Rroxscaffold_4G00288830

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
GWHEROQ00000004
OG0012533
Physical Location & Seq
Forward (+)
9491550 .. 9494039
2490 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_4G00288830.1

Sequence Viewer

Length: 1026 bp
ATGGCGAATCGATGGTGGGCTGGAAATGTGGCGATGGGAGCTCATGACTCAATCACCGCCTCGACACCACCGTCTCTTCATCTTAGAAACTCTGAAGCCGAGGAGCACAACAACAACAACACACCCACCAACAGCAGCACCAGCAACCCAAACAACACTCCACCTCAGAAGCAGGACGACGACCAGGACAGCCGTGACAACGATCGAGAAGTTGACAATCAAGACCCCAGCTCCGGCGGCCCCGACAGCCTCGAGCCTGGCTCCAGCAACCGCCGGCCCAGAGGCCAGTCTCCCAACGCTCTCCGGAGCCATGTCTTGGAAATCAGCAGCGGCAGCGACATCGTCGAGAGCATTGCCACCTTCGCACAGCGCAGGCACAGAGGAGTCTCCGTCCTAAGCGGCAGCGGCATTGTTTCTAACGTCACTCTTCGTCAGCCGGCCGCGCCGAGCGGGGTCATAACGCTCCACGGAAGGTTCGAGATTCTGTCCCTAAACGGTGCGTTTCTGCCTGCCCCGTCGCCGCCGGGGGCTAGTGGCCTGACCGTGTACTTGGGTGGCGGGCAGGGGCAGGTGGTTGGTGGGACTGTTGTTGGAGCTCTGTTGGCTTCCGGGCCAGTGATGATCATTGCGGCGACGTTCACTAATGCCACTTATGAGAGACTGCCGCTTGAGGATGAGAGCAATGAAGGGATGCAATTGCAACAGCAACAACAGCAGCAGCAATCCGGTGTGAATTCGGCAGGGACCGGAGGGAATTCGGGTTCTCAGGGCTTGAGTGATCAGCAGCAACAAGTGCCCATTTACGCTTTGCCTCCGACTTTACTTCCGAATGGTCAGATGCCGCCTGATGTGTACTGGGAGAGAACCAATAATTTCTTTGCCCTGGTCGTAGTTGTTGAAACTAGTAGTAGTTCCCCCACTTTGGAAACTGATGCTGGAAAGGTACAGAAAGCTCAAGTGGCAGTTATTATCTTGAAATTTTGGAGGTCTAGATCTTTGACTTCTGCTGTTAGGTGTAATGTTTGA
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

341

Amino Acids

36.07

Weight (kDa)

5.25

Isoelectric Point (pI)

