This gene encodes a nucleic acid binding protein which is highly expressed in germ cells. The encoded protein binds to a Y-box element in the promoters of certain genes but also binds to mRNA transcribed from these genes. Pseudogenes for this gene are located on chromosome 10 and 15. [provided by RefSeq, Feb 2012] See more...

Aliases for YBX2 Gene

Aliases for YBX2 Gene

  • Y-Box Binding Protein 2 2 3 5
  • CSDA3 2 3 4
  • MSY2 2 3 4
  • Y-Box-Binding Protein 2 3 4
  • DNA-Binding Protein C 3 4
  • Contrin 2 4
  • Epididymis Secretory Sperm Binding Protein 3
  • Germ Cell Specific Y-Box Binding Protein 3
  • Germ Cell-Specific Y-Box-Binding Protein 4
  • MSY2 Homolog 4
  • CONTRIN 3
  • DBPC 3
  • YBX2 5
  • Dbpc 4

External Ids for YBX2 Gene

Previous GeneCards Identifiers for YBX2 Gene

  • GC17M007549
  • GC17M007921
  • GC17M007134
  • GC17M007392
  • GC17M007132
  • GC17M007191
  • GC17M007083

Summaries for YBX2 Gene

Entrez Gene Summary for YBX2 Gene

  • This gene encodes a nucleic acid binding protein which is highly expressed in germ cells. The encoded protein binds to a Y-box element in the promoters of certain genes but also binds to mRNA transcribed from these genes. Pseudogenes for this gene are located on chromosome 10 and 15. [provided by RefSeq, Feb 2012]

GeneCards Summary for YBX2 Gene

YBX2 (Y-Box Binding Protein 2) is a Protein Coding gene. Diseases associated with YBX2 include Mastocytosis, Cutaneous and Mixed Germ Cell Cancer. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and lipid binding. An important paralog of this gene is YBX1.

UniProtKB/Swiss-Prot Summary for YBX2 Gene

  • Major constituent of messenger ribonucleoprotein particles (mRNPs). Involved in the regulation of the stability and/or translation of germ cell mRNAs. Binds to Y-box consensus promoter element. Binds to full-length mRNA with high affinity in a sequence-independent manner. Binds to short RNA sequences containing the consensus site 5'-UCCAUCA-3' with low affinity and limited sequence specificity. Its binding with maternal mRNAs is necessary for its cytoplasmic retention. May mark specific mRNAs (those transcribed from Y-box promoters) in the nucleus for cytoplasmic storage, thereby linking transcription and mRNA storage/translational delay (By similarity).

Gene Wiki entry for YBX2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for YBX2 Gene

Genomics for YBX2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for YBX2 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around YBX2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for YBX2

Top Transcription factor binding sites by QIAGEN in the YBX2 gene promoter:
  • AREB6
  • C/EBPbeta
  • COMP1
  • Gfi-1
  • LCR-F1
  • Nkx2-5
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for YBX2 Gene

Genomic Locations for YBX2 Gene
chr17:7,288,254-7,294,639
(GRCh38/hg38)
Size:
6,386 bases
Orientation:
Minus strand
chr17:7,191,571-7,197,934
(GRCh37/hg19)
Size:
6,364 bases
Orientation:
Minus strand

Genomic View for YBX2 Gene

Genes around YBX2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
YBX2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for YBX2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for YBX2 Gene

Proteins for YBX2 Gene

  • Protein details for YBX2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y2T7-YBOX2_HUMAN
    Recommended name:
    Y-box-binding protein 2
    Protein Accession:
    Q9Y2T7
    Secondary Accessions:
    • D3DTP1
    • Q8N4P0

    Protein attributes for YBX2 Gene

    Size:
    364 amino acids
    Molecular mass:
    38518 Da
    Quaternary structure:
    • Found in a mRNP complex with PABPC1 and YBX3.

neXtProt entry for YBX2 Gene

Post-translational modifications for YBX2 Gene

  • Phosphorylated during oocyte maturation and dephosphorylated following egg activation. Phosphorylated in vitro by a kinase activity associated with testicular mRNPs. Dephosphorylation leads to a decrease in its affinity to bind RNA in vitro (By similarity).
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for YBX2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for YBX2 Gene

Domains & Families for YBX2 Gene

Gene Families for YBX2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for YBX2 Gene

