Rh4AG036500

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
Chr4A
OG0004329
Physical Location & Seq
Reverse (-)
7945845 .. 7949127
3283 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh4AG036500.1

Sequence Viewer

Length: 849 bp
ATGGACCCGGCAGCCAATTCACCAGCAGCGCTAAACAAGCGAGAACTCGAGATTTCCATGAACGAAAACAGCGGCGGCAGAAGCAGTGGCGGTGGCAGAGACGACGACGAAGATAGAGATCAAGGAGAAGAGCCTAAAGAAGGGGCCGTCGAGATTGGATCTCGAAGGCCCCGAGGCCGCCCTCCCGGATCCAAAAACAAACCCAAACCGCCCATCTTCGTGACCAGGGACAGCCCCAACTCCCTTAGAAGCCACGTGATGGAAGTTGCCGGCGGTGCTGACGTGGCGGAGAGCGTGGCACAATTCGCACGGAGGCGTCAGAGAGGTGTTTGCGTGCTCAGCGGGAGTGGCTCAGTGGCCAACGTGACACTGAGACAACCCGCTGCCCCCGGGGCCGTTGTAGCACTCCATGGAAGGTTCGAGATCCTGTCCCTGAGCGGAGCGTTTCTGCCAGGACCTGCTCCGCCCGGGTCGACAGGCCTGACCGTCTACCTAGCAGGCGGTCAGGGTCAGGTGGTTGGGGGAAGCGTTGTTGGATCACTTGTTGCGGCTGGACCAGTTATGGTTGTGGCTGCTACTTTTGCTAATGCTACTTATGAGAGACTGCCTCTTGAGGAAGATGATGAGGCTGGAAGCGGTGGTGGTGGTGGAGGTCATGGAGCTTCTGGAAGCTCCCCTACTGGAGTTGGAAGTAGTGGCGGTCCTCAGTTGCAGCCACCCGGGCACGGCGGACAGCTGCCTGATCCGTCGTCGCTCCCCCTTTACGGTCTGCCACCCAATCTGATCCCCAACGGCGGCCCACTCGGGCATGACGCTTATGCTTGGACTCATTCAAGACCGCCTTACTAA
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

282

Amino Acids

28.38

Weight (kDa)

5.88

Isoelectric Point (pI)

