Rh1DG393000

Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands. Topoisomerase II makes double-strand breaks

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr1D
OG0020383
Physical Location & Seq
Forward (+)
61095771 .. 61097228
1458 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh1DG393000.1

Sequence Viewer

Length: 879 bp
ATGGTGGTGGTGGAGAAGACGATCGAGGAAATGTTGTACCTGCAGAAGGGCCAGGTGGAGCACATCTTGCACCGACCCGATACCTACATCGGGTCGATGTCGAGGCTCACGGAGACGCTGTGGGTCTTCGAGAACGACGAGATGGTCCATCGCTCCGTTTCCTACGTCCCAGGCCTTTGCAAGATCTTCGATGAGATTCTGGTGAACGCCGCCGAAAATAAACGGAGGGATCAGTGCATGGACTCTCTCAAGGTCACCATCGACCCTGAGAAGAACTGCGTCAGTGTTTATAACAACGGCGCCGGGATTCCAGTCGAGATTCACGGGCGGGCGAAGGCGTATGTTCCGGAAGTGATCTTCGGCCACCTCTTGACCGGGAACGGCTACGGCGCAAAGCTCACCAATATTTTCTCCACGGAATTCATCGTTGAAGTCGCCGACGGCAAGCAACAGAAGAAGTACAAGCAGGTGTTCACAAACAACATGCGGAAGAAATCTGAACCAGTCATCACTAAATGCAAAGAGAGTGAGAACTGGACCCGGGTGACATATAAGCCCGACTTGACAAAATTTAACATGACACATCTGGAAGATGATGTGGTAGCATTGATGAAAAAGCGAGTGATTGACATAGCTGGATGCCTCGGAAAGACTTTGAAGGTTGAGCTGAATGGAAACAGGGTCCCTGTAAAGTCATTTCTTCGTTATGTTGATCTCTACTTGCAATCTGCCGAAAAATTTAAAGACACTCAACTTCCAAGGATGATTGCGAAACTCAATGATAGGTGGGAAGTTTGTGTCAGTTTCAGTGATGGGCAGTTTCAACAGGTCAGCTTTGTGAATAGCATTGCTACAATCAAGGGGGGGAACTCATGTTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko01524 map01524
Pfam Domains
Protein Families
DNA_gyraseB DNA_topoisoIV HATPase_c TOPRIM_C Toprim

Protein Analysis

292

Amino Acids

33.27

Weight (kDa)

8.54

Isoelectric Point (pI)

34.72

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
HATPase_c PF02518 58 - 138 2.3e-06 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
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: OG0020383)

Species Orthologous Gene IDs
malus_domestica MD01G1165800.v1.1
prunus_persica Prupe.2G018500_v2.0.a1
pyrus_communis pycom11g13880
rosa_multiflora Rmu_co8187766.1_g000001
rosa_samantha Rh1CG375500 Rh1DG393000

