Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6A

Orthogroup ID

OG0002279

Physical Location & Seq

Genomic Coordinates Reverse (-)

27340085 .. 27387699

Gene Structure 47615 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6AG170000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 708 bp

ATGAATCGGAGCTGGGGAGCTCTGAGAATTTCTCAAAGGAATGGACGATTGCCGTTTTCCATCAATGCAGAATCAGCCAATCTCAATCCCCGCATTCATCCTCGTCTTCTTTTCATTCCTTCATTTCAGCTTGACACTGGGCCGGGTCAGCAGATCCTGAAATACTCATTCTCCCTTTTCCTTTTTATCATCCGGAAAGCATCAACATTTATAATAACTTATCCTATAAACAATGCTATTAATAAAGAGGGGAATGAAACTGAAAGAGCAGTGGCATGGGAGAAGGCCTTTATTGAGCTAGCAAAGGATGAGTTGTTGCAAATGGTGCAATCTAAAAACTTAACACTATCTTTCTCATCGGAAAGTTCCATTGAAGAAGAACTTAAGAGAGAAAGCACTGCAGATGCTATTACAATATTGATAAGCTATCTTGTGATGTTCGCTTATATTTCTCTTACTTTGGGTGACTCTCCTCGTTTGTCTTCCTTTTACATTTCATCTAAGGTATTGCTAGGTCTCTCTGGAGTTGTTCTTGTCATGCTCTCCATTCTTGGATCAGTGGAATTTTTCAGTGCCATTGGAGTTAAATCTACCCTAATTATTATGGAAGTCATCCCATTTCTTGTTCTACCTTGGTACACAGATGCAATGGTTTCACAAATTGTTGTTGGTGCAGTTGTTGCAGGTGATTGTAGAATTTGTGCTTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000323 GO:0003674 GO:0005488 GO:0005496 GO:0005575 GO:0005576 GO:0005622 GO:0005623 GO:0005634 GO:0005635 GO:0005737 GO:0005764 GO:0005773 GO:0005783 GO:0005886 GO:0005887 GO:0006082 GO:0006464 GO:0006486 GO:0006629 GO:0006807 GO:0006810 GO:0006869 GO:0007034 GO:0007041 GO:0008150 GO:0008152 GO:0008202 GO:0008206 GO:0008289 GO:0009058 GO:0009059 GO:0009100 GO:0009101 GO:0009987 GO:0010876 GO:0012505 GO:0015485 GO:0015850 GO:0015918 GO:0016020 GO:0016021 GO:0019538 GO:0019752 GO:0030301 GO:0031224 GO:0031226 GO:0031967 GO:0031975 GO:0032787 GO:0032934 GO:0033036 GO:0034645 GO:0036094 GO:0036211 GO:0042592 GO:0042632 GO:0043170 GO:0043178 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043412 GO:0043413 GO:0043436 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044267 GO:0044281 GO:0044422 GO:0044424 GO:0044425 GO:0044428 GO:0044444 GO:0044446 GO:0044459 GO:0044464 GO:0048471 GO:0048878 GO:0051179 GO:0051234 GO:0055088 GO:0055092 GO:0065007 GO:0065008 GO:0070085 GO:0071702 GO:0071704 GO:0071944 GO:0097159 GO:1901135 GO:1901137 GO:1901360 GO:1901564 GO:1901566 GO:1901576 GO:1901615

KEGG Pathways

Metabolic & Signaling

ko04142 ko04979 map04142 map04979

Pfam Domains

Protein Families

NPC1_N Patched

Protein Analysis

235

Amino Acids

26.07

Weight (kDa)

6.61

Isoelectric Point (pI)

39.99

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
NPC1_MLD	PF22314	65 - 121	1.4e-06	NPC1, middle luminal domain
Sterol-sensing	PF12349	165 - 211	3.7e-08	Sterol-sensing domain of SREBP cleavage-activation

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: OG0002279)

Species	Orthologous Gene IDs
malus_domestica	MD00G1080500.v1.1 MD16G1285200.v1.1
rosa_chinensis	RchiOBHm_Chr2g0175261 RchiOBHm_Chr6g0280801
rosa_laevigata	RLG00000013082 RLG00000019605 RLG00000033344 RLG00000034484 RLG00000036984
rosa_multiflora	Rmu_sc0000893.1_g000002 Rmu_sc0002494.1_g000006 Rmu_sc0007139.1_g000001
rosa_roxburghii	Rroxscaffold_4G00312410 Rroxscaffold_7G00187620
rosa_rugosa	Rorug01G0060900 Rorug02G0158200 Rorug02G0250000 Rorug06G0134700
rosa_samantha	Rh1AG184800 Rh1AG199900 Rh1AG262300 Rh1BG097700 Rh1BG103100 Rh2CG636900 Rh2DG687600 Rh3CG050700 Rh3DG112000 Rh4CG020800 Rh4CG194300 Rh4DG079900 Rh5AG202600 Rh5BG321300 Rh5CG365700 Rh6AG170000 Rh6CG250600 Rh6DG242200 Rh6DG280400 Rh7AG279500 Rh7CG298700 Rh7CG343600 Rh7DG079500
rosa_wichuraiana	Rw4G014860 Rw6G026540

