Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6C

Orthogroup ID

OG0012571

Physical Location & Seq

Genomic Coordinates Reverse (-)

412407 .. 415799

Gene Structure 3393 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6CG001900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1086 bp

ATGGAGGGATCCTCCTCCTCCTCCTCTTCCTGTTCCTCGCCGTCTTCGGCCATCTTCTATGACTTTCTCGACCGAATGCGAAACCCTGCTTCCCTCGATCTCGTCCGGTCCATAAAAAGCTTTATTGTATCGTTTTCGTTTTACCCTGCCAACCCTGAAAATGATGGCAAAAGAGTTCAAGAGTTCTTCGCGACAATGGAAGATTCAATTAGGGATCATCCCTTGTGGGCAGGTGCCACTGATCAAGAAGTTGAAAGTGCAATGGAGGGTTTGGAGAAGTATGTCATGACGAAATTGTTCTCCCGGACCTTTTCTTCATCTCCTGAGGATGCAAAGATTGACCTTGAAGTCTCACAGAAAATACAGTTGTTGCAGACTTTCTTGAAACCTGAGCATCTCGATATTCCGCTAGTTCTACGCAATGAAGCTTCATGGCTGCTTGCAGAAAAAGAGTTGCAGAAAATCAATGCTTTCAAAGCCCCTCGTGAGAAGCTTCTCTGTATCATGAATTGTTGCAAGGTCATTAACAATCTGTTGCTCAATGCATCAATGTCAGAAAAACATGTACTAGCTGGAGCTGATGACTTCCTTCCTGTCCTTATATATGTTACGATCAAGGCCAATCCTCCACAATTACATTCCAACCTCAAATTTATCCAGTTATATCGAAGGCAGGCAAAACTTGTGTCAGAAGCGGCCTATTACCTCACCAATCTTGTCTCAGCTAAAACATTTATCTCTGAGTTAAATGCTAAATCTCTTTCGATTGATGAAATCGAATTTGAAGAGAATATGCAAGCAGCGAGACTGACCAATAAAGAGACACAAAAGGAGGCCACACCCACTCTGGAAGAAATGACAACCTCACAAGATCATGAAGATCCTGGCCCTTCATTGAGATCGCATGATAAAGAAACAAGGGGTAAGTTTCAAACTATAACAATTTTCATTTTCCTATATGTTAGCCCTCACACCTGCCTCCCTTATAACTTTAATTGGTCTAGGATTGGTAACCAACATCCAATCACAGGCTCAACTAGTATGCGTTTTTTTTTTTTTTTCAAACTATATTACTTGGTTCAGTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

No ontology terms assigned.

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

VPS9

Protein Analysis

361

Amino Acids

41.21

Weight (kDa)

5.83

Isoelectric Point (pI)

43.25

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DUF5601	PF18151	36 - 100	1.2e-16	Domain of unknown function (DUF5601)
VPS9	PF02204	147 - 250	3.2e-32	Vacuolar sorting protein 9 (VPS9) domain

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: OG0012571)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_2g00230 FvH4_2g00230
malus_domestica	MD10G1001000.v1.1
prunus_persica	Prupe.8G002200_v2.0.a1 Prupe.8G002200_v2.0.a1 Prupe.8G002200_v2.0.a1 Prupe.8G002200_v2.0.a1
pyrus_communis	pycom05g00040 pycom10g00130
rosa_chinensis	RchiOBHm_Chr6g0249521
rosa_laevigata	RLG00000015573
rosa_roxburghii	Rroxscaffold_7G00217600
rosa_rugosa	Rorug05G0493100 Rorug05G0493200.1
rosa_samantha	Rh6AG002900 Rh6BG007200 Rh6CG001900 Rh6DG001900
rosa_wichuraiana	Rw6G000330