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 291
AarI CACCTGC 1 cut(s) 457
AasI GACNNNNNNGTC 1 cut(s) 143
Acc36I ACCTGC 2 cut(s) 48, 457
AccB1I GGYRCC 1 cut(s) 299
AccIII TCCGGA 1 cut(s) 346
AciI CCGC 3 cut(s) 210, 328, 487
AclWI GGATC 1 cut(s) 237
AcoI YGGCCR 1 cut(s) 361
AcsI RAATTY 3 cut(s) 419, 569, 737
AcyI GRCGYC 1 cut(s) 300
AfaI GTAC 2 cut(s) 38, 461
AfiI CCNNNNNNNGG 2 cut(s) 46, 90
AgsI TTSAA 3 cut(s) 431, 658, 824
AjnI CCWGG 2 cut(s) 51, 169
AluBI AGCT 4 cut(s) 397, 635, 667, 834
AluI AGCT 4 cut(s) 397, 635, 667, 834
Alw21I GWGCWC 1 cut(s) 63
Alw26I GTCTC 1 cut(s) 107
AlwI GGATC 1 cut(s) 237
Ama87I CYCGRG 1 cut(s) 540
Aor13HI TCCGGA 1 cut(s) 346
AoxI GGCC 3 cut(s) 49, 172, 361
ApoI RAATTY 3 cut(s) 419, 569, 737
AspLEI GCGC 2 cut(s) 302, 392
AspS9I GGNCC 4 cut(s) 49, 145, 537, 682
AsuC2I CCSGG 4 cut(s) 304, 376, 541, 542
AsuHPI GGTGA 4 cut(s) 214, 247, 391, 556
AvaI CYCGRG 1 cut(s) 540
AvaII GGWCC 3 cut(s) 145, 537, 682
BanI GGYRCC 1 cut(s) 299
BbsI GAAGAC 2 cut(s) 23, 118
Bbv12I GWGCWC 1 cut(s) 63
BccI CCATC 4 cut(s) 136, 156, 266, 806
BceAI ACGGC 4 cut(s) 313, 397, 403, 457
BcgI CGANNNNNNTGC 2 cut(s) 169, 203
BciT130I CCWGG 2 cut(s) 53, 171
BcnI CCSGG 4 cut(s) 304, 376, 541, 542
BcoDI GTCTC 1 cut(s) 107
BfmI CTRYAG 1 cut(s) 41
BfoI RGCGCY 1 cut(s) 303
BfuAI ACCTGC 2 cut(s) 48, 457
BglII AGATCT 1 cut(s) 183
BisI GCNGC 1 cut(s) 210
BlsI GCNGC 1 cut(s) 211
Bme1390I CCNGG 6 cut(s) 53, 171, 304, 376, 541, 542
Bme18I GGWCC 3 cut(s) 145, 537, 682
BmeT110I CYCGRG 1 cut(s) 540
BmgT120I GGNCC 4 cut(s) 49, 145, 537, 682
BmiI GGNNCC 4 cut(s) 301, 539, 683, 684
BmrFI CCNGG 6 cut(s) 53, 171, 304, 376, 541, 542
BmsI GCATC 1 cut(s) 629
BpiI GAAGAC 2 cut(s) 23, 118
BpuEI CTTGAG 1 cut(s) 233
BpuMI CCSGG 4 cut(s) 304, 376, 541, 542
BsaHI GRCGYC 1 cut(s) 300
BsaJI CCNNGG 5 cut(s) 169, 414, 540, 643, 758
BsaWI WCCGGW 1 cut(s) 346
BsaXI ACNNNNNCTCC 2 cut(s) 104, 134
Bsc4I CCNNNNNNNGG 2 cut(s) 46, 90
Bse1I ACTGG 3 cut(s) 311, 503, 539
Bse3DI GCAATG 1 cut(s) 846
BseAI TCCGGA 1 cut(s) 346
BseBI CCWGG 2 cut(s) 53, 171
BseDI CCNNGG 5 cut(s) 169, 414, 540, 643, 758
BseGI GGATG 2 cut(s) 644, 768
BseLI CCNNNNNNNGG 2 cut(s) 46, 90
BseMI GCAATG 1 cut(s) 846
BseMII CTCAG 1 cut(s) 258
BseNI ACTGG 3 cut(s) 311, 503, 539
Bsh1285I CGRYCG 1 cut(s) 24
BshFI GGCC 3 cut(s) 51, 174, 363
