RchiOBHm_Chr5g0000271

DNA-directed RNA polymerases IV and V subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
5
OG0005178
Physical Location & Seq
Reverse (-)
174489 .. 178305
3817 bp
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UTR
Exon/CDS
Intron
PRQ28184

Sequence Viewer

Length: 783 bp
ATGGGCATTCTGGACACAATGCAAACGAGAGTGTGGGTGGTATTGTATTGGTATAGCGAGCAAATTCGGTCCACTTCGAATCGACGCCGGCTTCTTCTTCGCTCGCTCCCTCCCTTTTCTGGAACGGACAAAGGGATTTCAAGGAAAGAGTGGCCAATGTCGGACAAAGGTGGAAAGGGTTTTACTTTGCCCAATGGAAAAGGAGTGAAATCCACTCCTCTCAAGGATGCTCCTCTCAAAGATAGCTCAGCCAAGTCCAAGAAGGCCAGAAATGTTCAGTTTTCTTCTCAAGGTTCAAAATCTGATAAGTCTGCTCCTGCTTCCAGCAAAGCTAATTCGGGAAAGGGAGGAAAAGGAGACAGTGGAATTGGAGGAAAGAAAGAACAAGAGCCACTGCAGCTCAAAGTTGAGAATGAACTGCCTAAGGGTGCCAAATGTCTGATGGATTGTGAGGCTGCGGATATCTTGCAAGGAATACAGGAGCAGATGGTCATACTGTCTAAAGATCCTACAATTAAACTCCCTGTATCCTTCGATAGGGGACTGCAGTACACCAAAAAAAGCACCCACTATACAGATCCTGAGTCTGTCAGACGAGTTCTTGAGAATCTCAAAACATATGGTGTCACAGACGGCGAGATATGTGTGATTGCCAATGTGTATCCAGAAACTGCCGATGAAGTTTTTGCTCTACTCCCTTCCTTGAAGGCTAGGAGAATCATGCTCGACGACCCAGTCAATGATGTTTTGAGTGAGCTAGCTAAGCTTAAAAAGTCAGCATAA
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

260

Amino Acids

28.52

Weight (kDa)

9.5

Isoelectric Point (pI)

