Abca1 ATP binding cassette subfamily A member 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Abca1provided by RGD
Official Full Name: ATP binding cassette subfamily A member 1provided by RGD
Primary source: RGD:631344
See related: EnsemblRapid:ENSRNOG00000018126 AllianceGenome:RGD:631344
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables ATPase-coupled transmembrane transporter activity and high-density lipoprotein particle binding activity. Involved in several processes, including cellular response to cholesterol; lipoprotein biosynthetic process; and response to vitamin B3. Located in basolateral plasma membrane and cell surface. Biomarker of several diseases, including end stage renal disease; extrahepatic cholestasis; liver disease (multiple); membranous glomerulonephritis; and premature menopause. Human ortholog(s) of this gene implicated in Alzheimer's disease; coronary artery disease; hypolipoproteinemia (multiple); obesity; and type 2 diabetes mellitus. Orthologous to human ABCA1 (ATP binding cassette subfamily A member 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Adrenal (RPKM 586.5), Liver (RPKM 371.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q23-q24

Exon count:: 51

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (72473676..72596563, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (67678267..67801162, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (69857717..69983042, complement)

Chromosome 5 - NC_086023.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A high-fat/high-cholesterol diet, but not high-cholesterol alone, increases free cholesterol and apoE-rich HDL serum levels in rats and upregulates hepatic ABCA1 expression.
Title: A high-fat/high-cholesterol diet, but not high-cholesterol alone, increases free cholesterol and apoE-rich HDL serum levels in rats and upregulates hepatic ABCA1 expression.
Geniposide Ameliorated Dexamethasone-Induced Cholesterol Accumulation in Osteoblasts by Mediating the GLP-1R/ABCA1 Axis.
Title: Geniposide Ameliorated Dexamethasone-Induced Cholesterol Accumulation in Osteoblasts by Mediating the GLP-1R/ABCA1 Axis.
MicroRNA-33a-5p sponges to inhibit pancreatic beta-cell function in gestational diabetes mellitus LncRNA DANCR.
Title: MicroRNA-33a-5p sponges to inhibit pancreatic β-cell function in gestational diabetes mellitus LncRNA DANCR.
We found abundant GAS5 expression and a reduction in RGC density in the retinal tissues of glaucoma rats. Silencing of GAS5 led to increased EZH2 expression and decreased ABCA1 expression in RGCs. In addition, upregulation of EZH2 promoted trimethylation of lysine 27 on histone H3, thereby suppressing ABCA1 expression and eventually leading to the inhibition of RGC apoptosis.
Title: Silencing of GAS5 Alleviates Glaucoma in Rat Models by Reducing Retinal Ganglion Cell Apoptosis.
ABCA1 suppressed PDGF-induced proliferation, migration, and contraction in rat airway smooth muscle cells at least partly through TLR2/NF-kappaB/NFATc1 signaling, which might offer hope for the future treatment of airway remodeling in asthma.
Title: ABCA1 inhibits PDGF-induced proliferation and migration of rat airway smooth muscle cell through blocking TLR2/NF-κB/NFATc1 signaling.
Increased expression of hepatic ABCA1 transporter is associated with hypercholesterolemia in a cholestatic rat model and primary biliary cholangitis patients.
Title: Increased hepatic ABCA1 transporter is associated with hypercholesterolemia in a cholestatic rat model and primary biliary cholangitis patients.
Advanced glycation end products affect cholesterol homeostasis by impairing ABCA1 expression on macrophages
Title: Advanced glycation end products affect cholesterol homeostasis by impairing ABCA1 expression on macrophages.
an important role for hepatic ABCA1 in regulating secretory trafficking and modulating VLDL expansion during the TG accretion phase of hepatic lipoprotein particle assembly
Title: Hepatic ABCA1 deficiency is associated with delayed apolipoprotein B secretory trafficking and augmented VLDL triglyceride secretion.
These studies showed that following brain ischemia, reactive astrocytes become phagocytic and engulf debris via the ABCA1 pathway.
Title: Reactive astrocytes function as phagocytes after brain ischemia via ABCA1-mediated pathway.
lnc-HC negatively regulates cholesterol metabolism within hepatocytes through physical interaction with hnRNPA2B1. By further binding to the target messenger RNA of Cyp7a1 or Abca1, the lnc-HC-hnRNPA2B1 complex decreases expressions of the two genes that are implicated in cellular cholesterol excretion.
Title: A novel long noncoding RNA Lnc-HC binds hnRNPA2B1 to regulate expressions of Cyp7a1 and Abca1 in hepatocytic cholesterol metabolism.

Submit: New GeneRIF Correction See all GeneRIFs (40)

