Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000002

Orthogroup ID

OG0001657

Physical Location & Seq

Genomic Coordinates Reverse (-)

20420237 .. 20422920

Gene Structure 2684 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_2G00098920.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 702 bp

ATGTTCGAACGACTCGTCACTCAGGTTCTTCACGGCTATCTCGGTCGCTACGTCAAGGATTTTCACAAGCACCAGCTCAAGATCACCATTTGGAATGAAGAAGTGTTCCTGGAAAACGTCGAGCTTAGTCTCGAAGCCTTCGATTATCTCCAGTTGCCTTTCGCTCTCAAACAAGGTCGGATTGGAAAGATAAGCATCAAAGTTCCATGGAAAACGCTTGGTCGGGACCCCTTTGTAATTAGTTTGGAAAATGTCTTCCTATGTGCATCCCAACGAGATGATGAAGAGTGGAGTTTGGATGAAGTTGAAAAACGAGAGTTTGCTGGAAAAAAGGCCAAACTTGCTGCAGCAGAACTGGCCAAATTATCAAAATGTGTATGCGAAAACCAGGCTGGGCTTAGATCAATAATTACTGCTAAGGTTCTTGACAGCATCCAAGTGTCAATCAGAGATTTTCATATCTTGTACCATGACAAGCTCAGTGGCTCGGTAGATTTCTTACTGGGTGTGCTTTATGTTTTCGTTTTTCCATTAGTTTTTGTTTTTATTTTCGAGAAGAAAAGTTTTATTCTAGAAGCATTACGATATGTTGACAAGCAGTCCACAGAAATAGAAGCATGTAATATTTTTGGTTTGAAGTTTTCCAGCTTGAGGACTATGAAGCCAAATCCTTCCGGGTATTCACAGGTTCCTTTGGGATAG

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

233

Amino Acids

26.73

Weight (kDa)

7.66

Isoelectric Point (pI)

33.19

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
VPS13_N	PF12624	1 - 170	2e-40	VPS13-like family N-terminal region