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	212
AarI	CACCTGC	1 cut(s)	674
Acc36I	ACCTGC	1 cut(s)	674
AccIII	TCCGGA	1 cut(s)	192
AciI	CCGC	1 cut(s)	91
AclWI	GGATC	2 cut(s)	148, 562
AcsI	RAATTY	3 cut(s)	27, 563, 696
AfaI	GTAC	1 cut(s)	638
AflII	CTTAAG	1 cut(s)	383
AgsI	TTSAA	1 cut(s)	374
AluBI	AGCT	5 cut(s)	12, 20, 130, 298, 426
AluI	AGCT	5 cut(s)	12, 20, 130, 298, 426
Alw21I	GWGCWC	1 cut(s)	22
Alw26I	GTCTC	1 cut(s)	521
AlwI	GGATC	2 cut(s)	148, 562
AlwNI	CAGNNNCTG	1 cut(s)	157
Aor13HI	TCCGGA	1 cut(s)	192
AoxI	GGCC	2 cut(s)	140, 285
ApoI	RAATTY	3 cut(s)	27, 563, 696
AseI	ATTAAT	1 cut(s)	240
AspS9I	GGNCC	1 cut(s)	140
AsuC2I	CCSGG	1 cut(s)	144
AsuHPI	GGTGA	2 cut(s)	476, 698
AsuNHI	GCTAGC	1 cut(s)	298
BanII	GRGCYC	1 cut(s)	22
BbsI	GAAGAC	2 cut(s)	98, 474
Bbv12I	GWGCWC	1 cut(s)	22
BccI	CCATC	1 cut(s)	68
BceAI	ACGGC	1 cut(s)	37
BcnI	CCSGG	1 cut(s)	144
BcoDI	GTCTC	1 cut(s)	521
BfaI	CTAG	2 cut(s)	299, 512
BfmI	CTRYAG	1 cut(s)	399
BfrI	CTTAAG	1 cut(s)	383
BfuAI	ACCTGC	1 cut(s)	674
Bme1390I	CCNGG	1 cut(s)	144
BmgT120I	GGNCC	1 cut(s)	140
BmrFI	CCNGG	1 cut(s)	144
BmrI	ACTGGG	1 cut(s)	147
BmsI	GCATC	3 cut(s)	209, 394, 634
BmtI	GCTAGC	1 cut(s)	302
BmuI	ACTGGG	1 cut(s)	147
BpiI	GAAGAC	2 cut(s)	98, 474
BplI	GAGNNNNNCTC	2 cut(s)	16, 48
BpmI	CTGGAG	1 cut(s)	543
BpuMI	CCSGG	1 cut(s)	144
BsaI	GGTCTC	1 cut(s)	521
BsaJI	CCNNGG	1 cut(s)	632
BsaWI	WCCGGW	1 cut(s)	192
BsaXI	ACNNNNNCTCC	2 cut(s)	155, 185
Bse1I	ACTGG	1 cut(s)	142
Bse3DI	GCAATG	1 cut(s)	654
BseAI	TCCGGA	1 cut(s)	192
BseDI	CCNNGG	1 cut(s)	632
BseGI	GGATG	4 cut(s)	97, 189, 313, 612
BseMI	GCAATG	1 cut(s)	654
BseMII	CTCAG	1 cut(s)	14
BseNI	ACTGG	1 cut(s)	142
BseRI	GAGGAG	1 cut(s)	462
BseYI	CCCAGC	1 cut(s)	12
BsgI	GTGCAG	1 cut(s)	693
BshFI	GGCC	2 cut(s)	142, 287
BsiHKAI	GWGCWC	1 cut(s)	22
BsiSI	CCGG	2 cut(s)	143, 193
BsmAI	GTCTC	1 cut(s)	521
BsmI	GAATGC	1 cut(s)	93
BsnI	GGCC	2 cut(s)	142, 287
Bso31I	GGTCTC	1 cut(s)	521
Bsp1286I	GDGCHC	1 cut(s)	22
Bsp13I	TCCGGA	1 cut(s)	192
Bsp143I	GATC	2 cut(s)	153, 554
BspACI	CCGC	1 cut(s)	91
BspANI	GGCC	2 cut(s)	142, 287
BspCNI	CTCAG	1 cut(s)	15
BspEI	TCCGGA	1 cut(s)	192
BspMAI	CTGCAG	1 cut(s)	403
BspMI	ACCTGC	1 cut(s)	674
BspOI	GCTAGC	1 cut(s)	302
BspPI	GGATC	2 cut(s)	148, 562
BspTI	CTTAAG	1 cut(s)	383
BspTNI	GGTCTC	1 cut(s)	521
