Rh2BG343800

RNA polymerase Rpb1, domain 5

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr2B
OG0017493
Physical Location & Seq
Reverse (-)
46083621 .. 46095168
11548 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh2BG343800.1

Sequence Viewer

Length: 651 bp
ATGGAGTCAAAATTCTTGGAAGGGAAACTGCTCAACTGCCTAGAGTGTAAACTGCCCAACTCCCCATTCGGACAACCGTCTAACTGCTCCGGTTTAGTGTCATCAGCTTCTGTCAGCAAACCAAACCGCAATCCCACATTCTCCTCCATAATACCATCAGTCAAACCCCCGGCAACTGCTTGCTCTTCCTATTTCCGATCACCATCCAAACCCAACTGCTCGGTGCACTGCCGTTTAGGTGAGTTGCCTATCATGAACTCATCAGCCTACAAGACCAGATCCATCTTCATGTCACCGTCAGAAGTACCTGGCACTGACAAATCGCCGGCTTTTTTCTCATCCCTAGTCCAAACAAAACCTGTCAAAGGGAGGTACCGGGCCACCATTCGCCAACCCTTCTTCAGTGCACTCCGCAAACCAAAGATCTATGATCAGCCAACAAGTGCACAAATTGGGGAAAGTATGGCCCTTCAACAAAGAGTATTGATAAGATTACAAGGAGCAAACAAGATGACTAGCAAAAGAAGTAATGAAACTTCTTGGGTCGTAATTGCTATTTTATTAGGTTCAGCCATTATAGCTGTTCGTAATCCACAAACCATTCCTACTGACGGTCAGAATTTCTTTGAATATGTCCTTGAATTCCTTTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko00190 ko00195 ko00230 ko00240 ko01100 ko03020 map00190 map00195 map00230 map00240 map01100 map03020
Pfam Domains
Protein Families
RNA_pol_Rpb1_3 RNA_pol_Rpb1_4 RNA_pol_Rpb1_5 Ribosomal_S2

Protein Analysis

216

Amino Acids

23.74

Weight (kDa)

9.83

Isoelectric Point (pI)

58.42

Instability Index
Protein Domains (Pfam)
No Pfam domains detected for this protein.
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0017493)

Species Orthologous Gene IDs
arabidopsis_thaliana ATCG00150
malus_domestica MD02G1261800.v1.1 MD16G1100100.v1.1 MD16G1263300.v1.1
pyrus_communis pycom08g10380
rosa_chinensis RchiOBHm_Chr2g0129011 RchiOBHm_CPg0502431
rosa_laevigata RLG00000004365 RLG00000004453
rosa_rugosa Rorug02G0490900
rosa_samantha Rh2BG343800 Rh6AG047100

