Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1C

Orthogroup ID

OG0000701

Physical Location & Seq

Genomic Coordinates Reverse (-)

38368833 .. 38369109

Gene Structure 277 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1CG173900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 204 bp

ATGAAAAGGGAGGACCTTACTATCAATTGGAGGAAGAGAGGTGACGAGTCTGATCAGATTTATGTGTTTTTCCCTGACGAACCAAAAGTTGGGTTCAAGACAATGAAGAGTTACATTACACGCATGAATCAGGAGAATGTGATTAGAGCAATCTTAATTAGTTGCTCAACAAAATCTGACTCCTTCTGCGAAGACCTCCATTAG

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

67

Amino Acids

7.96

Weight (kDa)

6.55

Isoelectric Point (pI)

37.6

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb5_N	PF03871	2 - 42	1.1e-10	RNA polymerase Rpb5, N-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)
AccB7I	CCANNNNNTGG	1 cut(s)	89
AfiI	CCNNNNNNNGG	1 cut(s)	89
AgsI	TTSAA	1 cut(s)	97
AjuI	GAANNNNNNNTTGG	2 cut(s)	72, 104
AspS9I	GGNCC	1 cut(s)	13
AsuHPI	GGTGA	1 cut(s)	53
AvaII	GGWCC	1 cut(s)	13
BbsI	GAAGAC	1 cut(s)	198
BclI	TGATCA	1 cut(s)	52
Bme18I	GGWCC	1 cut(s)	13
BmgT120I	GGNCC	1 cut(s)	13
BpiI	GAAGAC	1 cut(s)	198
Bsc4I	CCNNNNNNNGG	1 cut(s)	89
BseLI	CCNNNNNNNGG	1 cut(s)	89
BslI	CCNNNNNNNGG	1 cut(s)	89
Bsp143I	GATC	1 cut(s)	52
BssMI	GATC	1 cut(s)	52
Bst6I	CTCTTC	2 cut(s)	29, 101
BstKTI	GATC	1 cut(s)	55
BstMBI	GATC	1 cut(s)	52
BstV2I	GAAGAC	1 cut(s)	198
Cfr13I	GGNCC	1 cut(s)	13
CviAII	CATG	1 cut(s)	124
DpnI	GATC	1 cut(s)	54
DpnII	GATC	1 cut(s)	52
Eam1104I	CTCTTC	2 cut(s)	29, 101
EarI	CTCTTC	2 cut(s)	29, 101
Eco47I	GGWCC	1 cut(s)	13
EcoO109I	RGGNCCY	1 cut(s)	13
FaeI	CATG	1 cut(s)	127
FaiI	YATR	2 cut(s)	63, 125
FatI	CATG	1 cut(s)	123
FbaI	TGATCA	1 cut(s)	52
Hin1II	CATG	1 cut(s)	127
HinfI	GANTC	3 cut(s)	47, 127, 179
HphI	GGTGA	1 cut(s)	53
Hpy188I	TCNGA	3 cut(s)	52, 57, 178
Hpy188III	TCNNGA	2 cut(s)	97, 131
HpyAV	CCTTC	1 cut(s)	193
Hsp92II	CATG	1 cut(s)	127
Ksp22I	TGATCA	1 cut(s)	52
Kzo9I	GATC	1 cut(s)	52
LpnPI	CCDG	2 cut(s)	87, 116
MaeIII	GTNAC	2 cut(s)	41, 110
MalI	GATC	1 cut(s)	54
MboI	GATC	1 cut(s)	52
MboII	GAAGA	3 cut(s)	46, 118, 203
MfeI	CAATTG	1 cut(s)	25
MluCI	AATT	2 cut(s)	25, 156
MlyI	GAGTC	2 cut(s)	56, 173
MnlI	CCTC	3 cut(s)	4, 24, 32
MseI	TTAA	1 cut(s)	155
MunI	CAATTG	1 cut(s)	25
NdeII	GATC	1 cut(s)	52
NlaIII	CATG	1 cut(s)	127
NmuCI	GTSAC	1 cut(s)	41
PfeI	GAWTC	1 cut(s)	127
PflMI	CCANNNNNTGG	1 cut(s)	89
PleI	GAGTC	2 cut(s)	55, 173
PpsI	GAGTC	2 cut(s)	55, 173
PpuMI	RGGWCCY	1 cut(s)	13
Psp5II	RGGWCCY	1 cut(s)	13
PspPI	GGNCC	1 cut(s)	13
PspPPI	RGGWCCY	1 cut(s)	13
SaqAI	TTAA	1 cut(s)	155
Sau3AI	GATC	1 cut(s)	52
Sau96I	GGNCC	1 cut(s)	13
SchI	GAGTC	2 cut(s)	56, 173
SetI	ASST	3 cut(s)	18, 43, 198
SgeI	CNNG	6 cut(s)	58, 86, 109, 132, 136, 143
SinI	GGWCC	1 cut(s)	13
Sse9I	AATT	2 cut(s)	25, 156
TasI	AATT	2 cut(s)	25, 156
TfiI	GAWTC	1 cut(s)	127
Tru1I	TTAA	1 cut(s)	155
Tru9I	TTAA	1 cut(s)	155
TseFI	GTSAC	1 cut(s)	41
Tsp45I	GTSAC	1 cut(s)	41
TspDTI	ATGAA	3 cut(s)	17, 119, 140
Van91I	CCANNNNNTGG	1 cut(s)	89
VpaK11BI	GGWCC	1 cut(s)	13

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