RLG00000020564

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
Chr4
OG0014578
Physical Location & Seq
Reverse (-)
66308303 .. 66309103
801 bp
Loading structure...
UTR
Exon/CDS
Intron
RLM00000020564

Sequence Viewer

Length: 801 bp
ATGGCAGGAGGTGCGGATCTAACAGGACCTAATGTTGTGTCTAAAACTTCAGTAGACCGAAGCCAAGATGCAGATAAAGGTAATAATCACCACAGGCCTGGCATTGATGCATTGCTTATGGCACCAAAAATACCAAAGCCAGTGCAACCGGTTTCTTCAGCATCCGAGGGGGAGACAATCCGGCGACCTCGTGGCAGGCCGGCGGGTTCTAAAAACAAGCCAAAGCCACCTATCATTGTCACCCGTGATAGTGCTAATGCGCTTCGTGCGCATGCTATGGAAGTGAGTTCAGGCTGTGATGTGAGTGAAAGTTTAACCAACTTTGCAAGGAGGAAACAAAGAGGCATTTGCATACTGAGTGGAAGTGGTTGTGTAACCAATGTCACACTGAGGCAACCAGCTTCCTCCGGAGCCATTGTGACCCTCCACGGCCGTTTTGAGATTCTCTCATTGCTCGGATCAATCTTGCCTCCTCCAGCCCCTCCTGGGATTACAGGTCTAACTATCTACTTAGCTGGGGCTCAGGGGCAGGTTGTAGGTGGGAGTGTGGTAGGTGCACTCATTGCTTCGGGGCCTGTTGTGATCATGGCTGCATCGTTCATGAATGCAACGTTTGATCGTCTTCCACTGGATGAAGATGAAGTAGCTGCAGCTTTGCAAAACCAACAATACCAAAATGGTCGTCACCACCACCTGGATATGTCAGATTTTTATGGACTTCCACCAAATCTGCTCACTAATGGTAATGTGCCCCCTGAGGTTTACTCCTGGGCATCTGGCCGAACTATGTCAAAGACTTAA
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

267

Amino Acids

27.88

Weight (kDa)

9.27

Isoelectric Point (pI)

