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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
  • CONTRIN 3 4
  • CSDA3 3 4
  • DBPC 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

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. 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

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

Genomics for YBX2 Gene

Regulatory Elements for YBX2 Gene

Enhancers for YBX2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH17G007279 1.4 ENCODE dbSUPER 36.9 +13.3 13278 4.3 HDGF FOXA2 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 YBX2 ELP5 SNORD10 DVL2 PFAS SNORA48 CTC1 PER1 ENSG00000262089 SLC2A4
GH17G007256 1.6 Ensembl ENCODE dbSUPER 31.8 +33.8 33818 8.7 HNRNPUL1 HDGF FOXA2 MLX ARNT AGO1 ARID4B SIN3A FEZF1 DMAP1 ELP5 YBX2 CLDN7 GABARAP SLC2A4 DLG4 ENSG00000262302 PIR33341
GH17G007233 1.5 ENCODE dbSUPER 25.2 +55.9 55935 11.3 MLX CREB3L1 AGO1 ZFP64 FEZF1 DMAP1 YY1 ZNF416 ZNF143 ZNF263 DVL2 NLGN2 ELP5 SNORD10 NEURL4 ZBTB4 SNORA48 LOC100996842 SENP3 YBX2
GH17G007247 1.4 ENCODE dbSUPER 25.3 +43.9 43937 6.0 CREB3L1 MLX FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 NFYC ELP5 YBX2 CLDN7 DLG4 ENSG00000262526
GH17G007712 0.9 FANTOM5 28.3 -417.7 -417720 0.2 ATF1 MXI1 ZMYM3 CHD4 BMI1 KMT2B YY1 ZNF335 GLIS2 ZNF366 SPEM1 TMEM95 C17orf74 YBX2 DLG4 SLC35G6 CNTROB ELP5 GC17M007714 DNAH2
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around YBX2 on UCSC Golden Path with GeneCards custom track

Genomic Location for YBX2 Gene

Chromosome:
17
Start:
7,288,252 bp from pter
End:
7,294,615 bp from pter
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

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).

Gene Ontology (GO) - Molecular Function for YBX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
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

CRISPR Products

miRNA for YBX2 Gene

miRTarBase miRNAs that target YBX2

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones 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 5
cytosol 1

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:0006366 transcription from RNA polymerase II promoter TAS 10100484
GO:0007283 spermatogenesis TAS 10100484
GO:0009386 translational attenuation TAS 10100484
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

Unigene Clusters for YBX2 Gene

Y box binding protein 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones 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
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, PaxDb, 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

Primer Products

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 35
  • 99.35 (n)
cow
(Bos Taurus)
Mammalia YBX2 34 35
  • 90.58 (n)
dog
(Canis familiaris)
Mammalia -- 35
  • 90 (a)
OneToMany
YBX2 34
  • 88.89 (n)
-- 35
  • 75 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Ybx2 34
  • 89.74 (n)
mouse
(Mus musculus)
Mammalia Ybx2 34 16 35
  • 89.62 (n)
oppossum
(Monodelphis domestica)
Mammalia YBX2 35
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.7091 34
African clawed frog
(Xenopus laevis)
Amphibia FRGY2 34
fruit fly
(Drosophila melanogaster)
Insecta yps 35
  • 30 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea cey-1 35
  • 37 (a)
ManyToMany
cey-4 35
  • 25 (a)
ManyToMany
cey-2 35
  • 24 (a)
ManyToMany
cey-3 35
  • 23 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10127 35
  • 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)

Paralogs for YBX2 Gene

Paralogs for YBX2 Gene

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

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 Sequence Context AA Info Type
rs1000835919 -- 7,294,747(+) GCACC(G/T)CGGCC upstream-variant-2KB
rs1001013141 -- 7,288,156(+) GCAAG(A/G)ATGCC downstream-variant-500B
rs1001065455 -- 7,287,792(+) AAATG(-/TA)TATAT downstream-variant-500B, utr-variant-3-prime
rs1001076182 -- 7,292,105(+) AAGCC(C/T)TCAGC intron-variant
rs1001130264 -- 7,291,782(+) TTCCT(C/G)GAGTG intron-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)

Relevant External Links for YBX2 Gene

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

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: DISEASES and GeneCards

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

Relevant External Links for YBX2

Genetic Association Database (GAD)
YBX2
Human Genome Epidemiology (HuGE) Navigator
YBX2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
YBX2
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 N.B. (J. Androl. 1999) 2 3 4 22 64
  2. Sequence alterations in the YBX2 gene are associated with male factor infertility. (PMID: 18339382) Hammoud S. … Carrell D.T. (Fertil. Steril. 2009) 3 22 46 64
  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 46 64
  4. Expression of Y-box-binding protein dbpC/contrin, a potentially new cancer/testis antigen. (PMID: 16479255) Kohno Y. … Sasaguri Y. (Br. J. Cancer 2006) 3 4 22 64
  5. Evaluation of 172 candidate polymorphisms for association with oligozoospermia or azoospermia in a large cohort of men of European descent. (PMID: 20378615) Aston K.I. … Carrell D.T. (Hum. Reprod. 2010) 3 46 64

Products for YBX2 Gene

Sources for YBX2 Gene

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