Rroxscaffold_3G00224740

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
GWHEROQ00000003
OG0013067
Physical Location & Seq
Reverse (-)
8003825 .. 8006584
2760 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_3G00224740.1

Sequence Viewer

Length: 957 bp
ATGAAAGGTGAATACGGAGGTGGTGACACCAAGAGTGAAACCCAAAACATGTTCTCGAAGCTTCACCATCATAACAACCCACAATCTCATCCTCACCCTCACCCTCACCCTCACCACCCCCACCAGCAGCAGCAGTTCCACCACCATTTCTCCAACCCATTTCAGATTACCCCAGTCCGCGAATGTCAACCTCAAACTTCTGAAGAAGAAGACACCAGCCGAACCAGCAGCGGCACCGCCACCAAGCCGCTCGTTTCAGATCCCAACAACCTCACCGGCGGCGATGGCGCCACTATTGAAGTCGTCCGGAGGCCCAGGGGCCGCCCTCCCGGCTCCAAGAACAAGCCCAAGCCTCCCGTCATCATAACCCGCGACACCGAGCCCGCCATGAGCCCTTACATTCTTGAAGTCCCCGGCGGAAGCGACGTCGTCGACGCCGTCTCCCGATTCTGCTGCCGCAAGAACATCGGCCTCGTCATCCTCACCGGCTCCGGAACCGTCGCCAACGTTACTCTACGTCAGCCGTCGACTACTCCAGGAGCTACTGTTACCTTCCACGGCCGCTTCGACATCCTCTCGATCTCCGCCACCTTCCTTCCGCAAACGACGGCGGCCGGCCCGATCCCCAACGGCTTCACCATCTCCCTCGCCGGACCGCAGGGCCAGATCGTCGGAGGACTCGTCGCCGGTTCCTTGATAGCTGCCGGAACTGTTTACATCATCGCGGCGTCGTTCAACAGCCCTTCTTATCATCGGCTGCCGGTGGAGGACGAGGCGGCGCCCAGGAACTCGGTGTCGGGAGGGGAAGCGCAGTCGCCGCCTCTTTCGACTGGCGGGGAGAGTGGGGGTCACGCGCCGGCGCAGTCTTGTGGGATGGCCATGTACAGCTGTCACTTGCCTACCGATGTTATCTGGGCTCCGACTGCAAGACAACCACCACCTCCGCCACCCTACTGA

Protein Analysis

318

Amino Acids

33.61

Weight (kDa)

6.99

Isoelectric Point (pI)

57.94

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PCC PF03479 132 - 246 1.1e-19 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: OG0013067)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G14490 AT1G14490 AT5G49700
fragaria_vesca FvH4_5g35490
malus_domestica MD08G1196300.v1.1 MD15G1384100.v1.1
prunus_persica Prupe.1G530300_v2.0.a1
pyrus_communis pycom08g16870
rosa_chinensis RchiOBHm_Chr7g0236871
rosa_laevigata RLG00000001054
rosa_multiflora Rmu_sc0002867.1_g000011
rosa_roxburghii Rroxscaffold_3G00224740
rosa_rugosa Rorug07G0300400
rosa_samantha Rh7AG455300 Rh7BG426500 Rh7CG474000 Rh7DG443300
rosa_wichuraiana Rw7G037800