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	987
AarI	CACCTGC	2 cut(s)	221, 983
AasI	GACNNNNNNGTC	1 cut(s)	347
Acc36I	ACCTGC	2 cut(s)	221, 983
AccB1I	GGYRCC	1 cut(s)	233
AccII	CGCG	1 cut(s)	191
AciI	CCGC	2 cut(s)	407, 695
AclWI	GGATC	4 cut(s)	3, 16, 222, 875
AcoI	YGGCCR	1 cut(s)	48
AcsI	RAATTY	2 cut(s)	650, 779
AfaI	GTAC	1 cut(s)	567
AfiI	CCNNNNNNNGG	1 cut(s)	1028
AflIII	ACRYGT	1 cut(s)	562
AgsI	TTSAA	9 cut(s)	179, 207, 254, 347, 385, 475, 785, 932, 1063
AhlI	ACTAGT	1 cut(s)	1037
AjnI	CCWGG	1 cut(s)	883
AluBI	AGCT	6 cut(s)	120, 428, 493, 572, 578, 725
AluI	AGCT	6 cut(s)	120, 428, 493, 572, 578, 725
Alw26I	GTCTC	4 cut(s)	355, 724, 799, 815
AlwI	GGATC	4 cut(s)	3, 16, 222, 875
AoxI	GGCC	5 cut(s)	48, 618, 696, 834, 886
ApeKI	GCWGC	2 cut(s)	436, 800
ApoI	RAATTY	2 cut(s)	650, 779
ArsI	GACNNNNNNTTYG	2 cut(s)	671, 703
Asp700I	GAANNNNTTC	1 cut(s)	296
AspS9I	GGNCC	3 cut(s)	108, 306, 887
AsuC2I	CCSGG	1 cut(s)	304
AsuHPI	GGTGA	1 cut(s)	700
AvaII	GGWCC	2 cut(s)	108, 306
AxyI	CCTNAGG	1 cut(s)	324
BamHI	GGATCC	1 cut(s)	8
BanI	GGYRCC	1 cut(s)	233
BauI	CACGAG	1 cut(s)	483
BbsI	GAAGAC	1 cut(s)	36
BbvI	GCAGC	2 cut(s)	423, 812
BccI	CCATC	2 cut(s)	59, 158
BceAI	ACGGC	1 cut(s)	25
BciT130I	CCWGG	1 cut(s)	885
BclI	TGATCA	1 cut(s)	241
BcnI	CCSGG	1 cut(s)	304
BcoDI	GTCTC	4 cut(s)	355, 724, 799, 815
BcuI	ACTAGT	1 cut(s)	1037
BfaI	CTAG	4 cut(s)	410, 569, 1002, 1038
BfuAI	ACCTGC	2 cut(s)	221, 983
BisI	GCNGC	3 cut(s)	437, 696, 801
BlsI	GCNGC	3 cut(s)	438, 697, 802
Bme1390I	CCNGG	2 cut(s)	304, 885
Bme18I	GGWCC	2 cut(s)	108, 306
BmgT120I	GGNCC	3 cut(s)	108, 306, 887
BmiI	GGNNCC	2 cut(s)	10, 235
BmrFI	CCNGG	2 cut(s)	304, 885
BmsI	GCATC	3 cut(s)	319, 403, 554
BpiI	GAAGAC	1 cut(s)	36
BplI	GAGNNNNNCTC	1 cut(s)	28
BpmI	CTGGAG	1 cut(s)	594
Bpu10I	CCTNAGC	1 cut(s)	390
BpuMI	CCSGG	1 cut(s)	304
BsaWI	WCCGGW	1 cut(s)	105
Bsc4I	CCNNNNNNNGG	1 cut(s)	1028
Bse1I	ACTGG	1 cut(s)	658
Bse21I	CCTNAGG	1 cut(s)	324
Bse3DI	GCAATG	2 cut(s)	267, 427
BseBI	CCWGG	1 cut(s)	885
BseGI	GGATG	3 cut(s)	217, 334, 1018
BseLI	CCNNNNNNNGG	1 cut(s)	1028
BseMI	GCAATG	2 cut(s)	267, 427