40.85

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PCC PF03479 89 - 201 1.5e-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) 270
Acc36I ACCTGC 1 cut(s) 520
AccB1I GGYRCC 1 cut(s) 121
AccB7I CCANNNNNTGG 1 cut(s) 694
AccI GTMKAC 1 cut(s) 54
AccIII TCCGGA 1 cut(s) 407
AciI CCGC 2 cut(s) 14, 203
AclI AACGTT 1 cut(s) 611
AclWI GGATC 2 cut(s) 24, 466
AcoI YGGCCR 2 cut(s) 430, 778
AcuI CTGAAG 2 cut(s) 33, 141
AfiI CCNNNNNNNGG 2 cut(s) 486, 694
AgeI ACCGGT 1 cut(s) 148
AjnI CCWGG 4 cut(s) 97, 484, 693, 767
AluBI AGCT 4 cut(s) 401, 515, 647, 653
AluI AGCT 4 cut(s) 401, 515, 647, 653
Alw21I GWGCWC 1 cut(s) 559
Alw26I GTCTC 1 cut(s) 167
Alw44I GTGCAC 1 cut(s) 555
AlwI GGATC 2 cut(s) 24, 466
Aor13HI TCCGGA 1 cut(s) 407
AoxI GGCC 5 cut(s) 95, 197, 430, 572, 778
ApaLI GTGCAC 1 cut(s) 555
ApeKI GCWGC 3 cut(s) 590, 647, 650
ArsI GACNNNNNNTTYG 2 cut(s) 667, 699
AsiGI ACCGGT 1 cut(s) 148
AspLEI GCGC 2 cut(s) 262, 271
AspS9I GGNCC 2 cut(s) 26, 572
AsuHPI GGTGA 3 cut(s) 80, 232, 677
AvaII GGWCC 1 cut(s) 26
AxyI CCTNAGG 1 cut(s) 756
BaeGI GKGCMC 2 cut(s) 559, 753
BanI GGYRCC 1 cut(s) 121
BanII GRGCYC 1 cut(s) 523
BauI CACGAG 1 cut(s) 189
BbsI GAAGAC 1 cut(s) 614
Bbv12I GWGCWC 1 cut(s) 559
BbvI GCAGC 3 cut(s) 577, 634, 662
BceAI ACGGC 2 cut(s) 417, 445
BciT130I CCWGG 4 cut(s) 99, 486, 695, 769
BclI TGATCA 1 cut(s) 582
BcoDI GTCTC 1 cut(s) 167
BfmI CTRYAG 1 cut(s) 648
BfuAI ACCTGC 1 cut(s) 520
BisI GCNGC 3 cut(s) 591, 648, 651
BlsI GCNGC 3 cut(s) 592, 649, 652
Bme1390I CCNGG 4 cut(s) 99, 486, 695, 769
Bme18I GGWCC 1 cut(s) 26
BmgT120I GGNCC 2 cut(s) 26, 572
BmiI GGNNCC 3 cut(s) 123, 412, 573
BmrFI CCNGG 4 cut(s) 99, 486, 695, 769
BmsI GCATC 5 cut(s) 58, 97, 170, 602, 782
BpiI GAAGAC 1 cut(s) 614
BplI GAGNNNNNCTC 4 cut(s) 431, 463, 749, 781
BpmI CTGGAG 1 cut(s) 459
Bpu10I CCTNAGC 1 cut(s) 522
BsaJI CCNNGG 4 cut(s) 165, 427, 485, 768
BsaWI WCCGGW 2 cut(s) 148, 407
BsaXI ACNNNNNCTCC 2 cut(s) 402, 432
Bsc4I CCNNNNNNNGG 2 cut(s) 486, 694
Bse118I RCCGGY 2 cut(s) 148, 199
Bse1I ACTGG 2 cut(s) 140, 633
Bse21I CCTNAGG 1 cut(s) 756
Bse3DI GCAATG 3 cut(s) 110, 449, 561
BseAI TCCGGA 1 cut(s) 407
BseBI CCWGG 4 cut(s) 99, 486, 695, 769
BseDI CCNNGG 4 cut(s) 165, 427, 485, 768
BseGI GGATG 2 cut(s) 161, 637
BseLI CCNNNNNNNGG 2 cut(s) 486, 694
