Npc1l1 (NPC1 like intracellular cholesterol transporter 1) - Rat Genome Database

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Gene: Npc1l1 (NPC1 like intracellular cholesterol transporter 1) Mus musculus
Analyze
Symbol: Npc1l1
Name: NPC1 like intracellular cholesterol transporter 1
RGD ID: 1615659
MGI Page MGI
Description: Predicted to enable several functions, including cholesterol binding activity; myosin V binding activity; and protein homodimerization activity. Involved in cholesterol transport and intestinal cholesterol absorption. Acts upstream of or within cholesterol homeostasis. Predicted to be located in apical plasma membrane and brush border membrane. Predicted to be active in plasma membrane. Orthologous to human NPC1L1 (NPC1 like intracellular cholesterol transporter 1).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 9130221N23Rik; Gm243; Niemann-Pick C1-like protein 1; Niemann-Pick disease, type C1; Niemann-Pick disease, type C1-like 1; NPC1-like 1; NPC1-like intracellular cholesterol transporter 1; RP23-198N14.2
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39116,161,011 - 6,180,245 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl116,161,013 - 6,180,143 (-)EnsemblGRCm39 Ensembl
GRCm38116,211,011 - 6,230,245 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl116,211,013 - 6,230,143 (-)EnsemblGRCm38mm10GRCm38
MGSCv37116,111,014 - 6,130,248 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36116,111,461 - 6,130,126 (-)NCBIMGSCv36mm8
Celera116,693,602 - 6,712,842 (-)NCBICelera
Cytogenetic Map11A1NCBI
cM Map113.93NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Inactivation of NPC1L1 causes multiple lipid transport defects and protects against diet-induced hypercholesterolemia. Davies JP, etal., J Biol Chem. 2005 Apr 1;280(13):12710-20. Epub 2005 Jan 25.
2. Deficiency of Niemann-Pick C1 Like 1 prevents atherosclerosis in ApoE-/- mice. Davis HR Jr, etal., Arterioscler Thromb Vasc Biol. 2007 Apr;27(4):841-9. Epub 2007 Jan 11.
3. Genes that affect cholesterol synthesis, cholesterol absorption, and chylomicron assembly: the relationship between the liver and intestine in control and streptozotosin diabetic rats. Lally S, etal., Metabolism. 2007 Mar;56(3):430-8.
4. Mouse MP Annotation Import Pipeline RGD automated import 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
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:14976318   PMID:15173162   PMID:15544574   PMID:15604518   PMID:16141072   PMID:16141073  
PMID:16179600   PMID:16192643   PMID:16407187   PMID:16414355   PMID:17216601   PMID:17442616   PMID:17689140   PMID:18187667   PMID:18356535   PMID:18718999   PMID:18796403   PMID:18799693  
PMID:19141868   PMID:20601625   PMID:20699423   PMID:21071508   PMID:21187433   PMID:21507342   PMID:21602275   PMID:21683156   PMID:21844200   PMID:21873635   PMID:21929836   PMID:22231557  
PMID:23139223   PMID:24336247   PMID:24904062   PMID:25660144   PMID:25696002   PMID:25716431   PMID:25881076   PMID:28627641   PMID:29880681   PMID:29980051   PMID:31064810   PMID:31432115  
PMID:32410728   PMID:32872588   PMID:33760662   PMID:34465831   PMID:34943976   PMID:37833289  


