Rorug06G0409700

DNA-directed RNA-polymerase II subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_rugosa
GWHBQTZ00000006
OG0002628
Physical Location & Seq
Reverse (-)
55213792 .. 55216123
2332 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug06G0409700.1

Sequence Viewer

Length: 810 bp
ATGTTAGATAGTTGGTTGGGAGACTGGAGGCAAGCATTGACTGTTTTCTGGTCACACTATCAACAAAACATGAAATTTGAATTAAAGAAAAGATGGAAATCAATTGTCCCACTTCAGTTGAAACACAAATCAGCCACCCGTTTTTCTTTATTTCCCAAATCGAAGTCAGATTTTGGTCCGGGCAAAGCACCTGTATATCTCAATGTATATGACTTGACACCCATGAATGGCTATGTCTATTGGGCAGGCTTTGGAATTTTTCACTCTGGTGTTGAAGTTCATGGTGTTGAATATGCATTTGGAGCACATGACTACCCTACCAGTGGTGTTTTTGAGGTTGAACCTCGGCAATGCCCAGGATTCAAGTTCAGGAAATCTATATTTATTGGGACAACAAGCTTAGACCCTATTCAGGTTAGAGAGTTCATGGAGCGCCAGTCATTGAGGTACAATGGTGATACATATCACCTGATTGTCAAGAATTGCAACCATTTCTGCAGAGATATCTGTTACAAGCTAACTGGGAAATCAATTCCAAAGTGGGTAAATCGACTGGCAAGAATAGGTTCAATATGCAACTGCATACTTCCTGAAGCGCTAAAGATTTCTGCTGTACAACATGACCCTAACAACCAACCATATGATAGTGAGAAGAGGAGTTTGAGAAGTGCCTTCAGTTGCCTGTCTTCTATCTCAATGCGGCAGAAGCAATTGTCATCATCTTCATTGTTTCTACAGTCACCCTTGAAAGGCTGCTTGCCACCATGGGAATTAAGAAGGTCAAACAATGGTTCCTTGAAGGAAAGGTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko00230 ko00240 ko01100 ko03020 ko05016 ko05169 map00230 map00240 map01100 map03020 map05016 map05169
Pfam Domains
Protein Families
RNA_pol_Rpb4

Protein Analysis

269

Amino Acids

31.0

Weight (kDa)

9.58

Isoelectric Point (pI)

