Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6C

Orthogroup ID

OG0012693

Physical Location & Seq

Genomic Coordinates Reverse (-)

45987023 .. 45993247

Gene Structure 6225 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6CG282400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 600 bp

ATGCTCAACCATGGCTTCTCCGACTCTGCCTCCATTAGCTGCTTGCTCGGCCTAGACGACGGCGGCAGCGTGAACAATTCGGATTCGAGAGGAGGAGAAGCAGAGGCTTCTGCGGCGGTGAATTGCAGGATCAGAAGTCGTTTGGGTCAACATCGTCATCTTCGTCGTTGGCGAATTTTCCTCCGATTCGGCTCCACGTGGAAGATGGCGGTGGGAGTAGTCGCGGTGGGAATAAAGCGCAAGATCAGAAGTGATTCTAGTTTATCAAATGCTGCCTTATCTCACCCAAAACATGTAATTTATCAAGAACTAGTAGCTCAAATACTCGCTGCAACTAGATTTCTTGGAGGCTGTCAGGCATGCTTGAGGAACTATCTCAATCTTTTCTGCGAGCTATCATGCTCCCCAAATCAGAGCCTTTATATCAATGTGACGTCTGTCTCTGAGGTTAGTGGCAATATGACTGTGGCTGGGATTGACTATTACATAAGTGACACTTTTGGACAAGGACTACACAACTCCTGCAAGGATGTTAAATTCCGATCCGTAGACTTGGTAGGTGCCGGTGCTAAAAGTTTTGAAGGTGACCTGCTAATTTGA

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

199

Amino Acids

21.56

Weight (kDa)

8.9

Isoelectric Point (pI)

47.57

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
NPC1_N	PF16414	103 - 183	4.9e-22	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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Align Labels (Cladogram)

