Rroxscaffold_7G00173880

DNA-directed RNA polymerase II subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000007
OG0002628
Physical Location & Seq
Reverse (-)
13747355 .. 13748188
834 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_7G00173880.1

Sequence Viewer

Length: 534 bp
ATGGAGGAAGAAAACGCTGCCGAGCTCAAAATCGGGGATGAGTTCTTAAAGGCGAAGTGTCTAATGAAGTGCGAAGTTTCTTTGATTCTTGAACACAGGTTGGCGCAGCTTCAACAGATATCTGATGATCCCAACAACAACCAAGTTTCTCAAGTATTTGACAAGTCGCTGCAGTATGTGAAGCGCTTTAGCCGTTACAAGAATCCTGATGCTGTTAAACAAGTGCGAGAAACCCTTAGTAATTATCAATTGACTGAGTTTGAGCTCTGTGTTCTTGGCAATCTCTGCACTGAAACAGTTGACGAAGCTATTGCTATGGTGCCAACTCTGATGGCCAAAGGTCGACGGATGCATGATGATGATGATGCAATTCAAAACATGTTAAGAGACCTGGCTCTTATCAAGAAAGGCGCTGAAATTAAAGGACCACTGAGGATGACTATGACAGCTTCAGAACCTGCGATTCTTGCAAGTCGGGACAAGAAGCTAGCTTCTTTTGTTGCCATTACTCGACAGAAAAAAGTACAGAAGTAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0000288 GO:0000428 GO:0000932 GO:0000956 GO:0003674 GO:0003824 GO:0003899 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005665 GO:0005737 GO:0005829 GO:0006139 GO:0006351 GO:0006352 GO:0006366 GO:0006367 GO:0006396 GO:0006397 GO:0006401 GO:0006402 GO:0006403 GO:0006405 GO:0006406 GO:0006417 GO:0006446 GO:0006611 GO:0006725 GO:0006807 GO:0006810 GO:0006886 GO:0006913 GO:0006950 GO:0008104 GO:0008150 GO:0008152 GO:0009056 GO:0009057 GO:0009058 GO:0009059 GO:0009266 GO:0009408 GO:0009628 GO:0009889 GO:0009891 GO:0009892 GO:0009893 GO:0009987 GO:0010467 GO:0010468 GO:0010556 GO:0010557 GO:0010604 GO:0010605 GO:0010608 GO:0010628 GO:0010629 GO:0015031 GO:0015833 GO:0015931 GO:0016043 GO:0016070 GO:0016071 GO:0016591 GO:0016604 GO:0016607 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019222 GO:0019438 GO:0019439 GO:0022607 GO:0022613 GO:0022618 GO:0030880 GO:0031123 GO:0031124 GO:0031323 GO:0031325 GO:0031326 GO:0031328 GO:0031369 GO:0031503 GO:0031974 GO:0031981 GO:0031990 GO:0032268 GO:0032270 GO:0032774 GO:0032991 GO:0033036 GO:0033554 GO:0034062 GO:0034248 GO:0034250 GO:0034402 GO:0034605 GO:0034613 GO:0034622 GO:0034641 GO:0034645 GO:0034654 GO:0034655 GO:0035770 GO:0036464 GO:0042886 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043933 GO:0044085 GO:0044237 GO:0044238 GO:0044248 GO:0044249 GO:0044260 GO:0044265 GO:0044270 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044446 GO:0044451 GO:0044464 GO:0045184 GO:0045727 GO:0045948 GO:0046483 GO:0046700 GO:0046907 GO:0048518 GO:0048519 GO:0048522 GO:0050657 GO:0050658 GO:0050789 GO:0050794 GO:0050896 GO:0051028 GO:0051168 GO:0051169 GO:0051171 GO:0051173 GO:0051179 GO:0051234 GO:0051236 GO:0051246 GO:0051247 GO:0051641 GO:0051649 GO:0051716 GO:0055029 GO:0060255 GO:0061695 GO:0065003 GO:0065007 GO:0070013 GO:0070727 GO:0071166 GO:0071426 GO:0071427 GO:0071702 GO:0071704 GO:0071705 GO:0071826 GO:0071840 GO:0080090 GO:0090304 GO:0097659 GO:0097747 GO:0140098 GO:1901360 GO:1901361 GO:1901362 GO:1901575 GO:1901576 GO:1902494 GO:1990234 GO:1990904 GO:2000112
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

177

Amino Acids

20.1

Weight (kDa)

