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

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; 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: mouse all
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Genomic context

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
ARID1A in Gynecologic Precancers and Cancers.
Title: ARID1A in Gynecologic Precancers and Cancers.
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.
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.
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.
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.
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.
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.
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	Compare labs

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)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

MARC_11851-11852:1029349291:1 (e-PCR)
- UniSTS:267276

MARC_6181-6182:992006984:1 (e-PCR)
- UniSTS:231199

HSC27A052 (e-PCR)
- UniSTS:20016

SHGC-74444 (e-PCR)
- UniSTS:52310

D1S1417 (e-PCR)
- UniSTS:149613

Arid1a (e-PCR), detects polymorphism
- UniSTS:547183

SHGC-74487 (e-PCR)
- UniSTS:63376

D1S2243 (e-PCR)
- UniSTS:21138

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

NG_029965.1 RefSeqGene

Range

5001..91080

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_875

mRNA and Protein(s)

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
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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

26696015..26782104

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

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

NM_018450.4: Suppressed sequence

Description

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