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

Gene ID: 8289, updated on 29-Oct-2024

Summary

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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; AllianceGenome:HGNC:11110
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

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See ARID1A in Genome Data Viewer
Location:
1p36.11
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (26696015..26782104)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (26533960..26620059)
RS_2024_09 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 translation initiation factor IF-2-like Neighboring gene uncharacterized LOC101928728 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27019176-27019690 Neighboring gene hESC enhancers GRCh37_chr1:27021339-27022275 and GRCh37_chr1:27022276-27023211 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 489 Neighboring gene Sharpr-MPRA regulatory region 12508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27033907-27034406 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27048400-27048980 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27048981-27049560 Neighboring gene heart enhancer 10 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:27051301-27051880 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27051881-27052460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:27057943-27058472 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 517 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:27098665-27099864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 518 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 519 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27114367-27115193 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 521 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 522 Neighboring gene phosphatidylinositol glycan anchor biosynthesis class V Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27130608-27131323 Neighboring gene RNA, 7SL, cytoplasmic 165, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

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Related articles in PubMed

  1. ARID1A alteration in aggressive urothelial carcinoma and variants of urothelial carcinoma. Li J, et al. Hum Pathol, 2016 Sep. PMID 27137986
  2. ARID1A gene mutation in ovarian and endometrial cancers (Review). Takeda T, et al. Oncol Rep, 2016 Feb. PMID 26572704, Free PMC Article
  3. METTL8 mRNA Methyltransferase Enhances Cancer Cell Migration via Direct Binding to ARID1A. Lee SA, et al. Int J Mol Sci, 2021 May 21. PMID 34063990, Free PMC Article
  4. Identification and functional characterization of a novel bipartite nuclear localization sequence in ARID1A. Bateman NW, et al. Biochem Biophys Res Commun, 2016 Jan 1. PMID 26614907
  5. The effects of ARID1A mutations on colorectal cancer and associations with PD-L1 expression by stromal cells. Kamori T, et al. Cancer Rep (Hoboken), 2022 Jan. PMID 34042312, Free PMC Article

See all (480) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ARID1A-Deficient Tumors Acquire Immunogenic Neoantigens during the Development of Resistance to Targeted Therapy.
    Title: ARID1A-Deficient Tumors Acquire Immunogenic Neoantigens during the Development of Resistance to Targeted Therapy.
  2. ARID1A restrains EMT and stemness of ovarian cancer cells through the Hippo pathway.
    Title: ARID1A restrains EMT and stemness of ovarian cancer cells through the Hippo pathway.
  3. ARID1A in Gynecologic Precancers and Cancers.
    Title: ARID1A in Gynecologic Precancers and Cancers.
  4. ARID1A suppresses R-loop-mediated STING-type I interferon pathway activation of anti-tumor immunity.
    Title: ARID1A suppresses R-loop-mediated STING-type I interferon pathway activation of anti-tumor immunity.
  5. Genome-wide DNA methylation in relation to ARID1A deficiency in ovarian clear cell carcinoma.
    Title: Genome-wide DNA methylation in relation to ARID1A deficiency in ovarian clear cell carcinoma.
  6. Prognostic role of transcription factor ARID1A in patients with endometrial cancer of no specific molecular profile (NSMP) subtype.
    Title: Prognostic role of transcription factor ARID1A in patients with endometrial cancer of no specific molecular profile (NSMP) subtype.
  7. ARID1A regulates DNA repair through chromatin organization and its deficiency triggers DNA damage-mediated anti-tumor immune response.
    Title: ARID1A regulates DNA repair through chromatin organization and its deficiency triggers DNA damage-mediated anti-tumor immune response.
  8. Treatments, prognostic factors, and genetic heterogeneity in advanced cholangiocarcinoma: A multicenter real-world study.
    Title: Treatments, prognostic factors, and genetic heterogeneity in advanced cholangiocarcinoma: A multicenter real-world study.
  9. Deep-targeted gene sequencing reveals ARID1A mutation as an important driver of glioblastoma.
    Title: Deep-targeted gene sequencing reveals ARID1A mutation as an important driver of glioblastoma.
  10. ARID1A orchestrates SWI/SNF-mediated sequential binding of transcription factors with ARID1A loss driving pre-memory B cell fate and lymphomagenesis.
    Title: ARID1A orchestrates SWI/SNF-mediated sequential binding of transcription factors with ARID1A loss driving pre-memory B cell fate and lymphomagenesis.
Submit: New GeneRIF Correction See all GeneRIFs (298)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Intellectual disability, autosomal dominant 14
MedGen: C3553247 OMIM: 614607 GeneReviews: Not available
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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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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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 PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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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
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription coactivator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription coactivator activity NAS
Non-traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in chromatin remodeling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in chromatin remodeling NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in nervous system development IEA
Inferred from Electronic Annotation
more info
  
involved_in nucleosome disassembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of T cell differentiation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in positive regulation of cell differentiation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in positive regulation of double-strand break repair NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in positive regulation of myoblast differentiation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in positive regulation of stem cell population maintenance NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of G0 to G1 transition NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of G1/S transition of mitotic cell cycle NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of mitotic metaphase/anaphase transition NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of nucleotide-excision repair NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in transcription initiation-coupled chromatin remodeling TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of SWI/SNF complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of SWI/SNF complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of SWI/SNF complex NAS
Non-traceable Author Statement
more info
 PubMed 
part_of bBAF complex NAS
Non-traceable Author Statement
more info
 PubMed 
part_of brahma complex NAS
Non-traceable Author Statement
more info
 PubMed 
located_in chromatin IDA
Inferred from Direct Assay
more info
 PubMed 
located_in chromatin NAS
Non-traceable Author Statement
more info
 PubMed 
part_of nBAF complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of nBAF complex ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of nBAF complex NAS
Non-traceable Author Statement
more info
 PubMed 
part_of npBAF complex ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of npBAF complex NAS
Non-traceable Author Statement
more info
 PubMed 
is_active_in nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus TAS
Traceable Author Statement
more info
 PubMed 

General protein information

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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_006015.6 → NP_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
    D3DPL1, O14497, Q53FK9, Q5T0W1, Q5T0W2, Q5T0W3, Q8NFD6, Q96T89, Q9BY33, Q9HBJ5, Q9UPZ1
    UniProtKB/TrEMBL
    A0A0S2Q0B1
    Related
    ENSP00000320485.7, ENST00000324856.13
    Conserved Domains (5) summary
    TIGR01628
    Location:372 → 469
    PABP-1234; polyadenylate binding protein, human types 1, 2, 3, 4 family
    PRK07764
    Location:598 → 729
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    pfam09606
    Location:713 → 947
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    cd16876
    Location:1018 → 1110
    ARID_ARID1A; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1A (ARID1A) and similar proteins
    pfam12031
    Location:1976 → 2231
    BAF250_C; SWI/SNF-like complex subunit BAF250/Osa

  2. NM_139135.4 → NP_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/TrEMBL
    A0A0S2Q0B1
    Related
    ENSP00000387636.2, ENST00000457599.7
    Conserved Domains (3) summary
    smart00501
    Location:1018 → 1109
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
    pfam12004
    Location:596 → 881
    DUF3498; Domain of unknown function (DUF3498)
    pfam12031
    Location:1759 → 2014
    DUF3518; Domain of unknown function (DUF3518)

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_000001.11 Reference GRCh38.p14 Primary Assembly

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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    26533960..26620059
    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.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O14497.3 GenPept UniProtKB/Swiss-Prot:O14497

Gene LinkOut

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Chemical Information
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