Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr3

Orthogroup ID

OG0012693

Physical Location & Seq

Genomic Coordinates Forward (+)

21534272 .. 21537049

Gene Structure 2778 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000012711

Sequence Viewer

CDS Protein Promoter (2k)

Length: 945 bp

ATGGCGTCGTTTATCAGTATCTTTACTGCTTTCTTGTTGCTTCAGGTTGTGCATTCTGAAGAGTATTGTGCCATGTATGAAGTGTGTGGGAAGCGGAGTACTGATGGGGTAGTTCTGAATTGCCCTTATGGTTCTCCTTCTGTGAAGCCGGACAAGCTCTTCTCTGCACGAATCCAAAGTTTGTGCCCGACATTAACCGGAAATGTCTGTTGCACAGAGCTTCAGTTTGAGACATTGCGACTATGGGTCGACCCGGCAACCAGATTTCTTGGAGGCTGCCCGGCATGCTTGAGGAACTATCTCAATCTTTTCTGCGAGCTATCATGCTCCCCAAATCAGAGCCTCTATATCAATGTGACTTCCGTCTCCAAGGTTAGTGGCAATATGACTGTAGCTAGGATTGACTATTACATAAGTGACACTTTTGGACAAGGGCTATACAACTCCTGCAAGGATGTTAAATTCCGATCCATAGACTTGGTTGGTGCCGGTGCGAAAAGTTTTGAAGAATGGTTTGATTTTCTTGGGAAGAAAGCATCCCCTGCTGTCCCTGCTTCACCTTATGCCATTGACTTCAGGTTTCCGACTCGTGAATCATCCGAAATGCAGTTCATGAACATGTCAGCTTATTCATGTGCTGACACTCTATTAGGCTGCTCTTGTGATGATTGCCCTATTGCTTGTTCTAGCTCTGAAGTGATGCTACTCACCATCAAATTCTGGCCTGTTGAGGTGACAATCAATGTTACACGTATACTTGCCACATTCATGGCAGTTTTATGGGATTGTAGTCTGTTGGCTTGGGGAATGGCTAATCTTATGGGGATATGCAGTTTGTGGATGGTGACTGTTCTTTGGGGCATTATCTGGAATTTCAAGTTCTTGCTAGGTCTTGCTATTGGTTATCTATATGCTCATTTCGTTTGGTATTTTGAGCTAGGTTGA

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

315

Amino Acids

35.06

Weight (kDa)

5.13

Isoelectric Point (pI)

48.19

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
NPC1_N	PF16414	21 - 231	9e-57	Niemann-Pick C1 N terminus

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Align Labels (Cladogram)

