Rh4CG039800

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_samantha
Chr4C
OG0004329
Physical Location & Seq
Reverse (-)
8139361 .. 8146363
7003 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh4CG039800.1

Sequence Viewer

Length: 972 bp
ATGGCTGTTTTTCCTAAGGTGGCATGGCAGCGCCCCAAGGAATCGGCCAGCGTTATGCTTGGTTTCCGAACATGGTACACTCTGGCGAATCCGTGGTGGAGCGGTCAGCTGGGGCTGCCGGGAATGGACCCGGCAGCCAATTCACCAGCAGCGCTAAACAAGCGAGAACTCGAGATTTCCATGAACGAAAACAGCGGCGGCAGAAGCAGTGGCGGTGGCAGAGACGACGACGAAGATAGAGATCAAGGAGAAGAGCCTAAAGAAGGGGCCGTCGAGATTGGATCTCGAAGGCCCCGAGGCCGCCCTCCCGGATCCAAAAACAAACCCAAACCGCCCATCTTCGTGACCAGGGACAGCCCCAACTCCCTTAGAAGCCACGTGATGGAAGTTGCCGGCGGTGCTGACGTGGCGGAGAGCGTGGCACAATTCGCACGGAGGCGTCAGAGAGGTGTTTGCGTGCTCAGCGGGAGTGGCTCAGTGGCCAACGTGACACTGAGACAACCCGCTGCCCCCGGGGCCGTTGTAGCACTCCATGGAAGGTTCGAGATCCTGTCCCTGAGCGGAGCGTTTCTGCCAGGACCTGCTCCGCCCGGGTCGACAGGCCTGACCGTCTACCTAGCAGGCGGTCAGGGTCAGGTGGTTGGGGGAAGCGTTGTTGGATCACTTGTTGCGGCTGGACCAGTTATGGTTGTGGCTGCTACTTTTGCTAATGCTACTTATGAGAGACTGCCTCTTGAGGAAGATGATGAGGCTGGAAGCGGTGGTGGTGGTGGAGGTCATGGAGCTTCTGGAAGCTCCCCTACTGGAGTTGGAAGTAGTGGCGGTCCTCAGTTGCAGCCACCCGGGCACGGCGGACAGCTGCCTGATCCGTCGTCGCTCCCCCTTTACGGTCTGCCACCCAATCTGATCCCCAACGGCGGCCCACTCGGGCATGACGCTTATGCTTGGACTCATTCAAGACCGCCTTACTAA
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

33.03

Weight (kDa)

6.6

Isoelectric Point (pI)