56.06

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PCC PF03479 102 - 215 1.4e-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
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Publication-ready
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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) 559
AasI GACNNNNNNGTC 1 cut(s) 70
Acc36I ACCTGC 1 cut(s) 559
AccB7I CCANNNNNTGG 1 cut(s) 316
AccBSI CCGCTC 1 cut(s) 450
AccII CGCG 1 cut(s) 443
AccIII TCCGGA 1 cut(s) 303
AcoI YGGCCR 1 cut(s) 438
AcsI RAATTY 3 cut(s) 733, 754, 977
AcuI CTGAAG 1 cut(s) 114
AfaI GTAC 3 cut(s) 548, 854, 945
AfiI CCNNNNNNNGG 3 cut(s) 233, 316, 922
AgsI TTSAA 2 cut(s) 899, 976
AhlI ACTAGT 1 cut(s) 902
AjnI CCWGG 3 cut(s) 183, 256, 882
AloI GAACNNNNNNTCC 2 cut(s) 745, 777
AluBI AGCT 4 cut(s) 41, 231, 596, 953
AluI AGCT 4 cut(s) 41, 231, 596, 953
Alw21I GWGCWC 3 cut(s) 43, 108, 598
Alw26I GTCTC 4 cut(s) 78, 294, 391, 652
Ama87I CYCGRG 1 cut(s) 251
Aor13HI TCCGGA 1 cut(s) 303
AoxI GGCC 6 cut(s) 238, 275, 283, 438, 535, 611
ApeKI GCWGC 7 cut(s) 135, 327, 333, 402, 715, 718, 784
ApoI RAATTY 3 cut(s) 733, 754, 977
AspLEI GCGC 2 cut(s) 372, 445
AspS9I GGNCC 4 cut(s) 239, 276, 611, 744
AsuC2I CCSGG 2 cut(s) 525, 610
AsuHPI GGTGA 1 cut(s) 46
AvaI CYCGRG 1 cut(s) 251
AvaII GGWCC 1 cut(s) 744
BaeGI GKGCMC 1 cut(s) 798
BanII GRGCYC 2 cut(s) 43, 598
Bbv12I GWGCWC 3 cut(s) 43, 108, 598
BbvI GCAGC 7 cut(s) 147, 339, 345, 414, 727, 730, 796
BccI CCATC 2 cut(s) 6, 28
BceAI ACGGC 1 cut(s) 177
BcgI CGANNNNNNTGC 4 cut(s) 322, 335, 356, 369
BciT130I CCWGG 3 cut(s) 185, 258, 884
BclI TGATCA 2 cut(s) 621, 778
BcnI CCSGG 2 cut(s) 525, 610
BcoDI GTCTC 4 cut(s) 78, 294, 391, 652
BcuI ACTAGT 1 cut(s) 902
BfaI CTAG 3 cut(s) 531, 903, 990
BfuAI ACCTGC 1 cut(s) 559
BglII AGATCT 1 cut(s) 992
Bme1390I CCNGG 5 cut(s) 185, 258, 525, 610, 884
Bme18I GGWCC 1 cut(s) 744
BmeT110I CYCGRG 1 cut(s) 251
BmgT120I GGNCC 4 cut(s) 239, 276, 611, 744
BmiI GGNNCC 4 cut(s) 241, 262, 308, 745
BmrFI CCNGG 5 cut(s) 185, 258, 525, 610, 884
BmrI ACTGGG 1 cut(s) 865
BmsI GCATC 3 cut(s) 681, 828, 922
BmuI ACTGGG 1 cut(s) 865
BplI GAGNNNNNCTC 2 cut(s) 245, 277
BpmI CTGGAG 1 cut(s) 247
Bpu10I CCTNAGC 1 cut(s) 395
BpuEI CTTGAG 3 cut(s) 689, 793, 939
BpuMI CCSGG 2 cut(s) 525, 610
Bsa29I ATCGAT 1 cut(s) 10
BsaJI CCNNGG 4 cut(s) 99, 466, 524, 882
BsaWI WCCGGW 3 cut(s) 303, 725, 746
BsaXI ACNNNNNCTCC 4 cut(s) 215, 245, 375, 405
Bsc4I CCNNNNNNNGG 3 cut(s) 233, 316, 922
Bse118I RCCGGY 2 cut(s) 273, 436
Bse1I ACTGG 3 cut(s) 286, 614, 860
Bse3DI GCAATG 3 cut(s) 351, 624, 688
BseAI TCCGGA 1 cut(s) 303
BseBI CCWGG 3 cut(s) 185, 258, 884
BseCI ATCGAT 1 cut(s) 10
BseDI CCNNGG 4 cut(s) 99, 466, 524, 882