BseMI GCAATG 3 cut(s) 110, 449, 561
BseMII CTCAG 4 cut(s) 347, 380, 536, 747
BseNI ACTGG 2 cut(s) 140, 633
BseRI GAGGAG 1 cut(s) 462
BseSI GKGCMC 2 cut(s) 559, 753
BseX3I CGGCCG 1 cut(s) 430
BseXI GCAGC 3 cut(s) 577, 634, 662
BseYI CCCAGC 1 cut(s) 515
Bsh1285I CGRYCG 1 cut(s) 433
BshFI GGCC 5 cut(s) 97, 199, 432, 574, 780
BshNI GGYRCC 1 cut(s) 121
BshTI ACCGGT 1 cut(s) 148
BsiEI CGRYCG 1 cut(s) 433
BsiHKAI GWGCWC 1 cut(s) 559
BsiSI CCGG 4 cut(s) 149, 181, 200, 408
BslI CCNNNNNNNGG 2 cut(s) 486, 694
BsmAI GTCTC 1 cut(s) 167
BsmI GAATGC 1 cut(s) 610
BsnI GGCC 5 cut(s) 97, 199, 432, 574, 780
Bsp1286I GDGCHC 3 cut(s) 523, 559, 753
Bsp13I TCCGGA 1 cut(s) 407
Bsp143I GATC 4 cut(s) 16, 458, 582, 616
BspACI CCGC 2 cut(s) 14, 203
BspANI GGCC 5 cut(s) 97, 199, 432, 574, 780
BspCNI CTCAG 4 cut(s) 348, 381, 535, 748
BspEI TCCGGA 1 cut(s) 407
BspHI TCATGA 1 cut(s) 600
BspLI GGNNCC 3 cut(s) 123, 412, 573
BspMAI CTGCAG 1 cut(s) 652
BspMI ACCTGC 1 cut(s) 520
BspPI GGATC 2 cut(s) 24, 466
BspT107I GGYRCC 1 cut(s) 121
BsrDI GCAATG 3 cut(s) 110, 449, 561
BsrFI RCCGGY 2 cut(s) 148, 199
BsrI ACTGG 2 cut(s) 140, 633
BssAI RCCGGY 2 cut(s) 148, 199
BssECI CCNNGG 4 cut(s) 165, 427, 485, 768
BssMI GATC 4 cut(s) 16, 458, 582, 616
BssSI CACGAG 1 cut(s) 189
Bst2BI CACGAG 1 cut(s) 189
Bst2UI CCWGG 4 cut(s) 99, 486, 695, 769
BstAPI GCANNNNNTGC 2 cut(s) 11, 563
BstC8I GCNNGC 3 cut(s) 197, 201, 273
BstDEI CTNAG 5 cut(s) 356, 389, 511, 522, 756
BstDSI CCRYGG 1 cut(s) 427
BstF5I GGATG 2 cut(s) 161, 637
BstHHI GCGC 2 cut(s) 262, 271
BstKTI GATC 4 cut(s) 19, 461, 585, 619
BstMAI GTCTC 1 cut(s) 167
BstMBI GATC 4 cut(s) 16, 458, 582, 616
BstMCI CGRYCG 1 cut(s) 433
BstMWI GCNNNNNNNGC 4 cut(s) 11, 266, 268, 563
BstNI CCWGG 4 cut(s) 99, 486, 695, 769
BstNSI RCATGY 1 cut(s) 275
BstSCI CCNGG 4 cut(s) 97, 484, 693, 767
BstSFI CTRYAG 1 cut(s) 648
BstSLI GKGCMC 2 cut(s) 559, 753
BstV1I GCAGC 3 cut(s) 577, 634, 662
BstV2I GAAGAC 1 cut(s) 614
BstX2I RGATCY 1 cut(s) 16
BstXI CCANNNNNNTGG 1 cut(s) 98
BstYI RGATCY 1 cut(s) 16
BstZI CGGCCG 1 cut(s) 430
Bsu36I CCTNAGG 1 cut(s) 756
BsuRI GGCC 5 cut(s) 97, 199, 432, 574, 780
BtgI CCRYGG 1 cut(s) 427
BtsCI GGATG 2 cut(s) 161, 637
BtsIMutI CAGTG 3 cut(s) 147, 386, 626
BveI ACCTGC 1 cut(s) 520
