Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5C

Orthogroup ID

OG0001657

Physical Location & Seq

Genomic Coordinates Forward (+)

51005859 .. 51007721

Gene Structure 1863 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5CG387200.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 645 bp

ATGGATCTTGTAGGACTTGCCTACTCTGAGGGTTATCTTTCTATGTCATACAACGACCATATGGAAAACCATAGAACAAAGGCCAATGCTGGTTTTGTTGTTCCTGTTGTGTTTGATGTTTCAGTGCAGCAATACAGAAAGTTAATCCGATTATACTCAACGGTTATACTTTCAAATGCGACTTCAATGCCATTGGTGCTGCAATTTGATATTCCATTTGGTGTGTCCCCAAAGATCTTGGACCCCATATATCCAGTGAATAACTACCTTCCTGACGCATTGGCATTGACGACGATAGGAAGCGGTGGGATTACTCAGACCGCATTTCTTTCAGAGGTGGAAACTTCTTTTCATAATGTTGATCCTTCTCATCAGCTGAGATTGGAGATCCATATGCATGGCTTTAAACCAGCAGTTTTGGATTTCCCACATACTGAAATATTCTGTGAAGTGGCCAAGTTTGGTGGAGCGAAGTTCTCACTTTCTGAAGTTGTGGCCTTCGACTCCACAAATGGACCAATGTATGTCACAGTGGAAAAGGTGATGGATGCATTTTCTGGAGCCCACCCTTTATTTCCATTCCCTTTCTGTTATATAATTGCTCTGGTTTTCCACTCTTCATTTCTGAATCTGCCAGTGAAATGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000045 GO:0006810 GO:0006914 GO:0006996 GO:0007033 GO:0007034 GO:0008150 GO:0008152 GO:0009056 GO:0009987 GO:0016043 GO:0016192 GO:0016236 GO:0022607 GO:0030587 GO:0031154 GO:0032502 GO:0044085 GO:0044237 GO:0044248 GO:0045324 GO:0046907 GO:0048856 GO:0051179 GO:0051234 GO:0051641 GO:0051649 GO:0051703 GO:0051704 GO:0061919 GO:0070925 GO:0071840 GO:0090702 GO:0099120 GO:1905037

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

Chorein_N SHR-BD VPS13 VPS13_C VPS13_mid_rpt

Protein Analysis

214

Amino Acids

23.74

Weight (kDa)

5.63

Isoelectric Point (pI)

38.69

Instability Index

Protein Domains (Pfam)

No Pfam domains detected for this protein.

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)

Image

Tree File

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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: OG0001657)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G24740 AT5G24740 AT5G24740 AT5G24740 AT5G24740 AT5G24740
fragaria_vesca	FvH4_6g36300 FvH4_6g36300 FvH4_6g36300 FvH4_6g36300 FvH4_6g36300 FvH4_6g36300 FvH4_6g36300 FvH4_6g36300 FvH4_6g36300 FvH4_6g36300 FvH4_6g36300 FvH4_6g36300 FvH4_6g36300 FvH4_6g36300 FvH4_6g36300
malus_domestica	MD09G1170300.v1.1 MD17G1156800.v1.1
prunus_persica	Prupe.3G028500_v2.0.a1 Prupe.3G028500_v2.0.a1 Prupe.3G028500_v2.0.a1
pyrus_communis	pycom09g08790 pycom17g15020
rosa_chinensis	RchiOBHm_Chr2g0148301 RchiOBHm_Chr2g0148311 RchiOBHm_Chr5g0051461
rosa_laevigata	RLG00000020335
rosa_multiflora	Rmu_sc0004032.1_g000013 Rmu_sc0022189.1_g000006
rosa_roxburghii	Rroxscaffold_1G00027070 Rroxscaffold_2G00098910 Rroxscaffold_2G00098920
rosa_rugosa	Rorug02G0405600 Rorug05G0279200
rosa_samantha	Rh2AG464200 Rh2BG477200 Rh2CG450900 Rh2DG486000 Rh5AG350300 Rh5AG350400 Rh5BG362600 Rh5CG387200 Rh5DG377000
rosa_wichuraiana	Rw2G037840

