Rh3DG025500

DNA-binding protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr3D
OG0011499
Physical Location & Seq
Reverse (-)
1684042 .. 1690297
6256 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh3DG025500.1

Sequence Viewer

Length: 1095 bp
ATGGAACCAAACGAACACCAACTCAGCTCCTACTTCAACCCCCCCACCACCGCCGCCGCCGCCGCCTTGTCTCCGACCAATGGCCTCGCCGGCGGCCCAAGCACCCAACAACAACTCTCCTCGGCCGACAACAACAACAACATGGTCTACACTCCTCACTCCTCCTCCGCCGCCGCCGTGCCTCCGCCCTCGTCAGCCGTGACGTCACCGCTGGAGCCGGTGAAGAGGAAGCGCGGGAGGCCCAGGAAGTACGGCACGCCCGAGCAGGCCCTGGCGGCCAAGAAGGCCGCGACGACGTCGTCTCACTCCTCGTCTTCTAAGGAGAAGAAGGAGCAGCAGCTCCACCAGCAGCAGCAGCAACACGGCGGCGGCTCAGCCTCGCCGTCTTATTCTGGGTCCACCAAGAAATCTCAGCTCTCTGCTCTTGGCAATTCAGGGCAAGGTTTTACACCACATGTTCTAACTGTGGCTCCAGGAGAGGATGTGGGCCAGAAAATCATGGTTTTTATGCAACAGAATAAGCGTGACATATGCATTCTGTCCGCTTCTGGTTCAATCTCAAATGCATCTATTCGCCAGCCAGCTACTTCAGGAGGCAACATTACATATGAGGGTCGCTTTGAGATCATTTCACTGTCTGGATCTTATGTAACTGACCAAGGGGGAAAGACTGGTGGGCTCAGTGTGTGTCTCTCCAATACAAATGGGCAAATCATTGGGGGTGGAGTTGGTGGACCACTGAAGGCTGCAGGCCCTGTTCAGGTTATTGTTGGTACTTTTCTGATTGATAACAAAAAGGAAAAAGTCGAGGTTTCTATGCCCAGAATGCCATCGCCAGGTGGTGGAGCATCTATGATGAATGTAGGTTTCCGCTCAACGGTGGACTCTTCTGGAAGAAATATGGTCAGGGCAAATGATGAACAACAGCAAGCTATTGGCGGAAGTCATTTCATGATTCAGGGCATGCATGGATCCACAGATTGGAGGACTGGTCCAGATGCCAGAAGCACTGGTGCTTATGAATTGGCAGGAAGAGGTGGTCGTGCAGCCCACCAATCTCCAGAAAATGGGGACTATGATCAAATTCCAGATTAG
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

364

Amino Acids

37.8

Weight (kDa)

9.24

Isoelectric Point (pI)

47.41

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PCC PF03479 150 - 260 1.1e-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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Orthologous Genes (Group: OG0011499)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G04590 AT3G04590
fragaria_vesca FvH4_6g02360 FvH4_6g02360
malus_domestica MD00G1114400.v1.1 MD12G1245000.v1.1
prunus_persica Prupe.6G347600_v2.0.a1 Prupe.6G347600_v2.0.a1
pyrus_communis pycom04g20220 pycom12g22470
rosa_chinensis RchiOBHm_Chr3g0450121
rosa_laevigata RLG00000025754
rosa_multiflora Rmu_ssc0000116.1_g000066
rosa_roxburghii Rroxscaffold_6G00427890
rosa_rugosa Rorug02G0625700
rosa_samantha Rh3AG024900 Rh3BG025500 Rh3CG024400 Rh3DG025500
rosa_wichuraiana Rw3G001990

