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

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Gene: Npc1l1 (NPC1 like intracellular cholesterol transporter 1) Rattus norvegicus
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Symbol: Npc1l1
Name: NPC1 like intracellular cholesterol transporter 1
RGD ID: 1303135
Description: Enables heterocyclic compound binding activity. Involved in several processes, including cholesterol import; response to muscle activity; and vitamin transport. Located in apical plasma membrane and brush border membrane. Orthologous to human NPC1L1 (NPC1 like intracellular cholesterol transporter 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; endosulfan; furan.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: niemann-Pick C1-like protein 1; Niemann-Pick disease, type C1-like 1; NPC1 (Niemann-Pick disease, type C1, gene)-like 1; NPC1-like 1; NPC1-like intracellular cholesterol transporter 1; SLC66A2; solute carrier family 66 member 2
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
mRatBN7.21481,071,448 - 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_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01486,712,619 - 86,732,332 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01483,161,944 - 83,181,659 (-)NCBIRnor_WKY
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
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

References

References - curated
# Reference Title Reference Citation
1. Niemann-Pick C1 Like 1 protein is critical for intestinal cholesterol absorption. Altmann SW, etal., Science 2004 Feb 20;303(5661):1201-4.
2. An atherogenic diet decreases liver FXR gene expression and causes severe hepatic steatosis and hepatic cholesterol accumulation: effect of endurance training. Côté I, etal., Eur J Nutr. 2013 Aug;52(5):1523-32. doi: 10.1007/s00394-012-0459-5. Epub 2012 Nov 2.
3. 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.
4. 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.
5. The target of ezetimibe is Niemann-Pick C1-Like 1 (NPC1L1). Garcia-Calvo M, etal., Proc Natl Acad Sci U S A. 2005 Jun 7;102(23):8132-7. Epub 2005 May 31.
6. 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.
7. In vivo responsiveness to ezetimibe correlates with niemann-pick C1 like-1 (NPC1L1) binding affinity: Comparison of multiple species NPC1L1 orthologs. Hawes BE, etal., Mol Pharmacol. 2007 Jan;71(1):19-29. Epub 2006 Sep 27.
8. The genomic sequence and comparative analysis of the rat major histocompatibility complex. Hurt P, etal., Genome Res 2004 Apr;14(4):631-9.
9. Characterization of the putative native and recombinant rat sterol transporter Niemann-Pick C1 Like 1 (NPC1L1) protein. Iyer SP, etal., Biochim Biophys Acta. 2005 Apr 15;1722(3):282-92.
10. The different effect of pioglitazone as compared to insulin on expression of hepatic and intestinal genes regulating post-prandial lipoproteins in diabetes. Lally S, etal., Atherosclerosis. 2006 Nov 14;.
11. The different effect of pioglitazone as compared to insulin on expression of hepatic and intestinal genes regulating post-prandial lipoproteins in diabetes. Lally S, etal., Atherosclerosis. 2007 Aug;193(2):343-51. Epub 2006 Nov 15.
12. 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.
13. Niemann-pick C1-like 1 mediates alpha-tocopherol transport. Narushima K, etal., Mol Pharmacol. 2008 Jul;74(1):42-9. doi: 10.1124/mol.107.043034. Epub 2008 Apr 10.
14. GOA pipeline RGD automated data pipeline
15. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
16. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
17. Niemann-Pick C1-like 1 overexpression facilitates ezetimibe-sensitive cholesterol and beta-sitosterol uptake in CaCo-2 cells. Yamanashi Y, etal., J Pharmacol Exp Ther. 2007 Feb;320(2):559-64. doi: 10.1124/jpet.106.114181. Epub 2006 Nov 29.
Additional References at PubMed
PMID:17140581   PMID:18523240   PMID:19325169   PMID:19542231   PMID:21187433   PMID:21631994   PMID:21844200   PMID:25696002   PMID:25716431  


Genomics

Comparative Map Data
Npc1l1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01486,712,619 - 86,732,332 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01483,161,944 - 83,181,659 (-)NCBIRnor_WKY
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
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38744,512,535 - 44,541,330 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 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
(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
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
PanPan1.1745,296,365 - 45,324,692 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl745,297,271 - 45,324,692 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0745,227,289 - 45,256,094 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
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 (-)EnsemblSpeTri2.0
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
71 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:41
Count of miRNA genes:40
Interacting mature miRNAs:40
Transcripts:ENSRNOT00000075827
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144226252995023211Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)145002321195023211Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1455147478100147478Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)146875779683368335Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1470053989104886043Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1470053989104886043Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)147341532392554092Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)147341532392554092Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532395876975Rat
631213Bw60Body weight QTL604.51retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)147995092195876975Rat


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 endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system appendage
High
Medium 2
Low 1 12
Below cutoff 16 16 6 16 1 1 22 15 5 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000075827   ⟹   ENSRNOP00000065524
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1481,071,451 - 81,091,113 (-)Ensembl
Rnor_6.0 Ensembl1486,345,953 - 86,560,694 (-)Ensembl
RefSeq Acc Id: NM_001002025   ⟹   NP_001002025
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21481,071,448 - 81,091,113 (-)NCBI
Rnor_6.01486,345,946 - 86,560,694 (-)NCBI
Rnor_5.01487,307,372 - 87,319,081 (-)NCBI
Rnor_5.01487,516,291 - 87,523,225 (-)NCBI
Celera1479,954,434 - 79,974,086 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001002025 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAR97888 (Get FASTA)   NCBI Sequence Viewer  
  EDM00336 (Get FASTA)   NCBI Sequence Viewer  
  Q6T3U3 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001002025   ⟸   NM_001002025
- Peptide Label: precursor
- UniProtKB: Q6T3U3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000065524   ⟸   ENSRNOT00000075827
Protein Domains
SSD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6T3U3-F1-model_v2 AlphaFold Q6T3U3 1-1331 view protein structure

Transcriptome

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

Promoters
RGD ID:13699473
Promoter ID:EPDNEW_R9997
Type:initiation region
Name:Npc1l1_1
Description:NPC1 like intracellular cholesterol transporter 1
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_6.01486,560,760 - 86,560,820EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303135 AgrOrtholog
BioCyc Gene G2FUF-15102 BioCyc
Ensembl Genes ENSRNOG00000049955 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000065524 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000075827 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro NPC1-like UniProtKB/Swiss-Prot
  NPC1_N UniProtKB/Swiss-Prot
  Ptc/Disp UniProtKB/Swiss-Prot
  SSD UniProtKB/Swiss-Prot
KEGG Report rno:432367 UniProtKB/Swiss-Prot
NCBI Gene 432367 ENTREZGENE
Pfam NPC1_N UniProtKB/Swiss-Prot
  Patched UniProtKB/Swiss-Prot
  Sterol-sensing UniProtKB/Swiss-Prot
PharmGKB NPC1L1 RGD
PhenoGen Npc1l1 PhenoGen
PROSITE SSD UniProtKB/Swiss-Prot
TIGRFAMs 2A060601 UniProtKB/Swiss-Prot
UniProt NPCL1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-12 Npc1l1  NPC1 like intracellular cholesterol transporter 1  Npc1l1  NPC1-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-11-21 Npc1l1  NPC1-like 1  Npc1l1  NPC1 (Niemann-Pick disease, type C1, gene)-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-02-14 Npc1l1  NPC1 (Niemann-Pick disease, type C1, gene)-like 1      Symbol and Name status set to provisional 70820 PROVISIONAL