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AciI	CCGC	2 cut(s)	303, 321
AclWI	GGATC	3 cut(s)	12, 356, 382
AcoI	YGGCCR	1 cut(s)	453
AcuI	CTGAAG	1 cut(s)	507
AgsI	TTSAA	2 cut(s)	174, 186
AluBI	AGCT	1 cut(s)	376
AluI	AGCT	1 cut(s)	376
AlwI	GGATC	3 cut(s)	12, 356, 382
AoxI	GGCC	3 cut(s)	81, 453, 495
ApeKI	GCWGC	2 cut(s)	127, 199
AspS9I	GGNCC	2 cut(s)	241, 515
AsuHPI	GGTGA	1 cut(s)	553
AvaII	GGWCC	2 cut(s)	241, 515
BalI	TGGCCA	1 cut(s)	455
BanII	GRGCYC	1 cut(s)	565
BbvI	GCAGC	2 cut(s)	139, 186
BccI	CCATC	1 cut(s)	538
BcgI	CGANNNNNNTGC	2 cut(s)	169, 203
BglII	AGATCT	1 cut(s)	234
BisI	GCNGC	2 cut(s)	128, 200
BlsI	GCNGC	2 cut(s)	129, 201
Bme18I	GGWCC	2 cut(s)	241, 515
BmgT120I	GGNCC	2 cut(s)	241, 515
BmiI	GGNNCC	2 cut(s)	243, 562
BmsI	GCATC	1 cut(s)	538
BpmI	CTGGAG	1 cut(s)	579
Bse1I	ACTGG	2 cut(s)	254, 635
BseGI	GGATG	1 cut(s)	553
BseMII	CTCAG	3 cut(s)	18, 329, 368
BseNI	ACTGG	2 cut(s)	254, 635
BseXI	GCAGC	2 cut(s)	139, 186
BsgI	GTGCAG	1 cut(s)	146
BshFI	GGCC	3 cut(s)	83, 455, 497
BslFI	GGGAC	1 cut(s)	211
BsmFI	GGGAC	1 cut(s)	211
BsnI	GGCC	3 cut(s)	83, 455, 497
Bsp1286I	GDGCHC	1 cut(s)	565
Bsp143I	GATC	4 cut(s)	4, 234, 361, 387
BspACI	CCGC	2 cut(s)	303, 321
BspANI	GGCC	3 cut(s)	83, 455, 497
BspCNI	CTCAG	3 cut(s)	19, 328, 369
BspLI	GGNNCC	2 cut(s)	243, 562
BspPI	GGATC	3 cut(s)	12, 356, 382
BsrI	ACTGG	2 cut(s)	254, 635
BssMI	GATC	4 cut(s)	4, 234, 361, 387
Bst4CI	ACNGT	2 cut(s)	163, 532
Bst6I	CTCTTC	1 cut(s)	622
BstDEI	CTNAG	3 cut(s)	27, 315, 377
BstF5I	GGATG	1 cut(s)	553
BstKTI	GATC	4 cut(s)	7, 237, 364, 390
BstMBI	GATC	4 cut(s)	4, 234, 361, 387
BstMWI	GCNNNNNNNGC	1 cut(s)	196
BstV1I	GCAGC	2 cut(s)	139, 186
BstX2I	RGATCY	3 cut(s)	4, 234, 387
BstXI	CCANNNNNNTGG	1 cut(s)	398
BstYI	RGATCY	3 cut(s)	4, 234, 387
BsuRI	GGCC	3 cut(s)	83, 455, 497
BtsCI	GGATG	1 cut(s)	553
BtsIMutI	CAGTG	4 cut(s)	129, 261, 537, 642
Cfr13I	GGNCC	2 cut(s)	241, 515
CseI	GACGC	1 cut(s)	284
CspCI	CAANNNNNGTGG	2 cut(s)	445, 480
CviAII	CATG	1 cut(s)	398
CviJI	RGCY	6 cut(s)	83, 376, 402, 455, 497, 563
CviKI_1	RGCY	6 cut(s)	83, 376, 402, 455, 497, 563
DdeI	CTNAG	3 cut(s)	27, 315, 377
DpnI	GATC	4 cut(s)	6, 236, 363, 389
DpnII	GATC	4 cut(s)	4, 234, 361, 387
DraI	TTTAAA	1 cut(s)	406
EaeI	YGGCCR	1 cut(s)	453
Eam1104I	CTCTTC	1 cut(s)	622
EarI	CTCTTC	1 cut(s)	622
Eco24I	GRGCYC	1 cut(s)	565
Eco47I	GGWCC	2 cut(s)	241, 515
Eco57I	CTGAAG	1 cut(s)	507
EcoT22I	ATGCAT	2 cut(s)	399, 553
EcoT38I	GRGCYC	1 cut(s)	565
FaeI	CATG	1 cut(s)	401
FaqI	GGGAC	1 cut(s)	211
FatI	CATG	1 cut(s)	397
FauNDI	CATATG	2 cut(s)	60, 393
Fnu4HI	GCNGC	2 cut(s)	128, 200
FokI	GGATG	1 cut(s)	560