InterPro:
Blocks:
  • Cold-shock DNA-binding domain
  • Cold shock protein
ProtoNet:

Suggested Antigen Peptide Sequences for YBX2 Gene

GenScript: Design optimal peptide antigens:
  • MSY2 homolog (YBOX2_HUMAN)
genes like me logo Genes that share domains with YBX2: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for YBX2 Gene

Function for YBX2 Gene

Molecular function for YBX2 Gene

UniProtKB/Swiss-Prot Function:
Major constituent of messenger ribonucleoprotein particles (mRNPs). Involved in the regulation of the stability and/or translation of germ cell mRNAs. Binds to Y-box consensus promoter element. Binds to full-length mRNA with high affinity in a sequence-independent manner. Binds to short RNA sequences containing the consensus site 5'-UCCAUCA-3' with low affinity and limited sequence specificity. Its binding with maternal mRNAs is necessary for its cytoplasmic retention. May mark specific mRNAs (those transcribed from Y-box promoters) in the nucleus for cytoplasmic storage, thereby linking transcription and mRNA storage/translational delay (By similarity).

Phenotypes From GWAS Catalog for YBX2 Gene

Gene Ontology (GO) - Molecular Function for YBX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IBA 21873635
GO:0003677 DNA binding IEA --
GO:0003723 RNA binding IEA --
genes like me logo Genes that share ontologies with YBX2: view
genes like me logo Genes that share phenotypes with YBX2: view

Animal Models for YBX2 Gene

MGI Knock Outs for YBX2:

Animal Model Products

CRISPR Products

miRNA for YBX2 Gene

miRTarBase miRNAs that target YBX2

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for YBX2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for YBX2 Gene

Localization for YBX2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for YBX2 Gene

Cytoplasm. Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for YBX2 gene
Compartment Confidence
nucleus 4
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
cytosol 1

Gene Ontology (GO) - Cellular Components for YBX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS,IBA 21873635
GO:0005737 cytoplasm TAS,IEA --
genes like me logo Genes that share ontologies with YBX2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for YBX2 Gene

Pathways & Interactions for YBX2 Gene

PathCards logo

SuperPathways for YBX2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for YBX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006366 transcription by RNA polymerase II TAS 10100484
GO:0007283 spermatogenesis TAS 10100484
GO:0009386 translational attenuation TAS 10100484
GO:0010468 regulation of gene expression IBA 21873635
GO:0048599 oocyte development IEA --
genes like me logo Genes that share ontologies with YBX2: view

No data available for Pathways by source and SIGNOR curated interactions for YBX2 Gene

Drugs & Compounds for YBX2 Gene

(1) Additional Compounds for YBX2 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with YBX2: view

Transcripts for YBX2 Gene

mRNA/cDNA for YBX2 Gene

1 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for YBX2

Alternative Splicing Database (ASD) splice patterns (SP) for YBX2 Gene

No ASD Table

Relevant External Links for YBX2 Gene

GeneLoc Exon Structure for
YBX2

Expression for YBX2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for YBX2 Gene

mRNA differential expression in normal tissues according to GTEx for YBX2 Gene

This gene is overexpressed in Testis (x42.5).

Protein differential expression in normal tissues from HIPED for YBX2 Gene

This gene is overexpressed in Testis (43.0) and Ovary (25.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for YBX2 Gene



Protein tissue co-expression partners for YBX2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for YBX2

SOURCE GeneReport for Unigene cluster for YBX2 Gene:

Hs.567494

mRNA Expression by UniProt/SwissProt for YBX2 Gene:

Q9Y2T7-YBOX2_HUMAN
Tissue specificity: Expressed in oocytes and testicular germ cells in the stage of spermatogonia to spermatocyte. Also observed placental trophoblasts, as well as in vascular smooth muscle cells in the pulmonary artery, myocardium, and skeletal muscle. Undetectable in epithelial cells in respiratory, gastrointestinal, and urogenital tracts. Up-regulated in various carcinomas and germ cell tumors (at protein level).

Evidence on tissue expression from TISSUES for YBX2 Gene

  • Nervous system(4.5)
  • Blood(2)
  • Skin(2)
genes like me logo Genes that share expression patterns with YBX2: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for YBX2 Gene

Orthologs for YBX2 Gene

This gene was present in the common ancestor of animals.

