Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr2D

Orthogroup ID

OG0002279

Physical Location & Seq

Genomic Coordinates Reverse (-)

90534082 .. 90535233

Gene Structure 1152 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh2DG687600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 432 bp

ATGGATAACATTTTGAAATGTCACTACAAAAAAGAATTGCAACCGCCACAGCAGCTTGCATCTGCACATAAAGCTCCTCTTGATCCCAGCACTACTTTAGGTGGTTTCTGTGGAAAAAACTATTCCGAGGCATCAGCATTTATAATAACTTATCCTGTAAACAATGCTATTAATAAAGAGGGGAATGAAATTGAAAGAGCAGTGGCATGGGAGAAGGCCTTCATTGAGCTGGCAAAGGATGAGCTGTTGCAAATGGTGCAATCTAAAAACTTAACACTATCTTTCTCATCGGAGAGTTCCATTGAAGAAGAACTTAAGAGTGAAAGCACTGCAGATGCTATTACAATATTAGTCCATGAAGGTGCATTTGGTTCTATTGGTGATGATCAGTCACTTCTTAAATACTTGGAATCTCTGGGACAACATCAGTAA

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

143

Amino Acids

15.74

Weight (kDa)

4.83

Isoelectric Point (pI)

67.37

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
NPC1_MLD	PF22314	21 - 98	1.1e-14	NPC1, middle luminal domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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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)	143
AciI	CCGC	1 cut(s)	44
AclWI	GGATC	1 cut(s)	77
AflII	CTTAAG	1 cut(s)	314
AgsI	TTSAA	3 cut(s)	16, 194, 305
AjuI	GAANNNNNNNTTGG	2 cut(s)	351, 383
AluBI	AGCT	4 cut(s)	55, 74, 229, 244
AluI	AGCT	4 cut(s)	55, 74, 229, 244
AlwI	GGATC	1 cut(s)	77
AoxI	GGCC	1 cut(s)	216
ApeKI	GCWGC	1 cut(s)	52
AseI	ATTAAT	1 cut(s)	171
Asp700I	GAANNNNTTC	1 cut(s)	218
AsuHPI	GGTGA	1 cut(s)	392
BbvI	GCAGC	1 cut(s)	64
BclI	TGATCA	1 cut(s)	385
BfmI	CTRYAG	1 cut(s)	330
BfrI	CTTAAG	1 cut(s)	314
BisI	GCNGC	1 cut(s)	53
BlsI	GCNGC	1 cut(s)	54
BmsI	GCATC	3 cut(s)	68, 140, 325
BsaJI	CCNNGG	1 cut(s)	126
BseDI	CCNNGG	1 cut(s)	126
BseGI	GGATG	1 cut(s)	244
BseRI	GAGGAG	1 cut(s)	66
BseXI	GCAGC	1 cut(s)	64
BseYI	CCCAGC	1 cut(s)	86
BsgI	GTGCAG	1 cut(s)	48
BshFI	GGCC	1 cut(s)	218
BsnI	GGCC	1 cut(s)	218
Bsp143I	GATC	2 cut(s)	82, 385
BspACI	CCGC	1 cut(s)	44
BspANI	GGCC	1 cut(s)	218
BspMAI	CTGCAG	1 cut(s)	334
BspPI	GGATC	1 cut(s)	77
BspTI	CTTAAG	1 cut(s)	314
BssECI	CCNNGG	1 cut(s)	126
BssMI	GATC	2 cut(s)	82, 385
BstAFI	CTTAAG	1 cut(s)	314
BstAPI	GCANNNNNTGC	1 cut(s)	256
BstC8I	GCNNGC	2 cut(s)	57, 231
BstF5I	GGATG	1 cut(s)	244
BstKTI	GATC	2 cut(s)	85, 388
BstMBI	GATC	2 cut(s)	82, 385
BstMWI	GCNNNNNNNGC	3 cut(s)	52, 71, 256
BstSFI	CTRYAG	1 cut(s)	330
BstV1I	GCAGC	1 cut(s)	64
BsuRI	GGCC	1 cut(s)	218
BtsCI	GGATG	1 cut(s)	244
BtsI	GCAGTG	2 cut(s)	207, 327
BtsIMutI	CAGTG	2 cut(s)	207, 327
Cac8I	GCNNGC	2 cut(s)	57, 231