FriOI	GRGCYC	1 cut(s)	565
Fsp4HI	GCNGC	2 cut(s)	128, 200
GluI	GCNGC	2 cut(s)	128, 200
GsuI	CTGGAG	1 cut(s)	579
HaeIII	GGCC	3 cut(s)	83, 455, 497
HgaI	GACGC	1 cut(s)	284
Hin1II	CATG	1 cut(s)	401
HinfI	GANTC	2 cut(s)	503, 628
HphI	GGTGA	1 cut(s)	553
Hpy188I	TCNGA	6 cut(s)	28, 149, 318, 334, 487, 627
Hpy188III	TCNNGA	2 cut(s)	272, 558
Hpy99I	CGWCG	1 cut(s)	295
HpyAV	CCTTC	3 cut(s)	278, 375, 508
HpyCH4III	ACNGT	2 cut(s)	163, 532
HpyCH4V	TGCA	4 cut(s)	127, 202, 397, 551
HpyF10VI	GCNNNNNNNGC	1 cut(s)	196
HpyF3I	CTNAG	3 cut(s)	27, 315, 377
Hsp92II	CATG	1 cut(s)	401
Kzo9I	GATC	4 cut(s)	4, 234, 361, 387
LmnI	GCTCC	2 cut(s)	467, 560
LpnPI	CCDG	7 cut(s)	75, 117, 267, 285, 423, 543, 590
Lsp1109I	GCAGC	2 cut(s)	139, 186
LweI	GCATC	1 cut(s)	538
MaeIII	GTNAC	1 cut(s)	526
MalI	GATC	4 cut(s)	6, 236, 363, 389
MboI	GATC	4 cut(s)	4, 234, 361, 387
MboII	GAAGA	1 cut(s)	609
MflI	RGATCY	3 cut(s)	4, 234, 387
MhlI	GDGCHC	1 cut(s)	565
MlsI	TGGCCA	1 cut(s)	455
MluCI	AATT	2 cut(s)	203, 597
MluNI	TGGCCA	1 cut(s)	455
MlyI	GAGTC	1 cut(s)	497
MnlI	CCTC	2 cut(s)	22, 328
Mox20I	TGGCCA	1 cut(s)	455
Mph1103I	ATGCAT	2 cut(s)	399, 553
MscI	TGGCCA	1 cut(s)	455
MseI	TTAA	2 cut(s)	143, 405
MslI	CAYNNNNRTG	1 cut(s)	396
Msp20I	TGGCCA	1 cut(s)	455
MspA1I	CMGCKG	1 cut(s)	376
MwoI	GCNNNNNNNGC	1 cut(s)	196
NdeI	CATATG	2 cut(s)	60, 393
NdeII	GATC	4 cut(s)	4, 234, 361, 387
NlaIII	CATG	1 cut(s)	401
NlaIV	GGNNCC	2 cut(s)	243, 562
NmuCI	GTSAC	1 cut(s)	526
NsiI	ATGCAT	2 cut(s)	399, 553
PfeI	GAWTC	1 cut(s)	628
PkrI	GCNGC	2 cut(s)	129, 201
PleI	GAGTC	1 cut(s)	497
PpsI	GAGTC	1 cut(s)	497
PspN4I	GGNNCC	2 cut(s)	243, 562
PspPI	GGNCC	2 cut(s)	241, 515
PsuI	RGATCY	3 cut(s)	4, 234, 387
PvuII	CAGCTG	1 cut(s)	376
RseI	CAYNNNNRTG	1 cut(s)	396
SaqAI	TTAA	2 cut(s)	143, 405
SatI	GCNGC	2 cut(s)	128, 200
Sau3AI	GATC	4 cut(s)	4, 234, 361, 387
Sau96I	GGNCC	2 cut(s)	241, 515
SchI	GAGTC	1 cut(s)	497
SduI	GDGCHC	1 cut(s)	565
SetI	ASST	4 cut(s)	270, 339, 378, 543
SfaNI	GCATC	1 cut(s)	538
SinI	GGWCC	2 cut(s)	241, 515
SmiMI	CAYNNNNRTG	1 cut(s)	396
Sse9I	AATT	2 cut(s)	203, 597
SsiI	CCGC	2 cut(s)	303, 321
SspI	AATATT	1 cut(s)	441
TaaI	ACNGT	2 cut(s)	163, 532
TaqI	TCGA	1 cut(s)	501
TasI	AATT	2 cut(s)	203, 597
TfiI	GAWTC	1 cut(s)	628
Tru1I	TTAA	2 cut(s)	143, 405
Tru9I	TTAA	2 cut(s)	143, 405
TscAI	CASTG	4 cut(s)	129, 261, 537, 642
TseFI	GTSAC	1 cut(s)	526
TseI	GCWGC	2 cut(s)	127, 199
Tsp45I	GTSAC	1 cut(s)	526
TspDTI	ATGAA	2 cut(s)	341, 609
TspRI	CASTG	4 cut(s)	129, 261, 537, 642
VpaK11BI	GGWCC	2 cut(s)	241, 515
Zsp2I	ATGCAT	2 cut(s)	399, 553

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