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Gene: Npc2 (NPC intracellular cholesterol transporter 2) Rattus norvegicus

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Symbol:

Npc2

Name:

NPC intracellular cholesterol transporter 2

RGD ID:

628756

Description:

Predicted to enable cholesterol binding activity; cholesterol transfer activity; and enzyme binding activity. Predicted to be involved in cholesterol homeostasis; cholesterol transport; and response to virus. Predicted to act upstream of or within several processes, including cholesterol storage; sterol metabolic process; and sterol transport. Predicted to be located in extracellular space. Predicted to be active in lysosome. Human ortholog(s) of this gene implicated in Niemann-Pick disease and Niemann-Pick disease type C2. Orthologous to human NPC2 (NPC intracellular cholesterol transporter 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 4,4'-sulfonyldiphenol.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

epididymal secretory protein 1; epididymal secretory protein E1; Niemann Pick type C2; Niemann-Pick disease, type C2; re1

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	NPC2 (NPC intracellular cholesterol transporter 2)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Npc2 (NPC intracellular cholesterol transporter 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Npc2 (NPC intracellular cholesterol transporter 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	NPC2 (NPC intracellular cholesterol transporter 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	NPC2 (NPC intracellular cholesterol transporter 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Npc2 (NPC intracellular cholesterol transporter 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	NPC2 (NPC intracellular cholesterol transporter 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	NPC2 (NPC intracellular cholesterol transporter 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Npc2 (NPC intracellular cholesterol transporter 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Npc2 (NPC intracellular cholesterol transporter 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	NPC2 (NPC intracellular cholesterol transporter 2)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	NPC2 (NPC intracellular cholesterol transporter 2)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Npc2 (NPC intracellular cholesterol transporter 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Npc2 (NPC intracellular cholesterol transporter 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	zgc:193725	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	zgc:193725	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	npc2 (Niemann-Pick disease, type C2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	npc2 (Niemann-Pick disease, type C2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	heh-1	Alliance	DIOPT (Hieranoid\|OrthoFinder\|PANTHER)
Caenorhabditis elegans (roundworm):	heh-1	Alliance	DIOPT (Hieranoid\|OrthoFinder\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	Npc2a	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER)
Drosophila melanogaster (fruit fly):	Npc2a	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Npc2b	Alliance	DIOPT (Hieranoid\|OMA\|PANTHER)
Drosophila melanogaster (fruit fly):	Npc2b	Alliance	DIOPT (OrthoFinder\|OrthoInspector\|PANTHER)
Drosophila melanogaster (fruit fly):	Npc2c	Alliance	DIOPT (OrthoFinder\|PANTHER\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	npc2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	npc2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	6	110,128,325 - 110,149,245 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	6	110,128,325 - 110,150,004 (-)	Ensembl				GRCr8
mRatBN7.2	6	104,397,239 - 104,418,161 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	104,378,644 - 104,418,155 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	6	104,566,714 - 104,587,594 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	104,865,873 - 104,886,753 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	104,235,225 - 104,256,103 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	108,467,410 - 108,488,330 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	108,467,410 - 108,488,330 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	6	117,060,860 - 117,081,780 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	6	108,793,935 - 108,814,703 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	6	102,222,115 - 102,243,035 (-)	NCBI		Celera
RGSC_v3.1	6	108,797,391 - 108,818,159 (-)	NCBI
Cytogenetic Map	6	q31	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

Niemann-Pick disease (ISO,ISS)

Niemann-Pick disease type A (ISO)

Niemann-Pick disease type B (ISO)

Niemann-Pick disease type C1 (ISO)

Niemann-Pick disease type C2 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,4-dinitrotoluene (EXP)

4,4'-sulfonyldiphenol (EXP,ISO)

4-hydroxyphenyl retinamide (ISO)

5-aza-2'-deoxycytidine (ISO)

acrolein (ISO)

acrylamide (EXP)

all-trans-retinoic acid (ISO)

alpha-pinene (ISO)

ammonium chloride (EXP)

amphetamine (EXP)

ampicillin (EXP)

Archazolid B (ISO)

