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

Gene ID: 5926, updated on 11-Apr-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
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Genomic context

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Location:
14q23.1
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (58298555..58373876)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (52505552..52580897)
105.20220307 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
  • 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. 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
  2. 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
  3. Crystal structure of chromo barrel domain of RBBP1. Lei M, et al. Biochem Biophys Res Commun, 2018 Feb 19. PMID 29408527
  4. Retinoblastoma-binding protein 1 has an interdigitated double Tudor domain with DNA binding activity. Gong W, et al. J Biol Chem, 2014 Feb 21. PMID 24379399, Free PMC Article
  5. Recognition of an epitope of a breast cancer antigen by human antibody. Cao J, et al. Breast Cancer Res Treat, 1999 Feb. PMID 10369074

See all (58) 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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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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
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_2023_10

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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