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc65I GGTACC 1 cut(s) 372
AccB1I GGYRCC 1 cut(s) 372
AciI CCGC 2 cut(s) 127, 412
AclWI GGATC 1 cut(s) 273
AcsI RAATTY 3 cut(s) 11, 619, 641
AcuI CTGAAG 1 cut(s) 385
AfaI GTAC 2 cut(s) 306, 374
AfiI CCNNNNNNNGG 2 cut(s) 365, 611
AgsI TTSAA 3 cut(s) 473, 629, 641
AjnI CCWGG 1 cut(s) 307
AjuI GAANNNNNNNTTGG 2 cut(s) 50, 82
AluBI AGCT 2 cut(s) 107, 581
AluI AGCT 2 cut(s) 107, 581
Alw21I GWGCWC 3 cut(s) 228, 409, 448
Alw44I GTGCAC 3 cut(s) 224, 405, 444
AlwI GGATC 1 cut(s) 273
AlwNI CAGNNNCTG 1 cut(s) 110
AoxI GGCC 2 cut(s) 378, 465
ApaLI GTGCAC 3 cut(s) 224, 405, 444
ApoI RAATTY 3 cut(s) 11, 619, 641
Asp718I GGTACC 1 cut(s) 372
AspS9I GGNCC 2 cut(s) 378, 466
AsuC2I CCSGG 2 cut(s) 170, 377
AsuHPI GGTGA 3 cut(s) 192, 251, 285
BaeGI GKGCMC 3 cut(s) 228, 409, 448
BanI GGYRCC 1 cut(s) 372
BarI GAAGNNNNNNTAC 2 cut(s) 520, 552
Bbv12I GWGCWC 3 cut(s) 228, 409, 448
BccI CCATC 3 cut(s) 163, 211, 290
BceAI ACGGC 1 cut(s) 216
BciT130I CCWGG 1 cut(s) 309
BclI TGATCA 1 cut(s) 430
BcnI CCSGG 2 cut(s) 170, 377
BfaI CTAG 3 cut(s) 41, 344, 516
BglII AGATCT 1 cut(s) 423
Bme1390I CCNGG 3 cut(s) 170, 309, 377
BmgT120I GGNCC 2 cut(s) 378, 466
BmiI GGNNCC 1 cut(s) 374
BmrFI CCNGG 3 cut(s) 170, 309, 377
BoxI GACNNNNGTC 1 cut(s) 76
BpuMI CCSGG 2 cut(s) 170, 377
BsaBI GATNNNNATC 1 cut(s) 202
BsaJI CCNNGG 1 cut(s) 168
BsaWI WCCGGW 1 cut(s) 89
Bsc4I CCNNNNNNNGG 2 cut(s) 365, 611
Bse118I RCCGGY 1 cut(s) 325
Bse8I GATNNNNATC 1 cut(s) 202
BseBI CCWGG 1 cut(s) 309
BseDI CCNNGG 1 cut(s) 168
BseGI GGATG 2 cut(s) 203, 338
BseJI GATNNNNATC 1 cut(s) 202
BseLI CCNNNNNNNGG 2 cut(s) 365, 611
BseRI GAGGAG 1 cut(s) 133
BseSI GKGCMC 3 cut(s) 228, 409, 448
BshFI GGCC 2 cut(s) 380, 467
BshNI GGYRCC 1 cut(s) 372
BsiHKAI GWGCWC 3 cut(s) 228, 409, 448
BsiSI CCGG 4 cut(s) 90, 170, 326, 376
BslI CCNNNNNNNGG 2 cut(s) 365, 611
BsnI GGCC 2 cut(s) 380, 467
Bsp1286I GDGCHC 3 cut(s) 228, 409, 448
Bsp143I GATC 4 cut(s) 197, 278, 423, 430
BspACI CCGC 2 cut(s) 127, 412
BspANI GGCC 2 cut(s) 380, 467
BspHI TCATGA 1 cut(s) 252
BspLI GGNNCC 1 cut(s) 374
BspPI GGATC 1 cut(s) 273
BspQI GCTCTTC 1 cut(s) 190
BspT107I GGYRCC 1 cut(s) 372
BsrFI RCCGGY 1 cut(s) 325
BssAI RCCGGY 1 cut(s) 325
BssECI CCNNGG 1 cut(s) 168
BssMI GATC 4 cut(s) 197, 278, 423, 430
Bst2UI CCWGG 1 cut(s) 309
Bst4CI ACNGT 3 cut(s) 78, 297, 614
Bst6I CTCTTC 1 cut(s) 190
BstC8I GCNNGC 2 cut(s) 181, 327
BstENI CCTNNNNNAGG 1 cut(s) 363
BstF5I GGATG 2 cut(s) 203, 338
BstKTI GATC 4 cut(s) 200, 281, 426, 433
BstMBI GATC 4 cut(s) 197, 278, 423, 430
BstMWI GCNNNNNNNGC 1 cut(s) 578
BstNI CCWGG 1 cut(s) 309
BstPAI GACNNNNGTC 1 cut(s) 76
BstSCI CCNGG 3 cut(s) 168, 307, 375
BstSLI GKGCMC 3 cut(s) 228, 409, 448
BstX2I RGATCY 2 cut(s) 278, 423
BstYI RGATCY 2 cut(s) 278, 423
BsuRI GGCC 2 cut(s) 380, 467
BtsCI GGATG 2 cut(s) 203, 338
BtsI GCAGTG 1 cut(s) 226
BtsIMutI CAGTG 3 cut(s) 226, 312, 409
Cac8I GCNNGC 2 cut(s) 181, 327
CaiI CAGNNNCTG 1 cut(s) 110
CciI TCATGA 1 cut(s) 252
Cfr10I RCCGGY 1 cut(s) 325
Cfr13I GGNCC 2 cut(s) 378, 466
Csp6I GTAC 2 cut(s) 305, 373
CviAII CATG 2 cut(s) 253, 289
CviJI RGCY 8 cut(s) 107, 266, 329, 380, 436, 467, 572, 581
CviKI_1 RGCY 8 cut(s) 107, 266, 329, 380, 436, 467, 572, 581
