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

    Gene ID: 51742, updated on 15-Jun-2019

    Summary

    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
    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

    Genomic context

    See ARID4B in Genome Data Viewer
    Location:
    1q42.3
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (235166895..235328224, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (235330210..235491532, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105379283 Neighboring gene translocase of outer mitochondrial membrane 20 Neighboring gene small nucleolar RNA, H/ACA box 14B Neighboring gene RNA binding motif protein 34 Neighboring gene microRNA 4753 Neighboring gene ribosomal protein L23a pseudogene 23 Neighboring gene geranylgeranyl diphosphate synthase 1 Neighboring gene atrophin 1 pseudogene

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
      Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
    • Chromatin organization, organism-specific biosystem (from REACTOME)
      Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
    • Epigenetic regulation of gene expression, organism-specific biosystem (from REACTOME)
      Epigenetic regulation of gene expression, organism-specific biosystemEpigenetic processes regulate gene expression by modulating the frequency, rate, or extent of gene expression in a mitotically or meiotically heritable way that does not entail a change in the DNA se...
    • Gene Expression, organism-specific biosystem (from REACTOME)
      Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
    • HDACs deacetylate histones, organism-specific biosystem (from REACTOME)
      HDACs deacetylate histones, organism-specific biosystemLysine deacetylases (KDACs), historically referred to as histone deacetylases (HDACs), are divided into the Rpd3/Hda1 metal-dependent 'classical HDAC family' (de Ruijter et al. 2003, Verdin et al. 2...
    • Negative epigenetic regulation of rRNA expression, organism-specific biosystem (from REACTOME)
      Negative epigenetic regulation of rRNA expression, organism-specific biosystemTranscription of rRNA genes is controlled by epigenetic activation and repression (reviewed in McStay and Grummt 2008, Goodfellow and Zomerdijk 2012, Grummt and Langst 2013). About half of the roughl...
    • NoRC negatively regulates rRNA expression, organism-specific biosystem (from REACTOME)
      NoRC negatively regulates rRNA expression, organism-specific biosystemOnly about half of the rRNA gene copies in a cell are expressed. The remaining copies are silenced by modifications to histones and DNA (reviewed in Santoro and Grummt 2001, Grummt 2007, Preuss and P...
    • Pathways Affected in Adenoid Cystic Carcinoma, organism-specific biosystem (from WikiPathways)
      Pathways Affected in Adenoid Cystic Carcinoma, organism-specific biosystemProtein pathways altered by mutations in adenoid cystic carcinoma. Pathways include epigentic modification, DNA damage checkpoint signals, MYB/MYC signalling pathway, FGF/IGF/PI3K signalling, and not...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC163290, DKFZp313M2420

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
     
    molecular_function ND
    No biological Data available
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    transcription regulatory region DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Process Evidence Code Pubs
    biological_process ND
    No biological Data available
    more info
     
    establishment of Sertoli cell barrier IEA
    Inferred from Electronic Annotation
    more info
     
    histone H3-K9 trimethylation IEA
    Inferred from Electronic Annotation
    more info
     
    histone H4-K20 trimethylation IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of gene expression by genetic imprinting IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    spermatogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cellular_component ND
    No biological Data available
    more info
     
    cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    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)

    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
      5001..166323
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001206794.1NP_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, AI431949, AL391994
      Consensus CDS
      CCDS31061.1
      UniProtKB/Swiss-Prot
      Q4LE39
      UniProtKB/TrEMBL
      A0A024R3R1
      Related
      ENSP00000355562.2, ENST00000366603.6
      Conserved Domains (4) summary
      smart00333
      Location:58113
      TUDOR; Tudor domain
      smart01014
      Location:311394
      ARID; ARID/BRIGHT DNA binding domain
      pfam08169
      Location:170262
      RBB1NT; RBB1NT (NUC162) domain
      pfam11717
      Location:571624
      Tudor-knot; RNA binding activity-knot of a chromodomain
    2. NM_016374.6NP_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
      Q4LE39
      UniProtKB/TrEMBL
      A0A024R3R1
      Related
      ENSP00000264183.3, ENST00000264183.9
      Conserved Domains (4) summary
      smart00333
      Location:58113
      TUDOR; Tudor domain
      smart01014
      Location:311394
      ARID; ARID/BRIGHT DNA binding domain
      pfam08169
      Location:170262
      RBB1NT; RBB1NT (NUC162) domain
      pfam11717
      Location:571624
      Tudor-knot; RNA binding activity-knot of a chromodomain
    3. NM_031371.4NP_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:58113
      TUDOR; Tudor domain
      smart01014
      Location:311394
      ARID; ARID/BRIGHT DNA binding domain
      pfam08169
      Location:173262
      RBB1NT; RBB1NT (NUC162) domain
      cl26761
      Location:451728
      MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]

    RNA

    1. NR_135074.1 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, DA942288, DB100845
      Related
      ENST00000421364.5

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

      Range
      235166895..235328224 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011544212.3XP_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
      Q4LE39
      UniProtKB/TrEMBL
      A0A024R3R1
      Conserved Domains (4) summary
      smart00333
      Location:58113
      TUDOR; Tudor domain
      smart01014
      Location:311394
      ARID; ARID/BRIGHT DNA binding domain
      pfam08169
      Location:170262
      RBB1NT; RBB1NT (NUC162) domain
      pfam11717
      Location:571624
      Tudor-knot; RNA binding activity-knot of a chromodomain
    2. XM_024447626.1XP_024303394.1  AT-rich interactive domain-containing protein 4B isoform X3

      Conserved Domains (4) summary
      smart00333
      Location:58113
      TUDOR; Tudor domain
      smart01014
      Location:311394
      ARID; ARID/BRIGHT DNA binding domain
      pfam08169
      Location:173262
      RBB1NT; RBB1NT (NUC162) domain
      cl26761
      Location:451728
      MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
    3. XM_006711781.3XP_006711844.1  AT-rich interactive domain-containing protein 4B isoform X2

      Conserved Domains (3) summary
      smart00333
      Location:58113
      TUDOR; Tudor domain
      smart01014
      Location:311394
      ARID; ARID/BRIGHT DNA binding domain
      pfam08169
      Location:170262
      RBB1NT; RBB1NT (NUC162) domain
    4. XM_017001472.1XP_016856961.1  AT-rich interactive domain-containing protein 4B isoform X5

      Conserved Domains (2) summary
      smart01014
      Location:14101
      ARID; ARID/BRIGHT DNA binding domain
      pfam11717
      Location:278331
      Tudor-knot; RNA binding activity-knot of a chromodomain
    5. XM_024447628.1XP_024303396.1  AT-rich interactive domain-containing protein 4B isoform X4

      Conserved Domains (4) summary
      smart00333
      Location:58113
      TUDOR; Tudor domain
      smart01014
      Location:311394
      ARID; ARID/BRIGHT DNA binding domain
      pfam08169
      Location:173262
      RBB1NT; RBB1NT (NUC162) domain
      cl26761
      Location:451728
      MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]

    RNA

    1. XR_002956802.1 RNA Sequence

    2. XR_001737227.2 RNA Sequence

    3. XR_001737226.2 RNA Sequence

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