Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5D

Orthogroup ID

OG0006238

Physical Location & Seq

Genomic Coordinates Reverse (-)

4063537 .. 4065310

Gene Structure 1774 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5DG048700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 630 bp

ATGGAGGTCAAGCTATGGAATGACAAGCGTGAAAGAGAAATGTATGAAAATTTCTCCGAGTTATACGCCATTATAAAGGCCACTGAGAAGCTTGAAAGGGCATACATTCGCGACGTGATCTCTTCATCAGCGTATGAGACTGAATGCCAGAAACTCATTGCTCACTTTAAGACTTTGTCTTCCACGCTTAAAGACACCATCCCAAGCATTGAGCGCTTTGCAGATACATATAAGATGGACTGCCCAGCAGCTATAAACCGCCTTGTGACCTCTGGGGTTCCTGCCACAGTGGAGCACAGGGCTGCTGCAGCTTCTTCCATGACTTCATCGGCTGCTGCTGTGGCAGAGTGCACACAGAATTTCATTACGGCAATGGACTCATTGAAGTTGAATATGATTGCAGTTGATCAGGTGCACCCCCTACTCTCAGACCTCACAACATCTCTCAATAAGTTGACCTTTCTGCCACCGGATTTCTTGGGGAAGGTGAAGTTGAAGGAATGGATTGCAAGGCTGGCAAAGATGGGCGCAGCAGATGAGTTGACAGAGCAACAGGCAAGGCAGCTTCACTTTGATCTCGAATCATCCTACAACTCATTTATGGCAGCTTTACCCAATGCTGGTAATTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

No ontology terms assigned.

KEGG Pathways

Metabolic & Signaling

ko04144 map04144

Pfam Domains

Protein Families

VPS28

Protein Analysis

209

Amino Acids

23.32

Weight (kDa)

5.63

Isoelectric Point (pI)

33.27

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
VPS28	PF03997	18 - 204	9e-72	VPS28 protein

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: OG0006238)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT4G05000 AT4G05000 AT4G05000 AT4G21560 AT4G21560 AT4G21560
fragaria_vesca	FvH4_3g04140 FvH4_3g04140 FvH4_3g04140
malus_domestica	MD05G1324500.v1.1 MD10G1302300.v1.1
prunus_persica	Prupe.4G035900_v2.0.a1 Prupe.4G035900_v2.0.a1
pyrus_communis	pycom05g29870 pycom10g25480
rosa_chinensis	RchiOBHm_Chr5g0006591
rosa_laevigata	RLG00000031402
rosa_multiflora	Rmu_sc0001972.1_g000001 Rmu_sc0011154.1_g000006
rosa_roxburghii	Rroxscaffold_1G00069450
rosa_rugosa	Rorug04G0422800 Rorug04G0422800
rosa_samantha	Rh5AG050000 Rh5BG049300 Rh5CG057500 Rh5DG048700
rosa_wichuraiana	Rw5G005010

