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    ARID4A AT-rich interaction domain 4A [ Homo sapiens (human) ]

    Gene ID: 5926, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ARID4Aprovided by HGNC
    Official Full Name
    AT-rich interaction domain 4Aprovided by HGNC
    Primary source
    HGNC:HGNC:9885
    See related
    Ensembl:ENSG00000032219 MIM:180201; AllianceGenome:HGNC:9885
    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
    RBP1; RBBP1; RBP-1; RBBP-1
    Summary
    The protein encoded by this gene is a ubiquitously expressed nuclear protein. It binds directly, with several other proteins, to retinoblastoma protein (pRB) which regulates cell proliferation. pRB represses transcription by recruiting the encoded protein. This protein, in turn, serves as a bridging molecule to recruit HDACs and, in addition, provides a second HDAC-independent repression function. The encoded protein possesses transcriptional repression activity. Multiple alternatively spliced transcripts have been observed for this gene, although not all transcript variants have been fully described. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in bone marrow (RPKM 9.9), lymph node (RPKM 6.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ARID4A in Genome Data Viewer
    Location:
    14q23.1
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (58298555..58373876)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (52505552..52580897)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (58765273..58840594)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene PSMA3 antisense RNA 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:58764503-58765226 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5798 Neighboring gene long intergenic non-protein coding RNA 216 Neighboring gene RNA, U6 small nuclear 341, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8452 Neighboring gene TOMM20L divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5799 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5800 Neighboring gene translocase of outer mitochondrial membrane 20 like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:58892441-58893384 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8454 Neighboring gene translocase of inner mitochondrial membrane 9 Neighboring gene KIAA0586 Neighboring gene heat shock factor binding protein 1 pseudogene 1

    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. Crystal structure of chromo barrel domain of RBBP1. Lei M, et al. Biochem Biophys Res Commun, 2018 Feb 19. PMID 29408527
    2. Alternative splicing of the RBP1 gene clusters in an internal exon that encodes potential phosphorylation sites. Otterson GA, et al. Oncogene, 1993 Apr. PMID 8455946
    3. A novel heterozygous missense variant of the ARID4A gene identified in Han Chinese families with schizophrenia-diagnosed siblings that interferes with DNA-binding activity. Ren D, et al. Mol Psychiatry, 2022 Jun. PMID 35365808
    4. Recognition of an epitope of a breast cancer antigen by human antibody. Cao J, et al. Breast Cancer Res Treat, 1999 Feb. PMID 10369074
    5. Structural Insight into Chromatin Recognition by Multiple Domains of the Tumor Suppressor RBBP1. Gong W, et al. J Mol Biol, 2021 Oct 15. PMID 34506790

