RchiOBHm_Chr4g0389991

DNA-directed RNA polymerase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
4
OG0016814
Physical Location & Seq
Reverse (-)
5069775 .. 5071096
1322 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ36307

Sequence Viewer

Length: 528 bp
ATGTATCTCAAAGTAGAGTTACGCTGGAGTGTTGTAGTCCCTCCCAAAAGCCTGGACAAAGATGGAGTGAAATTCCAAACGGAATTGTCTCGCCGCTTGCTGGATGATTTTGCTACAAAAAGGGCAACAAAAGATCTGGGATACTTCCTGGCGGTGACGACTGTGGAGAGCATAGGAGAAGGAAAGGTGAGGCCGGACACTGGTGAAGTTAAGTTTCCGGTTGTTTTCAGCTGCATCACCTTCAAACTTTTCCGCGGAGAGATCATACATGCGGTTGTTTACAAGGTATTGAGGCACGGAGTTTGTCTGAGATGCGGTCCTGTCGAAAAGGTGTTTCTCTCTGCTAACAAGATACCGGATTATCAATATATCCCTAGAGAGGACGATTCTGTGTTCTTAAACCAAGAGAAGCCGTACTCTAGCATTGAAAAAGATGTCACAATTCGTTGCGTTGTCATTGGGACTCGATGGGTTGAAGCAGAAAGGGAATTCTGCGTACTGGTTGATTTGCCGAATGAGGATATCTAG
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_Rbc25 SHS2_Rpb7-N

Protein Analysis

175

Amino Acids

20.06

Weight (kDa)

6.74

Isoelectric Point (pI)

36.04

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
SHS2_Rpb7-N PF03876 13 - 68 1.6e-06 SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
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: OG0016814)

Species Orthologous Gene IDs
fragaria_vesca FvH4_4g02510 FvH4_4g02510
rosa_chinensis RchiOBHm_Chr4g0389991
rosa_laevigata RLG00000009941
rosa_multiflora Rmu_sc0003687.1_g000012 Rmu_sc0004336.1_g000019
rosa_rugosa Rorug03G0327700 Rorug03G0327700
rosa_samantha Rh4AG030900 Rh4BG024300 Rh4CG033600 Rh4DG024600
rosa_wichuraiana Rw4G002350 Rw4G002400

