Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6B

Orthogroup ID

OG0012571

Physical Location & Seq

Genomic Coordinates Forward (+)

1018074 .. 1021651

Gene Structure 3578 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6BG007200.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1167 bp

ATGGAGGGATCCTCCTCCTCCTCCTCCTCCTCTTCCTATTCCTCGCCGTCTTCGGCCATCTTCTATGACTTTCTCGACCGAATGCGAAACCCTGCTTCCCTCGATCTCGTCCGGTCCATAAAAAGCTTTATTGTATCGTTTTCGTTTTACCCTGCCAACCCTGAAAATGATGGCAAAAGAGTTCAAGAGTTCTTCGCGACAATGGAAGATTCAATTAGGGATCATCCCTTGTGGGCAGGTGCCACTGATCAAGAAGTTGAAAGTGCAATGGAGGGTTTGGAGAAGTATGTCATGACGAAATTGTTCTCCCGGACCTTTTCTTCATCTCCTGAGGATGCAAAGATTGACCTTGAAGTCTCACAGAAAATACAGTTGTTGCAGACTTTCTTGAAGCCTGAGCATCTCGATATTCCGCTAGTTCTACGCAATGAAGCTTCATGGCTGCTTGCAGAAAAAGAGTTGCAGAAAATCAATGCTTTCAAAGCCCCTCGTGAGAAGCTTCTCTGTATCATGAATTGTTGCAAGGTCATTAACAATCTGTTGCTCAATGCATCAATGTCAGAAAAACATGTACTAGCTGGAGCTGATGACTTCCTTCCTGTCCTTATATATGTTACGATCAAGGCCAATCCTCCACAATTACATTCCAACCTCAAATTTATCCAGTTATATCGAAGGCAGGCAAAACTTGTGTCAGAAGCGGCCTATTACCTCACCAATCTTGTCTCAGCTAAAACATTTATCTCTGAGTTAAATGCTAAATCTCTTTCGATTGATGAAATCGAATTTGAAGAGAATATGCAAGCAGCGAGACTGACCAATAAAGAGACACAAAAGGAGGCCACACCCACTCTGGAAGAAATGACAACCTCACAAGATCATGAAGATCCTGGCCCTTCATTGAGATCGCATGATAAAGAAACAAGGGGTGGGTCAAATTACCCCTATATGGACAAAGAAGCTGGGGATTTGACAGTTGGAGATGTGGAGAGGTTGCTGAGTGTGTACAAGGAAGTTGTTACCAAGTATACTAGCTTGTGCACCGCTTTTAGGCAGCTTTCATTATCTAGGATAGAAAACCATGTCACTAATATAGAAGATAGAAACGTCTCATCAACACAATCGGCAGAAACAGGTATGAATTCAGGTCAAAGAGATGGAGAGTGA

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

388

Amino Acids

43.65

Weight (kDa)

5.13

Isoelectric Point (pI)

47.68

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DUF5601	PF18151	38 - 102	1.4e-16	Domain of unknown function (DUF5601)
VPS9	PF02204	149 - 252	3.7e-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

