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

Gene ID: 22608, updated on 22-Jan-2023

Summary

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
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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)

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)
  • Gene trapped (1) 
  • Targeted (2)  1 citation
  • Endonuclease-mediated (2) 

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 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 
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
PubMed 
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 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
 
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
 
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
 
located_in plasma membrane 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

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_011732.2NP_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
    P43482, P62960
    UniProtKB/TrEMBL
    A0A8C6GXI3, 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

    UniProtKB/TrEMBL
    A0A8C6GWR6
    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