Rh5AG112100

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

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5A
OG0003607
Physical Location & Seq
Forward (+)
10333774 .. 10336195
2422 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5AG112100.1

Sequence Viewer

Length: 669 bp
ATGGCTACCGTGGTGTTGGACGACGCCGTTTCGGGTGGCGGTGGAGGAGGCCGGGCGGGATGCATGACGAGCCACGACGTCGTCGGTGGAGGGAGCTTGGAGAGCTACCGGTACTACGTGTCTCGTCGTACGGTGATGGAGATGCTGAGCGACCGAGGCTACAACGTCGCCGACTCGGACCTCACTCGCTCACTCACTGAGTTCCGTACCGCGTTCGGCCAAAACCCTGACCTCGACCACCTCACCATCTGCGCCTCTCTCCGCTCCAATTCCAAGAACAAGATTATGGTCATCTTCTGTGGAACTGATGAAATCAGAAAGGCGAGTGTTTGTGCCATTTATGCTAACCTCCTGAACAAAGATATAAGCTCTCTGATGCTTGTCCTGCAAAGTAAAATGAACTCCTATGCTAAAAAAGAGCTGGAAAACTATCCTTACAAAGTTGAAACTTTCCACACTCAAGTTATGGGAAAGCGTGGTATTGATGCATTGCCTGGCATGACAATTGTATCTGCTTACTTAGAAACTGTGAGTGGAGCAGGGCAAAGCTACAGCCGAGCAGAAGATCTTAATAGTTCCTTTGCCAGTGAAGCTTCTTGGGAACACCCGCCTGCTTCTTATCAAGGAACGCAGAGGCCAGCAACTGAAAGAAAATATGGTGCAATTTGA

Protein Analysis

222

Amino Acids

24.17

Weight (kDa)

6.43

Isoelectric Point (pI)