BseGI GGATG 2 cut(s) 679, 696
BseLI CCNNNNNNNGG 3 cut(s) 233, 316, 922
BseMI GCAATG 3 cut(s) 351, 624, 688
BseMII CTCAG 2 cut(s) 179, 779
BseNI ACTGG 3 cut(s) 286, 614, 860
BseRI GAGGAG 2 cut(s) 116, 396
BseSI GKGCMC 1 cut(s) 798
BseX3I CGGCCG 1 cut(s) 438
BseXI GCAGC 7 cut(s) 147, 339, 345, 414, 727, 730, 796
BseYI CCCAGC 1 cut(s) 227
Bsh1236I CGCG 1 cut(s) 443
Bsh1285I CGRYCG 2 cut(s) 205, 441
BshFI GGCC 6 cut(s) 240, 277, 285, 440, 537, 613
BshVI ATCGAT 1 cut(s) 10
BsiEI CGRYCG 2 cut(s) 205, 441
BsiHKAI GWGCWC 3 cut(s) 43, 108, 598
BsiHKCI CYCGRG 1 cut(s) 251
BsiSI CCGG 8 cut(s) 234, 274, 304, 437, 524, 609, 726, 747
BslFI GGGAC 3 cut(s) 472, 595, 757
BslI CCNNNNNNNGG 3 cut(s) 233, 316, 922
BsmAI GTCTC 4 cut(s) 78, 294, 391, 652
BsmBI CGTCTC 1 cut(s) 78
BsmFI GGGAC 3 cut(s) 472, 595, 757
BsnI GGCC 6 cut(s) 240, 277, 285, 440, 537, 613
BsoBI CYCGRG 1 cut(s) 251
Bsp1286I GDGCHC 4 cut(s) 43, 108, 598, 798
Bsp13I TCCGGA 1 cut(s) 303
Bsp143I GATC 4 cut(s) 202, 621, 778, 992
BspANI GGCC 6 cut(s) 240, 277, 285, 440, 537, 613
BspCNI CTCAG 2 cut(s) 178, 778
BspDI ATCGAT 1 cut(s) 10
BspEI TCCGGA 1 cut(s) 303
BspFNI CGCG 1 cut(s) 443
BspHI TCATGA 1 cut(s) 43
BspLI GGNNCC 4 cut(s) 241, 262, 308, 745
BspMI ACCTGC 1 cut(s) 559
BsrBI CCGCTC 1 cut(s) 450
BsrDI GCAATG 3 cut(s) 351, 624, 688
BsrFI RCCGGY 2 cut(s) 273, 436
BsrI ACTGG 3 cut(s) 286, 614, 860
BssAI RCCGGY 2 cut(s) 273, 436
BssECI CCNNGG 4 cut(s) 99, 466, 524, 882
BssMI GATC 4 cut(s) 202, 621, 778, 992
Bst2UI CCWGG 3 cut(s) 185, 258, 884
Bst4CI ACNGT 4 cut(s) 72, 497, 544, 586
Bst6I CTCTTC 2 cut(s) 81, 432
BstAPI GCANNNNNTGC 1 cut(s) 793
BstC8I GCNNGC 5 cut(s) 275, 374, 438, 510, 560
BstDEI CTNAG 4 cut(s) 83, 165, 395, 765
BstDSI CCRYGG 1 cut(s) 466
BstF5I GGATG 2 cut(s) 679, 696
BstFNI CGCG 1 cut(s) 443
BstHHI GCGC 2 cut(s) 372, 445
BstKTI GATC 4 cut(s) 205, 624, 781, 995
BstMAI GTCTC 4 cut(s) 78, 294, 391, 652
BstMBI GATC 4 cut(s) 202, 621, 778, 992
BstMCI CGRYCG 2 cut(s) 205, 441
BstNI CCWGG 3 cut(s) 185, 258, 884
BstSCI CCNGG 5 cut(s) 183, 256, 523, 608, 882
BstSLI GKGCMC 1 cut(s) 798
BstUI CGCG 1 cut(s) 443
BstV1I GCAGC 7 cut(s) 147, 339, 345, 414, 727, 730, 796
BstX2I RGATCY 1 cut(s) 992
BstYI RGATCY 1 cut(s) 992
BstZI CGGCCG 1 cut(s) 438
Bsu15I ATCGAT 1 cut(s) 10
BsuRI GGCC 6 cut(s) 240, 277, 285, 440, 537, 613
BsuTUI ATCGAT 1 cut(s) 10
BtgI CCRYGG 1 cut(s) 466
BtgZI GCGATG 1 cut(s) 47
BtsCI GGATG 2 cut(s) 679, 696
BtsIMutI CAGTG 1 cut(s) 621
BveI ACCTGC 1 cut(s) 559
Cac8I GCNNGC 5 cut(s) 275, 374, 438, 510, 560
CciI TCATGA 1 cut(s) 43
CfoI GCGC 2 cut(s) 372, 445
Cfr10I RCCGGY 2 cut(s) 273, 436
Cfr13I GGNCC 4 cut(s) 239, 276, 611, 744
ClaI ATCGAT 1 cut(s) 10
