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Ybx3 Y box protein 3 [ Mus musculus (house mouse) ]

Gene ID: 56449, updated on 6-Nov-2022

Summary

Official Symbol
Ybx3provided by MGI
Official Full Name
Y box protein 3provided by MGI
Primary source
MGI:MGI:2137670
See related
Ensembl:ENSMUSG00000030189 AllianceGenome:MGI:2137670
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
Yb2; Csda; Dpba; MSY3; MSY4; dbpA; oxyR
Summary
Enables nucleic acid binding activity and polysome binding activity. Involved in negative regulation of transcription by RNA polymerase II. Acts upstream of or within several processes, including male gonad development; negative regulation of skeletal muscle tissue development; and positive regulation of organ growth. Located in cytoplasm and nucleus. Is expressed in several structures, including brain; branchial arch; limb bud; sensory organ; and testis. Orthologous to human YBX3 (Y-box binding protein 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis adult (RPKM 404.0), liver E14 (RPKM 96.6) and 21 other tissues See more
Orthologs
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Genomic context

See Ybx3 in Genome Data Viewer
Location:
6; 6 F3
Exon count:
10
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (131341821..131365413, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (131364858..131388450, complement)

Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene mago homolog B, exon junction complex core component Neighboring gene serine/threonine/tyrosine kinase 1 Neighboring gene predicted gene, 22362 Neighboring gene ring finger and WD repeat domain 2 pseudogene Neighboring gene predicted gene 6619

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)
  • Targeted (1)  1 citation
  • Endonuclease-mediated (4) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables RNA binding IEA
Inferred from Electronic Annotation
more info
 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables mRNA 3'-UTR binding IDA
Inferred from Direct Assay
more info
PubMed 
enables nucleic acid binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables polysome binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables ribonucleoprotein complex 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
acts_upstream_of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cellular hyperosmotic response ISO
Inferred from Sequence Orthology
more info
 
involved_in cellular response to tumor necrosis factor ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of ectopic germ cell programmed cell death IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within fertilization 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 male gonad development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within negative regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within negative regulation of developmental process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of necroptotic process ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of reproductive process IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within negative regulation of skeletal muscle tissue development IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of organ growth IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within spermatogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol ISO
Inferred from Sequence Orthology
more info
 
located_in gap junction ISO
Inferred from Sequence Orthology
more info
PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus 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 3
Names
DNA-binding protein A
cold shock domain protein A
cold shock domain-containing protein A

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_011733.2NP_035863.1  Y-box-binding protein 3 short isoform

    See identical proteins and their annotated locations for NP_035863.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame segment in the coding region, compared to variant 1. The resulting protein, known as the short isoform, is shorter than the long isoform.
    Source sequence(s)
    BC027785, BC048242
    Consensus CDS
    CCDS20605.1
    UniProtKB/Swiss-Prot
    Q9JKB3
    UniProtKB/TrEMBL
    Q68G78
    Related
    ENSMUSP00000085172.3, ENSMUST00000087865.4
    Conserved Domains (1) summary
    pfam00313
    Location:83152
    CSD; 'Cold-shock' DNA-binding domain
  2. NM_139117.2NP_620817.2  Y-box-binding protein 3 long isoform

    See identical proteins and their annotated locations for NP_620817.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and it encodes the long isoform.
    Source sequence(s)
    BC027785, BC048242
    Consensus CDS
    CCDS20606.1
    UniProtKB/Swiss-Prot
    Q9EQF8, Q9JKB3
    UniProtKB/TrEMBL
    Q68G78
    Related
    ENSMUSP00000032309.7, ENSMUST00000032309.13
    Conserved Domains (1) summary
    pfam00313
    Location:83152
    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_000072.7 Reference GRCm39 C57BL/6J

    Range
    131341821..131365413 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)