Aroclor 1254 (ISO)

arsenite(3-) (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

beta-naphthoflavone (ISO)

bis(2-ethylhexyl) phthalate (EXP)

bisphenol A (EXP,ISO)

bisphenol AF (EXP,ISO)

Bisphenol B (ISO)

bisphenol F (EXP,ISO)

cadmium atom (ISO)

cadmium dichloride (EXP,ISO)

carbon nanotube (ISO)

CGP 52608 (ISO)

chloropicrin (ISO)

cisplatin (ISO)

clobetasol (ISO)

clofibrate (ISO)

cobalt dichloride (ISO)

copper atom (ISO)

copper(0) (ISO)

curcumin (ISO)

dibutyl phthalate (EXP)

dicrotophos (ISO)

diuron (ISO)

dorsomorphin (ISO)

ethanol (ISO)

ethyl methanesulfonate (ISO)

fenvalerate (EXP)

flutamide (EXP)

folic acid (ISO)

formaldehyde (ISO)

fulvestrant (ISO)

genistein (ISO)

gentamycin (EXP)

GSK-J4 (ISO)

isoflavones (ISO)

ivermectin (ISO)

methapyrilene (EXP)

methyl methanesulfonate (ISO)

metronidazole (EXP)

miconazole (ISO)

neomycin (EXP)

nimesulide (EXP)

okadaic acid (ISO)

ouabain (ISO)

ozone (ISO)

paracetamol (ISO)

perfluorooctanoic acid (ISO)

phenylmercury acetate (ISO)

phenylpropanolamine (ISO)

potassium dichromate (ISO)

resveratrol (ISO)

rotenone (ISO)

SB 431542 (ISO)

silicon dioxide (EXP)

sodium arsenite (ISO)

sodium dichromate (ISO)

sodium fluoride (ISO)

tamibarotene (ISO)

tetrachloromethane (EXP,ISO)

titanium dioxide (ISO)

trimellitic anhydride (ISO)

triphenyl phosphate (ISO)

urethane (ISO)

valproic acid (ISO)

vancomycin (EXP)

vinclozolin (EXP)

Yessotoxin (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

cholesterol efflux (IBA,IEA,ISO)

cholesterol homeostasis (IEA,ISO)

cholesterol storage (ISO)

cholesterol transport (IEA,ISO)

gene expression (ISO)

intracellular cholesterol transport (IBA,IEA,ISO)

intracellular sterol transport (IEA,ISO)

lysosome to ER cholesterol transport (IEA,ISO)

response to virus (IEA,ISO)

sterol metabolic process (ISO)

sterol transport (IEA,ISO)

Cellular Component

extracellular region (IEA)

extracellular space (IEA,ISO)

late endosome (IEA,ISO)

lysosomal lumen (IEA,ISO)

lysosome (IEA,ISO)

Molecular Function

cholesterol binding (IBA,IEA,ISO)

cholesterol transfer activity (IEA,ISO)

enzyme binding (IEA,ISO)

protein binding (ISO)

sterol binding (IEA)

References

References - curated

#	Reference Title	Reference Citation
1.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
3.	Niemann-Pick disease type C: spectrum of HE1 mutations and genotype/phenotype correlations in the NPC2 group.	Millat G, etal., Am J Hum Genet. 2001 Nov;69(5):1013-21. Epub 2001 Sep 20.
4.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
5.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
7.	Comprehensive gene review and curation	RGD comprehensive gene curation
8.	Information Derived from GenBank Report	RGD, Sept. 2003
9.	Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

Additional References at PubMed

PMID:10366780	PMID:11125141	PMID:12719428	PMID:15110773	PMID:15937921	PMID:16141411	PMID:16548883	PMID:17018531	PMID:18772377	PMID:18823126	PMID:19723497	PMID:21315718
PMID:22367786	PMID:23376485	PMID:23533145	PMID:24006456	PMID:27238017	PMID:29514215	PMID:29522534

