ARID1A AT rich interactive domain 1A (SWI-like) [Homo sapiens] - Gene

Help top of page

Summary

Official Symbol: ARID1Aprovided by HGNC
Official Full Name: AT rich interactive domain 1A (SWI-like)provided by HGNC
Primary source: HGNC:11110
Locus tag: RP1-50O24.1
See related: Ensembl:ENSG00000117713; HPRD:04319; 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; 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]

Help top of page

Genomic context

Location :: 1p35.3

Sequence :: Chromosome: 1; NC_000001.10 (27022522..27108601)

See ARID1A in Epigenomics, MapViewer

Chromosome 1 - NC_000001.10 Genomic Context describing neighboring genes

Help top of page

Genomic regions, transcripts, and products

Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

Help top of page

Bibliography

GeneRIFs: Gene References Into Functions What's a GeneRIF?

loss of ARID1A in ovarian clear cell carcinoma is a negative prognostic factor in patients treated with platinum-based chemotherapy
Title: Loss of ARID1A expression is related to shorter progression-free survival and chemoresistance in ovarian clear cell carcinoma.
The aberrant chromatin remodeling consequent to ARID1A inactivation contributes to a variety of different types of neoplasms.
Title: Somatic mutations in the chromatin remodeling gene ARID1A occur in several tumor types.
The mutation spectrum for ARID1A differs between molecular subtypes of gastric cancer, and mutation prevalence is negatively associated with mutations in TP53
Title: Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer.
ARID1A is a bona fide tumor suppressor that collaborates with p53 to regulate CDKN1A and SMAD3 transcription and tumor growth in gynecologic cancers.
Title: ARID1A, a factor that promotes formation of SWI/SNF-mediated chromatin remodeling, is a tumor suppressor in gynecologic cancers.
uterine low-grade endometrioid carcinoma is the predominant tumor type harboring ARID1A mutations and frequent loss of ARID1A expression
Title: Mutation and loss of expression of ARID1A in uterine low-grade endometrioid carcinoma.
genes mutated in ovarian clear cell carcinoma(OCCC);data suggest PPP2R1A functions as an oncogene and ARID1A as tumor-suppressor gene; in 42 OCCCs, 7% had mutations in PPP2R1A and 57% in ARID1A; suggests aberrant chromatin remodeling contributes to OCCC
Title: Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma.
These data implicate ARID1A as a tumor-suppressor gene frequently disrupted in ovarian clear-cell and endometrioid carcinomas.
Title: ARID1A mutations in endometriosis-associated ovarian carcinomas.
Results report that BAF250b complexes purified from mammalian cells contain elongin C (Elo C), a BC box binding component of an E3 ubiquitin ligase.
Title: Mammalian SWI/SNF--a subunit BAF250/ARID1 is an E3 ubiquitin ligase that targets histone H2B.
ARID1A/BAF250A was identified as a new HIC1 partner.
Title: HIC1 interacts with a specific subunit of SWI/SNF complexes, ARID1A/BAF250A.
in the primary breast carcinoma, transforming ARID1A sequence was an antisense cDNA, and was the product of a genomic rearrangement; identified a lung adenocarcinoma cell line with a highly localized homozygous genomic deletion in the 5' end of ARID1A
Title: Genomic and functional evidence for an ARID1A tumor suppressor role.

Submit: New GeneRIF Correction See all (16)