BsrDI	GCAATG	1 cut(s)	654
BsrI	ACTGG	1 cut(s)	142
BssECI	CCNNGG	1 cut(s)	632
BssMI	GATC	2 cut(s)	153, 554
BssT1I	CCWWGG	1 cut(s)	632
BstAFI	CTTAAG	1 cut(s)	383
BstAPI	GCANNNNNTGC	2 cut(s)	325, 680
BstC8I	GCNNGC	1 cut(s)	300
BstDEI	CTNAG	2 cut(s)	23, 501
BstF5I	GGATG	4 cut(s)	97, 189, 313, 612
BstKTI	GATC	2 cut(s)	156, 557
BstMAI	GTCTC	1 cut(s)	521
BstMBI	GATC	2 cut(s)	153, 554
BstMWI	GCNNNNNNNGC	4 cut(s)	74, 148, 325, 680
BstSCI	CCNGG	1 cut(s)	142
BstSFI	CTRYAG	1 cut(s)	399
BstV2I	GAAGAC	2 cut(s)	98, 474
BstX2I	RGATCY	1 cut(s)	153
BstYI	RGATCY	1 cut(s)	153
BsuRI	GGCC	2 cut(s)	142, 287
BtsCI	GGATG	4 cut(s)	97, 189, 313, 612
BtsI	GCAGTG	2 cut(s)	276, 396
BtsIMutI	CAGTG	5 cut(s)	135, 276, 396, 564, 577
BveI	ACCTGC	1 cut(s)	674
Cac8I	GCNNGC	1 cut(s)	300
CaiI	CAGNNNCTG	1 cut(s)	157
Cfr13I	GGNCC	1 cut(s)	140
Csp6I	GTAC	1 cut(s)	637
CviAII	CATG	2 cut(s)	276, 538
CviJI	RGCY	8 cut(s)	12, 20, 77, 130, 142, 287, 298, 426
CviKI_1	RGCY	8 cut(s)	12, 20, 77, 130, 142, 287, 298, 426
CviQI	GTAC	1 cut(s)	637
DdeI	CTNAG	2 cut(s)	23, 501
DpnI	GATC	2 cut(s)	155, 556
DpnII	GATC	2 cut(s)	153, 554
Ecl136II	GAGCTC	1 cut(s)	20
Eco130I	CCWWGG	1 cut(s)	632
Eco147I	AGGCCT	1 cut(s)	287
Eco24I	GRGCYC	1 cut(s)	22
Eco31I	GGTCTC	1 cut(s)	521
Eco53kI	GAGCTC	1 cut(s)	20
EcoICRI	GAGCTC	1 cut(s)	20
EcoT14I	CCWWGG	1 cut(s)	632
EcoT38I	GRGCYC	1 cut(s)	22
ErhI	CCWWGG	1 cut(s)	632
FaeI	CATG	2 cut(s)	279, 541
FaiI	YATR	6 cut(s)	212, 227, 277, 447, 539, 605
FalI	AAGNNNNNCTT	2 cut(s)	366, 398
FatI	CATG	2 cut(s)	275, 537
FauI	CCCGC	1 cut(s)	98
FokI	GGATG	4 cut(s)	84, 176, 320, 599
FriOI	GRGCYC	1 cut(s)	22
FspBI	CTAG	2 cut(s)	299, 512
GsaI	CCCAGC	1 cut(s)	16
GsuI	CTGGAG	1 cut(s)	543
HaeIII	GGCC	2 cut(s)	142, 287
HapII	CCGG	2 cut(s)	143, 193
Hin1II	CATG	2 cut(s)	279, 541
HinfI	GANTC	3 cut(s)	4, 71, 467
HpaII	CCGG	2 cut(s)	143, 193
HphI	GGTGA	2 cut(s)	476, 698
Hpy166II	GTNNAC	1 cut(s)	639
Hpy188I	TCNGA	3 cut(s)	9, 24, 361
Hpy188III	TCNNGA	3 cut(s)	157, 193, 522
Hpy8I	GTNNAC	1 cut(s)	639
HpyAV	CCTTC	2 cut(s)	129, 277
HpyCH4V	TGCA	7 cut(s)	68, 319, 328, 401, 647, 674, 683
HpyF10VI	GCNNNNNNNGC	4 cut(s)	74, 148, 325, 680
HpyF3I	CTNAG	2 cut(s)	23, 501
Hsp92II	CATG	2 cut(s)	279, 541
Kpn2I	TCCGGA	1 cut(s)	192
Kzo9I	GATC	2 cut(s)	153, 554
LmnI	GCTCC	2 cut(s)	9, 17