41.72

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb5_N PF03871 34 - 110 1.4e-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, 608
AcoI YGGCCR 1 cut(s) 217
AcyI GRCGYC 2 cut(s) 24, 78
AfaI GTAC 3 cut(s) 113, 130, 208
AflIII ACRYGT 1 cut(s) 117
AgeI ACCGGT 1 cut(s) 108
AgsI TTSAA 1 cut(s) 446
AjnI CCWGG 1 cut(s) 493
AluBI AGCT 6 cut(s) 96, 105, 369, 421, 549, 593
AluI AGCT 6 cut(s) 96, 105, 369, 421, 549, 593
Alw26I GTCTC 1 cut(s) 126
AlwNI CAGNNNCTG 1 cut(s) 644
AoxI GGCC 3 cut(s) 49, 217, 635
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
BaeI ACNNNNGTAYC 2 cut(s) 492, 525
BccI CCATC 2 cut(s) 130, 254
BceAI ACGGC 1 cut(s) 11
BciT130I CCWGG 1 cut(s) 495
BcnI CCSGG 1 cut(s) 53
BcoDI GTCTC 1 cut(s) 126
BfmI CTRYAG 1 cut(s) 550
BglII AGATCT 1 cut(s) 565
BlpI GCTNAGC 1 cut(s) 146
Bme1390I CCNGG 2 cut(s) 53, 495
Bme18I GGWCC 1 cut(s) 178
BmgT120I GGNCC 1 cut(s) 178
BmrFI CCNGG 2 cut(s) 53, 495
BmsI GCATC 4 cut(s) 50, 132, 366, 475
Bpu1102I GCTNAGC 1 cut(s) 146
BpuEI CTTGAG 1 cut(s) 444
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) 585
Bse3DI GCAATG 1 cut(s) 488
BseBI CCWGG 1 cut(s) 495
BseDI CCNNGG 2 cut(s) 9, 154
BseGI GGATG 1 cut(s) 65
BseMI GCAATG 1 cut(s) 488
BseMII CTCAG 2 cut(s) 137, 189
BseNI ACTGG 1 cut(s) 585
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, 637
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, 637
Bsp143I GATC 1 cut(s) 565
Bsp1720I GCTNAGC 1 cut(s) 146
BspACI CCGC 5 cut(s) 39, 56, 210, 262, 608
BspANI GGCC 3 cut(s) 51, 219, 637
BspCNI CTCAG 2 cut(s) 138, 190
BspFNI CGCG 1 cut(s) 212
BsrBI CCGCTC 1 cut(s) 264
BsrDI GCAATG 1 cut(s) 488
BsrFI RCCGGY 1 cut(s) 108
BsrI ACTGG 1 cut(s) 585
BssAI RCCGGY 1 cut(s) 108
BssECI CCNNGG 2 cut(s) 9, 154
BssMI GATC 1 cut(s) 565
BssNI GRCGYC 2 cut(s) 24, 78
Bst2UI CCWGG 1 cut(s) 495
Bst4CI ACNGT 3 cut(s) 10, 133, 529
BstACI GRCGYC 2 cut(s) 24, 78
BstBAI YACGTR 1 cut(s) 118
BstC8I GCNNGC 2 cut(s) 612, 639
BstDEI CTNAG 3 cut(s) 146, 198, 520
BstDSI CCRYGG 1 cut(s) 9
BstF5I GGATG 1 cut(s) 65
BstFNI CGCG 1 cut(s) 212
BstHHI GCGC 1 cut(s) 254
BstKTI GATC 1 cut(s) 568
BstMAI GTCTC 1 cut(s) 126
BstMBI GATC 1 cut(s) 565
BstMCI CGRYCG 1 cut(s) 154
BstMWI GCNNNNNNNGC 6 cut(s) 69, 102, 156, 341, 385, 590
BstNI CCWGG 1 cut(s) 495
BstSCI CCNGG 2 cut(s) 51, 493
BstSFI CTRYAG 1 cut(s) 550
BstUI CGCG 1 cut(s) 212
BstX2I RGATCY 1 cut(s) 565
BstYI RGATCY 1 cut(s) 565
BsuRI GGCC 3 cut(s) 51, 219, 637
BtgI CCRYGG 1 cut(s) 9
BtsCI GGATG 1 cut(s) 65
BtsIMutI CAGTG 2 cut(s) 195, 592
Cac8I GCNNGC 2 cut(s) 612, 639
CaiI CAGNNNCTG 1 cut(s) 644
CfoI GCGC 1 cut(s) 254
Cfr10I RCCGGY 1 cut(s) 108
Cfr13I GGNCC 1 cut(s) 178
CseI GACGC 1 cut(s) 32
Csp6I GTAC 3 cut(s) 112, 129, 207
CspAI ACCGGT 1 cut(s) 108
CviAII CATG 2 cut(s) 64, 499
CviQI GTAC 3 cut(s) 112, 129, 207
DdeI CTNAG 3 cut(s) 146, 198, 520
