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

Gene ID: 22608, updated on 11-Apr-2024

Summary

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Official Symbol
Ybx1provided by MGI
Official Full Name
Y box protein 1provided by MGI
Primary source
MGI:MGI:99146
See related
Ensembl:ENSMUSG00000028639 AllianceGenome:MGI:99146
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
EF1A; MSY1; YB-1; dbpB; Nsep1; mYB-1a; 1700102N10Rik
Summary
Enables chromatin binding activity; mRNA binding activity; and single-stranded DNA binding activity. Involved in epidermis development and negative regulation of cellular senescence. Acts upstream of or within several processes, including cellular response to interleukin-7; negative regulation of striated muscle cell differentiation; and negative regulation of transcription by RNA polymerase II. Located in cytoplasm and nucleus. Part of histone pre-mRNA 3'end processing complex. Is expressed in several structures, including branchial arch; central nervous system; facial prominence; gonad; and retina. Orthologous to human YBX1 (Y-box binding protein 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis adult (RPKM 192.5), CNS E11.5 (RPKM 174.7) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Ybx1 in Genome Data Viewer
Location:
4; 4 D2.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_02 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)

Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:118905472-118905581 Neighboring gene STARR-positive B cell enhancer ABC_E4654 Neighboring gene prolyl 3-hydroxylase 1 Neighboring gene predicted gene 12927 Neighboring gene claudin 19 Neighboring gene STARR-positive B cell enhancer ABC_E1652 Neighboring gene peptidyl prolyl isomerase H Neighboring gene STARR-positive B cell enhancer ABC_E10252 Neighboring gene coiled-coil domain containing 30 Neighboring gene lactate dehydrogenase A, pseudogene 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Long non-coding RNA KCND1 protects hearts from hypertrophy by targeting YBX1. Yang R, et al. Cell Death Dis, 2023 May 30. PMID 37253771, Free PMC Article
  2. DNA binding protein YB-1 is a part of the neutrophil extracellular trap mediation of kidney damage and cross-organ effects. Wang J, et al. Kidney Int, 2023 Jul. PMID 36963487
  3. YB-1 Expression Is Associated with Lymph Node Metastasis and Drug Resistance to Adriamycin in Breast Cancer. Dong H, et al. Dis Markers, 2023. PMID 36785738, Free PMC Article
  4. Transcriptional and post-transcriptional control of autophagy and adipogenesis by YBX1. Wu R, et al. Cell Death Dis, 2023 Jan 16. PMID 36642732, Free PMC Article
  5. Loss of YB-1 alleviates liver fibrosis by suppressing epithelial-mesenchymal transition in hepatic progenitor cells. Guo Y, et al. Biochim Biophys Acta Mol Basis Dis, 2022 Nov 1. PMID 35926755

See all (156) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. YBX1 promotes type H vessel-dependent bone formation in an m5C-dependent manner.
    Title: YBX1 promotes type H vessel-dependent bone formation in an m5C-dependent manner.
  2. Decreased YB-1 expression denervates brown adipose tissue and contributes to age-related metabolic dysfunction.
    Title: Decreased YB-1 expression denervates brown adipose tissue and contributes to age-related metabolic dysfunction.
  3. Y-box binding protein 1 promotes chromatin accessibility to aggravate liver fibrosis.
    Title: Y-box binding protein 1 promotes chromatin accessibility to aggravate liver fibrosis.
  4. YBX1 as an oncogenic factor in T-cell acute lymphoblastic leukemia.
    Title: YBX1 as an oncogenic factor in T-cell acute lymphoblastic leukemia.
  5. DNA binding protein YB-1 is a part of the neutrophil extracellular trap mediation of kidney damage and cross-organ effects.
    Title: DNA binding protein YB-1 is a part of the neutrophil extracellular trap mediation of kidney damage and cross-organ effects.
  6. Long non-coding RNA KCND1 protects hearts from hypertrophy by targeting YBX1.
    Title: Long non-coding RNA KCND1 protects hearts from hypertrophy by targeting YBX1.
  7. Splicing factor YBX1 regulates bone marrow stromal cell fate during aging.
    Title: Splicing factor YBX1 regulates bone marrow stromal cell fate during aging.
  8. YBX1 regulates the survival of chronic myeloid leukemia stem cells by modulating m[6]A-mediated YWHAZ stability.
    Title: YBX1 regulates the survival of chronic myeloid leukemia stem cells by modulating m(6)A-mediated YWHAZ stability.
  9. The formation of HuR/YB1 complex is required for the stabilization of target mRNA to promote myogenesis.
    Title: The formation of HuR/YB1 complex is required for the stabilization of target mRNA to promote myogenesis.
  10. YB-1 Expression Is Associated with Lymph Node Metastasis and Drug Resistance to Adriamycin in Breast Cancer.
    Title: YB-1 Expression Is Associated with Lymph Node Metastasis and Drug Resistance to Adriamycin in Breast Cancer.
Submit: New GeneRIF Correction See all GeneRIFs (70)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Gene trapped (1) 
  • Targeted (2)  1 citation
  • Endonuclease-mediated (3) 

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC118070

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables C5-methylcytidine-containing RNA reader activity 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
  
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 cellular senescence IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay 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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within positive regulation of cell division IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of cytoplasmic translation 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 DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
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
  
located_in P-body IDA
Inferred from Direct Assay
more info
 PubMed 
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 endoplasmic reticulum 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
  
located_in neuronal cell body ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IGI
Inferred from Genetic Interaction
more info
 PubMed 
located_in perinuclear region of cytoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
  
part_of protein-containing complex ISO
Inferred from Sequence Orthology
more info
  
part_of ribonucleoprotein complex ISO
Inferred from Sequence Orthology
more info
  
is_active_in synapse EXP
Inferred from Experiment
more info
 PubMed 
is_active_in synapse IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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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)

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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_011732.2 → NP_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, Q810K5
    Related
    ENSMUSP00000078589.7, ENSMUST00000079644.13
    Conserved Domains (1) summary
    pfam00313
    Location:57 → 126
    CSD; 'Cold-shock' DNA-binding domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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_030253407.1 → XP_030109267.1  Y-box-binding protein 1 isoform X3

    UniProtKB/TrEMBL
    Q810K5
    Conserved Domains (1) summary
    cd04458
    Location:59 → 88
    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_006502934.4 → XP_006502997.1  Y-box-binding protein 1 isoform X2

    UniProtKB/TrEMBL
    Q60951
    Conserved Domains (1) summary
    cd04458
    Location:59 → 88
    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_006502933.4 → XP_006502996.1  Y-box-binding protein 1 isoform X1

    UniProtKB/TrEMBL
    Q60951
    Conserved Domains (1) summary
    pfam00313
    Location:57 → 126
    CSD; 'Cold-shock' DNA-binding domain
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P62960.3 GenPept UniProtKB/Swiss-Prot:P62960

Gene LinkOut

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