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    YBX1 Y-box binding protein 1 [ Homo sapiens (human) ]

    Gene ID: 4904, updated on 17-Oct-2021

    Summary

    Official Symbol
    YBX1provided by HGNC
    Official Full Name
    Y-box binding protein 1provided by HGNC
    Primary source
    HGNC:HGNC:8014
    See related
    Ensembl:ENSG00000065978 MIM:154030
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    YB1; BP-8; CSDB; DBPB; YB-1; CBF-A; CSDA2; EFI-A; NSEP1; NSEP-1; MDR-NF1
    Summary
    This gene encodes a highly conserved cold shock domain protein that has broad nucleic acid binding properties. The encoded protein functions as both a DNA and RNA binding protein and has been implicated in numerous cellular processes including regulation of transcription and translation, pre-mRNA splicing, DNA reparation and mRNA packaging. This protein is also a component of messenger ribonucleoprotein (mRNP) complexes and may have a role in microRNA processing. This protein can be secreted through non-classical pathways and functions as an extracellular mitogen. Aberrant expression of the gene is associated with cancer proliferation in numerous tissues. This gene may be a prognostic marker for poor outcome and drug resistance in certain cancers. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on multiple chromosomes. [provided by RefSeq, Sep 2015]
    Expression
    Ubiquitous expression in testis (RPKM 220.6), fat (RPKM 121.2) and 25 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See YBX1 in Genome Data Viewer
    Location:
    1p34.2
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (42682418..42703805)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (43148089..43169476)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 30 Neighboring gene RNA, U6 small nuclear 536, pseudogene Neighboring gene peptidylprolyl isomerase H Neighboring gene claudin 19 Neighboring gene prolyl 3-hydroxylase 1

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    siRNA knockdown of YBX1 enhances HIV-1 replication; HIV-1 replication is restricted by EZR PubMed
    Knockdown of Y box binding protein 1 (YBX1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify Y box binding protein 1 (YBX1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify Y box binding protein 1 (YBX1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Nef nef Tandem affinity purification and mass spectrometry analysis identify Y box binding protein 1 (YBX1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify Y box binding protein 1 (YBX1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Tat tat YB-1 interacts with HIV-1 Tat and enhances Tat-induced activation of the HIV-1 LTR promoter PubMed
    tat Binding of YB-1 to HIV-1 Tat is mediated through the C-terminal region of Tat (amino acids 48-72) and through amino acids 75-203 of YB-1 PubMed
    matrix gag HIV-1 MA interacts with YBX1 PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC104858, MGC110976, MGC117250

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables C5-methylcytidine-containing RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables GTPase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables RNA binding HDA PubMed 
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables chromatin binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables double-stranded DNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables mRNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables miRNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables nucleic acid binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables single-stranded DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in CRD-mediated mRNA stabilization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in RNA splicing IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in RNA transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cellular response to interleukin-7 IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in embryonic morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in epidermis development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in in utero embryonic development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mRNA stabilization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in miRNA transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of cellular senescence ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of striated muscle cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of translation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of cell division IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein localization to cytoplasmic stress granule IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in tRNA transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of CRD-mediated mRNA stability complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of U12-type spliceosomal complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasmic stress granule IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in extracellular exosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    part_of histone pre-mRNA 3'end processing complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    part_of messenger ribonucleoprotein complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in nuclear membrane IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    part_of ribonucleoprotein complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    Y-box-binding protein 1
    Names
    CCAAT-binding transcription factor I subunit A
    DNA-binding protein B
    Y-box transcription factor
    enhancer factor I subunit A
    major histocompatibility complex, class II, Y box-binding protein I
    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_004559.5NP_004550.2  Y-box-binding protein 1

      See identical proteins and their annotated locations for NP_004550.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the functional protein.
      Source sequence(s)
      AC098484, BC090038, CN353145
      Consensus CDS
      CCDS470.1
      UniProtKB/Swiss-Prot
      P67809
      Related
      ENSP00000361626.3, ENST00000321358.12
      Conserved Domains (1) summary
      pfam00313
      Location:59128
      CSD; 'Cold-shock' DNA-binding domain

    RNA

    1. NR_132737.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate 5' exon and lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AC098484, BC013838

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

      Range
      42682418..42703805
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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