Rroxscaffold_3G00242760

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
OG0014937
Physical Location & Seq
Reverse (-)
35236741 .. 35237670
930 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_3G00242760.1

Sequence Viewer

Length: 930 bp
ATGGCGGGGTACAATGGCAGATCAGAATATATGCAACTCTTCCGTCCCGAACTGCACCTCCAGAGACCACCGTCACCATCCATCTCTGTTCCGCCGCAGCAACAACAACCTCAACCTTCTTCCGATTCTCAACAGCAAGAAGACTCGCCCGAAGGAGACCAAGAACACAAGATCGAGTCCGACACCGCTGCCACAAGTTCCGGAGGCGGCGGTGGCGGTAGCGGTGGGGGTTCAGGACGTCGTCCGCGGGGGCGTCCGGCGGGGTCAAAGAACAAGCCGAAGCCGCCGATCATCGTGACGCGCGACAGCCCCAACGCCCTCCGCTCGCACGTGCTGGAGGTCTCTGCCGGGACCGACGTGGTGGAGAGCGTGTCCCACTATGCGAGGCGGAGGGGGAGGGGAGTGTGCGTGCTCAGCGGCACCGGCACCGTCGCTAACGTCACCCTGCGTCAGCCGGCGGCGCCCGTGGGGAGCGTGGTCACTCTCCACGGGAGGTTCGAGATACTTTCGCTCTCGGGGACCGTGCTTCCGCCTCCGGCCCCGCCGGGCGCAGGGGGACTGTCGATTTTCCTGGCGGGCGGGCAGGGTCAGGTGGTTGGGGGCAGCGTGGTGGGCCCACTGCTGGCTTCGGGTCCGGTTGTTTTGATGGCTGCGTCGTTTGCGAATGCGGTGTTTGAGAGGCTGCCATTGGAGGAGGAAGAGGCAGCGGGCGGTGGTGGGTTACAAGTCCAGCAACCGACGGCTTCACAATCTTCAGGAGTGACAGGTGGTGGTGGTGGAGGACAACATCAGCAGCTTGGTGAGGGAAGCAGCAGCGGTCTCTTCAATCTGGGAGGGAACATGGGGGCGGGGAGCTATCCGGCGTTTTCGGGAACTGATTTGTATGGGTGGGGTAGCGGCGGAGCCACTCATCCGCGGCCTCCGTTTTAG
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

309

Amino Acids

31.11

Weight (kDa)

6.66

Isoelectric Point (pI)

73.59

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PCC PF03479 108 - 221 4.9e-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: OG0014937)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G20900 AT1G76500
fragaria_vesca FvH4_5g26230
malus_domestica MD06G1003000.v1.1
prunus_persica Prupe.5G004600_v2.0.a1
pyrus_communis pycom06g00310
rosa_chinensis RchiOBHm_Chr7g0216901
rosa_laevigata RLG00000002528
rosa_multiflora Rmu_sc0000854.1_g000020
rosa_roxburghii Rroxscaffold_3G00242760
rosa_rugosa Rorug07G0164300
rosa_samantha Rh7AG304600 Rh7BG296100 Rh7CG323000 Rh7DG304600
rosa_wichuraiana Rw7G025860

