Rw5G021040

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

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr5
OG0003607
Physical Location & Seq
Reverse (-)
27982930 .. 27985115
2186 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw5G021040.1

Sequence Viewer

Length: 750 bp
ATGGCTACCGTGGTGTTGGACGACGCCGTTTCGGGTGGCGGTGGAGGAGGCCGGGCGGGATGCATGACGAGCCACGACGTCGTCGGTGGAGGGAGCTTGGAGAGCTACCGGTACTACGTGTCTCGTCGTACGGTGATGGAGATGCTGAGCGACCGAGGCTACAACGTCGCCGACTCGGACCTCACTCGCTCACTCACTGAGTTCCGTACCGCGTTCGGCCAAAACCCTGACCTCGACCACCTCACCATCTGCGCCTCTCTCCGCTCCAATTCCAAGAACAAGATTATGGTCATCTTCTGTGGAACTGATGAAATCAGAAAGGCGAGTGTTTGTGCCATTTATGCTAACCTCCTGAACAAAGATATAAGCTCTCTGATGCTTGTCCTGCAAAGTAAAATGAACTCCTATGCTAAAAAAGAGCTGGAAAACTATCCTTACAAAGTTGAAACTTTCCACATTAATGAGCTTAAGTTGGCTCATCATAGACATGTTGGGCATCCTTACCTGGTTTGGCACATCATATCTAGATTTTCTAATGGTGTTTTGGGATACAAATATAGGGGAGTGGAGCAGGGCAAAGCTACAGCCGAGCAGAAGATCTTAATAGTTCCTTTGCCAGTGAAGCTTCTTGGGAACACCCGCCTGCTTCTTATCAAGGAACGCAGAGGCCAGCAACTGAAAGAAAATATGGTGCAATTTGAACGTTATGTACCTGTGACAGTGAATTTCAGCCAACTTGTACTAGTATGA

Protein Analysis

249

Amino Acids

27.93

Weight (kDa)

9.28

Isoelectric Point (pI)

