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

    Gene ID: 56449, updated on 31-Jan-2019

    Summary

    Official Symbol
    Ybx3provided by MGI
    Official Full Name
    Y box protein 3provided by MGI
    Primary source
    MGI:MGI:2137670
    See related
    Ensembl:ENSMUSG00000030189
    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
    Expression
    Broad expression in testis adult (RPKM 404.0), liver E14 (RPKM 96.6) and 21 other tissues See more
    Orthologs

    Genomic context

    See Ybx3 in Genome Data Viewer
    Location:
    6; 6 F3
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 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_000072.6Genomic Context describing neighboring genes Neighboring gene mago homolog B, exon junction complex core component Neighboring gene serine/threonine/tyrosine kinase 1 Neighboring gene ring finger and WD repeat domain 2 pseudogene Neighboring gene otolin-1-like

    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 FunctionsWhat'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 BioSystems

    • Tight junction, organism-specific biosystem (from KEGG)
      Tight junction, organism-specific biosystemTight junctions (TJs) are essential for establishing a selectively permeable barrier to diffusion through the paracellular space between neighboring cells. TJs are composed of at least three types of...
    • Tight junction, conserved biosystem (from KEGG)
      Tight junction, conserved biosystemTight junctions (TJs) are essential for establishing a selectively permeable barrier to diffusion through the paracellular space between neighboring cells. TJs are composed of at least three types of...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    PubMed 
    RNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    RNA polymerase II regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    mRNA 3'-UTR binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
     
    polysome binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    colocalizes_with ribonucleoprotein complex binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    single-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    single-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    gap junction ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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)

    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
      ENSMUSP00000085172.2, ENSMUST00000087865.3
      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
      ENSMUSP00000032309.6, ENSMUST00000032309.12
      Conserved Domains (1) summary
      pfam00313
      Location:83152
      CSD; 'Cold-shock' DNA-binding domain

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000072.6 Reference GRCm38.p4 C57BL/6J

      Range
      131364858..131388450 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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