Image

Tree File

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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)
AccB1I	GGYRCC	1 cut(s)	485
AccI	GTMKAC	2 cut(s)	249, 754
AciI	CCGC	1 cut(s)	94
AclWI	GGATC	1 cut(s)	462
AcsI	RAATTY	3 cut(s)	461, 716, 871
AcuI	CTGAAG	5 cut(s)	26, 78, 206, 559, 714
AcyI	GRCGYC	1 cut(s)	5
AfaI	GTAC	1 cut(s)	100
AflIII	ACRYGT	2 cut(s)	618, 749
AgsI	TTSAA	2 cut(s)	506, 877
AhdI	GACNNNNNGTC	1 cut(s)	245
AluBI	AGCT	7 cut(s)	157, 220, 319, 395, 626, 690, 937
AluI	AGCT	7 cut(s)	157, 220, 319, 395, 626, 690, 937
Alw26I	GTCTC	2 cut(s)	224, 370
AlwI	GGATC	1 cut(s)	462
AoxI	GGCC	1 cut(s)	722
ApeKI	GCWGC	2 cut(s)	276, 654
ApoI	RAATTY	3 cut(s)	461, 716, 871
AsuC2I	CCSGG	2 cut(s)	254, 281
AsuHPI	GGTGA	4 cut(s)	549, 700, 745, 856
BaeGI	GKGCMC	1 cut(s)	188
BanI	GGYRCC	1 cut(s)	485
BarI	GAAGNNNNNNTAC	2 cut(s)	687, 719
BauI	CACGAG	1 cut(s)	588
BbvI	GCAGC	2 cut(s)	263, 641
BccI	CCATC	3 cut(s)	98, 719, 835
BcnI	CCSGG	2 cut(s)	254, 281
BcoDI	GTCTC	2 cut(s)	224, 370
BfaI	CTAG	4 cut(s)	396, 687, 887, 938
BfmI	CTRYAG	1 cut(s)	390
BisI	GCNGC	2 cut(s)	277, 655
BlsI	GCNGC	2 cut(s)	278, 656
BmcAI	AGTACT	1 cut(s)	100
Bme1390I	CCNGG	2 cut(s)	254, 281
BmeRI	GACNNNNNGTC	1 cut(s)	245
BmiI	GGNNCC	1 cut(s)	487
BmrFI	CCNGG	2 cut(s)	254, 281
BmsI	GCATC	2 cut(s)	545, 690
BoxI	GACNNNNGTC	1 cut(s)	362
BpuEI	CTTGAG	1 cut(s)	310
BpuMI	CCSGG	2 cut(s)	254, 281
BsaAI	YACGTR	1 cut(s)	752
BsaHI	GRCGYC	1 cut(s)	5
BsaJI	CCNNGG	1 cut(s)	369
BsaWI	WCCGGW	1 cut(s)	197
Bse118I	RCCGGY	1 cut(s)	488
Bse3DI	GCAATG	1 cut(s)	233
BseDI	CCNNGG	1 cut(s)	369
BseGI	GGATG	4 cut(s)	460, 536, 596, 846
BseMI	GCAATG	1 cut(s)	233
BseSI	GKGCMC	1 cut(s)	188
BseXI	GCAGC	2 cut(s)	263, 641
BsgI	GTGCAG	1 cut(s)	150
BshFI	GGCC	1 cut(s)	724
BshNI	GGYRCC	1 cut(s)	485
BsiSI	CCGG	5 cut(s)	149, 198, 254, 281, 489
BslFI	GGGAC	1 cut(s)	533
BsmAI	GTCTC	2 cut(s)	224, 370
BsmBI	CGTCTC	1 cut(s)	370
BsmFI	GGGAC	1 cut(s)	533
BsmI	GAATGC	1 cut(s)	52
BsnI	GGCC	1 cut(s)	724
Bsp1286I	GDGCHC	1 cut(s)	188
Bsp143I	GATC	1 cut(s)	467
BspACI	CCGC	1 cut(s)	94
BspANI	GGCC	1 cut(s)	724
BspHI	TCATGA	1 cut(s)	612
BspLI	GGNNCC	1 cut(s)	487
BspPI	GGATC	1 cut(s)	462
BspQI	GCTCTTC	1 cut(s)	164
BspT107I	GGYRCC	1 cut(s)	485
BsrDI	GCAATG	1 cut(s)	233
BsrFI	RCCGGY	1 cut(s)	488
BssAI	RCCGGY	1 cut(s)	488
BssECI	CCNNGG	1 cut(s)	369
BssMI	GATC	1 cut(s)	467
BssNAI	GTATAC	1 cut(s)	755
BssNI	GRCGYC	1 cut(s)	5
BssSI	CACGAG	1 cut(s)	588
BssT1I	CCWWGG	1 cut(s)	369
Bst1107I	GTATAC	1 cut(s)	755
