Rh5DG002300

DNA-directed RNA polymerases IV and V subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5D
OG0005178
Physical Location & Seq
Reverse (-)
197333 .. 199986
2654 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5DG002300.1

Sequence Viewer

Length: 627 bp
ATGTCGGACAAAGGTGGAAAGGGTTTTACTTTGCCCAATGGAAAAGGAGTGAAATCCACTCCTCTCAAGGATGCTCCTCCCAAAGATAGCGCAGCCAAGTCCAAGAAGGCAAGAAATGTTCAGTTTTCTTCTCAAGGTTCAAAGTCTGATAAGTCTGCTCCTGCTTCCAGCAAAGCTAATTCGGGAAAGGGAGGAAAAGGAGACAGTGGAATTGGAGGAAAGAAAGAACAAGAACCACTGCAGCTCAAAGTTGAGAATGAACTGCCTAAGGGTGCCAAATGTCTGATGGATTGTGAGGCTGCGGATATCTTGCAAGGAATCCAGGAGCAGATGGTCATATTGTCTAAAGATCCTACAATTAAACTCCCTGTATCCTTCGATAGGGGACTGCAGTACACCAAAAAAAGCACCCACTATACAGATCCTGAGTCTGTCAGACGAGTTCTTGAGAATCTCAAAACATATGGTGTCACAGACGGCGAGATATGTGTGATTGCCAATGTGTATCCAGAAACTGCCGATGAAGTTTTTGCTCTACTCCCTTCCTTGAAGGCTAGGAGAATCATGCTCGACGACCCAGTCAATGATGTTTTGAGTGAGCTAGCTAAGCTTAAAAAGTCAGCATAA
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

208

Amino Acids

22.28

Weight (kDa)

9.18

Isoelectric Point (pI)

