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Aliases for YBX3 Gene

Aliases for YBX3 Gene

  • Y-Box Binding Protein 3 2 3 5
  • Single-Strand DNA-Binding Protein NF-GMB 3 4
  • Cold Shock Domain-Containing Protein A 3 4
  • Cold-Shock Domain Containing A1 2 3
  • DNA-Binding Protein A 3 4
  • CSDA 3 4
  • DBPA 3 4
  • ZO-1-Associated Nucleic Acid-Binding Protein 3
  • Cold Shock Domain Protein A 2
  • Cold-Shock Domain Protein A 3
  • Y-Box-Binding Protein 3 3
  • CSDA1 3
  • ZONAB 3

External Ids for YBX3 Gene

Previous HGNC Symbols for YBX3 Gene

  • CSDA

Previous GeneCards Identifiers for YBX3 Gene

  • GC12M010852
  • GC12M010711
  • GC12M010715
  • GC12M010842

Summaries for YBX3 Gene

GeneCards Summary for YBX3 Gene

YBX3 (Y-Box Binding Protein 3) is a Protein Coding gene. Diseases associated with YBX3 include Uterine Inflammatory Disease and Primary Bacterial Infectious Disease. Among its related pathways are Cytoskeleton remodeling Regulation of actin cytoskeleton by Rho GTPases and Tight junction. GO annotations related to this gene include nucleic acid binding and transcription factor activity, sequence-specific DNA binding. An important paralog of this gene is YBX1.

UniProtKB/Swiss-Prot for YBX3 Gene

  • Binds to the GM-CSF promoter. Seems to act as a repressor. Binds also to full length mRNA and to short RNA sequences containing the consensus site 5-UCCAUCA-3. May have a role in translation repression (By similarity).

Gene Wiki entry for YBX3 Gene

No data available for Entrez Gene Summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for YBX3 Gene

Genomics for YBX3 Gene

Regulatory Elements for YBX3 Gene

Enhancers for YBX3 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
- Elite enhancer/Elite enhancer-gene association

Enhancers around YBX3 on UCSC Golden Path with GeneCards custom track

Promoters for YBX3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around YBX3 on UCSC Golden Path with GeneCards custom track

Genomic Location for YBX3 Gene

Chromosome:
12
Start:
10,699,077 bp from pter
End:
10,723,448 bp from pter
Size:
24,372 bases
Orientation:
Minus strand

Genomic View for YBX3 Gene

Genes around YBX3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
YBX3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for YBX3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for YBX3 Gene

Proteins for YBX3 Gene

  • Protein details for YBX3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P16989-YBOX3_HUMAN
    Recommended name:
    Y-box-binding protein 3
    Protein Accession:
    P16989
    Secondary Accessions:
    • B2RBW6
    • Q14121
    • Q969N6
    • Q96B76

    Protein attributes for YBX3 Gene

    Size:
    372 amino acids
    Molecular mass:
    40090 Da
    Quaternary structure:
    • Found in a mRNP complex with YBX2.
    SequenceCaution:
    • Sequence=AAA35749.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for YBX3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for YBX3 Gene

Post-translational modifications for YBX3 Gene

  • Ubiquitination at Lys 268
  • Modification sites at PhosphoSitePlus

Other Protein References for YBX3 Gene

No data available for DME Specific Peptides for YBX3 Gene

Domains & Families for YBX3 Gene

Gene Families for YBX3 Gene

Suggested Antigen Peptide Sequences for YBX3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P16989

UniProtKB/Swiss-Prot:

YBOX3_HUMAN :
  • Contains 1 CSD (cold-shock) domain.
Domain:
  • Contains 1 CSD (cold-shock) domain.
genes like me logo Genes that share domains with YBX3: view

Function for YBX3 Gene

Molecular function for YBX3 Gene

UniProtKB/Swiss-Prot Function:
Binds to the GM-CSF promoter. Seems to act as a repressor. Binds also to full length mRNA and to short RNA sequences containing the consensus site 5-UCCAUCA-3. May have a role in translation repression (By similarity).

Gene Ontology (GO) - Molecular Function for YBX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IEA --
GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding IEA --
GO:0003677 DNA binding IEA --
GO:0003690 double-stranded DNA binding TAS 2977358
GO:0003697 single-stranded DNA binding IEA --
genes like me logo Genes that share ontologies with YBX3: view
genes like me logo Genes that share phenotypes with YBX3: view

Animal Models for YBX3 Gene

MGI Knock Outs for YBX3:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for YBX3 Gene

Localization for YBX3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for YBX3 Gene

Cytoplasm. Nucleus.