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AatII GACGTC 1 cut(s) 429
AccB1I GGYRCC 3 cut(s) 233, 287, 778
AccBSI CCGCTC 1 cut(s) 250
AccI GTMKAC 2 cut(s) 432, 527
AccII CGCG 4 cut(s) 180, 372, 725, 854
AccIII TCCGGA 2 cut(s) 306, 491
AclI AACGTT 1 cut(s) 507
AclWI GGATC 2 cut(s) 254, 616
AcoI YGGCCR 3 cut(s) 559, 612, 876
AcuI CTGAAG 1 cut(s) 222
AcyI GRCGYC 5 cut(s) 288, 426, 435, 728, 779
AfaI GTAC 1 cut(s) 884
AflIII ACRYGT 1 cut(s) 48
AgsI TTSAA 3 cut(s) 299, 407, 736
AjnI CCWGG 3 cut(s) 314, 535, 782
AluBI AGCT 4 cut(s) 61, 542, 701, 888
AluI AGCT 4 cut(s) 61, 542, 701, 888
Alw26I GTCTC 1 cut(s) 445
AlwI GGATC 2 cut(s) 254, 616
Aor13HI TCCGGA 2 cut(s) 306, 491
AoxI GGCC 8 cut(s) 311, 319, 469, 559, 612, 616, 661, 876
ApeKI GCWGC 6 cut(s) 127, 130, 228, 453, 701, 757
AspLEI GCGC 5 cut(s) 290, 781, 811, 856, 862
AspS9I GGNCC 5 cut(s) 312, 319, 617, 653, 661
AsuC2I CCSGG 2 cut(s) 330, 414
AvaII GGWCC 1 cut(s) 653
BalI TGGCCA 1 cut(s) 878
BanI GGYRCC 3 cut(s) 233, 287, 778
BanII GRGCYC 3 cut(s) 384, 395, 919
BbsI GAAGAC 1 cut(s) 216
BbvI GCAGC 6 cut(s) 139, 142, 240, 440, 688, 744
BccI CCATC 4 cut(s) 75, 278, 647, 868
BceAI ACGGC 5 cut(s) 422, 508, 574, 624, 646
BcgI CGANNNNNNTGC 4 cut(s) 435, 448, 469, 482
BciT130I CCWGG 3 cut(s) 316, 537, 784
BcnI CCSGG 2 cut(s) 330, 414
BcoDI GTCTC 1 cut(s) 445
BfoI RGCGCY 2 cut(s) 291, 782
BglI GCCNNNNNGGC 1 cut(s) 330
Bme1390I CCNGG 5 cut(s) 316, 330, 414, 537, 784
Bme18I GGWCC 1 cut(s) 653
BmgT120I GGNCC 5 cut(s) 312, 319, 617, 653, 661
BmiI GGNNCC 9 cut(s) 235, 289, 320, 334, 490, 496, 691, 780, 918
BmrFI CCNGG 5 cut(s) 316, 330, 414, 537, 784
BmrI ACTGGG 1 cut(s) 167
BmuI ACTGGG 1 cut(s) 167
BpiI GAAGAC 1 cut(s) 216
BpmI CTGGAG 1 cut(s) 519
BpuMI CCSGG 2 cut(s) 330, 414
BsaHI GRCGYC 5 cut(s) 288, 426, 435, 728, 779
BsaJI CCNNGG 5 cut(s) 314, 315, 412, 556, 782
BsaWI WCCGGW 2 cut(s) 306, 491
BsaXI ACNNNNNCTCC 8 cut(s) 134, 164, 425, 455, 531, 561, 666, 696
Bse118I RCCGGY 6 cut(s) 275, 485, 614, 686, 760, 856
Bse1I ACTGG 2 cut(s) 173, 835
BseAI TCCGGA 2 cut(s) 306, 491
BseBI CCWGG 3 cut(s) 316, 537, 784
BseDI CCNNGG 5 cut(s) 314, 315, 412, 556, 782
BseGI GGATG 4 cut(s) 88, 477, 570, 879
BseNI ACTGG 2 cut(s) 173, 835
BseX3I CGGCCG 2 cut(s) 559, 612
BseXI GCAGC 6 cut(s) 139, 142, 240, 440, 688, 744
Bsh1236I CGCG 4 cut(s) 180, 372, 725, 854
Bsh1285I CGRYCG 2 cut(s) 562, 615
BshFI GGCC 8 cut(s) 313, 321, 471, 561, 614, 618, 663, 878