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ABC-type transporter activity	IEA Inferred from Electronic Annotation more info
enables ATP binding	ISO Inferred from Sequence Orthology more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATPase binding	ISO Inferred from Sequence Orthology more info
enables ATPase-coupled transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATPase-coupled transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables ATPase-coupled transmembrane transporter activity	TAS Traceable Author Statement more info	PubMed
enables apolipoprotein A-I binding	ISO Inferred from Sequence Orthology more info
enables apolipoprotein A-I receptor activity	ISO Inferred from Sequence Orthology more info
enables apolipoprotein binding	ISO Inferred from Sequence Orthology more info
enables cholesterol transfer activity	ISO Inferred from Sequence Orthology more info
enables floppase activity	ISO Inferred from Sequence Orthology more info
enables high-density lipoprotein particle binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylcholine binding	ISO Inferred from Sequence Orthology more info
enables phosphatidylcholine floppase activity	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylcholine floppase activity	ISO Inferred from Sequence Orthology more info
enables phosphatidylserine floppase activity	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylserine floppase activity	ISO Inferred from Sequence Orthology more info
enables phospholipid transporter activity	ISO Inferred from Sequence Orthology more info
enables protein transmembrane transporter activity	ISO Inferred from Sequence Orthology more info
enables signaling receptor binding	ISO Inferred from Sequence Orthology more info
enables small GTPase binding	ISO Inferred from Sequence Orthology more info
enables sphingolipid floppase activity	ISO Inferred from Sequence Orthology more info
enables syntaxin binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in G protein-coupled receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in adenylate cyclase-activating G protein-coupled receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in apolipoprotein A-I-mediated signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in cellular response to cholesterol	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to cytokine stimulus	IEP Inferred from Expression Pattern more info	PubMed
NOT involved_in cellular response to high density lipoprotein particle stimulus	ISO Inferred from Sequence Orthology more info
involved_in cellular response to lipopolysaccharide	ISO Inferred from Sequence Orthology more info
involved_in cellular response to retinoic acid	ISO Inferred from Sequence Orthology more info
involved_in cellular response to xenobiotic stimulus	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within cholesterol efflux	ISO Inferred from Sequence Orthology more info
involved_in cholesterol efflux	ISO Inferred from Sequence Orthology more info
involved_in cholesterol homeostasis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cholesterol metabolic process	ISO Inferred from Sequence Orthology more info
involved_in cholesterol metabolic process	ISO Inferred from Sequence Orthology more info
involved_in cholesterol transport	IDA Inferred from Direct Assay more info	PubMed
involved_in cholesterol transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endosomal transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within establishment of localization in cell	ISO Inferred from Sequence Orthology more info
involved_in export across plasma membrane	ISO Inferred from Sequence Orthology more info
involved_in high-density lipoprotein particle assembly	ISO Inferred from Sequence Orthology more info
involved_in intracellular cholesterol transport	ISO Inferred from Sequence Orthology more info
involved_in lipoprotein biosynthetic process	IEP Inferred from Expression Pattern more info	PubMed
involved_in lipoprotein biosynthetic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within lipoprotein biosynthetic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lipoprotein metabolic process	ISO Inferred from Sequence Orthology more info
involved_in lysosome organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within peptide secretion	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within phagocytosis, engulfment	ISO Inferred from Sequence Orthology more info
involved_in phospholipid efflux	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within phospholipid efflux	ISO Inferred from Sequence Orthology more info
involved_in phospholipid efflux	ISO Inferred from Sequence Orthology more info
involved_in phospholipid homeostasis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within phospholipid translocation	ISO Inferred from Sequence Orthology more info
involved_in phospholipid translocation	ISO Inferred from Sequence Orthology more info
involved_in phospholipid transport	IDA Inferred from Direct Assay more info	PubMed
involved_in phospholipid transport	TAS Traceable Author Statement more info	PubMed
involved_in platelet dense granule organization	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cholesterol efflux	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of high-density lipoprotein particle assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein lipidation	ISO Inferred from Sequence Orthology more info
involved_in protein secretion	ISO Inferred from Sequence Orthology more info
involved_in protein transmembrane transport	ISO Inferred from Sequence Orthology more info
involved_in regulation of Cdc42 protein signal transduction	ISO Inferred from Sequence Orthology more info
involved_in response to laminar fluid shear stress	ISO Inferred from Sequence Orthology more info
involved_in response to nutrient	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to nutrient levels	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to vitamin B3	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to xenobiotic stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in reverse cholesterol transport	ISO Inferred from Sequence Orthology more info
involved_in signal release	ISO Inferred from Sequence Orthology more info
involved_in sphingolipid translocation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in apical plasma membrane	ISO Inferred from Sequence Orthology more info
located_in basolateral plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in basolateral plasma membrane	ISO Inferred from Sequence Orthology more info
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in endocytic vesicle	ISO Inferred from Sequence Orthology more info
located_in endosome	ISO Inferred from Sequence Orthology more info
located_in external side of plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in intracellular membrane-bounded organelle	IBA Inferred from Biological aspect of Ancestor more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in intracellular vesicle	ISO Inferred from Sequence Orthology more info
located_in membrane raft	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info
located_in phagocytic vesicle	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: phospholipid-transporting ATPase ABCA1

Names: ATP-binding cassette sub-family A member 1; ATP-binding cassette, sub-family A (ABC1), member 1; ATP-binding cassette, subfamily A (ABC1), member 1

NP_835196.2

EC 7.6.2.1

XP_038965774.1

EC 7.6.2.1

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_178095.3 → NP_835196.2 phospholipid-transporting ATPase ABCA1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

A6KDN7, F1LNL3

Related

ENSRNOP00000024564.9, ENSRNOT00000024564.9

Conserved Domains (1) summary

TIGR01257
Location:1 → 2236

rim_protein; retinal-specific rim ABC transporter

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086023.1 Reference GRCr8

Range

72473676..72596563 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039109846.2 → XP_038965774.1 phospholipid-transporting ATPase ABCA1 isoform X1

UniProtKB/TrEMBL

A0A8I5ZLK5, F1LNL3

Related

ENSRNOP00000078596.1, ENSRNOT00000110113.2

Conserved Domains (1) summary

TIGR01257
Location:1 → 2238

rim_protein; retinal-specific rim ABC transporter