Rorug06G0409600

DNA-directed RNA-polymerase II subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_rugosa
GWHBQTZ00000006
OG0002628
Physical Location & Seq
Reverse (-)
55209266 .. 55210685
1420 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug06G0409600.1

Sequence Viewer

Length: 774 bp
ATGGAGTCAGAAGCTTCAACTCCCTTGCTAAAAAAGGAAACCCCTATTGTTCAATCGAAGCCGAATAATAAAGACTTGTTGAACCACCTCGAAGCCTACCTCGCAAAGCGAGATGGCGTGGACAAGCTTCTAAAGATATCTAGATACGCCACCAAGATCATACTCGCCTCCTCAGCCCTCCCCGAAACCCTAACCCTAAATCAGCGCCTCAAGAGCTTCGAGTCGAGCGTGGGGGTCAGCCGCAAGGCCTTCAGGCTCGGCAAGTTCGTCCAAGACGTCAACGCCCTGAGAAATTCGCATTTCGATTCCAAGGAAGAGCTCGCCCTCTCGCTCGTCGCCTACGGCGGCGAGGGGTTGTACTTTTTCGTCGAGCAGTTCGTATGGCTGGTCAAATCGGGCTTGATTGACAAGAAGCACGCGCGGAGTTTGGGGCTGATCAGCGCGTGGGCGGAGTTGGTTGGGTACTTGGGGAGTGTTTCGCTGAAGATTAGGGATTTGAATCGGATTTCGGAGGACGAGAAGCGCGTGAAGATGAGCATCGAGGTTGCGATTACGAGAGGGATTAAGTGTGAGGAAGAGAAGGAGAGGCTGGGGAAGTTGATTCCGAAGAAACTGATGAAACGACTGTCTGTTGTTCAGGATTTGGCCGATGCGTTAATGGCGGTGGCTGATATTCGTGACGGAAAAGGACACTTTCTGGGGCCGCTGTCTGTATCAATTGCAGGGCTATTATCGGCATTGATCAGCACTCATAAGAATTGGGTTTCTTGCTGA
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_Rpb4

Protein Analysis

257

Amino Acids

28.53

Weight (kDa)

9.5

Isoelectric Point (pI)

31.68

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PEX11 PF05648 27 - 254 2.9e-43 Peroxisomal biogenesis factor 11 (PEX11)
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