Help top of page

Phenotypes

Review eQTL and phenotype association data in this region using PheGenI

Mental retardation, autosomal dominant 14

MIM: 614607

Help top of page

Products	Interactant	Other Gene	Source	Pubs	Description
O14497	Q03111	MLLT1	HPRD	PubMed
O14497	P51532	SMARCA4	HPRD	PubMed
BioGRID:113894	BioGRID:116967	ADNP	BioGRID	PubMed	Affinity Capture-MS
BioGRID:113894	BioGRID:121559	ARID1B	BioGRID	PubMed	Affinity Capture-Western
BioGRID:113894	BioGRID:114691	BCL7C	BioGRID	PubMed	Affinity Capture-MS
BioGRID:113894	BioGRID:198328	Bcl7b	BioGRID	PubMed	Affinity Capture-MS
BioGRID:113894	BioGRID:115760	CARM1	BioGRID	PubMed	Affinity Capture-Western; Co-purification
BioGRID:113894	BioGRID:120775	CHD7	BioGRID	PubMed	Affinity Capture-MS
BioGRID:113894	BioGRID:114031	CUL2	BioGRID	PubMed	Affinity Capture-Western
BioGRID:113894	BioGRID:111909	DPF2	BioGRID	PubMed	Affinity Capture-Western
BioGRID:113894	BioGRID:108893	GATA1	BioGRID	PubMed	Reconstituted Complex
BioGRID:113894	BioGRID:109337	HIC1	BioGRID	PubMed	Affinity Capture-Western; Two-hybrid
BioGRID:113894	BioGRID:109833	ING1	BioGRID	PubMed	Affinity Capture-MS
BioGRID:113894	BioGRID:123747	ITCH	BioGRID	PubMed	Affinity Capture-MS
BioGRID:113894	BioGRID:115904	KLF1	BioGRID	PubMed	Reconstituted Complex
BioGRID:113894	BioGRID:110811	NEDD4	BioGRID	PubMed	Affinity Capture-MS
BioGRID:113894	BioGRID:120490	PBRM1	BioGRID	PubMed	Affinity Capture-Western
BioGRID:113894	BioGRID:111260	PGR	BioGRID	PubMed	Reconstituted Complex
BioGRID:113894	BioGRID:111849	RARA	BioGRID	PubMed	Reconstituted Complex
BioGRID:113894	BioGRID:110262	SMAD2	BioGRID	PubMed	Affinity Capture-MS
BioGRID:113894	BioGRID:110263	SMAD3	BioGRID	PubMed	Affinity Capture-MS
BioGRID:113894	BioGRID:112479	SMARCA2	BioGRID	PubMed	Affinity Capture-MS; Co-purification
BioGRID:113894	BioGRID:112481	SMARCA4	BioGRID	PubMed	Affinity Capture-MS; Affinity Capture-Western; Co-purification
BioGRID:113894	BioGRID:112482	SMARCB1	BioGRID	PubMed	Affinity Capture-MS; Affinity Capture-Western; Co-purification
BioGRID:113894	BioGRID:112483	SMARCC1	BioGRID	PubMed	Affinity Capture-Western
BioGRID:113894	BioGRID:112485	SMARCC2	BioGRID	PubMed	Affinity Capture-MS; Affinity Capture-Western
BioGRID:113894	BioGRID:112486	SMARCD1	BioGRID	PubMed	Affinity Capture-MS
BioGRID:113894	BioGRID:112489	SMARCE1	BioGRID	PubMed	Affinity Capture-MS; Affinity Capture-Western
BioGRID:113894	BioGRID:112540	SOX2	BioGRID	PubMed	Affinity Capture-MS
BioGRID:113894	BioGRID:112592	SRC	BioGRID	PubMed	Reconstituted Complex
BioGRID:113894	BioGRID:113164	UBC	BioGRID	PubMed	Affinity Capture-MS
BioGRID:113894	BioGRID:1205541	tat	BioGRID	PubMed	Reconstituted Complex

Function	Evidence Code	Pubs
DNA binding	NAS Non-traceable Author Statement more info	PubMed
binding	IEA Inferred from Electronic Annotation more info
ligand-dependent nuclear receptor binding	IPI Inferred from Physical Interaction more info	PubMed
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
androgen receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
chromatin organization	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
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
nervous system development	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
positive regulation of transcription, DNA-dependent	IDA Inferred from Direct Assay more info	PubMed
regulation of transcription from RNA polymerase II promoter	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
SWI/SNF complex	IDA Inferred from Direct Assay more info	PubMed
SWI/SNF complex	IEA Inferred from Electronic Annotation more info
intracellular	IEA Inferred from Electronic Annotation more info
nBAF complex	IEA Inferred from Electronic Annotation more info
nBAF complex	ISS Inferred from Sequence or Structural Similarity more info
npBAF complex	IEA Inferred from Electronic Annotation more info
npBAF complex	ISS Inferred from Sequence or Structural Similarity more info
nuclear chromatin	IDA Inferred from Direct Assay more info	PubMed
NOT nucleolus	IDA Inferred from Direct Assay more info	PubMed
nucleus	IDA Inferred from Direct Assay more info	PubMed
nucleus	TAS Traceable Author Statement more info	PubMed
soluble fraction	IEA Inferred from Electronic Annotation more info

General protein information

Preferred Names: AT-rich interactive domain-containing protein 1A

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

Help top of page

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

NG_029965.1 RefSeqGene

Range

5001..91080

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_006015.4 → NP_006006.3 AT-rich interactive domain-containing protein 1A isoform a

Status: REVIEWED

Description

Transcript Variant: This variant (1) is the longer transcript and encodes the longer isoform (a).