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AatII GACGTC 1 cut(s) 241
AccB1I GGYRCC 3 cut(s) 419, 425, 460
AccBSI CCGCTC 1 cut(s) 324
AccII CGCG 4 cut(s) 247, 301, 303, 916
AccIII TCCGGA 1 cut(s) 200
AcuI CTGAAG 1 cut(s) 738
AcvI CACGTG 1 cut(s) 331
AcyI GRCGYC 3 cut(s) 238, 253, 461
AfaI GTAC 1 cut(s) 11
AfiI CCNNNNNNNGG 2 cut(s) 551, 622
AgsI TTSAA 1 cut(s) 826
AjiI CACGTC 1 cut(s) 358
AjnI CCWGG 1 cut(s) 570
AloI GAACNNNNNNTCC 2 cut(s) 42, 74
AluBI AGCT 2 cut(s) 796, 855
AluI AGCT 2 cut(s) 796, 855
Alw21I GWGCWC 1 cut(s) 414
Alw26I GTCTC 4 cut(s) 58, 150, 346, 824
Ama87I CYCGRG 1 cut(s) 514
Aor13HI TCCGGA 1 cut(s) 200
AoxI GGCC 3 cut(s) 537, 613, 917
ApaI GGGCCC 1 cut(s) 617
ApeKI GCWGC 9 cut(s) 97, 188, 603, 650, 682, 704, 793, 810, 813
AspLEI GCGC 3 cut(s) 303, 463, 551
AspS9I GGNCC 6 cut(s) 351, 519, 538, 613, 614, 632
AsuC2I CCSGG 2 cut(s) 349, 546
AsuHPI GGTGA 3 cut(s) 66, 433, 812
AvaI CYCGRG 1 cut(s) 514
AvaII GGWCC 3 cut(s) 351, 519, 632
BaeGI GKGCMC 1 cut(s) 617
BanI GGYRCC 3 cut(s) 419, 425, 460
BanII GRGCYC 1 cut(s) 617
BbrPI CACGTG 1 cut(s) 331
BbsI GAAGAC 1 cut(s) 147
Bbv12I GWGCWC 1 cut(s) 414
BbvI GCAGC 9 cut(s) 109, 175, 615, 637, 669, 716, 805, 822, 825
BccI CCATC 3 cut(s) 85, 89, 640
BceAI ACGGC 1 cut(s) 756
BcgI CGANNNNNNTGC 2 cut(s) 170, 204
BciT130I CCWGG 1 cut(s) 572
BcnI CCSGG 2 cut(s) 349, 546
BcoDI GTCTC 4 cut(s) 58, 150, 346, 824
BfoI RGCGCY 1 cut(s) 464
BlpI GCTNAGC 1 cut(s) 413
Bme1390I CCNGG 3 cut(s) 349, 546, 572
Bme18I GGWCC 3 cut(s) 351, 519, 632
BmeT110I CYCGRG 1 cut(s) 514
BmgBI CACGTC 1 cut(s) 358
BmgT120I GGNCC 6 cut(s) 351, 519, 538, 613, 614, 632
BmiI GGNNCC 9 cut(s) 352, 421, 427, 462, 520, 540, 615, 633, 904
BmrFI CCNGG 3 cut(s) 349, 546, 572
BoxI GACNNNNGTC 1 cut(s) 70
BpiI GAAGAC 1 cut(s) 147
BpmI CTGGAG 2 cut(s) 44, 356
Bpu1102I GCTNAGC 1 cut(s) 413
BpuMI CCSGG 2 cut(s) 349, 546
BsaAI YACGTR 1 cut(s) 331
BsaHI GRCGYC 3 cut(s) 238, 253, 461
BsaI GGTCTC 4 cut(s) 58, 150, 346, 824
BsaJI CCNNGG 4 cut(s) 245, 465, 487, 914
BsaWI WCCGGW 2 cut(s) 200, 634
BsaXI ACNNNNNCTCC 6 cut(s) 42, 72, 356, 386, 393, 423
Bsc4I CCNNNNNNNGG 2 cut(s) 551, 622
Bse118I RCCGGY 2 cut(s) 422, 454
BseAI TCCGGA 1 cut(s) 200
BseBI CCWGG 1 cut(s) 572
BseDI CCNNGG 4 cut(s) 245, 465, 487, 914
BseGI GGATG 2 cut(s) 77, 910
BseLI CCNNNNNNNGG 2 cut(s) 551, 622
BseMII CTCAG 1 cut(s) 427
BseRI GAGGAG 1 cut(s) 707
BseSI GKGCMC 1 cut(s) 617
