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    Ybx3 Y box protein 3 [ Mus musculus (house mouse) ]

    Gene ID: 56449, updated on 13-Jan-2025

    Summary

    Official Symbol
    Ybx3provided by MGI
    Official Full Name
    Y box protein 3provided by MGI
    Primary source
    MGI:MGI:2137670
    See related
    Ensembl:ENSMUSG00000030189 AllianceGenome:MGI:2137670
    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
    Yb2; Csda; Dpba; MSY3; MSY4; dbpA; oxyR
    Summary
    Enables RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; mRNA 3'-UTR binding activity; and ribonucleoprotein complex binding activity. Involved in negative regulation of transcription by RNA polymerase II. Acts upstream of or within several processes, including male gonad development; negative regulation of skeletal muscle tissue development; and positive regulation of organ growth. Located in cytoplasm and nucleus. Is active in synapse. Is expressed in several structures, including brain; branchial arch; jaw; limb bud; and sensory organ. Orthologous to human YBX3 (Y-box binding protein 3). [provided by Alliance of Genome Resources, Jan 2025]
    Expression
    Broad expression in testis adult (RPKM 404.0), liver E14 (RPKM 96.6) and 21 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Ybx3 in Genome Data Viewer
    Location:
    6 F3; 6 63.44 cM
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (131341821..131365413, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (131364858..131388450, complement)

    Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E9280 Neighboring gene CapStarr-seq enhancer MGSCv37_chr6:131243245-131243354 Neighboring gene mago homolog B, exon junction complex core component Neighboring gene serine/threonine/tyrosine kinase 1 Neighboring gene CapStarr-seq enhancer MGSCv37_chr6:131303559-131303777 Neighboring gene STARR-seq mESC enhancer starr_17494 Neighboring gene STARR-positive B cell enhancer mm9_chr6:131338351-131338652 Neighboring gene STARR-seq mESC enhancer starr_17495 Neighboring gene predicted gene, 22362 Neighboring gene STARR-seq mESC enhancer starr_17496 Neighboring gene ring finger and WD repeat domain 2 pseudogene Neighboring gene predicted gene 6619

    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 (6) 
    • Targeted (2)  1 citation

    Pathways from PubChem

    Interactions

    General gene information

    Gene Ontology Provided by MGI

    Process Evidence Code Pubs
    acts_upstream_of apoptotic process PubMed 
    involved_in cellular hyperosmotic response  
    involved_in cellular hyperosmotic response  
    involved_in cellular response to tumor necrosis factor  
    involved_in cellular response to tumor necrosis factor  
    acts_upstream_of ectopic germ cell programmed cell death PubMed 
    acts_upstream_of_or_within fertilization PubMed 
    acts_upstream_of_or_within in utero embryonic development PubMed 
    acts_upstream_of_or_within male gonad development PubMed 
    acts_upstream_of_or_within negative regulation of apoptotic process PubMed 
    acts_upstream_of_or_within negative regulation of developmental process PubMed 
    involved_in negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress  
    involved_in negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress  
    involved_in negative regulation of necroptotic process  
    involved_in negative regulation of necroptotic process  
    acts_upstream_of_or_within negative regulation of reproductive process PubMed 
    acts_upstream_of_or_within negative regulation of skeletal muscle tissue development PubMed 
    involved_in negative regulation of transcription by RNA polymerase II PubMed 
    involved_in negative regulation of transcription by RNA polymerase II  
    acts_upstream_of_or_within positive regulation of organ growth PubMed 
    involved_in regulation of gene expression  
    acts_upstream_of_or_within spermatogenesis PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm PubMed 
    located_in cytosol  
    located_in cytosol  
    located_in gap junction PubMed 
    is_active_in nucleus  
    located_in nucleus PubMed 
    is_active_in synapse PubMed 
    is_active_in synapse PubMed 

    General protein information

    Preferred Names
    Y-box-binding protein 3
    Names
    DNA-binding protein A
    cold shock domain protein A
    cold shock domain-containing protein A

    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_011733.2NP_035863.1  Y-box-binding protein 3 short isoform

      See identical proteins and their annotated locations for NP_035863.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame segment in the coding region, compared to variant 1. The resulting protein, known as the short isoform, is shorter than the long isoform.
      Source sequence(s)
      BC027785, BC048242
      Consensus CDS
      CCDS20605.1
      UniProtKB/TrEMBL
      Q68G78
      Related
      ENSMUSP00000085172.3, ENSMUST00000087865.4
      Conserved Domains (1) summary
      pfam00313
      Location:83152
      CSD; 'Cold-shock' DNA-binding domain
    2. NM_139117.2NP_620817.2  Y-box-binding protein 3 long isoform

      See identical proteins and their annotated locations for NP_620817.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and it encodes the long isoform.
      Source sequence(s)
      BC027785, BC048242
      Consensus CDS
      CCDS20606.1
      UniProtKB/Swiss-Prot
      Q80WG4, Q9EQF7, Q9EQF8, Q9JKB3
      UniProtKB/TrEMBL
      Q8BPG0
      Related
      ENSMUSP00000032309.7, ENSMUST00000032309.13
      Conserved Domains (1) summary
      pfam00313
      Location:83152
      CSD; 'Cold-shock' DNA-binding 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_000072.7 Reference GRCm39 C57BL/6J

      Range
      131341821..131365413 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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