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ARID4B AT-rich interaction domain 4B [ Homo sapiens (human) ]

Gene ID: 51742, updated on 13-Apr-2024

Summary

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Official Symbol
ARID4Bprovided by HGNC
Official Full Name
AT-rich interaction domain 4Bprovided by HGNC
Primary source
HGNC:HGNC:15550
See related
Ensembl:ENSG00000054267 MIM:609696; AllianceGenome:HGNC:15550
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
BCAA; BRCAA1; RBP1L1; SAP180; RBBP1L1
Summary
This gene encodes a protein with sequence similarity to retinoblastoma-binding protein-1. The encoded protein is a subunit of the histone deacetylase-dependant SIN3A transcriptional corepressor complex, which functions in diverse cellular processes including proliferation, differentiation, apoptosis, oncogenesis, and cell fate determination. The gene product is recognized by IgG antibody isolated from a breast cancer patient and appears to be a molecular marker associated with a broad range of human malignancies. Alternate transcriptional splice variants encoding different isoforms have been characterized. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 12.1), lymph node (RPKM 11.3) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
1q42.3
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (235166902..235328179, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (234558607..234719910, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (235330217..235491494, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105379283 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2793 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2794 Neighboring gene translocase of outer mitochondrial membrane 20 Neighboring gene small nucleolar RNA, H/ACA box 14B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2795 Neighboring gene RNA binding motif protein 34 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:235322928-235323532 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:235323819-235325018 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:235334884-235335090 Neighboring gene microRNA 4753 Neighboring gene Sharpr-MPRA regulatory region 13312 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:235434772-235435360 Neighboring gene ribosomal protein L23a pseudogene 23 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2797 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:235490383-235490908 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1987 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2798 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2800 Neighboring gene geranylgeranyl diphosphate synthase 1 Neighboring gene atrophin 1 pseudogene Neighboring gene uncharacterized LOC124904559 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:235530449-235531162

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. Overexpression of ARID4B predicts poor survival in patients with hepatocellular carcinoma. Wang R, et al. Hum Pathol, 2018 Mar. PMID 29288040
  2. ARID4B is a good biomarker to predict tumour behaviour and decide WHO grades in gliomas and meningiomas. Tsai WC, et al. J Clin Pathol, 2017 Feb. PMID 27451434
  3. RBP1L1, a retinoblastoma-binding protein-related gene encoding an antigenic epitope abundantly expressed in human carcinomas and normal testis. Cao J, et al. J Natl Cancer Inst, 2001 Aug 1. PMID 11481388
  4. Circ-SMARCA5 suppresses colorectal cancer progression via downregulating miR-39-3p and upregulating ARID4B. Miao X, et al. Dig Liver Dis, 2020 Dec. PMID 32807692
  5. miR-519b-3p promotes responsiveness to preoperative chemoradiotherapy in rectal cancer patients by targeting ARID4B. Luo J, et al. Gene, 2018 May 20. PMID 29477868

See all (70) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Circ-SMARCA5 suppresses colorectal cancer progression via downregulating miR-39-3p and upregulating ARID4B.
    Title: Circ-SMARCA5 suppresses colorectal cancer progression via downregulating miR-39-3p and upregulating ARID4B.
  2. 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.
  3. our results suggest that ARID4B acts as an oncogene in hepatocellular carcinoma and can therefore serve as a biomarker for the prognoses of patients with hepatocellular carcinoma
    Title: Overexpression of ARID4B predicts poor survival in patients with hepatocellular carcinoma.
  4. miR-519b-3p directly binds to the 3' UTR of ARID4B mRNA whose expression was inversely correlated with miR-519b-3p expression.
    Title: miR-519b-3p promotes responsiveness to preoperative chemoradiotherapy in rectal cancer patients by targeting ARID4B.
  5. ARID4B overexpression presented in most of primary brain tumors, rather than non-neoplastic brain tissue, and correlated with WHO grades in meningiomas and gliomas.
    Title: ARID4B is a good biomarker to predict tumour behaviour and decide WHO grades in gliomas and meningiomas.
  6. ARID4B was significantly elevated in the serum of excessive alcohol users.
    Title: Novel serum biomarkers for detection of excessive alcohol use.
  7. Consistent with our genetic analysis and in vivo experiments in our mouse model system, ARID4B expression was also an independent predictor of distant metastasis-free survival in breast cancer patients with ER+ tumors
    Title: Allelic variation and differential expression of the mSIN3A histone deacetylase complex gene Arid4b promote mammary tumor growth and metastasis.
  8. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  9. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
    Title: MicroRNAs and target site screening reveals a pre-microRNA-30e variant associated with schizophrenia.
  10. Immunohistochemistry analysis showed that the antigen epitope exhibited positive expression in 65% (39 of 60) breast cancer specimens and negative expression in 60 non-cancerous tissues. A novel breast cancer antigen epitope, SSKKQKRSHK, is identified
    Title: Characterization of BRCAA1 and its novel antigen epitope identification.
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