BshNI GGYRCC 3 cut(s) 233, 287, 778
BsiEI CGRYCG 2 cut(s) 562, 615
BslFI GGGAC 1 cut(s) 395
BsmAI GTCTC 1 cut(s) 445
BsmBI CGTCTC 1 cut(s) 445
BsmFI GGGAC 1 cut(s) 395
BsnI GGCC 8 cut(s) 313, 321, 471, 561, 614, 618, 663, 878
Bsp1286I GDGCHC 3 cut(s) 384, 395, 919
Bsp13I TCCGGA 2 cut(s) 306, 491
Bsp1407I TGTACA 1 cut(s) 882
Bsp143I GATC 4 cut(s) 259, 579, 621, 666
BspANI GGCC 8 cut(s) 313, 321, 471, 561, 614, 618, 663, 878
BspEI TCCGGA 2 cut(s) 306, 491
BspFNI CGCG 4 cut(s) 180, 372, 725, 854
BspLI GGNNCC 9 cut(s) 235, 289, 320, 334, 490, 496, 691, 780, 918
BspPI GGATC 2 cut(s) 254, 616
BspT107I GGYRCC 3 cut(s) 233, 287, 778
BsrBI CCGCTC 1 cut(s) 250
BsrFI RCCGGY 6 cut(s) 275, 485, 614, 686, 760, 856
BsrGI TGTACA 1 cut(s) 882
BsrI ACTGG 2 cut(s) 173, 835
BssAI RCCGGY 6 cut(s) 275, 485, 614, 686, 760, 856
BssECI CCNNGG 5 cut(s) 314, 315, 412, 556, 782
BssMI GATC 4 cut(s) 259, 579, 621, 666
BssNI GRCGYC 5 cut(s) 288, 426, 435, 728, 779
Bst2UI CCWGG 3 cut(s) 316, 537, 784
Bst4CI ACNGT 3 cut(s) 499, 547, 712
BstACI GRCGYC 5 cut(s) 288, 426, 435, 728, 779
BstAUI TGTACA 1 cut(s) 882
BstC8I GCNNGC 3 cut(s) 384, 616, 858
BstDSI CCRYGG 1 cut(s) 556
BstF5I GGATG 4 cut(s) 88, 477, 570, 879
BstFNI CGCG 4 cut(s) 180, 372, 725, 854
BstH2I RGCGCY 2 cut(s) 291, 782
BstHHI GCGC 5 cut(s) 290, 781, 811, 856, 862
BstKTI GATC 4 cut(s) 262, 582, 624, 669
BstMAI GTCTC 1 cut(s) 445
BstMBI GATC 4 cut(s) 259, 579, 621, 666
BstMCI CGRYCG 2 cut(s) 562, 615
BstMWI GCNNNNNNNGC 5 cut(s) 225, 285, 330, 817, 923
BstNI CCWGG 3 cut(s) 316, 537, 784
BstNSI RCATGY 1 cut(s) 52
BstSCI CCNGG 5 cut(s) 314, 328, 412, 535, 782
BstUI CGCG 4 cut(s) 180, 372, 725, 854
BstV1I GCAGC 6 cut(s) 139, 142, 240, 440, 688, 744
BstV2I GAAGAC 1 cut(s) 216
BstX2I RGATCY 1 cut(s) 259
BstYI RGATCY 1 cut(s) 259
BstZI CGGCCG 2 cut(s) 559, 612
BsuRI GGCC 8 cut(s) 313, 321, 471, 561, 614, 618, 663, 878
BtgI CCRYGG 1 cut(s) 556
BtgZI GCGATG 2 cut(s) 297, 706
BtsCI GGATG 4 cut(s) 88, 477, 570, 879
Cac8I GCNNGC 3 cut(s) 384, 616, 858
CfoI GCGC 5 cut(s) 290, 781, 811, 856, 862
Cfr10I RCCGGY 6 cut(s) 275, 485, 614, 686, 760, 856
Cfr13I GGNCC 5 cut(s) 312, 319, 617, 653, 661
CpoI CGGWCCG 1 cut(s) 653
CseI GACGC 2 cut(s) 443, 717
Csp6I GTAC 1 cut(s) 883
CspI CGGWCCG 1 cut(s) 653
CviAII CATG 3 cut(s) 49, 388, 880
CviQI GTAC 1 cut(s) 883
DinI GGCGCC 2 cut(s) 289, 780
DpnI GATC 4 cut(s) 261, 581, 623, 668
DpnII GATC 4 cut(s) 259, 579, 621, 666