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: 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)
AcoI	YGGCCR	1 cut(s)	357
AfaI	GTAC	1 cut(s)	467
AfiI	CCNNNNNNNGG	1 cut(s)	651
AgsI	TTSAA	2 cut(s)	308, 637
AhdI	GACNNNNNGTC	1 cut(s)	598
AjnI	CCWGG	2 cut(s)	108, 387
AluBI	AGCT	4 cut(s)	76, 124, 478, 648
AluI	AGCT	4 cut(s)	76, 124, 478, 648
Alw26I	GTCTC	1 cut(s)	134
AoxI	GGCC	2 cut(s)	333, 357
ApeKI	GCWGC	2 cut(s)	344, 347
ArsI	GACNNNNNNTTYG	1 cut(s)	32
AspS9I	GGNCC	1 cut(s)	226
AsuC2I	CCSGG	1 cut(s)	676
AsuHPI	GGTGA	1 cut(s)	76
AsuII	TTCGAA	1 cut(s)	6
AvaII	GGWCC	1 cut(s)	226
BalI	TGGCCA	1 cut(s)	359
BbsI	GAAGAC	1 cut(s)	247
BbvI	GCAGC	2 cut(s)	331, 359
BceAI	ACGGC	1 cut(s)	49
BciT130I	CCWGG	2 cut(s)	110, 389
BcnI	CCSGG	1 cut(s)	676
BcoDI	GTCTC	1 cut(s)	134
BfaI	CTAG	1 cut(s)	572
BfmI	CTRYAG	1 cut(s)	345
BisI	GCNGC	2 cut(s)	345, 348
BlsI	GCNGC	2 cut(s)	346, 349
Bme1390I	CCNGG	3 cut(s)	110, 389, 676
Bme18I	GGWCC	1 cut(s)	226
BmeRI	GACNNNNNGTC	1 cut(s)	598
BmgT120I	GGNCC	1 cut(s)	226
BmiI	GGNNCC	3 cut(s)	227, 228, 690
BmrFI	CCNGG	3 cut(s)	110, 389, 676
BmrI	ACTGGG	1 cut(s)	512
BmsI	GCATC	3 cut(s)	204, 275, 441
BmuI	ACTGGG	1 cut(s)	512
BpiI	GAAGAC	1 cut(s)	247
BpmI	CTGGAG	1 cut(s)	134
Bpu10I	CCTNAGC	1 cut(s)	417
Bpu14I	TTCGAA	1 cut(s)	6
BpuEI	CTTGAG	2 cut(s)	62, 670
BpuMI	CCSGG	1 cut(s)	676
BsaBI	GATNNNNATC	1 cut(s)	194
BsaJI	CCNNGG	1 cut(s)	206
Bsc4I	CCNNNNNNNGG	1 cut(s)	651
Bse1I	ACTGG	3 cut(s)	151, 360, 507
Bse8I	GATNNNNATC	1 cut(s)	194
BseBI	CCWGG	2 cut(s)	110, 389
BseDI	CCNNGG	1 cut(s)	206
BseGI	GGATG	3 cut(s)	266, 304, 432
BseJI	GATNNNNATC	1 cut(s)	194
BseLI	CCNNNNNNNGG	1 cut(s)	651
BseMII	CTCAG	2 cut(s)	35, 493
BseNI	ACTGG	3 cut(s)	151, 360, 507
BseXI	GCAGC	2 cut(s)	331, 359
BseYI	CCCAGC	1 cut(s)	392
Bsh1285I	CGRYCG	1 cut(s)	46
BshFI	GGCC	2 cut(s)	335, 359
BsiEI	CGRYCG	1 cut(s)	46
BsiSI	CCGG	1 cut(s)	675
BslFI	GGGAC	1 cut(s)	239
BslI	CCNNNNNNNGG	1 cut(s)	651
BsmAI	GTCTC	1 cut(s)	134
BsmFI	GGGAC	1 cut(s)	239
BsnI	GGCC	2 cut(s)	335, 359
Bsp119I	TTCGAA	1 cut(s)	6
Bsp143I	GATC	2 cut(s)	81, 401
Bsp19I	CCATGG	1 cut(s)	206
BspANI	GGCC	2 cut(s)	335, 359
BspCNI	CTCAG	2 cut(s)	34, 492
BspLI	GGNNCC	3 cut(s)	227, 228, 690
BspMAI	CTGCAG	1 cut(s)	349
BspT104I	TTCGAA	1 cut(s)	6
BsrI	ACTGG	3 cut(s)	151, 360, 507
BssECI	CCNNGG	1 cut(s)	206