39.83

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb5_N PF03871 34 - 110 1.8e-21 RNA polymerase Rpb5, N-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)
AatII GACGTC 1 cut(s) 81
AccBSI CCGCTC 1 cut(s) 264
AccII CGCG 1 cut(s) 212
AciI CCGC 5 cut(s) 39, 56, 210, 262, 640
AclI AACGTT 1 cut(s) 703
AcoI YGGCCR 1 cut(s) 217
AcsI RAATTY 1 cut(s) 724
AcyI GRCGYC 2 cut(s) 24, 78
AfaI GTAC 5 cut(s) 113, 130, 208, 711, 741
AflII CTTAAG 1 cut(s) 467
AflIII ACRYGT 2 cut(s) 117, 487
AgeI ACCGGT 1 cut(s) 108
AgsI TTSAA 2 cut(s) 446, 701
AhlI ACTAGT 1 cut(s) 742
AjnI CCWGG 1 cut(s) 504
AluBI AGCT 7 cut(s) 96, 105, 369, 421, 466, 581, 625
AluI AGCT 7 cut(s) 96, 105, 369, 421, 466, 581, 625
Alw26I GTCTC 1 cut(s) 126
AlwNI CAGNNNCTG 1 cut(s) 676
AoxI GGCC 3 cut(s) 49, 217, 667
ApoI RAATTY 1 cut(s) 724
AseI ATTAAT 1 cut(s) 459
AsiGI ACCGGT 1 cut(s) 108
AspLEI GCGC 1 cut(s) 254
AspS9I GGNCC 1 cut(s) 178
AsuC2I CCSGG 1 cut(s) 53
AsuHPI GGTGA 2 cut(s) 145, 235
AvaII GGWCC 1 cut(s) 178
BccI CCATC 2 cut(s) 130, 254
BceAI ACGGC 1 cut(s) 11
BciT130I CCWGG 1 cut(s) 506
BciVI GTATCC 1 cut(s) 542
BcnI CCSGG 1 cut(s) 53
BcoDI GTCTC 1 cut(s) 126
BcuI ACTAGT 1 cut(s) 742
BfaI CTAG 2 cut(s) 525, 743
BfmI CTRYAG 1 cut(s) 582
BfrI CTTAAG 1 cut(s) 467
BfuI GTATCC 1 cut(s) 542
BglII AGATCT 1 cut(s) 597
BlpI GCTNAGC 1 cut(s) 146
Bme1390I CCNGG 2 cut(s) 53, 506
Bme18I GGWCC 1 cut(s) 178
BmgT120I GGNCC 1 cut(s) 178
BmrFI CCNGG 2 cut(s) 53, 506
BmsI GCATC 4 cut(s) 50, 132, 366, 505
Bpu1102I GCTNAGC 1 cut(s) 146
BpuMI CCSGG 1 cut(s) 53
BsaAI YACGTR 1 cut(s) 118
BsaHI GRCGYC 2 cut(s) 24, 78
BsaJI CCNNGG 2 cut(s) 9, 154
BsaWI WCCGGW 1 cut(s) 108
Bse118I RCCGGY 1 cut(s) 108
Bse1I ACTGG 1 cut(s) 617
BseBI CCWGG 1 cut(s) 506
BseDI CCNNGG 2 cut(s) 9, 154
BseGI GGATG 2 cut(s) 65, 496
BseMII CTCAG 2 cut(s) 137, 189
BseNI ACTGG 1 cut(s) 617
BseRI GAGGAG 1 cut(s) 60
Bsh1236I CGCG 1 cut(s) 212
Bsh1285I CGRYCG 1 cut(s) 154
BshFI GGCC 3 cut(s) 51, 219, 669
BshTI ACCGGT 1 cut(s) 108
BsiEI CGRYCG 1 cut(s) 154
BsiSI CCGG 2 cut(s) 52, 109
BsiWI CGTACG 1 cut(s) 128
BsmAI GTCTC 1 cut(s) 126
BsnI GGCC 3 cut(s) 51, 219, 669
Bsp143I GATC 1 cut(s) 597
Bsp1720I GCTNAGC 1 cut(s) 146
BspACI CCGC 5 cut(s) 39, 56, 210, 262, 640
BspANI GGCC 3 cut(s) 51, 219, 669
BspCNI CTCAG 2 cut(s) 138, 190
BspFNI CGCG 1 cut(s) 212
BspTI CTTAAG 1 cut(s) 467
BsrBI CCGCTC 1 cut(s) 264
BsrFI RCCGGY 1 cut(s) 108
BsrI ACTGG 1 cut(s) 617
BssAI RCCGGY 1 cut(s) 108
BssECI CCNNGG 2 cut(s) 9, 154
BssMI GATC 1 cut(s) 597
