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    Ybx1 Y box protein 1 [ Mus musculus (house mouse) ]

    Gene ID: 22608, updated on 2-Aug-2021

    Summary

    Official Symbol
    Ybx1provided by MGI
    Official Full Name
    Y box protein 1provided by MGI
    Primary source
    MGI:MGI:99146
    See related
    Ensembl:ENSMUSG00000028639
    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
    Ns; EF1; MSY; dbp; EF1A; MSY1; YB-1; dbpB; Nsep1; C79409; mYB-1a; 1700102N10; 1700102N10Rik
    Expression
    Ubiquitous expression in testis adult (RPKM 192.5), CNS E11.5 (RPKM 174.7) and 28 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See Ybx1 in Genome Data Viewer
    Location:
    4; 4 D2.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    109 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (119134524..119153462, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (119277327..119296265, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 4 NC_000070.5 (118949932..118967118, complement)

    Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene prolyl 3-hydroxylase 1 Neighboring gene predicted gene 12927 Neighboring gene claudin 19 Neighboring gene peptidyl prolyl isomerase H Neighboring gene coiled-coil domain containing 30 Neighboring gene lactate dehydrogenase A, pseudogene 2

    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)

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC118070

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables C5-methylcytidine-containing RNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables GTPase binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables RNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables mRNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables mRNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables miRNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables nucleic acid binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables p53 binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    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 CRD-mediated mRNA stabilization ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within RNA splicing IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in RNA transport ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within cellular response to interleukin-7 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in epidermis development 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 in utero embryonic development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within mRNA processing IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mRNA stabilization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in miRNA transport ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of apoptotic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of cellular senescence IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of insulin receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within negative regulation of striated muscle cell differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    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 cell division IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in protein localization to cytoplasmic stress granule ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in tRNA transport ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    part_of CRD-mediated mRNA stability complex ISO
    Inferred from Sequence Orthology
    more info
     
    part_of U12-type spliceosomal complex ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytoplasmic stress granule ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    located_in dendrite ISO
    Inferred from Sequence Orthology
    more info
     
    located_in extracellular exosome ISO
    Inferred from Sequence Orthology
    more info
     
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
     
    part_of histone pre-mRNA 3'end processing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
     
    part_of messenger ribonucleoprotein complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    part_of messenger ribonucleoprotein complex ISO
    Inferred from Sequence Orthology
    more info
     
    located_in neuronal cell body ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nuclear membrane ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in nucleus IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in perinuclear region of cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    part_of ribonucleoprotein complex ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    Y-box-binding protein 1
    Names
    CBF-A
    CCAAT-binding transcription factor I subunit A
    DNA-binding protein B
    EFI-A
    Y-box transcription factor
    enhancer factor I subunit A
    nuclease-sensitive element-binding protein 1

    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_011732.2NP_035862.2  Y-box-binding protein 1

      See identical proteins and their annotated locations for NP_035862.2

      Status: VALIDATED

      Source sequence(s)
      AK150821, BG066506, BU512458, BX470153
      Consensus CDS
      CCDS18579.1
      UniProtKB/Swiss-Prot
      P62960
      UniProtKB/TrEMBL
      Q3UBT1
      Related
      ENSMUSP00000078589.7, ENSMUST00000079644.13
      Conserved Domains (1) summary
      pfam00313
      Location:57126
      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_000070.7 Reference GRCm39 C57BL/6J

      Range
      119134524..119153462 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030253407.1XP_030109267.1  Y-box-binding protein 1 isoform X3

      Conserved Domains (1) summary
      cd04458
      Location:5988
      CSP_CDS; Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. ...
    2. XM_006502934.4XP_006502997.1  Y-box-binding protein 1 isoform X2

      Conserved Domains (1) summary
      cd04458
      Location:5988
      CSP_CDS; Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. ...
    3. XM_006502933.4XP_006502996.1  Y-box-binding protein 1 isoform X1

      Conserved Domains (1) summary
      pfam00313
      Location:57126
      CSD; 'Cold-shock' DNA-binding domain
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