7.63

Isoelectric Point (pI)

36.48

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNA_pol_Rpb4 PF03874 20 - 132 5.5e-23 RNA polymerase Rpb4
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)
Acc36I ACCTGC 1 cut(s) 466
AccB1I GGYRCC 1 cut(s) 319
AccI GTMKAC 1 cut(s) 343
AclWI GGATC 1 cut(s) 122
AcoI YGGCCR 1 cut(s) 333
AcuI CTGAAG 1 cut(s) 435
AfaI GTAC 1 cut(s) 525
AfeI AGCGCT 1 cut(s) 185
AflIII ACRYGT 1 cut(s) 378
AgsI TTSAA 3 cut(s) 92, 113, 374
AjnI CCWGG 1 cut(s) 390
AluBI AGCT 7 cut(s) 25, 109, 265, 308, 449, 487, 491
AluI AGCT 7 cut(s) 25, 109, 265, 308, 449, 487, 491
Alw21I GWGCWC 2 cut(s) 27, 267
Alw26I GTCTC 1 cut(s) 381
AlwI GGATC 1 cut(s) 122
AlwNI CAGNNNCTG 1 cut(s) 458
Aor51HI AGCGCT 1 cut(s) 185
AoxI GGCC 1 cut(s) 333
ApeKI GCWGC 3 cut(s) 17, 106, 169
AspLEI GCGC 3 cut(s) 106, 186, 413
AspS9I GGNCC 1 cut(s) 425
AsuNHI GCTAGC 1 cut(s) 487
AvaII GGWCC 1 cut(s) 425
BalI TGGCCA 1 cut(s) 335
BanI GGYRCC 1 cut(s) 319
BanII GRGCYC 2 cut(s) 27, 267
Bbv12I GWGCWC 2 cut(s) 27, 267
BbvI GCAGC 3 cut(s) 4, 118, 156
BccI CCATC 1 cut(s) 325
BceAI ACGGC 1 cut(s) 177
BcgI CGANNNNNNTGC 2 cut(s) 293, 327
BciT130I CCWGG 1 cut(s) 392
BcoDI GTCTC 1 cut(s) 381
BfaI CTAG 1 cut(s) 488
BfmI CTRYAG 1 cut(s) 170
BfoI RGCGCY 2 cut(s) 187, 414
BfuAI ACCTGC 1 cut(s) 466
BisI GCNGC 3 cut(s) 18, 107, 170
BlsI GCNGC 3 cut(s) 19, 108, 171
Bme1390I CCNGG 1 cut(s) 392
Bme18I GGWCC 1 cut(s) 425
BmgT120I GGNCC 1 cut(s) 425
BmiI GGNNCC 1 cut(s) 321
BmrFI CCNGG 1 cut(s) 392
BmsI GCATC 3 cut(s) 199, 339, 355
BmtI GCTAGC 1 cut(s) 491
BpuEI CTTGAG 1 cut(s) 135
BsaI GGTCTC 1 cut(s) 381
BseBI CCWGG 1 cut(s) 392
BseGI GGATG 3 cut(s) 43, 354, 441
BseMII CTCAG 2 cut(s) 246, 422
BseXI GCAGC 3 cut(s) 4, 118, 156
BsgI GTGCAG 1 cut(s) 271
BshFI GGCC 1 cut(s) 335
BshNI GGYRCC 1 cut(s) 319
BsiHKAI GWGCWC 2 cut(s) 27, 267
BslFI GGGAC 1 cut(s) 491
BsmAI GTCTC 1 cut(s) 381
BsmFI GGGAC 1 cut(s) 491
BsnI GGCC 1 cut(s) 335
Bso31I GGTCTC 1 cut(s) 381
Bsp1286I GDGCHC 2 cut(s) 27, 267
Bsp143I GATC 1 cut(s) 127
BspANI GGCC 1 cut(s) 335
BspCNI CTCAG 2 cut(s) 247, 423
BspLI GGNNCC 1 cut(s) 321
BspMAI CTGCAG 1 cut(s) 174
BspMI ACCTGC 1 cut(s) 466
BspOI GCTAGC 1 cut(s) 491
BspPI GGATC 1 cut(s) 122
BspT107I GGYRCC 1 cut(s) 319
BspTNI GGTCTC 1 cut(s) 381
BssMI GATC 1 cut(s) 127
Bst2UI CCWGG 1 cut(s) 392
