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

    Gene ID: 8289, updated on 17-Feb-2019

    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

    Genomic context

    See ARID1A in Genome Data Viewer
    Location:
    1p36.11
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (26696033..26782110)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (27022522..27108601)

    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 FunctionsWhat's a GeneRIF?

    Phenotypes

    Associated conditions

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

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2017-10-12)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2017-10-12)

    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

    Pathways from BioSystems

    • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
      Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
    • Chromatin organization, organism-specific biosystem (from REACTOME)
      Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
    • Pathways Affected in Adenoid Cystic Carcinoma, organism-specific biosystem (from WikiPathways)
      Pathways Affected in Adenoid Cystic Carcinoma, organism-specific biosystemProtein pathways altered by mutations in adenoid cystic carcinoma. Pathways include epigentic modification, DNA damage checkpoint signals, MYB/MYC signalling pathway, FGF/IGF/PI3K signalling, and not...
    • RMTs methylate histone arginines, organism-specific biosystem (from REACTOME)
      RMTs methylate histone arginines, organism-specific biosystemArginine methylation is a common post-translational modification; around 2% of arginine residues are methylated in rat liver nuclei (Boffa et al. 1977). Arginine can be methylated in 3 different ways...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    DNA binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
     
    nuclear receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    nucleosome binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    transcription coactivator activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    ATP-dependent chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
     
    androgen receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cardiac chamber development IEA
    Inferred from Electronic Annotation
    more info
     
    cardiac muscle cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    chromatin remodeling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chromatin-mediated maintenance of transcription TAS
    Traceable Author Statement
    more info
    PubMed 
    embryo implantation IEA
    Inferred from Electronic Annotation
    more info
     
    forebrain development IEA
    Inferred from Electronic Annotation
    more info
     
    formation of primary germ layer IEA
    Inferred from Electronic Annotation
    more info
     
    glucocorticoid receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    intracellular estrogen receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    maintenance of chromatin silencing IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    neural tube closure IEA
    Inferred from Electronic Annotation
    more info
     
    nucleosome disassembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleosome mobilization TAS
    Traceable Author Statement
    more info
    PubMed 
    optic cup formation involved in camera-type eye development IEA
    Inferred from Electronic Annotation
    more info
     
    placenta blood vessel development IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of transcription by RNA polymerase II NAS
    Non-traceable Author Statement
    more info
    PubMed 
    stem cell population maintenance IEA
    Inferred from Electronic Annotation
    more info
     
    toxin transport IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    SWI/SNF complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nBAF complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    npBAF complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    nuclear chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    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)

    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, ENST00000324856.12
      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:19762231
      DUF3518; Domain of unknown function (DUF3518)
    2. NM_139135.3NP_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 Annotation Release 109

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

      Range
      26696033..26782110
      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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