Csp6I GTAC 3 cut(s) 547, 853, 944
CviAII CATG 2 cut(s) 44, 311
CviQI GTAC 3 cut(s) 547, 853, 944
DdeI CTNAG 4 cut(s) 83, 165, 395, 765
DpnI GATC 4 cut(s) 204, 623, 780, 994
DpnII GATC 4 cut(s) 202, 621, 778, 992
DrdI GACNNNNNNGTC 1 cut(s) 70
DseDI GACNNNNNNGTC 1 cut(s) 70
EaeI YGGCCR 1 cut(s) 438
EagI CGGCCG 1 cut(s) 438
Eam1104I CTCTTC 2 cut(s) 81, 432
EarI CTCTTC 2 cut(s) 81, 432
Ecl136II GAGCTC 2 cut(s) 41, 596
EclXI CGGCCG 1 cut(s) 438
Eco24I GRGCYC 2 cut(s) 43, 598
Eco47I GGWCC 1 cut(s) 744
Eco52I CGGCCG 1 cut(s) 438
Eco53kI GAGCTC 2 cut(s) 41, 596
Eco57I CTGAAG 1 cut(s) 114
Eco88I CYCGRG 1 cut(s) 251
EcoICRI GAGCTC 2 cut(s) 41, 596
EcoRI GAATTC 2 cut(s) 733, 754
EcoRII CCWGG 3 cut(s) 183, 256, 882
EcoT38I GRGCYC 2 cut(s) 43, 598
Esp3I CGTCTC 1 cut(s) 78
FaeI CATG 2 cut(s) 47, 314
FaiI YATR 4 cut(s) 45, 312, 458, 654
FaqI GGGAC 3 cut(s) 472, 595, 757
FatI CATG 2 cut(s) 43, 310
FauI CCCGC 2 cut(s) 443, 551
FbaI TGATCA 2 cut(s) 621, 778
FokI GGATG 2 cut(s) 686, 703
FriOI GRGCYC 2 cut(s) 43, 598
FspBI CTAG 3 cut(s) 531, 903, 990
GlaI GCGC 2 cut(s) 371, 444
GsaI CCCAGC 1 cut(s) 231
GsuI CTGGAG 1 cut(s) 247
HaeIII GGCC 6 cut(s) 240, 277, 285, 440, 537, 613
HapII CCGG 8 cut(s) 234, 274, 304, 437, 524, 609, 726, 747
HhaI GCGC 2 cut(s) 372, 445
Hin1II CATG 2 cut(s) 47, 314
Hin6I GCGC 2 cut(s) 370, 443
HinP1I GCGC 2 cut(s) 370, 443
HincII GTYRAC 1 cut(s) 214
HindII GTYRAC 1 cut(s) 214
HinfI GANTC 4 cut(s) 7, 47, 384, 481
HpaII CCGG 8 cut(s) 234, 274, 304, 437, 524, 609, 726, 747
HphI GGTGA 1 cut(s) 46
Hpy166II GTNNAC 4 cut(s) 214, 547, 639, 853
Hpy188I TCNGA 5 cut(s) 94, 168, 816, 828, 837
Hpy188III TCNNGA 8 cut(s) 44, 206, 221, 304, 346, 478, 973, 990
Hpy8I GTNNAC 4 cut(s) 214, 547, 639, 853
Hpy99I CGWCG 4 cut(s) 182, 347, 520, 637
HpyAV CCTTC 3 cut(s) 370, 465, 680
HpyCH4III ACNGT 4 cut(s) 72, 497, 544, 586
HpyCH4IV ACGT 2 cut(s) 420, 635
HpyCH4V TGCA 2 cut(s) 694, 700
HpyF3I CTNAG 4 cut(s) 83, 165, 395, 765
HpySE526I ACGT 2 cut(s) 420, 635
Hsp92II CATG 2 cut(s) 47, 314
HspAI GCGC 2 cut(s) 370, 443
Kpn2I TCCGGA 1 cut(s) 303
KroI GCCGGC 2 cut(s) 273, 436
KroNI GCCGGC 2 cut(s) 275, 438
Ksp22I TGATCA 2 cut(s) 621, 778
Kzo9I GATC 4 cut(s) 202, 621, 778, 992
LmnI GCTCC 7 cut(s) 38, 103, 236, 266, 306, 468, 593
Lsp1109I GCAGC 7 cut(s) 147, 339, 345, 414, 727, 730, 796
LweI GCATC 3 cut(s) 681, 828, 922
MaeI CTAG 3 cut(s) 531, 903, 990
MaeII ACGT 2 cut(s) 420, 635
MaeIII GTNAC 2 cut(s) 194, 421
MalI GATC 4 cut(s) 204, 623, 780, 994
MbiI CCGCTC 1 cut(s) 450
MboI GATC 4 cut(s) 202, 621, 778, 992
MboII GAAGA 2 cut(s) 68, 419
MfeI CAATTG 1 cut(s) 695
MflI RGATCY 1 cut(s) 992
MhlI GDGCHC 4 cut(s) 43, 108, 598, 798
MluCI AATT 5 cut(s) 695, 733, 754, 871, 977
