Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1C

Orthogroup ID

OG0000701

Physical Location & Seq

Genomic Coordinates Forward (+)

39849232 .. 39849612

Gene Structure 381 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1CG180700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 186 bp

ATGCTGAAAGATTGGGACTGCATTTATGTGTTTTTCCCTGACGAACCAAAAGTTGGGGTCAAGACAATCAAGAATTACATCAAACGCGTGGTTCTGGAGGATATGGACACAGGCATCATGGTTATTCAACAAAATCTGACTCCTTTTGCAAAACTCGTCATAAGTGAGATGAGATCAAAGTGGTAG

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

61

Amino Acids

7.22

Weight (kDa)

7.84

Isoelectric Point (pI)

24.79

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb5_N	PF03871	6 - 30	7.5e-06	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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Publication-ready

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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)	53
AccII	CGCG	1 cut(s)	87
AfiI	CCNNNNNNNGG	1 cut(s)	53
AflIII	ACRYGT	1 cut(s)	85
AgsI	TTSAA	1 cut(s)	128
AjuI	GAANNNNNNNTTGG	2 cut(s)	36, 68
BmsI	GCATC	1 cut(s)	123
BpmI	CTGGAG	1 cut(s)	116
Bsc4I	CCNNNNNNNGG	1 cut(s)	53
BseLI	CCNNNNNNNGG	1 cut(s)	53
Bsh1236I	CGCG	1 cut(s)	87
BslFI	GGGAC	1 cut(s)	29
BslI	CCNNNNNNNGG	1 cut(s)	53
BsmFI	GGGAC	1 cut(s)	29
Bsp143I	GATC	1 cut(s)	173
BspFNI	CGCG	1 cut(s)	87
BssMI	GATC	1 cut(s)	173
BstFNI	CGCG	1 cut(s)	87
BstKTI	GATC	1 cut(s)	176
BstMBI	GATC	1 cut(s)	173
BstUI	CGCG	1 cut(s)	87
CviAII	CATG	1 cut(s)	118
DpnI	GATC	1 cut(s)	175
DpnII	GATC	1 cut(s)	173
FaeI	CATG	1 cut(s)	121
FaiI	YATR	4 cut(s)	27, 104, 119, 161
FaqI	GGGAC	1 cut(s)	29
FatI	CATG	1 cut(s)	117
GsuI	CTGGAG	1 cut(s)	116
Hin1II	CATG	1 cut(s)	121
HinfI	GANTC	1 cut(s)	139
Hpy188I	TCNGA	1 cut(s)	138
Hpy188III	TCNNGA	3 cut(s)	61, 70, 95
HpyCH4V	TGCA	2 cut(s)	21, 149
Hsp92II	CATG	1 cut(s)	121
Kzo9I	GATC	1 cut(s)	173
LpnPI	CCDG	3 cut(s)	51, 80, 96
LweI	GCATC	1 cut(s)	123
MalI	GATC	1 cut(s)	175
MboI	GATC	1 cut(s)	173
MluCI	AATT	1 cut(s)	73
MluI	ACGCGT	1 cut(s)	85
MlyI	GAGTC	1 cut(s)	133
MnlI	CCTC	1 cut(s)	91
MslI	CAYNNNNRTG	1 cut(s)	26
MvnI	CGCG	1 cut(s)	87
NdeII	GATC	1 cut(s)	173
NlaIII	CATG	1 cut(s)	121
PflMI	CCANNNNNTGG	1 cut(s)	53
PleI	GAGTC	1 cut(s)	133
PpsI	GAGTC	1 cut(s)	133
RseI	CAYNNNNRTG	1 cut(s)	26
Sau3AI	GATC	1 cut(s)	173
SchI	GAGTC	1 cut(s)	133
SfaNI	GCATC	1 cut(s)	123
SgeI	CNNG	9 cut(s)	50, 73, 82, 98, 100, 107, 123, 130, 167
SmiMI	CAYNNNNRTG	1 cut(s)	26
Sse9I	AATT	1 cut(s)	73
TasI	AATT	1 cut(s)	73
Van91I	CCANNNNNTGG	1 cut(s)	53

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