Rroxscaffold_2G00094580

DNA-directed RNA polymerases I, II, and III subunit RPABC1-like

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000002
OG0016960
Physical Location & Seq
Reverse (-)
15934848 .. 15937980
3133 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_2G00094580.1

Sequence Viewer

Length: 381 bp
ATGCATAGACTCCTGCCTCCGCATGCCATCCTCCAAGCTGCGACGCTGCTGTTCCCTTACCTTCATCAATTTCTGGCAGCCATCTCGCAACACCTCCACCACCGCTTTGATTCAGTAAATTTTGAACTCTCCTTTTTGTCAAAATCGAAGCTTTATTTGAGTGCTGAAGCAGAGGAGAGTGGTTATGAATACGAGATGGTTCAAAGGCAGAGAAAGATTTCTGAACTGCTAGTCAATGTTACAAAGCATGTTTTACAGCCAAAGTATGAGATACTTACGGCTGAAGAAAAGAAACAGCTGCTAAGGAAGTACAAGTTGGAAGACAAGAAGATCAAGCAACCACTTATGGGAAATTTTGTATCAAACTGCTCAAGGCTTTGA

Protein Analysis

126

Amino Acids

14.82

Weight (kDa)

9.35

Isoelectric Point (pI)

42.93

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb5_C PF01191 78 - 111 5.1e-09 RNA polymerase Rpb5, C-terminal domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AciI CCGC 2 cut(s) 20, 103
AcsI RAATTY 2 cut(s) 118, 352
AcuI CTGAAG 2 cut(s) 186, 303
AfaI GTAC 1 cut(s) 311
AfiI CCNNNNNNNGG 1 cut(s) 347
AgsI TTSAA 2 cut(s) 125, 203
AjuI GAANNNNNNNTTGG 2 cut(s) 299, 331
AluBI AGCT 3 cut(s) 38, 151, 298
AluI AGCT 3 cut(s) 38, 151, 298
ApeKI GCWGC 4 cut(s) 38, 46, 77, 298
ApoI RAATTY 2 cut(s) 118, 352
Asp700I GAANNNNTTC 1 cut(s) 217
BbsI GAAGAC 1 cut(s) 327
BbvI GCAGC 4 cut(s) 25, 33, 89, 285
BccI CCATC 3 cut(s) 35, 89, 190
BceAI ACGGC 1 cut(s) 294
BcgI CGANNNNNNTGC 2 cut(s) 66, 100
BfaI CTAG 1 cut(s) 230
BisI GCNGC 4 cut(s) 39, 47, 78, 299
BlsI GCNGC 4 cut(s) 40, 48, 79, 300
BpiI GAAGAC 1 cut(s) 327
Bpu10I CCTNAGC 1 cut(s) 302
BpuEI CTTGAG 1 cut(s) 355
Bsc4I CCNNNNNNNGG 1 cut(s) 347
BseGI GGATG 1 cut(s) 27
BseLI CCNNNNNNNGG 1 cut(s) 347
BseRI GAGGAG 1 cut(s) 188
BseXI GCAGC 4 cut(s) 25, 33, 89, 285
BslI CCNNNNNNNGG 1 cut(s) 347
Bsp143I GATC 1 cut(s) 330
BspACI CCGC 2 cut(s) 20, 103
BssMI GATC 1 cut(s) 330
BstC8I GCNNGC 1 cut(s) 24
BstDEI CTNAG 1 cut(s) 302
BstF5I GGATG 1 cut(s) 27
BstKTI GATC 1 cut(s) 333
BstMBI GATC 1 cut(s) 330
BstNSI RCATGY 2 cut(s) 26, 251
BstV1I GCAGC 4 cut(s) 25, 33, 89, 285
BstV2I GAAGAC 1 cut(s) 327
BtsCI GGATG 1 cut(s) 27
Cac8I GCNNGC 1 cut(s) 24
CseI GACGC 1 cut(s) 52