CviQI GTAC 2 cut(s) 305, 373
DpnI GATC 4 cut(s) 199, 280, 425, 432
DpnII GATC 4 cut(s) 197, 278, 423, 430
Eam1104I CTCTTC 1 cut(s) 190
EarI CTCTTC 1 cut(s) 190
Eco57I CTGAAG 1 cut(s) 385
EcoNI CCTNNNNNAGG 1 cut(s) 363
EcoRI GAATTC 1 cut(s) 641
EcoRII CCWGG 1 cut(s) 307
FaeI CATG 2 cut(s) 256, 292
FaiI YATR 7 cut(s) 149, 254, 290, 429, 464, 578, 633
FatI CATG 2 cut(s) 252, 288
FbaI TGATCA 1 cut(s) 430
FokI GGATG 2 cut(s) 190, 325
FspBI CTAG 3 cut(s) 41, 344, 516
HaeIII GGCC 2 cut(s) 380, 467
HapII CCGG 4 cut(s) 90, 170, 326, 376
Hin1II CATG 2 cut(s) 256, 292
HinfI GANTC 1 cut(s) 5
HpaII CCGG 4 cut(s) 90, 170, 326, 376
HphI GGTGA 3 cut(s) 192, 251, 285
Hpy166II GTNNAC 4 cut(s) 50, 226, 407, 446
Hpy188I TCNGA 4 cut(s) 71, 197, 301, 618
Hpy188III TCNNGA 1 cut(s) 253
Hpy8I GTNNAC 4 cut(s) 50, 226, 407, 446
HpyAV CCTTC 3 cut(s) 14, 406, 479
HpyCH4III ACNGT 3 cut(s) 78, 297, 614
HpyCH4V TGCA 3 cut(s) 226, 407, 446
HpyF10VI GCNNNNNNNGC 1 cut(s) 578
Hsp92II CATG 2 cut(s) 256, 292
KpnI GGTACC 1 cut(s) 376
KroI GCCGGC 1 cut(s) 325
KroNI GCCGGC 1 cut(s) 327
Ksp22I TGATCA 1 cut(s) 430
Kzo9I GATC 4 cut(s) 197, 278, 423, 430
LguI GCTCTTC 1 cut(s) 190
LmnI GCTCC 2 cut(s) 92, 500
LpnPI CCDG 8 cut(s) 103, 183, 289, 294, 321, 339, 372, 389
MaeI CTAG 3 cut(s) 41, 344, 516
MaeIII GTNAC 1 cut(s) 291
MalI GATC 4 cut(s) 199, 280, 425, 432
MboI GATC 4 cut(s) 197, 278, 423, 430
MboII GAAGA 3 cut(s) 177, 277, 391
MflI RGATCY 2 cut(s) 278, 423
MhlI GDGCHC 3 cut(s) 228, 409, 448
MluCI AATT 5 cut(s) 11, 450, 549, 619, 641
MlyI GAGTC 1 cut(s) 14
MnlI CCTC 2 cut(s) 154, 363
MroNI GCCGGC 1 cut(s) 325
MslI CAYNNNNRTG 1 cut(s) 287
MspI CCGG 4 cut(s) 90, 170, 326, 376
MspR9I CCNGG 3 cut(s) 170, 309, 377
MvaI CCWGG 1 cut(s) 309
MwoI GCNNNNNNNGC 1 cut(s) 578
NaeI GCCGGC 1 cut(s) 327
NciI CCSGG 2 cut(s) 170, 377
NdeII GATC 4 cut(s) 197, 278, 423, 430
NgoMIV GCCGGC 1 cut(s) 325
NlaIII CATG 2 cut(s) 256, 292
NlaIV GGNNCC 1 cut(s) 374
NmuCI GTSAC 1 cut(s) 291
PagI TCATGA 1 cut(s) 252
PciSI GCTCTTC 1 cut(s) 190
PdiI GCCGGC 1 cut(s) 327
PleI GAGTC 1 cut(s) 13
PpsI GAGTC 1 cut(s) 13
PshAI GACNNNNGTC 1 cut(s) 76
Psp6I CCWGG 1 cut(s) 307
PspGI CCWGG 1 cut(s) 307
PspN4I GGNNCC 1 cut(s) 374
PspPI GGNCC 2 cut(s) 378, 466
PstNI CAGNNNCTG 1 cut(s) 110
PsuI RGATCY 2 cut(s) 278, 423
RsaI GTAC 2 cut(s) 306, 374
RsaNI GTAC 2 cut(s) 305, 373
RseI CAYNNNNRTG 1 cut(s) 287
SapI GCTCTTC 1 cut(s) 190
Sau3AI GATC 4 cut(s) 197, 278, 423, 430
Sau96I GGNCC 2 cut(s) 378, 466
SchI GAGTC 1 cut(s) 14
ScrFI CCNGG 3 cut(s) 170, 309, 377
SduI GDGCHC 3 cut(s) 228, 409, 448
SetI ASST 7 cut(s) 109, 241, 310, 361, 374, 568, 583
SmiMI CAYNNNNRTG 1 cut(s) 287
Sse9I AATT 5 cut(s) 11, 450, 549, 619, 641
SsiI CCGC 2 cut(s) 127, 412
SspMI CTAG 3 cut(s) 41, 344, 516
StyD4I CCNGG 3 cut(s) 168, 307, 375
TaaI ACNGT 3 cut(s) 78, 297, 614
TasI AATT 5 cut(s) 11, 450, 549, 619, 641
TscAI CASTG 3 cut(s) 233, 319, 409
TseFI GTSAC 1 cut(s) 291
Tsp45I GTSAC 1 cut(s) 291
TspDTI ATGAA 3 cut(s) 269, 277, 546
TspRI CASTG 3 cut(s) 233, 319, 409
VneI GTGCAC 3 cut(s) 224, 405, 444
XagI CCTNNNNNAGG 1 cut(s) 363
XapI RAATTY 3 cut(s) 11, 619, 641
XspI CTAG 3 cut(s) 41, 344, 516
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.