DpnI GATC 1 cut(s) 567
DpnII GATC 1 cut(s) 565
EaeI YGGCCR 1 cut(s) 217
Eco47I GGWCC 1 cut(s) 178
EcoRII CCWGG 1 cut(s) 493
EcoT22I ATGCAT 2 cut(s) 65, 490
FaeI CATG 2 cut(s) 67, 502
FaiI YATR 8 cut(s) 65, 287, 342, 365, 408, 467, 500, 657
FatI CATG 2 cut(s) 63, 498
FauI CCCGC 2 cut(s) 49, 615
FokI GGATG 1 cut(s) 72
GlaI GCGC 1 cut(s) 253
HaeIII GGCC 3 cut(s) 51, 219, 637
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, 502
Hin6I GCGC 1 cut(s) 252
HinP1I GCGC 1 cut(s) 252
HindIII AAGCTT 1 cut(s) 591
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 1 cut(s) 352
Hpy99I CGWCG 6 cut(s) 26, 80, 83, 86, 129, 170
HpyCH4III ACNGT 3 cut(s) 10, 133, 529
HpyCH4IV ACGT 3 cut(s) 78, 117, 165
HpyCH4V TGCA 4 cut(s) 63, 388, 488, 662
HpyF10VI GCNNNNNNNGC 6 cut(s) 69, 102, 156, 341, 385, 590
HpyF3I CTNAG 3 cut(s) 146, 198, 520
HpySE526I ACGT 3 cut(s) 78, 117, 165
Hsp92I GRCGYC 2 cut(s) 24, 78
Hsp92II CATG 2 cut(s) 67, 502
HspAI GCGC 1 cut(s) 252
Kzo9I GATC 1 cut(s) 565
LmnI GCTCC 3 cut(s) 93, 269, 536
LweI GCATC 4 cut(s) 50, 132, 366, 475
MaeII ACGT 3 cut(s) 78, 117, 165
MalI GATC 1 cut(s) 567
MbiI CCGCTC 1 cut(s) 264
MboI GATC 1 cut(s) 565
MboII GAAGA 2 cut(s) 286, 575
MfeI CAATTG 1 cut(s) 504
MflI RGATCY 1 cut(s) 565
MluCI AATT 3 cut(s) 268, 504, 663
MlyI GAGTC 1 cut(s) 167
Mph1103I ATGCAT 2 cut(s) 65, 490
MseI TTAA 1 cut(s) 570
MspI CCGG 2 cut(s) 52, 109
MspR9I CCNGG 2 cut(s) 53, 495
MunI CAATTG 1 cut(s) 504
MvaI CCWGG 1 cut(s) 495
MvnI CGCG 1 cut(s) 212
MwoI GCNNNNNNNGC 6 cut(s) 69, 102, 156, 341, 385, 590
NciI CCSGG 1 cut(s) 53
NdeII GATC 1 cut(s) 565
NlaIII CATG 2 cut(s) 67, 502
NmeAIII GCCGAG 1 cut(s) 581
NsiI ATGCAT 2 cut(s) 65, 490
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
Psp6I CCWGG 1 cut(s) 493
PspGI CCWGG 1 cut(s) 493
PspLI CGTACG 1 cut(s) 128
PspPI GGNCC 1 cut(s) 178
PstNI CAGNNNCTG 1 cut(s) 644
PsuI RGATCY 1 cut(s) 565
PsyI GACNNNGTC 1 cut(s) 80
RsaI GTAC 3 cut(s) 113, 130, 208
RsaNI GTAC 3 cut(s) 112, 129, 207
SaqAI TTAA 1 cut(s) 570
Sau3AI GATC 1 cut(s) 565
Sau96I GGNCC 1 cut(s) 178
SchI GAGTC 1 cut(s) 167
ScrFI CCNGG 2 cut(s) 53, 495
SfaNI GCATC 4 cut(s) 50, 132, 366, 475
SfcI CTRYAG 1 cut(s) 550
SinI GGWCC 1 cut(s) 178
SmlI CTYRAG 1 cut(s) 459
SmoI CTYRAG 1 cut(s) 459
Sse9I AATT 3 cut(s) 268, 504, 663
SsiI CCGC 5 cut(s) 39, 56, 210, 262, 608
StyD4I CCNGG 2 cut(s) 51, 493
TaaI ACNGT 3 cut(s) 10, 133, 529
TaiI ACGT 3 cut(s) 81, 120, 168
TaqI TCGA 1 cut(s) 234
TaqII GACCGA 1 cut(s) 168
TasI AATT 3 cut(s) 268, 504, 663
Tru1I TTAA 1 cut(s) 570
Tru9I TTAA 1 cut(s) 570
TscAI CASTG 2 cut(s) 202, 592
TspDTI ATGAA 2 cut(s) 324, 413
TspGWI ACGGA 1 cut(s) 194
TspRI CASTG 2 cut(s) 202, 592
Tth111I GACNNNGTC 1 cut(s) 80
VpaK11BI GGWCC 1 cut(s) 178
ZraI GACGTC 1 cut(s) 79
Zsp2I ATGCAT 2 cut(s) 65, 490
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.