npc1 Niemann-Pick disease, type C1 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: npc1provided by ZNC
Official Full Name: Niemann-Pick disease, type C1provided by ZNC
Primary source: ZFIN:ZDB-GENE-030131-3161
See related: Ensembl:ENSDARG00000017180 AllianceGenome:ZFIN:ZDB-GENE-030131-3161
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: im:7149020; wu:fb53a12; wu:fc29a12
Summary: Predicted to enable lipid transporter activity. Acts upstream of or within several processes, including cholesterol homeostasis; epiboly involved in gastrulation with mouth forming second; and megakaryocyte development. Predicted to be located in membrane. Predicted to be integral component of membrane. Is expressed in several structures, including heart; liver; nervous system; pleuroperitoneal region; and yolk syncytial layer. Used to study Niemann-Pick disease type C1. Human ortholog(s) of this gene implicated in Niemann-Pick disease type C1. Orthologous to human NPC1 (NPC intracellular cholesterol transporter 1). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 2

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	2	NC_007113.7 (3823767..3866975)
105	previous assembly	GRCz10 (GCF_000002035.5)	2	NC_007113.6 (3992875..4036082)

Chromosome 2 - NC_007113.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

this is the first report, showing a role of NPC1 in platelet function and formation but further studies are needed to define how cholesterol storage interferes with these processes
Title: NPC1 defect results in abnormal platelet formation and function: studies in Niemann-Pick disease type C1 patients and zebrafish.
npc1 is required early for proper cell movement and cholesterol localization and later for cell survival
Title: Requirement of Npc1 and availability of cholesterol for early embryonic cell movements in zebrafish.

Submit: New GeneRIF Correction

General gene information

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Markers

fb53a12.x1 (e-PCR)
- UniSTS:203300

AI722583 (e-PCR)
- UniSTS:206001

G47242 (e-PCR)
- UniSTS:108025

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables cholesterol binding	IBA Inferred from Biological aspect of Ancestor more info
enables lipid transporter activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within blood circulation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cellular homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within central nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cholesterol homeostasis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cholesterol homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cholesterol transport	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within chordate embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within epiboly involved in gastrulation with mouth forming second	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intestinal cholesterol absorption	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within lipid metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lipid storage	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lipid transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within lipid transport	ISS Inferred from Sequence or Structural Similarity more info	PubMed
acts_upstream_of_or_within megakaryocyte development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within notochord morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within otic vesicle development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within otolith formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of intracellular cholesterol transport	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to hypoxia	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: NPC intracellular cholesterol transporter 1; Niemann-Pick C1 protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001243875.1 → NP_001230804.1 NPC intracellular cholesterol transporter 1 precursor

Status: VALIDATED

Source sequence(s)

FP236166, FP245481

UniProtKB/TrEMBL

A0A0R4IZV0, A0A8M1P234

Related

ENSDARP00000141736.2, ENSDART00000161880.2

Conserved Domains (3) summary

TIGR00917
Location:28 → 1246

2A060601; Niemann-Pick C type protein family

pfam12349
Location:646 → 799

Sterol-sensing; Sterol-sensing domain of SREBP cleavage-activation

pfam16414
Location:26 → 247

NPC1_N; Niemann-Pick C1 N terminus

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCz11 Primary Assembly

Genomic

NC_007113.7 Reference GRCz11 Primary Assembly

Range

3823767..3866975

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005163659.4 → XP_005163716.1 Niemann-Pick C1 protein isoform X2

UniProtKB/TrEMBL

A0A8M2BAS9, F1QNG7

Related

ENSDARP00000094372.4, ENSDART00000103596.6

Conserved Domains (3) summary

TIGR00917
Location:28 → 1251

2A060601; Niemann-Pick C type protein family

pfam12349
Location:651 → 804

Sterol-sensing; Sterol-sensing domain of SREBP cleavage-activation

pfam16414
Location:26 → 247

NPC1_N; Niemann-Pick C1 N terminus
XM_005163658.4 → XP_005163715.1 Niemann-Pick C1 protein isoform X1

UniProtKB/TrEMBL

A0A2R8Q2J0, A0A8M2BAZ2

Related

ENSDARP00000144951.1, ENSDART00000185408.1

Conserved Domains (3) summary

TIGR00917
Location:28 → 1251

2A060601; Niemann-Pick C type protein family

pfam12349
Location:651 → 804

Sterol-sensing; Sterol-sensing domain of SREBP cleavage-activation

pfam16414
Location:26 → 247

NPC1_N; Niemann-Pick C1 N terminus