53.14

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PCC PF03479 124 - 236 1.6e-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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 589
AccB7I CCANNNNNTGG 1 cut(s) 382
AccBSI CCGCTC 2 cut(s) 102, 561
AccI GTMKAC 2 cut(s) 596, 612
AclWI GGATC 7 cut(s) 289, 306, 319, 541, 667, 860, 901
AcoI YGGCCR 2 cut(s) 45, 480
AcvI CACGTG 1 cut(s) 379
AcyI GRCGYC 1 cut(s) 439
AfaI GTAC 1 cut(s) 77
AfeI AGCGCT 1 cut(s) 153
AfiI CCNNNNNNNGG 5 cut(s) 263, 382, 848, 887, 917
AgsI TTSAA 1 cut(s) 957
AjiI CACGTC 1 cut(s) 406
AjnI CCWGG 2 cut(s) 347, 574
AluBI AGCT 4 cut(s) 109, 785, 795, 859
AluI AGCT 4 cut(s) 109, 785, 795, 859
Alw21I GWGCWC 1 cut(s) 462
Alw26I GTCTC 3 cut(s) 216, 490, 718
AlwI GGATC 7 cut(s) 289, 306, 319, 541, 667, 860, 901
AlwNI CAGNNNCTG 1 cut(s) 581
Ama87I CYCGRG 6 cut(s) 170, 294, 512, 590, 842, 926
Aor51HI AGCGCT 1 cut(s) 153
AoxI GGCC 8 cut(s) 45, 267, 290, 298, 480, 516, 601, 919
ApeKI GCWGC 8 cut(s) 28, 115, 134, 149, 506, 695, 835, 859
AspLEI GCGC 2 cut(s) 33, 154
AspS9I GGNCC 8 cut(s) 127, 267, 291, 516, 578, 677, 824, 920
AsuC2I CCSGG 9 cut(s) 120, 131, 309, 513, 514, 591, 592, 843, 844
AsuHPI GGTGA 1 cut(s) 135
AvaI CYCGRG 6 cut(s) 170, 294, 512, 590, 842, 926
AvaII GGWCC 4 cut(s) 127, 578, 677, 824
AxyI CCTNAGG 1 cut(s) 15
BaeGI GKGCMC 1 cut(s) 849
BalI TGGCCA 1 cut(s) 482
BamHI GGATCC 1 cut(s) 311
BarI GAAGNNNNNNTAC 2 cut(s) 784, 816
BbrPI CACGTG 1 cut(s) 379
Bbv12I GWGCWC 1 cut(s) 462
BbvI GCAGC 8 cut(s) 40, 102, 146, 161, 493, 682, 846, 847
BccI CCATC 2 cut(s) 344, 376
BceAI ACGGC 4 cut(s) 254, 503, 865, 931
BciT130I CCWGG 2 cut(s) 349, 576
BcnI CCSGG 9 cut(s) 120, 131, 309, 513, 514, 591, 592, 843, 844
BcoDI GTCTC 3 cut(s) 216, 490, 718
BfaI CTAG 1 cut(s) 617
BfoI RGCGCY 2 cut(s) 34, 155
BfuAI ACCTGC 1 cut(s) 589
BglI GCCNNNNNGGC 2 cut(s) 515, 844
BlpI GCTNAGC 1 cut(s) 461
Bme18I GGWCC 4 cut(s) 127, 578, 677, 824
BmeT110I CYCGRG 6 cut(s) 170, 294, 512, 590, 842, 926
BmgBI CACGTC 1 cut(s) 406
BmgT120I GGNCC 8 cut(s) 127, 267, 291, 516, 578, 677, 824, 920
BmiI GGNNCC 5 cut(s) 129, 268, 293, 313, 517
BplI GAGNNNNNCTC 2 cut(s) 715, 747
BpmI CTGGAG 1 cut(s) 825
Bpu10I CCTNAGC 1 cut(s) 557
Bpu1102I GCTNAGC 1 cut(s) 461
BpuEI CTTGAG 1 cut(s) 755
BpuMI CCSGG 9 cut(s) 120, 131, 309, 513, 514, 591, 592, 843, 844
BsaAI YACGTR 1 cut(s) 379
BsaBI GATNNNNATC 1 cut(s) 240
BsaHI GRCGYC 1 cut(s) 439
Bsc4I CCNNNNNNNGG 5 cut(s) 263, 382, 848, 887, 917
Bse118I RCCGGY 1 cut(s) 392
Bse1I ACTGG 2 cut(s) 680, 808
Bse21I CCTNAGG 1 cut(s) 15
Bse8I GATNNNNATC 1 cut(s) 240
BseBI CCWGG 2 cut(s) 349, 576
BseJI GATNNNNATC 1 cut(s) 240
BseLI CCNNNNNNNGG 5 cut(s) 263, 382, 848, 887, 917