57.58

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PCC PF03479 83 - 195 1.2e-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) 466
AccB7I CCANNNNNTGG 1 cut(s) 259
AccBSI CCGCTC 1 cut(s) 438
AccI GTMKAC 2 cut(s) 473, 489
AclWI GGATC 7 cut(s) 166, 183, 196, 418, 544, 737, 778
AcoI YGGCCR 1 cut(s) 357
AcvI CACGTG 1 cut(s) 256
AcyI GRCGYC 1 cut(s) 316
AfeI AGCGCT 1 cut(s) 30
AfiI CCNNNNNNNGG 5 cut(s) 140, 259, 725, 764, 794
AgsI TTSAA 1 cut(s) 834
AjiI CACGTC 1 cut(s) 283
AjnI CCWGG 2 cut(s) 224, 451
AluBI AGCT 3 cut(s) 662, 672, 736
AluI AGCT 3 cut(s) 662, 672, 736
Alw21I GWGCWC 1 cut(s) 339
Alw26I GTCTC 3 cut(s) 93, 367, 595
AlwI GGATC 7 cut(s) 166, 183, 196, 418, 544, 737, 778
AlwNI CAGNNNCTG 1 cut(s) 458
Ama87I CYCGRG 6 cut(s) 47, 171, 389, 467, 719, 803
Aor51HI AGCGCT 1 cut(s) 30
AoxI GGCC 7 cut(s) 144, 167, 175, 357, 393, 478, 796
ApeKI GCWGC 6 cut(s) 11, 26, 383, 572, 712, 736
AspLEI GCGC 1 cut(s) 31
AspS9I GGNCC 8 cut(s) 4, 144, 168, 393, 455, 554, 701, 797
AsuC2I CCSGG 8 cut(s) 8, 186, 390, 391, 468, 469, 720, 721
AsuHPI GGTGA 1 cut(s) 12
AvaI CYCGRG 6 cut(s) 47, 171, 389, 467, 719, 803
AvaII GGWCC 4 cut(s) 4, 455, 554, 701
BaeGI GKGCMC 1 cut(s) 726
BalI TGGCCA 1 cut(s) 359
BamHI GGATCC 1 cut(s) 188
BarI GAAGNNNNNNTAC 2 cut(s) 661, 693
BbrPI CACGTG 1 cut(s) 256
Bbv12I GWGCWC 1 cut(s) 339
BbvI GCAGC 6 cut(s) 23, 38, 370, 559, 723, 724
BccI CCATC 2 cut(s) 221, 253
BceAI ACGGC 4 cut(s) 131, 380, 742, 808
BciT130I CCWGG 2 cut(s) 226, 453
BcnI CCSGG 8 cut(s) 8, 186, 390, 391, 468, 469, 720, 721
BcoDI GTCTC 3 cut(s) 93, 367, 595
BfaI CTAG 1 cut(s) 494
BfoI RGCGCY 1 cut(s) 32
BfuAI ACCTGC 1 cut(s) 466
BglI GCCNNNNNGGC 2 cut(s) 392, 721
BlpI GCTNAGC 1 cut(s) 338
Bme18I GGWCC 4 cut(s) 4, 455, 554, 701
BmeT110I CYCGRG 6 cut(s) 47, 171, 389, 467, 719, 803
BmgBI CACGTC 1 cut(s) 283
BmgT120I GGNCC 8 cut(s) 4, 144, 168, 393, 455, 554, 701, 797
BmiI GGNNCC 5 cut(s) 6, 145, 170, 190, 394
BplI GAGNNNNNCTC 2 cut(s) 592, 624
BpmI CTGGAG 1 cut(s) 702
Bpu10I CCTNAGC 1 cut(s) 434
Bpu1102I GCTNAGC 1 cut(s) 338
BpuEI CTTGAG 1 cut(s) 632
BpuMI CCSGG 8 cut(s) 8, 186, 390, 391, 468, 469, 720, 721
BsaAI YACGTR 1 cut(s) 256
BsaBI GATNNNNATC 1 cut(s) 117
BsaHI GRCGYC 1 cut(s) 316
BsaJI CCNNGG 8 cut(s) 172, 225, 388, 389, 390, 409, 467, 719
Bsc4I CCNNNNNNNGG 5 cut(s) 140, 259, 725, 764, 794
Bse118I RCCGGY 1 cut(s) 269
Bse1I ACTGG 2 cut(s) 557, 685
Bse8I GATNNNNATC 1 cut(s) 117
BseBI CCWGG 2 cut(s) 226, 453
BseDI CCNNGG 8 cut(s) 172, 225, 388, 389, 390, 409, 467, 719
BseJI GATNNNNATC 1 cut(s) 117
