Npc2 (NPC intracellular cholesterol transporter 2) - Rat Genome Database

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Gene: Npc2 (NPC intracellular cholesterol transporter 2) Rattus norvegicus
Analyze
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 be located in extracellular space and 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; acrylamide.
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
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26104,397,239 - 104,418,161 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl6104,378,644 - 104,418,155 (-)Ensembl
Rnor_6.06108,467,410 - 108,488,330 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6108,467,410 - 108,488,330 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06117,060,860 - 117,081,780 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46108,793,935 - 108,814,703 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16108,797,391 - 108,818,159 (-)NCBI
Celera6102,222,115 - 102,243,035 (-)NCBICelera
Cytogenetic Map6q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
4,4'-sulfonyldiphenol  (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)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,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)
dorsomorphin  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
fenvalerate  (EXP)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
genistein  (ISO)
gentamycin  (EXP)
isoflavones  (ISO)
ivermectin  (ISO)
methapyrilene  (EXP)
methyl methanesulfonate  (ISO)
metronidazole  (EXP)
miconazole  (ISO)
neomycin  (EXP)
nimesulide  (EXP)
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)
trimellitic anhydride  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vancomycin  (EXP)
vinclozolin  (EXP)
Yessotoxin  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26104,397,239 - 104,418,161 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl6104,378,644 - 104,418,155 (-)Ensembl
Rnor_6.06108,467,410 - 108,488,330 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6108,467,410 - 108,488,330 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06117,060,860 - 117,081,780 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46108,793,935 - 108,814,703 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16108,797,391 - 108,818,159 (-)NCBI
Celera6102,222,115 - 102,243,035 (-)NCBICelera
Cytogenetic Map6q31NCBI
NPC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381474,479,935 - 74,493,512 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1474,476,192 - 74,494,177 (-)EnsemblGRCh38hg38GRCh38
GRCh371474,946,638 - 74,960,215 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361474,016,396 - 74,029,837 (-)NCBINCBI36hg18NCBI36
Build 341474,016,396 - 74,029,837NCBI
Celera1454,985,030 - 54,998,469 (-)NCBI
Cytogenetic Map14q24.3NCBI
HuRef1455,115,095 - 55,128,528 (-)NCBIHuRef
CHM1_11474,886,183 - 74,899,622 (-)NCBICHM1_1
T2T-CHM13v2.01468,688,905 - 68,702,483 (-)NCBI
Npc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391284,801,333 - 84,819,886 (-)NCBIGRCm39mm39
GRCm39 Ensembl1284,801,336 - 84,819,926 (-)Ensembl
GRCm381284,754,559 - 84,773,112 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1284,754,562 - 84,773,152 (-)EnsemblGRCm38mm10GRCm38
MGSCv371286,095,509 - 86,114,062 (-)NCBIGRCm37mm9NCBIm37
MGSCv361285,644,307 - 85,662,860 (-)NCBImm8
Celera1286,210,583 - 86,229,366 (-)NCBICelera
Cytogenetic Map12D1NCBI
Npc2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555231,010,976 - 1,021,144 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555231,010,976 - 1,021,048 (+)NCBIChiLan1.0ChiLan1.0
NPC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11473,875,856 - 73,894,628 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1473,875,889 - 73,894,628 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01455,033,129 - 55,046,564 (-)NCBIMhudiblu_PPA_v0panPan3
NPC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1847,641,185 - 47,650,543 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl847,628,077 - 47,650,576 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha847,325,075 - 47,334,437 (-)NCBI
ROS_Cfam_1.0847,868,101 - 47,877,468 (-)NCBI
ROS_Cfam_1.0 Ensembl847,866,650 - 47,877,427 (-)Ensembl
UMICH_Zoey_3.1847,539,316 - 47,548,676 (-)NCBI
UNSW_CanFamBas_1.0847,560,539 - 47,569,881 (-)NCBI
UU_Cfam_GSD_1.0847,958,527 - 47,967,885 (-)NCBI
Npc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864028,392,518 - 28,404,797 (+)NCBI
SpeTri2.0NW_0049364883,664,171 - 3,676,438 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NPC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl797,730,516 - 97,740,331 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1797,730,532 - 97,740,087 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.27103,573,100 - 103,582,358 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NPC2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12451,685,699 - 51,700,557 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2451,685,609 - 51,700,557 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605339,920,625 - 39,935,553 (-)NCBIVero_WHO_p1.0
Npc2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473427,166,880 - 27,177,229 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462473427,166,867 - 27,177,229 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
RH128345  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26104,397,491 - 104,397,693 (+)MAPPERmRatBN7.2
Rnor_6.06108,467,663 - 108,467,864NCBIRnor6.0
Rnor_5.06117,081,326 - 117,081,527UniSTSRnor5.0
RGSC_v3.46108,794,101 - 108,794,302UniSTSRGSC3.4
Celera6102,222,368 - 102,222,569UniSTS
RH 3.4 Map6780.5UniSTS
Cytogenetic Map6q31UniSTS
RH143366  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26104,418,809 - 104,419,046 (+)MAPPERmRatBN7.2
mRatBN7.21467,719,188 - 67,719,310 (+)MAPPERmRatBN7.2
Rnor_6.01472,259,518 - 72,259,639NCBIRnor6.0
Rnor_6.06108,488,979 - 108,489,215NCBIRnor6.0
Rnor_5.01472,287,979 - 72,288,100UniSTSRnor5.0
Rnor_5.06117,059,975 - 117,060,211UniSTSRnor5.0
RGSC_v3.46108,815,417 - 108,815,653UniSTSRGSC3.4
RGSC_v3.41472,887,023 - 72,887,144UniSTSRGSC3.4
Celera1466,671,454 - 66,671,575UniSTS
Celera6102,243,684 - 102,243,920UniSTS
RH 3.4 Map14486.07UniSTS
Cytogenetic Map14q21UniSTS
Cytogenetic Map6q31UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)661747639106747639Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)667262953112262953Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)671201409116201409Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)672202632115200186Rat
70196BpQTLcluster7Blood pressure QTL cluster 76.82arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)672202632117202632Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)672202632130729475Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)672202632130919985Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)672227641130729205Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)672227641130729205Rat
724524Uae2Urinary albumin excretion QTL 22.70.0005urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)673463459109394713Rat
737827Hcar11Hepatocarcinoma resistance QTL 114.4liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)682523650110548006Rat
1576302Schws4Schwannoma susceptibility QTL 40.0078nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)683190345106747639Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)684130881129130881Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)685140138130140138Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)685140138130140138Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)685311061133478515Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)686894788131894788Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (CMO:0000132)688047916133047916Rat
1331722Thshl1Thyroid stimulating hormone level QTL 111.70.0001blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)689762877106752806Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)693701310128713626Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)694968928137848904Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)694968928139968928Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)696833997140994061Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6100364669140994061Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6100671796132340886Rat
1331797Bp213Blood pressure QTL 2133.291arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)6104085867128713626Rat

