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

    Gene ID: 56449, updated on 24-Apr-2022

    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 nucleic acid binding activity and polysome 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 expressed in several structures, including brain; branchial arch; limb bud; sensory organ; and testis. Orthologous to human YBX3 (Y-box binding protein 3). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in testis adult (RPKM 404.0), liver E14 (RPKM 96.6) and 21 other tissues See more
    Orthologs
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    Genomic context

    See Ybx3 in Genome Data Viewer
    Location:
    6; 6 F3
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    109 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)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 6 NC_000072.5 (131314876..131338468, complement)

    Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene mago homolog B, exon junction complex core component Neighboring gene serine/threonine/tyrosine kinase 1 Neighboring gene predicted gene, 22362 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)
    • Targeted (1)  1 citation
    • Endonuclease-mediated (1) 

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables mRNA 3'-UTR binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables nucleic acid binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables polysome binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables ribonucleoprotein complex binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables single-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables single-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    involved_in cellular hyperosmotic response ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cellular response to tumor necrosis factor ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within fertilization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within in utero embryonic development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within male gonad development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of necroptotic process ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of skeletal muscle tissue development IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within positive regulation of organ growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    acts_upstream_of_or_within spermatogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    located_in gap junction ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     

    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/Swiss-Prot
      Q9JKB3
      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
      Q9JKB3
      UniProtKB/TrEMBL
      Q68G78
      Related
      ENSMUSP00000032309.7, ENSMUST00000032309.13
      Conserved Domains (1) summary
      pfam00313
      Location:83152
      CSD; 'Cold-shock' DNA-binding domain

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

    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)