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	74
AccII	CGCG	1 cut(s)	111
AciI	CCGC	1 cut(s)	259
AcsI	RAATTY	2 cut(s)	49, 358
AfeI	AGCGCT	1 cut(s)	215
AfiI	CCNNNNNNNGG	1 cut(s)	620
AgsI	TTSAA	4 cut(s)	95, 385, 391, 496
AjiI	CACGTC	1 cut(s)	115
AluBI	AGCT	6 cut(s)	13, 91, 251, 311, 565, 608
AluI	AGCT	6 cut(s)	13, 91, 251, 311, 565, 608
Alw21I	GWGCWC	3 cut(s)	297, 353, 417
Alw26I	GTCTC	1 cut(s)	131
Alw44I	GTGCAC	2 cut(s)	349, 413
Aor51HI	AGCGCT	1 cut(s)	215
AoxI	GGCC	1 cut(s)	78
ApaLI	GTGCAC	2 cut(s)	349, 413
ApeKI	GCWGC	9 cut(s)	248, 302, 305, 308, 332, 335, 530, 562, 605
ApoI	RAATTY	2 cut(s)	49, 358
AspLEI	GCGC	2 cut(s)	216, 530
AsuHPI	GGTGA	1 cut(s)	499
BaeGI	GKGCMC	2 cut(s)	353, 417
BbsI	GAAGAC	1 cut(s)	171
Bbv12I	GWGCWC	3 cut(s)	297, 353, 417
BbvI	GCAGC	9 cut(s)	260, 289, 292, 319, 320, 322, 542, 574, 617
BccI	CCATC	3 cut(s)	206, 229, 517
BceAI	ACGGC	1 cut(s)	384
BclI	TGATCA	1 cut(s)	406
BcoDI	GTCTC	1 cut(s)	131
BfmI	CTRYAG	1 cut(s)	306
BfoI	RGCGCY	1 cut(s)	217
BisI	GCNGC	9 cut(s)	249, 303, 306, 309, 333, 336, 531, 563, 606
BlsI	GCNGC	9 cut(s)	250, 304, 307, 310, 334, 337, 532, 564, 607
BmgBI	CACGTC	1 cut(s)	115
BmiI	GGNNCC	1 cut(s)	279
BpiI	GAAGAC	1 cut(s)	171
BsaWI	WCCGGW	1 cut(s)	469
Bsc4I	CCNNNNNNNGG	1 cut(s)	620
Bse3DI	GCAATG	2 cut(s)	156, 378
BseGI	GGATG	2 cut(s)	198, 584
BseLI	CCNNNNNNNGG	1 cut(s)	620
BseMI	GCAATG	2 cut(s)	156, 378
BseMII	CTCAG	2 cut(s)	75, 441
BseSI	GKGCMC	2 cut(s)	353, 417
BseXI	GCAGC	9 cut(s)	260, 289, 292, 319, 320, 322, 542, 574, 617
BseYI	CCCAGC	1 cut(s)	244
Bsh1236I	CGCG	1 cut(s)	111
BshFI	GGCC	1 cut(s)	80
BsiHKAI	GWGCWC	3 cut(s)	297, 353, 417
BsiSI	CCGG	1 cut(s)	470
BslI	CCNNNNNNNGG	1 cut(s)	620
BsmAI	GTCTC	1 cut(s)	131
BsmI	GAATGC	1 cut(s)	149
BsnI	GGCC	1 cut(s)	80
Bsp1286I	GDGCHC	3 cut(s)	297, 353, 417
Bsp143I	GATC	3 cut(s)	117, 406, 574
Bsp68I	TCGCGA	1 cut(s)	111
BspACI	CCGC	1 cut(s)	259
BspANI	GGCC	1 cut(s)	80
BspCNI	CTCAG	2 cut(s)	76, 440
BspFNI	CGCG	1 cut(s)	111
BspLI	GGNNCC	1 cut(s)	279
BspMAI	CTGCAG	1 cut(s)	310
BsrDI	GCAATG	2 cut(s)	156, 378
BssMI	GATC	3 cut(s)	117, 406, 574
Bst4CI	ACNGT	1 cut(s)	289
Bst6I	CTCTTC	1 cut(s)	127
BstC8I	GCNNGC	1 cut(s)	516
BstDEI	CTNAG	2 cut(s)	84, 427
BstF5I	GGATG	2 cut(s)	198, 584
BstFNI	CGCG	1 cut(s)	111
BstH2I	RGCGCY	1 cut(s)	217
BstHHI	GCGC	2 cut(s)	216, 530
BstKTI	GATC	3 cut(s)	120, 409, 577
BstMAI	GTCTC	1 cut(s)	131
BstMBI	GATC	3 cut(s)	117, 406, 574
BstMWI	GCNNNNNNNGC	4 cut(s)	213, 308, 341, 515
BstSFI	CTRYAG	1 cut(s)	306
BstSLI	GKGCMC	2 cut(s)	353, 417
BstUI	CGCG	1 cut(s)	111
BstV1I	GCAGC	9 cut(s)	260, 289, 292, 319, 320, 322, 542, 574, 617
BstV2I	GAAGAC	1 cut(s)	171
BsuRI	GGCC	1 cut(s)	80
BtrI	CACGTC	1 cut(s)	115
BtsCI	GGATG	2 cut(s)	198, 584
BtsIMutI	CAGTG	2 cut(s)	81, 294
BtuMI	TCGCGA	1 cut(s)	111
Cac8I	GCNNGC	1 cut(s)	516
CfoI	GCGC	2 cut(s)	216, 530
CviAII	CATG	1 cut(s)	319
DdeI	CTNAG	2 cut(s)	84, 427
DpnI	GATC	3 cut(s)	119, 408, 576
DpnII	GATC	3 cut(s)	117, 406, 574
Eam1104I	CTCTTC	1 cut(s)	127
EarI	CTCTTC	1 cut(s)	127
Eco47III	AGCGCT	1 cut(s)	215
FaeI	CATG	1 cut(s)	322