BshNI GGYRCC 1 cut(s) 299
BsiEI CGRYCG 1 cut(s) 24
BsiHKAI GWGCWC 1 cut(s) 63
BsiHKCI CYCGRG 1 cut(s) 540
BsiSI CCGG 4 cut(s) 303, 347, 375, 541
BslFI GGGAC 2 cut(s) 152, 668
BslI CCNNNNNNNGG 2 cut(s) 46, 90
BsmAI GTCTC 1 cut(s) 107
BsmBI CGTCTC 1 cut(s) 107
BsmFI GGGAC 2 cut(s) 152, 668
BsnI GGCC 3 cut(s) 51, 174, 363
BsoBI CYCGRG 1 cut(s) 540
Bsp1286I GDGCHC 1 cut(s) 63
Bsp13I TCCGGA 1 cut(s) 346
Bsp143I GATC 5 cut(s) 21, 183, 229, 354, 712
BspACI CCGC 3 cut(s) 210, 328, 487
BspANI GGCC 3 cut(s) 51, 174, 363
BspCNI CTCAG 1 cut(s) 259
BspEI TCCGGA 1 cut(s) 346
BspLI GGNNCC 4 cut(s) 301, 539, 683, 684
BspMAI CTGCAG 1 cut(s) 45
BspMI ACCTGC 2 cut(s) 48, 457
BspPI GGATC 1 cut(s) 237
BspT107I GGYRCC 1 cut(s) 299
BsrDI GCAATG 1 cut(s) 846
BsrI ACTGG 3 cut(s) 311, 503, 539
BssECI CCNNGG 5 cut(s) 169, 414, 540, 643, 758
BssMI GATC 5 cut(s) 21, 183, 229, 354, 712
BssNI GRCGYC 1 cut(s) 300
BssT1I CCWWGG 1 cut(s) 758
Bst2UI CCWGG 2 cut(s) 53, 171
BstACI GRCGYC 1 cut(s) 300
BstAPI GCANNNNNTGC 1 cut(s) 67
BstC8I GCNNGC 2 cut(s) 330, 446
BstDEI CTNAG 1 cut(s) 267
BstDSI CCRYGG 1 cut(s) 414
BstEII GGTNACC 1 cut(s) 253
BstENI CCTNNNNNAGG 1 cut(s) 44
BstF5I GGATG 2 cut(s) 644, 768
BstH2I RGCGCY 1 cut(s) 303
BstHHI GCGC 2 cut(s) 302, 392
BstKTI GATC 5 cut(s) 24, 186, 232, 357, 715
BstMAI GTCTC 1 cut(s) 107
BstMBI GATC 5 cut(s) 21, 183, 229, 354, 712
BstMCI CGRYCG 1 cut(s) 24
BstMWI GCNNNNNNNGC 1 cut(s) 67
BstNI CCWGG 2 cut(s) 53, 171
BstNSI RCATGY 1 cut(s) 487
BstPI GGTNACC 1 cut(s) 253
BstSCI CCNGG 6 cut(s) 51, 169, 302, 374, 539, 540
BstSFI CTRYAG 1 cut(s) 41
BstV2I GAAGAC 2 cut(s) 23, 118
BstX2I RGATCY 1 cut(s) 183
BstYI RGATCY 1 cut(s) 183
BsuRI GGCC 3 cut(s) 51, 174, 363
BtgI CCRYGG 1 cut(s) 414
BtgZI GCGATG 1 cut(s) 134
BtsCI GGATG 2 cut(s) 644, 768
BtsIMutI CAGTG 3 cut(s) 239, 289, 814
BveI ACCTGC 2 cut(s) 48, 457
Cac8I GCNNGC 2 cut(s) 330, 446
CfoI GCGC 2 cut(s) 302, 392
Cfr13I GGNCC 4 cut(s) 49, 145, 537, 682
Cfr9I CCCGGG 1 cut(s) 540
CseI GACGC 2 cut(s) 124, 268
Csp6I GTAC 2 cut(s) 37, 460
CviAII CATG 4 cut(s) 238, 484, 577, 873
CviQI GTAC 2 cut(s) 37, 460
DdeI CTNAG 1 cut(s) 267
DinI GGCGCC 1 cut(s) 301
DpnI GATC 5 cut(s) 23, 185, 231, 356, 714
DpnII GATC 5 cut(s) 21, 183, 229, 354, 712
DraI TTTAAA 1 cut(s) 742
DrdI GACNNNNNNGTC 1 cut(s) 143
DseDI GACNNNNNNGTC 1 cut(s) 143