BssNI GRCGYC 2 cut(s) 24, 78
Bst2UI CCWGG 1 cut(s) 506
Bst4CI ACNGT 3 cut(s) 10, 133, 721
BstACI GRCGYC 2 cut(s) 24, 78
BstAFI CTTAAG 1 cut(s) 467
BstBAI YACGTR 1 cut(s) 118
BstC8I GCNNGC 2 cut(s) 644, 671
BstDEI CTNAG 2 cut(s) 146, 198
BstDSI CCRYGG 1 cut(s) 9
BstF5I GGATG 2 cut(s) 65, 496
BstFNI CGCG 1 cut(s) 212
BstHHI GCGC 1 cut(s) 254
BstKTI GATC 1 cut(s) 600
BstMAI GTCTC 1 cut(s) 126
BstMBI GATC 1 cut(s) 597
BstMCI CGRYCG 1 cut(s) 154
BstMWI GCNNNNNNNGC 6 cut(s) 69, 102, 156, 341, 385, 622
BstNI CCWGG 1 cut(s) 506
BstNSI RCATGY 1 cut(s) 491
BstSCI CCNGG 2 cut(s) 51, 504
BstSFI CTRYAG 1 cut(s) 582
BstUI CGCG 1 cut(s) 212
BstX2I RGATCY 1 cut(s) 597
BstYI RGATCY 1 cut(s) 597
BsuI GTATCC 1 cut(s) 542
BsuRI GGCC 3 cut(s) 51, 219, 669
BtgI CCRYGG 1 cut(s) 9
BtsCI GGATG 2 cut(s) 65, 496
BtsIMutI CAGTG 3 cut(s) 195, 624, 726
Cac8I GCNNGC 2 cut(s) 644, 671
CaiI CAGNNNCTG 1 cut(s) 676
CfoI GCGC 1 cut(s) 254
Cfr10I RCCGGY 1 cut(s) 108
Cfr13I GGNCC 1 cut(s) 178
CseI GACGC 1 cut(s) 32
CsiI ACCWGGT 1 cut(s) 504
Csp6I GTAC 5 cut(s) 112, 129, 207, 710, 740
CspAI ACCGGT 1 cut(s) 108
CviAII CATG 2 cut(s) 64, 488
CviQI GTAC 5 cut(s) 112, 129, 207, 710, 740
DdeI CTNAG 2 cut(s) 146, 198
DpnI GATC 1 cut(s) 599
DpnII GATC 1 cut(s) 597
EaeI YGGCCR 1 cut(s) 217
Eco47I GGWCC 1 cut(s) 178
EcoRII CCWGG 1 cut(s) 504
EcoT22I ATGCAT 1 cut(s) 65
FaeI CATG 2 cut(s) 67, 491
FatI CATG 2 cut(s) 63, 487
FauI CCCGC 2 cut(s) 49, 647
FokI GGATG 2 cut(s) 72, 483
FspBI CTAG 2 cut(s) 525, 743
GlaI GCGC 1 cut(s) 253
HaeIII GGCC 3 cut(s) 51, 219, 669
HapII CCGG 2 cut(s) 52, 109
HgaI GACGC 1 cut(s) 32
HhaI GCGC 1 cut(s) 254
Hin1I GRCGYC 2 cut(s) 24, 78
Hin1II CATG 2 cut(s) 67, 491
Hin6I GCGC 1 cut(s) 252
HinP1I GCGC 1 cut(s) 252
HindIII AAGCTT 1 cut(s) 623
HinfI GANTC 1 cut(s) 173
HpaII CCGG 2 cut(s) 52, 109
HphI GGTGA 2 cut(s) 145, 235
Hpy188I TCNGA 3 cut(s) 178, 317, 375
Hpy188III TCNNGA 2 cut(s) 352, 525
Hpy99I CGWCG 6 cut(s) 26, 80, 83, 86, 129, 170
HpyCH4III ACNGT 3 cut(s) 10, 133, 721
HpyCH4IV ACGT 4 cut(s) 78, 117, 165, 703
HpyCH4V TGCA 3 cut(s) 63, 388, 694
HpyF10VI GCNNNNNNNGC 6 cut(s) 69, 102, 156, 341, 385, 622
HpyF3I CTNAG 2 cut(s) 146, 198
HpySE526I ACGT 4 cut(s) 78, 117, 165, 703
Hsp92I GRCGYC 2 cut(s) 24, 78
Hsp92II CATG 2 cut(s) 67, 491
HspAI GCGC 1 cut(s) 252
Kzo9I GATC 1 cut(s) 597
LmnI GCTCC 3 cut(s) 93, 269, 568
LweI GCATC 4 cut(s) 50, 132, 366, 505
MabI ACCWGGT 1 cut(s) 504
MaeI CTAG 2 cut(s) 525, 743
MaeII ACGT 4 cut(s) 78, 117, 165, 703
MaeIII GTNAC 1 cut(s) 715