BssMI	GATC	2 cut(s)	81, 401
BssT1I	CCWWGG	1 cut(s)	206
Bst2UI	CCWGG	2 cut(s)	110, 389
Bst6I	CTCTTC	1 cut(s)	279
BstBI	TTCGAA	1 cut(s)	6
BstDEI	CTNAG	5 cut(s)	21, 125, 398, 417, 479
BstDSI	CCRYGG	1 cut(s)	206
BstF5I	GGATG	3 cut(s)	266, 304, 432
BstKTI	GATC	2 cut(s)	84, 404
BstMAI	GTCTC	1 cut(s)	134
BstMBI	GATC	2 cut(s)	81, 401
BstMCI	CGRYCG	1 cut(s)	46
BstMWI	GCNNNNNNNGC	2 cut(s)	341, 356
BstNI	CCWGG	2 cut(s)	110, 389
BstNSI	RCATGY	1 cut(s)	621
BstSCI	CCNGG	3 cut(s)	108, 387, 674
BstSFI	CTRYAG	1 cut(s)	345
BstV1I	GCAGC	2 cut(s)	331, 359
BstV2I	GAAGAC	1 cut(s)	247
BsuRI	GGCC	2 cut(s)	335, 359
BtgI	CCRYGG	1 cut(s)	206
BtsCI	GGATG	3 cut(s)	266, 304, 432
BtsIMutI	CAGTG	1 cut(s)	487
Cfr13I	GGNCC	1 cut(s)	226
Csp6I	GTAC	1 cut(s)	466
CspCI	CAANNNNNGTGG	2 cut(s)	463, 498
CviAII	CATG	3 cut(s)	207, 470, 618
CviQI	GTAC	1 cut(s)	466
DdeI	CTNAG	5 cut(s)	21, 125, 398, 417, 479
DpnI	GATC	2 cut(s)	83, 403
DpnII	GATC	2 cut(s)	81, 401
DriI	GACNNNNNGTC	1 cut(s)	598
EaeI	YGGCCR	1 cut(s)	357
Eam1104I	CTCTTC	1 cut(s)	279
Eam1105I	GACNNNNNGTC	1 cut(s)	598
EarI	CTCTTC	1 cut(s)	279
Eco130I	CCWWGG	1 cut(s)	206
Eco47I	GGWCC	1 cut(s)	226
EcoO109I	RGGNCCY	1 cut(s)	226
EcoRII	CCWGG	2 cut(s)	108, 387
EcoT14I	CCWWGG	1 cut(s)	206
ErhI	CCWWGG	1 cut(s)	206
FaeI	CATG	3 cut(s)	210, 473, 621
FaiI	YATR	9 cut(s)	208, 262, 379, 459, 471, 516, 588, 619, 659
FaqI	GGGAC	1 cut(s)	239
FatI	CATG	3 cut(s)	206, 469, 617
Fnu4HI	GCNGC	2 cut(s)	345, 348
FokI	GGATG	3 cut(s)	253, 311, 419
Fsp4HI	GCNGC	2 cut(s)	345, 348
FspBI	CTAG	1 cut(s)	572
GluI	GCNGC	2 cut(s)	345, 348
GsaI	CCCAGC	1 cut(s)	396
GsuI	CTGGAG	1 cut(s)	134
HaeIII	GGCC	2 cut(s)	335, 359
HapII	CCGG	1 cut(s)	675
Hin1II	CATG	3 cut(s)	210, 473, 621
HincII	GTYRAC	1 cut(s)	592
HindII	GTYRAC	1 cut(s)	592
HinfI	GANTC	1 cut(s)	12
HpaII	CCGG	1 cut(s)	675
HphI	GGTGA	1 cut(s)	76
Hpy166II	GTNNAC	2 cut(s)	592, 603
Hpy188I	TCNGA	2 cut(s)	180, 449
Hpy188III	TCNNGA	6 cut(s)	79, 131, 224, 425, 553, 572
Hpy8I	GTNNAC	2 cut(s)	592, 603
Hpy99I	CGWCG	1 cut(s)	122
HpyAV	CCTTC	2 cut(s)	148, 681
HpyCH4IV	ACGT	2 cut(s)	51, 117
HpyCH4V	TGCA	2 cut(s)	266, 347
HpyF10VI	GCNNNNNNNGC	2 cut(s)	341, 356
HpyF3I	CTNAG	5 cut(s)	21, 125, 398, 417, 479
HpySE526I	ACGT	2 cut(s)	51, 117
Hsp92II	CATG	3 cut(s)	210, 473, 621
KflI	GGGWCCC	1 cut(s)	226
