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

Gene ID: 4904, updated on 29-Mar-2020

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

Genomic context

See YBX1 in Genome Data Viewer
Location:
1p34.2
Exon count:
9
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (42682418..42703805)
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 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
DNA binding TAS
Traceable Author Statement
more info
PubMed 
DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity TAS
Traceable Author Statement
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
GTPase binding IPI
Inferred from Physical Interaction
more info
PubMed 
RNA binding HDA PubMed 
RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
double-stranded DNA binding TAS
Traceable Author Statement
more info
PubMed 
mRNA binding IEA
Inferred from Electronic Annotation
more info
 
miRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
nucleic acid binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
single-stranded DNA binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
CRD-mediated mRNA stabilization IMP
Inferred from Mutant Phenotype
more info
PubMed 
Notch signaling pathway TAS
Traceable Author Statement
more info
 
RNA transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to interleukin-7 IEA
Inferred from Electronic Annotation
more info
 
embryonic morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
epidermis development ISS
Inferred from Sequence or Structural Similarity
more info
 
in utero embryonic development IEA
Inferred from Electronic Annotation
more info
 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
mRNA stabilization IDA
Inferred from Direct Assay
more info
PubMed 
miRNA transport IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of cellular senescence ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of striated muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
negative regulation of translation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of cell division IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
protein localization to cytoplasmic stress granule IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
tRNA transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
transcription by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
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 
cytosol IDA
Inferred from Direct Assay
more info
 
extracellular exosome HDA PubMed 
extracellular exosome IDA
Inferred from Direct Assay
more info
PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
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
 
messenger ribonucleoprotein complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear membrane IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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)

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.

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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