BseMII CTCAG 5 cut(s) 475, 485, 489, 548, 842
BseNI ACTGG 2 cut(s) 680, 808
BseSI GKGCMC 1 cut(s) 849
BseXI GCAGC 8 cut(s) 40, 102, 146, 161, 493, 682, 846, 847
BseYI CCCAGC 1 cut(s) 109
BshFI GGCC 8 cut(s) 47, 269, 292, 300, 482, 518, 603, 921
BsiHKAI GWGCWC 1 cut(s) 462
BsiHKCI CYCGRG 6 cut(s) 170, 294, 512, 590, 842, 926
BsiSI CCGG 7 cut(s) 119, 131, 309, 393, 513, 591, 843
BslFI GGGAC 2 cut(s) 365, 538
BslI CCNNNNNNNGG 5 cut(s) 263, 382, 848, 887, 917
BsmAI GTCTC 3 cut(s) 216, 490, 718
BsmBI CGTCTC 1 cut(s) 216
BsmFI GGGAC 2 cut(s) 365, 538
BsnI GGCC 8 cut(s) 47, 269, 292, 300, 482, 518, 603, 921
BsoBI CYCGRG 6 cut(s) 170, 294, 512, 590, 842, 926
Bsp1286I GDGCHC 2 cut(s) 462, 849
Bsp143I GATC 7 cut(s) 241, 281, 311, 546, 659, 865, 906
Bsp1720I GCTNAGC 1 cut(s) 461
Bsp19I CCATGG 1 cut(s) 532
BspANI GGCC 8 cut(s) 47, 269, 292, 300, 482, 518, 603, 921
BspCNI CTCAG 5 cut(s) 474, 486, 488, 549, 841
BspLI GGNNCC 5 cut(s) 129, 268, 293, 313, 517
BspMI ACCTGC 1 cut(s) 589
BspPI GGATC 7 cut(s) 289, 306, 319, 541, 667, 860, 901
BspQI GCTCTTC 1 cut(s) 246
BsrBI CCGCTC 2 cut(s) 102, 561
BsrFI RCCGGY 1 cut(s) 392
BsrI ACTGG 2 cut(s) 680, 808
BssAI RCCGGY 1 cut(s) 392
BssMI GATC 7 cut(s) 241, 281, 311, 546, 659, 865, 906
BssNI GRCGYC 1 cut(s) 439
BssT1I CCWWGG 2 cut(s) 36, 532
Bst2UI CCWGG 2 cut(s) 349, 576
Bst4CI ACNGT 2 cut(s) 610, 890
Bst6I CTCTTC 1 cut(s) 246
BstACI GRCGYC 1 cut(s) 439
BstBAI YACGTR 1 cut(s) 379
BstC8I GCNNGC 4 cut(s) 49, 394, 458, 622
BstDEI CTNAG 7 cut(s) 15, 368, 461, 475, 494, 557, 828
BstDSI CCRYGG 2 cut(s) 92, 532
BstENI CCTNNNNNAGG 1 cut(s) 261
BstH2I RGCGCY 2 cut(s) 34, 155
BstHHI GCGC 2 cut(s) 33, 154
BstKTI GATC 7 cut(s) 244, 284, 314, 549, 662, 868, 909
BstMAI GTCTC 3 cut(s) 216, 490, 718
BstMBI GATC 7 cut(s) 241, 281, 311, 546, 659, 865, 906
BstNI CCWGG 2 cut(s) 349, 576
BstSLI GKGCMC 1 cut(s) 849
BstV1I GCAGC 8 cut(s) 40, 102, 146, 161, 493, 682, 846, 847
BstX2I RGATCY 3 cut(s) 281, 311, 546
BstYI RGATCY 3 cut(s) 281, 311, 546
Bsu36I CCTNAGG 1 cut(s) 15
BsuRI GGCC 8 cut(s) 47, 269, 292, 300, 482, 518, 603, 921
BtgI CCRYGG 2 cut(s) 92, 532
BtrI CACGTC 1 cut(s) 406
BtsI GCAGTG 1 cut(s) 214
BtsIMutI CAGTG 3 cut(s) 214, 483, 491
BveI ACCTGC 1 cut(s) 589
Cac8I GCNNGC 4 cut(s) 49, 394, 458, 622
CaiI CAGNNNCTG 1 cut(s) 581
CfoI GCGC 2 cut(s) 33, 154
Cfr10I RCCGGY 1 cut(s) 392
Cfr13I GGNCC 8 cut(s) 127, 267, 291, 516, 578, 677, 824, 920
Cfr9I CCCGGG 3 cut(s) 512, 590, 842
CseI GACGC 2 cut(s) 428, 944
Csp6I GTAC 1 cut(s) 76
CviAII CATG 6 cut(s) 24, 72, 181, 533, 779, 932
CviQI GTAC 1 cut(s) 76
DdeI CTNAG 7 cut(s) 15, 368, 461, 475, 494, 557, 828
DpnI GATC 7 cut(s) 243, 283, 313, 548, 661, 867, 908
DpnII GATC 7 cut(s) 241, 281, 311, 546, 659, 865, 906