BseLI CCNNNNNNNGG 5 cut(s) 140, 259, 725, 764, 794
BseMII CTCAG 5 cut(s) 352, 362, 366, 425, 719
BseNI ACTGG 2 cut(s) 557, 685
BseSI GKGCMC 1 cut(s) 726
BseXI GCAGC 6 cut(s) 23, 38, 370, 559, 723, 724
BshFI GGCC 7 cut(s) 146, 169, 177, 359, 395, 480, 798
BsiHKAI GWGCWC 1 cut(s) 339
BsiHKCI CYCGRG 6 cut(s) 47, 171, 389, 467, 719, 803
BsiSI CCGG 6 cut(s) 8, 186, 270, 390, 468, 720
BslFI GGGAC 2 cut(s) 242, 415
BslI CCNNNNNNNGG 5 cut(s) 140, 259, 725, 764, 794
BsmAI GTCTC 3 cut(s) 93, 367, 595
BsmBI CGTCTC 1 cut(s) 93
BsmFI GGGAC 2 cut(s) 242, 415
BsnI GGCC 7 cut(s) 146, 169, 177, 359, 395, 480, 798
BsoBI CYCGRG 6 cut(s) 47, 171, 389, 467, 719, 803
Bsp1286I GDGCHC 2 cut(s) 339, 726
Bsp143I GATC 7 cut(s) 118, 158, 188, 423, 536, 742, 783
Bsp1720I GCTNAGC 1 cut(s) 338
Bsp19I CCATGG 1 cut(s) 409
BspANI GGCC 7 cut(s) 146, 169, 177, 359, 395, 480, 798
BspCNI CTCAG 5 cut(s) 351, 363, 365, 426, 718
BspLI GGNNCC 5 cut(s) 6, 145, 170, 190, 394
BspMI ACCTGC 1 cut(s) 466
BspPI GGATC 7 cut(s) 166, 183, 196, 418, 544, 737, 778
BspQI GCTCTTC 1 cut(s) 123
BsrBI CCGCTC 1 cut(s) 438
BsrFI RCCGGY 1 cut(s) 269
BsrI ACTGG 2 cut(s) 557, 685
BssAI RCCGGY 1 cut(s) 269
BssECI CCNNGG 8 cut(s) 172, 225, 388, 389, 390, 409, 467, 719
BssMI GATC 7 cut(s) 118, 158, 188, 423, 536, 742, 783
BssNI GRCGYC 1 cut(s) 316
BssT1I CCWWGG 1 cut(s) 409
Bst2UI CCWGG 2 cut(s) 226, 453
Bst4CI ACNGT 2 cut(s) 487, 767
Bst6I CTCTTC 1 cut(s) 123
BstACI GRCGYC 1 cut(s) 316
BstBAI YACGTR 1 cut(s) 256
BstC8I GCNNGC 3 cut(s) 271, 335, 499
BstDEI CTNAG 6 cut(s) 245, 338, 352, 371, 434, 705
BstDSI CCRYGG 1 cut(s) 409
BstENI CCTNNNNNAGG 1 cut(s) 138
BstH2I RGCGCY 1 cut(s) 32
BstHHI GCGC 1 cut(s) 31
BstKTI GATC 7 cut(s) 121, 161, 191, 426, 539, 745, 786
BstMAI GTCTC 3 cut(s) 93, 367, 595
BstMBI GATC 7 cut(s) 118, 158, 188, 423, 536, 742, 783
BstNI CCWGG 2 cut(s) 226, 453
BstSLI GKGCMC 1 cut(s) 726
BstV1I GCAGC 6 cut(s) 23, 38, 370, 559, 723, 724
BstX2I RGATCY 3 cut(s) 158, 188, 423
BstYI RGATCY 3 cut(s) 158, 188, 423
BsuRI GGCC 7 cut(s) 146, 169, 177, 359, 395, 480, 798
BtgI CCRYGG 1 cut(s) 409
BtrI CACGTC 1 cut(s) 283
BtsI GCAGTG 1 cut(s) 91
BtsIMutI CAGTG 3 cut(s) 91, 360, 368
BveI ACCTGC 1 cut(s) 466
Cac8I GCNNGC 3 cut(s) 271, 335, 499
CaiI CAGNNNCTG 1 cut(s) 458
CfoI GCGC 1 cut(s) 31
Cfr10I RCCGGY 1 cut(s) 269
Cfr13I GGNCC 8 cut(s) 4, 144, 168, 393, 455, 554, 701, 797
Cfr9I CCCGGG 3 cut(s) 389, 467, 719
CseI GACGC 2 cut(s) 305, 821
CviAII CATG 4 cut(s) 58, 410, 656, 809
DdeI CTNAG 6 cut(s) 245, 338, 352, 371, 434, 705
DpnI GATC 7 cut(s) 120, 160, 190, 425, 538, 744, 785