42.11

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb4 PF03874 146 - 256 5.9e-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) 734
AccB1I GGYRCC 1 cut(s) 428
AciI CCGC 1 cut(s) 458
AclWI GGATC 2 cut(s) 500, 572
AcoI YGGCCR 1 cut(s) 152
AcsI RAATTY 1 cut(s) 63
AcyI GRCGYC 1 cut(s) 85
AfaI GTAC 1 cut(s) 551
AfiI CCNNNNNNNGG 2 cut(s) 119, 537
AgsI TTSAA 3 cut(s) 141, 297, 706
AluBI AGCT 6 cut(s) 246, 332, 400, 757, 761, 766
AluI AGCT 6 cut(s) 246, 332, 400, 757, 761, 766
Alw26I GTCTC 1 cut(s) 351
AlwI GGATC 2 cut(s) 500, 572
AlwNI CAGNNNCTG 2 cut(s) 581, 671
AoxI GGCC 2 cut(s) 152, 264
ApeKI GCWGC 2 cut(s) 397, 455
ApoI RAATTY 1 cut(s) 63
AspS9I GGNCC 1 cut(s) 69
AsuII TTCGAA 1 cut(s) 77
AsuNHI GCTAGC 1 cut(s) 757
AvaII GGWCC 1 cut(s) 69
AxyI CCTNAGG 1 cut(s) 423
BalI TGGCCA 1 cut(s) 154
BanI GGYRCC 1 cut(s) 428
BbvI GCAGC 2 cut(s) 409, 442
BccI CCATC 2 cut(s) 436, 481
BceAI ACGGC 1 cut(s) 649
BciVI GTATCC 2 cut(s) 538, 672
BcoDI GTCTC 1 cut(s) 351
BfaI CTAG 2 cut(s) 711, 758
BfmI CTRYAG 2 cut(s) 395, 545
BfuI GTATCC 2 cut(s) 538, 672
BisI GCNGC 2 cut(s) 398, 456
BlpI GCTNAGC 2 cut(s) 247, 762
BlsI GCNGC 2 cut(s) 399, 457
Bme18I GGWCC 1 cut(s) 69
BmgT120I GGNCC 1 cut(s) 69
BmiI GGNNCC 1 cut(s) 430
BmrI ACTGGG 1 cut(s) 728
BmsI GCATC 1 cut(s) 217
BmtI GCTAGC 1 cut(s) 761
BmuI ACTGGG 1 cut(s) 728
Bpu1102I GCTNAGC 2 cut(s) 247, 762
Bpu14I TTCGAA 1 cut(s) 77
BpuEI CTTGAG 3 cut(s) 206, 273, 623
BsaHI GRCGYC 1 cut(s) 85
Bsc4I CCNNNNNNNGG 2 cut(s) 119, 537
Bse118I RCCGGY 1 cut(s) 87
Bse1I ACTGG 1 cut(s) 734
Bse21I CCTNAGG 1 cut(s) 423
BseGI GGATG 1 cut(s) 232
BseLI CCNNNNNNNGG 2 cut(s) 119, 537
BseMII CTCAG 2 cut(s) 261, 573
BseNI ACTGG 1 cut(s) 734
BseRI GAGGAG 2 cut(s) 207, 222
BseXI GCAGC 2 cut(s) 409, 442
BshFI GGCC 2 cut(s) 154, 266
BshNI GGYRCC 1 cut(s) 428
BsiSI CCGG 1 cut(s) 88
BslFI GGGAC 1 cut(s) 555
BslI CCNNNNNNNGG 2 cut(s) 119, 537
BsmAI GTCTC 1 cut(s) 351
BsmFI GGGAC 1 cut(s) 555
BsmI GAATGC 1 cut(s) 6
BsnI GGCC 2 cut(s) 154, 266
Bsp119I TTCGAA 1 cut(s) 77
Bsp143I GATC 2 cut(s) 505, 577
Bsp1720I GCTNAGC 2 cut(s) 247, 762
BspACI CCGC 1 cut(s) 458
BspANI GGCC 2 cut(s) 154, 266
BspCNI CTCAG 2 cut(s) 260, 574
BspLI GGNNCC 1 cut(s) 430
BspMAI CTGCAG 2 cut(s) 399, 549
BspOI GCTAGC 1 cut(s) 761
BspPI GGATC 2 cut(s) 500, 572
BspT104I TTCGAA 1 cut(s) 77
BspT107I GGYRCC 1 cut(s) 428
BsrFI RCCGGY 1 cut(s) 87