EaeI YGGCCR 1 cut(s) 361
Eco130I CCWWGG 1 cut(s) 758
Eco147I AGGCCT 1 cut(s) 174
Eco47I GGWCC 3 cut(s) 145, 537, 682
Eco88I CYCGRG 1 cut(s) 540
Eco91I GGTNACC 1 cut(s) 253
EcoNI CCTNNNNNAGG 1 cut(s) 44
EcoO109I RGGNCCY 1 cut(s) 682
EcoO65I GGTNACC 1 cut(s) 253
EcoRI GAATTC 1 cut(s) 419
EcoRII CCWGG 2 cut(s) 51, 169
EcoT14I CCWWGG 1 cut(s) 758
EgeI GGCGCC 1 cut(s) 301
EheI GGCGCC 1 cut(s) 301
ErhI CCWWGG 1 cut(s) 758
Esp3I CGTCTC 1 cut(s) 107
FaeI CATG 4 cut(s) 241, 487, 580, 876
FalI AAGNNNNNCTT 2 cut(s) 545, 577
FaqI GGGAC 2 cut(s) 152, 668
FatI CATG 4 cut(s) 237, 483, 576, 872
FauI CCCGC 1 cut(s) 321
Fnu4HI GCNGC 1 cut(s) 210
FokI GGATG 2 cut(s) 651, 775
Fsp4HI GCNGC 1 cut(s) 210
GlaI GCGC 2 cut(s) 301, 391
GluI GCNGC 1 cut(s) 210
HaeII RGCGCY 1 cut(s) 303
HaeIII GGCC 3 cut(s) 51, 174, 363
HapII CCGG 4 cut(s) 303, 347, 375, 541
HgaI GACGC 2 cut(s) 124, 268
HhaI GCGC 2 cut(s) 302, 392
Hin1I GRCGYC 1 cut(s) 300
Hin1II CATG 4 cut(s) 241, 487, 580, 876
Hin6I GCGC 2 cut(s) 300, 390
HinP1I GCGC 2 cut(s) 300, 390
HinfI GANTC 4 cut(s) 196, 242, 307, 319
HpaII CCGG 4 cut(s) 303, 347, 375, 541
HphI GGTGA 4 cut(s) 214, 247, 391, 556
Hpy166II GTNNAC 2 cut(s) 205, 474
Hpy188I TCNGA 2 cut(s) 499, 647
Hpy188III TCNNGA 5 cut(s) 130, 316, 347, 370, 587
Hpy8I GTNNAC 2 cut(s) 205, 474
Hpy99I CGWCG 2 cut(s) 140, 443
HpyAV CCTTC 3 cut(s) 40, 328, 652
HpyCH4IV ACGT 1 cut(s) 165
HpyCH4V TGCA 6 cut(s) 43, 70, 180, 237, 519, 724
HpyF10VI GCNNNNNNNGC 1 cut(s) 67
HpyF3I CTNAG 1 cut(s) 267
HpySE526I ACGT 1 cut(s) 165
Hsp92I GRCGYC 1 cut(s) 300
Hsp92II CATG 4 cut(s) 241, 487, 580, 876
HspAI GCGC 2 cut(s) 300, 390
KasI GGCGCC 1 cut(s) 299
KflI GGGWCCC 1 cut(s) 682
Kpn2I TCCGGA 1 cut(s) 346
Kzo9I GATC 5 cut(s) 21, 183, 229, 354, 712
LmnI GCTCC 2 cut(s) 58, 158
LweI GCATC 1 cut(s) 629
MaeII ACGT 1 cut(s) 165
MaeIII GTNAC 2 cut(s) 253, 544
MalI GATC 5 cut(s) 23, 185, 231, 356, 714
MboI GATC 5 cut(s) 21, 183, 229, 354, 712
MboII GAAGA 9 cut(s) 28, 118, 178, 283, 349, 466, 502, 602, 692
MflI RGATCY 1 cut(s) 183
MhlI GDGCHC 1 cut(s) 63
MluCI AATT 3 cut(s) 419, 569, 737
Mly113I GGCGCC 1 cut(s) 300
MlyI GAGTC 1 cut(s) 236
MnlI CCTC 5 cut(s) 19, 96, 219, 377, 653
MroI TCCGGA 1 cut(s) 346
MseI TTAA 2 cut(s) 573, 741
MspI CCGG 4 cut(s) 303, 347, 375, 541
MspR9I CCNGG 6 cut(s) 53, 171, 304, 376, 541, 542