BseMII	CTCAG	4 cut(s)	315, 381, 732, 735
BseNI	ACTGG	1 cut(s)	658
BseRI	GAGGAG	4 cut(s)	4, 7, 10, 13
BseXI	GCAGC	2 cut(s)	423, 812
Bsh1236I	CGCG	1 cut(s)	191
Bsh1285I	CGRYCG	1 cut(s)	73
BshFI	GGCC	5 cut(s)	50, 620, 698, 836, 888
BshNI	GGYRCC	1 cut(s)	233
BsiEI	CGRYCG	1 cut(s)	73
BsiSI	CCGG	2 cut(s)	106, 304
BslI	CCNNNNNNNGG	1 cut(s)	1028
BsmAI	GTCTC	4 cut(s)	355, 724, 799, 815
BsmI	GAATGC	1 cut(s)	81
BsnI	GGCC	5 cut(s)	50, 620, 698, 836, 888
Bsp143I	GATC	8 cut(s)	8, 97, 214, 241, 612, 871, 880, 899
Bsp68I	TCGCGA	1 cut(s)	191
BspACI	CCGC	2 cut(s)	407, 695
BspANI	GGCC	5 cut(s)	50, 620, 698, 836, 888
BspCNI	CTCAG	4 cut(s)	316, 382, 733, 734
BspFNI	CGCG	1 cut(s)	191
BspHI	TCATGA	3 cut(s)	285, 504, 874
BspLI	GGNNCC	2 cut(s)	10, 235
BspMI	ACCTGC	2 cut(s)	221, 983
BspPI	GGATC	4 cut(s)	3, 16, 222, 875
BspT107I	GGYRCC	1 cut(s)	233
BsrDI	GCAATG	2 cut(s)	267, 427
BsrI	ACTGG	1 cut(s)	658
BssMI	GATC	8 cut(s)	8, 97, 214, 241, 612, 871, 880, 899
BssSI	CACGAG	1 cut(s)	483
Bst2BI	CACGAG	1 cut(s)	483
Bst2UI	CCWGG	1 cut(s)	885
Bst4CI	ACNGT	1 cut(s)	366
Bst6I	CTCTTC	2 cut(s)	31, 780
BstC8I	GCNNGC	3 cut(s)	441, 675, 798
BstDEI	CTNAG	4 cut(s)	324, 390, 721, 741
BstEII	GGTNACC	1 cut(s)	1010
BstF5I	GGATG	3 cut(s)	217, 334, 1018
BstFNI	CGCG	1 cut(s)	191
BstKTI	GATC	8 cut(s)	11, 100, 217, 244, 615, 874, 883, 902
BstMAI	GTCTC	4 cut(s)	355, 724, 799, 815
BstMBI	GATC	8 cut(s)	8, 97, 214, 241, 612, 871, 880, 899
BstMCI	CGRYCG	1 cut(s)	73
BstMWI	GCNNNNNNNGC	1 cut(s)	476
BstNI	CCWGG	1 cut(s)	885
BstNSI	RCATGY	1 cut(s)	566
BstPI	GGTNACC	1 cut(s)	1010
BstSCI	CCNGG	2 cut(s)	302, 883
BstUI	CGCG	1 cut(s)	191
BstV1I	GCAGC	2 cut(s)	423, 812
BstV2I	GAAGAC	1 cut(s)	36
BstX2I	RGATCY	2 cut(s)	8, 880
BstYI	RGATCY	2 cut(s)	8, 880
Bsu36I	CCTNAGG	1 cut(s)	324
BsuRI	GGCC	5 cut(s)	50, 620, 698, 836, 888
BtsCI	GGATG	3 cut(s)	217, 334, 1018
BtsIMutI	CAGTG	1 cut(s)	237
BtuMI	TCGCGA	1 cut(s)	191
BveI	ACCTGC	2 cut(s)	221, 983
Cac8I	GCNNGC	3 cut(s)	441, 675, 798
CciI	TCATGA	3 cut(s)	285, 504, 874
Cfr13I	GGNCC	3 cut(s)	108, 306, 887
Csp6I	GTAC	1 cut(s)	566
