Basic Information

Type: gene

Biological Identity

Species

rosa_wichuraiana

Chromosome

Chr1

Orthogroup ID

OG0000701

Physical Location & Seq

Genomic Coordinates Forward (+)

35998115 .. 35999680

Gene Structure 1566 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rw1G016200.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 426 bp

ATGGAGAGTTACATCACACGCATGAATCAGGAGAATGTGATTAGAGCAATCTTAGTTGCTCAACAAAATCTGACTCCTTTTCCAAGGACCTCCATTAGTGAGATGGGTTCAGAGTACCACTTGGAGATTTTCCAGGAGGCAGAATTGTTGGTGAATATTAAAGAGCATGTTCTAGTTCTTGCGCATCGGGTTCATGCAAATGAGGAATATAAGAGTTTGCTGGAGAGGTACATTGTGAAAGAAACACAGCTTCCTCTTATTCAGGTGATTGATCCAATTGCAAGATATTACGGGCTTAATCGTGGACAAGTTGTGAAGATAATCCGGCCAATTGGGATTTTGCAAAGGCCTCCATTAGTGAAATGGGTTCAAAGTACCACTTGGAGATTTGAAGGATTGGAGAGTGGAGAAAGAAGCCATGCTTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000418 GO:0000428 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005665 GO:0005666 GO:0005730 GO:0005736 GO:0006139 GO:0006351 GO:0006366 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0010467 GO:0016070 GO:0016591 GO:0018130 GO:0019438 GO:0030880 GO:0031974 GO:0031981 GO:0032774 GO:0032991 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044452 GO:0044464 GO:0046483 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0090304 GO:0097659 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko04623 ko05016 ko05169 map00230 map00240 map01100 map03020 map04623 map05016 map05169

Pfam Domains

Protein Families

RNA_pol_Rpb5_C RNA_pol_Rpb5_N

Protein Analysis

141

Amino Acids

16.43

Weight (kDa)

6.98

Isoelectric Point (pI)

36.2

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb5_C	PF01191	51 - 110	7.7e-21	RNA polymerase Rpb5, C-terminal domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

Font Size (px)

Line Width

Align Labels (Cladogram)

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

Orthologous Genes (Group: OG0000701)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G22320
fragaria_vesca	FvH4_5g21560 FvH4_7g09301 FvH4_7g09301
malus_domestica	MD02G1080800.v1.1 MD02G1093900.v1.1 MD15G1208600.v1.1
prunus_persica	Prupe.2G121300_v2.0.a1 Prupe.2G121300_v2.0.a1 Prupe.2G121400_v2.0.a1 Prupe.2G121400_v2.0.a1
pyrus_communis	pycom02g06410 pycom02g07430 pycom15g18470
rosa_chinensis	RchiOBHm_Chr1g0332791 RchiOBHm_Chr1g0344101 RchiOBHm_Chr1g0344151 RchiOBHm_Chr1g0344171 RchiOBHm_Chr1g0345361 RchiOBHm_Chr1g0345421 RchiOBHm_Chr1g0345561 RchiOBHm_Chr1g0345591 RchiOBHm_Chr1g0345671 RchiOBHm_Chr1g0345701 RchiOBHm_Chr1g0345711 RchiOBHm_Chr1g0345721 RchiOBHm_Chr1g0345801 RchiOBHm_Chr1g0345851 RchiOBHm_Chr1g0345901 RchiOBHm_Chr1g0345921 RchiOBHm_Chr1g0345931 RchiOBHm_Chr1g0345951 RchiOBHm_Chr1g0345961 RchiOBHm_Chr7g0208981
rosa_laevigata	RLG00000003175 RLG00000029644
rosa_multiflora	Rmu_co8382943.1_g000001 Rmu_sc0000532.1_g000035 Rmu_sc0001292.1_g000003 Rmu_sc0001349.1_g000004 Rmu_sc0001692.1_g000006 Rmu_sc0001692.1_g000027 Rmu_sc0002329.1_g000024 Rmu_sc0002329.1_g000032 Rmu_sc0004239.1_g000023 Rmu_sc0008115.1_g000011
rosa_roxburghii	Rroxscaffold_3G00238160 Rroxscaffold_3G00249920 Rroxscaffold_4G00310020 Rroxscaffold_4G00317980 Rroxscaffold_5G00344600
rosa_rugosa	Rorug01G0103700 Rorug01G0103800 Rorug01G0103900 Rorug01G0171800 Rorug07G0107800
rosa_samantha	Rh1BG097500 Rh1BG161500 Rh1CG122000 Rh1CG173900 Rh1CG180700 Rh1CG181100 Rh1DG133900 Rh1DG191900 Rh7AG242600 Rh7BG237400 Rh7DG249500
rosa_wichuraiana	Rw1G010510 Rw1G016120 Rw1G016200 Rw1G016220 Rw1G016430 Rw1G016490 Rw7G020550

