FvH4_3g00201

DNA-directed RNA polymerases IV and V subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb3
OG0005178
Physical Location & Seq
Reverse (-)
116625 .. 119962
3338 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_3g00201.t7

Sequence Viewer

Length: 636 bp
ATGTCGGACAAAGGTGGAAAGGGGTTCACTGCTGTACCTAAGGGAAAGGGAAAAGGAGGCAAATCTTCACTCAAGGAAGCTACTCCCAAAGGCAAGGACGATGGCCCAGCAAAGTCCAAGAAGACCAGAAATGTTCAGTTTTCTTCTCAAGCTGCTGCTTCCACCAAAGCCAATTCAGGAAAGGGGGGACAAGCCGATGGTGGAGCAAAGAAAGATAAAGAACCACTGCAGCTCAAACTTGAGAATGAATTGCCAAAGGGTGCCAAATGTCTGATGGATTGTGAGGCTGCGGATATCTTGCAAGGAGTTCAGGACCATATGGTCATATTGTCCAAAGATCCATCAATTAAACTCCCTGTATCCTTCGATAGGGCACTGCAGTACACAGAAAAAAGCACCAACTATACAGATCCTGAGTCTGTCAGACAAGTTCTTCAGAATCTCAAAACATATGGTGTCACAGATGGCGAGATTTGTGTGATGGCTAATGTGTATCCAGAAACTGCTGATGAAGTTTTTGCTCTACTCCCGTCCTTGAAGGCTAGGAGAATCATGCTCGACGACCCAGTCAATGATGTTTTGAGTGAGCTAGCTAAGCTTAAAAAGCGTCTAGATGCAGTTGGAGCACTGATATGA
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

212

Amino Acids

22.55

Weight (kDa)

9.07

Isoelectric Point (pI)