Orthologs for YBX2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia YBX2 30 31
  • 99.35 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia YBX2 30 31
  • 90.58 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia -- 31
  • 90 (a)
OneToMany
YBX2 30
  • 88.89 (n)
-- 31
  • 75 (a)
OneToMany
Rat
(Rattus norvegicus)
Mammalia Ybx2 30
  • 89.74 (n)
Mouse
(Mus musculus)
Mammalia Ybx2 30 17 31
  • 89.62 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia YBX2 31
  • 71 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia FRGY2 30
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia Str.7091 30
Fruit Fly
(Drosophila melanogaster)
Insecta yps 31
  • 30 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea cey-1 31
  • 37 (a)
ManyToMany
cey-4 31
  • 25 (a)
ManyToMany
cey-2 31
  • 24 (a)
ManyToMany
cey-3 31
  • 23 (a)
ManyToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.10127 31
  • 36 (a)
OneToMany
Species where no ortholog for YBX2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Zebrafish (Danio rerio)

Evolution for YBX2 Gene

ENSEMBL:
Gene Tree for YBX2 (if available)
TreeFam:
Gene Tree for YBX2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for YBX2: view image

Paralogs for YBX2 Gene

Paralogs for YBX2 Gene

(3) SIMAP similar genes for YBX2 Gene using alignment to 3 proteins:

  • YBOX2_HUMAN
  • I3L2D6_HUMAN
  • L8EAU5_HUMAN

Pseudogenes.org Pseudogenes for YBX2 Gene

genes like me logo Genes that share paralogs with YBX2: view

Variants for YBX2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for YBX2 Gene

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
rs222859 - p.Gly9Val
rs8069533 - p.Ser63Pro

Additional dbSNP identifiers (rs#s) for YBX2 Gene

Structural Variations from Database of Genomic Variants (DGV) for YBX2 Gene

Variant ID Type Subtype PubMed ID
esv2422288 CNV deletion 17116639
esv2665200 CNV deletion 23128226
esv3639863 CNV loss 21293372
esv3639865 CNV loss 21293372
esv3639866 CNV gain 21293372
nsv1071330 CNV deletion 25765185
nsv1112699 CNV deletion 24896259
nsv1963 CNV deletion 18451855
nsv457659 CNV loss 19166990
nsv574322 CNV loss 21841781
nsv952118 CNV deletion 24416366

Variation tolerance for YBX2 Gene

Residual Variation Intolerance Score: 59.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.38; 88.47% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for YBX2 Gene

Human Gene Mutation Database (HGMD)
YBX2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
YBX2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for YBX2 Gene

Disorders for YBX2 Gene

MalaCards: The human disease database

(7) MalaCards diseases for YBX2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
mastocytosis, cutaneous
  • mastc
mixed germ cell cancer
  • mixed germ cell neoplasm
peach allergy
  • prunus persica fruit allergy
corticosteroid allergy
dysgerminoma of ovary
  • ovarian dysgerminoma
- elite association - COSMIC cancer census association via MalaCards
Search YBX2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for YBX2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with YBX2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for YBX2 Gene

Publications for YBX2 Gene

  1. Contrin, the human homologue of a germ-cell Y-box-binding protein: cloning, expression, and chromosomal localization. (PMID: 10100484) Tekur S … Hecht NB (Journal of andrology 1999) 2 3 4 23
  2. Sequence alterations in the YBX2 gene are associated with male factor infertility. (PMID: 18339382) Hammoud S … Carrell DT (Fertility and sterility 2009) 3 23 41
  3. Some single nucleotide polymorphisms of MSY2 gene might contribute to susceptibility to spermatogenic impairment in idiopathic infertile men. (PMID: 18372033) Deng Y … Zhang S (Urology 2008) 3 23 41
  4. Expression of Y-box-binding protein dbpC/contrin, a potentially new cancer/testis antigen. (PMID: 16479255) Kohno Y … Sasaguri Y (British journal of cancer 2006) 3 4 23
  5. Evaluation of 172 candidate polymorphisms for association with oligozoospermia or azoospermia in a large cohort of men of European descent. (PMID: 20378615) Aston KI … Carrell DT (Human reproduction (Oxford, England) 2010) 3 41

Products for YBX2 Gene

Sources for YBX2 Gene