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ARID2 AT-rich interaction domain 2 [ Homo sapiens (human) ]

Gene ID: 196528, updated on 6-Oct-2018

Summary

Official Symbol
ARID2provided by HGNC
Official Full Name
AT-rich interaction domain 2provided by HGNC
Primary source
HGNC:HGNC:18037
See related
Ensembl:ENSG00000189079 MIM:609539; Vega:OTTHUMG00000150487
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
CSS6; p200; BAF200
Summary
This gene encodes a member of the AT-rich interactive domain (ARID)-containing family of DNA-binding proteins. Members of the ARID family have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation and chromatin structure modification. This protein functions as a subunit of the polybromo- and BRG1-associated factor or PBAF (SWI/SNF-B) chromatin remodeling complex which facilitates ligand-dependent transcriptional activation by nuclear receptors. Mutations in this gene are associated with hepatocellular carcinomas. A pseudogene of this gene is found on chromosome1. [provided by RefSeq, Dec 2016]
Expression
Broad expression in testis (RPKM 13.8), thyroid (RPKM 5.2) and 25 other tissues See more
Orthologs

Genomic context

See ARID2 in Genome Data Viewer
Location:
12q12
Exon count:
24
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (45729706..45908040)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (46123494..46301820)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369744 Neighboring gene long intergenic non-protein coding RNA 938 Neighboring gene uncharacterized LOC105369745 Neighboring gene RNA, 7SL, cytoplasmic 246, pseudogene Neighboring gene lysine rich nucleolar protein 1 pseudogene 2 Neighboring gene SR-related CTD associated factor 11 Neighboring gene ribosomal protein L13a pseudogene 21

Genomic regions, transcripts, and products

Expression

  • 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

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
COFFIN-SIRIS SYNDROME 6
MedGen: C4540499 OMIM: 617808 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2018-09-26)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2018-09-26)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
NHGRI GWA Catalog
Hippocampal atrophy as a quantitative trait in a genome-wide association study identifying novel susceptibility genes for Alzheimer's disease.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat A PBAF-specific component BAF200 is required for HIV-1 Tat-mediated activation of HIV LTR PubMed
tat Acetylated HIV-1 Tat binds efficiently to BRG1 and BAF200 (component of PBAF complex) and weakly to BAF250 (component of BAF complex) PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • 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...
  • 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ30619, KIAA1557, DKFZp686G052, DKFZp779P0222

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cardiac muscle cell proliferation IEA
Inferred from Electronic Annotation
more info
 
coronary artery morphogenesis IEA
Inferred from Electronic Annotation
more info
 
embryonic organ development IEA
Inferred from Electronic Annotation
more info
 
heart morphogenesis IEA
Inferred from Electronic Annotation
more info
 
homeostatic process IEA
Inferred from Electronic Annotation
more info
 
negative regulation of cell migration IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
nucleosome disassembly IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nucleoplasm IDA
Inferred from Direct Assay
more info
 
plasma membrane IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
AT-rich interactive domain-containing protein 2
Names
ARID domain-containing protein 2
AT rich interactive domain 2 (ARID, RFX-like)
BRG1-associated factor 200
zinc finger protein with activation potential
zipzap/p200

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

  1. NG_052800.1 RefSeqGene

    Range
    5045..183376
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001347839.1NP_001334768.1  AT-rich interactive domain-containing protein 2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and 3' coding region compared to isoform 1. The encoded isoform (2) has a shorter C-terminus compared to isoform 1.
    Source sequence(s)
    AC008124, AC009464, CR749833
    UniProtKB/Swiss-Prot
    Q68CP9
    Related
    ENSP00000415650.1, ENST00000422737.5
  2. NM_152641.3NP_689854.2  AT-rich interactive domain-containing protein 2 isoform 1

    See identical proteins and their annotated locations for NP_689854.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform 1.
    Source sequence(s)
    AC008124, AC009464, BX537879, DQ096628
    Consensus CDS
    CCDS31783.1
    UniProtKB/Swiss-Prot
    Q68CP9
    Related
    ENSP00000335044.6, OTTHUMP00000197509, ENST00000334344.10, OTTHUMT00000318380
    Conserved Domains (2) summary
    pfam01388
    Location:19101
    ARID; ARID/BRIGHT DNA binding domain
    pfam02257
    Location:521601
    RFX_DNA_binding; RFX DNA-binding domain

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_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    45729706..45908040
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006719272.4XP_006719335.1  AT-rich interactive domain-containing protein 2 isoform X1

    See identical proteins and their annotated locations for XP_006719335.1

    Conserved Domains (2) summary
    pfam01388
    Location:19101
    ARID; ARID/BRIGHT DNA binding domain
    pfam02257
    Location:521601
    RFX_DNA_binding; RFX DNA-binding domain
  2. XM_011538025.1XP_011536327.1  AT-rich interactive domain-containing protein 2 isoform X2

    Related
    ENSP00000397307.1, OTTHUMP00000197511, ENST00000444670.5, OTTHUMT00000318382
    Conserved Domains (1) summary
    pfam02257
    Location:157
    RFX_DNA_binding; RFX DNA-binding domain

RNA

  1. XR_944505.3 RNA Sequence

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