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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)
AarI	CACCTGC	1 cut(s)	227
AasI	GACNNNNNNGTC	1 cut(s)	353
Acc36I	ACCTGC	1 cut(s)	227
AccB1I	GGYRCC	1 cut(s)	239
AccI	GTMKAC	1 cut(s)	1028
AccII	CGCG	1 cut(s)	197
AciI	CCGC	3 cut(s)	413, 701, 1044
AclWI	GGATC	4 cut(s)	3, 16, 228, 881
AcoI	YGGCCR	1 cut(s)	54
AcsI	RAATTY	3 cut(s)	656, 785, 1141
AfaI	GTAC	2 cut(s)	573, 1007
AfiI	CCNNNNNNNGG	2 cut(s)	949, 1050
AflIII	ACRYGT	1 cut(s)	568
AgsI	TTSAA	7 cut(s)	185, 213, 260, 353, 391, 481, 791
AjnI	CCWGG	1 cut(s)	889
AluBI	AGCT	9 cut(s)	126, 434, 499, 578, 584, 731, 962, 1035, 1057
AluI	AGCT	9 cut(s)	126, 434, 499, 578, 584, 731, 962, 1035, 1057
Alw21I	GWGCWC	1 cut(s)	1043
Alw26I	GTCTC	5 cut(s)	361, 730, 805, 821, 1114
Alw44I	GTGCAC	1 cut(s)	1039
AlwI	GGATC	4 cut(s)	3, 16, 228, 881
AoxI	GGCC	5 cut(s)	54, 624, 702, 840, 892
ApaLI	GTGCAC	1 cut(s)	1039
ApeKI	GCWGC	3 cut(s)	442, 806, 1054
ApoI	RAATTY	3 cut(s)	656, 785, 1141
ArsI	GACNNNNNNTTYG	2 cut(s)	677, 709
Asp700I	GAANNNNTTC	1 cut(s)	302
AspS9I	GGNCC	3 cut(s)	114, 312, 893
AsuC2I	CCSGG	1 cut(s)	310
AsuHPI	GGTGA	1 cut(s)	706
AvaII	GGWCC	2 cut(s)	114, 312
AxyI	CCTNAGG	1 cut(s)	330
BaeGI	GKGCMC	1 cut(s)	1043
BamHI	GGATCC	1 cut(s)	8
BanI	GGYRCC	1 cut(s)	239
BauI	CACGAG	1 cut(s)	489
BbsI	GAAGAC	1 cut(s)	42
Bbv12I	GWGCWC	1 cut(s)	1043
BbvI	GCAGC	3 cut(s)	429, 818, 1066
BccI	CCATC	3 cut(s)	65, 164, 1151
BceAI	ACGGC	1 cut(s)	31
BciT130I	CCWGG	1 cut(s)	891
BclI	TGATCA	1 cut(s)	247
BcnI	CCSGG	1 cut(s)	310
BcoDI	GTCTC	5 cut(s)	361, 730, 805, 821, 1114
BfaI	CTAG	4 cut(s)	416, 575, 1032, 1068
BfuAI	ACCTGC	1 cut(s)	227
BisI	GCNGC	4 cut(s)	443, 702, 807, 1055
BlsI	GCNGC	4 cut(s)	444, 703, 808, 1056
Bme1390I	CCNGG	2 cut(s)	310, 891
Bme18I	GGWCC	2 cut(s)	114, 312
BmgT120I	GGNCC	3 cut(s)	114, 312, 893
BmiI	GGNNCC	2 cut(s)	10, 241
BmrFI	CCNGG	2 cut(s)	310, 891
BmsI	GCATC	3 cut(s)	325, 409, 560
BpiI	GAAGAC	1 cut(s)	42
BplI	GAGNNNNNCTC	1 cut(s)	28
BpmI	CTGGAG	1 cut(s)	600
Bpu10I	CCTNAGC	1 cut(s)	396
BpuMI	CCSGG	1 cut(s)	310
BsaWI	WCCGGW	1 cut(s)	111
Bsc4I	CCNNNNNNNGG	2 cut(s)	949, 1050
Bse1I	ACTGG	1 cut(s)	664
Bse21I	CCTNAGG	1 cut(s)	330
Bse3DI	GCAATG	2 cut(s)	273, 433
BseBI	CCWGG	1 cut(s)	891
BseGI	GGATG	2 cut(s)	223, 340
BseLI	CCNNNNNNNGG	2 cut(s)	949, 1050
BseMI	GCAATG	2 cut(s)	273, 433