Source sequence(s)

AF521670, AL034380, AL512408

Consensus CDS

CCDS285.1

UniProtKB/Swiss-Prot

O14497

Related

ENSP00000320485, OTTHUMP00000004117, ENST00000324856, OTTHUMT00000011437

Conserved Domains (2) summary

pfam12031
Location:1975 – 2231
Blast Score: 1173

DUF3518; Domain of unknown function (DUF3518)

cl02633
Location:1017 – 1104
Blast Score: 273

ARID; ARID/BRIGHT DNA binding domain
NM_139135.2 → NP_624361.1 AT-rich interactive domain-containing protein 1A isoform b

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)

AF268913, AF521670, AL034380, AL512408

Consensus CDS

CCDS44091.1

UniProtKB/Swiss-Prot

O14497

Related

ENSP00000387636, OTTHUMP00000004118, ENST00000457599, OTTHUMT00000011438

Conserved Domains (2) summary

pfam12031
Location:1758 – 2014
Blast Score: 1168

DUF3518; Domain of unknown function (DUF3518)

cl02633
Location:1017 – 1104
Blast Score: 274

ARID; ARID/BRIGHT DNA binding domain

RefSeqs of Annotated Genomes: Build 37.3

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

Reference GRCh37.p5 Primary Assembly

Genomic

NC_000001.10 Reference GRCh37.p5 Primary Assembly

Range

27022522..27108601

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000133.1 Alternate HuRef

Range

25309350..25361809

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.

Help top of page

Related Sequences

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	AB024075.2	BAA83073.1
genomic	AL034380.26	CAI21621.1
		CAI21622.1
		CAI21623.1
		CAI21629.1
genomic	AL034380.26	CAI21621.1
		CAI21622.1
		CAI21623.1
		CAI21629.1
genomic	AL512408.12	CAI23482.1
		CAI23483.1
		CAI23484.1
genomic	CH471059.2	EAX07793.1
		EAX07794.1
		EAX07795.1
		EAX07796.1
		EAX07797.1
mRNA	AB001895.1	BAA23269.1
mRNA	AB210022.1	BAE06104.1
mRNA	AF217506.1	AAF67617.1
mRNA	AF219114.1	AAG17549.2
mRNA	AF231056.1	AAG33967.1
mRNA	AF265208.1	AAF75765.1
mRNA	AF268913.1	AAK54505.1
mRNA	AF521670.1	AAN03446.1
mRNA	AK027442.1	BAB55114.1
mRNA	AK027467.1	BAB55132.1
mRNA	AK027655.1	BAB55270.1
mRNA	AK074940.1	BAC11306.1
mRNA	AK223275.1	BAD96995.1
mRNA	AK308363.1	None
mRNA	BC112895.1	AAI12896.1

Protein Accession	Links
Protein Accession	GenPept Link	UniProtKB Link
O14497.3	GenPept	UniProtKB/Swiss-Prot:O14497
Q4LE49	GenPept	UniProtKB/TrEMBL:Q4LE49
Q5JYH3	GenPept	UniProtKB/TrEMBL:Q5JYH3
Q8NC65	GenPept	UniProtKB/TrEMBL:Q8NC65
Q96SM7	GenPept	UniProtKB/TrEMBL:Q96SM7
Q96SY8	GenPept	UniProtKB/TrEMBL:Q96SY8
Q96T01	GenPept	UniProtKB/TrEMBL:Q96T01
Q96TA9	GenPept	UniProtKB/TrEMBL:Q96TA9
Q9NZ92	GenPept	UniProtKB/TrEMBL:Q9NZ92