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc16I	TGCGCA	1 cut(s)	183
AclWI	GGATC	1 cut(s)	266
AcoI	YGGCCR	1 cut(s)	326
AfaI	GTAC	3 cut(s)	116, 230, 376
AgsI	TTSAA	2 cut(s)	371, 392
AjnI	CCWGG	1 cut(s)	132
AluBI	AGCT	1 cut(s)	250
AluI	AGCT	1 cut(s)	250
AlwI	GGATC	1 cut(s)	266
AoxI	GGCC	2 cut(s)	326, 347
AspLEI	GCGC	1 cut(s)	184
AspS9I	GGNCC	1 cut(s)	87
AsuHPI	GGTGA	2 cut(s)	163, 277
AvaII	GGWCC	1 cut(s)	87
BccI	CCATC	1 cut(s)	97
BciT130I	CCWGG	1 cut(s)	134
BfaI	CTAG	1 cut(s)	173
Bme1390I	CCNGG	1 cut(s)	134
Bme18I	GGWCC	1 cut(s)	87
BmgT120I	GGNCC	1 cut(s)	87
BmrFI	CCNGG	1 cut(s)	134
BmsI	GCATC	1 cut(s)	193
BpmI	CTGGAG	1 cut(s)	242
BsaJI	CCNNGG	1 cut(s)	83
BseBI	CCWGG	1 cut(s)	134
BseDI	CCNNGG	1 cut(s)	83
BshFI	GGCC	2 cut(s)	328, 349
BsiSI	CCGG	1 cut(s)	325
BsnI	GGCC	2 cut(s)	328, 349
Bsp143I	GATC	1 cut(s)	271
BspANI	GGCC	2 cut(s)	328, 349
BspPI	GGATC	1 cut(s)	266
BssECI	CCNNGG	1 cut(s)	83
BssMI	GATC	1 cut(s)	271
BssT1I	CCWWGG	1 cut(s)	83
Bst2UI	CCWGG	1 cut(s)	134
BstDEI	CTNAG	2 cut(s)	52, 423
BstHHI	GCGC	1 cut(s)	184
BstKTI	GATC	1 cut(s)	274
BstMBI	GATC	1 cut(s)	271
BstNI	CCWGG	1 cut(s)	134
BstNSI	RCATGY	1 cut(s)	170
BstSCI	CCNGG	1 cut(s)	132
BsuRI	GGCC	2 cut(s)	328, 349
CfoI	GCGC	1 cut(s)	184
Cfr13I	GGNCC	1 cut(s)	87
Csp6I	GTAC	3 cut(s)	115, 229, 375
CviAII	CATG	4 cut(s)	22, 167, 194, 419
CviJI	RGCY	5 cut(s)	250, 295, 328, 349, 417
CviKI_1	RGCY	5 cut(s)	250, 295, 328, 349, 417
CviQI	GTAC	3 cut(s)	115, 229, 375
DdeI	CTNAG	2 cut(s)	52, 423
DpnI	GATC	1 cut(s)	273
DpnII	GATC	1 cut(s)	271
EaeI	YGGCCR	1 cut(s)	326
Eco130I	CCWWGG	1 cut(s)	83
Eco147I	AGGCCT	1 cut(s)	349
Eco47I	GGWCC	1 cut(s)	87
EcoO109I	RGGNCCY	1 cut(s)	87
EcoRII	CCWGG	1 cut(s)	132
EcoT14I	CCWWGG	1 cut(s)	83
ErhI	CCWWGG	1 cut(s)	83
FaeI	CATG	4 cut(s)	25, 170, 197, 422
FaiI	YATR	5 cut(s)	23, 168, 195, 210, 420
FalI	AAGNNNNNCTT	3 cut(s)	364, 396, 406
FatI	CATG	4 cut(s)	21, 166, 193, 418
FspBI	CTAG	1 cut(s)	173
FspI	TGCGCA	1 cut(s)	183
GlaI	GCGC	1 cut(s)	183
GsuI	CTGGAG	1 cut(s)	242
HaeIII	GGCC	2 cut(s)	328, 349
HapII	CCGG	1 cut(s)	325
HhaI	GCGC	1 cut(s)	184
Hin1II	CATG	4 cut(s)	25, 170, 197, 422
Hin6I	GCGC	1 cut(s)	182