BseXI GCAGC 9 cut(s) 109, 175, 615, 637, 669, 716, 805, 822, 825
BsgI GTGCAG 1 cut(s) 38
Bsh1236I CGCG 4 cut(s) 247, 301, 303, 916
BshFI GGCC 3 cut(s) 539, 615, 919
BshNI GGYRCC 3 cut(s) 419, 425, 460
BsiHKAI GWGCWC 1 cut(s) 414
BsiHKCI CYCGRG 1 cut(s) 514
BsiSI CCGG 9 cut(s) 201, 257, 348, 423, 455, 536, 545, 635, 860
BslFI GGGAC 5 cut(s) 30, 358, 364, 532, 570
BslI CCNNNNNNNGG 2 cut(s) 551, 622
BsmAI GTCTC 4 cut(s) 58, 150, 346, 824
BsmFI GGGAC 5 cut(s) 30, 358, 364, 532, 570
BsmI GAATGC 1 cut(s) 670
BsnI GGCC 3 cut(s) 539, 615, 919
Bso31I GGTCTC 4 cut(s) 58, 150, 346, 824
BsoBI CYCGRG 1 cut(s) 514
Bsp120I GGGCCC 1 cut(s) 613
Bsp1286I GDGCHC 2 cut(s) 414, 617
Bsp13I TCCGGA 1 cut(s) 200
Bsp143I GATC 3 cut(s) 20, 171, 288
Bsp1720I GCTNAGC 1 cut(s) 413
BspANI GGCC 3 cut(s) 539, 615, 919
BspCNI CTCAG 1 cut(s) 426
BspEI TCCGGA 1 cut(s) 200
BspFNI CGCG 4 cut(s) 247, 301, 303, 916
BspLI GGNNCC 9 cut(s) 352, 421, 427, 462, 520, 540, 615, 633, 904
BspT107I GGYRCC 3 cut(s) 419, 425, 460
BspTNI GGTCTC 4 cut(s) 58, 150, 346, 824
BsrBI CCGCTC 1 cut(s) 324
BsrFI RCCGGY 2 cut(s) 422, 454
BssAI RCCGGY 2 cut(s) 422, 454
BssECI CCNNGG 4 cut(s) 245, 465, 487, 914
BssMI GATC 3 cut(s) 20, 171, 288
BssNI GRCGYC 3 cut(s) 238, 253, 461
Bst2UI CCWGG 1 cut(s) 572
Bst4CI ACNGT 4 cut(s) 72, 430, 523, 561
Bst6I CTCTTC 3 cut(s) 44, 693, 827
BstACI GRCGYC 3 cut(s) 238, 253, 461
BstBAI YACGTR 1 cut(s) 331
BstC8I GCNNGC 7 cut(s) 326, 410, 456, 577, 581, 624, 709
BstDEI CTNAG 1 cut(s) 413
BstDSI CCRYGG 4 cut(s) 245, 465, 487, 914
BstF5I GGATG 2 cut(s) 77, 910
BstFNI CGCG 4 cut(s) 247, 301, 303, 916
BstH2I RGCGCY 1 cut(s) 464
BstHHI GCGC 3 cut(s) 303, 463, 551
BstKTI GATC 3 cut(s) 23, 174, 291
BstMAI GTCTC 4 cut(s) 58, 150, 346, 824
BstMBI GATC 3 cut(s) 20, 171, 288
BstMWI GCNNNNNNNGC 7 cut(s) 213, 283, 414, 423, 460, 612, 659
BstNI CCWGG 1 cut(s) 572
BstPAI GACNNNNGTC 1 cut(s) 70
BstSCI CCNGG 3 cut(s) 347, 544, 570
BstSLI GKGCMC 1 cut(s) 617
BstUI CGCG 4 cut(s) 247, 301, 303, 916
BstV1I GCAGC 9 cut(s) 109, 175, 615, 637, 669, 716, 805, 822, 825
BstV2I GAAGAC 1 cut(s) 147
BsuRI GGCC 3 cut(s) 539, 615, 919
BtgI CCRYGG 4 cut(s) 245, 465, 487, 914
BtrI CACGTC 1 cut(s) 358
BtsCI GGATG 2 cut(s) 77, 910
BtsI GCAGTG 1 cut(s) 617
BtsIMutI CAGTG 1 cut(s) 617
Cac8I GCNNGC 7 cut(s) 326, 410, 456, 577, 581, 624, 709
CfoI GCGC 3 cut(s) 303, 463, 551
Cfr10I RCCGGY 2 cut(s) 422, 454
Cfr13I GGNCC 6 cut(s) 351, 519, 538, 613, 614, 632