BsrI ACTGG 1 cut(s) 734
BssAI RCCGGY 1 cut(s) 87
BssMI GATC 2 cut(s) 505, 577
BssNI GRCGYC 1 cut(s) 85
Bst4CI ACNGT 2 cut(s) 362, 498
BstACI GRCGYC 1 cut(s) 85
BstBI TTCGAA 1 cut(s) 77
BstC8I GCNNGC 4 cut(s) 59, 89, 104, 759
BstDEI CTNAG 4 cut(s) 247, 423, 582, 762
BstENI CCTNNNNNAGG 1 cut(s) 535
BstF5I GGATG 1 cut(s) 232
BstKTI GATC 2 cut(s) 508, 580
BstMAI GTCTC 1 cut(s) 351
BstMBI GATC 2 cut(s) 505, 577
BstMWI GCNNNNNNNGC 2 cut(s) 397, 763
BstSFI CTRYAG 2 cut(s) 395, 545
BstV1I GCAGC 2 cut(s) 409, 442
BstX2I RGATCY 2 cut(s) 505, 577
BstYI RGATCY 2 cut(s) 505, 577
Bsu36I CCTNAGG 1 cut(s) 423
BsuI GTATCC 2 cut(s) 538, 672
BsuRI GGCC 2 cut(s) 154, 266
BtsCI GGATG 1 cut(s) 232
BtsI GCAGTG 1 cut(s) 392
BtsIMutI CAGTG 2 cut(s) 367, 392
Cac8I GCNNGC 4 cut(s) 59, 89, 104, 759
CaiI CAGNNNCTG 2 cut(s) 581, 671
Cfr10I RCCGGY 1 cut(s) 87
Cfr13I GGNCC 1 cut(s) 69
CseI GACGC 1 cut(s) 93
Csp6I GTAC 1 cut(s) 550
CviAII CATG 1 cut(s) 721
CviQI GTAC 1 cut(s) 550
DdeI CTNAG 4 cut(s) 247, 423, 582, 762
DpnI GATC 2 cut(s) 507, 579
DpnII GATC 2 cut(s) 505, 577
DrdI GACNNNNNNGTC 1 cut(s) 734
DseDI GACNNNNNNGTC 1 cut(s) 734
EaeI YGGCCR 1 cut(s) 152
Eco32I GATATC 1 cut(s) 463
Eco47I GGWCC 1 cut(s) 69
Eco81I CCTNAGG 1 cut(s) 423
EcoNI CCTNNNNNAGG 1 cut(s) 535
EcoRV GATATC 1 cut(s) 463
FaeI CATG 1 cut(s) 724
FaiI YATR 8 cut(s) 54, 494, 573, 619, 621, 643, 722, 781
FaqI GGGAC 1 cut(s) 555
FatI CATG 1 cut(s) 720
FauNDI CATATG 1 cut(s) 619
Fnu4HI GCNGC 2 cut(s) 398, 456
FokI GGATG 1 cut(s) 239
Fsp4HI GCNGC 2 cut(s) 398, 456
FspBI CTAG 2 cut(s) 711, 758
GluI GCNGC 2 cut(s) 398, 456
HaeIII GGCC 2 cut(s) 154, 266
HapII CCGG 1 cut(s) 88
HgaI GACGC 1 cut(s) 93
Hin1I GRCGYC 1 cut(s) 85
Hin1II CATG 1 cut(s) 724
HindIII AAGCTT 1 cut(s) 764
HinfI GANTC 4 cut(s) 79, 584, 607, 717
HpaII CCGG 1 cut(s) 88
Hpy166II GTNNAC 2 cut(s) 72, 552
Hpy188I TCNGA 4 cut(s) 163, 304, 441, 593
Hpy188III TCNNGA 6 cut(s) 11, 120, 339, 581, 602, 665
Hpy8I GTNNAC 2 cut(s) 72, 552
Hpy99I CGWCG 2 cut(s) 87, 731
HpyAV CCTTC 4 cut(s) 256, 541, 700, 708
HpyCH4III ACNGT 2 cut(s) 362, 498
HpyCH4V TGCA 4 cut(s) 22, 397, 469, 547
HpyF10VI GCNNNNNNNGC 2 cut(s) 397, 763
HpyF3I CTNAG 4 cut(s) 247, 423, 582, 762
Hsp92I GRCGYC 1 cut(s) 85
Hsp92II CATG 1 cut(s) 724
KroI GCCGGC 1 cut(s) 87
KroNI GCCGGC 1 cut(s) 89
Kzo9I GATC 2 cut(s) 505, 577
LmnI GCTCC 4 cut(s) 111, 235, 319, 481
Lsp1109I GCAGC 2 cut(s) 409, 442