Genomics

Comparative Map Data

Npc2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	6	110,128,325 - 110,149,245 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	6	110,128,325 - 110,150,004 (-)	Ensembl				GRCr8
mRatBN7.2	6	104,397,239 - 104,418,161 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	104,378,644 - 104,418,155 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	6	104,566,714 - 104,587,594 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	104,865,873 - 104,886,753 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	104,235,225 - 104,256,103 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	108,467,410 - 108,488,330 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	108,467,410 - 108,488,330 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	6	117,060,860 - 117,081,780 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	6	108,793,935 - 108,814,703 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	6	102,222,115 - 102,243,035 (-)	NCBI		Celera
RGSC_v3.1	6	108,797,391 - 108,818,159 (-)	NCBI
Cytogenetic Map	6	q31	NCBI

NPC2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	14	74,479,935 - 74,493,512 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	14	74,476,192 - 74,494,177 (-)	Ensembl			hg38	GRCh38
GRCh37	14	74,946,638 - 74,960,215 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	14	74,016,396 - 74,029,837 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	14	74,016,396 - 74,029,837	NCBI
Celera	14	54,985,030 - 54,998,469 (-)	NCBI		Celera
Cytogenetic Map	14	q24.3	NCBI
HuRef	14	55,115,095 - 55,128,528 (-)	NCBI		HuRef
CHM1_1	14	74,886,183 - 74,899,622 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	14	68,688,905 - 68,702,483 (-)	NCBI		T2T-CHM13v2.0

Npc2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	12	84,801,333 - 84,819,886 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	12	84,801,336 - 84,819,926 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	12	84,754,559 - 84,773,112 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	12	84,754,562 - 84,773,152 (-)	Ensembl			mm10	GRCm38
MGSCv37	12	86,095,509 - 86,114,062 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	12	85,644,307 - 85,662,860 (-)	NCBI		MGSCv36	mm8
Celera	12	86,210,583 - 86,229,366 (-)	NCBI		Celera
Cytogenetic Map	12	D1	NCBI
cM Map	12	39.37	NCBI

Npc2
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955523	1,010,976 - 1,021,144 (+)	Ensembl
ChiLan1.0	NW_004955523	1,010,976 - 1,021,048 (+)	NCBI	ChiLan1.0	ChiLan1.0

NPC2
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	15	75,563,794 - 75,577,953 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	14	74,780,300 - 74,794,459 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	14	55,033,129 - 55,046,564 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	14	73,875,856 - 73,894,628 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	14	73,875,889 - 73,894,628 (-)	Ensembl			panPan2	panpan1.1

NPC2
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	8	47,641,185 - 47,650,543 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	8	47,628,077 - 47,650,576 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	8	47,325,075 - 47,334,437 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	8	47,868,101 - 47,877,468 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	8	47,866,650 - 47,877,427 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	8	47,539,316 - 47,548,676 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	8	47,560,539 - 47,569,881 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	8	47,958,527 - 47,967,885 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Npc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024408640	28,392,518 - 28,404,797 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936488	3,663,655 - 3,676,505 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936488	3,664,171 - 3,676,438 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

NPC2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	7	97,730,516 - 97,740,331 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	7	97,730,532 - 97,740,087 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	103,573,100 - 103,582,358 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

