Format

Send to:

Choose Destination

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

Gene ID: 8289, updated on 8-Jul-2018
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; Vega:OTTHUMG00000004004
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
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

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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

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

  • 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...
Products Interactant Other Gene Complex Source Pubs Description

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 
RNA polymerase II transcription factor activity, sequence-specific DNA binding 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
 
cellular response to calcium ion HEP PubMed 
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
 
transcription, DNA-templated 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 
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

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_006015.5NP_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, OTTHUMP00000004117, 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, OTTHUMP00000004118, 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 details...Open this link in a new tab

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.
Support Center