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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)
AatII	GACGTC	1 cut(s)	437
AccB1I	GGYRCC	1 cut(s)	560
AccI	GTMKAC	1 cut(s)	549
AccII	CGCG	1 cut(s)	224
AciI	CCGC	5 cut(s)	63, 113, 116, 209, 224
AclWI	GGATC	2 cut(s)	137, 537
AcsI	RAATTY	2 cut(s)	174, 536
AcvI	CACGTG	1 cut(s)	198
AcyI	GRCGYC	1 cut(s)	434
AflIII	ACRYGT	1 cut(s)	292
AgsI	TTSAA	1 cut(s)	581
AhlI	ACTAGT	1 cut(s)	310
AluBI	AGCT	3 cut(s)	39, 317, 394
AluI	AGCT	3 cut(s)	39, 317, 394
Alw26I	GTCTC	1 cut(s)	445
AlwI	GGATC	2 cut(s)	137, 537
AoxI	GGCC	1 cut(s)	49
ApeKI	GCWGC	4 cut(s)	39, 66, 272, 329
ApoI	RAATTY	2 cut(s)	174, 536
Asp700I	GAANNNNTTC	1 cut(s)	253
AspLEI	GCGC	1 cut(s)	240
AsuHPI	GGTGA	3 cut(s)	130, 275, 596
BanI	GGYRCC	1 cut(s)	560
BbrPI	CACGTG	1 cut(s)	198
BbvI	GCAGC	4 cut(s)	26, 78, 259, 316
BccI	CCATC	1 cut(s)	199
BceAI	ACGGC	1 cut(s)	76
BcoDI	GTCTC	1 cut(s)	445
BcuI	ACTAGT	1 cut(s)	310
BfaI	CTAG	4 cut(s)	53, 258, 311, 336
BisI	GCNGC	6 cut(s)	40, 64, 67, 114, 273, 330
BlsI	GCNGC	6 cut(s)	41, 65, 68, 115, 274, 331
BmiI	GGNNCC	2 cut(s)	193, 562
BoxI	GACNNNNGTC	1 cut(s)	437
BpuEI	CTTGAG	1 cut(s)	385
BsaAI	YACGTR	1 cut(s)	198
BsaHI	GRCGYC	1 cut(s)	434
BsaJI	CCNNGG	1 cut(s)	10
BsaXI	ACNNNNNCTCC	2 cut(s)	14, 44
Bse118I	RCCGGY	1 cut(s)	563
BseDI	CCNNGG	1 cut(s)	10
BseGI	GGATG	1 cut(s)	535
BseMII	CTCAG	1 cut(s)	435
BseRI	GAGGAG	2 cut(s)	105, 108
BseXI	GCAGC	4 cut(s)	26, 78, 259, 316
BseYI	CCCAGC	1 cut(s)	470
Bsh1236I	CGCG	1 cut(s)	224
BshFI	GGCC	1 cut(s)	51
BshNI	GGYRCC	1 cut(s)	560
BsiSI	CCGG	1 cut(s)	564
BsmAI	GTCTC	1 cut(s)	445
BsnI	GGCC	1 cut(s)	51
Bsp143I	GATC	3 cut(s)	129, 243, 542
Bsp19I	CCATGG	1 cut(s)	10
BspACI	CCGC	5 cut(s)	63, 113, 116, 209, 224
BspANI	GGCC	1 cut(s)	51
BspCNI	CTCAG	1 cut(s)	436
BspFNI	CGCG	1 cut(s)	224
BspLI	GGNNCC	2 cut(s)	193, 562
BspPI	GGATC	2 cut(s)	137, 537
BspT107I	GGYRCC	1 cut(s)	560
BsrFI	RCCGGY	1 cut(s)	563
BssAI	RCCGGY	1 cut(s)	563
BssECI	CCNNGG	1 cut(s)	10
BssMI	GATC	3 cut(s)	129, 243, 542
BssNI	GRCGYC	1 cut(s)	434
BssT1I	CCWWGG	1 cut(s)	10
Bst4CI	ACNGT	1 cut(s)	466
BstACI	GRCGYC	1 cut(s)	434
BstBAI	YACGTR	1 cut(s)	198
BstC8I	GCNNGC	3 cut(s)	44, 361, 392
BstDEI	CTNAG	1 cut(s)	444
BstDSI	CCRYGG	1 cut(s)	10
BstEII	GGTNACC	1 cut(s)	584
BstF5I	GGATG	1 cut(s)	535
BstFNI	CGCG	1 cut(s)	224
BstHHI	GCGC	1 cut(s)	240
BstKTI	GATC	3 cut(s)	132, 246, 545
BstMAI	GTCTC	1 cut(s)	445
BstMBI	GATC	3 cut(s)	129, 243, 542
BstMWI	GCNNNNNNNGC	2 cut(s)	48, 113
BstNSI	RCATGY	2 cut(s)	296, 363
BstPAI	GACNNNNGTC	1 cut(s)	437
BstPI	GGTNACC	1 cut(s)	584
BstUI	CGCG	1 cut(s)	224
BstV1I	GCAGC	4 cut(s)	26, 78, 259, 316
BsuRI	GGCC	1 cut(s)	51
BtgI	CCRYGG	1 cut(s)	10
BtsCI	GGATG	1 cut(s)	535
Cac8I	GCNNGC	3 cut(s)	44, 361, 392
CfoI	GCGC	1 cut(s)	240
Cfr10I	RCCGGY	1 cut(s)	563
CviAII	CATG	4 cut(s)	11, 293, 360, 399
DdeI	CTNAG	1 cut(s)	444
DpnI	GATC	3 cut(s)	131, 245, 544
DpnII	GATC	3 cut(s)	129, 243, 542
Eco130I	CCWWGG	1 cut(s)	10
Eco72I	CACGTG	1 cut(s)	198
Eco91I	GGTNACC	1 cut(s)	584
EcoO65I	GGTNACC	1 cut(s)	584
EcoT14I	CCWWGG	1 cut(s)	10
ErhI	CCWWGG	1 cut(s)	10
FaeI	CATG	4 cut(s)	14, 296, 363, 402
FaiI	YATR	7 cut(s)	12, 294, 361, 400, 423, 461, 488
FalI	AAGNNNNNCTT	2 cut(s)	481, 513
FatI	CATG	4 cut(s)	10, 292, 359, 398
FblI	GTMKAC	1 cut(s)	549
Fnu4HI	GCNGC	6 cut(s)	40, 64, 67, 114, 273, 330
FokI	GGATG	1 cut(s)	542
Fsp4HI	GCNGC	6 cut(s)	40, 64, 67, 114, 273, 330
FspBI	CTAG	4 cut(s)	53, 258, 311, 336
