Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6A

Orthogroup ID

OG0012693

Physical Location & Seq

Genomic Coordinates Reverse (-)

47459706 .. 47465062

Gene Structure 5357 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6AG280100.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 462 bp

ATGATTTCGGTTAGTGGCAATATGACTGTGGTTGGGATTGACTATTACATAAGTGACACTTTTGGACACGGACTACACAACCCCTGCAAGGATGTTAAATTCCGATCCGTAGACTTGGTAGATGCCGGTGCTAAACGTTTTGAAGAATGCTTTGATTTTCTTGGAAAGAAAGCATCCCCTGCTGTCCCTGCTTCACCTTATGCCATTGACTTCAAGTTTCCGACTCGTGAATCATCTGAAATGCAGTTCATGAACATGTCAGCTTATTCATGTGCTGACACTTCATCAGGCTACTCTTGTGATGATTTCCCTAACGCGTGTTCTAGTTCTGAAGCGATGCTACTCTCCATCAAACTCTGGCCTGTTGAGTTTGTGGATGGTGACTGTTATTTGGGGCATTATCTGGAATTTCAAGTTCTTGCTATTGATTATCAACATCCTGAATTACGTTTGTTATTTTGA

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

153

Amino Acids

17.11

Weight (kDa)

4.61

Isoelectric Point (pI)

49.87

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
NPC1_N	PF16414	6 - 111	2.9e-14	Niemann-Pick C1 N terminus

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Orthologous Genes (Group: OG0012693)

Species	Orthologous Gene IDs
rosa_chinensis	RchiOBHm_Chr4g0443141 RchiOBHm_Chr6g0284841
rosa_laevigata	RLG00000008014 RLG00000012711 RLG00000034684
rosa_roxburghii	Rroxscaffold_1G00068590
rosa_rugosa	Rorug06G0167400
rosa_samantha	Rh2AG448000 Rh3BG307600 Rh4BG390400 Rh4CG426100 Rh5BG126000 Rh6AG280100 Rh6BG280200 Rh6BG370100 Rh6CG282400 Rh6DG259200 Rh6DG275300 Rh6DG275500

