Abca2 ATP binding cassette subfamily A member 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Abca2provided by RGD
Official Full Name: ATP binding cassette subfamily A member 2provided by RGD
Primary source: RGD:620238
See related: Ensembl:ENSRNOG00000014268 AllianceGenome:RGD:620238
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Abc2
Summary: Enables ATP binding activity. Involved in central nervous system myelin formation; negative regulation of lipid biosynthetic process; and positive regulation of amyloid-beta formation. Located in cytoplasmic vesicle; lysosomal membrane; and microtubule organizing center. Orthologous to human ABCA2 (ATP binding cassette subfamily A member 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Kidney (RPKM 257.8), Brain (RPKM 186.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 3p13

Exon count:: 49

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (28642660..28662689)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (8244515..8264545)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (2648787..2668770)

Chromosome 3 - NC_086021.1 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
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?

control of ABCA2 expression level may be a key locus of regulation for esterification of plasma membrane-derived cholesterol through modulation of sphingolipid metabolism.
Title: The ATP-binding cassette transporter-2 (ABCA2) regulates esterification of plasma membrane cholesterol by modulation of sphingolipid metabolism.
Down-regulation of the ATP-binding cassette transporter 2 (Abca2) reduces amyloid-beta production by altering Nicastrin maturation and intracellular localization.
Title: Down-regulation of the ATP-binding cassette transporter 2 (Abca2) reduces amyloid-β production by altering Nicastrin maturation and intracellular localization.
ATP-binding cassette transporter ABCA2 (ABC2) expression in the developing spinal cord and PNS during myelination.
Title: ATP-binding cassette transporter ABCA2 (ABC2) expression in the developing spinal cord and PNS during myelination.
ABCA2 is a marker of neural progenitors and neuronal subsets in the adult rodent brain.
Title: ABCA2 is a marker of neural progenitors and neuronal subsets in the adult rodent brain.
ABCA2 protein is expressed predominantly in oligodendrocytes, and the expression of the protein is upregulated in the brain during maturation, especially between postnatal days 6 and 19.
Title: Temporal and spatial profiles of ABCA2-expressing oligodendrocytes in the developing rat brain.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

