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ARID3A AT-rich interaction domain 3A [ Homo sapiens (human) ]

Gene ID: 1820, updated on 2-Nov-2024

Summary

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Official Symbol
ARID3Aprovided by HGNC
Official Full Name
AT-rich interaction domain 3Aprovided by HGNC
Primary source
HGNC:HGNC:3031
See related
Ensembl:ENSG00000116017 MIM:603265; AllianceGenome:HGNC:3031
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
DRIL1; DRIL3; BRIGHT; E2FBP1
Summary
This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA binding proteins. It was found by homology to the Drosophila dead ringer gene, which is important for normal embryogenesis. Other ARID family members have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation, and possibly in chromatin structure modification. [provided by RefSeq, Jul 2008]
Expression
Broad expression in placenta (RPKM 13.1), bone marrow (RPKM 2.3) and 16 other tissues See more
Orthologs
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Genomic context

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See ARID3A in Genome Data Viewer
Location:
19p13.3
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (925732..975939)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (888464..938643)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (926035..975939)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak3217 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:904059-904817 Neighboring gene R3H domain containing 4 Neighboring gene Sharpr-MPRA regulatory region 9324 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9627 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9630 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:918907-919847 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:919848-920787 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9633 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9635 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9634 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9636 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:926209-926969 Neighboring gene KISS1 receptor Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:932426-932957 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:932958-933488 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:934552-935082 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9640 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:947299-947798 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9642 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13576 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:952365-953066 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:953067-953768 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:953750-953958 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:955173-955874 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:956577-957278 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:957654-957846 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:962809-963327 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:965021-965198 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:980065-980655 Neighboring gene HNF4 motif-containing MPRA enhancer 174 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9644 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:983939-984880 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:990841-991786 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9647 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:993929-994462 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:994463-994995 Neighboring gene WD repeat domain 18 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:996475-997094 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9648 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:1009528-1009718 Neighboring gene glutamate ionotropic receptor NMDA type subunit 3B Neighboring gene transmembrane protein 259

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Disease activity in systemic lupus erythematosus correlates with expression of the transcription factor AT-rich-interactive domain 3A. Ward JM, et al. Arthritis Rheumatol, 2014 Dec. PMID 25185498, Free PMC Article
  2. TLR engagement induces ARID3a in human blood hematopoietic progenitors and modulates IFNα production. Ratliff ML, et al. Cell Immunol, 2020 Nov. PMID 32979763, Free PMC Article
  3. New Frontiers: ARID3a in SLE. Garton J, et al. Cells, 2019 Sep 24. PMID 31554207, Free PMC Article
  4. ARID3A Positivity Correlated With Favorable Prognosis in Patients With Residual Rectal Cancer After Neoadjuvant Chemoradiotherapy. Yoon G, et al. Anticancer Res, 2019 Jun. PMID 31177122
  5. ARID3a gene profiles are strongly associated with human interferon alpha production. Ratliff ML, et al. J Autoimmun, 2019 Jan. PMID 30297159, Free PMC Article

See all (88) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ARID3A variant and the risk of primary biliary cholangitis in a Central European cohort.
    Title: ARID3A variant and the risk of primary biliary cholangitis in a Central European cohort.
  2. A regulatory variant at 19p13.3 is associated with primary biliary cholangitis risk and ARID3A expression.
    Title: A regulatory variant at 19p13.3 is associated with primary biliary cholangitis risk and ARID3A expression.
  3. Several genetic variants associated with systemic sclerosis in a Chinese Han population.
    Title: Several genetic variants associated with systemic sclerosis in a Chinese Han population.
  4. Hepatic ARID3A facilitates liver cancer malignancy by cooperating with CEP131 to regulate an embryonic stem cell-like gene signature.
    Title: Hepatic ARID3A facilitates liver cancer malignancy by cooperating with CEP131 to regulate an embryonic stem cell-like gene signature.
  5. ARID3A promotes the chemosensitivity of colon cancer by inhibiting AKR1C3.
    Title: ARID3A promotes the chemosensitivity of colon cancer by inhibiting AKR1C3.
  6. MiR-361-3p promotes tumorigenesis of osteosarcoma cells via targeting ARID3A.
    Title: MiR-361-3p promotes tumorigenesis of osteosarcoma cells via targeting ARID3A.
  7. The megakaryocytic transcription factor ARID3A suppresses leukemia pathogenesis.
    Title: The megakaryocytic transcription factor ARID3A suppresses leukemia pathogenesis.
  8. Deficiencies in the DNA Binding Protein ARID3a Alter Chromatin Structures Important for Early Human Erythropoiesis.
    Title: Deficiencies in the DNA Binding Protein ARID3a Alter Chromatin Structures Important for Early Human Erythropoiesis.
  9. ARID3A regulates autophagy related gene BECN1 expression and inhibits proliferation of osteosarcoma cells.
    Title: ARID3A regulates autophagy related gene BECN1 expression and inhibits proliferation of osteosarcoma cells.
  10. Distinct and overlapping roles of ARID3A and ARID3B in regulating E2Fdependent transcription via direct binding to E2F target genes.
    Title: Distinct and overlapping roles of ARID3A and ARID3B in regulating E2F‑dependent transcription via direct binding to E2F target genes.
Submit: New GeneRIF Correction See all GeneRIFs (40)