EaeI YGGCCR 3 cut(s) 559, 612, 876
EagI CGGCCG 2 cut(s) 559, 612
EciI GGCGGA 3 cut(s) 432, 574, 933
EclXI CGGCCG 2 cut(s) 559, 612
Eco24I GRGCYC 3 cut(s) 384, 395, 919
Eco47I GGWCC 1 cut(s) 653
Eco52I CGGCCG 2 cut(s) 559, 612
Eco57I CTGAAG 1 cut(s) 222
EcoRII CCWGG 3 cut(s) 314, 535, 782
EcoT38I GRGCYC 3 cut(s) 384, 395, 919
EgeI GGCGCC 2 cut(s) 289, 780
EheI GGCGCC 2 cut(s) 289, 780
Esp3I CGTCTC 1 cut(s) 445
FaeI CATG 3 cut(s) 52, 391, 883
FaiI YATR 5 cut(s) 50, 72, 365, 389, 881
FaqI GGGAC 1 cut(s) 395
FatI CATG 3 cut(s) 48, 387, 879
FauI CCCGC 3 cut(s) 377, 391, 827
FblI GTMKAC 2 cut(s) 432, 527
FokI GGATG 4 cut(s) 75, 464, 557, 886
FriOI GRGCYC 3 cut(s) 384, 395, 919
FseI GGCCGGCC 1 cut(s) 618
GlaI GCGC 5 cut(s) 289, 780, 810, 855, 861
GsuI CTGGAG 1 cut(s) 519
HaeII RGCGCY 2 cut(s) 291, 782
HaeIII GGCC 8 cut(s) 313, 321, 471, 561, 614, 618, 663, 878
HgaI GACGC 2 cut(s) 443, 717
HhaI GCGC 5 cut(s) 290, 781, 811, 856, 862
Hin1I GRCGYC 5 cut(s) 288, 426, 435, 728, 779
Hin1II CATG 3 cut(s) 52, 391, 883
Hin6I GCGC 5 cut(s) 288, 779, 809, 854, 860
HinP1I GCGC 5 cut(s) 288, 779, 809, 854, 860
HincII GTYRAC 3 cut(s) 188, 433, 528
HindII GTYRAC 3 cut(s) 188, 433, 528
HindIII AAGCTT 1 cut(s) 59
HinfI GANTC 2 cut(s) 447, 678
Hpy166II GTNNAC 4 cut(s) 188, 433, 528, 715
Hpy188I TCNGA 5 cut(s) 165, 202, 259, 674, 921
Hpy188III TCNNGA 7 cut(s) 55, 307, 404, 444, 492, 577, 798
Hpy8I GTNNAC 4 cut(s) 188, 433, 528, 715
HpyAV CCTTC 4 cut(s) 562, 601, 605, 753
HpyCH4III ACNGT 3 cut(s) 499, 547, 712
HpyCH4IV ACGT 3 cut(s) 426, 507, 517
HpyCH4V TGCA 1 cut(s) 926
HpyF10VI GCNNNNNNNGC 5 cut(s) 225, 285, 330, 817, 923
HpySE526I ACGT 3 cut(s) 426, 507, 517
Hsp92I GRCGYC 5 cut(s) 288, 426, 435, 728, 779
Hsp92II CATG 3 cut(s) 52, 391, 883
HspAI GCGC 5 cut(s) 288, 779, 809, 854, 860
KasI GGCGCC 2 cut(s) 287, 778
Kpn2I TCCGGA 2 cut(s) 306, 491
KroI GCCGGC 2 cut(s) 614, 856
KroNI GCCGGC 2 cut(s) 616, 858
Kzo9I GATC 4 cut(s) 259, 579, 621, 666
LmnI GCTCC 4 cut(s) 338, 494, 539, 922
Lsp1109I GCAGC 6 cut(s) 139, 142, 240, 440, 688, 744
MaeII ACGT 3 cut(s) 426, 507, 517
MaeIII GTNAC 5 cut(s) 23, 508, 547, 848, 890
MalI GATC 4 cut(s) 261, 581, 623, 668
MbiI CCGCTC 1 cut(s) 250
MboI GATC 4 cut(s) 259, 579, 621, 666
MboII GAAGA 3 cut(s) 215, 218, 221
MflI RGATCY 1 cut(s) 259
MhlI GDGCHC 3 cut(s) 384, 395, 919
MlsI TGGCCA 1 cut(s) 878
MluNI TGGCCA 1 cut(s) 878
Mly113I GGCGCC 2 cut(s) 288, 779