38.52

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb4 PF03874 94 - 204 3.4e-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 1 cut(s) 578
AccB1I GGYRCC 1 cut(s) 272
AciI CCGC 1 cut(s) 302
AclWI GGATC 2 cut(s) 344, 416
AfaI GTAC 1 cut(s) 395
AfiI CCNNNNNNNGG 1 cut(s) 381
AgsI TTSAA 2 cut(s) 141, 550
AjnI CCWGG 1 cut(s) 321
AluBI AGCT 5 cut(s) 176, 244, 601, 605, 610
AluI AGCT 5 cut(s) 176, 244, 601, 605, 610
Alw26I GTCTC 1 cut(s) 195
AlwI GGATC 2 cut(s) 344, 416
AlwNI CAGNNNCTG 2 cut(s) 425, 515
ApeKI GCWGC 3 cut(s) 92, 241, 299
AspLEI GCGC 1 cut(s) 92
AsuNHI GCTAGC 1 cut(s) 601
AxyI CCTNAGG 1 cut(s) 267
BanI GGYRCC 1 cut(s) 272
BbvI GCAGC 3 cut(s) 104, 253, 286
BccI CCATC 2 cut(s) 280, 325
BceAI ACGGC 1 cut(s) 493
BciT130I CCWGG 1 cut(s) 323
BciVI GTATCC 2 cut(s) 382, 516
BcoDI GTCTC 1 cut(s) 195
BfaI CTAG 2 cut(s) 555, 602
BfmI CTRYAG 2 cut(s) 239, 389
BfuI GTATCC 2 cut(s) 382, 516
BisI GCNGC 3 cut(s) 93, 242, 300
BlpI GCTNAGC 1 cut(s) 606
BlsI GCNGC 3 cut(s) 94, 243, 301
Bme1390I CCNGG 1 cut(s) 323
BmiI GGNNCC 1 cut(s) 274
BmrFI CCNGG 1 cut(s) 323
BmrI ACTGGG 1 cut(s) 572
BmsI GCATC 1 cut(s) 61
BmtI GCTAGC 1 cut(s) 605
BmuI ACTGGG 1 cut(s) 572
Bpu1102I GCTNAGC 1 cut(s) 606
BpuEI CTTGAG 3 cut(s) 50, 117, 467
Bsc4I CCNNNNNNNGG 1 cut(s) 381
Bse1I ACTGG 1 cut(s) 578
Bse21I CCTNAGG 1 cut(s) 267
BseBI CCWGG 1 cut(s) 323
BseGI GGATG 1 cut(s) 76
BseLI CCNNNNNNNGG 1 cut(s) 381
BseMII CTCAG 1 cut(s) 417
BseNI ACTGG 1 cut(s) 578
BseRI GAGGAG 2 cut(s) 51, 66
BseXI GCAGC 3 cut(s) 104, 253, 286
BshNI GGYRCC 1 cut(s) 272
BslFI GGGAC 1 cut(s) 399
BslI CCNNNNNNNGG 1 cut(s) 381
BsmAI GTCTC 1 cut(s) 195
BsmFI GGGAC 1 cut(s) 399
Bsp143I GATC 2 cut(s) 349, 421
Bsp1720I GCTNAGC 1 cut(s) 606
BspACI CCGC 1 cut(s) 302
BspCNI CTCAG 1 cut(s) 418
BspLI GGNNCC 1 cut(s) 274
BspMAI CTGCAG 2 cut(s) 243, 393
BspOI GCTAGC 1 cut(s) 605
BspPI GGATC 2 cut(s) 344, 416
BspT107I GGYRCC 1 cut(s) 272
BsrI ACTGG 1 cut(s) 578
BssMI GATC 2 cut(s) 349, 421
Bst2UI CCWGG 1 cut(s) 323
Bst4CI ACNGT 1 cut(s) 206
BstC8I GCNNGC 1 cut(s) 603
BstDEI CTNAG 3 cut(s) 267, 426, 606
BstENI CCTNNNNNAGG 1 cut(s) 379
BstF5I GGATG 1 cut(s) 76
BstHHI GCGC 1 cut(s) 92
BstKTI GATC 2 cut(s) 352, 424
BstMAI GTCTC 1 cut(s) 195
BstMBI GATC 2 cut(s) 349, 421
BstMWI GCNNNNNNNGC 1 cut(s) 607
BstNI CCWGG 1 cut(s) 323
BstSCI CCNGG 1 cut(s) 321
BstSFI CTRYAG 2 cut(s) 239, 389
BstV1I GCAGC 3 cut(s) 104, 253, 286
BstX2I RGATCY 2 cut(s) 349, 421
BstYI RGATCY 2 cut(s) 349, 421
Bsu36I CCTNAGG 1 cut(s) 267
BsuI GTATCC 2 cut(s) 382, 516
BtsCI GGATG 1 cut(s) 76
BtsI GCAGTG 1 cut(s) 236
BtsIMutI CAGTG 2 cut(s) 211, 236
Cac8I GCNNGC 1 cut(s) 603
CaiI CAGNNNCTG 2 cut(s) 425, 515
CfoI GCGC 1 cut(s) 92
Csp6I GTAC 1 cut(s) 394
CviAII CATG 1 cut(s) 565
CviJI RGCY 8 cut(s) 95, 176, 244, 299, 554, 601, 605, 610
CviKI_1 RGCY 8 cut(s) 95, 176, 244, 299, 554, 601, 605, 610
CviQI GTAC 1 cut(s) 394
DdeI CTNAG 3 cut(s) 267, 426, 606
DpnI GATC 2 cut(s) 351, 423
DpnII GATC 2 cut(s) 349, 421
DrdI GACNNNNNNGTC 1 cut(s) 578
DseDI GACNNNNNNGTC 1 cut(s) 578
Eco32I GATATC 1 cut(s) 307
Eco81I CCTNAGG 1 cut(s) 267
