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Aliases for YBX2 Gene

Aliases for YBX2 Gene

  • Y-Box Binding Protein 2 2 3 5
  • DNA-Binding Protein C 3 4
  • CSDA3 3 4
  • MSY2 3 4
  • Germ Cell Specific Y-Box Binding Protein 3
  • Germ Cell-Specific Y-Box-Binding Protein 4
  • Y-Box-Binding Protein 2 3
  • MSY2 Homolog 4
  • CONTRIN 3
  • Contrin 4
  • DBPC 3
  • 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 Peach Allergy and Fruit Allergy. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and lipid binding. An important paralog of this gene is YBX3.

UniProtKB/Swiss-Prot 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

Additional gene information for YBX2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for YBX2 Gene

Genomics for YBX2 Gene

GeneHancer (GH) Regulatory Elements for YBX2 Gene

Promoters and enhancers for YBX2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J007293 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE 659 -0.5 -511 3.9 CLOCK MLX ARID4B SIN3A DMAP1 ZNF2 SLC30A9 ZNF766 ZNF143 KLF13 YBX2 PIR50100 GC17M007299 GC17M007298 ENSG00000262067 SPEM1 EIF5A LOC105371517 ELP5
GH17J007279 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 36.8 +13.3 13277 4.3 HDGF FOXA2 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B IRF4 SLC2A4 YBX2 ELP5 PFAS DVL2 CTC1 ENSG00000262089 CNTROB WRAP53 SNORD10
GH17J007256 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 31.8 +33.8 33817 8.7 HDGF FOXA2 MLX ARNT ARID4B NEUROD1 SIN3A FEZF1 DMAP1 ZNF2 CLDN7 PIR33341 GC17M007249 ENSG00000262302 CTDNEP1 ELP5 YBX2 WRAP53 POLR2A CNTROB
GH17J007233 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 25.2 +56.0 55956 11.3 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF416 DVL2 GABARAP PHF23 CNTROB SNORD10 WRAP53 NEURL4 POLR2A KIAA0753 KCTD11
GH17J007247 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 25.3 +43.9 43937 6 HDGF PKNOX1 CLOCK SMAD1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ELP5 CTDNEP1 PIR48144 YBX2 DVL2 CTC1 ENSG00000262089 CNTROB WRAP53 PFAS
- 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 UCSC Golden Path with GeneCards custom track

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

Genomic Locations for YBX2 Gene

Genomic Locations for YBX2 Gene
chr17:7,288,252-7,294,615
(GRCh38/hg38)
Size:
6,364 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

Suggested Antigen Peptide Sequences for YBX2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

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

No data available for 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:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding ISA --
GO:0003676 nucleic acid binding IEA --
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

miRNA for YBX2 Gene

miRTarBase miRNAs that target YBX2

Clone Products

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 5
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli fibrillar center (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for YBX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001650 fibrillar center IDA --
GO:0005634 nucleus TAS 10100484
GO:0005737 cytoplasm IEA,TAS --
genes like me logo Genes that share ontologies with YBX2: view

Pathways & Interactions for YBX2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for YBX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0006366 transcription by RNA polymerase II TAS 10100484
GO:0007283 spermatogenesis TAS 10100484
GO:0009386 translational attenuation TAS 10100484
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

Unigene Clusters for YBX2 Gene

Y box binding protein 2:
Representative Sequences:

Clone Products

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

No ASD Table

Relevant External Links for YBX2 Gene

GeneLoc Exon Structure for
YBX2
ECgene alternative splicing isoforms for
YBX2

Expression for YBX2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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

NURSA nuclear receptor signaling pathways regulating expression of YBX2 Gene:

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(4.3)
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 34 33
  • 99.35 (n)
OneToOne
cow
(Bos Taurus)
Mammalia YBX2 34 33
  • 90.58 (n)
OneToOne
dog
(Canis familiaris)
Mammalia -- 34
  • 90 (a)
OneToMany
YBX2 33
  • 88.89 (n)
-- 34
  • 75 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Ybx2 33
  • 89.74 (n)
mouse
(Mus musculus)
Mammalia Ybx2 16 34 33
  • 89.62 (n)
oppossum
(Monodelphis domestica)
Mammalia YBX2 34
  • 71 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia FRGY2 33
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.7091 33
fruit fly
(Drosophila melanogaster)
Insecta yps 34
  • 30 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea cey-1 34
  • 37 (a)
ManyToMany
cey-4 34
  • 25 (a)
ManyToMany
cey-2 34
  • 24 (a)
ManyToMany
cey-3 34
  • 23 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10127 34
  • 36 (a)
OneToMany
Species where no ortholog for YBX2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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 from dbSNP and Humsavar for YBX2 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1000835919 -- 7,294,747(-) G/T upstream_transcript_variant
rs1001013141 -- 7,288,156(-) G/A downstream_transcript_variant
rs1001076182 -- 7,292,105(-) C/T intron_variant
rs1001130264 -- 7,291,782(-) G/C intron_variant
rs1001289118 -- 7,294,579(-) G/T 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant

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

(2) MalaCards diseases for YBX2 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
peach allergy
  • prunus persica fruit allergy
fruit allergy
  • allergy to fruit
- 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
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 22 58
  2. Sequence alterations in the YBX2 gene are associated with male factor infertility. (PMID: 18339382) Hammoud S … Carrell DT (Fertility and sterility 2009) 3 22 44 58
  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 22 44 58
  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 22 58
  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 44 58

Products for YBX2 Gene

Sources for YBX2 Gene

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