About   Help   FAQ
Ybx3
Gene Detail
Symbol

Name
ID
Ybx3
Y box protein 3
MGI:2137670
Synonyms
Csda, dbpA, Dpba, MSY3, MSY4, oxyR, Yb2
Feature Type
protein coding gene
Genetic Map
Chromosome 6
63.44 cM
Detailed Genetic Map ± 1 cM


Mapping data(1)
Sequence Map
Chr6:131364858-131388450 bp, - strand
From NCBI annotation of GRCm38

  23593 bp   ±  kb flank

VEGA Genome Browser | Ensembl Genome Browser | UCSC Browser | NCBI Map Viewer


Mouse Genome Browser
Vertebrate
homology
HomoloGene:2708  Vertebrate Homology Class
1 human; 1 mouse; 1 rat; 1 chimpanzee; 1 rhesus macaque; 1 cattle; 1 dog; 1 chicken; 1 western clawed frog

Protein SuperFamily: Y box-binding protein 1
Gene Tree: Ybx3

Human
homologs
Human Homolog YBX3, Y box binding protein 3
NCBI Gene ID 8531
neXtProt AC  NX_P16989
Human Synonyms  CSDA, CSDA1, DBPA, ZONAB
Human Chr (Location)  12p13.1; chr12:10699077-10723354 (-)  GRCh38
Mutations,
alleles, and
phenotypes
All mutations/alleles(23) : Gene trapped(21) Targeted(2)
 
Half of mice homozygous for a knock-out allele exhibit male infertility associated with smaller testes and reduced sperm production, partly due to increased spermatocyte apoptosis during mid to late spermatogenesis and progressive seminiferous tubule degeneration.
 
Interactions
Ybx3 interacts with 173 markers (Mir7-1, Mir9-1, Mir9-2, ...)
Gene Ontology
(GO)
classifications
All GO classifications: (35 annotations)
Process cellular hyperosmotic response, cellular response to tumor necrosis factor, ...
Component cytoplasm, gap junction, ...
Function DNA binding, mRNA 3'-UTR binding, ...
This is a GO Consortium Reference Genome Project gene.
External Resources: FuncBase
Expression
Literature Summary: (9 records)
Data Summary: Results (101)    Tissues (82)    Images (10)    Tissue x Stage Matrix (view)
Assay TypeResults
Immunohistochemistry 5
RNA in situ 68
Western blot 25
RT-PCR 3
cDNA source data(210)
External Resources: Allen Institute   GEO   Expression Atlas
Molecular
reagents
All nucleic(214) cDNA(213) Primer pair(1)
Microarray probesets(4)
Other database
links
Ensembl Gene ModelENSMUSG00000030189 (Evidence)
Entrez Gene56449 (Evidence)
UniGene458000
DFCITC1572736, TC1584267
DoTSDT.101403643, DT.110485248, DT.536906
Consensus CDS ProjectCCDS20605.1, CCDS20606.1
International Mouse Knockout Project StatusYbx3
Sequences
Representative SequencesLengthStrain/SpeciesFlank
genomic 56449 NCBI Gene Model | MGI Sequence Detail 23593 C57BL/6J ±  kb
transcript NM_139117 RefSeq | MGI Sequence Detail 1862 Not Specified 
polypeptide Q9JKB3 UniProt | EBI | MGI Sequence Detail 361 Not Applicable 

For the selected sequences
All sequences(37) RefSeq(4) UniProt(7)
Polymorphisms
SNPs within 2kb(283 from dbSNP Build 137)
Protein-related
information
ResourceIDDescription
InterPro IPR019844 Cold-shock conserved site
InterPro IPR011129 Cold shock protein
InterPro IPR002059 Cold-shock protein, DNA-binding
InterPro IPR012340 Nucleic acid-binding, OB-fold
Protein Ontology PR:000003243 Y-box-binding protein 3
Graphical View of Protein Domain Structure
References
(Earliest) J:64916 Sakura H, et al., Two human genes isolated by a novel method encode DNA-binding proteins containing a common region of homology. Gene. 1988 Dec 20;73(2):499-507
(Latest) J:209112 Shimizu H, et al., The AERO system: a 3D-like approach for recording gene expression patterns in the whole mouse embryo. PLoS One. 2013;8(10):e75754
All references(52)
Other
accession IDs
MGI:1096351

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
Citing These Resources
Funding Information
Warranty Disclaimer & Copyright Notice
Send questions and comments to User Support.
last database update
10/21/2014
MGI 5.20
The Jackson Laboratory