Cfr42I CCGCGG 2 cut(s) 248, 917
CseI GACGC 4 cut(s) 242, 307, 437, 642
Csp6I GTAC 1 cut(s) 10
CviAII CATG 1 cut(s) 841
CviQI GTAC 1 cut(s) 10
DdeI CTNAG 1 cut(s) 413
DinI GGCGCC 1 cut(s) 462
DpnI GATC 3 cut(s) 22, 173, 290
DpnII GATC 3 cut(s) 20, 171, 288
Eam1104I CTCTTC 3 cut(s) 44, 693, 827
EarI CTCTTC 3 cut(s) 44, 693, 827
EciI GGCGGA 4 cut(s) 81, 403, 519, 915
Eco24I GRGCYC 1 cut(s) 617
Eco31I GGTCTC 4 cut(s) 58, 150, 346, 824
Eco47I GGWCC 3 cut(s) 351, 519, 632
Eco57I CTGAAG 1 cut(s) 738
Eco72I CACGTG 1 cut(s) 331
Eco88I CYCGRG 1 cut(s) 514
EcoRII CCWGG 1 cut(s) 570
EcoT38I GRGCYC 1 cut(s) 617
EgeI GGCGCC 1 cut(s) 462
EheI GGCGCC 1 cut(s) 462
FaeI CATG 1 cut(s) 844
FaiI YATR 5 cut(s) 30, 32, 381, 842, 885
FaqI GGGAC 5 cut(s) 30, 358, 364, 532, 570
FatI CATG 1 cut(s) 840
FauI CCCGC 7 cut(s) 240, 253, 549, 568, 572, 700, 841
FokI GGATG 2 cut(s) 64, 897
FriOI GRGCYC 1 cut(s) 617
GlaI GCGC 3 cut(s) 302, 462, 550
GsuI CTGGAG 2 cut(s) 44, 356
HaeII RGCGCY 1 cut(s) 464
HaeIII GGCC 3 cut(s) 539, 615, 919
HapII CCGG 9 cut(s) 201, 257, 348, 423, 455, 536, 545, 635, 860
HgaI GACGC 4 cut(s) 242, 307, 437, 642
HhaI GCGC 3 cut(s) 303, 463, 551
Hin1I GRCGYC 3 cut(s) 238, 253, 461
Hin1II CATG 1 cut(s) 844
Hin6I GCGC 3 cut(s) 301, 461, 549
HinP1I GCGC 3 cut(s) 301, 461, 549
HinfI GANTC 3 cut(s) 125, 143, 176
HpaII CCGG 9 cut(s) 201, 257, 348, 423, 455, 536, 545, 635, 860
HphI GGTGA 3 cut(s) 66, 433, 812
Hpy188I TCNGA 3 cut(s) 25, 124, 181
Hpy188III TCNNGA 8 cut(s) 47, 61, 201, 234, 295, 499, 756, 870
Hpy99I CGWCG 5 cut(s) 243, 359, 434, 658, 742
HpyAV CCTTC 2 cut(s) 126, 146
HpyCH4III ACNGT 4 cut(s) 72, 430, 523, 561
HpyCH4IV ACGT 4 cut(s) 238, 330, 357, 438
HpyCH4V TGCA 2 cut(s) 34, 55
HpyF10VI GCNNNNNNNGC 7 cut(s) 213, 283, 414, 423, 460, 612, 659
HpyF3I CTNAG 1 cut(s) 413
HpySE526I ACGT 4 cut(s) 238, 330, 357, 438
Hsp92I GRCGYC 3 cut(s) 238, 253, 461
Hsp92II CATG 1 cut(s) 844
HspAI GCGC 3 cut(s) 301, 461, 549
KasI GGCGCC 1 cut(s) 460
Kpn2I TCCGGA 1 cut(s) 200
KroI GCCGGC 1 cut(s) 454
KroNI GCCGGC 1 cut(s) 456
KspI CCGCGG 2 cut(s) 248, 917
Kzo9I GATC 3 cut(s) 20, 171, 288
LmnI GCTCC 3 cut(s) 471, 852, 902
Lsp1109I GCAGC 9 cut(s) 109, 175, 615, 637, 669, 716, 805, 822, 825
MaeII ACGT 4 cut(s) 238, 330, 357, 438
MaeIII GTNAC 6 cut(s) 72, 295, 439, 478, 720, 760
MalI GATC 3 cut(s) 22, 173, 290
MbiI CCGCTC 1 cut(s) 324
MboI GATC 3 cut(s) 20, 171, 288