Bst2BI	CACGAG	1 cut(s)	588
Bst4CI	ACNGT	2 cut(s)	391, 850
Bst6I	CTCTTC	2 cut(s)	54, 164
BstACI	GRCGYC	1 cut(s)	5
BstAPI	GCANNNNNTGC	1 cut(s)	542
BstBAI	YACGTR	1 cut(s)	752
BstC8I	GCNNGC	2 cut(s)	286, 317
BstF5I	GGATG	4 cut(s)	460, 536, 596, 846
BstKTI	GATC	1 cut(s)	470
BstMAI	GTCTC	2 cut(s)	224, 370
BstMBI	GATC	1 cut(s)	467
BstMWI	GCNNNNNNNGC	4 cut(s)	154, 285, 542, 551
BstNSI	RCATGY	2 cut(s)	288, 622
BstPAI	GACNNNNGTC	1 cut(s)	362
BstSCI	CCNGG	2 cut(s)	252, 279
BstSFI	CTRYAG	1 cut(s)	390
BstSLI	GKGCMC	1 cut(s)	188
BstV1I	GCAGC	2 cut(s)	263, 641
BstXI	CCANNNNNNTGG	2 cut(s)	478, 769
BstZ17I	GTATAC	1 cut(s)	755
BsuRI	GGCC	1 cut(s)	724
BtsCI	GGATG	4 cut(s)	460, 536, 596, 846
Cac8I	GCNNGC	2 cut(s)	286, 317
CciI	TCATGA	1 cut(s)	612
Cfr10I	RCCGGY	1 cut(s)	488
Csp6I	GTAC	1 cut(s)	99
CspCI	CAANNNNNGTGG	2 cut(s)	358, 393
CviAII	CATG	7 cut(s)	73, 285, 324, 613, 619, 633, 769
CviQI	GTAC	1 cut(s)	99
DpnI	GATC	1 cut(s)	469
DpnII	GATC	1 cut(s)	467
DriI	GACNNNNNGTC	1 cut(s)	245
Eam1104I	CTCTTC	2 cut(s)	54, 164
Eam1105I	GACNNNNNGTC	1 cut(s)	245
EarI	CTCTTC	2 cut(s)	54, 164
Eco130I	CCWWGG	1 cut(s)	369
Eco57I	CTGAAG	5 cut(s)	26, 78, 206, 559, 714
EcoT14I	CCWWGG	1 cut(s)	369
ErhI	CCWWGG	1 cut(s)	369
Esp3I	CGTCTC	1 cut(s)	370
FaeI	CATG	7 cut(s)	76, 288, 327, 616, 622, 636, 772
FalI	AAGNNNNNCTT	2 cut(s)	406, 438
FaqI	GGGAC	1 cut(s)	533
FatI	CATG	7 cut(s)	72, 284, 323, 612, 618, 632, 768
FblI	GTMKAC	2 cut(s)	249, 754
Fnu4HI	GCNGC	2 cut(s)	277, 655
FokI	GGATG	4 cut(s)	467, 523, 583, 853
Fsp4HI	GCNGC	2 cut(s)	277, 655
FspBI	CTAG	4 cut(s)	396, 687, 887, 938
GluI	GCNGC	2 cut(s)	277, 655
HaeIII	GGCC	1 cut(s)	724
HapII	CCGG	5 cut(s)	149, 198, 254, 281, 489
Hin1I	GRCGYC	1 cut(s)	5
Hin1II	CATG	7 cut(s)	76, 288, 327, 616, 622, 636, 772
HincII	GTYRAC	1 cut(s)	250
HindII	GTYRAC	1 cut(s)	250
HinfI	GANTC	3 cut(s)	171, 586, 593
HpaII	CCGG	5 cut(s)	149, 198, 254, 281, 489
HphI	GGTGA	4 cut(s)	549, 700, 745, 856
Hpy166II	GTNNAC	2 cut(s)	250, 755
Hpy188I	TCNGA	7 cut(s)	58, 117, 339, 467, 585, 601, 694
Hpy188III	TCNNGA	3 cut(s)	590, 613, 868
Hpy8I	GTNNAC	2 cut(s)	250, 755
Hpy99I	CGWCG	1 cut(s)	10
HpyAV	CCTTC	1 cut(s)	147
HpyCH4III	ACNGT	2 cut(s)	391, 850
HpyCH4IV	ACGT	1 cut(s)	751
HpyCH4V	TGCA	6 cut(s)	52, 167, 213, 450, 607, 831
HpyF10VI	GCNNNNNNNGC	4 cut(s)	154, 285, 542, 551
HpySE526I	ACGT	1 cut(s)	751
Hsp92I	GRCGYC	1 cut(s)	5
Hsp92II	CATG	7 cut(s)	76, 288, 327, 616, 622, 636, 772
Kzo9I	GATC	1 cut(s)	467
LguI	GCTCTTC	1 cut(s)	164
