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    Arid4b AT-rich interaction domain 4B [ Rattus norvegicus (Norway rat) ]

    Gene ID: 84481, updated on 9-Dec-2024

    Summary

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    Symbol
    Arid4bprovided by RGD
    Full Name
    AT-rich interaction domain 4Bprovided by RGD
    Primary source
    RGD:619919
    See related
    EnsemblRapid:ENSRNOG00000016391 AllianceGenome:RGD:619919
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Bcaa
    Summary
    Predicted to enable transcription cis-regulatory region binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within establishment of Sertoli cell barrier; regulation of gene expression; and spermatogenesis. Predicted to be located in cytosol; mitochondrion; and nucleoplasm. Predicted to be active in nucleus. Orthologous to human ARID4B (AT-rich interaction domain 4B). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 158.9), Adrenal (RPKM 130.5) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Arid4b in Genome Data Viewer
    Location:
    17q12.1
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 17 NC_086035.1 (55833908..55958382, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 17 NC_051352.1 (51138419..51262894, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 17 NC_005116.4 (53831353..53955897, complement)

    Chromosome 17 - NC_086035.1Genomic Context describing neighboring genes Neighboring gene HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1 Neighboring gene 40S ribosomal protein S19 pseudogene Neighboring gene Y-box-binding protein 1-like Neighboring gene geranylgeranyl diphosphate synthase 1 Neighboring gene tubulin folding cofactor E Neighboring gene beta-1,3-N-acetylgalactosaminyltransferase 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Characterization of BRCAA1 and its novel antigen epitope identification. Cui D, et al. Cancer Epidemiol Biomarkers Prev, 2004 Jul. PMID 15247124
    2. ARID4A and ARID4B regulate male fertility, a functional link to the AR and RB pathways. Wu RC, et al. Proc Natl Acad Sci U S A, 2013 Mar 19. PMID 23487765, Free PMC Article
    3. Deficiency of Rbbp1/Arid4a and Rbbp1l1/Arid4b alters epigenetic modifications and suppresses an imprinting defect in the PWS/AS domain. Wu MY, et al. Genes Dev, 2006 Oct 15. PMID 17043311, Free PMC Article
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription cis-regulatory region binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within chromatin organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in establishment of Sertoli cell barrier IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within establishment of Sertoli cell barrier ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in genomic imprinting IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within genomic imprinting ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    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
    		  
    acts_upstream_of_or_within spermatogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in mitochondrion ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    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)
    AT-rich interactive domain-containing protein 4B-like
    histone deacetylase complex subunit SAP180
    retinoblastoma-binding protein 1-like 1
    retinoblastoma-binding protein 1-related protein
    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.

    mRNA and Protein(s)

    1. NM_001414215.1 → NP_001401144.1  AT-rich interactive domain-containing protein 4B isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000017
      UniProtKB/Swiss-Prot
      Q9JKB5
      UniProtKB/TrEMBL
      A0A0G2JVS0

    2. NM_053421.3 → NP_445873.2  AT-rich interactive domain-containing protein 4B isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000017
      UniProtKB/Swiss-Prot
      Q9JKB5
      UniProtKB/TrEMBL
      A6K9C7, F1LMH4, F1LYA4
      Related
      ENSRNOP00000010836.7, ENSRNOT00000010836.8
      Conserved Domains (5) summary
      PTZ00121
      Location:450 → 763
      PTZ00121; MAEBL; Provisional
      cd16883
      Location:308 → 399
      ARID_ARID4B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
      pfam08169
      Location:168 → 263
      RBB1NT; RBB1NT (NUC162) domain
      cd20460
      Location:1 → 61
      Tudor_ARID4B_rpt1; first Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
      cd20462
      Location:62 → 118
      Tudor_ARID4B_rpt2; second Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086035.1 Reference GRCr8

      Range
      55833908..55958382 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_008771766.4 → XP_008769988.1  AT-rich interactive domain-containing protein 4B isoform X4

      UniProtKB/Swiss-Prot
      Q9JKB5
      Conserved Domains (3) summary
      smart00333
      Location:58 → 113
      TUDOR; Tudor domain
      smart01014
      Location:311 → 394
      ARID; ARID/BRIGHT DNA binding domain
      pfam08169
      Location:169 → 262
      RBB1NT; RBB1NT (NUC162) domain

    2. XM_063276774.1 → XP_063132844.1  AT-rich interactive domain-containing protein 4B isoform X3

      UniProtKB/Swiss-Prot
      Q9JKB5

    3. XM_008771765.4 → XP_008769987.1  AT-rich interactive domain-containing protein 4B isoform X2

      UniProtKB/Swiss-Prot
      Q9JKB5
      Conserved Domains (3) summary
      smart00333
      Location:58 → 113
      TUDOR; Tudor domain
      smart01014
      Location:311 → 394
      ARID; ARID/BRIGHT DNA binding domain
      pfam08169
      Location:169 → 262
      RBB1NT; RBB1NT (NUC162) domain

    4. XM_008771764.4 → XP_008769986.1  AT-rich interactive domain-containing protein 4B isoform X1

      UniProtKB/Swiss-Prot
      Q9JKB5
      Related
      ENSRNOP00000069593.3, ENSRNOT00000078643.3
      Conserved Domains (4) summary
      smart00333
      Location:58 → 113
      TUDOR; Tudor domain
      smart01014
      Location:311 → 394
      ARID; ARID/BRIGHT DNA binding domain
      pfam08169
      Location:169 → 262
      RBB1NT; RBB1NT (NUC162) domain
      pfam11717
      Location:571 → 624
      Tudor-knot; RNA binding activity-knot of a chromodomain

    5. XM_039096118.2 → XP_038952046.1  AT-rich interactive domain-containing protein 4B isoform X5

      Conserved Domains (2) summary
      cl28902
      Location:1 → 80
      ARID; ARID/BRIGHT DNA binding domain family
      cl28914
      Location:254 → 311
      CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains

    RNA

    1. XR_361039.5 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9JKB5.1 GenPept UniProtKB/Swiss-Prot:Q9JKB5

    Gene LinkOut

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