Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3C

Orthogroup ID

OG0001513

Physical Location & Seq

Genomic Coordinates Reverse (-)

24227742 .. 24230315

Gene Structure 2574 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3CG249700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 291 bp

ATGTGCTTGTTGTATTTCAAGGAAATGTGTGAAAAGGGTGTTCAGCCTGATTTGCTTACTTACACTGCAGTCATTGATAGGTTGGGGAGGTCAGGGGACATTGAGGAGTCGTTGAAGTTGTTTGGTGAGATGAAGGAGAGGCGGATTCGGCCTTCGTTGTATCTTTATAGAGCAATGATTAGTAATTTGAAGAAGTTGGGGAAGGTGGAGATGGCAACGAGTTTTATGGAGGAGATGAATTCGTGTGCTTCAAGTCTTTGTGCTAGTTGTAAATCGAATAAACGCGAGTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0003676 GO:0003723 GO:0003824 GO:0004518 GO:0004519 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0006139 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009451 GO:0009987 GO:0016070 GO:0016787 GO:0016788 GO:0034641 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043412 GO:0044237 GO:0044238 GO:0044424 GO:0044464 GO:0046483 GO:0071704 GO:0090304 GO:0090305 GO:0097159 GO:1901360 GO:1901363

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

DYW_deaminase PPR PPR_2 PPR_3

Protein Analysis

96

Amino Acids

11.02

Weight (kDa)

8.63

Isoelectric Point (pI)

45.03

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_3	PF13812	6 - 61	1.7e-10	Pentatricopeptide repeat domain
PPR_1	PF12854	12 - 45	3.4e-08	PPR repeat
PPR_2	PF13041	20 - 63	2.1e-09	PPR repeat family
PPR	PF01535	20 - 49	5.1e-08	PPR repeat

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Align Labels (Cladogram)

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Publication-ready

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

Orthologous Genes (Group: OG0001513)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G11900
fragaria_vesca	FvH4_6g24020 FvH4_6g44590 FvH4_6g44590 FvH4_6g44590 FvH4_6g44590 FvH4_6g44590 FvH4_6g44670 FvH4_6g44670 FvH4_6g44670
malus_domestica	MD14G1065400.v1.1 MD17G1084400.v1.1
prunus_persica	Prupe.3G231200_v2.0.a1
pyrus_communis	pycom17g08150
rosa_chinensis	RchiOBHm_Chr1g0342741 RchiOBHm_Chr1g0342831 RchiOBHm_Chr2g0161831
rosa_laevigata	RLG00000021301 RLG00000029118 RLG00000029172 RLG00000029191
rosa_multiflora	Rmu_co8023038.1_g000001 Rmu_sc0001993.1_g000024 Rmu_sc0004502.1_g000002 Rmu_sc0011563.1_g000011
rosa_roxburghii	Rroxscaffold_2G00088520 Rroxscaffold_2G00088540 Rroxscaffold_2G00118030 Rroxscaffold_3G00231880 Rroxscaffold_4G00313190 Rroxscaffold_4G00313220 Rroxscaffold_7G00197130
rosa_rugosa	Rorug01G0146200.1 Rorug02G0492600
rosa_samantha	Rh1AG162400 Rh1AG162900 Rh1AG163800 Rh1AG164600 Rh1BG129700 Rh1CG152900 Rh1CG153400 Rh2AG558200 Rh2AG558300 Rh2CG541900 Rh2CG542300 Rh2DG581000 Rh2DG581900 Rh3CG249700
rosa_wichuraiana	Rw1G013300 Rw1G013340 Rw1G013680

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccII	CGCG	1 cut(s)	285
AciI	CCGC	1 cut(s)	142
AcsI	RAATTY	1 cut(s)	238
AgsI	TTSAA	4 cut(s)	19, 115, 190, 252
AoxI	GGCC	1 cut(s)	149
ApoI	RAATTY	1 cut(s)	238
AsuHPI	GGTGA	1 cut(s)	137
BccI	CCATC	1 cut(s)	205
BfaI	CTAG	1 cut(s)	264
BfmI	CTRYAG	1 cut(s)	66
Bse3DI	GCAATG	1 cut(s)	180
BseMI	GCAATG	1 cut(s)	180
BseRI	GAGGAG	2 cut(s)	119, 245
Bsh1236I	CGCG	1 cut(s)	285
BshFI	GGCC	1 cut(s)	151
BslFI	GGGAC	1 cut(s)	110
BsmFI	GGGAC	1 cut(s)	110
BsnI	GGCC	1 cut(s)	151
BspACI	CCGC	1 cut(s)	142
BspANI	GGCC	1 cut(s)	151
BspFNI	CGCG	1 cut(s)	285
BspMAI	CTGCAG	1 cut(s)	70
BsrDI	GCAATG	1 cut(s)	180
BstFNI	CGCG	1 cut(s)	285
BstMWI	GCNNNNNNNGC	2 cut(s)	52, 148
BstSFI	CTRYAG	1 cut(s)	66
BstUI	CGCG	1 cut(s)	285
BsuRI	GGCC	1 cut(s)	151
BtsI	GCAGTG	1 cut(s)	63
BtsIMutI	CAGTG	1 cut(s)	63
CviJI	RGCY	2 cut(s)	46, 151
CviKI_1	RGCY	2 cut(s)	46, 151
EciI	GGCGGA	1 cut(s)	157
EcoRI	GAATTC	1 cut(s)	238
FaiI	YATR	2 cut(s)	168, 227
FaqI	GGGAC	1 cut(s)	110
FspBI	CTAG	1 cut(s)	264
HaeIII	GGCC	1 cut(s)	151
HinfI	GANTC	2 cut(s)	107, 145
HphI	GGTGA	1 cut(s)	137
HpyAV	CCTTC	3 cut(s)	127, 162, 196
HpyCH4V	TGCA	1 cut(s)	68
HpyF10VI	GCNNNNNNNGC	2 cut(s)	52, 148
LpnPI	CCDG	2 cut(s)	60, 78
MaeI	CTAG	1 cut(s)	264
MboII	GAAGA	1 cut(s)	202
MluCI	AATT	2 cut(s)	184, 238
MlyI	GAGTC	1 cut(s)	116
MnlI	CCTC	4 cut(s)	81, 97, 132, 223
MvnI	CGCG	1 cut(s)	285
MwoI	GCNNNNNNNGC	2 cut(s)	52, 148
PfeI	GAWTC	1 cut(s)	145
PleI	GAGTC	1 cut(s)	115
PpsI	GAGTC	1 cut(s)	115
PstI	CTGCAG	1 cut(s)	70
SchI	GAGTC	1 cut(s)	116
SetI	ASST	3 cut(s)	83, 92, 207
SfcI	CTRYAG	1 cut(s)	66
SgeI	CNNG	8 cut(s)	19, 31, 59, 105, 231, 255, 264, 276
Sse9I	AATT	2 cut(s)	184, 238
SsiI	CCGC	1 cut(s)	142
SspMI	CTAG	1 cut(s)	264
TaqI	TCGA	1 cut(s)	275
TasI	AATT	2 cut(s)	184, 238
TfiI	GAWTC	1 cut(s)	145
TscAI	CASTG	1 cut(s)	70
TspDTI	ATGAA	2 cut(s)	146, 251
TspRI	CASTG	1 cut(s)	70
XapI	RAATTY	1 cut(s)	238
XspI	CTAG	1 cut(s)	264

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