LmnI	GCTCC	1 cut(s)	332
Lsp1109I	GCAGC	2 cut(s)	263, 641
LweI	GCATC	2 cut(s)	545, 690
MaeI	CTAG	4 cut(s)	396, 687, 887, 938
MaeII	ACGT	1 cut(s)	751
MaeIII	GTNAC	5 cut(s)	355, 416, 733, 745, 844
MalI	GATC	1 cut(s)	469
MboI	GATC	1 cut(s)	467
MboII	GAAGA	4 cut(s)	71, 151, 518, 541
MhlI	GDGCHC	1 cut(s)	188
MluCI	AATT	4 cut(s)	118, 461, 716, 871
MlyI	GAGTC	1 cut(s)	580
MmeI	TCCRAC	1 cut(s)	608
MnlI	CCTC	4 cut(s)	266, 285, 353, 724
MseI	TTAA	2 cut(s)	194, 459
MslI	CAYNNNNRTG	2 cut(s)	617, 767
MspI	CCGG	5 cut(s)	149, 198, 254, 281, 489
MspR9I	CCNGG	2 cut(s)	254, 281
Mva1269I	GAATGC	1 cut(s)	52
MwoI	GCNNNNNNNGC	4 cut(s)	154, 285, 542, 551
NciI	CCSGG	2 cut(s)	254, 281
NdeII	GATC	1 cut(s)	467
NlaIII	CATG	7 cut(s)	76, 288, 327, 616, 622, 636, 772
NlaIV	GGNNCC	1 cut(s)	487
NmuCI	GTSAC	4 cut(s)	355, 416, 733, 844
NspI	RCATGY	2 cut(s)	288, 622
PaeI	GCATGC	1 cut(s)	288
PagI	TCATGA	1 cut(s)	612
PciI	ACATGT	1 cut(s)	618
PciSI	GCTCTTC	1 cut(s)	164
PctI	GAATGC	1 cut(s)	52
PfeI	GAWTC	2 cut(s)	171, 593
PkrI	GCNGC	2 cut(s)	278, 656
PleI	GAGTC	1 cut(s)	580
PpsI	GAGTC	1 cut(s)	580
Ppu21I	YACGTR	1 cut(s)	752
PscI	ACATGT	1 cut(s)	618
PshAI	GACNNNNGTC	1 cut(s)	362
PspN4I	GGNNCC	1 cut(s)	487
RsaI	GTAC	1 cut(s)	100
RsaNI	GTAC	1 cut(s)	99
RseI	CAYNNNNRTG	2 cut(s)	617, 767
SalI	GTCGAC	1 cut(s)	248
SapI	GCTCTTC	1 cut(s)	164
SaqAI	TTAA	2 cut(s)	194, 459
SatI	GCNGC	2 cut(s)	277, 655
Sau3AI	GATC	1 cut(s)	467
ScaI	AGTACT	1 cut(s)	100
SchI	GAGTC	1 cut(s)	580
ScrFI	CCNGG	2 cut(s)	254, 281
SduI	GDGCHC	1 cut(s)	188
SfaNI	GCATC	2 cut(s)	545, 690
SfcI	CTRYAG	1 cut(s)	390
SmiMI	CAYNNNNRTG	2 cut(s)	617, 767
SmlI	CTYRAG	1 cut(s)	289
SmoI	CTYRAG	1 cut(s)	289
SphI	GCATGC	1 cut(s)	288
Sse9I	AATT	4 cut(s)	118, 461, 716, 871
SsiI	CCGC	1 cut(s)	94
SspMI	CTAG	4 cut(s)	396, 687, 887, 938
StyD4I	CCNGG	2 cut(s)	252, 279
StyI	CCWWGG	1 cut(s)	369
TaaI	ACNGT	2 cut(s)	391, 850
TaiI	ACGT	1 cut(s)	754
TaqI	TCGA	1 cut(s)	249
TasI	AATT	4 cut(s)	118, 461, 716, 871
TatI	WGTACW	1 cut(s)	98
TfiI	GAWTC	2 cut(s)	171, 593
Tru1I	TTAA	2 cut(s)	194, 459
Tru9I	TTAA	2 cut(s)	194, 459
TseFI	GTSAC	4 cut(s)	355, 416, 733, 844
TseI	GCWGC	2 cut(s)	276, 654
Tsp45I	GTSAC	4 cut(s)	355, 416, 733, 844
TspDTI	ATGAA	5 cut(s)	93, 601, 621, 629, 757
TspGWI	ACGGA	1 cut(s)	352
XapI	RAATTY	3 cut(s)	461, 716, 871
XceI	RCATGY	2 cut(s)	288, 622
XmiI	GTMKAC	2 cut(s)	249, 754
XspI	CTAG	4 cut(s)	396, 687, 887, 938
ZrmI	AGTACT	1 cut(s)	100

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