    See all (63) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A novel heterozygous missense variant of the ARID4A gene identified in Han Chinese families with schizophrenia-diagnosed siblings that interferes with DNA-binding activity.
      Title: A novel heterozygous missense variant of the ARID4A gene identified in Han Chinese families with schizophrenia-diagnosed siblings that interferes with DNA-binding activity.
    2. Structural Insight into Chromatin Recognition by Multiple Domains of the Tumor Suppressor RBBP1.
      Title: Structural Insight into Chromatin Recognition by Multiple Domains of the Tumor Suppressor RBBP1.
    3. ARID4A and ARID4B may play the role as tumor suppressor gene in prostate cancer by inhibiting cell proliferation, migration, and invasion. Moreover, co-downregulation of ARID4A and ARID4B can predict poorer prognosis in prostate cancer, suggesting they might be the novel marker of prognosis and potential therapeutic targets for prostate cancer in human.
      Title: Downregulation of ARID4A and ARID4B promote tumor progression and directly regulated by microRNA-30d in patient with prostate cancer.
    4. Consistently, our ITC assays also showed that DNA does not significantly enhance the histone binding ability of the chromo barrel domain of RBBP1.
      Title: Crystal structure of chromo barrel domain of RBBP1.
    5. The RBBP1 Tudor domain binds both double- and single-stranded DNA with an affinity of 10-100 muM; no apparent DNA sequence specificity was detected.
      Title: Retinoblastoma-binding protein 1 has an interdigitated double Tudor domain with DNA binding activity.
    6. ARID4a (AT-rich interacting domain 4a, also known as RBP1) and CCL5 (C-C motif ligand 5) are targets for miR-302.
      Title: Reactive oxygen species mediate microRNA-302 regulation of AT-rich interacting domain 4a and C-C motif ligand 5 expression during transitions between quiescence and proliferation.
    7. chromobarrel domain of RBBP1 is responsible for recognizing methylated histone tails in chromatin remodeling and epigenetic regulation
      Title: Structural insight into recognition of methylated histone tails by retinoblastoma-binding protein 1.
    8. Alterations of BRMS1-ARID4A interaction modify gene expression but still suppress metastasis in human breast cancer cells.
      Title: Alterations of BRMS1-ARID4A interaction modify gene expression but still suppress metastasis in human breast cancer cells.
    9. RBP1 and the mSin3 histone deacetylase complex bind to BRMS1 and repress transcription
      Title: Breast cancer metastasis suppressor 1 (BRMS1) forms complexes with retinoblastoma-binding protein 1 (RBP1) and the mSin3 histone deacetylase complex and represses transcription.
    10. there is an E2-dependent, ER isoform-specific transcriptional activation of the RBBP1 gene, which in part, is explained by the differential activity of ER AF1 and enhancer element binding
      Title: Estrogen receptor isoform-specific regulation of the retinoblastoma-binding protein 1 (RBBP1) gene: roles of AF1 and enhancer elements.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription cis-regulatory region binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in erythrocyte development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in establishment of Sertoli cell barrier IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in genomic imprinting IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of cell migration NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of stem cell population maintenance NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of transforming growth factor beta receptor signaling pathway NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of stem cell population maintenance NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    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
    		  
    involved_in spermatogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of Sin3-type complex NAS
    Non-traceable Author Statement
    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
    		  
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  
    part_of transcription repressor complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    AT-rich interactive domain-containing protein 4A
    Names
    ARID domain-containing protein 4A
    AT rich interactive domain 4A (RBP1-like)
    retinoblastoma-binding 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.

    Genomic

    1. NG_052999.1 RefSeqGene

      Range
      5171..80492
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_002892.4 → NP_002883.3  AT-rich interactive domain-containing protein 4A isoform I

      See identical proteins and their annotated locations for NP_002883.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the full length isoform.
      Source sequence(s)
      AL139021, BC026230, BX279740, DB218466, S57153
      Consensus CDS
      CCDS9732.1
      UniProtKB/Swiss-Prot
      P29374, Q15991, Q15992, Q15993
      Related
      ENSP00000347602.3, ENST00000355431.8
      Conserved Domains (4) summary
      smart00501
      Location:312 → 401
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00333
      Location:58 → 113
      TUDOR; Tudor domain
      pfam08169
      Location:171 → 261
      RBB1NT; RBB1NT (NUC162) domain
      pfam11717
      Location:575 → 629
      Tudor-knot; RNA binding activity-knot of a chromodomain

    2. NM_023000.3 → NP_075376.2  AT-rich interactive domain-containing protein 4A isoform II

      See identical proteins and their annotated locations for NP_075376.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks 162 bp in the coding region, as compared to variant 1, but maintains the same reading frame. The encoded protein lacks 54 internal codons and is thought to lack phosphorylation sites.
      Source sequence(s)
      AL139021, BC026230, BX279740, DB218466, S57160
      Consensus CDS
      CCDS45114.1
      Related
      ENSP00000378597.3, ENST00000395168.7
      Conserved Domains (5) summary
      cd16882
      Location:311 → 397
      ARID_ARID4A; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins
      cd18641
      Location:577 → 635
      CBD_RBP1_like; chromo barrel domain of retinoblastoma binding protein 1, and similar proteins
      pfam08169
      Location:170 → 262
      RBB1NT; RBB1NT (NUC162) domain
      cd20390
      Location:62 → 114
      Tudor_ARID4_rpt2; second Tudor domain found in AT-rich interactive domain-containing protein ARID4 family
      cd20459
      Location:4 → 61
      Tudor_ARID4A_rpt1; first Tudor domain found in AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins

    3. NM_023001.3 → NP_075377.2  AT-rich interactive domain-containing protein 4A isoform III

      See identical proteins and their annotated locations for NP_075377.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks 207 bp in the coding region, as compared to variant 1, but maintains the same reading frame. The encoded protein lacks 69 internal codons and is thought to lack phosphorylation sites.
      Source sequence(s)
      AL139021, BC026230, BX279740, DB218466, S57162
      Consensus CDS
      CCDS9733.1
      Related
      ENSP00000344556.3, ENST00000348476.7
      Conserved Domains (4) summary
      smart00501
      Location:312 → 401
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00333
      Location:58 → 113
      TUDOR; Tudor domain
      pfam08169
      Location:171 → 261
      RBB1NT; RBB1NT (NUC162) domain
      pfam11717
      Location:575 → 629
      Tudor-knot; RNA binding activity-knot of a chromodomain

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      58298555..58373876
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005267964.3 → XP_005268021.1  AT-rich interactive domain-containing protein 4A isoform X1

      See identical proteins and their annotated locations for XP_005268021.1

      Conserved Domains (4) summary
      smart00501
      Location:312 → 401
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00333
      Location:58 → 113
      TUDOR; Tudor domain
      pfam08169
      Location:171 → 261
      RBB1NT; RBB1NT (NUC162) domain
      pfam11717
      Location:575 → 629
      Tudor-knot; RNA binding activity-knot of a chromodomain

    2. XM_005267965.3 → XP_005268022.1  AT-rich interactive domain-containing protein 4A isoform X2

      Conserved Domains (4) summary
      smart00501
      Location:312 → 401
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00333
      Location:58 → 113
      TUDOR; Tudor domain
      pfam08169
      Location:171 → 261
      RBB1NT; RBB1NT (NUC162) domain
      pfam11717
      Location:575 → 629
      Tudor-knot; RNA binding activity-knot of a chromodomain

    3. XM_047431656.1 → XP_047287612.1  AT-rich interactive domain-containing protein 4A isoform X6

    4. XM_047431652.1 → XP_047287608.1  AT-rich interactive domain-containing protein 4A isoform X1

    5. XM_047431653.1 → XP_047287609.1  AT-rich interactive domain-containing protein 4A isoform X3

    6. XM_047431654.1 → XP_047287610.1  AT-rich interactive domain-containing protein 4A isoform X4

    7. XM_047431655.1 → XP_047287611.1  AT-rich interactive domain-containing protein 4A isoform X5

    RNA

    1. XR_001750495.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      52505552..52580897
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054376532.1 → XP_054232507.1  AT-rich interactive domain-containing protein 4A isoform X1

    2. XM_054376534.1 → XP_054232509.1  AT-rich interactive domain-containing protein 4A isoform X2

    3. XM_054376538.1 → XP_054232513.1  AT-rich interactive domain-containing protein 4A isoform X6

    4. XM_054376533.1 → XP_054232508.1  AT-rich interactive domain-containing protein 4A isoform X1

    5. XM_054376535.1 → XP_054232510.1  AT-rich interactive domain-containing protein 4A isoform X3

    6. XM_054376536.1 → XP_054232511.1  AT-rich interactive domain-containing protein 4A isoform X4

    7. XM_054376537.1 → XP_054232512.1  AT-rich interactive domain-containing protein 4A isoform X5

    RNA

    1. XR_008488891.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P29374.3 GenPept UniProtKB/Swiss-Prot:P29374

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