Arid1a AT-rich interaction domain 1A [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Arid1aprovided by MGI
Official Full Name: AT-rich interaction domain 1Aprovided by MGI
Primary source: MGI:MGI:1935147
See related: Ensembl:ENSMUSG00000007880 AllianceGenome:MGI:1935147
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Osa1; BAF250; BAF250a; Smarcf1; 1110030E03Rik
Summary: Enables ATP-dependent chromatin remodeler activity. Contributes to nucleosome binding activity. Acts upstream of or within several processes, including animal organ development; embryonic morphogenesis; and toxin transport. Located in chromatin. Part of SWI/SNF complex; nBAF complex; and npBAF complex. Is expressed in several structures, including alimentary system; brain; early conceptus; genitourinary system; and sensory organ. Used to study Coffin-Siris syndrome. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 2; breast cancer; carcinoma (multiple); gastrointestinal system cancer (multiple); and neuroblastoma. Orthologous to human ARID1A (AT-rich interaction domain 1A). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in thymus adult (RPKM 94.0), spleen adult (RPKM 52.9) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 4 D2.3; 4 66.25 cM

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	4	NC_000070.7 (133406319..133484682, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	4	NC_000070.6 (133679008..133756769, complement)

Chromosome 4 - NC_000070.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Neuropathic pain development following nerve injury is mediated by SOX11-ARID1A-SOCS3 transcriptional regulation in the spinal cord.
Title: Neuropathic pain development following nerve injury is mediated by SOX11-ARID1A-SOCS3 transcriptional regulation in the spinal cord.
Abnormal chromatin remodeling caused by ARID1A deletion leads to malformation of the dentate gyrus.
Title: Abnormal chromatin remodeling caused by ARID1A deletion leads to malformation of the dentate gyrus.
GLS1 is a protective factor in patients with ovarian clear cell carcinoma and its expression does not correlate with ARID1A-mutated tumors.
Title: GLS1 is a protective factor in patients with ovarian clear cell carcinoma and its expression does not correlate with ARID1A-mutated tumors.
Endothelial Arid1a deletion disrupts the balance among angiogenesis, neurogenesis and gliogenesis in the developing brain.
Title: Endothelial Arid1a deletion disrupts the balance among angiogenesis, neurogenesis and gliogenesis in the developing brain.
ARID1A Regulates Progesterone Receptor Expression in Early Endometrial Endometrioid Carcinoma Pathogenesis.
Title: ARID1A Regulates Progesterone Receptor Expression in Early Endometrial Endometrioid Carcinoma Pathogenesis.
Arid1a loss potentiates pancreatic beta-cell regeneration through activation of EGF signaling.
Title: Arid1a loss potentiates pancreatic β-cell regeneration through activation of EGF signaling.
Abnormal microglial polarization induced by Arid1a deletion leads to neuronal differentiation deficits.
Title: Abnormal microglial polarization induced by Arid1a deletion leads to neuronal differentiation deficits.
Arid1a mutation suppresses TGF-beta signaling and induces cholangiocarcinoma.
Title: Arid1a mutation suppresses TGF-β signaling and induces cholangiocarcinoma.
Loss of Arid1a and Pten in Pancreatic Ductal Cells Induces Intraductal Tubulopapillary Neoplasm via the YAP/TAZ Pathway.
Title: Loss of Arid1a and Pten in Pancreatic Ductal Cells Induces Intraductal Tubulopapillary Neoplasm via the YAP/TAZ Pathway.

Submit: New GeneRIF Correction See all GeneRIFs (58)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Chemically induced (ENU) (2) 1 citation
Endonuclease-mediated (3)
Targeted (7) 1 citation