44.06

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Peptidase_C97 PF05903 64 - 199 7.7e-50 PPPDE putative peptidase 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)
AciI CCGC 1 cut(s) 700
AcsI RAATTY 2 cut(s) 74, 255
AcuI CTGAAG 3 cut(s) 98, 612, 658
AfaI GTAC 2 cut(s) 449, 615
AfeI AGCGCT 1 cut(s) 597
AfiI CCNNNNNNNGG 4 cut(s) 227, 323, 412, 749
AgsI TTSAA 9 cut(s) 80, 121, 275, 290, 341, 364, 570, 748, 799
AjnI CCWGG 1 cut(s) 355
AjuI GAANNNNNNNTTGG 2 cut(s) 282, 314
AleI CACNNNNGTG 1 cut(s) 267
AluBI AGCT 2 cut(s) 399, 517
AluI AGCT 2 cut(s) 399, 517
Alw21I GWGCWC 1 cut(s) 307
Alw26I GTCTC 1 cut(s) 15
Aor51HI AGCGCT 1 cut(s) 597
ApeKI GCWGC 1 cut(s) 753
ApoI RAATTY 2 cut(s) 74, 255
Asp700I GAANNNNTTC 1 cut(s) 565
AspLEI GCGC 2 cut(s) 435, 598
AspS9I GGNCC 1 cut(s) 176
AsuC2I CCSGG 1 cut(s) 180
AsuHPI GGTGA 3 cut(s) 458, 467, 732
AvaII GGWCC 1 cut(s) 176
BaeI ACNNNNGTAYC 2 cut(s) 439, 472
BbsI GAAGAC 1 cut(s) 678
Bbv12I GWGCWC 1 cut(s) 307
BbvI GCAGC 1 cut(s) 740
BccI CCATC 1 cut(s) 87
BciT130I CCWGG 1 cut(s) 357
BcnI CCSGG 1 cut(s) 180
BcoDI GTCTC 1 cut(s) 15
BfmI CTRYAG 2 cut(s) 496, 734
BfoI RGCGCY 2 cut(s) 436, 599
BisI GCNGC 2 cut(s) 701, 754
BlsI GCNGC 2 cut(s) 702, 755
Bme1390I CCNGG 2 cut(s) 180, 357
Bme18I GGWCC 1 cut(s) 176
BmgT120I GGNCC 1 cut(s) 176
BmiI GGNNCC 1 cut(s) 793
BmrFI CCNGG 2 cut(s) 180, 357
BmrI ACTGGG 1 cut(s) 531
BmuI ACTGGG 1 cut(s) 531
BpiI GAAGAC 1 cut(s) 678
BpmI CTGGAG 1 cut(s) 46
BpuMI CCSGG 1 cut(s) 180
BsaBI GATNNNNATC 2 cut(s) 97, 462
BsaJI CCNNGG 3 cut(s) 344, 355, 764
BsaXI ACNNNNNCTCC 2 cut(s) 422, 452
Bsc4I CCNNNNNNNGG 4 cut(s) 227, 323, 412, 749
Bse1I ACTGG 5 cut(s) 29, 321, 436, 526, 558
Bse3DI GCAATG 1 cut(s) 356
Bse8I GATNNNNATC 2 cut(s) 97, 462
BseBI CCWGG 1 cut(s) 357
BseDI CCNNGG 3 cut(s) 344, 355, 764
BseJI GATNNNNATC 2 cut(s) 97, 462
BseLI CCNNNNNNNGG 4 cut(s) 227, 323, 412, 749
BseMI GCAATG 1 cut(s) 356
BseNI ACTGG 5 cut(s) 29, 321, 436, 526, 558
BseRI GAGGAG 1 cut(s) 670
BseXI GCAGC 1 cut(s) 740
BsiHKAI GWGCWC 1 cut(s) 307
BsiSI CCGG 1 cut(s) 179
BslFI GGGAC 2 cut(s) 92, 403
BslI CCNNNNNNNGG 4 cut(s) 227, 323, 412, 749
BsmAI GTCTC 1 cut(s) 15
BsmFI GGGAC 2 cut(s) 92, 403
Bsp1286I GDGCHC 1 cut(s) 307
Bsp1407I TGTACA 1 cut(s) 613
Bsp19I CCATGG 1 cut(s) 764
BspACI CCGC 1 cut(s) 700
BspLI GGNNCC 1 cut(s) 793
BspMAI CTGCAG 1 cut(s) 500
BsrDI GCAATG 1 cut(s) 356
BsrGI TGTACA 1 cut(s) 613
BsrI ACTGG 5 cut(s) 29, 321, 436, 526, 558
BssECI CCNNGG 3 cut(s) 344, 355, 764
BssT1I CCWWGG 1 cut(s) 764
Bst2UI CCWGG 1 cut(s) 357
Bst4CI ACNGT 2 cut(s) 43, 738
Bst6I CTCTTC 1 cut(s) 647
BstAUI TGTACA 1 cut(s) 613
BstC8I GCNNGC 3 cut(s) 33, 247, 758
BstDEI CTNAG 1 cut(s) 400
BstDSI CCRYGG 1 cut(s) 764
BstH2I RGCGCY 2 cut(s) 436, 599
BstHHI GCGC 2 cut(s) 435, 598
BstMAI GTCTC 1 cut(s) 15
BstMWI GCNNNNNNNGC 2 cut(s) 302, 706
BstNI CCWGG 1 cut(s) 357
BstSCI CCNGG 2 cut(s) 178, 355
BstSFI CTRYAG 2 cut(s) 496, 734
BstV1I GCAGC 1 cut(s) 740
BstV2I GAAGAC 1 cut(s) 678
BtgI CCRYGG 1 cut(s) 764
BtsIMutI CAGTG 1 cut(s) 328
Cac8I GCNNGC 3 cut(s) 33, 247, 758
CfoI GCGC 2 cut(s) 435, 598
Cfr13I GGNCC 1 cut(s) 176
Csp6I GTAC 2 cut(s) 448, 614
CspCI CAANNNNNGTGG 2 cut(s) 99, 134
CviAII CATG 7 cut(s) 70, 223, 281, 308, 427, 620, 765
CviJI RGCY 6 cut(s) 134, 231, 249, 399, 517, 753
CviKI_1 RGCY 6 cut(s) 134, 231, 249, 399, 517, 753
CviQI GTAC 2 cut(s) 448, 614
