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ABCA2 ATP binding cassette subfamily A member 2 [ Homo sapiens (human) ]

Gene ID: 20, updated on 4-Jan-2025

Summary

Official Symbol
ABCA2provided by HGNC
Official Full Name
ATP binding cassette subfamily A member 2provided by HGNC
Primary source
HGNC:HGNC:32
See related
Ensembl:ENSG00000107331 MIM:600047; AllianceGenome:HGNC:32
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ABC2; IDPOGSA
Summary
The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. This protein is highly expressed in brain tissue and may play a role in macrophage lipid metabolism and neural development. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Broad expression in brain (RPKM 47.6), thyroid (RPKM 9.5) and 20 other tissues See more
Orthologs
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Genomic context

See ABCA2 in Genome Data Viewer
Location:
9q34.3
Exon count:
50
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (137007234..137028922, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (149241651..149263357, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (139901686..139923374, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20565 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139887067-139887609 Neighboring gene PAXX non-homologous end joining factor Neighboring gene chloride intracellular channel 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29337 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:139904888-139906087 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139917045-139917624 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139922830-139923574 Neighboring gene long intergenic non-protein coding RNA 2908 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139929142-139930030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139930031-139930917 Neighboring gene fucosyltransferase 7 Neighboring gene neural proliferation, differentiation and control 1

Genomic regions, transcripts, and products

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

General gene information

Clone Names

  • MGC129761

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ABC-type transporter activity  
enables ATP binding PubMed 
enables ATP binding  
enables ATP hydrolysis activity  
enables ATPase-coupled transmembrane transporter activity  
enables ATPase-coupled transmembrane transporter activity PubMed 
enables ceramide floppase activity PubMed 
enables endopeptidase regulator activity PubMed 
enables lipid transporter activity  
enables nucleotide binding PubMed 
Items 1 - 25 of 37
Process Evidence Code Pubs
acts_upstream_of_or_within central nervous system myelin formation  
involved_in central nervous system myelin formation  
involved_in ceramide translocation PubMed 
involved_in cholesterol homeostasis PubMed 
involved_in ganglioside metabolic process  
involved_in glycosphingolipid metabolic process  
involved_in intracellular sphingolipid homeostasis PubMed 
involved_in lipid metabolic process PubMed 
involved_in lipid transport  
involved_in locomotory behavior  
acts_upstream_of negative regulation of cholesterol efflux PubMed 
acts_upstream_of negative regulation of intracellular cholesterol transport PubMed 
involved_in negative regulation of phospholipid biosynthetic process PubMed 
acts_upstream_of negative regulation of receptor-mediated endocytosis involved in cholesterol transport PubMed 
involved_in negative regulation of sphingolipid biosynthetic process PubMed 
acts_upstream_of negative regulation of steroid metabolic process PubMed 
involved_in positive regulation of amyloid precursor protein biosynthetic process PubMed 
acts_upstream_of positive regulation of amyloid precursor protein catabolic process PubMed 
acts_upstream_of positive regulation of amyloid precursor protein catabolic process PubMed 
acts_upstream_of positive regulation of amyloid-beta formation PubMed 
involved_in positive regulation of amyloid-beta formation PubMed 
acts_upstream_of positive regulation of low-density lipoprotein particle receptor catabolic process PubMed 
NOT involved_in regulation of cholesterol biosynthetic process PubMed 
involved_in regulation of intracellular cholesterol transport PubMed 
involved_in regulation of intracellular cholesterol transport  
acts_upstream_of regulation of post-translational protein modification PubMed 
involved_in regulation of protein glycosylation PubMed 
involved_in regulation of protein localization to cell periphery PubMed 
involved_in regulation of protein localization to cell surface PubMed 
acts_upstream_of regulation of steroid metabolic process PubMed 
involved_in response to cholesterol PubMed 
involved_in response to steroid hormone PubMed 
involved_in response to xenobiotic stimulus PubMed 
involved_in sphingomyelin metabolic process  
acts_upstream_of_positive_effect sphingosine biosynthetic process PubMed 
involved_in transmembrane transport PubMed 
involved_in transport across blood-brain barrier PubMed 
Items 1 - 25 of 37
Component Evidence Code Pubs
part_of ATP-binding cassette (ABC) transporter complex PubMed 
located_in cytoplasmic vesicle  
located_in endosome PubMed 
located_in endosome membrane PubMed 
located_in endosome membrane  
is_active_in intracellular membrane-bounded organelle  
located_in intracellular membrane-bounded organelle  
located_in lysosomal membrane PubMed 
located_in lysosomal membrane  
located_in lysosomal membrane PubMed 
located_in lysosome PubMed 
located_in membrane PubMed 
located_in membrane PubMed 
located_in membrane PubMed 
located_in microtubule organizing center  
is_active_in plasma membrane PubMed 
located_in plasma membrane PubMed 

General protein information

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, sub-family A, 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.

Genomic

  1. NG_011789.1 RefSeqGene

    Range
    5686..26689
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001411042.1NP_001397971.1  ATP-binding cassette sub-family A member 2 isoform c

    Status: REVIEWED

    Source sequence(s)
    AL807752, KF458947
    Consensus CDS
    CCDS94538.1
    UniProtKB/Swiss-Prot
    A6NED5, Q5SPY5, Q5W9G5, Q76MW7, Q9BZC7, Q9HC28
    UniProtKB/TrEMBL
    A0A087WXK5
    Related
    ENSP00000360666.3, ENST00000371605.7
  2. NM_001606.5NP_001597.2  ATP-binding cassette sub-family A member 2 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the predominant isoform (a).
    Source sequence(s)
    AF178941, AL525193, AL807752, BC029282, BE273611, BF516223, BM474929, BM921499, CD676110, DB168116
    Consensus CDS
    CCDS43909.1
    UniProtKB/TrEMBL
    A0A087WXK5
    Related
    ENSP00000344155.6, ENST00000341511.11
    Conserved Domains (2) summary
    TIGR01257
    Location:12368
    rim_protein; retinal-specific rim ABC transporter
    cd03263
    Location:20512274
    ABC_subfamily_A; ATP-binding cassette domain of the lipid transporters, subfamily A
  3. NM_212533.3NP_997698.1  ATP-binding cassette sub-family A member 2 isoform b

    See identical proteins and their annotated locations for NP_997698.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding region compared to variant 1. The resulting isoform (b) is longer and has a distinct N-terminus compared to isoform a.
    Source sequence(s)
    AF178941, AL525193, AL807752, BC029282, BE273611, BF516223, BM474929, BM921499, DB168116
    Consensus CDS
    CCDS94539.1
    UniProtKB/TrEMBL
    A0A087WXK5
    Related
    ENSP00000481105.2, ENST00000614293.5
    Conserved Domains (2) summary
    TIGR01257
    Location:582398
    rim_protein; retinal-specific rim ABC transporter
    cd03263
    Location:20812304
    ABC_subfamily_A; ATP-binding cassette domain of the lipid transporters, subfamily A

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    137007234..137028922 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047422921.1XP_047278877.1  ATP-binding cassette sub-family A member 2 isoform X1

    UniProtKB/TrEMBL
    A0A087WXK5
    Related
    ENST00000459850.5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    149241651..149263357 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054362255.1XP_054218230.1  ATP-binding cassette sub-family A member 2 isoform X1

    UniProtKB/TrEMBL
    A0A087WXK5
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