BseMII	CTCAG	5 cut(s)	321, 387, 738, 741, 989
BseNI	ACTGG	1 cut(s)	664
BseRI	GAGGAG	6 cut(s)	4, 7, 10, 13, 16, 19
BseSI	GKGCMC	1 cut(s)	1043
BseXI	GCAGC	3 cut(s)	429, 818, 1066
BseYI	CCCAGC	1 cut(s)	962
Bsh1236I	CGCG	1 cut(s)	197
Bsh1285I	CGRYCG	1 cut(s)	79
BshFI	GGCC	5 cut(s)	56, 626, 704, 842, 894
BshNI	GGYRCC	1 cut(s)	239
BsiEI	CGRYCG	1 cut(s)	79
BsiHKAI	GWGCWC	1 cut(s)	1043
BsiSI	CCGG	2 cut(s)	112, 310
BslI	CCNNNNNNNGG	2 cut(s)	949, 1050
BsmAI	GTCTC	5 cut(s)	361, 730, 805, 821, 1114
BsmBI	CGTCTC	1 cut(s)	1114
BsmI	GAATGC	1 cut(s)	87
BsnI	GGCC	5 cut(s)	56, 626, 704, 842, 894
Bsp1286I	GDGCHC	1 cut(s)	1043
Bsp1407I	TGTACA	1 cut(s)	1005
Bsp143I	GATC	8 cut(s)	8, 103, 220, 247, 618, 877, 886, 905
Bsp68I	TCGCGA	1 cut(s)	197
BspACI	CCGC	3 cut(s)	413, 701, 1044
BspANI	GGCC	5 cut(s)	56, 626, 704, 842, 894
BspCNI	CTCAG	5 cut(s)	322, 388, 739, 740, 990
BspFNI	CGCG	1 cut(s)	197
BspHI	TCATGA	3 cut(s)	291, 510, 880
BspLI	GGNNCC	2 cut(s)	10, 241
BspMI	ACCTGC	1 cut(s)	227
BspPI	GGATC	4 cut(s)	3, 16, 228, 881
BspT107I	GGYRCC	1 cut(s)	239
BsrDI	GCAATG	2 cut(s)	273, 433
BsrGI	TGTACA	1 cut(s)	1005
BsrI	ACTGG	1 cut(s)	664
BssMI	GATC	8 cut(s)	8, 103, 220, 247, 618, 877, 886, 905
BssNAI	GTATAC	1 cut(s)	1029
BssSI	CACGAG	1 cut(s)	489
Bst1107I	GTATAC	1 cut(s)	1029
Bst2BI	CACGAG	1 cut(s)	489
Bst2UI	CCWGG	1 cut(s)	891
Bst4CI	ACNGT	2 cut(s)	372, 976
Bst6I	CTCTTC	2 cut(s)	37, 786
BstAUI	TGTACA	1 cut(s)	1005
BstC8I	GCNNGC	3 cut(s)	447, 681, 804
BstDEI	CTNAG	5 cut(s)	330, 396, 727, 747, 998
BstF5I	GGATG	2 cut(s)	223, 340
BstFNI	CGCG	1 cut(s)	197
BstKTI	GATC	8 cut(s)	11, 106, 223, 250, 621, 880, 889, 908
BstMAI	GTCTC	5 cut(s)	361, 730, 805, 821, 1114
BstMBI	GATC	8 cut(s)	8, 103, 220, 247, 618, 877, 886, 905
BstMCI	CGRYCG	1 cut(s)	79
BstMWI	GCNNNNNNNGC	1 cut(s)	482
BstNI	CCWGG	1 cut(s)	891
BstNSI	RCATGY	1 cut(s)	572
BstSCI	CCNGG	2 cut(s)	308, 889
BstSLI	GKGCMC	1 cut(s)	1043
BstUI	CGCG	1 cut(s)	197
BstV1I	GCAGC	3 cut(s)	429, 818, 1066
BstV2I	GAAGAC	1 cut(s)	42
BstX2I	RGATCY	2 cut(s)	8, 886
BstYI	RGATCY	2 cut(s)	8, 886
BstZ17I	GTATAC	1 cut(s)	1029
Bsu36I	CCTNAGG	1 cut(s)	330
BsuRI	GGCC	5 cut(s)	56, 626, 704, 842, 894
BtsCI	GGATG	2 cut(s)	223, 340
BtsIMutI	CAGTG	1 cut(s)	243
BtuMI	TCGCGA	1 cut(s)	197
BveI	ACCTGC	1 cut(s)	227
Cac8I	GCNNGC	3 cut(s)	447, 681, 804
CciI	TCATGA	3 cut(s)	291, 510, 880