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 1 cut(s) 298
AatII GACGTC 2 cut(s) 206, 299
AccB7I CCANNNNNTGG 3 cut(s) 842, 981, 1067
AccBSI CCGCTC 1 cut(s) 873
AccI GTMKAC 1 cut(s) 147
AccII CGCG 2 cut(s) 234, 290
AclWI GGATC 3 cut(s) 649, 966, 979
AcoI YGGCCR 2 cut(s) 123, 276
AcsI RAATTY 1 cut(s) 1083
AcuI CTGAAG 2 cut(s) 573, 761
AcyI GRCGYC 2 cut(s) 203, 296
AfaI GTAC 2 cut(s) 251, 775
AfiI CCNNNNNNNGG 7 cut(s) 80, 760, 836, 842, 877, 981, 1067
AflIII ACRYGT 1 cut(s) 454
AgsI TTSAA 2 cut(s) 37, 555
AjnI CCWGG 4 cut(s) 242, 270, 472, 835
AluBI AGCT 5 cut(s) 27, 340, 415, 584, 932
AluI AGCT 5 cut(s) 27, 340, 415, 584, 932
Alw26I GTCTC 3 cut(s) 75, 306, 695
AlwI GGATC 3 cut(s) 649, 966, 979
AlwNI CAGNNNCTG 2 cut(s) 271, 755
Ama87I CYCGRG 1 cut(s) 260
AoxI GGCC 9 cut(s) 82, 94, 123, 239, 267, 276, 285, 487, 751
ApeKI GCWGC 7 cut(s) 334, 337, 349, 352, 355, 746, 1046
ApoI RAATTY 1 cut(s) 1083
AspLEI GCGC 1 cut(s) 234
AspS9I GGNCC 8 cut(s) 95, 240, 268, 396, 487, 734, 752, 992
AsuHPI GGTGA 2 cut(s) 198, 232
AvaI CYCGRG 1 cut(s) 260
AvaII GGWCC 3 cut(s) 396, 734, 992
BamHI GGATCC 1 cut(s) 971
BanII GRGCYC 1 cut(s) 681
BbsI GAAGAC 1 cut(s) 306
BbvI GCAGC 7 cut(s) 346, 349, 361, 364, 367, 733, 1058
BccI CCATC 1 cut(s) 838
BceAI ACGGC 5 cut(s) 161, 182, 268, 367, 379
BciT130I CCWGG 4 cut(s) 244, 272, 474, 837
BclI TGATCA 1 cut(s) 1078
BcoDI GTCTC 3 cut(s) 75, 306, 695
BfmI CTRYAG 1 cut(s) 747
BglI GCCNNNNNGGC 3 cut(s) 90, 275, 284
BlpI GCTNAGC 1 cut(s) 373
Bme1390I CCNGG 4 cut(s) 244, 272, 474, 837
Bme18I GGWCC 3 cut(s) 396, 734, 992
BmeT110I CYCGRG 1 cut(s) 260
BmgT120I GGNCC 8 cut(s) 95, 240, 268, 396, 487, 734, 752, 992
BmiI GGNNCC 5 cut(s) 6, 216, 397, 471, 973
BmrFI CCNGG 4 cut(s) 244, 272, 474, 837
BmsI GCATC 3 cut(s) 575, 857, 988
BpiI GAAGAC 1 cut(s) 306
BpmI CTGGAG 3 cut(s) 233, 456, 1044
Bpu1102I GCTNAGC 1 cut(s) 373
BsaHI GRCGYC 2 cut(s) 203, 296
BsaJI CCNNGG 4 cut(s) 120, 242, 270, 658
BsaXI ACNNNNNCTCC 8 cut(s) 149, 179, 454, 468, 484, 498, 976, 1006
Bsc4I CCNNNNNNNGG 7 cut(s) 80, 760, 836, 842, 877, 981, 1067
Bse118I RCCGGY 2 cut(s) 89, 217
Bse1I ACTGG 3 cut(s) 676, 994, 1015
BseBI CCWGG 4 cut(s) 244, 272, 474, 837
BseDI CCNNGG 4 cut(s) 120, 242, 270, 658
BseGI GGATG 1 cut(s) 487
BseLI CCNNNNNNNGG 7 cut(s) 80, 760, 836, 842, 877, 981, 1067
BseMII CTCAG 4 cut(s) 37, 387, 425, 694
BseNI ACTGG 3 cut(s) 676, 994, 1015
BseRI GAGGAG 5 cut(s) 109, 144, 151, 154, 298
BseX3I CGGCCG 1 cut(s) 123
BseXI GCAGC 7 cut(s) 346, 349, 361, 364, 367, 733, 1058
BsgI GTGCAG 1 cut(s) 1065