Kzo9I	GATC	2 cut(s)	81, 401
Lsp1109I	GCAGC	2 cut(s)	331, 359
LweI	GCATC	3 cut(s)	204, 275, 441
MaeI	CTAG	1 cut(s)	572
MaeII	ACGT	2 cut(s)	51, 117
MaeIII	GTNAC	1 cut(s)	16
MalI	GATC	2 cut(s)	83, 403
MboI	GATC	2 cut(s)	81, 401
MboII	GAAGA	5 cut(s)	20, 110, 247, 296, 568
MlsI	TGGCCA	1 cut(s)	359
MluCI	AATT	3 cut(s)	237, 362, 408
MluNI	TGGCCA	1 cut(s)	359
MlyI	GAGTC	1 cut(s)	6
MmeI	TCCRAC	1 cut(s)	158
MnlI	CCTC	1 cut(s)	645
Mox20I	TGGCCA	1 cut(s)	359
MscI	TGGCCA	1 cut(s)	359
MslI	CAYNNNNRTG	1 cut(s)	437
Msp20I	TGGCCA	1 cut(s)	359
MspI	CCGG	1 cut(s)	675
MspR9I	CCNGG	3 cut(s)	110, 389, 676
MvaI	CCWGG	2 cut(s)	110, 389
MwoI	GCNNNNNNNGC	2 cut(s)	341, 356
NciI	CCSGG	1 cut(s)	676
NcoI	CCATGG	1 cut(s)	206
NdeII	GATC	2 cut(s)	81, 401
NlaIII	CATG	3 cut(s)	210, 473, 621
NlaIV	GGNNCC	3 cut(s)	227, 228, 690
NmuCI	GTSAC	1 cut(s)	16
NspI	RCATGY	1 cut(s)	621
NspV	TTCGAA	1 cut(s)	6
PcsI	WCGNNNNNNNCGW	3 cut(s)	12, 48, 138
PfoI	TCCNGGA	1 cut(s)	108
PkrI	GCNGC	2 cut(s)	346, 349
PleI	GAGTC	1 cut(s)	6
PpsI	GAGTC	1 cut(s)	6
PpuMI	RGGWCCY	1 cut(s)	226
Psp5II	RGGWCCY	1 cut(s)	226
Psp6I	CCWGG	2 cut(s)	108, 387
PspFI	CCCAGC	1 cut(s)	392
PspGI	CCWGG	2 cut(s)	108, 387
PspN4I	GGNNCC	3 cut(s)	227, 228, 690
PspPI	GGNCC	1 cut(s)	226
PspPPI	RGGWCCY	1 cut(s)	226
PstI	CTGCAG	1 cut(s)	349
RsaI	GTAC	1 cut(s)	467
RsaNI	GTAC	1 cut(s)	466
RseI	CAYNNNNRTG	1 cut(s)	437
SatI	GCNGC	2 cut(s)	345, 348
Sau3AI	GATC	2 cut(s)	81, 401
Sau96I	GGNCC	1 cut(s)	226
SchI	GAGTC	1 cut(s)	6
ScrFI	CCNGG	3 cut(s)	110, 389, 676
SfaNI	GCATC	3 cut(s)	204, 275, 441
SfcI	CTRYAG	1 cut(s)	345
SfuI	TTCGAA	1 cut(s)	6
SinI	GGWCC	1 cut(s)	226
SmiMI	CAYNNNNRTG	1 cut(s)	437
SmlI	CTYRAG	2 cut(s)	77, 649
SmoI	CTYRAG	2 cut(s)	77, 649
Sse9I	AATT	3 cut(s)	237, 362, 408
SspI	AATATT	1 cut(s)	625
SspMI	CTAG	1 cut(s)	572
StyD4I	CCNGG	3 cut(s)	108, 387, 674
StyI	CCWWGG	1 cut(s)	206
TaiI	ACGT	2 cut(s)	54, 120
TaqI	TCGA	5 cut(s)	6, 120, 132, 141, 552
TaqII	GACCGA	1 cut(s)	32
TasI	AATT	3 cut(s)	237, 362, 408
TscAI	CASTG	1 cut(s)	487
TseFI	GTSAC	1 cut(s)	16
TseI	GCWGC	2 cut(s)	344, 347
Tsp45I	GTSAC	1 cut(s)	16
TspDTI	ATGAA	5 cut(s)	111, 297, 315, 446, 674
TspRI	CASTG	1 cut(s)	487
VpaK11BI	GGWCC	1 cut(s)	226
XbaI	TCTAGA	1 cut(s)	571
XceI	RCATGY	1 cut(s)	621
XspI	CTAG	1 cut(s)	572

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