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccI	GTMKAC	1 cut(s)	111
AccII	CGCG	1 cut(s)	317
AclI	AACGTT	1 cut(s)	136
AclWI	GGATC	1 cut(s)	99
AcsI	RAATTY	2 cut(s)	98, 407
AcuI	CTGAAG	1 cut(s)	351
AfiI	CCNNNNNNNGG	1 cut(s)	88
AflIII	ACRYGT	2 cut(s)	255, 315
AgsI	TTSAA	3 cut(s)	143, 214, 413
AluBI	AGCT	1 cut(s)	263
AluI	AGCT	1 cut(s)	263
AlwI	GGATC	1 cut(s)	99
AoxI	GGCC	1 cut(s)	359
ApoI	RAATTY	2 cut(s)	98, 407
AsuHPI	GGTGA	2 cut(s)	186, 392
BarI	GAAGNNNNNNTAC	2 cut(s)	324, 356
BauI	CACGAG	1 cut(s)	225
BccI	CCATC	2 cut(s)	356, 371
BfaI	CTAG	1 cut(s)	324
BmsI	GCATC	3 cut(s)	112, 182, 327
Bsc4I	CCNNNNNNNGG	1 cut(s)	88
Bse118I	RCCGGY	1 cut(s)	125
BseGI	GGATG	4 cut(s)	97, 173, 382, 436
BseLI	CCNNNNNNNGG	1 cut(s)	88
Bsh1236I	CGCG	1 cut(s)	317
BshFI	GGCC	1 cut(s)	361
BsiSI	CCGG	1 cut(s)	126
BslFI	GGGAC	1 cut(s)	170
BslI	CCNNNNNNNGG	1 cut(s)	88
BsmFI	GGGAC	1 cut(s)	170
BsmI	GAATGC	1 cut(s)	152
BsnI	GGCC	1 cut(s)	361
Bsp143I	GATC	1 cut(s)	104
BspANI	GGCC	1 cut(s)	361
BspFNI	CGCG	1 cut(s)	317
BspHI	TCATGA	1 cut(s)	249
BspPI	GGATC	1 cut(s)	99
BsrFI	RCCGGY	1 cut(s)	125
BssAI	RCCGGY	1 cut(s)	125
BssMI	GATC	1 cut(s)	104
BssSI	CACGAG	1 cut(s)	225
Bst2BI	CACGAG	1 cut(s)	225
Bst4CI	ACNGT	2 cut(s)	28, 386
BstAPI	GCANNNNNTGC	1 cut(s)	179
BstF5I	GGATG	4 cut(s)	97, 173, 382, 436
BstFNI	CGCG	1 cut(s)	317
BstKTI	GATC	1 cut(s)	107
BstMBI	GATC	1 cut(s)	104
BstMWI	GCNNNNNNNGC	2 cut(s)	179, 188
BstNSI	RCATGY	1 cut(s)	259
BstUI	CGCG	1 cut(s)	317
BsuRI	GGCC	1 cut(s)	361
BtgZI	GCGATG	1 cut(s)	350
BtsCI	GGATG	4 cut(s)	97, 173, 382, 436
CciI	TCATGA	1 cut(s)	249
Cfr10I	RCCGGY	1 cut(s)	125
CviAII	CATG	3 cut(s)	250, 256, 270
CviJI	RGCY	3 cut(s)	263, 291, 361
CviKI_1	RGCY	3 cut(s)	263, 291, 361
DpnI	GATC	1 cut(s)	106
DpnII	GATC	1 cut(s)	104
Eco57I	CTGAAG	1 cut(s)	351
FaeI	CATG	3 cut(s)	253, 259, 273
FaiI	YATR	6 cut(s)	23, 50, 201, 251, 257, 271
FalI	AAGNNNNNCTT	2 cut(s)	43, 75
FaqI	GGGAC	1 cut(s)	170
FatI	CATG	3 cut(s)	249, 255, 269
FblI	GTMKAC	1 cut(s)	111
FokI	GGATG	4 cut(s)	104, 160, 389, 423
FspBI	CTAG	1 cut(s)	324
HaeIII	GGCC	1 cut(s)	361
HapII	CCGG	1 cut(s)	126
Hin1II	CATG	3 cut(s)	253, 259, 273
HinfI	GANTC	2 cut(s)	223, 230
HpaII	CCGG	1 cut(s)	126
HphI	GGTGA	2 cut(s)	186, 392
Hpy166II	GTNNAC	1 cut(s)	112
Hpy188I	TCNGA	4 cut(s)	104, 222, 238, 331
Hpy188III	TCNNGA	4 cut(s)	227, 250, 404, 440
Hpy8I	GTNNAC	1 cut(s)	112
HpyCH4III	ACNGT	2 cut(s)	28, 386
HpyCH4IV	ACGT	2 cut(s)	136, 448
HpyCH4V	TGCA	2 cut(s)	87, 244
HpyF10VI	GCNNNNNNNGC	2 cut(s)	179, 188
HpySE526I	ACGT	2 cut(s)	136, 448
Hsp92II	CATG	3 cut(s)	253, 259, 273
Kzo9I	GATC	1 cut(s)	104
LpnPI	CCDG	9 cut(s)	97, 139, 192, 201, 273, 343, 375, 389, 453
LweI	GCATC	3 cut(s)	112, 182, 327
MaeI	CTAG	1 cut(s)	324
MaeII	ACGT	2 cut(s)	136, 448
MaeIII	GTNAC	2 cut(s)	53, 380
MalI	GATC	1 cut(s)	106
MboI	GATC	1 cut(s)	104
MboII	GAAGA	1 cut(s)	155
MluCI	AATT	3 cut(s)	98, 407, 443
MluI	ACGCGT	1 cut(s)	315
MlyI	GAGTC	1 cut(s)	217
MmeI	TCCRAC	1 cut(s)	245
MseI	TTAA	1 cut(s)	96
MslI	CAYNNNNRTG	1 cut(s)	254
MspI	CCGG	1 cut(s)	126
Mva1269I	GAATGC	1 cut(s)	152
MvnI	CGCG	1 cut(s)	317
MwoI	GCNNNNNNNGC	2 cut(s)	179, 188
NdeII	GATC	1 cut(s)	104
NlaIII	CATG	3 cut(s)	253, 259, 273
NmuCI	GTSAC	2 cut(s)	53, 380
NspI	RCATGY	1 cut(s)	259
PagI	TCATGA	1 cut(s)	249
PciI	ACATGT	1 cut(s)	255
PctI	GAATGC	1 cut(s)	152
PfeI	GAWTC	1 cut(s)	230
PleI	GAGTC	1 cut(s)	217
PpsI	GAGTC	1 cut(s)	217
PscI	ACATGT	1 cut(s)	255
Psp1406I	AACGTT	1 cut(s)	136
RseI	CAYNNNNRTG	1 cut(s)	254
SaqAI	TTAA	1 cut(s)	96
Sau3AI	GATC	1 cut(s)	104
SchI	GAGTC	1 cut(s)	217
SetI	ASST	4 cut(s)	139, 199, 265, 451
SfaNI	GCATC	3 cut(s)	112, 182, 327
SmiMI	CAYNNNNRTG	1 cut(s)	254
Sse9I	AATT	3 cut(s)	98, 407, 443
SspMI	CTAG	1 cut(s)	324
TaaI	ACNGT	2 cut(s)	28, 386
TaiI	ACGT	2 cut(s)	139, 451
TasI	AATT	3 cut(s)	98, 407, 443
TfiI	GAWTC	1 cut(s)	230
Tru1I	TTAA	1 cut(s)	96
Tru9I	TTAA	1 cut(s)	96
TseFI	GTSAC	2 cut(s)	53, 380
Tsp45I	GTSAC	2 cut(s)	53, 380
TspDTI	ATGAA	4 cut(s)	238, 258, 266, 273
TspGWI	ACGGA	2 cut(s)	84, 97
XapI	RAATTY	2 cut(s)	98, 407
XceI	RCATGY	1 cut(s)	259
XmiI	GTMKAC	1 cut(s)	111
XspI	CTAG	1 cut(s)	324

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