CviAII	CATG	2 cut(s)	207, 356
CviJI	RGCY	5 cut(s)	55, 74, 218, 229, 244
CviKI_1	RGCY	5 cut(s)	55, 74, 218, 229, 244
DpnI	GATC	2 cut(s)	84, 387
DpnII	GATC	2 cut(s)	82, 385
Eco147I	AGGCCT	1 cut(s)	218
FaeI	CATG	2 cut(s)	210, 359
FaiI	YATR	4 cut(s)	69, 143, 208, 357
FalI	AAGNNNNNCTT	4 cut(s)	63, 95, 297, 329
FatI	CATG	2 cut(s)	206, 355
FbaI	TGATCA	1 cut(s)	385
Fnu4HI	GCNGC	1 cut(s)	53
FokI	GGATG	1 cut(s)	251
Fsp4HI	GCNGC	1 cut(s)	53
GluI	GCNGC	1 cut(s)	53
GsaI	CCCAGC	1 cut(s)	90
HaeIII	GGCC	1 cut(s)	218
Hin1II	CATG	2 cut(s)	210, 359
HinfI	GANTC	1 cut(s)	410
HphI	GGTGA	1 cut(s)	392
Hpy166II	GTNNAC	1 cut(s)	160
Hpy188I	TCNGA	2 cut(s)	127, 292
Hpy188III	TCNNGA	1 cut(s)	80
Hpy8I	GTNNAC	1 cut(s)	160
HpyAV	CCTTC	3 cut(s)	208, 229, 353
HpyCH4V	TGCA	7 cut(s)	40, 59, 65, 250, 259, 332, 365
HpyF10VI	GCNNNNNNNGC	3 cut(s)	52, 71, 256
Hsp92II	CATG	2 cut(s)	210, 359
Ksp22I	TGATCA	1 cut(s)	385
Kzo9I	GATC	2 cut(s)	82, 385
LmnI	GCTCC	1 cut(s)	79
LpnPI	CCDG	4 cut(s)	100, 168, 215, 401
Lsp1109I	GCAGC	1 cut(s)	64
LweI	GCATC	3 cut(s)	68, 140, 325
MaeIII	GTNAC	2 cut(s)	20, 390
MalI	GATC	2 cut(s)	84, 387
MboI	GATC	2 cut(s)	82, 385
MboII	GAAGA	2 cut(s)	317, 320
MluCI	AATT	2 cut(s)	35, 189
MnlI	CCTC	3 cut(s)	87, 121, 172
MroXI	GAANNNNTTC	1 cut(s)	218
MseI	TTAA	4 cut(s)	171, 272, 315, 399
MslI	CAYNNNNRTG	1 cut(s)	360
MspCI	CTTAAG	1 cut(s)	314
MwoI	GCNNNNNNNGC	3 cut(s)	52, 71, 256
NdeII	GATC	2 cut(s)	82, 385
NlaIII	CATG	2 cut(s)	210, 359
NmuCI	GTSAC	2 cut(s)	20, 390
PceI	AGGCCT	1 cut(s)	218
PdmI	GAANNNNTTC	1 cut(s)	218
PfeI	GAWTC	1 cut(s)	410
PkrI	GCNGC	1 cut(s)	54
PshBI	ATTAAT	1 cut(s)	171
PsiI	TTATAA	1 cut(s)	143
PspFI	CCCAGC	1 cut(s)	86
PstI	CTGCAG	1 cut(s)	334
RseI	CAYNNNNRTG	1 cut(s)	360
SaqAI	TTAA	4 cut(s)	171, 272, 315, 399
SatI	GCNGC	1 cut(s)	53
Sau3AI	GATC	2 cut(s)	82, 385
SetI	ASST	6 cut(s)	57, 76, 103, 231, 246, 364
SfaNI	GCATC	3 cut(s)	68, 140, 325
SfcI	CTRYAG	1 cut(s)	330
SmiMI	CAYNNNNRTG	1 cut(s)	360
SmlI	CTYRAG	1 cut(s)	314
SmoI	CTYRAG	1 cut(s)	314
Sse9I	AATT	2 cut(s)	35, 189
SseBI	AGGCCT	1 cut(s)	218
SsiI	CCGC	1 cut(s)	44
SspI	AATATT	1 cut(s)	348
StuI	AGGCCT	1 cut(s)	218
TasI	AATT	2 cut(s)	35, 189
TfiI	GAWTC	1 cut(s)	410
Tru1I	TTAA	4 cut(s)	171, 272, 315, 399
Tru9I	TTAA	4 cut(s)	171, 272, 315, 399
TscAI	CASTG	2 cut(s)	207, 334
TseFI	GTSAC	2 cut(s)	20, 390
TseI	GCWGC	1 cut(s)	52
Tsp45I	GTSAC	2 cut(s)	20, 390
TspDTI	ATGAA	3 cut(s)	201, 211, 372
TspRI	CASTG	2 cut(s)	207, 334
Vha464I	CTTAAG	1 cut(s)	314
VspI	ATTAAT	1 cut(s)	171
XmnI	GAANNNNTTC	1 cut(s)	218

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