GlaI	GCGC	1 cut(s)	239
GluI	GCNGC	6 cut(s)	40, 64, 67, 114, 273, 330
GsaI	CCCAGC	1 cut(s)	474
HaeIII	GGCC	1 cut(s)	51
HapII	CCGG	1 cut(s)	564
HhaI	GCGC	1 cut(s)	240
Hin1I	GRCGYC	1 cut(s)	434
Hin1II	CATG	4 cut(s)	14, 296, 363, 402
Hin6I	GCGC	1 cut(s)	238
HinP1I	GCGC	1 cut(s)	238
HincII	GTYRAC	1 cut(s)	149
HindII	GTYRAC	1 cut(s)	149
HinfI	GANTC	4 cut(s)	23, 83, 186, 254
HpaII	CCGG	1 cut(s)	564
HphI	GGTGA	3 cut(s)	130, 275, 596
Hpy166II	GTNNAC	3 cut(s)	73, 149, 550
Hpy188I	TCNGA	8 cut(s)	22, 82, 134, 185, 248, 414, 445, 542
Hpy188III	TCNNGA	2 cut(s)	87, 305
Hpy8I	GTNNAC	3 cut(s)	73, 149, 550
Hpy99I	CGWCG	2 cut(s)	62, 168
HpyAV	CCTTC	1 cut(s)	575
HpyCH4III	ACNGT	1 cut(s)	466
HpyCH4IV	ACGT	2 cut(s)	197, 434
HpyCH4V	TGCA	3 cut(s)	126, 332, 525
HpyF10VI	GCNNNNNNNGC	2 cut(s)	48, 113
HpyF3I	CTNAG	1 cut(s)	444
HpySE526I	ACGT	2 cut(s)	197, 434
Hsp92I	GRCGYC	1 cut(s)	434
Hsp92II	CATG	4 cut(s)	14, 296, 363, 402
HspAI	GCGC	1 cut(s)	238
Kzo9I	GATC	3 cut(s)	129, 243, 542
LmnI	GCTCC	2 cut(s)	197, 407
LpnPI	CCDG	5 cut(s)	112, 341, 456, 535, 577
Lsp1109I	GCAGC	4 cut(s)	26, 78, 259, 316
MaeI	CTAG	4 cut(s)	53, 258, 311, 336
MaeII	ACGT	2 cut(s)	197, 434
MaeIII	GTNAC	3 cut(s)	430, 491, 584
MalI	GATC	3 cut(s)	131, 245, 544
MboI	GATC	3 cut(s)	129, 243, 542
MboII	GAAGA	2 cut(s)	152, 214
MluCI	AATT	6 cut(s)	76, 121, 174, 297, 536, 594
MlyI	GAGTC	1 cut(s)	17
MmeI	TCCRAC	1 cut(s)	45
MnlI	CCTC	8 cut(s)	40, 83, 86, 97, 191, 341, 360, 439
MroXI	GAANNNNTTC	1 cut(s)	253
MseI	TTAA	1 cut(s)	534
MspI	CCGG	1 cut(s)	564
MvnI	CGCG	1 cut(s)	224
MwoI	GCNNNNNNNGC	2 cut(s)	48, 113
NcoI	CCATGG	1 cut(s)	10
NdeII	GATC	3 cut(s)	129, 243, 542
NlaIII	CATG	4 cut(s)	14, 296, 363, 402
NlaIV	GGNNCC	2 cut(s)	193, 562
NmeAIII	GCCGAG	1 cut(s)	27
NmuCI	GTSAC	3 cut(s)	430, 491, 584
NspI	RCATGY	2 cut(s)	296, 363
PaeI	GCATGC	1 cut(s)	363
PciI	ACATGT	1 cut(s)	292
PcsI	WCGNNNNNNNCGW	4 cut(s)	54, 66, 160, 169
PdmI	GAANNNNTTC	1 cut(s)	253
PfeI	GAWTC	3 cut(s)	83, 186, 254
PkrI	GCNGC	6 cut(s)	41, 65, 68, 115, 274, 331
PleI	GAGTC	1 cut(s)	17
PmaCI	CACGTG	1 cut(s)	198
PmlI	CACGTG	1 cut(s)	198
PpsI	GAGTC	1 cut(s)	17
Ppu21I	YACGTR	1 cut(s)	198
PscI	ACATGT	1 cut(s)	292
PshAI	GACNNNNGTC	1 cut(s)	437
PspCI	CACGTG	1 cut(s)	198
PspEI	GGTNACC	1 cut(s)	584
PspFI	CCCAGC	1 cut(s)	470
PspN4I	GGNNCC	2 cut(s)	193, 562
SaqAI	TTAA	1 cut(s)	534
SatI	GCNGC	6 cut(s)	40, 64, 67, 114, 273, 330
Sau3AI	GATC	3 cut(s)	129, 243, 542
SchI	GAGTC	1 cut(s)	17
SetI	ASST	9 cut(s)	41, 200, 319, 396, 437, 450, 562, 586, 591
SmlI	CTYRAG	1 cut(s)	364
SmoI	CTYRAG	1 cut(s)	364
SpeI	ACTAGT	1 cut(s)	310
SphI	GCATGC	1 cut(s)	363
Sse9I	AATT	6 cut(s)	76, 121, 174, 297, 536, 594
SsiI	CCGC	5 cut(s)	63, 113, 116, 209, 224
SspMI	CTAG	4 cut(s)	53, 258, 311, 336
StyI	CCWWGG	1 cut(s)	10
TaaI	ACNGT	1 cut(s)	466
TaiI	ACGT	2 cut(s)	200, 437
TaqI	TCGA	1 cut(s)	86
TasI	AATT	6 cut(s)	76, 121, 174, 297, 536, 594
TauI	GCSGC	2 cut(s)	66, 116
TfiI	GAWTC	3 cut(s)	83, 186, 254
Tru1I	TTAA	1 cut(s)	534
Tru9I	TTAA	1 cut(s)	534
TseFI	GTSAC	3 cut(s)	430, 491, 584
TseI	GCWGC	4 cut(s)	39, 66, 272, 329
Tsp45I	GTSAC	3 cut(s)	430, 491, 584
TspGWI	ACGGA	1 cut(s)	535
XapI	RAATTY	2 cut(s)	174, 536
XceI	RCATGY	2 cut(s)	296, 363
XcmI	CCANNNNNNNNNTGG	1 cut(s)	202
XmiI	GTMKAC	1 cut(s)	549
XmnI	GAANNNNTTC	1 cut(s)	253
XspI	CTAG	4 cut(s)	53, 258, 311, 336
ZraI	GACGTC	1 cut(s)	435

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