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    Arid4b AT-rich interaction domain 4B [ Mus musculus (house mouse) ]

    Gene ID: 94246, updated on 9-Dec-2024

    Summary

    Official Symbol
    Arid4bprovided by MGI
    Official Full Name
    AT-rich interaction domain 4Bprovided by MGI
    Primary source
    MGI:MGI:2137512
    See related
    Ensembl:ENSMUSG00000039219 AllianceGenome:MGI:2137512
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    BCAA; BRCAA1; Rbp1l1; SAP180; RBBP1L1
    Summary
    Predicted to enable transcription cis-regulatory region binding activity. Acts 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. Is expressed in testis. Orthologous to human ARID4B (AT-rich interaction domain 4B). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 10.1), CNS E14 (RPKM 7.3) and 26 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Arid4b in Genome Data Viewer
    Location:
    13 A1; 13 5.29 cM
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 13 NC_000079.7 (14238334..14374188)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 13 NC_000079.6 (14063609..14199603)

    Chromosome 13 - NC_000079.7Genomic Context describing neighboring genes Neighboring gene UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 2 Neighboring gene STARR-seq mESC enhancer starr_33708 Neighboring gene STARR-positive B cell enhancer ABC_E5369 Neighboring gene tubulin-specific chaperone E Neighboring gene STARR-positive B cell enhancer ABC_E9866 Neighboring gene STARR-positive B cell enhancer ABC_E32 Neighboring gene STARR-seq mESC enhancer starr_33710 Neighboring gene geranylgeranyl diphosphate synthase 1 Neighboring gene predicted gene, 26129 Neighboring gene zinc finger and SCAN domain containing 5B pseudogene Neighboring gene HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1 Neighboring gene STARR-seq mESC enhancer starr_33711 Neighboring gene STARR-seq mESC enhancer starr_33713 Neighboring gene STARR-seq mESC enhancer starr_33714 Neighboring gene STARR-seq mESC enhancer starr_33715 Neighboring gene predicted gene, 30893

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (4) 
    • Targeted (5)  1 citation

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • 5930400I17, 6330417L24Rik, 6720480E17Rik

    Gene Ontology Provided by MGI

    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 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
     
    Component Evidence Code Pubs
    part_of Sin3-type complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    located_in mitochondrion IEA
    Inferred from Electronic Annotation
    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 NAS
    Non-traceable Author Statement
    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)
    breast cancer-associated antigen
    histone deacetylase complex subunit SAP180
    retinoblastoma binding protein 1-like 1
    sin3-associated polypeptide p180

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_194262.2NP_919238.1  AT-rich interactive domain-containing protein 4B isoform 1

      See identical proteins and their annotated locations for NP_919238.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK034400, AK041414, BC137783, BY720039
      Consensus CDS
      CCDS36599.1
      UniProtKB/Swiss-Prot
      A2CG61, A2CG62, A2CG63, A2CG64, B2RQ67, Q8BMI8, Q8BYA5
      Related
      ENSMUSP00000106163.2, ENSMUST00000110534.8
      Conserved Domains (4) summary
      smart00333
      Location:58113
      TUDOR; Tudor domain
      cd16883
      Location:308399
      ARID_ARID4B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
      pfam08169
      Location:168263
      RBB1NT; RBB1NT (NUC162) domain
      cl28914
      Location:573630
      CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains
    2. NM_198122.2NP_937755.1  AT-rich interactive domain-containing protein 4B isoform 2

      See identical proteins and their annotated locations for NP_937755.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      AK034400, AK041414, BC137783, BY720039
      Consensus CDS
      CCDS36600.1
      UniProtKB/Swiss-Prot
      A2CG63
      Related
      ENSMUSP00000043889.9, ENSMUST00000039538.15
      Conserved Domains (3) summary
      smart00333
      Location:58113
      TUDOR; Tudor domain
      smart01014
      Location:311394
      ARID; ARID/BRIGHT DNA binding domain
      pfam08169
      Location:169262
      RBB1NT; RBB1NT (NUC162) domain

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000079.7 Reference GRCm39 C57BL/6J

      Range
      14238334..14374188
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006516808.4XP_006516871.1  AT-rich interactive domain-containing protein 4B isoform X2

      Conserved Domains (4) summary
      cd16883
      Location:308399
      ARID_ARID4B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
      pfam08169
      Location:168263
      RBB1NT; RBB1NT (NUC162) domain
      cd20460
      Location:161
      Tudor_ARID4B_rpt1; first Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
      cd20462
      Location:62118
      Tudor_ARID4B_rpt2; second Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
    2. XM_006516806.4XP_006516869.1  AT-rich interactive domain-containing protein 4B isoform X1

      See identical proteins and their annotated locations for XP_006516869.1

      UniProtKB/Swiss-Prot
      A2CG61, A2CG62, A2CG63, A2CG64, B2RQ67, Q8BMI8, Q8BYA5
      Conserved Domains (4) summary
      smart00333
      Location:58113
      TUDOR; Tudor domain
      cd16883
      Location:308399
      ARID_ARID4B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
      pfam08169
      Location:168263
      RBB1NT; RBB1NT (NUC162) domain
      cl28914
      Location:573630
      CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains
    3. XM_036158231.1XP_036014124.1  AT-rich interactive domain-containing protein 4B isoform X2

      Conserved Domains (4) summary
      cd16883
      Location:308399
      ARID_ARID4B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
      pfam08169
      Location:168263
      RBB1NT; RBB1NT (NUC162) domain
      cd20460
      Location:161
      Tudor_ARID4B_rpt1; first Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
      cd20462
      Location:62118
      Tudor_ARID4B_rpt2; second Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
    4. XM_006516807.4XP_006516870.1  AT-rich interactive domain-containing protein 4B isoform X1

      See identical proteins and their annotated locations for XP_006516870.1

      UniProtKB/Swiss-Prot
      A2CG61, A2CG62, A2CG63, A2CG64, B2RQ67, Q8BMI8, Q8BYA5
      Conserved Domains (4) summary
      smart00333
      Location:58113
      TUDOR; Tudor domain
      cd16883
      Location:308399
      ARID_ARID4B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins
      pfam08169
      Location:168263
      RBB1NT; RBB1NT (NUC162) domain
      cl28914
      Location:573630
      CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains
    5. XM_030247479.2XP_030103339.1  AT-rich interactive domain-containing protein 4B isoform X3

      Conserved Domains (2) summary
      cl28902
      Location:180
      ARID; ARID/BRIGHT DNA binding domain family
      cl28914
      Location:254311
      CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains
    6. XM_030247480.2XP_030103340.1  AT-rich interactive domain-containing protein 4B isoform X4

      Conserved Domains (1) summary
      cl28902
      Location:180
      ARID; ARID/BRIGHT DNA binding domain family

    RNA

    1. XR_003950495.2 RNA Sequence