EcoNI CCTNNNNNAGG 1 cut(s) 379
EcoRII CCWGG 1 cut(s) 321
EcoRV GATATC 1 cut(s) 307
FaeI CATG 1 cut(s) 568
FaiI YATR 7 cut(s) 338, 417, 463, 465, 487, 566, 625
FaqI GGGAC 1 cut(s) 399
FatI CATG 1 cut(s) 564
FauNDI CATATG 1 cut(s) 463
Fnu4HI GCNGC 3 cut(s) 93, 242, 300
FokI GGATG 1 cut(s) 83
Fsp4HI GCNGC 3 cut(s) 93, 242, 300
FspBI CTAG 2 cut(s) 555, 602
GlaI GCGC 1 cut(s) 91
GluI GCNGC 3 cut(s) 93, 242, 300
HhaI GCGC 1 cut(s) 92
Hin1II CATG 1 cut(s) 568
Hin6I GCGC 1 cut(s) 90
HinP1I GCGC 1 cut(s) 90
HindIII AAGCTT 1 cut(s) 608
HinfI GANTC 4 cut(s) 318, 428, 451, 561
Hpy166II GTNNAC 1 cut(s) 396
Hpy188I TCNGA 4 cut(s) 7, 148, 285, 437
Hpy188III TCNNGA 4 cut(s) 183, 425, 446, 509
Hpy8I GTNNAC 1 cut(s) 396
Hpy99I CGWCG 1 cut(s) 575
HpyAV CCTTC 4 cut(s) 100, 385, 544, 552
HpyCH4III ACNGT 1 cut(s) 206
HpyCH4V TGCA 3 cut(s) 241, 313, 391
HpyF10VI GCNNNNNNNGC 1 cut(s) 607
HpyF3I CTNAG 3 cut(s) 267, 426, 606
Hsp92II CATG 1 cut(s) 568
HspAI GCGC 1 cut(s) 90
Kzo9I GATC 2 cut(s) 349, 421
LmnI GCTCC 3 cut(s) 79, 163, 325
LpnPI CCDG 8 cut(s) 174, 181, 308, 335, 381, 438, 522, 591
Lsp1109I GCAGC 3 cut(s) 104, 253, 286
LweI GCATC 1 cut(s) 61
MaeI CTAG 2 cut(s) 555, 602
MaeIII GTNAC 1 cut(s) 469
MalI GATC 2 cut(s) 351, 423
MboI GATC 2 cut(s) 349, 421
MboII GAAGA 1 cut(s) 120
MflI RGATCY 2 cut(s) 349, 421
MluCI AATT 3 cut(s) 178, 210, 357
MlyI GAGTC 1 cut(s) 437
MnlI CCTC 5 cut(s) 72, 87, 185, 209, 289
MseI TTAA 2 cut(s) 360, 612
MspR9I CCNGG 1 cut(s) 323
MvaI CCWGG 1 cut(s) 323
MwoI GCNNNNNNNGC 1 cut(s) 607
NdeI CATATG 1 cut(s) 463
NdeII GATC 2 cut(s) 349, 421
NheI GCTAGC 1 cut(s) 601
NlaIII CATG 1 cut(s) 568
NlaIV GGNNCC 1 cut(s) 274
NmuCI GTSAC 1 cut(s) 469
PfeI GAWTC 3 cut(s) 318, 451, 561
PflFI GACNNNGTC 1 cut(s) 578
PfoI TCCNGGA 1 cut(s) 321
PkrI GCNGC 3 cut(s) 94, 243, 301
PleI GAGTC 1 cut(s) 436
PpsI GAGTC 1 cut(s) 436
Psp6I CCWGG 1 cut(s) 321
PspGI CCWGG 1 cut(s) 321
PspN4I GGNNCC 1 cut(s) 274
PstI CTGCAG 2 cut(s) 243, 393
PstNI CAGNNNCTG 2 cut(s) 425, 515
PsuI RGATCY 2 cut(s) 349, 421
PsyI GACNNNGTC 1 cut(s) 578
RsaI GTAC 1 cut(s) 395
RsaNI GTAC 1 cut(s) 394
SaqAI TTAA 2 cut(s) 360, 612
SatI GCNGC 3 cut(s) 93, 242, 300
Sau3AI GATC 2 cut(s) 349, 421
SchI GAGTC 1 cut(s) 437
ScrFI CCNGG 1 cut(s) 323
SetI ASST 7 cut(s) 16, 139, 178, 246, 603, 607, 612
SfaNI GCATC 1 cut(s) 61
SfcI CTRYAG 2 cut(s) 239, 389
SmlI CTYRAG 3 cut(s) 65, 132, 446
SmoI CTYRAG 3 cut(s) 65, 132, 446
Sse9I AATT 3 cut(s) 178, 210, 357
SsiI CCGC 1 cut(s) 302
SspMI CTAG 2 cut(s) 555, 602
StyD4I CCNGG 1 cut(s) 321
TaaI ACNGT 1 cut(s) 206
TaqI TCGA 2 cut(s) 378, 570
TasI AATT 3 cut(s) 178, 210, 357
TatI WGTACW 1 cut(s) 393
TfiI GAWTC 3 cut(s) 318, 451, 561
Tru1I TTAA 2 cut(s) 360, 612
Tru9I TTAA 2 cut(s) 360, 612
TscAI CASTG 2 cut(s) 211, 243
TseFI GTSAC 1 cut(s) 469
TseI GCWGC 3 cut(s) 92, 241, 299
Tsp45I GTSAC 1 cut(s) 469
TspDTI ATGAA 2 cut(s) 273, 537
TspRI CASTG 2 cut(s) 211, 243
Tth111I GACNNNGTC 1 cut(s) 578
XagI CCTNNNNNAGG 1 cut(s) 379
XcmI CCANNNNNNNNNTGG 1 cut(s) 283
XspI CTAG 2 cut(s) 555, 602
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.