HinP1I	GCGC	1 cut(s)	182
HinfI	GANTC	2 cut(s)	25, 73
HpaII	CCGG	1 cut(s)	325
HphI	GGTGA	2 cut(s)	163, 277
Hpy166II	GTNNAC	1 cut(s)	305
Hpy188I	TCNGA	2 cut(s)	72, 112
Hpy188III	TCNNGA	1 cut(s)	29
Hpy8I	GTNNAC	1 cut(s)	305
HpyAV	CCTTC	1 cut(s)	386
HpyCH4V	TGCA	3 cut(s)	197, 281, 343
HpyF3I	CTNAG	2 cut(s)	52, 423
Hsp92II	CATG	4 cut(s)	25, 170, 197, 422
HspAI	GCGC	1 cut(s)	182
Kzo9I	GATC	1 cut(s)	271
LpnPI	CCDG	6 cut(s)	14, 119, 146, 206, 248, 338
LweI	GCATC	1 cut(s)	193
MaeI	CTAG	1 cut(s)	173
MaeIII	GTNAC	1 cut(s)	8
MalI	GATC	1 cut(s)	273
MboI	GATC	1 cut(s)	271
MboII	GAAGA	1 cut(s)	328
MfeI	CAATTG	2 cut(s)	276, 330
MluCI	AATT	3 cut(s)	143, 276, 330
MlyI	GAGTC	1 cut(s)	67
MnlI	CCTC	6 cut(s)	100, 130, 196, 219, 264, 360
MseI	TTAA	2 cut(s)	159, 297
MslI	CAYNNNNRTG	2 cut(s)	20, 198
MspI	CCGG	1 cut(s)	325
MspR9I	CCNGG	1 cut(s)	134
MunI	CAATTG	2 cut(s)	276, 330
MvaI	CCWGG	1 cut(s)	134
NdeII	GATC	1 cut(s)	271
NlaIII	CATG	4 cut(s)	25, 170, 197, 422
NsbI	TGCGCA	1 cut(s)	183
NspI	RCATGY	1 cut(s)	170
PceI	AGGCCT	1 cut(s)	349
PfeI	GAWTC	1 cut(s)	25
PfoI	TCCNGGA	1 cut(s)	132
PleI	GAGTC	1 cut(s)	67
PpsI	GAGTC	1 cut(s)	67
PpuMI	RGGWCCY	1 cut(s)	87
Psp5II	RGGWCCY	1 cut(s)	87
Psp6I	CCWGG	1 cut(s)	132
PspGI	CCWGG	1 cut(s)	132
PspPI	GGNCC	1 cut(s)	87
PspPPI	RGGWCCY	1 cut(s)	87
RsaI	GTAC	3 cut(s)	116, 230, 376
RsaNI	GTAC	3 cut(s)	115, 229, 375
RseI	CAYNNNNRTG	2 cut(s)	20, 198
SaqAI	TTAA	2 cut(s)	159, 297
Sau3AI	GATC	1 cut(s)	271
Sau96I	GGNCC	1 cut(s)	87
SchI	GAGTC	1 cut(s)	67
ScrFI	CCNGG	1 cut(s)	134
SetI	ASST	4 cut(s)	92, 230, 252, 267
SfaNI	GCATC	1 cut(s)	193
SinI	GGWCC	1 cut(s)	87
SmiMI	CAYNNNNRTG	2 cut(s)	20, 198
Sse9I	AATT	3 cut(s)	143, 276, 330
SseBI	AGGCCT	1 cut(s)	349
SspI	AATATT	1 cut(s)	157
SspMI	CTAG	1 cut(s)	173
StuI	AGGCCT	1 cut(s)	349
StyD4I	CCNGG	1 cut(s)	132
StyI	CCWWGG	1 cut(s)	83
TasI	AATT	3 cut(s)	143, 276, 330
TfiI	GAWTC	1 cut(s)	25
Tru1I	TTAA	2 cut(s)	159, 297
Tru9I	TTAA	2 cut(s)	159, 297
TspDTI	ATGAA	2 cut(s)	38, 182
VpaK11BI	GGWCC	1 cut(s)	87
XceI	RCATGY	1 cut(s)	170
XcmI	CCANNNNNNNNNTGG	2 cut(s)	100, 360
XspI	CTAG	1 cut(s)	173

Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.