Arid1a AT-rich interaction domain 1A [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Arid1aprovided by RGD
Official Full Name: AT-rich interaction domain 1Aprovided by RGD
Primary source: RGD:1310500
See related: EnsemblRapid:ENSRNOG00000006137 AllianceGenome:RGD:1310500
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable several functions, including ATP-dependent chromatin remodeler activity; nuclear receptor binding activity; and transcription coactivator activity. Predicted to contribute to nucleosome binding activity. Predicted to be involved in nucleosome disassembly; positive regulation of DNA-templated transcription; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including circulatory system development; embryo implantation; and embryonic morphogenesis. Predicted to be located in chromatin. Predicted to be part of SWI/SNF complex; nBAF complex; and npBAF complex. Predicted to be active in nucleoplasm. 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, Nov 2024]
Expression: Biased expression in Thymus (RPKM 176.2), Spleen (RPKM 163.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q36

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (151192014..151269291, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (145908173..145981552, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (151904687..151977973, complement)

Chromosome 5 - NC_086023.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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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

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

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

AA818481 (e-PCR)
- UniSTS:249715

RH143105 (e-PCR)
- UniSTS:232352

RH143917 (e-PCR)
- UniSTS:233163

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP-dependent chromatin remodeler activity	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
enables transcription coactivator activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within cardiac chamber development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cardiac muscle cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within chromatin organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryo implantation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within forebrain development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within formation of primary germ layer	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within gastrulation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neural tube closure	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within placenta blood vessel development	ISO Inferred from Sequence Orthology more info
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 regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within stem cell population maintenance	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of SWI/SNF complex	IBA Inferred from Biological aspect of Ancestor more info
part_of SWI/SNF complex	ISO Inferred from Sequence Orthology more info
part_of brahma complex	IEA Inferred from Electronic Annotation more info
located_in chromatin	ISO Inferred from Sequence Orthology more info
part_of nBAF complex	IBA Inferred from Biological aspect of Ancestor more info
part_of nBAF complex	ISO Inferred from Sequence Orthology more info
part_of npBAF complex	ISO Inferred from Sequence Orthology more info
is_active_in nucleoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info

General protein information

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

Names: AT rich interactive domain 1A (SWI-like); AT rich interactive domain 1A (Swi1 like)

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_001401278.1 → NP_001388207.1 AT-rich interactive domain-containing protein 1A isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

A0A8I6AJE2

Related

ENSRNOP00000009173.8, ENSRNOT00000009173.9
NM_001401279.1 → NP_001388208.1 AT-rich interactive domain-containing protein 1A isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086023.1 Reference GRCr8

Range

151192014..151269291 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063287285.1 → XP_063143355.1 AT-rich interactive domain-containing protein 1A isoform X2

Related

ENSRNOP00000088707.2, ENSRNOT00000102003.2
XM_063287284.1 → XP_063143354.1 AT-rich interactive domain-containing protein 1A isoform X1
XM_063287286.1 → XP_063143356.1 AT-rich interactive domain-containing protein 1A isoform X3