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

Smarcf1 (e-PCR), detects polymorphism
- UniSTS:226146

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

AA818481 (e-PCR)
- UniSTS:249715

RH143917 (e-PCR)
- UniSTS:233163

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables ATP-dependent chromatin remodeler activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables nuclear receptor binding	ISO Inferred from Sequence Orthology more info
contributes_to nucleosome binding	IBA Inferred from Biological aspect of Ancestor more info
contributes_to nucleosome binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in androgen receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cardiac chamber development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cardiac muscle cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within chromatin organization	IPI Inferred from Physical Interaction more info	PubMed
acts_upstream_of_or_within chromatin remodeling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within embryo implantation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within forebrain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within formation of primary germ layer	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within gastrulation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular estrogen receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in intracellular glucocorticoid receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nervous system development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neural tube closure	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nucleosome disassembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within optic cup formation involved in camera-type eye development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within placenta blood vessel development	IMP Inferred from Mutant Phenotype 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	ISO Inferred from Sequence Orthology more info
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
acts_upstream_of_or_within stem cell population maintenance	IMP Inferred from Mutant Phenotype 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	ISO Inferred from Sequence Orthology more info
part_of SWI/SNF complex	NAS Non-traceable Author Statement more info	PubMed
part_of SWI/SNF superfamily-type complex	IDA Inferred from Direct Assay 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
part_of chromatin	IDA Inferred from Direct Assay more info	PubMed
part_of chromatin	ISO Inferred from Sequence Orthology more info
part_of 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	IDA Inferred from Direct Assay more info	PubMed
part_of nBAF complex	NAS Non-traceable Author Statement more info	PubMed
part_of npBAF complex	IDA Inferred from Direct Assay more info	PubMed
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	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

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); AT rich interactive domain 1A (Swi1 like); BRG1-associated factor 250a; SWI-like protein; SWI/SNF complex protein p270; SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin subfamily F member 1; 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.

mRNA and Protein(s)

NM_001080819.2 → NP_001074288.1 AT-rich interactive domain-containing protein 1A isoform 1

See identical proteins and their annotated locations for NP_001074288.1

Status: VALIDATED

Source sequence(s)

BX537327, CR751606, CR925752

Consensus CDS

CCDS38908.1

UniProtKB/Swiss-Prot

A2BH40, Q640Q1, Q925Q1

Related

ENSMUSP00000101517.4, ENSMUST00000105897.10

Conserved Domains (2) summary

smart00501
Location:1019 → 1110

BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

pfam12031
Location:1974 → 2229

DUF3518; Domain of unknown function (DUF3518)
NM_001363070.2 → NP_001349999.1 AT-rich interactive domain-containing protein 1A isoform 2

Status: VALIDATED

Source sequence(s)

BX537327, CR751606, CR925752

Consensus CDS

CCDS89836.1

Related

ENSMUSP00000008024.7, ENSMUST00000008024.7

Conserved Domains (4) summary

PHA03247
Location:726 → 1279

PHA03247; large tegument protein UL36; Provisional

pfam09606
Location:232 → 596

Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

cd16876
Location:634 → 726

ARID_ARID1A; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1A (ARID1A) and similar proteins

pfam12031
Location:1593 → 1848

BAF250_C; SWI/SNF-like complex subunit BAF250/Osa
NM_001401271.1 → NP_001388200.1 AT-rich interactive domain-containing protein 1A isoform 3

Status: VALIDATED

Source sequence(s)

BX537327, CR751606, CR925752
NM_001401273.1 → NP_001388202.1 AT-rich interactive domain-containing protein 1A isoform 4

Status: VALIDATED

Source sequence(s)

BX537327, CR751606, CR925752

UniProtKB/TrEMBL

E9QAQ7

Related

ENSMUSP00000122354.3, ENSMUST00000145664.9
NM_001401275.1 → NP_001388204.1 AT-rich interactive domain-containing protein 1A isoform 2

Status: VALIDATED

Source sequence(s)

BX537327, CR751606, CR925752
NM_001401276.1 → NP_001388205.1 AT-rich interactive domain-containing protein 1A isoform 2

Status: VALIDATED

Source sequence(s)

BX537327, CR751606, CR925752

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000070.7 Reference GRCm39 C57BL/6J

Range

133406319..133484682 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006539327.5 → XP_006539390.1 AT-rich interactive domain-containing protein 1A isoform X3

UniProtKB/Swiss-Prot

A2BH40

Conserved Domains (4) summary

PHA03247
Location:726 → 1280

PHA03247; large tegument protein UL36; Provisional

cd16876
Location:634 → 726

ARID_ARID1A; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1A (ARID1A) and similar proteins

pfam12004
Location:212 → 501

DUF3498; Domain of unknown function (DUF3498)

pfam12031
Location:1594 → 1849

BAF250_C; SWI/SNF-like complex subunit BAF250/Osa
XM_030253943.2 → XP_030109803.1 AT-rich interactive domain-containing protein 1A isoform X3

Conserved Domains (4) summary

PHA03247
Location:726 → 1280

PHA03247; large tegument protein UL36; Provisional

cd16876
Location:634 → 726

ARID_ARID1A; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1A (ARID1A) and similar proteins

pfam12004
Location:212 → 501

DUF3498; Domain of unknown function (DUF3498)

pfam12031
Location:1594 → 1849

BAF250_C; SWI/SNF-like complex subunit BAF250/Osa