Cfr13I	GGNCC	3 cut(s)	114, 312, 893
Csp6I	GTAC	2 cut(s)	572, 1006
CviAII	CATG	7 cut(s)	292, 438, 511, 569, 881, 911, 1082
CviQI	GTAC	2 cut(s)	572, 1006
DdeI	CTNAG	5 cut(s)	330, 396, 727, 747, 998
DpnI	GATC	8 cut(s)	10, 105, 222, 249, 620, 879, 888, 907
DpnII	GATC	8 cut(s)	8, 103, 220, 247, 618, 877, 886, 905
DrdI	GACNNNNNNGTC	1 cut(s)	353
DseDI	GACNNNNNNGTC	1 cut(s)	353
EaeI	YGGCCR	1 cut(s)	54
Eam1104I	CTCTTC	2 cut(s)	37, 786
EarI	CTCTTC	2 cut(s)	37, 786
Eco47I	GGWCC	2 cut(s)	114, 312
Eco81I	CCTNAGG	1 cut(s)	330
EcoRI	GAATTC	1 cut(s)	1141
EcoRII	CCWGG	1 cut(s)	889
EcoT22I	ATGCAT	1 cut(s)	553
Esp3I	CGTCTC	1 cut(s)	1114
FaeI	CATG	7 cut(s)	295, 441, 514, 572, 884, 914, 1085
FatI	CATG	7 cut(s)	291, 437, 510, 568, 880, 910, 1081
FbaI	TGATCA	1 cut(s)	247
FblI	GTMKAC	1 cut(s)	1028
Fnu4HI	GCNGC	4 cut(s)	443, 702, 807, 1055
FokI	GGATG	2 cut(s)	210, 347
Fsp4HI	GCNGC	4 cut(s)	443, 702, 807, 1055
FspBI	CTAG	4 cut(s)	416, 575, 1032, 1068
GluI	GCNGC	4 cut(s)	443, 702, 807, 1055
GsaI	CCCAGC	1 cut(s)	966
GsuI	CTGGAG	1 cut(s)	600
HaeIII	GGCC	5 cut(s)	56, 626, 704, 842, 894
HapII	CCGG	2 cut(s)	112, 310
Hin1II	CATG	7 cut(s)	295, 441, 514, 572, 884, 914, 1085
HindIII	AAGCTT	3 cut(s)	124, 432, 497
HinfI	GANTC	1 cut(s)	209
HpaII	CCGG	2 cut(s)	112, 310
HphI	GGTGA	1 cut(s)	706
Hpy166II	GTNNAC	3 cut(s)	1006, 1029, 1041
Hpy188I	TCNGA	3 cut(s)	562, 697, 748
Hpy8I	GTNNAC	3 cut(s)	1006, 1029, 1041
HpyAV	CCTTC	3 cut(s)	605, 669, 906
HpyCH4III	ACNGT	2 cut(s)	372, 976
HpyCH4IV	ACGT	1 cut(s)	1107
HpyCH4V	TGCA	9 cut(s)	266, 338, 379, 449, 463, 522, 551, 802, 1041
HpyF10VI	GCNNNNNNNGC	1 cut(s)	482
HpyF3I	CTNAG	5 cut(s)	330, 396, 727, 747, 998
HpySE526I	ACGT	1 cut(s)	1107
Hsp92II	CATG	7 cut(s)	295, 441, 514, 572, 884, 914, 1085
Ksp22I	TGATCA	1 cut(s)	247
Kzo9I	GATC	8 cut(s)	8, 103, 220, 247, 618, 877, 886, 905
LmnI	GCTCC	1 cut(s)	581
Lsp1109I	GCAGC	3 cut(s)	429, 818, 1066
LweI	GCATC	3 cut(s)	325, 409, 560
MaeI	CTAG	4 cut(s)	416, 575, 1032, 1068
MaeII	ACGT	1 cut(s)	1107
MaeIII	GTNAC	3 cut(s)	613, 1018, 1084
MalI	GATC	8 cut(s)	10, 105, 222, 249, 620, 879, 888, 907
MboI	GATC	8 cut(s)	8, 103, 220, 247, 618, 877, 886, 905
MflI	RGATCY	2 cut(s)	8, 886
MhlI	GDGCHC	1 cut(s)	1043
MluCI	AATT	8 cut(s)	213, 299, 514, 638, 656, 785, 937, 1141
MmeI	TCCRAC	2 cut(s)	672, 958
Mph1103I	ATGCAT	1 cut(s)	553
