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

    Gene ID: 10865, updated on 2-Nov-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
    mouse all
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    Genomic context

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    See ARID5A in Genome Data Viewer
    Location:
    2q11.2
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (96536752..96552638)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (97043371..97059257)
    RS_2024_09 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 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. Noncanonical STAT1 phosphorylation expands its transcriptional activity into promoting LPS-induced IL-6 and IL-12p40 production. Metwally H, et al. Sci Signal, 2020 Mar 24. PMID 32209697

    See all (24) 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 mRNA 3'-UTR AU-rich region binding IDA
    Inferred from Direct Assay
    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 3'-UTR-mediated mRNA stabilization IMP
    Inferred from Mutant Phenotype
    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, ENST00000454558.3
      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_2024_08

    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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