NPC2 (NPC intracellular cholesterol transporter 2) - Rat Genome Database

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Gene: NPC2 (NPC intracellular cholesterol transporter 2) Canis lupus familiaris
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Symbol: NPC2
Name: NPC intracellular cholesterol transporter 2
RGD ID: 12277643
Description: ENCODES a protein that exhibits cholesterol binding (ortholog); cholesterol transfer activity (ortholog); enzyme binding (ortholog); INVOLVED IN cholesterol efflux (ortholog); cholesterol homeostasis (ortholog); cholesterol storage (ortholog); ASSOCIATED WITH Developmental Disabilities (ortholog); genetic disease (ortholog); intellectual disability (ortholog); FOUND IN extracellular space (ortholog); lysosome (ortholog)
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: CE1; epididymal secretory protein E1; niemann Pick type C2 protein homolog
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0847,868,101 - 47,877,468 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl847,866,650 - 47,877,427 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1847,539,316 - 47,548,676 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0847,560,539 - 47,569,881 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0847,958,527 - 47,967,885 (-)NCBIUU_Cfam_GSD_1.0
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
Additional References at PubMed
PMID:7744511   PMID:7744512   PMID:22301074   PMID:26995145   PMID:30032202  


Genomics

Comparative Map Data
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0847,868,101 - 47,877,468 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl847,866,650 - 47,877,427 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1847,539,316 - 47,548,676 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0847,560,539 - 47,569,881 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0847,958,527 - 47,967,885 (-)NCBIUU_Cfam_GSD_1.0
NPC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381474,479,935 - 74,493,512 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1474,476,192 - 74,494,177 (-)EnsemblGRCh38hg38GRCh38
GRCh371474,946,638 - 74,960,215 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361474,016,396 - 74,029,837 (-)NCBINCBI36Build 36hg18NCBI36
Build 341474,016,396 - 74,029,837NCBI
Celera1454,985,030 - 54,998,469 (-)NCBICelera
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 (-)NCBIT2T-CHM13v2.0
Npc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391284,801,333 - 84,819,886 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1284,801,336 - 84,819,926 (-)EnsemblGRCm39 Ensembl
GRCm381284,754,559 - 84,773,112 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1284,754,562 - 84,773,152 (-)EnsemblGRCm38mm10GRCm38
MGSCv371286,095,509 - 86,114,062 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361285,644,307 - 85,662,860 (-)NCBIMGSCv36mm8
Celera1286,210,583 - 86,229,366 (-)NCBICelera
Cytogenetic Map12D1NCBI
cM Map1239.37NCBI
Npc2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr86110,128,325 - 110,149,245 (-)NCBIGRCr8
mRatBN7.26104,397,239 - 104,418,161 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6104,378,644 - 104,418,155 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx6104,566,714 - 104,587,594 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.06104,865,873 - 104,886,753 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.06104,235,225 - 104,256,103 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.16108,797,391 - 108,818,159 (-)NCBI
Celera6102,222,115 - 102,243,035 (-)NCBICelera
Cytogenetic Map6q31NCBI
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
NHGRI_mPanPan1-v21575,563,794 - 75,577,953 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11474,780,300 - 74,794,459 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01455,033,129 - 55,046,564 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11473,875,856 - 73,894,628 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1473,875,889 - 73,894,628 (-)Ensemblpanpan1.1panPan2
Npc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864028,392,518 - 28,404,797 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364883,663,655 - 3,676,505 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
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 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2451,685,609 - 51,700,557 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605339,920,625 - 39,935,553 (-)NCBIVero_WHO_p1.0Vero_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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473427,166,867 - 27,177,229 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in NPC2
123 total Variants

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 reproductive system respiratory system adipose tissue
High 5 7
Medium 5 5 17 6 6 6 6 5 12 8 3 6
Low 1
Below cutoff

Sequence


RefSeq Acc Id: ENSCAFT00000026786   ⟹   ENSCAFP00000024889
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl847,641,184 - 47,650,576 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000087082   ⟹   ENSCAFP00000055843
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl847,628,077 - 47,650,473 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845025548   ⟹   ENSCAFP00845020117
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl847,866,650 - 47,877,427 (-)Ensembl
RefSeq Acc Id: NM_001003242   ⟹   NP_001003242
RefSeq Status: VALIDATED
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1847,641,185 - 47,650,543 (-)NCBI
Dog10K_Boxer_Tasha847,325,075 - 47,334,437 (-)NCBI
ROS_Cfam_1.0847,868,101 - 47,877,468 (-)NCBI
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
Sequence:
Protein Sequences
Protein RefSeqs NP_001003242 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB34263 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCAFP00000052889.1
  ENSCAFP00000068617.1
  ENSCAFP00030033028.1
  ENSCAFP00030033507.1
  ENSCAFP00040023849.1
  ENSCAFP00845020117
  ENSCAFP00845020117.1
  ENSCAFP00845029941.1
GenBank Protein Q28895 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001003242   ⟸   NM_001003242
- Peptide Label: precursor
- UniProtKB: A0A8C0JQN0 (UniProtKB/TrEMBL),   A0A8C0P355 (UniProtKB/TrEMBL),   A0A8I3NVN8 (UniProtKB/TrEMBL),   A0A8C0P0J0 (UniProtKB/TrEMBL),   A0A8I3PDV0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000055843   ⟸   ENSCAFT00000087082
RefSeq Acc Id: ENSCAFP00000024889   ⟸   ENSCAFT00000026786
RefSeq Acc Id: ENSCAFP00845020117   ⟸   ENSCAFT00845025548
Promoters
RGD ID:13684280
Promoter ID:EPDNEW_C2348
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:
Dog AssemblyChrPosition (strand)Source
CanFam3.1847,650,506 - 47,650,566EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000013780 UniProtKB/TrEMBL
  ENSCAFG00000016932 Ensembl
  ENSCAFG00000051920 UniProtKB/TrEMBL
  ENSCAFG00030020631 UniProtKB/TrEMBL
  ENSCAFG00030020933 UniProtKB/TrEMBL
  ENSCAFG00040014896 UniProtKB/TrEMBL
  ENSCAFG00845014286 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSCAFG00845021667 UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000021869.3 UniProtKB/TrEMBL
  ENSCAFT00000098764.1 UniProtKB/TrEMBL
  ENSCAFT00030037850.1 UniProtKB/TrEMBL
  ENSCAFT00030038407.1 UniProtKB/TrEMBL
  ENSCAFT00040027450.1 UniProtKB/TrEMBL
  ENSCAFT00845025548 ENTREZGENE
  ENSCAFT00845025548.1 UniProtKB/TrEMBL
  ENSCAFT00845038223.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.770 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Ig_E-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ML_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ML_Npc2-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NPC2-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report cfa:403920 UniProtKB/TrEMBL
NCBI Gene NPC2 ENTREZGENE
PANTHER NPC INTRACELLULAR CHOLESTEROL TRANSPORTER 2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11306 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam E1_DerP2_DerF2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00737 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF81296 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8C0JQN0 ENTREZGENE
  A0A8C0P0J0 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0P355 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3NVN8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3PDV0 ENTREZGENE, UniProtKB/TrEMBL
  NPC2_CANLF UniProtKB/Swiss-Prot, ENTREZGENE
VGNC ID VGNC:43914 ENTREZGENE