DpnII GATC 7 cut(s) 118, 158, 188, 423, 536, 742, 783
EaeI YGGCCR 1 cut(s) 357
Eam1104I CTCTTC 1 cut(s) 123
EarI CTCTTC 1 cut(s) 123
EciI GGCGGA 3 cut(s) 302, 453, 744
Eco130I CCWWGG 1 cut(s) 409
Eco147I AGGCCT 1 cut(s) 480
Eco47I GGWCC 4 cut(s) 4, 455, 554, 701
Eco47III AGCGCT 1 cut(s) 30
Eco72I CACGTG 1 cut(s) 256
Eco88I CYCGRG 6 cut(s) 47, 171, 389, 467, 719, 803
EcoNI CCTNNNNNAGG 1 cut(s) 138
EcoO109I RGGNCCY 2 cut(s) 168, 455
EcoRII CCWGG 2 cut(s) 224, 451
EcoT14I CCWWGG 1 cut(s) 409
ErhI CCWWGG 1 cut(s) 409
Esp3I CGTCTC 1 cut(s) 93
FaeI CATG 4 cut(s) 61, 413, 659, 812
FaiI YATR 7 cut(s) 59, 411, 563, 597, 657, 810, 819
FalI AAGNNNNNCTT 1 cut(s) 826
FaqI GGGAC 2 cut(s) 242, 415
FatI CATG 4 cut(s) 57, 409, 655, 808
FauI CCCGC 2 cut(s) 335, 388
FblI GTMKAC 2 cut(s) 473, 489
FspBI CTAG 1 cut(s) 494
GlaI GCGC 1 cut(s) 30
GsuI CTGGAG 1 cut(s) 702
HaeII RGCGCY 1 cut(s) 32
HaeIII GGCC 7 cut(s) 146, 169, 177, 359, 395, 480, 798
HapII CCGG 6 cut(s) 8, 186, 270, 390, 468, 720
HgaI GACGC 2 cut(s) 305, 821
HhaI GCGC 1 cut(s) 31
Hin1I GRCGYC 1 cut(s) 316
Hin1II CATG 4 cut(s) 61, 413, 659, 812
Hin6I GCGC 1 cut(s) 29
HinP1I GCGC 1 cut(s) 29
HincII GTYRAC 1 cut(s) 474
HindII GTYRAC 1 cut(s) 474
HinfI GANTC 1 cut(s) 826
HpaII CCGG 6 cut(s) 8, 186, 270, 390, 468, 720
HphI GGTGA 1 cut(s) 12
Hpy166II GTNNAC 2 cut(s) 474, 490
Hpy188I TCNGA 2 cut(s) 321, 783
Hpy188III TCNNGA 8 cut(s) 49, 151, 162, 220, 421, 611, 666, 834
Hpy8I GTNNAC 2 cut(s) 474, 490
Hpy99I CGWCG 5 cut(s) 107, 110, 152, 751, 754
HpyAV CCTTC 3 cut(s) 134, 159, 408
HpyCH4III ACNGT 2 cut(s) 487, 767
HpyCH4IV ACGT 3 cut(s) 255, 282, 363
HpyCH4V TGCA 1 cut(s) 712
HpyF3I CTNAG 6 cut(s) 245, 338, 352, 371, 434, 705
HpySE526I ACGT 3 cut(s) 255, 282, 363
Hsp92I GRCGYC 1 cut(s) 316
Hsp92II CATG 4 cut(s) 61, 413, 659, 812
HspAI GCGC 1 cut(s) 29
KroI GCCGGC 1 cut(s) 269
KroNI GCCGGC 1 cut(s) 271
Kzo9I GATC 7 cut(s) 118, 158, 188, 423, 536, 742, 783
LguI GCTCTTC 1 cut(s) 123
LmnI GCTCC 5 cut(s) 440, 466, 659, 677, 759
Lsp1109I GCAGC 6 cut(s) 23, 38, 370, 559, 723, 724
MaeI CTAG 1 cut(s) 494
MaeII ACGT 3 cut(s) 255, 282, 363
MaeIII GTNAC 2 cut(s) 220, 364
MalI GATC 7 cut(s) 120, 160, 190, 425, 538, 744, 785
MbiI CCGCTC 1 cut(s) 438
MboI GATC 7 cut(s) 118, 158, 188, 423, 536, 742, 783
MboII GAAGA 4 cut(s) 122, 140, 208, 629
MflI RGATCY 3 cut(s) 158, 188, 423
MhlI GDGCHC 2 cut(s) 339, 726
MlsI TGGCCA 1 cut(s) 359
MluCI AATT 2 cut(s) 16, 302
MluNI TGGCCA 1 cut(s) 359
MlyI GAGTC 1 cut(s) 820
MmeI TCCRAC 2 cut(s) 514, 667
MnlI CCTC 9 cut(s) 167, 192, 306, 317, 607, 618, 619, 644, 714