Bst4CI ACNGT 1 cut(s) 298
BstAPI GCANNNNNTGC 1 cut(s) 285
BstC8I GCNNGC 1 cut(s) 489
BstDEI CTNAG 3 cut(s) 236, 255, 431
BstF5I GGATG 3 cut(s) 43, 354, 441
BstH2I RGCGCY 2 cut(s) 187, 414
BstHHI GCGC 3 cut(s) 106, 186, 413
BstKTI GATC 1 cut(s) 130
BstMAI GTCTC 1 cut(s) 381
BstMBI GATC 1 cut(s) 127
BstMWI GCNNNNNNNGC 2 cut(s) 285, 467
BstNI CCWGG 1 cut(s) 392
BstNSI RCATGY 1 cut(s) 382
BstSCI CCNGG 1 cut(s) 390
BstSFI CTRYAG 1 cut(s) 170
BstV1I GCAGC 3 cut(s) 4, 118, 156
BsuRI GGCC 1 cut(s) 335
BtsCI GGATG 3 cut(s) 43, 354, 441
BtsIMutI CAGTG 2 cut(s) 288, 428
BveI ACCTGC 1 cut(s) 466
Cac8I GCNNGC 1 cut(s) 489
CaiI CAGNNNCTG 1 cut(s) 458
CfoI GCGC 3 cut(s) 106, 186, 413
Cfr13I GGNCC 1 cut(s) 425
Csp6I GTAC 1 cut(s) 524
CviAII CATG 2 cut(s) 353, 379
CviQI GTAC 1 cut(s) 524
DdeI CTNAG 3 cut(s) 236, 255, 431
DpnI GATC 1 cut(s) 129
DpnII GATC 1 cut(s) 127
EaeI YGGCCR 1 cut(s) 333
Ecl136II GAGCTC 2 cut(s) 25, 265
Eco24I GRGCYC 2 cut(s) 27, 267
Eco31I GGTCTC 1 cut(s) 381
Eco32I GATATC 1 cut(s) 120
Eco47I GGWCC 1 cut(s) 425
Eco47III AGCGCT 1 cut(s) 185
Eco53kI GAGCTC 2 cut(s) 25, 265
Eco57I CTGAAG 1 cut(s) 435
EcoICRI GAGCTC 2 cut(s) 25, 265
EcoRII CCWGG 1 cut(s) 390
EcoRV GATATC 1 cut(s) 120
EcoT22I ATGCAT 1 cut(s) 354
EcoT38I GRGCYC 2 cut(s) 27, 267
FaeI CATG 2 cut(s) 356, 382
FaiI YATR 5 cut(s) 177, 317, 354, 380, 443
FaqI GGGAC 1 cut(s) 491
FatI CATG 2 cut(s) 352, 378
FblI GTMKAC 1 cut(s) 343
Fnu4HI GCNGC 3 cut(s) 18, 107, 170
FokI GGATG 3 cut(s) 50, 361, 448
FriOI GRGCYC 2 cut(s) 27, 267
Fsp4HI GCNGC 3 cut(s) 18, 107, 170
FspBI CTAG 1 cut(s) 488
GlaI GCGC 3 cut(s) 105, 185, 412
GluI GCNGC 3 cut(s) 18, 107, 170
HaeII RGCGCY 2 cut(s) 187, 414
HaeIII GGCC 1 cut(s) 335
HhaI GCGC 3 cut(s) 106, 186, 413
Hin1II CATG 2 cut(s) 356, 382
Hin6I GCGC 3 cut(s) 104, 184, 411
HinP1I GCGC 3 cut(s) 104, 184, 411
HincII GTYRAC 2 cut(s) 301, 344
HindII GTYRAC 2 cut(s) 301, 344
HinfI GANTC 3 cut(s) 85, 202, 463
Hpy166II GTNNAC 2 cut(s) 301, 344
Hpy188I TCNGA 3 cut(s) 124, 330, 454
Hpy188III TCNNGA 4 cut(s) 89, 206, 403, 476
Hpy8I GTNNAC 2 cut(s) 301, 344
Hpy99I CGWCG 1 cut(s) 348
HpyCH4III ACNGT 1 cut(s) 298
HpyCH4V TGCA 5 cut(s) 172, 288, 352, 368, 470
HpyF10VI GCNNNNNNNGC 2 cut(s) 285, 467
HpyF3I CTNAG 3 cut(s) 236, 255, 431
Hsp92II CATG 2 cut(s) 356, 382
HspAI GCGC 3 cut(s) 104, 184, 411
Kzo9I GATC 1 cut(s) 127