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

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AatII GACGTC 1 cut(s) 279
AccII CGCG 4 cut(s) 419, 421, 443, 525
AciI CCGC 6 cut(s) 241, 345, 421, 449, 662, 704
AcoI YGGCCR 1 cut(s) 645
AcsI RAATTY 1 cut(s) 292
AcuI CTGAAG 2 cut(s) 235, 503
AcyI GRCGYC 1 cut(s) 276
AfaI GTAC 2 cut(s) 359, 464
AgsI TTSAA 4 cut(s) 18, 53, 82, 499
AluBI AGCT 4 cut(s) 14, 127, 216, 319
AluI AGCT 4 cut(s) 14, 127, 216, 319
Alw21I GWGCWC 1 cut(s) 321
AoxI GGCC 3 cut(s) 246, 645, 701
ApoI RAATTY 1 cut(s) 292
AspLEI GCGC 4 cut(s) 207, 421, 443, 525
AspS9I GGNCC 1 cut(s) 701
BanII GRGCYC 1 cut(s) 321
Bbv12I GWGCWC 1 cut(s) 321
BbvCI CCTCAGC 1 cut(s) 172
BccI CCATC 1 cut(s) 107
BceAI ACGGC 1 cut(s) 358
BclI TGATCA 2 cut(s) 435, 741
BfaI CTAG 1 cut(s) 141
BfoI RGCGCY 1 cut(s) 208
BisI GCNGC 3 cut(s) 241, 346, 704
BlsI GCNGC 3 cut(s) 242, 347, 705
BmgT120I GGNCC 1 cut(s) 701
BmiI GGNNCC 1 cut(s) 702
BmsI GCATC 2 cut(s) 546, 640
Bpu10I CCTNAGC 1 cut(s) 172
BpuEI CTTGAG 1 cut(s) 194
BsaBI GATNNNNATC 2 cut(s) 498, 536
BsaHI GRCGYC 1 cut(s) 276
BsaJI CCNNGG 1 cut(s) 309
Bse8I GATNNNNATC 2 cut(s) 498, 536
BseDI CCNNGG 1 cut(s) 309
BseJI GATNNNNATC 2 cut(s) 498, 536
BseMII CTCAG 2 cut(s) 186, 278
BseRI GAGGAG 1 cut(s) 160
BseYI CCCAGC 1 cut(s) 589
Bsh1236I CGCG 4 cut(s) 419, 421, 443, 525
BshFI GGCC 3 cut(s) 248, 647, 703
BsiHKAI GWGCWC 1 cut(s) 321
BsnI GGCC 3 cut(s) 248, 647, 703
Bsp1286I GDGCHC 1 cut(s) 321
Bsp143I GATC 3 cut(s) 156, 435, 741
BspACI CCGC 6 cut(s) 241, 345, 421, 449, 662, 704
BspANI GGCC 3 cut(s) 248, 647, 703
BspCNI CTCAG 2 cut(s) 185, 279
BspFNI CGCG 4 cut(s) 419, 421, 443, 525
BspLI GGNNCC 1 cut(s) 702
BspQI GCTCTTC 1 cut(s) 309
BssECI CCNNGG 1 cut(s) 309
BssMI GATC 3 cut(s) 156, 435, 741
BssNI GRCGYC 1 cut(s) 276
BssT1I CCWWGG 1 cut(s) 309
Bst4CI ACNGT 1 cut(s) 627
Bst6I CTCTTC 2 cut(s) 309, 570
BstACI GRCGYC 1 cut(s) 276
BstC8I GCNNGC 2 cut(s) 321, 417
BstDEI CTNAG 2 cut(s) 172, 287
BstFNI CGCG 4 cut(s) 419, 421, 443, 525
BstH2I RGCGCY 1 cut(s) 208
BstHHI GCGC 4 cut(s) 207, 421, 443, 525
BstKTI GATC 3 cut(s) 159, 438, 744
BstMBI GATC 3 cut(s) 156, 435, 741
BstMWI GCNNNNNNNGC 4 cut(s) 101, 173, 213, 659
BstUI CGCG 4 cut(s) 419, 421, 443, 525
BsuRI GGCC 3 cut(s) 248, 647, 703
Cac8I GCNNGC 2 cut(s) 321, 417
CfoI GCGC 4 cut(s) 207, 421, 443, 525
Cfr13I GGNCC 1 cut(s) 701
Csp6I GTAC 2 cut(s) 358, 463
CviQI GTAC 2 cut(s) 358, 463
DdeI CTNAG 2 cut(s) 172, 287
DpnI GATC 3 cut(s) 158, 437, 743
DpnII GATC 3 cut(s) 156, 435, 741
EaeI YGGCCR 1 cut(s) 645
Eam1104I CTCTTC 2 cut(s) 309, 570
EarI CTCTTC 2 cut(s) 309, 570
EciI GGCGGA 1 cut(s) 464
Ecl136II GAGCTC 1 cut(s) 319
Eco130I CCWWGG 1 cut(s) 309
Eco147I AGGCCT 1 cut(s) 248
Eco24I GRGCYC 1 cut(s) 321
Eco32I GATATC 1 cut(s) 138
Eco53kI GAGCTC 1 cut(s) 319
Eco57I CTGAAG 2 cut(s) 235, 503
EcoICRI GAGCTC 1 cut(s) 319
EcoRV GATATC 1 cut(s) 138
EcoT14I CCWWGG 1 cut(s) 309
EcoT38I GRGCYC 1 cut(s) 321
ErhI CCWWGG 1 cut(s) 309
FaiI YATR 3 cut(s) 161, 382, 753
FbaI TGATCA 2 cut(s) 435, 741
Fnu4HI GCNGC 3 cut(s) 241, 346, 704
FriOI GRGCYC 1 cut(s) 321
Fsp4HI GCNGC 3 cut(s) 241, 346, 704
FspBI CTAG 1 cut(s) 141