NPC2
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	24	51,685,699 - 51,700,557 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	24	51,685,609 - 51,700,557 (-)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666053	39,920,625 - 39,935,553 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Npc2
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624734	27,166,880 - 27,177,229 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624734	27,166,867 - 27,177,229 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Npc2
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	7	98,860,259 - 98,881,423 (-)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Npc2
121 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	321
Count of miRNA genes:	197
Interacting mature miRNAs:	223
Transcripts:	ENSRNOT00000016076
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
4145119	Mcs25	Mammary carcinoma susceptibility QTL 25		0.0001	mammary gland integrity trait (VT:0010552)	ratio of deaths to total study population during a period of time (CMO:0001023)	6	71278722	116278722	Rat
2293088	Iddm28	Insulin dependent diabetes mellitus QTL 28	5.21		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	6	68767270	135411972	Rat
1331799	Bp211	Blood pressure QTL 211	3.66407		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	6	88019181	136741135	Rat
1581563	Uae33	Urinary albumin excretion QTL 33			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	93560258	136550638	Rat
10054138	Gmadr3	Adrenal mass QTL 3	3.68	0.00045	adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	6	90871046	135871046	Rat
1641917	Colcr5	Colorectal carcinoma resistance QTL 5	3.18	0.0009	intestine integrity trait (VT:0010554)	benign colorectal tumor number (CMO:0001795)	6	98944780	143944780	Rat
61414	Pia3	Pristane induced arthritis QTL 3	4.5		joint integrity trait (VT:0010548)	post-insult time to onset of experimental arthritis (CMO:0001450)	6	100704576	136029228	Rat
724524	Uae2	Urinary albumin excretion QTL 2	2.7	0.0005	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	79198463	144254945	Rat
1358355	Srcrt4	Stress Responsive Cort QTL 4	6.39		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	6	106095977	147156653	Rat
737827	Hcar11	Hepatocarcinoma resistance QTL 11	4.4		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	6	46050607	116278722	Rat
2303624	Vencon5	Ventilatory control QTL 5	4.45		respiration trait (VT:0001943)	minute ventilation (CMO:0000132)	6	93778632	138778632	Rat
1576309	Emca7	Estrogen-induced mammary cancer QTL 7	4		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	20859430	113082285	Rat
61329	Eae9	Experimental allergic encephalomyelitis QTL 9	3.7		body mass (VT:0001259)	change in body weight (CMO:0002045)	6	84490437	129490437	Rat
10054123	Srcrt6	Stress Responsive Cort QTL 6	2.5	0.0043	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	6	90871046	135871046	Rat
724536	Uae7	Urinary albumin excretion QTL 7	3.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	6	93560258	136550638	Rat
2313399	Anxrr28	Anxiety related response QTL 28			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	6	101593607	138161926	Rat
1576302	Schws4	Schwannoma susceptibility QTL 4		0.0078	nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	6	78204640	123204640	Rat
1581550	Pur8	Proteinuria QTL 8			urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	6	93560258	136550638	Rat
1300075	Glom7	Glomerulus QTL 7	5.6	0.0000002	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)	6	76937178	121937178	Rat
1331725	Bp212	Blood pressure QTL 212	3.52475		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	6	99437079	125323237	Rat
1331789	Rf37	Renal function QTL 37	3.224		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	6	86494122	112380234	Rat
12801471	Schws9	Schwannoma susceptibility QTL 9			nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	6	101593607	146593607	Rat
1331722	Thshl1	Thyroid stimulating hormone level QTL 1	11.7	0.0001	blood thyroid-stimulating hormone amount (VT:0005119)	serum thyroid stimulating hormone level (CMO:0001248)	6	99708426	112483760	Rat

Markers in Region

RH128345

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	104,397,491 - 104,397,693 (+)	MAPPER	mRatBN7.2
Rnor_6.0	6	108,467,663 - 108,467,864	NCBI	Rnor6.0
Rnor_5.0	6	117,081,326 - 117,081,527	UniSTS	Rnor5.0
RGSC_v3.4	6	108,794,101 - 108,794,302	UniSTS	RGSC3.4
Celera	6	102,222,368 - 102,222,569	UniSTS
RH 3.4 Map	6	780.5	UniSTS
Cytogenetic Map	6	q31	UniSTS

RH143366

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	104,418,809 - 104,419,046 (+)	MAPPER	mRatBN7.2
mRatBN7.2	14	67,719,188 - 67,719,310 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	72,259,518 - 72,259,639	NCBI	Rnor6.0
Rnor_6.0	6	108,488,979 - 108,489,215	NCBI	Rnor6.0
Rnor_5.0	14	72,287,979 - 72,288,100	UniSTS	Rnor5.0
Rnor_5.0	6	117,059,975 - 117,060,211	UniSTS	Rnor5.0
RGSC_v3.4	6	108,815,417 - 108,815,653	UniSTS	RGSC3.4
RGSC_v3.4	14	72,887,023 - 72,887,144	UniSTS	RGSC3.4
Celera	14	66,671,454 - 66,671,575	UniSTS
Celera	6	102,243,684 - 102,243,920	UniSTS
RH 3.4 Map	14	486.07	UniSTS
Cytogenetic Map	14	q21	UniSTS
Cytogenetic Map	6	q31	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
16	12	67	165	91	90	59	92	59	6	356	192	11	144	81	92	31	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_173118	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC113727	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AJ515237	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC058132	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473982	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ214040	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ216545	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ219301	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ219367	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ219863	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ220225	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ220524	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ220660	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ220919	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ228456	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ229422	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ229782	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ229783	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ230107	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000006	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000016076 ⟹ ENSRNOP00000016076

