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ARID5A AT-rich interaction domain 5A [ Homo sapiens (human) ]

Gene ID: 10865, updated on 3-Apr-2024

Summary

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Official Symbol
ARID5Aprovided by HGNC
Official Full Name
AT-rich interaction domain 5Aprovided by HGNC
Primary source
HGNC:HGNC:17361
See related
Ensembl:ENSG00000196843 MIM:611583; AllianceGenome:HGNC:17361
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
MRF1; MRF-1; RP11-363D14
Summary
Members of the ARID protein family, including ARID5A, have diverse functions but all appear to play important roles in development, tissue-specific gene expression, and regulation of cell growth (Patsialou et al., 2005 [PubMed 15640446]).[supplied by OMIM, Mar 2008]
Expression
Ubiquitous expression in bone marrow (RPKM 12.1), appendix (RPKM 8.5) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
2q11.2
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (96536752..96552638)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (97043371..97059257)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (97202489..97218375)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97162590-97163590 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97163591-97164590 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16218 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11767 Neighboring gene neuralized E3 ubiquitin protein ligase 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97190085-97190604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11768 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11769 Neighboring gene uncharacterized LOC105373496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16219 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97196747-97197538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97197539-97198328 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11771 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11772 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16221 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:97204265-97204810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97219546-97220071 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:97230045-97230545 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:97230616-97231116 Neighboring gene KAT8 regulatory NSL complex subunit 3 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:97273727-97274926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16223 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11773 Neighboring gene fer-1 like family member 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:97326800-97327300 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:97327301-97327801 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:97351655-97352380 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97359457-97359958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97360677-97361221 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97361222-97361765

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
  • 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. Differentially regulated gene expression in quiescence versus senescence and identification of ARID5A as a quiescence associated marker. Anwar T, et al. J Cell Physiol, 2018 May. PMID 29044508
  2. AT-rich-interactive domain-containing protein 5A functions as a negative regulator of retinoic acid receptor-related orphan nuclear receptor γt-induced Th17 cell differentiation. Saito Y, et al. Arthritis Rheumatol, 2014 May. PMID 24782182
  3. Repression by a differentiation-specific factor of the human cytomegalovirus enhancer. Huang TH, et al. Nucleic Acids Res, 1996 May 1. PMID 8649988, Free PMC Article
  4. Genome-wide association study of theta band event-related oscillations identifies serotonin receptor gene HTR7 influencing risk of alcohol dependence. Zlojutro M, et al. Am J Med Genet B Neuropsychiatr Genet, 2011 Jan. PMID 21184583, Free PMC Article
  5. Modulator recognition factor 1, an AT-rich interaction domain family member, is a novel corepressor for estrogen receptor alpha. Georgescu SP, et al. Mol Endocrinol, 2005 Oct. PMID 15941852

See all (23) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Overexpression of ARID5A resulted in more number of cells in G0/G1 phase of cell cycle
    Title: Differentially regulated gene expression in quiescence versus senescence and identification of ARID5A as a quiescence associated marker.
  2. AT-rich-interactive domain-containing protein 5A functions as a negative regulator of retinoic acid receptor-related orphan nuclear receptor gammat-induced Th17 cell differentiation.
    Title: AT-rich-interactive domain-containing protein 5A functions as a negative regulator of retinoic acid receptor-related orphan nuclear receptor γt-induced Th17 cell differentiation.
Submit: New GeneRIF Correction

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
Genome-wide association study of theta band event-related oscillations identifies serotonin receptor gene HTR7 influencing risk of alcohol dependence.
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

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of AT rich interactive domain 5A (ARID5A) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

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 TAS
Traceable Author Statement
more info
 PubMed 
enables RNA stem-loop binding IEA
Inferred from Electronic Annotation
more info
  
enables chromatin binding IEA
Inferred from Electronic Annotation
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables nuclear androgen receptor binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables nuclear estrogen receptor binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables nuclear retinoid X receptor binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables nuclear thyroid hormone receptor binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription cis-regulatory region binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables transcription corepressor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription factor binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in cellular response to estrogen stimulus IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to lipopolysaccharide IEA
Inferred from Electronic Annotation
more info
  
involved_in chondrocyte differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in innate immune response IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of DNA-templated transcription TAS
Traceable Author Statement
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of T-helper 1 cell cytokine production IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of T-helper 17 type immune response IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of interleukin-17 production IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of interleukin-6 production IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of protein acetylation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of tumor necrosis factor production IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of type II interferon production 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 nucleolus IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of transcription regulator complex IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
AT-rich interactive domain-containing protein 5A
Names
ARID domain-containing protein 5A
AT rich interactive domain 5A (MRF1-like)
RFVG5814
modulator recognition factor 1
modulator recognition factor I