GlaI GCGC 4 cut(s) 206, 420, 442, 524
GluI GCNGC 3 cut(s) 241, 346, 704
GsaI CCCAGC 1 cut(s) 593
HaeII RGCGCY 1 cut(s) 208
HaeIII GGCC 3 cut(s) 248, 647, 703
HhaI GCGC 4 cut(s) 207, 421, 443, 525
Hin1I GRCGYC 1 cut(s) 276
Hin6I GCGC 4 cut(s) 205, 419, 441, 523
HinP1I GCGC 4 cut(s) 205, 419, 441, 523
HincII GTYRAC 1 cut(s) 280
HindII GTYRAC 1 cut(s) 280
HindIII AAGCTT 2 cut(s) 12, 125
HinfI GANTC 5 cut(s) 5, 221, 305, 499, 601
Hpy166II GTNNAC 2 cut(s) 121, 280
Hpy188I TCNGA 4 cut(s) 10, 504, 511, 606
Hpy188III TCNNGA 4 cut(s) 141, 211, 638, 677
Hpy8I GTNNAC 2 cut(s) 121, 280
Hpy99I CGWCG 2 cut(s) 338, 371
HpyAV CCTTC 2 cut(s) 259, 574
HpyCH4III ACNGT 1 cut(s) 627
HpyCH4IV ACGT 1 cut(s) 276
HpyCH4V TGCA 1 cut(s) 722
HpyF10VI GCNNNNNNNGC 4 cut(s) 101, 173, 213, 659
HpyF3I CTNAG 2 cut(s) 172, 287
HpySE526I ACGT 1 cut(s) 276
Hsp92I GRCGYC 1 cut(s) 276
HspAI GCGC 4 cut(s) 205, 419, 441, 523
Ksp22I TGATCA 2 cut(s) 435, 741
Kzo9I GATC 3 cut(s) 156, 435, 741
LguI GCTCTTC 1 cut(s) 309
LpnPI CCDG 7 cut(s) 238, 299, 371, 575, 623, 683, 708
LweI GCATC 2 cut(s) 546, 640
MaeI CTAG 1 cut(s) 141
MaeII ACGT 1 cut(s) 276
MaeIII GTNAC 1 cut(s) 677
MalI GATC 3 cut(s) 158, 437, 743
MboI GATC 3 cut(s) 156, 435, 741
MboII GAAGA 5 cut(s) 326, 496, 541, 587, 619
MfeI CAATTG 1 cut(s) 717
MhlI GDGCHC 1 cut(s) 321
MluCI AATT 3 cut(s) 292, 717, 757
MlyI GAGTC 2 cut(s) 14, 230
MseI TTAA 2 cut(s) 564, 656
MspA1I CMGCKG 1 cut(s) 706
MunI CAATTG 1 cut(s) 717
MvnI CGCG 4 cut(s) 419, 421, 443, 525
MwoI GCNNNNNNNGC 4 cut(s) 101, 173, 213, 659
NdeII GATC 3 cut(s) 156, 435, 741
NlaIV GGNNCC 1 cut(s) 702
NmeAIII GCCGAG 1 cut(s) 237
NmuCI GTSAC 1 cut(s) 677
PceI AGGCCT 1 cut(s) 248
PciSI GCTCTTC 1 cut(s) 309
PcsI WCGNNNNNNNCGW 5 cut(s) 225, 264, 273, 375, 522
PfeI GAWTC 3 cut(s) 305, 499, 601
PkrI GCNGC 3 cut(s) 242, 347, 705
PleI GAGTC 2 cut(s) 13, 229
PpsI GAGTC 2 cut(s) 13, 229
Psp124BI GAGCTC 1 cut(s) 321
PspFI CCCAGC 1 cut(s) 589
PspN4I GGNNCC 1 cut(s) 702
PspPI GGNCC 1 cut(s) 701
RsaI GTAC 2 cut(s) 359, 464
RsaNI GTAC 2 cut(s) 358, 463
SacI GAGCTC 1 cut(s) 321
SapI GCTCTTC 1 cut(s) 309
SaqAI TTAA 2 cut(s) 564, 656
SatI GCNGC 3 cut(s) 241, 346, 704
Sau3AI GATC 3 cut(s) 156, 435, 741
Sau96I GGNCC 1 cut(s) 701
SchI GAGTC 2 cut(s) 14, 230
SduI GDGCHC 1 cut(s) 321
SetI ASST 8 cut(s) 16, 90, 102, 129, 218, 279, 321, 546
SfaNI GCATC 2 cut(s) 546, 640
SmlI CTYRAG 1 cut(s) 209
SmoI CTYRAG 1 cut(s) 209
Sse9I AATT 3 cut(s) 292, 717, 757
SseBI AGGCCT 1 cut(s) 248
SsiI CCGC 6 cut(s) 241, 345, 421, 449, 662, 704
SspMI CTAG 1 cut(s) 141
SstI GAGCTC 1 cut(s) 321
StuI AGGCCT 1 cut(s) 248
StyI CCWWGG 1 cut(s) 309
TaaI ACNGT 1 cut(s) 627
TaiI ACGT 1 cut(s) 279
TaqI TCGA 7 cut(s) 56, 90, 219, 224, 303, 369, 540
TasI AATT 3 cut(s) 292, 717, 757
TatI WGTACW 1 cut(s) 357
TauI GCSGC 3 cut(s) 243, 348, 706
TfiI GAWTC 3 cut(s) 305, 499, 601
Tru1I TTAA 2 cut(s) 564, 656
Tru9I TTAA 2 cut(s) 564, 656
TseFI GTSAC 1 cut(s) 677
Tsp45I GTSAC 1 cut(s) 677
TspDTI ATGAA 1 cut(s) 632
TspGWI ACGGA 1 cut(s) 696
XapI RAATTY 1 cut(s) 292
XbaI TCTAGA 1 cut(s) 140
XspI CTAG 1 cut(s) 141
ZraI GACGTC 1 cut(s) 277
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.