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	6	110,128,325 - 110,150,004 (-)	Ensembl
mRatBN7.2 Ensembl	6	104,378,644 - 104,418,155 (-)	Ensembl
Rnor_6.0 Ensembl	6	108,467,410 - 108,488,330 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000117875 ⟹ ENSRNOP00000093242

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	6	110,128,325 - 110,139,552 (-)	Ensembl
mRatBN7.2 Ensembl	6	104,397,393 - 104,418,141 (-)	Ensembl

RefSeq Acc Id:

NM_173118 ⟹ NP_775141

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	6	110,128,325 - 110,149,245 (-)	NCBI
mRatBN7.2	6	104,397,239 - 104,418,161 (-)	NCBI
Rnor_6.0	6	108,467,410 - 108,488,330 (-)	NCBI
Rnor_5.0	6	117,060,860 - 117,081,780 (+)	NCBI
RGSC_v3.4	6	108,793,935 - 108,814,703 (-)	RGD
Celera	6	102,222,115 - 102,243,035 (-)	NCBI

Sequence:

show sequence

ACAAGTGGCCTGACCTGGCTCCACCCTCGGTCTGCCGGGACAAGTTTATCTTGTGACTGTCGGG
CTGCTTTCCCTTCCTAGATTGCACAGCGTTCATGCCCAGGATGAGCTTCCTGACCCCCACGATC
CTGCTGCTGGCGCTGGTCGCCGCCACCCAGGCCGAGCCCCTGCACTTCAAGGACTGCGGCTCTA
AGGTGGGCGTTATAAAGGAAGTGAATGTGAGCCCGTGCCCTACCCAGCCCTGTCAGCTACACAA
AGGCCAGTCCTACAGTGTCAACGTCACCTTTACTAGCGGCACTCAGTCCCAGAACAGCACGGCC
TTGGTCCACGGCATCTTGGCAGGGGTCCCAGTCTACTTCCCTATTCCTGAGCCTGACGGTTGTA
AATGTGGAATCAACTGCCCCATCCAGAAAGACAAGGTCTACAGCTACCTGAATAAGCTGCCGGT
GAAGAGCGAATATCCCTCTCTAAAACTGGTGGTGGAATGGAAACTTCAAGATGACAAAAAGGAT
AACCTCTTCTGCTGGGAGATCCCAGTAGAGATCAAAGGCTAGGCTGCTTGGTGCCCTGTGTCTG
TGCAGGGTGAGAGGCCATGGGCGGAGGGAGGGGAAGGAAGAGAAATCAGACCTGAAATTGAGTC
GGTGCCATAAGACGAACAGAACTTCAAGAATGCTGTTTTATGCCTTTCAGCCTCCAAAAACATA
CCTGCAGCCCTACTACTCTTGAGAGCCAGAGCCATGGCCCCCTGAGATAGCCTTTGTGGAGGCT
TCGGGAGGGAAAGGGGAGACTGGAGAGATTAGATTAGTGTCCATGGCTGTTTGCTGTTGGATTA
CGTCGGCAGGTCCAGGCAAGATGAGGCAGGGATGCTTGAGGATGTCAGATAACCTGTCAATCCA
CTGTGAAGGATGGCTTCCCAGAATCTTCTGGCTGGCCGGGAGTATTACCTCTTCTGTATCTAAG
TGCCTCCTGAGTCCCAAGCACCCTGCTTATCGATCCGATGAGTCTCCATGGTAGCCTCTGCCCA
ACGCTTCAACAGCAGTGACTAACTCTCCATGGTCCAGAGACGGCCTGAGGGAAGGTCTGCGCAG
AAACTTAGCTCTGACTGGCTGCTGCTTTGCGGTTAGCTCTTGTTCTTTGGTAGTTTTCATTAAA
GCCAATACTTGGTTGCAGGTGCTTGGTTTTGTTTTTTAACAGTATTAGTCTGTATCCTCTCTCC
GCACGTGAGATGGAGCCTCCCCATAAATTCTAACTTGCCA