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

EBI GWAS Catalog

Description
A genome-wide association study of optic disc parameters.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables chromatin binding IEA
Inferred from Electronic Annotation
more info
  
enables identical protein binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription coregulator activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in membrane raft IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
AT-rich interactive domain-containing protein 3A
Names
ARID domain-containing 3A
ARID domain-containing protein 3A
AT rich interactive domain 3A (BRIGHT- like) protein
AT rich interactive domain 3A (BRIGHT-like)
B-cell regulator of IgH transcription
E2F-binding protein 1
dead ringer-like 1
dead ringer-like protein 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)

  1. NM_005224.3 → NP_005215.1  AT-rich interactive domain-containing protein 3A

    See identical proteins and their annotated locations for NP_005215.1

    Status: REVIEWED

    Source sequence(s)
    AC005379, AC005391, BC060828, U88047
    Consensus CDS
    CCDS12050.1
    UniProtKB/Swiss-Prot
    Q5I858, Q6P9C6, Q8IZA7, Q8N4Z3, Q99856
    Related
    ENSP00000263620.2, ENST00000263620.8
    Conserved Domains (1) summary
    smart00501
    Location:239 → 331
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

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

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    925732..975939
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017026445.2 → XP_016881934.1  AT-rich interactive domain-containing protein 3A isoform X1

    UniProtKB/Swiss-Prot
    Q5I858, Q6P9C6, Q8IZA7, Q8N4Z3, Q99856
    Conserved Domains (1) summary
    smart00501
    Location:239 → 331
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

  2. XM_005259514.5 → XP_005259571.1  AT-rich interactive domain-containing protein 3A isoform X1

    See identical proteins and their annotated locations for XP_005259571.1

    UniProtKB/Swiss-Prot
    Q5I858, Q6P9C6, Q8IZA7, Q8N4Z3, Q99856
    Conserved Domains (1) summary
    smart00501
    Location:239 → 331
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

  3. XM_005259513.6 → XP_005259570.1  AT-rich interactive domain-containing protein 3A isoform X1

    See identical proteins and their annotated locations for XP_005259570.1

    UniProtKB/Swiss-Prot
    Q5I858, Q6P9C6, Q8IZA7, Q8N4Z3, Q99856
    Conserved Domains (1) summary
    smart00501
    Location:239 → 331
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

  4. XM_047438380.1 → XP_047294336.1  AT-rich interactive domain-containing protein 3A isoform X2

  5. XM_047438381.1 → XP_047294337.1  AT-rich interactive domain-containing protein 3A isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    888464..938643
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054320138.1 → XP_054176113.1  AT-rich interactive domain-containing protein 3A isoform X1

  2. XM_054320139.1 → XP_054176114.1  AT-rich interactive domain-containing protein 3A isoform X1

  3. XM_054320137.1 → XP_054176112.1  AT-rich interactive domain-containing protein 3A isoform X1

  4. XM_054320140.1 → XP_054176115.1  AT-rich interactive domain-containing protein 3A isoform X2

  5. XM_054320142.1 → XP_054176117.1  AT-rich interactive domain-containing protein 3A isoform X4

  6. XM_054320141.1 → XP_054176116.1  AT-rich interactive domain-containing protein 3A isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q99856.2 GenPept UniProtKB/Swiss-Prot:Q99856

Gene LinkOut

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