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

Gene ID: 4904, updated on 8-May-2016
Official Symbol
YBX1provided by HGNC
Official Full Name
Y-box binding protein 1provided by HGNC
Primary source
HGNC:HGNC:8014
See related
Ensembl:ENSG00000065978 HPRD:01095; MIM:154030; Vega:OTTHUMG00000007523
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]
Orthologs
Location:
1p34
Exon count:
8
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 1 NC_000001.11 (42682389..42702363)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (43148060..43168024)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 30 Neighboring gene thymosin beta 4, X-linked pseudogene 1 Neighboring gene uncharacterized LOC105378681 Neighboring gene peptidylprolyl isomerase H Neighboring gene claudin 19 Neighboring gene prolyl 3-hydroxylase 1

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Replication interactions

Interaction Pubs
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

Go to the HIV-1, Human Interaction Database

  • BDNF signaling pathway, organism-specific biosystem (from WikiPathways)
    BDNF signaling pathway, organism-specific biosystemBrain-derived neurotrophic factor (BDNF) is a neurotrophin essential for growth, differentiation, plasticity, and survival of neurons. BDNF is also required for processes such as energy metabolism, b...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • SIDS Susceptibility Pathways, organism-specific biosystem (from WikiPathways)
    SIDS Susceptibility Pathways, organism-specific biosystemIn this model, we provide an integrated view of Sudden Infant Death Syndrome (SIDS) at the level of implicated tissues, signaling networks and genetics. The purpose of this model is to serve as an ov...
  • Signaling events mediated by PTP1B, organism-specific biosystem (from Pathway Interaction Database)
    Signaling events mediated by PTP1B, organism-specific biosystem
    Signaling events mediated by PTP1B
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...
  • mRNA Splicing - Minor Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Minor Pathway, organism-specific biosystemThe splicing of a subset of pre-mRNA introns occurs by a second pathway, designated the AT-AC or U12-dependent splicing pathway. AT-AC introns have highly conserved, non-canonical splice sites that ...
  • mRNA processing, organism-specific biosystem (from WikiPathways)
    mRNA processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • MGC104858, MGC110976, MGC117250

Gene Ontology Provided by GOA

Component Evidence Code Pubs
CRD-mediated mRNA stability complex IDA
Inferred from Direct Assay
more info
PubMed 
U12-type spliceosomal complex IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic stress granule IDA
Inferred from Direct Assay
more info
PubMed 
extracellular exosome IDA
Inferred from Direct Assay
more info
PubMed 
histone pre-mRNA 3'end processing complex ISS
Inferred from Sequence or Structural Similarity
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
intracellular ribonucleoprotein complex IDA
Inferred from Direct Assay
more info
PubMed 
nuclear membrane IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus TAS
Traceable Author Statement
more info
PubMed 
Preferred Names
nuclease-sensitive element-binding protein 1
Names
CCAAT-binding transcription factor I subunit A
DNA-binding protein B
Y box binding protein 1
Y-box transcription factor
Y-box-binding protein 1
enhancer factor I subunit A
major histocompatibility complex, class II, Y box-binding protein I
nuclease sensitive element binding protein 1

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_004559.4NP_004550.2  nuclease-sensitive element-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, OTTHUMP00000008731, ENST00000321358, OTTHUMT00000019786
    Conserved Domains (1) summary
    cd04458
    Location:61127
    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. ...

RNA

  1. NR_132737.1 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 Annotation Release 107 details...

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p2 Primary Assembly

    Range
    42682389..42702363
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005270904.2XP_005270961.1  

    See identical proteins and their annotated locations for XP_005270961.1

    Conserved Domains (1) summary
    cd04458
    Location:6190
    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. ...

Alternate CHM1_1.1

Genomic

  1. NC_018912.2 Alternate CHM1_1.1

    Range
    43264924..43284881
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)