Genomics

Comparative Map Data
Npc1l1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39116,161,011 - 6,180,245 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl116,161,013 - 6,180,143 (-)EnsemblGRCm39 Ensembl
GRCm38116,211,011 - 6,230,245 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl116,211,013 - 6,230,143 (-)EnsemblGRCm38mm10GRCm38
MGSCv37116,111,014 - 6,130,248 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36116,111,461 - 6,130,126 (-)NCBIMGSCv36mm8
Celera116,693,602 - 6,712,842 (-)NCBICelera
Cytogenetic Map11A1NCBI
cM Map113.93NCBI
NPC1L1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38744,512,535 - 44,541,330 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl744,512,535 - 44,541,330 (-)EnsemblGRCh38hg38GRCh38
GRCh37744,552,134 - 44,580,929 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36744,518,659 - 44,547,439 (-)NCBINCBI36Build 36hg18NCBI36
Build 34744,325,376 - 44,354,154NCBI
Celera744,651,139 - 44,679,899 (-)NCBICelera
Cytogenetic Map7p13NCBI
HuRef744,436,243 - 44,465,023 (-)NCBIHuRef
CHM1_1744,556,489 - 44,585,261 (-)NCBICHM1_1
T2T-CHM13v2.0744,672,255 - 44,701,030 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2744,591,658 - 44,620,428 (-)NCBI
Npc1l1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81485,285,387 - 85,305,050 (-)NCBIGRCr8
mRatBN7.21481,071,448 - 81,091,113 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1481,071,451 - 81,091,113 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1485,472,534 - 85,492,247 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01486,712,619 - 86,732,332 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01483,161,944 - 83,181,659 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01486,345,946 - 86,560,694 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1486,345,953 - 86,560,694 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01487,307,372 - 87,319,081 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01487,516,291 - 87,523,225 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1479,954,434 - 79,974,086 (-)NCBICelera
Cytogenetic Map14q21NCBI
Npc1l1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554567,528,423 - 7,547,720 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554567,528,452 - 7,547,714 (+)NCBIChiLan1.0ChiLan1.0
NPC1L1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2649,424,993 - 49,453,745 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1797,749,732 - 97,778,483 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0745,227,289 - 45,256,094 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1745,296,365 - 45,324,692 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl745,297,271 - 45,324,692 (-)Ensemblpanpan1.1panPan2
NPC1L1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha162,311,494 - 2,327,591 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01614,518,743 - 14,550,434 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1614,534,022 - 14,550,425 (+)EnsemblROS_Cfam_1.0 Ensembl
UNSW_CanFamBas_1.01614,165,465 - 14,181,751 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01614,146,247 - 14,162,328 (+)NCBIUU_Cfam_GSD_1.0
Npc1l1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118100,222,063 - 100,240,594 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647819,434,557 - 19,452,248 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647819,434,557 - 19,452,245 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NPC1L1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1850,726,922 - 50,757,649 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11850,726,854 - 50,757,676 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21855,630,239 - 55,657,272 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NPC1L1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12114,129,413 - 14,163,916 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2114,130,767 - 14,163,907 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660628,377,157 - 8,405,655 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Npc1l1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247407,590,046 - 7,609,420 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247407,590,041 - 7,609,574 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Npc1l1
598 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:136
Count of miRNA genes:128
Interacting mature miRNAs:132
Transcripts:ENSMUST00000004505
Prediction methods:Miranda, Rnahybrid
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357722Vtbt11_mvertebral trabecular bone trait 11 (mouse)Not determined11123880487Mouse
1300768Tshp9_mtooth shape 9 (mouse)Not determined11125976374Mouse
1301765Skull15_mskull morphology 15 (mouse)Not determined11125976374Mouse
1300661Lmr6_mleishmaniasis resistance 6 (mouse)Not determined11125976374Mouse
10044008Hbnr15_mHeligmosomoides bakeri nematode resistance 15 (mouse)Not determined1122705234227232Mouse
1300599Cocrb11_mcocaine related behavior 11 (mouse)Not determined11267035536671472Mouse
27095914Pglq16_mpelvic girdle length QTL 16, 16 week (mouse)11325000018150000Mouse
27095919Pglq10_mpelvic girdle length QTL 10, 10 week (mouse)11325000018450000Mouse
27095925Pglq5_mpelvic girdle length QTL 5, 5 week (mouse)11325000019750000Mouse
27095904Scvln12_msacral vertebrae length 2, 10 week (mouse)11325000034495048Mouse
27095909Scvln6_msacral vertebrae length 2, 5 week (mouse)11325000044090827Mouse
27226798Scvln18_msacral vertebrae length 2, 16 week (mouse)11325000060690826Mouse
26884446Sklq10_mskull length QTL 10, 10 week (mouse)11325000062890826Mouse
26884453Sklq16_mskull length QTL 16, 16 week (mouse)11325000072690826Mouse
13208559Wght10_mweight 10 (mouse)11395000088890826Mouse
13208558Lgth12_mbody length 12 (mouse)11395000094890826Mouse
10053676Eae44a_mexperimental allergic encephalomyelitis susceptibility 44a (mouse)Not determined11450789621379532Mouse
27226741Metcl5_mmetatarsal-calcaneal length 5, 5 week (mouse)11465000046290827Mouse
27226735Metcl16_mmetatarsal-calcaneal length 16, 16 week (mouse)11525000035090827Mouse