miRNA Target Status

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.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 1
Medium 3 43 57 41 19 41 8 11 74 35 41 10 8
Low
Below cutoff

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
  JACYVU010000166 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000016076   ⟹   ENSRNOP00000016076
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6104,378,644 - 104,418,155 (-)Ensembl
Rnor_6.0 Ensembl6108,467,410 - 108,488,330 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000117875   ⟹   ENSRNOP00000093242
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6104,397,393 - 104,418,141 (-)Ensembl
RefSeq Acc Id: NM_173118   ⟹   NP_775141
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26104,397,239 - 104,418,161 (-)NCBI
Rnor_6.06108,467,410 - 108,488,330 (-)NCBI
Rnor_5.06117,060,860 - 117,081,780 (+)NCBI
RGSC_v3.46108,793,935 - 108,814,703 (-)RGD
Celera6102,222,115 - 102,243,035 (-)NCBI
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  
Reference Sequences
RefSeq Acc Id: NP_775141   ⟸   NM_173118
- Peptide Label: precursor
- UniProtKB: F7FJQ3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000016076   ⟸   ENSRNOT00000016076
RefSeq Acc Id: ENSRNOP00000093242   ⟸   ENSRNOT00000117875
Protein Domains
ML

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 AssemblyChrPosition (strand)Source
Rnor_6.06108,488,253 - 108,488,313EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:628756 AgrOrtholog
BioCyc Gene G2FUF-36808 BioCyc
Ensembl Genes ENSRNOG00000012062 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000016076 ENTREZGENE
  ENSRNOP00000016076.3 UniProtKB/TrEMBL
  ENSRNOP00000093242.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016076 ENTREZGENE
  ENSRNOT00000016076.6 UniProtKB/TrEMBL
  ENSRNOT00000117875.1 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 PTHR11306 UniProtKB/TrEMBL
Pfam E1_DerP2_DerF2 UniProtKB/TrEMBL
PhenoGen Npc2 PhenoGen
SMART SM00737 UniProtKB/TrEMBL
Superfamily-SCOP Ig_E-set UniProtKB/TrEMBL
UniProt A0A8I6AWS0_RAT UniProtKB/TrEMBL
  F7FJQ3 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