LpnPI	CCDG	6 cut(s)	123, 156, 170, 206, 507, 669
LweI	GCATC	3 cut(s)	209, 394, 634
MaeI	CTAG	2 cut(s)	299, 512
MaeIII	GTNAC	1 cut(s)	464
MalI	GATC	2 cut(s)	155, 556
MboI	GATC	2 cut(s)	153, 554
MboII	GAAGA	4 cut(s)	98, 386, 389, 474
MflI	RGATCY	1 cut(s)	153
MhlI	GDGCHC	1 cut(s)	22
MluCI	AATT	5 cut(s)	27, 563, 597, 660, 696
MlyI	GAGTC	1 cut(s)	461
MnlI	CCTC	3 cut(s)	111, 241, 483
MroI	TCCGGA	1 cut(s)	192
MseI	TTAA	5 cut(s)	240, 341, 384, 585, 706
MspCI	CTTAAG	1 cut(s)	383
MspI	CCGG	2 cut(s)	143, 193
MspR9I	CCNGG	1 cut(s)	144
Mva1269I	GAATGC	1 cut(s)	93
MwoI	GCNNNNNNNGC	4 cut(s)	74, 148, 325, 680
NciI	CCSGG	1 cut(s)	144
NdeII	GATC	2 cut(s)	153, 554
NheI	GCTAGC	1 cut(s)	298
NlaIII	CATG	2 cut(s)	279, 541
NmuCI	GTSAC	1 cut(s)	464
PaqCI	CACCTGC	1 cut(s)	674
PceI	AGGCCT	1 cut(s)	287
PctI	GAATGC	1 cut(s)	93
PfeI	GAWTC	2 cut(s)	4, 71
PleI	GAGTC	1 cut(s)	461
PpsI	GAGTC	1 cut(s)	461
PshBI	ATTAAT	1 cut(s)	240
PsiI	TTATAA	1 cut(s)	212
Psp124BI	GAGCTC	1 cut(s)	22
PspFI	CCCAGC	1 cut(s)	12
PspPI	GGNCC	1 cut(s)	140
PstI	CTGCAG	1 cut(s)	403
PstNI	CAGNNNCTG	1 cut(s)	157
PsuI	RGATCY	1 cut(s)	153
RsaI	GTAC	1 cut(s)	638
RsaNI	GTAC	1 cut(s)	637
SacI	GAGCTC	1 cut(s)	22
SaqAI	TTAA	5 cut(s)	240, 341, 384, 585, 706
Sau3AI	GATC	2 cut(s)	153, 554
Sau96I	GGNCC	1 cut(s)	140
SchI	GAGTC	1 cut(s)	461
ScrFI	CCNGG	1 cut(s)	144
SduI	GDGCHC	1 cut(s)	22
SetI	ASST	9 cut(s)	14, 22, 132, 300, 428, 507, 517, 634, 688
SfaNI	GCATC	3 cut(s)	209, 394, 634
SfcI	CTRYAG	1 cut(s)	399
SmlI	CTYRAG	1 cut(s)	383
SmoI	CTYRAG	1 cut(s)	383
Sse9I	AATT	5 cut(s)	27, 563, 597, 660, 696
SseBI	AGGCCT	1 cut(s)	287
SsiI	CCGC	1 cut(s)	91
SspI	AATATT	1 cut(s)	417
SspMI	CTAG	2 cut(s)	299, 512
SstI	GAGCTC	1 cut(s)	22
StuI	AGGCCT	1 cut(s)	287
StyD4I	CCNGG	1 cut(s)	142
StyI	CCWWGG	1 cut(s)	632
TasI	AATT	5 cut(s)	27, 563, 597, 660, 696
TfiI	GAWTC	2 cut(s)	4, 71
Tru1I	TTAA	5 cut(s)	240, 341, 384, 585, 706
Tru9I	TTAA	5 cut(s)	240, 341, 384, 585, 706
TscAI	CASTG	5 cut(s)	142, 276, 403, 564, 577
TseFI	GTSAC	1 cut(s)	464
Tsp45I	GTSAC	1 cut(s)	464
TspDTI	ATGAA	6 cut(s)	17, 86, 103, 111, 270, 486
TspRI	CASTG	5 cut(s)	142, 276, 403, 564, 577
Vha464I	CTTAAG	1 cut(s)	383
VspI	ATTAAT	1 cut(s)	240
XapI	RAATTY	3 cut(s)	27, 563, 696
XspI	CTAG	2 cut(s)	299, 512

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