MalI GATC 1 cut(s) 599
MbiI CCGCTC 1 cut(s) 264
MboI GATC 1 cut(s) 597
MboII GAAGA 2 cut(s) 286, 607
MflI RGATCY 1 cut(s) 597
MluCI AATT 3 cut(s) 268, 695, 724
MlyI GAGTC 1 cut(s) 167
Mph1103I ATGCAT 1 cut(s) 65
MseI TTAA 3 cut(s) 459, 468, 602
MslI CAYNNNNRTG 2 cut(s) 459, 486
MspCI CTTAAG 1 cut(s) 467
MspI CCGG 2 cut(s) 52, 109
MspR9I CCNGG 2 cut(s) 53, 506
MvaI CCWGG 1 cut(s) 506
MvnI CGCG 1 cut(s) 212
MwoI GCNNNNNNNGC 6 cut(s) 69, 102, 156, 341, 385, 622
NciI CCSGG 1 cut(s) 53
NdeII GATC 1 cut(s) 597
NlaIII CATG 2 cut(s) 67, 491
NmeAIII GCCGAG 1 cut(s) 613
NmuCI GTSAC 1 cut(s) 715
NsiI ATGCAT 1 cut(s) 65
NspI RCATGY 1 cut(s) 491
PciI ACATGT 1 cut(s) 487
Pfl23II CGTACG 1 cut(s) 128
PflFI GACNNNGTC 1 cut(s) 80
PinAI ACCGGT 1 cut(s) 108
PleI GAGTC 1 cut(s) 167
PpsI GAGTC 1 cut(s) 167
Ppu21I YACGTR 1 cut(s) 118
PscI ACATGT 1 cut(s) 487
PshBI ATTAAT 1 cut(s) 459
Psp1406I AACGTT 1 cut(s) 703
Psp6I CCWGG 1 cut(s) 504
PspGI CCWGG 1 cut(s) 504
PspLI CGTACG 1 cut(s) 128
PspPI GGNCC 1 cut(s) 178
PsrI GAACNNNNNNTAC 2 cut(s) 693, 725
PstNI CAGNNNCTG 1 cut(s) 676
PsuI RGATCY 1 cut(s) 597
PsyI GACNNNGTC 1 cut(s) 80
RsaI GTAC 5 cut(s) 113, 130, 208, 711, 741
RsaNI GTAC 5 cut(s) 112, 129, 207, 710, 740
RseI CAYNNNNRTG 2 cut(s) 459, 486
SaqAI TTAA 3 cut(s) 459, 468, 602
Sau3AI GATC 1 cut(s) 597
Sau96I GGNCC 1 cut(s) 178
SchI GAGTC 1 cut(s) 167
ScrFI CCNGG 2 cut(s) 53, 506
SexAI ACCWGGT 1 cut(s) 504
SfaNI GCATC 4 cut(s) 50, 132, 366, 505
SfcI CTRYAG 1 cut(s) 582
SinI GGWCC 1 cut(s) 178
SmiMI CAYNNNNRTG 2 cut(s) 459, 486
SmlI CTYRAG 1 cut(s) 467
SmoI CTYRAG 1 cut(s) 467
SpeI ACTAGT 1 cut(s) 742
Sse9I AATT 3 cut(s) 268, 695, 724
SsiI CCGC 5 cut(s) 39, 56, 210, 262, 640
SspMI CTAG 2 cut(s) 525, 743
StyD4I CCNGG 2 cut(s) 51, 504
TaaI ACNGT 3 cut(s) 10, 133, 721
TaiI ACGT 4 cut(s) 81, 120, 168, 706
TaqI TCGA 1 cut(s) 234
TaqII GACCGA 1 cut(s) 168
TasI AATT 3 cut(s) 268, 695, 724
TatI WGTACW 1 cut(s) 739
Tru1I TTAA 3 cut(s) 459, 468, 602
Tru9I TTAA 3 cut(s) 459, 468, 602
TscAI CASTG 3 cut(s) 202, 624, 726
TseFI GTSAC 1 cut(s) 715
Tsp45I GTSAC 1 cut(s) 715
TspDTI ATGAA 2 cut(s) 324, 413
TspGWI ACGGA 1 cut(s) 194
TspRI CASTG 3 cut(s) 202, 624, 726
Tth111I GACNNNGTC 1 cut(s) 80
Vha464I CTTAAG 1 cut(s) 467
VpaK11BI GGWCC 1 cut(s) 178
VspI ATTAAT 1 cut(s) 459
XapI RAATTY 1 cut(s) 724
XbaI TCTAGA 1 cut(s) 524
XceI RCATGY 1 cut(s) 491
XspI CTAG 2 cut(s) 525, 743
ZraI GACGTC 1 cut(s) 79
Zsp2I ATGCAT 1 cut(s) 65
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.