LweI GCATC 1 cut(s) 217
MaeI CTAG 2 cut(s) 711, 758
MaeIII GTNAC 1 cut(s) 625
MalI GATC 2 cut(s) 507, 579
MboI GATC 2 cut(s) 505, 577
MboII GAAGA 3 cut(s) 86, 89, 276
MflI RGATCY 2 cut(s) 505, 577
MlsI TGGCCA 1 cut(s) 154
MluCI AATT 4 cut(s) 63, 334, 366, 513
MluNI TGGCCA 1 cut(s) 154
MlyI GAGTC 1 cut(s) 593
MmeI TCCRAC 1 cut(s) 141
MnlI CCTC 6 cut(s) 120, 228, 243, 341, 365, 445
Mox20I TGGCCA 1 cut(s) 154
MroNI GCCGGC 1 cut(s) 87
MscI TGGCCA 1 cut(s) 154
MseI TTAA 2 cut(s) 516, 768
Msp20I TGGCCA 1 cut(s) 154
MspI CCGG 1 cut(s) 88
Mva1269I GAATGC 1 cut(s) 6
MwoI GCNNNNNNNGC 2 cut(s) 397, 763
NaeI GCCGGC 1 cut(s) 89
NdeI CATATG 1 cut(s) 619
NdeII GATC 2 cut(s) 505, 577
NgoMIV GCCGGC 1 cut(s) 87
NheI GCTAGC 1 cut(s) 757
NlaIII CATG 1 cut(s) 724
NlaIV GGNNCC 1 cut(s) 430
NmuCI GTSAC 1 cut(s) 625
NspV TTCGAA 1 cut(s) 77
PctI GAATGC 1 cut(s) 6
PdiI GCCGGC 1 cut(s) 89
PfeI GAWTC 3 cut(s) 79, 607, 717
PflFI GACNNNGTC 1 cut(s) 734
PkrI GCNGC 2 cut(s) 399, 457
PleI GAGTC 1 cut(s) 592
PpsI GAGTC 1 cut(s) 592
PspN4I GGNNCC 1 cut(s) 430
PspPI GGNCC 1 cut(s) 69
PstI CTGCAG 2 cut(s) 399, 549
PstNI CAGNNNCTG 2 cut(s) 581, 671
PsuI RGATCY 2 cut(s) 505, 577
PsyI GACNNNGTC 1 cut(s) 734
RsaI GTAC 1 cut(s) 551
RsaNI GTAC 1 cut(s) 550
SaqAI TTAA 2 cut(s) 516, 768
SatI GCNGC 2 cut(s) 398, 456
Sau3AI GATC 2 cut(s) 505, 577
Sau96I GGNCC 1 cut(s) 69
SchI GAGTC 1 cut(s) 593
SetI ASST 8 cut(s) 172, 248, 295, 334, 402, 759, 763, 768
SfaNI GCATC 1 cut(s) 217
SfcI CTRYAG 2 cut(s) 395, 545
SfuI TTCGAA 1 cut(s) 77
SinI GGWCC 1 cut(s) 69
SmlI CTYRAG 3 cut(s) 221, 288, 602
SmoI CTYRAG 3 cut(s) 221, 288, 602
Sse9I AATT 4 cut(s) 63, 334, 366, 513
SsiI CCGC 1 cut(s) 458
SspMI CTAG 2 cut(s) 711, 758
TaaI ACNGT 2 cut(s) 362, 498
TaqI TCGA 4 cut(s) 77, 82, 534, 726
TaqII GACCGA 1 cut(s) 57
TasI AATT 4 cut(s) 63, 334, 366, 513
TatI WGTACW 1 cut(s) 549
TfiI GAWTC 3 cut(s) 79, 607, 717
Tru1I TTAA 2 cut(s) 516, 768
Tru9I TTAA 2 cut(s) 516, 768
TscAI CASTG 2 cut(s) 367, 399
TseFI GTSAC 1 cut(s) 625
TseI GCWGC 2 cut(s) 397, 455
Tsp45I GTSAC 1 cut(s) 625
TspDTI ATGAA 2 cut(s) 429, 693
TspGWI ACGGA 1 cut(s) 140
TspRI CASTG 2 cut(s) 367, 399
Tth111I GACNNNGTC 1 cut(s) 734
VpaK11BI GGWCC 1 cut(s) 69
XagI CCTNNNNNAGG 1 cut(s) 535
XapI RAATTY 1 cut(s) 63
XcmI CCANNNNNNNNNTGG 1 cut(s) 439
XspI CTAG 2 cut(s) 711, 758
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.