EaeI YGGCCR 2 cut(s) 45, 480
Eam1104I CTCTTC 1 cut(s) 246
EarI CTCTTC 1 cut(s) 246
EciI GGCGGA 3 cut(s) 425, 576, 867
Eco130I CCWWGG 2 cut(s) 36, 532
Eco147I AGGCCT 1 cut(s) 603
Eco47I GGWCC 4 cut(s) 127, 578, 677, 824
Eco47III AGCGCT 1 cut(s) 153
Eco72I CACGTG 1 cut(s) 379
Eco81I CCTNAGG 1 cut(s) 15
Eco88I CYCGRG 6 cut(s) 170, 294, 512, 590, 842, 926
EcoNI CCTNNNNNAGG 1 cut(s) 261
EcoO109I RGGNCCY 2 cut(s) 291, 578
EcoRII CCWGG 2 cut(s) 347, 574
EcoT14I CCWWGG 2 cut(s) 36, 532
ErhI CCWWGG 2 cut(s) 36, 532
Esp3I CGTCTC 1 cut(s) 216
FaeI CATG 6 cut(s) 27, 75, 184, 536, 782, 935
FalI AAGNNNNNCTT 1 cut(s) 949
FaqI GGGAC 2 cut(s) 365, 538
FatI CATG 6 cut(s) 23, 71, 180, 532, 778, 931
FauI CCCGC 2 cut(s) 458, 511
FblI GTMKAC 2 cut(s) 596, 612
FspBI CTAG 1 cut(s) 617
GlaI GCGC 2 cut(s) 32, 153
GsaI CCCAGC 1 cut(s) 113
GsuI CTGGAG 1 cut(s) 825
HaeII RGCGCY 2 cut(s) 34, 155
HaeIII GGCC 8 cut(s) 47, 269, 292, 300, 482, 518, 603, 921
HapII CCGG 7 cut(s) 119, 131, 309, 393, 513, 591, 843
HgaI GACGC 2 cut(s) 428, 944
HhaI GCGC 2 cut(s) 33, 154
Hin1I GRCGYC 1 cut(s) 439
Hin1II CATG 6 cut(s) 27, 75, 184, 536, 782, 935
Hin6I GCGC 2 cut(s) 31, 152
HinP1I GCGC 2 cut(s) 31, 152
HincII GTYRAC 1 cut(s) 597
HindII GTYRAC 1 cut(s) 597
HinfI GANTC 3 cut(s) 41, 88, 949
HpaII CCGG 7 cut(s) 119, 131, 309, 393, 513, 591, 843
HphI GGTGA 1 cut(s) 135
Hpy166II GTNNAC 3 cut(s) 78, 597, 613
Hpy188I TCNGA 3 cut(s) 68, 444, 906
Hpy188III TCNNGA 8 cut(s) 172, 274, 285, 343, 544, 734, 789, 957
Hpy8I GTNNAC 3 cut(s) 78, 597, 613
Hpy99I CGWCG 5 cut(s) 230, 233, 275, 874, 877
HpyAV CCTTC 3 cut(s) 257, 282, 531
HpyCH4III ACNGT 2 cut(s) 610, 890
HpyCH4IV ACGT 3 cut(s) 378, 405, 486
HpyCH4V TGCA 1 cut(s) 835
HpyF3I CTNAG 7 cut(s) 15, 368, 461, 475, 494, 557, 828
HpySE526I ACGT 3 cut(s) 378, 405, 486
Hsp92I GRCGYC 1 cut(s) 439
Hsp92II CATG 6 cut(s) 27, 75, 184, 536, 782, 935
HspAI GCGC 2 cut(s) 31, 152
KroI GCCGGC 1 cut(s) 392
KroNI GCCGGC 1 cut(s) 394
Kzo9I GATC 7 cut(s) 241, 281, 311, 546, 659, 865, 906
LguI GCTCTTC 1 cut(s) 246
LmnI GCTCC 6 cut(s) 99, 563, 589, 782, 800, 882
Lsp1109I GCAGC 8 cut(s) 40, 102, 146, 161, 493, 682, 846, 847
MaeI CTAG 1 cut(s) 617
MaeII ACGT 3 cut(s) 378, 405, 486
MaeIII GTNAC 2 cut(s) 343, 487
MalI GATC 7 cut(s) 243, 283, 313, 548, 661, 867, 908
MbiI CCGCTC 2 cut(s) 102, 561
MboI GATC 7 cut(s) 241, 281, 311, 546, 659, 865, 906
MboII GAAGA 4 cut(s) 245, 263, 331, 752
MflI RGATCY 3 cut(s) 281, 311, 546
MhlI GDGCHC 2 cut(s) 462, 849
MlsI TGGCCA 1 cut(s) 482
MluCI AATT 2 cut(s) 139, 425
MluNI TGGCCA 1 cut(s) 482
MlyI GAGTC 1 cut(s) 943
MmeI TCCRAC 2 cut(s) 637, 790
MnlI CCTC 9 cut(s) 290, 315, 429, 440, 730, 741, 742, 767, 837
Mox20I TGGCCA 1 cut(s) 482