MvaI CCWGG 2 cut(s) 53, 171
MwoI GCNNNNNNNGC 1 cut(s) 67
NarI GGCGCC 1 cut(s) 300
NciI CCSGG 4 cut(s) 304, 376, 541, 542
NdeII GATC 5 cut(s) 21, 183, 229, 354, 712
NlaIII CATG 4 cut(s) 241, 487, 580, 876
NlaIV GGNNCC 4 cut(s) 301, 539, 683, 684
NmuCI GTSAC 2 cut(s) 253, 544
NspI RCATGY 1 cut(s) 487
PaqCI CACCTGC 1 cut(s) 457
PceI AGGCCT 1 cut(s) 174
PcsI WCGNNNNNNNCGW 1 cut(s) 135
PfeI GAWTC 3 cut(s) 196, 307, 319
PkrI GCNGC 1 cut(s) 211
Ple19I CGATCG 1 cut(s) 24
PleI GAGTC 1 cut(s) 236
PluTI GGCGCC 1 cut(s) 303
PpsI GAGTC 1 cut(s) 236
PpuMI RGGWCCY 1 cut(s) 682
PsiI TTATAA 1 cut(s) 291
Psp5II RGGWCCY 1 cut(s) 682
Psp6I CCWGG 2 cut(s) 51, 169
PspEI GGTNACC 1 cut(s) 253
PspGI CCWGG 2 cut(s) 51, 169
PspN4I GGNNCC 4 cut(s) 301, 539, 683, 684
PspPI GGNCC 4 cut(s) 49, 145, 537, 682
PspPPI RGGWCCY 1 cut(s) 682
PstI CTGCAG 1 cut(s) 45
PsuI RGATCY 1 cut(s) 183
PvuI CGATCG 1 cut(s) 24
RsaI GTAC 2 cut(s) 38, 461
RsaNI GTAC 2 cut(s) 37, 460
SaqAI TTAA 2 cut(s) 573, 741
SatI GCNGC 1 cut(s) 210
Sau3AI GATC 5 cut(s) 21, 183, 229, 354, 712
Sau96I GGNCC 4 cut(s) 49, 145, 537, 682
SchI GAGTC 1 cut(s) 236
ScrFI CCNGG 6 cut(s) 53, 171, 304, 376, 541, 542
SduI GDGCHC 1 cut(s) 63
SfaNI GCATC 1 cut(s) 629
SfcI CTRYAG 1 cut(s) 41
SfoI GGCGCC 1 cut(s) 301
SinI GGWCC 3 cut(s) 145, 537, 682
SmaI CCCGGG 1 cut(s) 542
SmlI CTYRAG 1 cut(s) 248
SmoI CTYRAG 1 cut(s) 248
Sse9I AATT 3 cut(s) 419, 569, 737
SseBI AGGCCT 1 cut(s) 174
SsiI CCGC 3 cut(s) 210, 328, 487
SspDI GGCGCC 1 cut(s) 299
SspI AATATT 1 cut(s) 406
StuI AGGCCT 1 cut(s) 174
StyD4I CCNGG 6 cut(s) 51, 169, 302, 374, 539, 540
StyI CCWWGG 1 cut(s) 758
TaiI ACGT 1 cut(s) 168
TaqI TCGA 7 cut(s) 24, 95, 101, 129, 189, 261, 315
TasI AATT 3 cut(s) 419, 569, 737
TatI WGTACW 1 cut(s) 459
TauI GCSGC 1 cut(s) 212
TfiI GAWTC 3 cut(s) 196, 307, 319
Tru1I TTAA 2 cut(s) 573, 741
Tru9I TTAA 2 cut(s) 573, 741
TscAI CASTG 3 cut(s) 239, 289, 814
TseFI GTSAC 2 cut(s) 253, 544
Tsp45I GTSAC 2 cut(s) 253, 544
TspDTI ATGAA 2 cut(s) 412, 626
TspGWI ACGGA 4 cut(s) 125, 145, 238, 431
TspMI CCCGGG 1 cut(s) 540
TspRI CASTG 3 cut(s) 239, 289, 814
VpaK11BI GGWCC 3 cut(s) 145, 537, 682
XagI CCTNNNNNAGG 1 cut(s) 44
XapI RAATTY 3 cut(s) 419, 569, 737
XceI RCATGY 1 cut(s) 487
XmaI CCCGGG 1 cut(s) 540
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.