MroXI	GAANNNNTTC	1 cut(s)	302
MseI	TTAA	2 cut(s)	531, 752
MspI	CCGG	2 cut(s)	112, 310
MspR9I	CCNGG	2 cut(s)	310, 891
Mva1269I	GAATGC	1 cut(s)	87
MvaI	CCWGG	1 cut(s)	891
MvnI	CGCG	1 cut(s)	197
MwoI	GCNNNNNNNGC	1 cut(s)	482
NciI	CCSGG	1 cut(s)	310
NdeII	GATC	8 cut(s)	8, 103, 220, 247, 618, 877, 886, 905
NlaIII	CATG	7 cut(s)	295, 441, 514, 572, 884, 914, 1085
NlaIV	GGNNCC	2 cut(s)	10, 241
NmuCI	GTSAC	1 cut(s)	1084
NruI	TCGCGA	1 cut(s)	197
NsiI	ATGCAT	1 cut(s)	553
NspI	RCATGY	1 cut(s)	572
PagI	TCATGA	3 cut(s)	291, 510, 880
PaqCI	CACCTGC	1 cut(s)	227
PciI	ACATGT	1 cut(s)	568
PctI	GAATGC	1 cut(s)	87
PdmI	GAANNNNTTC	1 cut(s)	302
PfeI	GAWTC	1 cut(s)	209
PfoI	TCCNGGA	1 cut(s)	308
PkrI	GCNGC	4 cut(s)	444, 703, 808, 1056
PscI	ACATGT	1 cut(s)	568
Psp6I	CCWGG	1 cut(s)	889
PspFI	CCCAGC	1 cut(s)	962
PspGI	CCWGG	1 cut(s)	889
PspN4I	GGNNCC	2 cut(s)	10, 241
PspPI	GGNCC	3 cut(s)	114, 312, 893
PsuI	RGATCY	2 cut(s)	8, 886
RruI	TCGCGA	1 cut(s)	197
RsaI	GTAC	2 cut(s)	573, 1007
RsaNI	GTAC	2 cut(s)	572, 1006
SaqAI	TTAA	2 cut(s)	531, 752
SatI	GCNGC	4 cut(s)	443, 702, 807, 1055
Sau3AI	GATC	8 cut(s)	8, 103, 220, 247, 618, 877, 886, 905
Sau96I	GGNCC	3 cut(s)	114, 312, 893
ScrFI	CCNGG	2 cut(s)	310, 891
SduI	GDGCHC	1 cut(s)	1043
SfaNI	GCATC	3 cut(s)	325, 409, 560
SinI	GGWCC	2 cut(s)	114, 312
Sse9I	AATT	8 cut(s)	213, 299, 514, 638, 656, 785, 937, 1141
SsiI	CCGC	3 cut(s)	413, 701, 1044
SspMI	CTAG	4 cut(s)	416, 575, 1032, 1068
StyD4I	CCNGG	2 cut(s)	308, 889
TaaI	ACNGT	2 cut(s)	372, 976
TaiI	ACGT	1 cut(s)	1110
TaqI	TCGA	6 cut(s)	75, 102, 405, 673, 770, 783
TaqII	GACCGA	1 cut(s)	93
TasI	AATT	8 cut(s)	213, 299, 514, 638, 656, 785, 937, 1141
TatI	WGTACW	2 cut(s)	571, 1005
TauI	GCSGC	1 cut(s)	704
TfiI	GAWTC	1 cut(s)	209
Tru1I	TTAA	2 cut(s)	531, 752
Tru9I	TTAA	2 cut(s)	531, 752
TscAI	CASTG	1 cut(s)	250
TseFI	GTSAC	1 cut(s)	1084
TseI	GCWGC	3 cut(s)	442, 806, 1054
Tsp45I	GTSAC	1 cut(s)	1084
TspDTI	ATGAA	9 cut(s)	312, 426, 444, 527, 792, 888, 897, 1050, 1154
TspRI	CASTG	1 cut(s)	250
VneI	GTGCAC	1 cut(s)	1039
VpaK11BI	GGWCC	2 cut(s)	114, 312
XapI	RAATTY	3 cut(s)	656, 785, 1141
XceI	RCATGY	1 cut(s)	572
XcmI	CCANNNNNNNNNTGG	1 cut(s)	850
XmiI	GTMKAC	1 cut(s)	1028
XmnI	GAANNNNTTC	1 cut(s)	302
XspI	CTAG	4 cut(s)	416, 575, 1032, 1068
Zsp2I	ATGCAT	1 cut(s)	553

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