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

    Gene ID: 20, updated on 27-Nov-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    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: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC129761

    Gene Ontology Provided by GOA

    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 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 ATPase-coupled transmembrane transporter activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables ceramide floppase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables endopeptidase regulator activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables lipid transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables nucleotide binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within central nervous system myelin formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in central nervous system myelin formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in ceramide translocation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cholesterol homeostasis IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in ganglioside metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in glycosphingolipid metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in intracellular sphingolipid homeostasis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in lipid metabolic process NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in lipid transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in locomotory behavior ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of negative regulation of cholesterol efflux IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of negative regulation of intracellular cholesterol transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of phospholipid biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of negative regulation of receptor-mediated endocytosis involved in cholesterol transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of sphingolipid biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of negative regulation of steroid metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in positive regulation of amyloid precursor protein biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of positive regulation of amyloid precursor protein catabolic process IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of positive regulation of amyloid precursor protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of positive regulation of amyloid-beta formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of amyloid-beta formation ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    acts_upstream_of positive regulation of low-density lipoprotein particle receptor catabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    NOT involved_in regulation of cholesterol biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of intracellular cholesterol transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of intracellular cholesterol transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of regulation of post-translational protein modification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of protein glycosylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in regulation of protein localization to cell periphery ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in regulation of protein localization to cell surface ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    acts_upstream_of regulation of steroid metabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to cholesterol IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to steroid hormone IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to xenobiotic stimulus TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in sphingomyelin metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_positive_effect sphingosine biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in transmembrane transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in transport across blood-brain barrier NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of ATP-binding cassette (ABC) transporter complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in cytoplasmic vesicle ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in intracellular membrane-bounded organelle IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosomal membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in lysosomal membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in membrane HDA PubMed 
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in microtubule organizing center ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    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)

    NEW Try the new Transcript table

    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
      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

      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