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	IDA Inferred from Direct Assay more info	PubMed
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP binding	ISO Inferred from Sequence Orthology more info
enables ATP binding	ISS Inferred from Sequence or Structural Similarity more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATPase-coupled transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables ceramide floppase activity	IEA Inferred from Electronic Annotation more info
enables ceramide floppase activity	ISO Inferred from Sequence Orthology more info
enables endopeptidase regulator activity	IEA Inferred from Electronic Annotation more info
enables endopeptidase regulator activity	ISO Inferred from Sequence Orthology more info
enables lipid transporter activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in central nervous system myelin formation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within central nervous system myelin formation	ISO Inferred from Sequence Orthology more info
involved_in ceramide translocation	IEA Inferred from Electronic Annotation more info
involved_in ceramide translocation	ISO Inferred from Sequence Orthology more info
involved_in cholesterol homeostasis	IEA Inferred from Electronic Annotation more info
involved_in cholesterol homeostasis	ISO Inferred from Sequence Orthology more info
involved_in cholesterol homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in ganglioside metabolic process	ISO Inferred from Sequence Orthology more info
involved_in ganglioside metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in glycosphingolipid metabolic process	ISO Inferred from Sequence Orthology more info
involved_in glycosphingolipid metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in intracellular sphingolipid homeostasis	IEA Inferred from Electronic Annotation more info
involved_in intracellular sphingolipid homeostasis	ISO Inferred from Sequence Orthology more info
involved_in lipid transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in locomotory behavior	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cholesterol efflux	IEA Inferred from Electronic Annotation more info
acts_upstream_of negative regulation of cholesterol efflux	ISO Inferred from Sequence Orthology more info
acts_upstream_of negative regulation of intracellular cholesterol transport	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of phospholipid biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of phospholipid biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of receptor-mediated endocytosis involved in cholesterol transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of negative regulation of receptor-mediated endocytosis involved in cholesterol transport	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of sphingolipid biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of sphingolipid biosynthetic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of negative regulation of steroid metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of amyloid precursor protein biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of amyloid precursor protein biosynthetic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of positive regulation of amyloid precursor protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of amyloid-beta formation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of amyloid-beta formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of positive regulation of amyloid-beta formation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of low-density lipoprotein particle receptor catabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of positive regulation of low-density lipoprotein particle receptor catabolic process	ISO Inferred from Sequence Orthology more info
NOT involved_in regulation of cholesterol biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of intracellular cholesterol transport	ISO Inferred from Sequence Orthology more info
involved_in regulation of intracellular cholesterol transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of post-translational protein modification	IEA Inferred from Electronic Annotation more info
acts_upstream_of regulation of post-translational protein modification	ISO Inferred from Sequence Orthology more info
involved_in regulation of protein glycosylation	ISO Inferred from Sequence Orthology more info
involved_in regulation of protein localization to cell periphery	ISO Inferred from Sequence Orthology more info
involved_in regulation of protein localization to cell surface	ISO Inferred from Sequence Orthology more info
involved_in regulation of steroid metabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of regulation of steroid metabolic process	ISO Inferred from Sequence Orthology more info
involved_in response to cholesterol	IEA Inferred from Electronic Annotation more info
involved_in response to cholesterol	ISO Inferred from Sequence Orthology more info
involved_in response to steroid hormone	IEA Inferred from Electronic Annotation more info
involved_in response to steroid hormone	ISO Inferred from Sequence Orthology more info
involved_in response to steroid hormone	ISS Inferred from Sequence or Structural Similarity more info
involved_in sphingomyelin metabolic process	ISO Inferred from Sequence Orthology more info
involved_in sphingomyelin metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in sphingosine biosynthetic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_positive_effect sphingosine biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in transmembrane transport	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasmic vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in endosome	IEA Inferred from Electronic Annotation more info
located_in endosome	ISO Inferred from Sequence Orthology more info
located_in endosome	ISS Inferred from Sequence or Structural Similarity more info
located_in endosome membrane	IEA Inferred from Electronic Annotation more info
located_in endosome 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 lysosomal membrane	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal membrane	ISO Inferred from Sequence Orthology more info
located_in lysosomal membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in lysosome	IEA Inferred from Electronic Annotation more info
located_in lysosome	ISO Inferred from Sequence Orthology more info
located_in lysosome	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in membrane	ISO Inferred from Sequence Orthology more info
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in microtubule organizing center	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	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: ATP-binding cassette sub-family A member 2

Names: ATP-binding cassette 2; ATP-binding cassette transporter 2; ATP-binding cassette, sub-family A (ABC1), member 2; ATP-binding cassette, subfamily A (ABC1), member 2

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_024396.1 → NP_077372.1 ATP-binding cassette sub-family A member 2

See identical proteins and their annotated locations for NP_077372.1

Status: PROVISIONAL

Source sequence(s)

AB037937

UniProtKB/Swiss-Prot

Q9ESR9

UniProtKB/TrEMBL

A6JT60

Related

ENSRNOP00000020339.6, ENSRNOT00000020339.8

Conserved Domains (2) summary

TIGR01257
Location:1 → 2368

rim_protein; retinal-specific rim ABC transporter

cd03263
Location:2051 → 2274

ABC_subfamily_A; ATP-binding cassette domain of the lipid transporters, subfamily A

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_086021.1 Reference GRCr8

Range

28642660..28662689

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063284607.1 → XP_063140677.1 ATP-binding cassette sub-family A member 2 isoform X4
XM_063284605.1 → XP_063140675.1 ATP-binding cassette sub-family A member 2 isoform X2
XM_063284604.1 → XP_063140674.1 ATP-binding cassette sub-family A member 2 isoform X1

UniProtKB/TrEMBL

G3V7X4
XM_063284606.1 → XP_063140676.1 ATP-binding cassette sub-family A member 2 isoform X3