Clone Names

  • MGC163290, DKFZp313M2420

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding EXP
Inferred from Experiment
more info
 PubMed 
enables DNA binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables molecular_function ND
No biological Data available
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription cis-regulatory region binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
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 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 cytosol IDA
Inferred from Direct Assay
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
  
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 

General protein information

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Preferred Names
AT-rich interactive domain-containing protein 4B
Names
180 kDa Sin3-associated polypeptide
ARID domain-containing protein 4B
AT rich interactive domain 4B (RBP1-like)
Rb-binding protein homolog
SIN3A-associated protein 180
breast cancer-associated antigen 1
breast cancer-associated antigen BRCAA1
breast carcinoma-associated antigen
histone deacetylase complex subunit SAP180
retinoblastoma-binding protein 1-like 1
sin3-associated polypeptide p180

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_029484.1 RefSeqGene

    Range
    5039..166316
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001206794.2 → NP_001193723.1  AT-rich interactive domain-containing protein 4B isoform 1

    See identical proteins and their annotated locations for NP_001193723.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1 and 3 encode the same protein (isoform 1).
    Source sequence(s)
    AB210032, AF208045, AL391994
    Consensus CDS
    CCDS31061.1
    UniProtKB/Swiss-Prot
    A1L465, Q3MHV4, Q4LE39, Q5HY99, Q5T2C2, Q5T2C3, Q5T2C4, Q5T2C5, Q5T2C6, Q6P600, Q86UX1, Q86WR4, Q9H915, Q9NYU3, Q9NZB6, Q9NZG4, Q9P2W4, Q9UF62, Q9Y6E1
    Related
    ENSP00000355562.2, ENST00000366603.6
    Conserved Domains (4) summary
    smart00333
    Location:58 → 113
    TUDOR; Tudor domain
    smart01014
    Location:311 → 394
    ARID; ARID/BRIGHT DNA binding domain
    pfam08169
    Location:170 → 262
    RBB1NT; RBB1NT (NUC162) domain
    pfam11717
    Location:571 → 624
    Tudor-knot; RNA binding activity-knot of a chromodomain

  2. NM_016374.6 → NP_057458.4  AT-rich interactive domain-containing protein 4B isoform 1

    See identical proteins and their annotated locations for NP_057458.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1 and 3 encode the same isoform.
    Source sequence(s)
    AB210032, AL133418, AL391994
    Consensus CDS
    CCDS31061.1
    UniProtKB/Swiss-Prot
    A1L465, Q3MHV4, Q4LE39, Q5HY99, Q5T2C2, Q5T2C3, Q5T2C4, Q5T2C5, Q5T2C6, Q6P600, Q86UX1, Q86WR4, Q9H915, Q9NYU3, Q9NZB6, Q9NZG4, Q9P2W4, Q9UF62, Q9Y6E1
    Related
    ENSP00000264183.3, ENST00000264183.9
    Conserved Domains (4) summary
    smart00333
    Location:58 → 113
    TUDOR; Tudor domain
    smart01014
    Location:311 → 394
    ARID; ARID/BRIGHT DNA binding domain
    pfam08169
    Location:170 → 262
    RBB1NT; RBB1NT (NUC162) domain
    pfam11717
    Location:571 → 624
    Tudor-knot; RNA binding activity-knot of a chromodomain

  3. NM_031371.4 → NP_112739.2  AT-rich interactive domain-containing protein 4B isoform 2

    See identical proteins and their annotated locations for NP_112739.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon compared to variant 1 but maintains the reading frame. The resulting protein (isoform 2) is shorter than isoform 1.
    Source sequence(s)
    AB210032, AL133418, AL391994, BC048959
    Consensus CDS
    CCDS31060.1
    UniProtKB/Swiss-Prot
    Q4LE39
    Related
    ENSP00000264184.4, ENST00000349213.7
    Conserved Domains (4) summary
    smart00333
    Location:58 → 113
    TUDOR; Tudor domain
    smart01014
    Location:311 → 394
    ARID; ARID/BRIGHT DNA binding domain
    pfam08169
    Location:173 → 262
    RBB1NT; RBB1NT (NUC162) domain
    cl26761
    Location:451 → 728
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]