MlyI GAGTC 1 cut(s) 672
MmeI TCCRAC 3 cut(s) 177, 652, 944
Mox20I TGGCCA 1 cut(s) 878
MreI CGCCGGCG 1 cut(s) 856
MroI TCCGGA 2 cut(s) 306, 491
MroNI GCCGGC 2 cut(s) 614, 856
MscI TGGCCA 1 cut(s) 878
Msp20I TGGCCA 1 cut(s) 878
MspA1I CMGCKG 2 cut(s) 231, 888
MspR9I CCNGG 5 cut(s) 316, 330, 414, 537, 784
MvaI CCWGG 3 cut(s) 316, 537, 784
MvnI CGCG 4 cut(s) 180, 372, 725, 854
MwoI GCNNNNNNNGC 5 cut(s) 225, 285, 330, 817, 923
NaeI GCCGGC 2 cut(s) 616, 858
NarI GGCGCC 2 cut(s) 288, 779
NciI CCSGG 2 cut(s) 330, 414
NdeII GATC 4 cut(s) 259, 579, 621, 666
NgoMIV GCCGGC 2 cut(s) 614, 856
NlaIII CATG 3 cut(s) 52, 391, 883
NlaIV GGNNCC 9 cut(s) 235, 289, 320, 334, 490, 496, 691, 780, 918
NmuCI GTSAC 3 cut(s) 23, 848, 890
NspI RCATGY 1 cut(s) 52
PasI CCCWGGG 1 cut(s) 315
PciI ACATGT 1 cut(s) 48
PcsI WCGNNNNNNNCGW 3 cut(s) 435, 564, 678
PdiI GCCGGC 2 cut(s) 616, 858
PfeI GAWTC 1 cut(s) 447
PflFI GACNNNGTC 2 cut(s) 428, 437
PfoI TCCNGGA 1 cut(s) 535
PleI GAGTC 1 cut(s) 672
PluTI GGCGCC 2 cut(s) 291, 782
PpsI GAGTC 1 cut(s) 672
PscI ACATGT 1 cut(s) 48
Psp1406I AACGTT 1 cut(s) 507
Psp6I CCWGG 3 cut(s) 314, 535, 782
PspGI CCWGG 3 cut(s) 314, 535, 782
PspN4I GGNNCC 9 cut(s) 235, 289, 320, 334, 490, 496, 691, 780, 918
PspPI GGNCC 5 cut(s) 312, 319, 617, 653, 661
PsuI RGATCY 1 cut(s) 259
PsyI GACNNNGTC 2 cut(s) 428, 437
PvuII CAGCTG 1 cut(s) 888
RigI GGCCGGCC 1 cut(s) 618
RsaI GTAC 1 cut(s) 884
RsaNI GTAC 1 cut(s) 883
Rsr2I CGGWCCG 1 cut(s) 653
RsrII CGGWCCG 1 cut(s) 653
SalI GTCGAC 2 cut(s) 431, 526
Sau3AI GATC 4 cut(s) 259, 579, 621, 666
Sau96I GGNCC 5 cut(s) 312, 319, 617, 653, 661
SchI GAGTC 1 cut(s) 672
ScrFI CCNGG 5 cut(s) 316, 330, 414, 537, 784
SduI GDGCHC 3 cut(s) 384, 395, 919
SfoI GGCGCC 2 cut(s) 289, 780
SgrAI CRCCGGYG 2 cut(s) 275, 856
SgrDI CGTCGACG 1 cut(s) 431
SinI GGWCC 1 cut(s) 653
SspDI GGCGCC 2 cut(s) 287, 778
StyD4I CCNGG 5 cut(s) 314, 328, 412, 535, 782
TaaI ACNGT 3 cut(s) 499, 547, 712
TaiI ACGT 3 cut(s) 429, 510, 520
TaqI TCGA 6 cut(s) 56, 432, 527, 567, 578, 827
TatI WGTACW 1 cut(s) 882
TfiI GAWTC 1 cut(s) 447
TseFI GTSAC 3 cut(s) 23, 848, 890
TseI GCWGC 6 cut(s) 127, 130, 228, 453, 701, 757
Tsp45I GTSAC 3 cut(s) 23, 848, 890
TspDTI ATGAA 1 cut(s) 17
TspGWI ACGGA 1 cut(s) 30
Tth111I GACNNNGTC 2 cut(s) 428, 437
VpaK11BI GGWCC 1 cut(s) 653
XceI RCATGY 1 cut(s) 52
XmiI GTMKAC 2 cut(s) 432, 527
ZraI GACGTC 1 cut(s) 427
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.