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_001319085.2 → NP_001306014.1  AT-rich interactive domain-containing protein 5A isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    BC067301, BX396215, HY002073
    Conserved Domains (2) summary
    PHA03247
    Location:132 → 440
    PHA03247; large tegument protein UL36; Provisional
    cl28902
    Location:61 → 197
    ARID; ARID/BRIGHT DNA binding domain family

  2. NM_001319087.2 → NP_001306016.1  AT-rich interactive domain-containing protein 5A isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is 1 aa shorter compared to isoform a.
    Source sequence(s)
    BC067301, CR981009, HY002073
    Conserved Domains (1) summary
    smart00501
    Location:61 → 201
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

  3. NM_001319092.1 → NP_001306021.1  AT-rich interactive domain-containing protein 5A isoform d

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (d) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform a.
    Source sequence(s)
    AC013270, AI085152, BC047390
    Consensus CDS
    CCDS82484.1
    UniProtKB/Swiss-Prot
    Q03989
    Related
    ENSP00000400785.1, ENST00000454558.2
    Conserved Domains (1) summary
    smart00501
    Location:1 → 80
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

  4. NM_001319093.2 → NP_001306022.1  AT-rich interactive domain-containing protein 5A isoform e

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) uses two alternate splice junctions and lacks an alternate exon compared to variant 1. The resulting isoform (e) is shorter at the N-terminus compared to isoform a. Variants 5, 6, and 7 all encode the same isoform (e).
    Source sequence(s)
    AC013270, BC067301, HY076710

  5. NM_001319094.2 → NP_001306023.1  AT-rich interactive domain-containing protein 5A isoform e

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) uses two alternate splice junctions compared to variant 1. The resulting isoform (e) is shorter at the N-terminus compared to isoform a. Variants 5, 6, and 7 all encode the same isoform (e).
    Source sequence(s)
    BC067301, BM556343, HY002073

  6. NM_001319096.2 → NP_001306025.1  AT-rich interactive domain-containing protein 5A isoform e

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) uses lacks an alternate exon compared to variant 1. The resulting isoform (e) is shorter at the N-terminus compared to isoform a. Variants 5, 6, and 7 all encode the same isoform (e).
    Source sequence(s)
    AI085152, BX648918
    Related
    ENST00000497920.1

  7. NM_212481.3 → NP_997646.1  AT-rich interactive domain-containing protein 5A isoform c

    See identical proteins and their annotated locations for NP_997646.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AI085152, HY002073, M62324
    Consensus CDS
    CCDS33251.1
    UniProtKB/Swiss-Prot
    C9J1Q0, Q03989, Q6NX37
    UniProtKB/TrEMBL
    B4DTE1
    Related
    ENSP00000350078.3, ENST00000357485.8
    Conserved Domains (1) summary
    smart00501
    Location:61 → 148
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    96536752..96552638
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047443000.1 → XP_047298956.1  AT-rich interactive domain-containing protein 5A isoform X1

  2. XM_011510499.3 → XP_011508801.1  AT-rich interactive domain-containing protein 5A isoform X2

    See identical proteins and their annotated locations for XP_011508801.1

    UniProtKB/TrEMBL
    B4DTE1
    Conserved Domains (1) summary
    smart00501
    Location:71 → 158
    BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

  3. XM_017003183.2 → XP_016858672.1  AT-rich interactive domain-containing protein 5A isoform X1

  4. XM_047443001.1 → XP_047298957.1  AT-rich interactive domain-containing protein 5A isoform X2

  5. XM_047443002.1 → XP_047298958.1  AT-rich interactive domain-containing protein 5A isoform X3

  6. XM_047443003.1 → XP_047298959.1  AT-rich interactive domain-containing protein 5A isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    97043371..97059257
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054340223.1 → XP_054196198.1  AT-rich interactive domain-containing protein 5A isoform X1

  2. XM_054340224.1 → XP_054196199.1  AT-rich interactive domain-containing protein 5A isoform X2

  3. XM_054340225.1 → XP_054196200.1  AT-rich interactive domain-containing protein 5A isoform X3

  4. XM_054340226.1 → XP_054196201.1  AT-rich interactive domain-containing protein 5A isoform X4

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_006673.2: Suppressed sequence

    Description
    NM_006673.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q03989.2 GenPept UniProtKB/Swiss-Prot:Q03989

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