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    ARID1A AT-rich interaction domain 1A [ Homo sapiens (human) ]

    Gene ID: 8289, updated on 12-Sep-2021

    Summary

    Official Symbol
    ARID1Aprovided by HGNC
    Official Full Name
    AT-rich interaction domain 1Aprovided by HGNC
    Primary source
    HGNC:HGNC:11110
    See related
    Ensembl:ENSG00000117713 MIM:603024
    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
    ELD; B120; CSS2; OSA1; P270; hELD; BM029; MRD14; hOSA1; BAF250; C1orf4; BAF250a; SMARCF1
    Summary
    This gene encodes a member of the SWI/SNF family, whose members have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI, which is required for transcriptional activation of genes normally repressed by chromatin. It possesses at least two conserved domains that could be important for its function. First, it has a DNA-binding domain that can specifically bind an AT-rich DNA sequence known to be recognized by a SNF/SWI complex at the beta-globin locus. Second, the C-terminus of the protein can stimulate glucocorticoid receptor-dependent transcriptional activation. It is thought that the protein encoded by this gene confers specificity to the SNF/SWI complex and may recruit the complex to its targets through either protein-DNA or protein-protein interactions. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in spleen (RPKM 14.3), lymph node (RPKM 13.2) and 25 other tissues See more
    Orthologs
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    Genomic context

    See ARID1A in Genome Data Viewer
    Location:
    1p36.11
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (26696015..26782104)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (27022506..27108595)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376888 Neighboring gene uncharacterized LOC101928728 Neighboring gene heart enhancer 10 Neighboring gene phosphatidylinositol glycan anchor biosynthesis class V Neighboring gene RNA, 7SL, cytoplasmic 165, pseudogene

    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?

    Phenotypes

    Associated conditions

    Description Tests
    Mental retardation, autosomal dominant 14
    MedGen: C3553247 OMIM: 614607 GeneReviews: Not available
    not available

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2020-05-27)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2020-05-27)

    ClinGen Genome Curation PagePubMed

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of AT rich interactive domain 1A, SWI-like (ARID1A; BAF250) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Most of the components of the SWI2/SNF2 chromatin remodeling complex (BRG1/BRM, BAF250, BAF180, BAF170, BAF155, BAF60a, BAF53A, actin and InI) except BRM, BAF155 and BAF57, are identified to interact with HIV-1 Tat in Jurkat cell PubMed
    tat Acetylated HIV-1 Tat binds efficiently to BRG1 and BAF200 (component of PBAF complex) and weakly to BAF250 (component of BAF complex). BAF250 has a preference to bind to unmodified Tat PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables nuclear receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    contributes_to nucleosome binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription coactivator activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of SWI/SNF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    part_of SWI/SNF complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of brahma complex IEA
    Inferred from Electronic Annotation
    more info
     
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of nBAF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    part_of nBAF complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of npBAF complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleus TAS
    Traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    AT-rich interactive domain-containing protein 1A
    Names
    ARID domain-containing protein 1A
    AT rich interactive domain 1A (SWI-like)
    BRG1-associated factor 250a
    OSA1 nuclear protein
    SWI-like protein
    SWI/SNF complex protein p270
    SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin subfamily F member 1
    brain protein 120
    chromatin remodeling factor p250
    osa homolog 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.

    Genomic

    1. NG_029965.1 RefSeqGene

      Range
      5001..91080
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_875

    mRNA and Protein(s)

    1. NM_006015.6NP_006006.3  AT-rich interactive domain-containing protein 1A isoform a

      See identical proteins and their annotated locations for NP_006006.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) is the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AF231056, AF521670, AL034380, AL512408
      Consensus CDS
      CCDS285.1
      UniProtKB/Swiss-Prot
      O14497
      Related
      ENSP00000320485.7, ENST00000324856.13
      Conserved Domains (5) summary
      TIGR01628
      Location:372469
      PABP-1234; polyadenylate binding protein, human types 1, 2, 3, 4 family
      PRK07764
      Location:598729
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam09606
      Location:713947
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
      cd16876
      Location:10181110
      ARID_ARID1A; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1A (ARID1A) and similar proteins
      pfam12031
      Location:19762231
      BAF250_C; SWI/SNF-like complex subunit BAF250/Osa
    2. NM_139135.4NP_624361.1  AT-rich interactive domain-containing protein 1A isoform b

      See identical proteins and their annotated locations for NP_624361.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks a segment in the coding region compared to variant 1. Variant 2 encodes isoform b, which lacks an internal segment compared to isoform a.
      Source sequence(s)
      AF231056, AF268913, AF521670, AL034380, AL512408
      Consensus CDS
      CCDS44091.1
      UniProtKB/Swiss-Prot
      O14497
      Related
      ENSP00000387636.2, ENST00000457599.6
      Conserved Domains (3) summary
      smart00501
      Location:10181109
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      pfam12004
      Location:596881
      DUF3498; Domain of unknown function (DUF3498)
      pfam12031
      Location:17592014
      DUF3518; Domain of unknown function (DUF3518)

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

      Range
      26696015..26782104
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_018450.4: Suppressed sequence

      Description
      NM_018450.4: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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