Cac8I GCNNGC 3 cut(s) 197, 201, 273
CciI TCATGA 1 cut(s) 600
CfoI GCGC 2 cut(s) 262, 271
Cfr10I RCCGGY 2 cut(s) 148, 199
Cfr13I GGNCC 2 cut(s) 26, 572
CspAI ACCGGT 1 cut(s) 148
CviAII CATG 3 cut(s) 272, 586, 601
DdeI CTNAG 5 cut(s) 356, 389, 511, 522, 756
DpnI GATC 4 cut(s) 18, 460, 584, 618
DpnII GATC 4 cut(s) 16, 458, 582, 616
EaeI YGGCCR 2 cut(s) 430, 778
EagI CGGCCG 1 cut(s) 430
EclXI CGGCCG 1 cut(s) 430
Eco147I AGGCCT 1 cut(s) 97
Eco24I GRGCYC 1 cut(s) 523
Eco47I GGWCC 1 cut(s) 26
Eco52I CGGCCG 1 cut(s) 430
Eco57I CTGAAG 2 cut(s) 33, 141
Eco81I CCTNAGG 1 cut(s) 756
EcoO109I RGGNCCY 2 cut(s) 26, 572
EcoRII CCWGG 4 cut(s) 97, 484, 693, 767
EcoT22I ATGCAT 1 cut(s) 112
EcoT38I GRGCYC 1 cut(s) 523
FaeI CATG 3 cut(s) 275, 589, 604
FaiI YATR 9 cut(s) 119, 273, 278, 353, 587, 602, 701, 714, 788
FatI CATG 3 cut(s) 271, 585, 600
FauI CCCGC 1 cut(s) 196
FbaI TGATCA 1 cut(s) 582
FblI GTMKAC 1 cut(s) 54
Fnu4HI GCNGC 3 cut(s) 591, 648, 651
FokI GGATG 2 cut(s) 148, 644
FriOI GRGCYC 1 cut(s) 523
Fsp4HI GCNGC 3 cut(s) 591, 648, 651
FspAI RTGCGCAY 1 cut(s) 270
FspI TGCGCA 1 cut(s) 270
GlaI GCGC 2 cut(s) 261, 270
GluI GCNGC 3 cut(s) 591, 648, 651
GsaI CCCAGC 1 cut(s) 519
GsuI CTGGAG 1 cut(s) 459
HaeIII GGCC 5 cut(s) 97, 199, 432, 574, 780
HapII CCGG 4 cut(s) 149, 181, 200, 408
HhaI GCGC 2 cut(s) 262, 271
Hin1II CATG 3 cut(s) 275, 589, 604
Hin6I GCGC 2 cut(s) 260, 269
HinP1I GCGC 2 cut(s) 260, 269
HinfI GANTC 1 cut(s) 442
HpaII CCGG 4 cut(s) 149, 181, 200, 408
HphI GGTGA 3 cut(s) 80, 232, 677
Hpy166II GTNNAC 3 cut(s) 55, 557, 763
Hpy188I TCNGA 3 cut(s) 166, 458, 706
Hpy188III TCNNGA 2 cut(s) 408, 601
Hpy8I GTNNAC 3 cut(s) 55, 557, 763
HpyCH4IV ACGT 1 cut(s) 611
HpyF10VI GCNNNNNNNGC 4 cut(s) 11, 266, 268, 563
HpyF3I CTNAG 5 cut(s) 356, 389, 511, 522, 756
HpySE526I ACGT 1 cut(s) 611
Hsp92II CATG 3 cut(s) 275, 589, 604
HspAI GCGC 2 cut(s) 260, 269
Kpn2I TCCGGA 1 cut(s) 407
KroI GCCGGC 1 cut(s) 199
KroNI GCCGGC 1 cut(s) 201
Ksp22I TGATCA 1 cut(s) 582
Kzo9I GATC 4 cut(s) 16, 458, 582, 616
LmnI GCTCC 1 cut(s) 410
Lsp1109I GCAGC 3 cut(s) 577, 634, 662
LweI GCATC 5 cut(s) 58, 97, 170, 602, 782
MaeII ACGT 1 cut(s) 611
MaeIII GTNAC 5 cut(s) 238, 373, 382, 418, 683
MalI GATC 4 cut(s) 18, 460, 584, 618
MboI GATC 4 cut(s) 16, 458, 582, 616