MroNI GCCGGC 1 cut(s) 392
MscI TGGCCA 1 cut(s) 482
MslI CAYNNNNRTG 1 cut(s) 341
Msp20I TGGCCA 1 cut(s) 482
MspA1I CMGCKG 5 cut(s) 109, 195, 465, 506, 859
MspI CCGG 7 cut(s) 119, 131, 309, 393, 513, 591, 843
MvaI CCWGG 2 cut(s) 349, 576
NaeI GCCGGC 1 cut(s) 394
NciI CCSGG 9 cut(s) 120, 131, 309, 513, 514, 591, 592, 843, 844
NcoI CCATGG 1 cut(s) 532
NdeII GATC 7 cut(s) 241, 281, 311, 546, 659, 865, 906
NgoMIV GCCGGC 1 cut(s) 392
NlaIII CATG 6 cut(s) 27, 75, 184, 536, 782, 935
NlaIV GGNNCC 5 cut(s) 129, 268, 293, 313, 517
NmuCI GTSAC 2 cut(s) 343, 487
PaeR7I CTCGAG 1 cut(s) 170
PceI AGGCCT 1 cut(s) 603
PciSI GCTCTTC 1 cut(s) 246
PcsI WCGNNNNNNNCGW 1 cut(s) 292
PdiI GCCGGC 1 cut(s) 394
PfeI GAWTC 2 cut(s) 41, 88
PflMI CCANNNNNTGG 1 cut(s) 382
PfoI TCCNGGA 1 cut(s) 307
PleI GAGTC 1 cut(s) 943
PmaCI CACGTG 1 cut(s) 379
PmlI CACGTG 1 cut(s) 379
PpsI GAGTC 1 cut(s) 943
Ppu21I YACGTR 1 cut(s) 379
PpuMI RGGWCCY 1 cut(s) 578
Psp5II RGGWCCY 1 cut(s) 578
Psp6I CCWGG 2 cut(s) 347, 574
PspCI CACGTG 1 cut(s) 379
PspFI CCCAGC 1 cut(s) 109
PspGI CCWGG 2 cut(s) 347, 574
PspN4I GGNNCC 5 cut(s) 129, 268, 293, 313, 517
PspPI GGNCC 8 cut(s) 127, 267, 291, 516, 578, 677, 824, 920
PspPPI RGGWCCY 1 cut(s) 578
PstNI CAGNNNCTG 1 cut(s) 581
PsuI RGATCY 3 cut(s) 281, 311, 546
PvuII CAGCTG 2 cut(s) 109, 859
RsaI GTAC 1 cut(s) 77
RsaNI GTAC 1 cut(s) 76
RseI CAYNNNNRTG 1 cut(s) 341
SalI GTCGAC 1 cut(s) 595
SapI GCTCTTC 1 cut(s) 246
Sau3AI GATC 7 cut(s) 241, 281, 311, 546, 659, 865, 906
Sau96I GGNCC 8 cut(s) 127, 267, 291, 516, 578, 677, 824, 920
SchI GAGTC 1 cut(s) 943
SduI GDGCHC 2 cut(s) 462, 849
Sfr274I CTCGAG 1 cut(s) 170
SinI GGWCC 4 cut(s) 127, 578, 677, 824
SlaI CTCGAG 1 cut(s) 170
SmaI CCCGGG 3 cut(s) 514, 592, 844
SmiMI CAYNNNNRTG 1 cut(s) 341
SmlI CTYRAG 2 cut(s) 170, 734
SmoI CTYRAG 2 cut(s) 170, 734
Sse9I AATT 2 cut(s) 139, 425
SseBI AGGCCT 1 cut(s) 603
SspMI CTAG 1 cut(s) 617
StuI AGGCCT 1 cut(s) 603
StyI CCWWGG 2 cut(s) 36, 532
TaaI ACNGT 2 cut(s) 610, 890
TaiI ACGT 3 cut(s) 381, 408, 489
TaqI TCGA 5 cut(s) 171, 273, 286, 543, 596
TasI AATT 2 cut(s) 139, 425
TauI GCSGC 5 cut(s) 198, 201, 303, 674, 921
TfiI GAWTC 2 cut(s) 41, 88
TscAI CASTG 3 cut(s) 214, 483, 498
TseFI GTSAC 2 cut(s) 343, 487
TseI GCWGC 8 cut(s) 28, 115, 134, 149, 506, 695, 835, 859
Tsp45I GTSAC 2 cut(s) 343, 487
TspDTI ATGAA 1 cut(s) 197
TspGWI ACGGA 3 cut(s) 81, 448, 858
TspMI CCCGGG 3 cut(s) 512, 590, 842
TspRI CASTG 3 cut(s) 214, 483, 498
Van91I CCANNNNNTGG 1 cut(s) 382
VpaK11BI GGWCC 4 cut(s) 127, 578, 677, 824
XagI CCTNNNNNAGG 1 cut(s) 261
XhoI CTCGAG 1 cut(s) 170
XmaI CCCGGG 3 cut(s) 512, 590, 842
XmiI GTMKAC 2 cut(s) 596, 612
XspI CTAG 1 cut(s) 617
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.