAC 1 cut(s) 217
HindII GTYRAC 1 cut(s) 217
HinfI GANTC 5 cut(s) 7, 47, 341, 438, 535
HphI GGTGA 3 cut(s) 46, 325, 682
Hpy166II GTNNAC 4 cut(s) 217, 601, 693, 928
Hpy188I TCNGA 4 cut(s) 94, 171, 891, 912
Hpy188III TCNNGA 7 cut(s) 31, 44, 209, 224, 358, 400, 532
Hpy8I GTNNAC 4 cut(s) 217, 601, 693, 928
Hpy99I CGWCG 3 cut(s) 185, 401, 691
HpyAV CCTTC 3 cut(s) 424, 519, 734
HpyCH4III ACNGT 4 cut(s) 72, 551, 598, 640
HpyCH4IV ACGT 2 cut(s) 474, 689
HpyCH4V TGCA 1 cut(s) 754
HpyF3I CTNAG 3 cut(s) 83, 168, 831
HpySE526I ACGT 2 cut(s) 474, 689
Hsp92II CATG 1 cut(s) 368
HspAI GCGC 1 cut(s) 497
Kpn2I TCCGGA 1 cut(s) 357
KroI GCCGGC 1 cut(s) 490
KroNI GCCGGC 1 cut(s) 492
Ksp22I TGATCA 2 cut(s) 675, 844
Kzo9I GATC 3 cut(s) 205, 675, 844
LguI GCTCTTC 1 cut(s) 96
LmnI GCTCC 6 cut(s) 38, 239, 269, 360, 522, 647
Lsp1109I GCAGC 7 cut(s) 150, 393, 399, 468, 793, 796, 862
LweI GCATC 2 cut(s) 735, 903
MaeI CTAG 4 cut(s) 209, 231, 585, 948
MaeII ACGT 2 cut(s) 474, 689
MaeIII GTNAC 2 cut(s) 197, 475
MalI GATC 3 cut(s) 207, 677, 846
MbiI CCGCTC 1 cut(s) 504
MboI GATC 3 cut(s) 205, 675, 844
MboII GAAGA 3 cut(s) 68, 113, 473
MhlI GDGCHC 4 cut(s) 43, 108, 652, 873
MluCI AATT 2 cut(s) 799, 820
MlyI GAGTC 3 cut(s) 41, 350, 447
MmeI TCCRAC 2 cut(s) 625, 914
MroI TCCGGA 1 cut(s) 357
MroNI GCCGGC 1 cut(s) 490
MseI TTAA 1 cut(s) 449
MspA1I CMGCKG 3 cut(s) 384, 424, 459
MspCI CTTAAG 1 cut(s) 448
MspR9I CCNGG 4 cut(s) 261, 297, 579, 664
MvaI CCWGG 1 cut(s) 261
MvnI CGCG 2 cut(s) 32, 497
NaeI GCCGGC 1 cut(s) 492
NciI CCSGG 3 cut(s) 297, 579, 664
NdeII GATC 3 cut(s) 205, 675, 844
NgoMIV GCCGGC 1 cut(s) 490
NlaIII CATG 1 cut(s) 368
NlaIV GGNNCC 5 cut(s) 244, 265, 362, 811, 936
NmeAIII GCCGAG 1 cut(s) 525
NmuCI GTSAC 2 cut(s) 197, 475
NruI TCGCGA 1 cut(s) 32
PaeR7I CTCGAG 1 cut(s) 254
PaqCI CACCTGC 1 cut(s) 613
PciSI GCTCTTC 1 cut(s) 96
PcsI WCGNNNNNNNCGW 2 cut(s) 68, 528
PdiI GCCGGC 1 cut(s) 492
PfeI GAWTC 2 cut(s) 7, 535
PflFI GACNNNGTC 1 cut(s) 395
PflMI CCANNNNNTGG 1 cut(s) 370
PleI GAGTC 3 cut(s) 41, 349, 446
PpsI GAGTC 3 cut(s) 41, 349, 446
PpuMI RGGWCCY 1 cut(s) 935
Psp124BI GAGCTC 2 cut(s) 43, 652
Psp5II RGGWCCY 1 cut(s) 935
Psp6I CCWGG 1 cut(s) 259
PspGI CCWGG 1 cut(s) 259
PspN4I GGNNCC 5 cut(s) 244, 265, 362, 811, 936
PspPI GGNCC 5 cut(s) 242, 279, 665, 810, 935
PspPPI RGGWCCY 1 cut(s) 935
PspXI VCTCGAGB 1 cut(s) 254
PsyI GACNNNGTC 1 cut(s) 395
RruI TCGCGA 1 cut(s) 32
RsaI GTAC 2 cut(s) 602, 929
RsaNI GTAC 2 cut(s) 601, 928
SacI GAGCTC 2 cut(s) 43, 652
SapI GCTCTTC 1 cut(s) 96
SaqAI TTAA 1 cut(s) 449
Sau3AI GATC 3 cut(s) 205, 675, 844
Sau96I GGNCC 5 cut(s) 242, 279, 665, 810, 935
SchI GAGTC 3 cut(s) 41, 350, 447
ScrFI CCNGG 4 cut(s) 261, 297, 579, 664
SduI GDGCHC 4 cut(s) 43, 108, 652, 873
SfaNI GCATC 2 cut(s) 735, 903
Sfr274I CTCGAG 1 cut(s) 254
SinI GGWCC 2 cut(s) 810, 935
SlaI CTCGAG 1 cut(s) 254
SmlI CTYRAG 4 cut(s) 254, 448, 722, 838
SmoI CTYRAG 4 cut(s) 254, 448, 722, 838
Sse9I AATT 2 cut(s) 799, 820
SspMI CTAG 4 cut(s) 209, 231, 585, 948
SstI GAGCTC 2 cut(s) 43, 652
StyD4I CCNGG 4 cut(s) 259, 295, 577, 662
TaaI ACNGT 4 cut(s) 72, 551, 598, 640
TaiI ACGT 2 cut(s) 477, 692
TaqI TCGA 6 cut(s) 10, 62, 255, 302, 399, 531
TasI AATT 2 cut(s) 799, 820
TatI WGTACW 2 cut(s) 600, 927
TfiI GAWTC 2 cut(s) 7, 535
Tru1I TTAA 1 cut(s) 449
Tru9I TTAA 1 cut(s) 449
TseFI GTSAC 2 cut(s) 197, 475
TseI GCWGC 7 cut(s) 138, 381, 387, 456, 781, 784, 850
Tsp45I GTSAC 2 cut(s) 197, 475
TspDTI ATGAA 2 cut(s) 68, 753
TspGWI ACGGA 2 cut(s) 433, 537
Tth111I GACNNNGTC 1 cut(s) 395
Van91I CCANNNNNTGG 1 cut(s) 370
Vha464I CTTAAG 1 cut(s) 448
VpaK11BI GGWCC 2 cut(s) 810, 935
XapI RAATTY 2 cut(s) 799, 820
XbaI TCTAGA 1 cut(s) 208
XhoI CTCGAG 1 cut(s) 254
XspI CTAG 4 cut(s) 209, 231, 585, 948
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.