Mox20I TGGCCA 1 cut(s) 359
MroNI GCCGGC 1 cut(s) 269
MscI TGGCCA 1 cut(s) 359
MslI CAYNNNNRTG 1 cut(s) 218
Msp20I TGGCCA 1 cut(s) 359
MspA1I CMGCKG 4 cut(s) 72, 342, 383, 736
MspI CCGG 6 cut(s) 8, 186, 270, 390, 468, 720
MvaI CCWGG 2 cut(s) 226, 453
NaeI GCCGGC 1 cut(s) 271
NciI CCSGG 8 cut(s) 8, 186, 390, 391, 468, 469, 720, 721
NcoI CCATGG 1 cut(s) 409
NdeII GATC 7 cut(s) 118, 158, 188, 423, 536, 742, 783
NgoMIV GCCGGC 1 cut(s) 269
NlaIII CATG 4 cut(s) 61, 413, 659, 812
NlaIV GGNNCC 5 cut(s) 6, 145, 170, 190, 394
NmuCI GTSAC 2 cut(s) 220, 364
PaeR7I CTCGAG 1 cut(s) 47
PceI AGGCCT 1 cut(s) 480
PciSI GCTCTTC 1 cut(s) 123
PcsI WCGNNNNNNNCGW 1 cut(s) 169
PdiI GCCGGC 1 cut(s) 271
PflMI CCANNNNNTGG 1 cut(s) 259
PfoI TCCNGGA 1 cut(s) 184
PleI GAGTC 1 cut(s) 820
PmaCI CACGTG 1 cut(s) 256
PmlI CACGTG 1 cut(s) 256
PpsI GAGTC 1 cut(s) 820
Ppu21I YACGTR 1 cut(s) 256
PpuMI RGGWCCY 1 cut(s) 455
Psp5II RGGWCCY 1 cut(s) 455
Psp6I CCWGG 2 cut(s) 224, 451
PspCI CACGTG 1 cut(s) 256
PspGI CCWGG 2 cut(s) 224, 451
PspN4I GGNNCC 5 cut(s) 6, 145, 170, 190, 394
PspPI GGNCC 8 cut(s) 4, 144, 168, 393, 455, 554, 701, 797
PspPPI RGGWCCY 1 cut(s) 455
PstNI CAGNNNCTG 1 cut(s) 458
PsuI RGATCY 3 cut(s) 158, 188, 423
PvuII CAGCTG 1 cut(s) 736
RseI CAYNNNNRTG 1 cut(s) 218
SalI GTCGAC 1 cut(s) 472
SapI GCTCTTC 1 cut(s) 123
Sau3AI GATC 7 cut(s) 118, 158, 188, 423, 536, 742, 783
Sau96I GGNCC 8 cut(s) 4, 144, 168, 393, 455, 554, 701, 797
SchI GAGTC 1 cut(s) 820
SduI GDGCHC 2 cut(s) 339, 726
Sfr274I CTCGAG 1 cut(s) 47
SinI GGWCC 4 cut(s) 4, 455, 554, 701
SlaI CTCGAG 1 cut(s) 47
SmaI CCCGGG 3 cut(s) 391, 469, 721
SmiMI CAYNNNNRTG 1 cut(s) 218
SmlI CTYRAG 2 cut(s) 47, 611
SmoI CTYRAG 2 cut(s) 47, 611
Sse9I AATT 2 cut(s) 16, 302
SseBI AGGCCT 1 cut(s) 480
SspMI CTAG 1 cut(s) 494
StuI AGGCCT 1 cut(s) 480
StyI CCWWGG 1 cut(s) 409
TaaI ACNGT 2 cut(s) 487, 767
TaiI ACGT 3 cut(s) 258, 285, 366
TaqI TCGA 5 cut(s) 48, 150, 163, 420, 473
TasI AATT 2 cut(s) 16, 302
TauI GCSGC 5 cut(s) 75, 78, 180, 551, 798
TscAI CASTG 3 cut(s) 91, 360, 375
TseFI GTSAC 2 cut(s) 220, 364
TseI GCWGC 6 cut(s) 11, 26, 383, 572, 712, 736
Tsp45I GTSAC 2 cut(s) 220, 364
TspDTI ATGAA 1 cut(s) 74
TspGWI ACGGA 2 cut(s) 325, 735
TspMI CCCGGG 3 cut(s) 389, 467, 719
TspRI CASTG 3 cut(s) 91, 360, 375
Van91I CCANNNNNTGG 1 cut(s) 259
VpaK11BI GGWCC 4 cut(s) 4, 455, 554, 701
XagI CCTNNNNNAGG 1 cut(s) 138
XhoI CTCGAG 1 cut(s) 47
XmaI CCCGGG 3 cut(s) 389, 467, 719
XmiI GTMKAC 2 cut(s) 473, 489
XspI CTAG 1 cut(s) 494
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.