CviAII	CATG	6 cut(s)	286, 432, 505, 563, 875, 905
CviQI	GTAC	1 cut(s)	566
DdeI	CTNAG	4 cut(s)	324, 390, 721, 741
DpnI	GATC	8 cut(s)	10, 99, 216, 243, 614, 873, 882, 901
DpnII	GATC	8 cut(s)	8, 97, 214, 241, 612, 871, 880, 899
DrdI	GACNNNNNNGTC	1 cut(s)	347
DseDI	GACNNNNNNGTC	1 cut(s)	347
EaeI	YGGCCR	1 cut(s)	48
Eam1104I	CTCTTC	2 cut(s)	31, 780
EarI	CTCTTC	2 cut(s)	31, 780
Eco47I	GGWCC	2 cut(s)	108, 306
Eco81I	CCTNAGG	1 cut(s)	324
Eco91I	GGTNACC	1 cut(s)	1010
EcoO65I	GGTNACC	1 cut(s)	1010
EcoRII	CCWGG	1 cut(s)	883
EcoT22I	ATGCAT	1 cut(s)	547
FaeI	CATG	6 cut(s)	289, 435, 508, 566, 878, 908
FatI	CATG	6 cut(s)	285, 431, 504, 562, 874, 904
FbaI	TGATCA	1 cut(s)	241
Fnu4HI	GCNGC	3 cut(s)	437, 696, 801
FokI	GGATG	3 cut(s)	204, 341, 1005
Fsp4HI	GCNGC	3 cut(s)	437, 696, 801
FspBI	CTAG	4 cut(s)	410, 569, 1002, 1038
GluI	GCNGC	3 cut(s)	437, 696, 801
GsuI	CTGGAG	1 cut(s)	594
HaeIII	GGCC	5 cut(s)	50, 620, 698, 836, 888
HapII	CCGG	2 cut(s)	106, 304
Hin1II	CATG	6 cut(s)	289, 435, 508, 566, 878, 908
HindIII	AAGCTT	3 cut(s)	118, 426, 491
HinfI	GANTC	1 cut(s)	203
HpaII	CCGG	2 cut(s)	106, 304
HphI	GGTGA	1 cut(s)	700
Hpy188I	TCNGA	3 cut(s)	556, 691, 742
HpyAV	CCTTC	3 cut(s)	599, 663, 900
HpyCH4III	ACNGT	1 cut(s)	366
HpyCH4V	TGCA	8 cut(s)	260, 332, 373, 443, 457, 516, 545, 796
HpyF10VI	GCNNNNNNNGC	1 cut(s)	476
HpyF3I	CTNAG	4 cut(s)	324, 390, 721, 741
Hsp92II	CATG	6 cut(s)	289, 435, 508, 566, 878, 908
Ksp22I	TGATCA	1 cut(s)	241
Kzo9I	GATC	8 cut(s)	8, 97, 214, 241, 612, 871, 880, 899
LmnI	GCTCC	1 cut(s)	575
Lsp1109I	GCAGC	2 cut(s)	423, 812
LweI	GCATC	3 cut(s)	319, 403, 554
MaeI	CTAG	4 cut(s)	410, 569, 1002, 1038
MaeIII	GTNAC	2 cut(s)	607, 1010
MalI	GATC	8 cut(s)	10, 99, 216, 243, 614, 873, 882, 901
MboI	GATC	8 cut(s)	8, 97, 214, 241, 612, 871, 880, 899
MboII	GAAGA	9 cut(s)	18, 36, 46, 178, 212, 306, 797, 863, 890
MflI	RGATCY	2 cut(s)	8, 880
MluCI	AATT	8 cut(s)	207, 293, 508, 632, 650, 779, 942, 994
MmeI	TCCRAC	1 cut(s)	666
Mph1103I	ATGCAT	1 cut(s)	547
MroXI	GAANNNNTTC	1 cut(s)	296
MseI	TTAA	3 cut(s)	525, 746, 993
MspI	CCGG	2 cut(s)	106, 304