MboII GAAGA 6 cut(s) 31, 111, 152, 710, 744, 814
MhlI GDGCHC 2 cut(s) 414, 617
Mly113I GGCGCC 1 cut(s) 461
MlyI GAGTC 2 cut(s) 137, 185
MmeI TCCRAC 1 cut(s) 204
MroI TCCGGA 1 cut(s) 200
MroNI GCCGGC 1 cut(s) 454
MspA1I CMGCKG 6 cut(s) 188, 247, 417, 707, 816, 916
MspI CCGG 9 cut(s) 201, 257, 348, 423, 455, 536, 545, 635, 860
MspR9I CCNGG 3 cut(s) 349, 546, 572
Mva1269I GAATGC 1 cut(s) 670
MvaI CCWGG 1 cut(s) 572
MvnI CGCG 4 cut(s) 247, 301, 303, 916
MwoI GCNNNNNNNGC 7 cut(s) 213, 283, 414, 423, 460, 612, 659
NaeI GCCGGC 1 cut(s) 456
NarI GGCGCC 1 cut(s) 461
NciI CCSGG 2 cut(s) 349, 546
NdeII GATC 3 cut(s) 20, 171, 288
NgoMIV GCCGGC 1 cut(s) 454
NlaIII CATG 1 cut(s) 844
NlaIV GGNNCC 9 cut(s) 352, 421, 427, 462, 520, 540, 615, 633, 904
NmuCI GTSAC 5 cut(s) 72, 295, 439, 478, 760
PcsI WCGNNNNNNNCGW 2 cut(s) 300, 495
PctI GAATGC 1 cut(s) 670
PdiI GCCGGC 1 cut(s) 456
PfeI GAWTC 1 cut(s) 125
PflFI GACNNNGTC 1 cut(s) 240
PleI GAGTC 2 cut(s) 137, 184
PluTI GGCGCC 1 cut(s) 464
PmaCI CACGTG 1 cut(s) 331
PmlI CACGTG 1 cut(s) 331
PpsI GAGTC 2 cut(s) 137, 184
Ppu21I YACGTR 1 cut(s) 331
PshAI GACNNNNGTC 1 cut(s) 70
Psp6I CCWGG 1 cut(s) 570
PspCI CACGTG 1 cut(s) 331
PspGI CCWGG 1 cut(s) 570
PspN4I GGNNCC 9 cut(s) 352, 421, 427, 462, 520, 540, 615, 633, 904
PspOMI GGGCCC 1 cut(s) 613
PspPI GGNCC 6 cut(s) 351, 519, 538, 613, 614, 632
PsyI GACNNNGTC 1 cut(s) 240
RsaI GTAC 1 cut(s) 11
RsaNI GTAC 1 cut(s) 10
SacII CCGCGG 2 cut(s) 248, 917
Sau3AI GATC 3 cut(s) 20, 171, 288
Sau96I GGNCC 6 cut(s) 351, 519, 538, 613, 614, 632
SchI GAGTC 2 cut(s) 137, 185
ScrFI CCNGG 3 cut(s) 349, 546, 572
SduI GDGCHC 2 cut(s) 414, 617
SfoI GGCGCC 1 cut(s) 462
Sfr303I CCGCGG 2 cut(s) 248, 917
SgrBI CCGCGG 2 cut(s) 248, 917
SinI GGWCC 3 cut(s) 351, 519, 632
SspDI GGCGCC 1 cut(s) 460
StyD4I CCNGG 3 cut(s) 347, 544, 570
TaaI ACNGT 4 cut(s) 72, 430, 523, 561
TaiI ACGT 4 cut(s) 241, 333, 360, 441
TaqI TCGA 3 cut(s) 174, 498, 563
TaqII GACCGA 1 cut(s) 368
TauI GCSGC 7 cut(s) 97, 210, 286, 420, 461, 900, 919
TfiI GAWTC 1 cut(s) 125
TscAI CASTG 1 cut(s) 624
TseFI GTSAC 5 cut(s) 72, 295, 439, 478, 760
TseI GCWGC 9 cut(s) 97, 188, 603, 650, 682, 704, 793, 810, 813
Tsp45I GTSAC 5 cut(s) 72, 295, 439, 478, 760
TspGWI ACGGA 2 cut(s) 32, 912
TspRI CASTG 1 cut(s) 624
Tth111I GACNNNGTC 1 cut(s) 240
VpaK11BI GGWCC 3 cut(s) 351, 519, 632
ZraI GACGTC 1 cut(s) 239
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.