LpnPI CCDG 5 cut(s) 82, 219, 377, 404, 471
Lsp1109I GCAGC 3 cut(s) 4, 118, 156
LweI GCATC 3 cut(s) 199, 339, 355
MaeI CTAG 1 cut(s) 488
MaeIII GTNAC 1 cut(s) 194
MalI GATC 1 cut(s) 129
MboI GATC 1 cut(s) 127
MboII GAAGA 1 cut(s) 20
MfeI CAATTG 1 cut(s) 248
MhlI GDGCHC 2 cut(s) 27, 267
MlsI TGGCCA 1 cut(s) 335
MluCI AATT 4 cut(s) 241, 248, 369, 417
MluNI TGGCCA 1 cut(s) 335
MnlI CCTC 1 cut(s) 426
Mox20I TGGCCA 1 cut(s) 335
Mph1103I ATGCAT 1 cut(s) 354
MscI TGGCCA 1 cut(s) 335
MseI TTAA 4 cut(s) 47, 216, 383, 420
MslI CAYNNNNRTG 1 cut(s) 357
Msp20I TGGCCA 1 cut(s) 335
MspR9I CCNGG 1 cut(s) 392
MunI CAATTG 1 cut(s) 248
MvaI CCWGG 1 cut(s) 392
MwoI GCNNNNNNNGC 2 cut(s) 285, 467
NdeII GATC 1 cut(s) 127
NheI GCTAGC 1 cut(s) 487
NlaIII CATG 2 cut(s) 356, 382
NlaIV GGNNCC 1 cut(s) 321
NmeAIII GCCGAG 1 cut(s) 46
NsiI ATGCAT 1 cut(s) 354
NspI RCATGY 1 cut(s) 382
PciI ACATGT 1 cut(s) 378
PfeI GAWTC 3 cut(s) 85, 202, 463
PkrI GCNGC 3 cut(s) 19, 108, 171
PscI ACATGT 1 cut(s) 378
Psp124BI GAGCTC 2 cut(s) 27, 267
Psp6I CCWGG 1 cut(s) 390
PspGI CCWGG 1 cut(s) 390
PspN4I GGNNCC 1 cut(s) 321
PspPI GGNCC 1 cut(s) 425
PstI CTGCAG 1 cut(s) 174
PstNI CAGNNNCTG 1 cut(s) 458
RsaI GTAC 1 cut(s) 525
RsaNI GTAC 1 cut(s) 524
RseI CAYNNNNRTG 1 cut(s) 357
SacI GAGCTC 2 cut(s) 27, 267
SalI GTCGAC 1 cut(s) 342
SaqAI TTAA 4 cut(s) 47, 216, 383, 420
SatI GCNGC 3 cut(s) 18, 107, 170
Sau3AI GATC 1 cut(s) 127
Sau96I GGNCC 1 cut(s) 425
ScrFI CCNGG 1 cut(s) 392
SduI GDGCHC 2 cut(s) 27, 267
SfaNI GCATC 3 cut(s) 199, 339, 355
SfcI CTRYAG 1 cut(s) 170
SinI GGWCC 1 cut(s) 425
SmiMI CAYNNNNRTG 1 cut(s) 357
SmlI CTYRAG 1 cut(s) 150
SmoI CTYRAG 1 cut(s) 150
Sse9I AATT 4 cut(s) 241, 248, 369, 417
SspMI CTAG 1 cut(s) 488
SstI GAGCTC 2 cut(s) 27, 267
StyD4I CCNGG 1 cut(s) 390
TaaI ACNGT 1 cut(s) 298
TaqI TCGA 2 cut(s) 343, 511
TasI AATT 4 cut(s) 241, 248, 369, 417
TatI WGTACW 1 cut(s) 523
TfiI GAWTC 3 cut(s) 85, 202, 463
Tru1I TTAA 4 cut(s) 47, 216, 383, 420
Tru9I TTAA 4 cut(s) 47, 216, 383, 420
TscAI CASTG 2 cut(s) 295, 435
TseI GCWGC 3 cut(s) 17, 106, 169
TspDTI ATGAA 1 cut(s) 80
TspGWI ACGGA 1 cut(s) 361
TspRI CASTG 2 cut(s) 295, 435
VpaK11BI GGWCC 1 cut(s) 425
XceI RCATGY 1 cut(s) 382
XmiI GTMKAC 1 cut(s) 343
XspI CTAG 1 cut(s) 488
Zsp2I ATGCAT 1 cut(s) 354
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.