Bsh1236I CGCG 2 cut(s) 234, 290
Bsh1285I CGRYCG 1 cut(s) 126
BshFI GGCC 9 cut(s) 84, 96, 125, 241, 269, 278, 287, 489, 753
BsiEI CGRYCG 1 cut(s) 126
BsiHKCI CYCGRG 1 cut(s) 260
BsiSI CCGG 2 cut(s) 90, 218
BslFI GGGAC 1 cut(s) 1085
BslI CCNNNNNNNGG 7 cut(s) 80, 760, 836, 842, 877, 981, 1067
BsmAI GTCTC 3 cut(s) 75, 306, 695
BsmBI CGTCTC 1 cut(s) 306
BsmFI GGGAC 1 cut(s) 1085
BsmI GAATGC 2 cut(s) 534, 831
BsnI GGCC 9 cut(s) 84, 96, 125, 241, 269, 278, 287, 489, 753
BsoBI CYCGRG 1 cut(s) 260
Bsp1286I GDGCHC 1 cut(s) 681
Bsp143I GATC 4 cut(s) 624, 641, 971, 1078
Bsp1720I GCTNAGC 1 cut(s) 373
BspANI GGCC 9 cut(s) 84, 96, 125, 241, 269, 278, 287, 489, 753
BspCNI CTCAG 4 cut(s) 36, 386, 424, 693
BspFNI CGCG 2 cut(s) 234, 290
BspHI TCATGA 1 cut(s) 951
BspLI GGNNCC 5 cut(s) 6, 216, 397, 471, 973
BspMAI CTGCAG 1 cut(s) 751
BspPI GGATC 3 cut(s) 649, 966, 979
BsrBI CCGCTC 1 cut(s) 873
BsrFI RCCGGY 2 cut(s) 89, 217
BsrI ACTGG 3 cut(s) 676, 994, 1015
BssAI RCCGGY 2 cut(s) 89, 217
BssECI CCNNGG 4 cut(s) 120, 242, 270, 658
BssMI GATC 4 cut(s) 624, 641, 971, 1078
BssNI GRCGYC 2 cut(s) 203, 296
BssT1I CCWWGG 1 cut(s) 658
Bst2UI CCWGG 4 cut(s) 244, 272, 474, 837
Bst4CI ACNGT 3 cut(s) 466, 636, 880
Bst6I CTCTTC 3 cut(s) 218, 892, 1027
BstACI GRCGYC 2 cut(s) 203, 296
BstC8I GCNNGC 8 cut(s) 91, 257, 267, 578, 582, 751, 930, 965
BstDEI CTNAG 5 cut(s) 23, 318, 373, 411, 680
BstF5I GGATG 1 cut(s) 487
BstFNI CGCG 2 cut(s) 234, 290
BstHHI GCGC 1 cut(s) 234
BstKTI GATC 4 cut(s) 627, 644, 974, 1081
BstMAI GTCTC 3 cut(s) 75, 306, 695
BstMBI GATC 4 cut(s) 624, 641, 971, 1078
BstMCI CGRYCG 1 cut(s) 126
BstNI CCWGG 4 cut(s) 244, 272, 474, 837
BstNSI RCATGY 2 cut(s) 458, 967
BstSCI CCNGG 4 cut(s) 242, 270, 472, 835
BstSFI CTRYAG 1 cut(s) 747
BstUI CGCG 2 cut(s) 234, 290
BstV1I GCAGC 7 cut(s) 346, 349, 361, 364, 367, 733, 1058
BstV2I GAAGAC 1 cut(s) 306
BstX2I RGATCY 2 cut(s) 641, 971
BstYI RGATCY 2 cut(s) 641, 971
BstZI CGGCCG 1 cut(s) 123
BsuRI GGCC 9 cut(s) 84, 96, 125, 241, 269, 278, 287, 489, 753
BtgZI GCGATG 1 cut(s) 816
BtsCI GGATG 1 cut(s) 487
BtsIMutI CAGTG 4 cut(s) 632, 688, 737, 1008
Cac8I GCNNGC 8 cut(s) 91, 257, 267, 578, 582, 751, 930, 965
CaiI CAGNNNCTG 2 cut(s) 271, 755
CciI TCATGA 1 cut(s) 951
CfoI GCGC 1 cut(s) 234
Cfr10I RCCGGY 2 cut(s) 89, 217
Cfr13I GGNCC 8 cut(s) 95, 240, 268, 396, 487, 734, 752, 992
Csp6I GTAC 2 cut(s) 250, 774
CviAII CATG 6 cut(s) 142, 455, 499, 952, 964, 968
CviQI GTAC 2 cut(s) 250, 774
DdeI CTNAG 5 cut(s) 23, 318, 373, 411, 680
DpnI GATC 4 cut(s) 626, 643, 973, 1080