MlyI GAGTC 2 cut(s) 41, 393
MmeI TCCRAC 2 cut(s) 571, 839
MroI TCCGGA 1 cut(s) 303
MroNI GCCGGC 2 cut(s) 273, 436
MspA1I CMGCKG 2 cut(s) 330, 405
MspI CCGG 8 cut(s) 234, 274, 304, 437, 524, 609, 726, 747
MspR9I CCNGG 5 cut(s) 185, 258, 525, 610, 884
MunI CAATTG 1 cut(s) 695
MvaI CCWGG 3 cut(s) 185, 258, 884
MvnI CGCG 1 cut(s) 443
NaeI GCCGGC 2 cut(s) 275, 438
NciI CCSGG 2 cut(s) 525, 610
NdeII GATC 4 cut(s) 202, 621, 778, 992
NgoMIV GCCGGC 2 cut(s) 273, 436
NlaIII CATG 2 cut(s) 47, 314
NlaIV GGNNCC 4 cut(s) 241, 262, 308, 745
NmeAIII GCCGAG 2 cut(s) 124, 471
NmuCI GTSAC 2 cut(s) 194, 421
PaeR7I CTCGAG 1 cut(s) 251
PagI TCATGA 1 cut(s) 43
PaqCI CACCTGC 1 cut(s) 559
PcsI WCGNNNNNNNCGW 2 cut(s) 68, 474
PdiI GCCGGC 2 cut(s) 275, 438
PfeI GAWTC 2 cut(s) 7, 481
PflFI GACNNNGTC 1 cut(s) 341
PflMI CCANNNNNTGG 1 cut(s) 316
Ple19I CGATCG 1 cut(s) 205
PleI GAGTC 2 cut(s) 41, 392
PpsI GAGTC 2 cut(s) 41, 392
Psp124BI GAGCTC 2 cut(s) 43, 598
Psp6I CCWGG 3 cut(s) 183, 256, 882
PspFI CCCAGC 1 cut(s) 227
PspGI CCWGG 3 cut(s) 183, 256, 882
PspN4I GGNNCC 4 cut(s) 241, 262, 308, 745
PspPI GGNCC 4 cut(s) 239, 276, 611, 744
PspXI VCTCGAGB 1 cut(s) 251
PsuI RGATCY 1 cut(s) 992
PsyI GACNNNGTC 1 cut(s) 341
PvuI CGATCG 1 cut(s) 205
RsaI GTAC 3 cut(s) 548, 854, 945
RsaNI GTAC 3 cut(s) 547, 853, 944
SacI GAGCTC 2 cut(s) 43, 598
Sau3AI GATC 4 cut(s) 202, 621, 778, 992
Sau96I GGNCC 4 cut(s) 239, 276, 611, 744
SchI GAGTC 2 cut(s) 41, 393
ScrFI CCNGG 5 cut(s) 185, 258, 525, 610, 884
SduI GDGCHC 4 cut(s) 43, 108, 598, 798
SfaNI GCATC 3 cut(s) 681, 828, 922
Sfr274I CTCGAG 1 cut(s) 251
SinI GGWCC 1 cut(s) 744
SlaI CTCGAG 1 cut(s) 251
SmlI CTYRAG 4 cut(s) 251, 668, 772, 954
SmoI CTYRAG 4 cut(s) 251, 668, 772, 954
SpeI ACTAGT 1 cut(s) 902
Sse9I AATT 5 cut(s) 695, 733, 754, 871, 977
SspMI CTAG 3 cut(s) 531, 903, 990
SstI GAGCTC 2 cut(s) 43, 598
StyD4I CCNGG 5 cut(s) 183, 256, 523, 608, 882
TaaI ACNGT 4 cut(s) 72, 497, 544, 586
TaiI ACGT 2 cut(s) 423, 638
TaqI TCGA 6 cut(s) 10, 62, 205, 252, 345, 477
TasI AATT 5 cut(s) 695, 733, 754, 871, 977
TatI WGTACW 2 cut(s) 546, 852
TauI GCSGC 9 cut(s) 240, 333, 402, 408, 443, 523, 632, 667, 844
TfiI GAWTC 2 cut(s) 7, 481
TscAI CASTG 1 cut(s) 621
TseFI GTSAC 2 cut(s) 194, 421
TseI GCWGC 7 cut(s) 135, 327, 333, 402, 715, 718, 784
Tsp45I GTSAC 2 cut(s) 194, 421
TspDTI ATGAA 2 cut(s) 68, 699
TspGWI ACGGA 2 cut(s) 379, 483
TspRI CASTG 1 cut(s) 621
Tth111I GACNNNGTC 1 cut(s) 341
Van91I CCANNNNNTGG 1 cut(s) 316
VpaK11BI GGWCC 1 cut(s) 744
XapI RAATTY 3 cut(s) 733, 754, 977
XbaI TCTAGA 1 cut(s) 989
XhoI CTCGAG 1 cut(s) 251
XspI CTAG 3 cut(s) 531, 903, 990
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.