hide sequence

Protein Sequences


Protein RefSeqs	NP_775141	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH58132	(Get FASTA)	NCBI Sequence Viewer
	CAD56199	(Get FASTA)	NCBI Sequence Viewer
	EDL81526	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000016076
	ENSRNOP00000016076.4
	ENSRNOP00000093242.1

RefSeq Acc Id:	NP_775141 ⟸ NM_173118
- Peptide Label:	precursor
- UniProtKB:	F7FJQ3 (UniProtKB/TrEMBL), A6JDY2 (UniProtKB/TrEMBL), Q8CHN5 (UniProtKB/TrEMBL)
- Sequence:	show sequence MPRMSFLTPTILLLALVAATQAEPLHFKDCGSKVGVIKEVNVSPCPTQPCQLHKGQSYSVNVTF TSGTQSQNSTALVHGILAGVPVYFPIPEPDGCKCGINCPIQKDKVYSYLNKLPVKSEYPSLKLV VEWKLQDDKKDNLFCWEIPVEIKG hide sequence

Ensembl Acc Id:

ENSRNOP00000016076 ⟸ ENSRNOT00000016076

Ensembl Acc Id:

ENSRNOP00000093242 ⟸ ENSRNOT00000117875

Protein Domains

MD-2-related lipid-recognition

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-F7FJQ3-F1-model_v2	AlphaFold	F7FJQ3	1-152	view protein structure

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13694730

Promoter ID:

EPDNEW_R5254

Type:

initiation region

Name:

Npc2_1

Description:

NPC intracellular cholesterol transporter 2

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	6	108,488,253 - 108,488,313	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:628756	AgrOrtholog
BioCyc Gene	G2FUF-36808	BioCyc
Ensembl Genes	ENSRNOG00000012062	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000016076	ENTREZGENE
	ENSRNOT00000016076.7	UniProtKB/TrEMBL
	ENSRNOT00000117875.2	UniProtKB/TrEMBL
Gene3D-CATH	2.60.40.770	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:6920130	IMAGE-MGC_LOAD
InterPro	Ig_E-set	UniProtKB/TrEMBL
	MD-2_lipid-recog	UniProtKB/TrEMBL
	ML_Npc2-like	UniProtKB/TrEMBL
	NPC2-like	UniProtKB/TrEMBL
KEGG Report	rno:286898	UniProtKB/TrEMBL
MGC_CLONE	MGC:72659	IMAGE-MGC_LOAD
NCBI Gene	286898	ENTREZGENE
PANTHER	NPC INTRACELLULAR CHOLESTEROL TRANSPORTER 2	UniProtKB/TrEMBL
	PTHR11306	UniProtKB/TrEMBL
Pfam	E1_DerP2_DerF2	UniProtKB/TrEMBL
PhenoGen	Npc2	PhenoGen
RatGTEx	ENSRNOG00000012062	RatGTEx
SMART	SM00737	UniProtKB/TrEMBL
Superfamily-SCOP	Ig_E-set	UniProtKB/TrEMBL
UniProt	A0A8I6AWS0_RAT	UniProtKB/TrEMBL
	A6JDY2	ENTREZGENE, UniProtKB/TrEMBL
	F7FJQ3	ENTREZGENE, UniProtKB/TrEMBL
	Q8CHN5	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-05-12	Npc2	NPC intracellular cholesterol transporter 2	Npc2	Niemann-Pick disease, type C2	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-08-29	Npc2	Niemann-Pick disease, type C2	Npc2	Niemann Pick type C2	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-01-20	Npc2	Niemann Pick type C2	re1	epididymal secretory protein 1	Symbol and Name updated	1299863	APPROVED
2003-02-27	re1	epididymal secretory protein 1			Symbol and Name status set to provisional	70820	PROVISIONAL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Disease Annotations - MGI

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