MspR9I	CCNGG	2 cut(s)	304, 885
Mva1269I	GAATGC	1 cut(s)	81
MvaI	CCWGG	1 cut(s)	885
MvnI	CGCG	1 cut(s)	191
MwoI	GCNNNNNNNGC	1 cut(s)	476
NciI	CCSGG	1 cut(s)	304
NdeII	GATC	8 cut(s)	8, 97, 214, 241, 612, 871, 880, 899
NlaIII	CATG	6 cut(s)	289, 435, 508, 566, 878, 908
NlaIV	GGNNCC	2 cut(s)	10, 235
NruI	TCGCGA	1 cut(s)	191
NsiI	ATGCAT	1 cut(s)	547
NspI	RCATGY	1 cut(s)	566
PagI	TCATGA	3 cut(s)	285, 504, 874
PaqCI	CACCTGC	2 cut(s)	221, 983
PciI	ACATGT	1 cut(s)	562
PctI	GAATGC	1 cut(s)	81
PdmI	GAANNNNTTC	1 cut(s)	296
PfeI	GAWTC	1 cut(s)	203
PfoI	TCCNGGA	1 cut(s)	302
PkrI	GCNGC	3 cut(s)	438, 697, 802
PscI	ACATGT	1 cut(s)	562
PsiI	TTATAA	1 cut(s)	987
Psp6I	CCWGG	1 cut(s)	883
PspEI	GGTNACC	1 cut(s)	1010
PspGI	CCWGG	1 cut(s)	883
PspN4I	GGNNCC	2 cut(s)	10, 235
PspPI	GGNCC	3 cut(s)	108, 306, 887
PsuI	RGATCY	2 cut(s)	8, 880
RruI	TCGCGA	1 cut(s)	191
RsaI	GTAC	1 cut(s)	567
RsaNI	GTAC	1 cut(s)	566
SaqAI	TTAA	3 cut(s)	525, 746, 993
SatI	GCNGC	3 cut(s)	437, 696, 801
Sau3AI	GATC	8 cut(s)	8, 97, 214, 241, 612, 871, 880, 899
Sau96I	GGNCC	3 cut(s)	108, 306, 887
ScrFI	CCNGG	2 cut(s)	304, 885
SfaNI	GCATC	3 cut(s)	319, 403, 554
SinI	GGWCC	2 cut(s)	108, 306
SpeI	ACTAGT	1 cut(s)	1037
Sse9I	AATT	8 cut(s)	207, 293, 508, 632, 650, 779, 942, 994
SsiI	CCGC	2 cut(s)	407, 695
SspMI	CTAG	4 cut(s)	410, 569, 1002, 1038
StyD4I	CCNGG	2 cut(s)	302, 883
TaaI	ACNGT	1 cut(s)	366
TaqI	TCGA	6 cut(s)	69, 96, 399, 667, 764, 777
TaqII	GACCGA	1 cut(s)	87
TasI	AATT	8 cut(s)	207, 293, 508, 632, 650, 779, 942, 994
TatI	WGTACW	1 cut(s)	565
TauI	GCSGC	1 cut(s)	698
TfiI	GAWTC	1 cut(s)	203
Tru1I	TTAA	3 cut(s)	525, 746, 993
Tru9I	TTAA	3 cut(s)	525, 746, 993
TscAI	CASTG	1 cut(s)	244
TseI	GCWGC	2 cut(s)	436, 800
TspDTI	ATGAA	8 cut(s)	306, 420, 438, 521, 786, 882, 891, 937
TspRI	CASTG	1 cut(s)	244
VpaK11BI	GGWCC	2 cut(s)	108, 306
XapI	RAATTY	2 cut(s)	650, 779
XceI	RCATGY	1 cut(s)	566
XcmI	CCANNNNNNNNNTGG	1 cut(s)	844
XmnI	GAANNNNTTC	1 cut(s)	296
XspI	CTAG	4 cut(s)	410, 569, 1002, 1038
Zsp2I	ATGCAT	1 cut(s)	547

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