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000004505   ⟹   ENSMUSP00000004505
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl116,161,013 - 6,180,143 (-)Ensembl
GRCm38.p6 Ensembl116,211,013 - 6,230,143 (-)Ensembl
RefSeq Acc Id: NM_207242   ⟹   NP_997125
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39116,161,011 - 6,180,245 (-)NCBI
GRCm38116,211,011 - 6,230,245 (-)ENTREZGENE
MGSCv37116,111,014 - 6,130,248 (-)RGD
Celera116,693,602 - 6,712,842 (-)RGD
cM Map11 ENTREZGENE
Sequence:
RefSeq Acc Id: XR_004936946
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39116,167,818 - 6,180,237 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_997125 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI31789 (Get FASTA)   NCBI Sequence Viewer  
  AAI31790 (Get FASTA)   NCBI Sequence Viewer  
  AAR97887 (Get FASTA)   NCBI Sequence Viewer  
  EDL40576 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000004505
  ENSMUSP00000004505.3
GenBank Protein Q6T3U4 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_997125   ⟸   NM_207242
- Peptide Label: precursor
- UniProtKB: Q6T3U4 (UniProtKB/Swiss-Prot),   Q5SVX1 (UniProtKB/Swiss-Prot),   Z4YJC9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000004505   ⟸   ENSMUST00000004505
Protein Domains
SSD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6T3U4-F1-model_v2 AlphaFold Q6T3U4 1-1333 view protein structure

Promoters
RGD ID:8673888
Promoter ID:EPDNEW_M14974
Type:initiation region
Name:Npc1l1_1
Description:Mus musculus NPC1 like intracellular cholesterol transporter1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38116,230,184 - 6,230,244EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2685089 AgrOrtholog
Ensembl Genes ENSMUSG00000020447 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000004505 ENTREZGENE
  ENSMUST00000004505.3 UniProtKB/TrEMBL
Gene3D-CATH Multidrug efflux transporter AcrB transmembrane domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro NPC1-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NPC1_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ptc/Disp UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:237636 UniProtKB/TrEMBL
MGD MGI:2685089 ENTREZGENE
NCBI Gene 237636 ENTREZGENE
PANTHER NPC INTRACELLULAR CHOLESTEROL TRANSPORTER 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NPC1-LIKE INTRACELLULAR CHOLESTEROL TRANSPORTER 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam NPC1_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Patched UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sterol-sensing UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB NPC1L1 RGD
PhenoGen Npc1l1 PhenoGen
PROSITE SSD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Multidrug efflux transporter AcrB transmembrane domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A2RRR0_MOUSE UniProtKB/TrEMBL
  A3KMG9_MOUSE UniProtKB/TrEMBL
  NPCL1_MOUSE UniProtKB/Swiss-Prot
  Q5SVX1 ENTREZGENE
  Q6T3U4 ENTREZGENE
  Z4YJC9 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary Q5SVX1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-09-05 Npc1l1  NPC1 like intracellular cholesterol transporter 1    NPC1-like 1  Symbol and/or name change 5135510 APPROVED