DpnII GATC 4 cut(s) 624, 641, 971, 1078
DrdI GACNNNNNNGTC 1 cut(s) 298
DseDI GACNNNNNNGTC 1 cut(s) 298
EaeI YGGCCR 2 cut(s) 123, 276
EagI CGGCCG 1 cut(s) 123
Eam1104I CTCTTC 3 cut(s) 218, 892, 1027
EarI CTCTTC 3 cut(s) 218, 892, 1027
EciI GGCGGA 3 cut(s) 157, 174, 954
EclXI CGGCCG 1 cut(s) 123
Eco130I CCWWGG 1 cut(s) 658
Eco24I GRGCYC 1 cut(s) 681
Eco47I GGWCC 3 cut(s) 396, 734, 992
Eco52I CGGCCG 1 cut(s) 123
Eco57I CTGAAG 2 cut(s) 573, 761
Eco88I CYCGRG 1 cut(s) 260
EcoO109I RGGNCCY 2 cut(s) 268, 752
EcoRII CCWGG 4 cut(s) 242, 270, 472, 835
EcoT14I CCWWGG 1 cut(s) 658
EcoT22I ATGCAT 3 cut(s) 536, 568, 969
EcoT38I GRGCYC 1 cut(s) 681
ErhI CCWWGG 1 cut(s) 658
Esp3I CGTCTC 1 cut(s) 306
FaeI CATG 6 cut(s) 145, 458, 502, 955, 967, 971
FaqI GGGAC 1 cut(s) 1085
FatI CATG 6 cut(s) 141, 454, 498, 951, 963, 967
FauI CCCGC 1 cut(s) 227
FauNDI CATATG 2 cut(s) 530, 607
FbaI TGATCA 1 cut(s) 1078
FblI GTMKAC 1 cut(s) 147
FokI GGATG 1 cut(s) 494
FriOI GRGCYC 1 cut(s) 681
GlaI GCGC 1 cut(s) 233
GsuI CTGGAG 3 cut(s) 233, 456, 1044
HaeIII GGCC 9 cut(s) 84, 96, 125, 241, 269, 278, 287, 489, 753
HapII CCGG 2 cut(s) 90, 218
HhaI GCGC 1 cut(s) 234
Hin1I GRCGYC 2 cut(s) 203, 296
Hin1II CATG 6 cut(s) 145, 458, 502, 955, 967, 971
Hin6I GCGC 1 cut(s) 232
HinP1I GCGC 1 cut(s) 232
HinfI GANTC 2 cut(s) 884, 955
HpaII CCGG 2 cut(s) 90, 218
HphI GGTGA 2 cut(s) 198, 232
Hpy166II GTNNAC 4 cut(s) 148, 399, 734, 883
Hpy188I TCNGA 2 cut(s) 75, 783
Hpy188III TCNNGA 7 cut(s) 591, 639, 891, 952, 995, 1061, 1088
Hpy8I GTNNAC 4 cut(s) 148, 399, 734, 883
Hpy99I CGWCG 3 cut(s) 295, 298, 301
HpyAV CCTTC 3 cut(s) 277, 322, 736
HpyCH4III ACNGT 3 cut(s) 466, 636, 880
HpyCH4IV ACGT 2 cut(s) 203, 296
HpyCH4V TGCA 6 cut(s) 511, 534, 566, 749, 967, 1046
HpyF3I CTNAG 5 cut(s) 23, 318, 373, 411, 680
HpySE526I ACGT 2 cut(s) 203, 296
Hsp92I GRCGYC 2 cut(s) 203, 296
Hsp92II CATG 6 cut(s) 145, 458, 502, 955, 967, 971
HspAI GCGC 1 cut(s) 232
KroI GCCGGC 1 cut(s) 89
KroNI GCCGGC 1 cut(s) 91
Ksp22I TGATCA 1 cut(s) 1078
Kzo9I GATC 4 cut(s) 624, 641, 971, 1078
LmnI GCTCC 6 cut(s) 32, 214, 331, 345, 475, 845
Lsp1109I GCAGC 7 cut(s) 346, 349, 361, 364, 367, 733, 1058
LweI GCATC 3 cut(s) 575, 857, 988
MaeII ACGT 2 cut(s) 203, 296
MaeIII GTNAC 4 cut(s) 199, 204, 524, 649
MalI GATC 4 cut(s) 626, 643, 973, 1080
MbiI CCGCTC 1 cut(s) 873
MboI GATC 4 cut(s) 624, 641, 971, 1078
MboII GAAGA 6 cut(s) 235, 306, 337, 879, 906, 1044
MflI RGATCY 2 cut(s) 641, 971
MhlI GDGCHC 1 cut(s) 681
MluCI AATT 3 cut(s) 430, 1022, 1083
MlyI GAGTC 1 cut(s) 878
MmeI TCCRAC 1 cut(s) 98