FalI	AAGNNNNNCTT	2 cut(s)	443, 475
FatI	CATG	1 cut(s)	318
FbaI	TGATCA	1 cut(s)	406
Fnu4HI	GCNGC	9 cut(s)	249, 303, 306, 309, 333, 336, 531, 563, 606
FokI	GGATG	2 cut(s)	185, 571
Fsp4HI	GCNGC	9 cut(s)	249, 303, 306, 309, 333, 336, 531, 563, 606
GlaI	GCGC	2 cut(s)	215, 529
GluI	GCNGC	9 cut(s)	249, 303, 306, 309, 333, 336, 531, 563, 606
GsaI	CCCAGC	1 cut(s)	248
HaeII	RGCGCY	1 cut(s)	217
HaeIII	GGCC	1 cut(s)	80
HapII	CCGG	1 cut(s)	470
HhaI	GCGC	2 cut(s)	216, 530
Hin1II	CATG	1 cut(s)	322
Hin6I	GCGC	2 cut(s)	214, 528
HinP1I	GCGC	2 cut(s)	214, 528
HincII	GTYRAC	2 cut(s)	456, 543
HindII	GTYRAC	2 cut(s)	456, 543
HindIII	AAGCTT	1 cut(s)	89
HinfI	GANTC	2 cut(s)	377, 581
HpaII	CCGG	1 cut(s)	470
HphI	GGTGA	1 cut(s)	499
Hpy166II	GTNNAC	4 cut(s)	351, 415, 456, 543
Hpy188I	TCNGA	2 cut(s)	58, 430
Hpy188III	TCNNGA	2 cut(s)	110, 578
Hpy8I	GTNNAC	4 cut(s)	351, 415, 456, 543
Hpy99I	CGWCG	1 cut(s)	116
HpyAV	CCTTC	2 cut(s)	478, 490
HpyCH4III	ACNGT	1 cut(s)	289
HpyCH4IV	ACGT	1 cut(s)	114
HpyCH4V	TGCA	6 cut(s)	221, 308, 351, 401, 415, 509
HpyF10VI	GCNNNNNNNGC	4 cut(s)	213, 308, 341, 515
HpyF3I	CTNAG	2 cut(s)	84, 427
HpySE526I	ACGT	1 cut(s)	114
Hsp92II	CATG	1 cut(s)	322
HspAI	GCGC	2 cut(s)	214, 528
Ksp22I	TGATCA	1 cut(s)	406
Kzo9I	GATC	3 cut(s)	117, 406, 574
LmnI	GCTCC	1 cut(s)	292
Lsp1109I	GCAGC	9 cut(s)	260, 289, 292, 319, 320, 322, 542, 574, 617
MaeII	ACGT	1 cut(s)	114
MaeIII	GTNAC	1 cut(s)	265
MalI	GATC	3 cut(s)	119, 408, 576
MboI	GATC	3 cut(s)	117, 406, 574
MboII	GAAGA	3 cut(s)	114, 171, 306
MhlI	GDGCHC	3 cut(s)	297, 353, 417
MluCI	AATT	3 cut(s)	49, 358, 625
MlyI	GAGTC	1 cut(s)	371
MnlI	CCTC	2 cut(s)	280, 443
MseI	TTAA	2 cut(s)	168, 189
MspI	CCGG	1 cut(s)	470
Mva1269I	GAATGC	1 cut(s)	149
MvnI	CGCG	1 cut(s)	111
MwoI	GCNNNNNNNGC	4 cut(s)	213, 308, 341, 515
NdeII	GATC	3 cut(s)	117, 406, 574
NlaIII	CATG	1 cut(s)	322
NlaIV	GGNNCC	1 cut(s)	279
NmuCI	GTSAC	1 cut(s)	265
NruI	TCGCGA	1 cut(s)	111
PctI	GAATGC	1 cut(s)	149
PfeI	GAWTC	1 cut(s)	581
PflFI	GACNNNGTC	1 cut(s)	175
PkrI	GCNGC	9 cut(s)	250, 304, 307, 310, 334, 337, 532, 564, 607
PleI	GAGTC	1 cut(s)	371
PpsI	GAGTC	1 cut(s)	371
PsiI	TTATAA	1 cut(s)	74
PspFI	CCCAGC	1 cut(s)	244
PspN4I	GGNNCC	1 cut(s)	279
PstI	CTGCAG	1 cut(s)	310
PsyI	GACNNNGTC	1 cut(s)	175
RruI	TCGCGA	1 cut(s)	111
SaqAI	TTAA	2 cut(s)	168, 189
SatI	GCNGC	9 cut(s)	249, 303, 306, 309, 333, 336, 531, 563, 606
Sau3AI	GATC	3 cut(s)	117, 406, 574
SchI	GAGTC	1 cut(s)	371
SduI	GDGCHC	3 cut(s)	297, 353, 417
SfcI	CTRYAG	1 cut(s)	306
Sse9I	AATT	3 cut(s)	49, 358, 625
SsiI	CCGC	1 cut(s)	259
TaaI	ACNGT	1 cut(s)	289
TaiI	ACGT	1 cut(s)	117
TaqI	TCGA	1 cut(s)	579
TasI	AATT	3 cut(s)	49, 358, 625
TfiI	GAWTC	1 cut(s)	581
Tru1I	TTAA	2 cut(s)	168, 189
Tru9I	TTAA	2 cut(s)	168, 189
TscAI	CASTG	2 cut(s)	88, 294
TseFI	GTSAC	1 cut(s)	265
TseI	GCWGC	9 cut(s)	248, 302, 305, 308, 332, 335, 530, 562, 605
Tsp45I	GTSAC	1 cut(s)	265
TspDTI	ATGAA	4 cut(s)	60, 114, 315, 352
TspRI	CASTG	2 cut(s)	88, 294
Tth111I	GACNNNGTC	1 cut(s)	175
VneI	GTGCAC	2 cut(s)	349, 413
XapI	RAATTY	2 cut(s)	49, 358

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