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccII CGCG 1 cut(s) 255
AciI CCGC 6 cut(s) 94, 152, 253, 255, 272, 315
AcsI RAATTY 2 cut(s) 71, 488
AfaI GTAC 2 cut(s) 416, 498
AfiI CCNNNNNNNGG 3 cut(s) 100, 200, 379
AgsI TTSAA 3 cut(s) 244, 428, 476
AjnI CCWGG 2 cut(s) 51, 147
AluBI AGCT 1 cut(s) 231
AluI AGCT 1 cut(s) 231
Alw26I GTCTC 1 cut(s) 93
AoxI GGCC 1 cut(s) 191
ApeKI GCWGC 1 cut(s) 231
ApoI RAATTY 2 cut(s) 71, 488
AspS9I GGNCC 1 cut(s) 317
AsuHPI GGTGA 4 cut(s) 166, 199, 215, 229
AvaII GGWCC 1 cut(s) 317
BbvI GCAGC 1 cut(s) 218
BccI CCATC 2 cut(s) 56, 462
BceAI ACGGC 1 cut(s) 397
BciT130I CCWGG 2 cut(s) 53, 149
BciVI GTATCC 1 cut(s) 134
BcoDI GTCTC 1 cut(s) 93
BfaI CTAG 3 cut(s) 375, 420, 526
BfuI GTATCC 1 cut(s) 134
BglII AGATCT 1 cut(s) 133
BisI GCNGC 2 cut(s) 94, 232
BlsI GCNGC 2 cut(s) 95, 233
Bme1390I CCNGG 2 cut(s) 53, 149
Bme18I GGWCC 1 cut(s) 317
BmgT120I GGNCC 1 cut(s) 317
BmrFI CCNGG 2 cut(s) 53, 149
BmsI GCATC 2 cut(s) 243, 302
BpmI CTGGAG 1 cut(s) 46
BsaJI CCNNGG 1 cut(s) 253
BsaWI WCCGGW 2 cut(s) 217, 355
Bsc4I CCNNNNNNNGG 3 cut(s) 100, 200, 379
Bse1I ACTGG 2 cut(s) 205, 504
BseBI CCWGG 2 cut(s) 53, 149
BseDI CCNNGG 1 cut(s) 253
BseGI GGATG 1 cut(s) 109
BseLI CCNNNNNNNGG 3 cut(s) 100, 200, 379
BseMII CTCAG 1 cut(s) 299
BseNI ACTGG 2 cut(s) 205, 504
BseXI GCAGC 1 cut(s) 218
Bsh1236I CGCG 1 cut(s) 255
BshFI GGCC 1 cut(s) 193
BsiSI CCGG 3 cut(s) 194, 218, 356
BslFI GGGAC 2 cut(s) 23, 475
BslI CCNNNNNNNGG 3 cut(s) 100, 200, 379
BsmAI GTCTC 1 cut(s) 93
BsmFI GGGAC 2 cut(s) 23, 475
BsnI GGCC 1 cut(s) 193
Bsp143I GATC 2 cut(s) 133, 261
BspACI CCGC 6 cut(s) 94, 152, 253, 255, 272, 315
BspANI GGCC 1 cut(s) 193
BspCNI CTCAG 1 cut(s) 300
BspFNI CGCG 1 cut(s) 255
BsrI ACTGG 2 cut(s) 205, 504
BssECI CCNNGG 1 cut(s) 253
BssMI GATC 2 cut(s) 133, 261
Bst2UI CCWGG 2 cut(s) 53, 149
Bst4CI ACNGT 1 cut(s) 163
BstC8I GCNNGC 1 cut(s) 98
BstDEI CTNAG 1 cut(s) 308
BstDSI CCRYGG 1 cut(s) 253
BstF5I GGATG 1 cut(s) 109
BstFNI CGCG 1 cut(s) 255
BstKTI GATC 2 cut(s) 136, 264
BstMAI GTCTC 1 cut(s) 93
BstMBI GATC 2 cut(s) 133, 261
BstNI CCWGG 2 cut(s) 53, 149
BstNSI RCATGY 1 cut(s) 272
BstSCI CCNGG 2 cut(s) 51, 147
BstUI CGCG 1 cut(s) 255
BstV1I GCAGC 1 cut(s) 218
BstX2I RGATCY 1 cut(s) 133
BstXI CCANNNNNNTGG 1 cut(s) 52
BstYI RGATCY 1 cut(s) 133
BsuI GTATCC 1 cut(s) 134
BsuRI GGCC 1 cut(s) 193
BtgI CCRYGG 1 cut(s) 253
BtsCI GGATG 1 cut(s) 109
BtsIMutI CAGTG 1 cut(s) 198
Cac8I GCNNGC 1 cut(s) 98
Cfr13I GGNCC 1 cut(s) 317
Cfr42I CCGCGG 1 cut(s) 256
Csp6I GTAC 2 cut(s) 415, 497
CviAII CATG 1 cut(s) 269
CviJI RGCY 4 cut(s) 51, 193, 231, 412
CviKI_1 RGCY 4 cut(s) 51, 193, 231, 412
CviQI GTAC 2 cut(s) 415, 497
DdeI CTNAG 1 cut(s) 308
DpnI GATC 2 cut(s) 135, 263
DpnII GATC 2 cut(s) 133, 261
Eco32I GATATC 1 cut(s) 523