31.18

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb4 PF03874 87 - 197 1.1e-11 RNA polymerase Rpb4
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)
AasI GACNNNNNNGTC 2 cut(s) 320, 566
AccB1I GGYRCC 1 cut(s) 260
AciI CCGC 1 cut(s) 290
AclWI GGATC 2 cut(s) 332, 404
AcuI CTGAAG 1 cut(s) 419
AfaI GTAC 2 cut(s) 36, 383
AfiI CCNNNNNNNGG 1 cut(s) 369
AgsI TTSAA 1 cut(s) 538
AluBI AGCT 6 cut(s) 80, 152, 232, 589, 593, 598
AluI AGCT 6 cut(s) 80, 152, 232, 589, 593, 598
Alw21I GWGCWC 1 cut(s) 628
AlwI GGATC 2 cut(s) 332, 404
AlwNI CAGNNNCTG 2 cut(s) 413, 503
AoxI GGCC 1 cut(s) 103
ApeKI GCWGC 4 cut(s) 152, 155, 229, 287
AspS9I GGNCC 2 cut(s) 104, 313
AsuNHI GCTAGC 1 cut(s) 589
AvaII GGWCC 1 cut(s) 313
AxyI CCTNAGG 1 cut(s) 39
BaeGI GKGCMC 1 cut(s) 376
BaeI ACNNNNGTAYC 2 cut(s) 18, 51
BanI GGYRCC 1 cut(s) 260
BbsI GAAGAC 1 cut(s) 128
Bbv12I GWGCWC 1 cut(s) 628
BbvI GCAGC 4 cut(s) 139, 142, 241, 274
BccI CCATC 6 cut(s) 95, 191, 268, 349, 458, 475
BciVI GTATCC 2 cut(s) 370, 504
BfaI CTAG 3 cut(s) 543, 590, 611
BfmI CTRYAG 2 cut(s) 227, 377
BfuI GTATCC 2 cut(s) 370, 504
BisI GCNGC 4 cut(s) 153, 156, 230, 288
BlpI GCTNAGC 1 cut(s) 594
BlsI GCNGC 4 cut(s) 154, 157, 231, 289
Bme18I GGWCC 1 cut(s) 313
BmgT120I GGNCC 2 cut(s) 104, 313
BmiI GGNNCC 1 cut(s) 262
BmrI ACTGGG 1 cut(s) 560
BmsI GCATC 1 cut(s) 604
BmtI GCTAGC 1 cut(s) 593
BmuI ACTGGG 1 cut(s) 560
BpiI GAAGAC 1 cut(s) 128
Bpu1102I GCTNAGC 1 cut(s) 594
BpuEI CTTGAG 3 cut(s) 56, 132, 260
Bsc4I CCNNNNNNNGG 1 cut(s) 369
Bse1I ACTGG 1 cut(s) 566
Bse21I CCTNAGG 1 cut(s) 39
BseLI CCNNNNNNNGG 1 cut(s) 369
BseMII CTCAG 1 cut(s) 405
BseNI ACTGG 1 cut(s) 566
BseSI GKGCMC 1 cut(s) 376
BseXI GCAGC 4 cut(s) 139, 142, 241, 274
BseYI CCCAGC 1 cut(s) 106
BshFI GGCC 1 cut(s) 105
BshNI GGYRCC 1 cut(s) 260
BsiHKAI GWGCWC 1 cut(s) 628
BslFI GGGAC 1 cut(s) 201
BslI CCNNNNNNNGG 1 cut(s) 369
BsmFI GGGAC 1 cut(s) 201
BsnI GGCC 1 cut(s) 105
Bsp1286I GDGCHC 2 cut(s) 376, 628
Bsp143I GATC 2 cut(s) 337, 409
Bsp1720I GCTNAGC 1 cut(s) 594
BspACI CCGC 1 cut(s) 290
BspANI GGCC 1 cut(s) 105
BspCNI CTCAG 1 cut(s) 406
BspLI GGNNCC 1 cut(s) 262
BspMAI CTGCAG 2 cut(s) 231, 381
BspOI GCTAGC 1 cut(s) 593
BspPI GGATC 2 cut(s) 332, 404
BspT107I GGYRCC 1 cut(s) 260
BsrI ACTGG 1 cut(s) 566
BssMI GATC 2 cut(s) 337, 409
BstC8I GCNNGC 1 cut(s) 591
BstDEI CTNAG 3 cut(s) 39, 414, 594
BstENI CCTNNNNNAGG 1 cut(s) 367
BstKTI GATC 2 cut(s) 340, 412
BstMBI GATC 2 cut(s) 337, 409
BstMWI GCNNNNNNNGC 3 cut(s) 595, 604, 623
BstSFI CTRYAG 2 cut(s) 227, 377
BstSLI GKGCMC 1 cut(s) 376
BstV1I GCAGC 4 cut(s) 139, 142, 241, 274
BstV2I GAAGAC 1 cut(s) 128
BstX2I RGATCY 2 cut(s) 337, 409
BstYI RGATCY 2 cut(s) 337, 409
Bsu36I CCTNAGG 1 cut(s) 39
BsuI GTATCC 2 cut(s) 370, 504
BsuRI GGCC 1 cut(s) 105
BtsI GCAGTG 3 cut(s) 27, 224, 374
BtsIMutI CAGTG 4 cut(s) 27, 224, 374, 626
Cac8I GCNNGC 1 cut(s) 591
CaiI CAGNNNCTG 2 cut(s) 413, 503
Cfr13I GGNCC 2 cut(s) 104, 313
CseI GACGC 1 cut(s) 596
Csp6I GTAC 2 cut(s) 35, 382
CviAII CATG 1 cut(s) 553
CviQI GTAC 2 cut(s) 35, 382
DdeI CTNAG 3 cut(s) 39, 414, 594
DpnI GATC 2 cut(s) 339, 411
DpnII GATC 2 cut(s) 337, 409
DrdI GACNNNNNNGTC 2 cut(s) 320, 566
DseDI GACNNNNNNGTC 2 cut(s) 320, 566
Eco32I GATATC 1 cut(s) 295
Eco47I GGWCC 1 cut(s) 313
Eco57I CTGAAG 1 cut(s) 419