Csp6I GTAC 1 cut(s) 310
CviAII CATG 2 cut(s) 23, 248
CviJI RGCY 7 cut(s) 38, 80, 151, 259, 281, 298, 376
CviKI_1 RGCY 7 cut(s) 38, 80, 151, 259, 281, 298, 376
CviQI GTAC 1 cut(s) 310
DdeI CTNAG 1 cut(s) 302
DpnI GATC 1 cut(s) 332
DpnII GATC 1 cut(s) 330
Eco57I CTGAAG 2 cut(s) 186, 303
EcoT22I ATGCAT 1 cut(s) 6
FaeI CATG 2 cut(s) 26, 251
FaiI YATR 6 cut(s) 6, 24, 186, 249, 267, 347
FatI CATG 2 cut(s) 22, 247
Fnu4HI GCNGC 4 cut(s) 39, 47, 78, 299
FokI GGATG 1 cut(s) 14
Fsp4HI GCNGC 4 cut(s) 39, 47, 78, 299
FspBI CTAG 1 cut(s) 230
GluI GCNGC 4 cut(s) 39, 47, 78, 299
HgaI GACGC 1 cut(s) 52
Hin1II CATG 2 cut(s) 26, 251
HindIII AAGCTT 1 cut(s) 149
HinfI GANTC 2 cut(s) 9, 110
Hpy188I TCNGA 1 cut(s) 223
Hpy99I CGWCG 1 cut(s) 46
HpyAV CCTTC 1 cut(s) 71
HpyCH4V TGCA 1 cut(s) 4
HpyF3I CTNAG 1 cut(s) 302
Hsp92II CATG 2 cut(s) 26, 251
Kzo9I GATC 1 cut(s) 330
LpnPI CCDG 2 cut(s) 26, 59
Lsp1109I GCAGC 4 cut(s) 25, 33, 89, 285
MaeI CTAG 1 cut(s) 230
MaeIII GTNAC 1 cut(s) 238
MalI GATC 1 cut(s) 332
MboI GATC 1 cut(s) 330
MboII GAAGA 3 cut(s) 296, 332, 340
MluCI AATT 3 cut(s) 68, 118, 352
MlyI GAGTC 1 cut(s) 3
MmeI TCCRAC 1 cut(s) 297
MnlI CCTC 4 cut(s) 27, 41, 104, 166
Mph1103I ATGCAT 1 cut(s) 6
MroXI GAANNNNTTC 1 cut(s) 217
MspA1I CMGCKG 1 cut(s) 298
NdeII GATC 1 cut(s) 330
NlaIII CATG 2 cut(s) 26, 251
NsiI ATGCAT 1 cut(s) 6
NspI RCATGY 2 cut(s) 26, 251
PaeI GCATGC 1 cut(s) 26
PdmI GAANNNNTTC 1 cut(s) 217
PfeI GAWTC 1 cut(s) 110
PkrI GCNGC 4 cut(s) 40, 48, 79, 300
PleI GAGTC 1 cut(s) 3
PpsI GAGTC 1 cut(s) 3
PvuII CAGCTG 1 cut(s) 298
RsaI GTAC 1 cut(s) 311
RsaNI GTAC 1 cut(s) 310
SatI GCNGC 4 cut(s) 39, 47, 78, 299
Sau3AI GATC 1 cut(s) 330
SchI GAGTC 1 cut(s) 3
SetI ASST 5 cut(s) 40, 63, 96, 153, 300
SmlI CTYRAG 1 cut(s) 370
SmoI CTYRAG 1 cut(s) 370
SphI GCATGC 1 cut(s) 26
Sse9I AATT 3 cut(s) 68, 118, 352
SsiI CCGC 2 cut(s) 20, 103
SspMI CTAG 1 cut(s) 230
TaqI TCGA 1 cut(s) 146
TasI AATT 3 cut(s) 68, 118, 352
TatI WGTACW 1 cut(s) 309
TfiI GAWTC 1 cut(s) 110
TseI GCWGC 4 cut(s) 38, 46, 77, 298
TspDTI ATGAA 2 cut(s) 53, 201
XapI RAATTY 2 cut(s) 118, 352
XceI RCATGY 2 cut(s) 26, 251
XmnI GAANNNNTTC 1 cut(s) 217
XspI CTAG 1 cut(s) 230
Zsp2I ATGCAT 1 cut(s) 6
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.