DdeI CTNAG 1 cut(s) 400
Eam1104I CTCTTC 1 cut(s) 647
EarI CTCTTC 1 cut(s) 647
Eco130I CCWWGG 1 cut(s) 764
Eco32I GATATC 1 cut(s) 505
Eco47I GGWCC 1 cut(s) 176
Eco47III AGCGCT 1 cut(s) 597
Eco57I CTGAAG 3 cut(s) 98, 612, 658
EcoRII CCWGG 1 cut(s) 355
EcoRV GATATC 1 cut(s) 505
EcoT14I CCWWGG 1 cut(s) 764
EcoT22I ATGCAT 1 cut(s) 298
ErhI CCWWGG 1 cut(s) 764
FaeI CATG 7 cut(s) 73, 226, 284, 311, 430, 623, 768
FaqI GGGAC 2 cut(s) 92, 403
FatI CATG 7 cut(s) 69, 222, 280, 307, 426, 619, 764
FauNDI CATATG 1 cut(s) 640
Fnu4HI GCNGC 2 cut(s) 701, 754
Fsp4HI GCNGC 2 cut(s) 701, 754
GlaI GCGC 2 cut(s) 434, 597
GluI GCNGC 2 cut(s) 701, 754
GsuI CTGGAG 1 cut(s) 46
HaeII RGCGCY 2 cut(s) 436, 599
HapII CCGG 1 cut(s) 179
HhaI GCGC 2 cut(s) 435, 598
Hin1II CATG 7 cut(s) 73, 226, 284, 311, 430, 623, 768
Hin6I GCGC 2 cut(s) 433, 596
HinP1I GCGC 2 cut(s) 433, 596
HindIII AAGCTT 1 cut(s) 397
HinfI GANTC 1 cut(s) 360
HpaII CCGG 1 cut(s) 179
HphI GGTGA 3 cut(s) 458, 467, 732
Hpy188I TCNGA 1 cut(s) 169
Hpy188III TCNNGA 3 cut(s) 370, 478, 590
HpyAV CCTTC 3 cut(s) 682, 771, 793
HpyCH4III ACNGT 2 cut(s) 43, 738
HpyCH4V TGCA 5 cut(s) 296, 486, 498, 576, 582
HpyF10VI GCNNNNNNNGC 2 cut(s) 302, 706
HpyF3I CTNAG 1 cut(s) 400
Hsp92II CATG 7 cut(s) 73, 226, 284, 311, 430, 623, 768
HspAI GCGC 2 cut(s) 433, 596
LmnI GCTCC 2 cut(s) 302, 430
Lsp1109I GCAGC 1 cut(s) 740
MaeIII GTNAC 3 cut(s) 51, 509, 738
MboII GAAGA 3 cut(s) 664, 678, 714
MfeI CAATTG 2 cut(s) 102, 710
MhlI GDGCHC 1 cut(s) 307
MluCI AATT 8 cut(s) 74, 80, 102, 255, 481, 531, 710, 770
MnlI CCTC 5 cut(s) 21, 328, 354, 438, 648
Mph1103I ATGCAT 1 cut(s) 298
MroXI GAANNNNTTC 1 cut(s) 565
MseI TTAA 2 cut(s) 83, 773
MslI CAYNNNNRTG 1 cut(s) 267
MspI CCGG 1 cut(s) 179
MspR9I CCNGG 2 cut(s) 180, 357
MunI CAATTG 2 cut(s) 102, 710
MvaI CCWGG 1 cut(s) 357
MwoI GCNNNNNNNGC 2 cut(s) 302, 706
NciI CCSGG 1 cut(s) 180
NcoI CCATGG 1 cut(s) 764
NdeI CATATG 1 cut(s) 640
NlaIII CATG 7 cut(s) 73, 226, 284, 311, 430, 623, 768
NlaIV GGNNCC 1 cut(s) 793
NmeAIII GCCGAG 1 cut(s) 325
NmuCI GTSAC 2 cut(s) 51, 738
NsiI ATGCAT 1 cut(s) 298
OliI CACNNNNGTG 1 cut(s) 267
PdmI GAANNNNTTC 1 cut(s) 565
PfeI GAWTC 1 cut(s) 360
PkrI GCNGC 2 cut(s) 702, 755
Psp6I CCWGG 1 cut(s) 355
PspGI CCWGG 1 cut(s) 355
PspN4I GGNNCC 1 cut(s) 793
PspPI GGNCC 1 cut(s) 176
PstI CTGCAG 1 cut(s) 500
RsaI GTAC 2 cut(s) 449, 615
RsaNI GTAC 2 cut(s) 448, 614
RseI CAYNNNNRTG 1 cut(s) 267
SaqAI TTAA 2 cut(s) 83, 773
SatI GCNGC 2 cut(s) 701, 754
Sau96I GGNCC 1 cut(s) 176
ScrFI CCNGG 2 cut(s) 180, 357
SduI GDGCHC 1 cut(s) 307
SfcI CTRYAG 2 cut(s) 496, 734
SinI GGWCC 1 cut(s) 176
SmiMI CAYNNNNRTG 1 cut(s) 267
Sse9I AATT 8 cut(s) 74, 80, 102, 255, 481, 531, 710, 770
SsiI CCGC 1 cut(s) 700
StyD4I CCNGG 2 cut(s) 178, 355
StyI CCWWGG 1 cut(s) 764
TaaI ACNGT 2 cut(s) 43, 738
TaqI TCGA 2 cut(s) 161, 550
TasI AATT 8 cut(s) 74, 80, 102, 255, 481, 531, 710, 770
TatI WGTACW 1 cut(s) 613
TauI GCSGC 1 cut(s) 703
TfiI GAWTC 1 cut(s) 360
Tru1I TTAA 2 cut(s) 83, 773
Tru9I TTAA 2 cut(s) 83, 773
TscAI CASTG 1 cut(s) 328
TseFI GTSAC 2 cut(s) 51, 738
TseI GCWGC 1 cut(s) 753
Tsp45I GTSAC 2 cut(s) 51, 738
TspDTI ATGAA 5 cut(s) 86, 239, 269, 415, 714
TspRI CASTG 1 cut(s) 328
VpaK11BI GGWCC 1 cut(s) 176
XapI RAATTY 2 cut(s) 74, 255
XmnI GAANNNNTTC 1 cut(s) 565
Zsp2I ATGCAT 1 cut(s) 298
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.