Eco47I GGWCC 1 cut(s) 317
EcoRI GAATTC 1 cut(s) 488
EcoRII CCWGG 2 cut(s) 51, 147
EcoRV GATATC 1 cut(s) 523
FaeI CATG 1 cut(s) 272
FaiI YATR 4 cut(s) 173, 266, 270, 369
FaqI GGGAC 2 cut(s) 23, 475
FatI CATG 1 cut(s) 268
Fnu4HI GCNGC 2 cut(s) 94, 232
FokI GGATG 1 cut(s) 116
Fsp4HI GCNGC 2 cut(s) 94, 232
FspBI CTAG 3 cut(s) 375, 420, 526
GluI GCNGC 2 cut(s) 94, 232
GsuI CTGGAG 1 cut(s) 46
HaeIII GGCC 1 cut(s) 193
HapII CCGG 3 cut(s) 194, 218, 356
Hin1II CATG 1 cut(s) 272
HinfI GANTC 2 cut(s) 386, 463
HpaII CCGG 3 cut(s) 194, 218, 356
HphI GGTGA 4 cut(s) 166, 199, 215, 229
Hpy166II GTNNAC 1 cut(s) 280
Hpy188I TCNGA 1 cut(s) 309
Hpy8I GTNNAC 1 cut(s) 280
HpyAV CCTTC 2 cut(s) 173, 250
HpyCH4III ACNGT 1 cut(s) 163
HpyCH4V TGCA 1 cut(s) 234
HpyF3I CTNAG 1 cut(s) 308
Hsp92II CATG 1 cut(s) 272
KspI CCGCGG 1 cut(s) 256
Kzo9I GATC 2 cut(s) 133, 261
Lsp1109I GCAGC 1 cut(s) 218
LweI GCATC 2 cut(s) 243, 302
MaeI CTAG 3 cut(s) 375, 420, 526
MaeIII GTNAC 3 cut(s) 18, 154, 436
MalI GATC 2 cut(s) 135, 263
MboI GATC 2 cut(s) 133, 261
MflI RGATCY 1 cut(s) 133
MluCI AATT 4 cut(s) 71, 83, 441, 488
MlyI GAGTC 1 cut(s) 457
MnlI CCTC 5 cut(s) 51, 183, 285, 373, 511
MseI TTAA 2 cut(s) 210, 398
MspA1I CMGCKG 2 cut(s) 231, 255
MspI CCGG 3 cut(s) 194, 218, 356
MspR9I CCNGG 2 cut(s) 53, 149
MvaI CCWGG 2 cut(s) 53, 149
MvnI CGCG 1 cut(s) 255
NdeII GATC 2 cut(s) 133, 261
NlaIII CATG 1 cut(s) 272
NmuCI GTSAC 2 cut(s) 154, 436
NspI RCATGY 1 cut(s) 272
PfeI GAWTC 1 cut(s) 386
PkrI GCNGC 2 cut(s) 95, 233
PleI GAGTC 1 cut(s) 457
PpsI GAGTC 1 cut(s) 457
Psp6I CCWGG 2 cut(s) 51, 147
PspGI CCWGG 2 cut(s) 51, 147
PspPI GGNCC 1 cut(s) 317
PsuI RGATCY 1 cut(s) 133
PvuII CAGCTG 1 cut(s) 231
RsaI GTAC 2 cut(s) 416, 498
RsaNI GTAC 2 cut(s) 415, 497
SacII CCGCGG 1 cut(s) 256
SaqAI TTAA 2 cut(s) 210, 398
SatI GCNGC 2 cut(s) 94, 232
Sau3AI GATC 2 cut(s) 133, 261
Sau96I GGNCC 1 cut(s) 317
SchI GAGTC 1 cut(s) 457
ScrFI CCNGG 2 cut(s) 53, 149
SetI ASST 5 cut(s) 189, 233, 242, 288, 333
SfaNI GCATC 2 cut(s) 243, 302
Sfr303I CCGCGG 1 cut(s) 256
SgrBI CCGCGG 1 cut(s) 256
SinI GGWCC 1 cut(s) 317
Sse9I AATT 4 cut(s) 71, 83, 441, 488
SsiI CCGC 6 cut(s) 94, 152, 253, 255, 272, 315
SspMI CTAG 3 cut(s) 375, 420, 526
StyD4I CCNGG 2 cut(s) 51, 147
TaaI ACNGT 1 cut(s) 163
TaqI TCGA 2 cut(s) 324, 466
TasI AATT 4 cut(s) 71, 83, 441, 488
TauI GCSGC 1 cut(s) 96
TfiI GAWTC 1 cut(s) 386
Tru1I TTAA 2 cut(s) 210, 398
Tru9I TTAA 2 cut(s) 210, 398
TscAI CASTG 1 cut(s) 205
TseFI GTSAC 2 cut(s) 154, 436
TseI GCWGC 1 cut(s) 231
Tsp45I GTSAC 2 cut(s) 154, 436
TspGWI ACGGA 2 cut(s) 95, 312
TspRI CASTG 1 cut(s) 205
VpaK11BI GGWCC 1 cut(s) 317
XapI RAATTY 2 cut(s) 71, 488
XceI RCATGY 1 cut(s) 272
XspI CTAG 3 cut(s) 375, 420, 526
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.