MboII GAAGA 3 cut(s) 147, 614, 647
MflI RGATCY 1 cut(s) 16
MhlI GDGCHC 3 cut(s) 523, 559, 753
Mph1103I ATGCAT 1 cut(s) 112
MroI TCCGGA 1 cut(s) 407
MroNI GCCGGC 1 cut(s) 199
MseI TTAA 2 cut(s) 314, 799
MspI CCGG 4 cut(s) 149, 181, 200, 408
MspR9I CCNGG 4 cut(s) 99, 486, 695, 769
Mva1269I GAATGC 1 cut(s) 610
MvaI CCWGG 4 cut(s) 99, 486, 695, 769
MwoI GCNNNNNNNGC 4 cut(s) 11, 266, 268, 563
NaeI GCCGGC 1 cut(s) 201
NdeII GATC 4 cut(s) 16, 458, 582, 616
NgoMIV GCCGGC 1 cut(s) 199
NlaIII CATG 3 cut(s) 275, 589, 604
NlaIV GGNNCC 3 cut(s) 123, 412, 573
NmuCI GTSAC 4 cut(s) 238, 382, 418, 683
NsbI TGCGCA 1 cut(s) 270
NsiI ATGCAT 1 cut(s) 112
NspI RCATGY 1 cut(s) 275
PaeI GCATGC 1 cut(s) 275
PagI TCATGA 1 cut(s) 600
PceI AGGCCT 1 cut(s) 97
PctI GAATGC 1 cut(s) 610
PdiI GCCGGC 1 cut(s) 201
PfeI GAWTC 1 cut(s) 442
PflMI CCANNNNNTGG 1 cut(s) 694
PinAI ACCGGT 1 cut(s) 148
PkrI GCNGC 3 cut(s) 592, 649, 652
PpuMI RGGWCCY 1 cut(s) 26
Psp1406I AACGTT 1 cut(s) 611
Psp5II RGGWCCY 1 cut(s) 26
Psp6I CCWGG 4 cut(s) 97, 484, 693, 767
PspFI CCCAGC 1 cut(s) 515
PspGI CCWGG 4 cut(s) 97, 484, 693, 767
PspN4I GGNNCC 3 cut(s) 123, 412, 573
PspPI GGNCC 2 cut(s) 26, 572
PspPPI RGGWCCY 1 cut(s) 26
PstI CTGCAG 1 cut(s) 652
PsuI RGATCY 1 cut(s) 16
SaqAI TTAA 2 cut(s) 314, 799
SatI GCNGC 3 cut(s) 591, 648, 651
Sau3AI GATC 4 cut(s) 16, 458, 582, 616
Sau96I GGNCC 2 cut(s) 26, 572
ScrFI CCNGG 4 cut(s) 99, 486, 695, 769
SduI GDGCHC 3 cut(s) 523, 559, 753
SfaNI GCATC 5 cut(s) 58, 97, 170, 602, 782
SfcI CTRYAG 1 cut(s) 648
SinI GGWCC 1 cut(s) 26
SphI GCATGC 1 cut(s) 275
SseBI AGGCCT 1 cut(s) 97
SsiI CCGC 2 cut(s) 14, 203
StuI AGGCCT 1 cut(s) 97
StyD4I CCNGG 4 cut(s) 97, 484, 693, 767
TaiI ACGT 1 cut(s) 614
TaqII GACCGA 1 cut(s) 72
TfiI GAWTC 1 cut(s) 442
Tru1I TTAA 2 cut(s) 314, 799
Tru9I TTAA 2 cut(s) 314, 799
TscAI CASTG 3 cut(s) 147, 393, 633
TseFI GTSAC 4 cut(s) 238, 382, 418, 683
TseI GCWGC 3 cut(s) 590, 647, 650
Tsp45I GTSAC 4 cut(s) 238, 382, 418, 683
TspDTI ATGAA 4 cut(s) 589, 617, 648, 654
TspRI CASTG 3 cut(s) 147, 393, 633
Van91I CCANNNNNTGG 1 cut(s) 694
VneI GTGCAC 1 cut(s) 555
VpaK11BI GGWCC 1 cut(s) 26
XceI RCATGY 1 cut(s) 275
XmiI GTMKAC 1 cut(s) 54
Zsp2I ATGCAT 1 cut(s) 112
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.