Eco81I CCTNAGG 1 cut(s) 39
EcoNI CCTNNNNNAGG 1 cut(s) 367
EcoRV GATATC 1 cut(s) 295
FaeI CATG 1 cut(s) 556
FaiI YATR 8 cut(s) 318, 320, 326, 405, 451, 453, 554, 634
FaqI GGGAC 1 cut(s) 201
FatI CATG 1 cut(s) 552
FauNDI CATATG 2 cut(s) 318, 451
Fnu4HI GCNGC 4 cut(s) 153, 156, 230, 288
Fsp4HI GCNGC 4 cut(s) 153, 156, 230, 288
FspBI CTAG 3 cut(s) 543, 590, 611
GluI GCNGC 4 cut(s) 153, 156, 230, 288
GsaI CCCAGC 1 cut(s) 110
HaeIII GGCC 1 cut(s) 105
HgaI GACGC 1 cut(s) 596
Hin1II CATG 1 cut(s) 556
HindIII AAGCTT 1 cut(s) 596
HinfI GANTC 3 cut(s) 416, 439, 549
Hpy166II GTNNAC 2 cut(s) 27, 384
Hpy188I TCNGA 4 cut(s) 7, 273, 425, 438
Hpy188III TCNNGA 5 cut(s) 177, 311, 413, 497, 611
Hpy8I GTNNAC 2 cut(s) 27, 384
Hpy99I CGWCG 1 cut(s) 563
HpyAV CCTTC 2 cut(s) 373, 532
HpyCH4V TGCA 4 cut(s) 229, 301, 379, 617
HpyF10VI GCNNNNNNNGC 3 cut(s) 595, 604, 623
HpyF3I CTNAG 3 cut(s) 39, 414, 594
Hsp92II CATG 1 cut(s) 556
Kzo9I GATC 2 cut(s) 337, 409
LmnI GCTCC 2 cut(s) 203, 623
LpnPI CCDG 8 cut(s) 120, 139, 162, 296, 369, 426, 510, 579
Lsp1109I GCAGC 4 cut(s) 139, 142, 241, 274
LweI GCATC 1 cut(s) 604
MaeI CTAG 3 cut(s) 543, 590, 611
MaeIII GTNAC 1 cut(s) 457
MalI GATC 2 cut(s) 339, 411
MboI GATC 2 cut(s) 337, 409
MboII GAAGA 4 cut(s) 57, 133, 135, 425
MflI RGATCY 2 cut(s) 337, 409
MhlI GDGCHC 2 cut(s) 376, 628
MluCI AATT 3 cut(s) 172, 248, 345
MlyI GAGTC 1 cut(s) 425
MmeI TCCRAC 1 cut(s) 601
MnlI CCTC 2 cut(s) 50, 277
MseI TTAA 2 cut(s) 348, 600
MslI CAYNNNNRTG 1 cut(s) 631
MwoI GCNNNNNNNGC 3 cut(s) 595, 604, 623
NdeI CATATG 2 cut(s) 318, 451
NdeII GATC 2 cut(s) 337, 409
NheI GCTAGC 1 cut(s) 589
NlaIII CATG 1 cut(s) 556
NlaIV GGNNCC 1 cut(s) 262
NmuCI GTSAC 1 cut(s) 457
PfeI GAWTC 2 cut(s) 439, 549
PflFI GACNNNGTC 1 cut(s) 566
PkrI GCNGC 4 cut(s) 154, 157, 231, 289
PleI GAGTC 1 cut(s) 424
PpsI GAGTC 1 cut(s) 424
PspFI CCCAGC 1 cut(s) 106
PspN4I GGNNCC 1 cut(s) 262
PspPI GGNCC 2 cut(s) 104, 313
PstI CTGCAG 2 cut(s) 231, 381
PstNI CAGNNNCTG 2 cut(s) 413, 503
PsuI RGATCY 2 cut(s) 337, 409
PsyI GACNNNGTC 1 cut(s) 566
RsaI GTAC 2 cut(s) 36, 383
RsaNI GTAC 2 cut(s) 35, 382
RseI CAYNNNNRTG 1 cut(s) 631
SaqAI TTAA 2 cut(s) 348, 600
SatI GCNGC 4 cut(s) 153, 156, 230, 288
Sau3AI GATC 2 cut(s) 337, 409
Sau96I GGNCC 2 cut(s) 104, 313
SchI GAGTC 1 cut(s) 425
SduI GDGCHC 2 cut(s) 376, 628
SetI ASST 8 cut(s) 16, 40, 82, 154, 234, 591, 595, 600
SfaNI GCATC 1 cut(s) 604
SfcI CTRYAG 2 cut(s) 227, 377
SinI GGWCC 1 cut(s) 313
SmiMI CAYNNNNRTG 1 cut(s) 631
SmlI CTYRAG 3 cut(s) 71, 147, 239
SmoI CTYRAG 3 cut(s) 71, 147, 239
Sse9I AATT 3 cut(s) 172, 248, 345
SsiI CCGC 1 cut(s) 290
SspMI CTAG 3 cut(s) 543, 590, 611
TaqI TCGA 2 cut(s) 366, 558
TasI AATT 3 cut(s) 172, 248, 345
TatI WGTACW 1 cut(s) 381
TfiI GAWTC 2 cut(s) 439, 549
Tru1I TTAA 2 cut(s) 348, 600
Tru9I TTAA 2 cut(s) 348, 600
TscAI CASTG 4 cut(s) 34, 231, 381, 633
TseFI GTSAC 1 cut(s) 457
TseI GCWGC 4 cut(s) 152, 155, 229, 287
Tsp45I GTSAC 1 cut(s) 457
TspDTI ATGAA 2 cut(s) 261, 525
TspRI CASTG 4 cut(s) 34, 231, 381, 633
Tth111I GACNNNGTC 1 cut(s) 566
VpaK11BI GGWCC 1 cut(s) 313
XagI CCTNNNNNAGG 1 cut(s) 367
XbaI TCTAGA 1 cut(s) 610
XcmI CCANNNNNNNNNTGG 1 cut(s) 271
XspI CTAG 3 cut(s) 543, 590, 611
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.