Mph1103I ATGCAT 3 cut(s) 536, 568, 969
MreI CGCCGGCG 1 cut(s) 89
MroNI GCCGGC 1 cut(s) 89
MspA1I CMGCKG 1 cut(s) 211
MspI CCGG 2 cut(s) 90, 218
MspR9I CCNGG 4 cut(s) 244, 272, 474, 837
Mva1269I GAATGC 2 cut(s) 534, 831
MvaI CCWGG 4 cut(s) 244, 272, 474, 837
MvnI CGCG 2 cut(s) 234, 290
NaeI GCCGGC 1 cut(s) 91
NdeI CATATG 2 cut(s) 530, 607
NdeII GATC 4 cut(s) 624, 641, 971, 1078
NgoMIV GCCGGC 1 cut(s) 89
NlaIII CATG 6 cut(s) 145, 458, 502, 955, 967, 971
NlaIV GGNNCC 5 cut(s) 6, 216, 397, 471, 973
NmeAIII GCCGAG 1 cut(s) 101
NmuCI GTSAC 3 cut(s) 199, 204, 524
NsiI ATGCAT 3 cut(s) 536, 568, 969
NspI RCATGY 2 cut(s) 458, 967
PaeI GCATGC 1 cut(s) 967
PagI TCATGA 1 cut(s) 951
PciI ACATGT 1 cut(s) 454
PcsI WCGNNNNNNNCGW 1 cut(s) 258
PctI GAATGC 2 cut(s) 534, 831
PdiI GCCGGC 1 cut(s) 91
PfeI GAWTC 1 cut(s) 955
PflFI GACNNNGTC 2 cut(s) 295, 298
PflMI CCANNNNNTGG 3 cut(s) 842, 981, 1067
PfoI TCCNGGA 1 cut(s) 472
PleI GAGTC 1 cut(s) 878
PpsI GAGTC 1 cut(s) 878
PscI ACATGT 1 cut(s) 454
Psp6I CCWGG 4 cut(s) 242, 270, 472, 835
PspGI CCWGG 4 cut(s) 242, 270, 472, 835
PspN4I GGNNCC 5 cut(s) 6, 216, 397, 471, 973
PspPI GGNCC 8 cut(s) 95, 240, 268, 396, 487, 734, 752, 992
PstI CTGCAG 1 cut(s) 751
PstNI CAGNNNCTG 2 cut(s) 271, 755
PsuI RGATCY 2 cut(s) 641, 971
PsyI GACNNNGTC 2 cut(s) 295, 298
RsaI GTAC 2 cut(s) 251, 775
RsaNI GTAC 2 cut(s) 250, 774
Sau3AI GATC 4 cut(s) 624, 641, 971, 1078
Sau96I GGNCC 8 cut(s) 95, 240, 268, 396, 487, 734, 752, 992
SchI GAGTC 1 cut(s) 878
ScrFI CCNGG 4 cut(s) 244, 272, 474, 837
SduI GDGCHC 1 cut(s) 681
SfaNI GCATC 3 cut(s) 575, 857, 988
SfcI CTRYAG 1 cut(s) 747
SfiI GGCCNNNNNGGCC 2 cut(s) 275, 284
SgrAI CRCCGGYG 1 cut(s) 89
SinI GGWCC 3 cut(s) 396, 734, 992
SphI GCATGC 1 cut(s) 967
Sse9I AATT 3 cut(s) 430, 1022, 1083
StyD4I CCNGG 4 cut(s) 242, 270, 472, 835
StyI CCWWGG 1 cut(s) 658
TaaI ACNGT 3 cut(s) 466, 636, 880
TaiI ACGT 2 cut(s) 206, 299
TaqI TCGA 1 cut(s) 807
TasI AATT 3 cut(s) 430, 1022, 1083
TfiI GAWTC 1 cut(s) 955
TscAI CASTG 4 cut(s) 639, 688, 744, 1015
TseFI GTSAC 3 cut(s) 199, 204, 524
TseI GCWGC 7 cut(s) 334, 337, 349, 352, 355, 746, 1046
Tsp45I GTSAC 3 cut(s) 199, 204, 524
TspDTI ATGAA 4 cut(s) 872, 933, 940, 1035
TspRI CASTG 4 cut(s) 639, 688, 744, 1015
Tth111I GACNNNGTC 2 cut(s) 295, 298
Van91I CCANNNNNTGG 3 cut(s) 842, 981, 1067
VpaK11BI GGWCC 3 cut(s) 396, 734, 992
XapI RAATTY 1 cut(s) 1083
XceI RCATGY 2 cut(s) 458, 967
XmiI GTMKAC 1 cut(s) 147
ZraI GACGTC 2 cut(s) 204, 297
Zsp2I ATGCAT 3 cut(s) 536, 568, 969
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.