RNA

  1. NR_135074.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB210032, AY220790, BC130418, CB048003, DB100845
    Related
    ENST00000421364.5

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    235166902..235328179 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024447626.2 → XP_024303394.1  AT-rich interactive domain-containing protein 4B isoform X3

    Conserved Domains (4) summary
    smart00333
    Location:58 → 113
    TUDOR; Tudor domain
    smart01014
    Location:311 → 394
    ARID; ARID/BRIGHT DNA binding domain
    pfam08169
    Location:173 → 262
    RBB1NT; RBB1NT (NUC162) domain
    cl26761
    Location:451 → 728
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]

  2. XM_047422531.1 → XP_047278487.1  AT-rich interactive domain-containing protein 4B isoform X2

  3. XM_011544212.4 → XP_011542514.1  AT-rich interactive domain-containing protein 4B isoform X1

    See identical proteins and their annotated locations for XP_011542514.1

    UniProtKB/Swiss-Prot
    A1L465, Q3MHV4, Q4LE39, Q5HY99, Q5T2C2, Q5T2C3, Q5T2C4, Q5T2C5, Q5T2C6, Q6P600, Q86UX1, Q86WR4, Q9H915, Q9NYU3, Q9NZB6, Q9NZG4, Q9P2W4, Q9UF62, Q9Y6E1
    Conserved Domains (4) summary
    smart00333
    Location:58 → 113
    TUDOR; Tudor domain
    smart01014
    Location:311 → 394
    ARID; ARID/BRIGHT DNA binding domain
    pfam08169
    Location:170 → 262
    RBB1NT; RBB1NT (NUC162) domain
    pfam11717
    Location:571 → 624
    Tudor-knot; RNA binding activity-knot of a chromodomain

  4. XM_006711781.4 → XP_006711844.1  AT-rich interactive domain-containing protein 4B isoform X2

    Conserved Domains (3) summary
    smart00333
    Location:58 → 113
    TUDOR; Tudor domain
    smart01014
    Location:311 → 394
    ARID; ARID/BRIGHT DNA binding domain
    pfam08169
    Location:170 → 262
    RBB1NT; RBB1NT (NUC162) domain

  5. XM_017001472.2 → XP_016856961.1  AT-rich interactive domain-containing protein 4B isoform X5

    Conserved Domains (2) summary
    smart01014
    Location:14 → 101
    ARID; ARID/BRIGHT DNA binding domain
    pfam11717
    Location:278 → 331
    Tudor-knot; RNA binding activity-knot of a chromodomain

  6. XM_047422533.1 → XP_047278489.1  AT-rich interactive domain-containing protein 4B isoform X6

  7. XM_047422532.1 → XP_047278488.1  AT-rich interactive domain-containing protein 4B isoform X4

    Related
    ENST00000491632.5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    234558607..234719910 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337003.1 → XP_054192978.1  AT-rich interactive domain-containing protein 4B isoform X3

  2. XM_054337002.1 → XP_054192977.1  AT-rich interactive domain-containing protein 4B isoform X2

  3. XM_054337000.1 → XP_054192975.1  AT-rich interactive domain-containing protein 4B isoform X1

    UniProtKB/Swiss-Prot
    A1L465, Q3MHV4, Q4LE39, Q5HY99, Q5T2C2, Q5T2C3, Q5T2C4, Q5T2C5, Q5T2C6, Q6P600, Q86UX1, Q86WR4, Q9H915, Q9NYU3, Q9NZB6, Q9NZG4, Q9P2W4, Q9UF62, Q9Y6E1

  4. XM_054337001.1 → XP_054192976.1  AT-rich interactive domain-containing protein 4B isoform X2

  5. XM_054337005.1 → XP_054192980.1  AT-rich interactive domain-containing protein 4B isoform X5

  6. XM_054337006.1 → XP_054192981.1  AT-rich interactive domain-containing protein 4B isoform X6

  7. XM_054337004.1 → XP_054192979.1  AT-rich interactive domain-containing protein 4B isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q4LE39.2 GenPept UniProtKB/Swiss-Prot:Q4LE39

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