Gene Ontology (GO) - Cellular Components for YBX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,ISS 22711822
GO:0005737 cytoplasm IEA,IDA --
GO:0005844 polysome IEA --
GO:0005923 bicellular tight junction ISS 22711822
GO:0030529 intracellular ribonucleoprotein complex IEA --
genes like me logo Genes that share ontologies with YBX3: view

No data available for Subcellular locations from COMPARTMENTS for YBX3 Gene

Pathways & Interactions for YBX3 Gene

genes like me logo Genes that share pathways with YBX3: view

Pathways by source for YBX3 Gene

1 BioSystems pathway for YBX3 Gene
1 KEGG pathway for YBX3 Gene
1 GeneGo (Thomson Reuters) pathway for YBX3 Gene

Gene Ontology (GO) - Biological Process for YBX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IEA --
GO:0001701 in utero embryonic development IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0007283 spermatogenesis IEA --
GO:0008584 male gonad development IEA --
genes like me logo Genes that share ontologies with YBX3: view

No data available for SIGNOR curated interactions for YBX3 Gene

Drugs & Compounds for YBX3 Gene

(1) Drugs for YBX3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(3) Additional Compounds for YBX3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with YBX3: view

Transcripts for YBX3 Gene

Unigene Clusters for YBX3 Gene

Y box binding protein 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for YBX3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b · 11c ^ 12a · 12b ^ 13 ^ 14a · 14b · 14c
SP1: - - - - - - - - - -
SP2: - - - - - - - - - - -
SP3: - - - - - - -
SP4: - -
SP5: - - - - -
SP6: -
SP7:
SP8: - - - - -
SP9: - -
SP10:
SP11:
SP12: -

Relevant External Links for YBX3 Gene

GeneLoc Exon Structure for
YBX3
ECgene alternative splicing isoforms for
YBX3

Expression for YBX3 Gene

mRNA expression in normal human tissues for YBX3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for YBX3 Gene

This gene is overexpressed in Muscle - Skeletal (x19.6).

Protein differential expression in normal tissues from HIPED for YBX3 Gene

This gene is overexpressed in Nasal epithelium (30.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for YBX3 Gene



Protein tissue co-expression partners for YBX3 Gene

NURSA nuclear receptor signaling pathways regulating expression of YBX3 Gene:

YBX3

SOURCE GeneReport for Unigene cluster for YBX3 Gene:

Hs.221889

mRNA Expression by UniProt/SwissProt for YBX3 Gene:

P16989-YBOX3_HUMAN
Tissue specificity: Highly expressed in skeletal muscle and heart.
genes like me logo Genes that share expression patterns with YBX3: view

Primer Products

Orthologs for YBX3 Gene

This gene was present in the common ancestor of animals.

Orthologs for YBX3 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia CSDA 34
  • 87.9 (n)
  • 87.81 (a)
CSDA 35
  • 85 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CSDA 34
  • 91.4 (n)
  • 89.75 (a)
CSDA 35
  • 79 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ybx3 34
  • 86.89 (n)
  • 86.43 (a)
Ybx3 16
Ybx3 35
  • 89 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia CSDA 34
  • 100 (n)
  • 100 (a)
YBX3 35
  • 94 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ybx3 34
  • 87.9 (n)
  • 87.53 (a)
oppossum
(Monodelphis domestica)
Mammalia YBX3 35
  • 81 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia YBX3 35
  • 83 (a)
OneToOne
chicken
(Gallus gallus)
Aves CSDA 34
  • 74.26 (n)
  • 76.24 (a)
YBX3 35
  • 63 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ybx3 34
  • 62.31 (n)
  • 64.86 (a)
fruit fly
(Drosophila melanogaster)
Insecta yps 35
  • 34 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea cey-1 35
  • 44 (a)
ManyToMany
cey-2 35
  • 28 (a)
ManyToMany
cey-3 35
  • 28 (a)
ManyToMany
cey-4 35
  • 31 (a)
ManyToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5400 34
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10127 35
  • 40 (a)
OneToMany
Species where no ortholog for YBX3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)
  • 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 YBX3 Gene

ENSEMBL:
Gene Tree for YBX3 (if available)
TreeFam:
Gene Tree for YBX3 (if available)

Paralogs for YBX3 Gene

Paralogs for YBX3 Gene

(2) SIMAP similar genes for YBX3 Gene using alignment to 2 proteins:

Pseudogenes.org Pseudogenes for YBX3 Gene

genes like me logo Genes that share paralogs with YBX3: view

Variants for YBX3 Gene

Sequence variations from dbSNP and Humsavar for YBX3 Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
VAR_013114 -
rs7302837 -- 10,714,801(+) gtccc(C/T)caggc intron-variant
rs7304148 -- 10,717,632(+) AGTTT(C/T)CTCAT intron-variant
rs2166066 -- 10,699,059(+) AGGTC(A/G)GCAAA downstream-variant-500B
rs7953251 -- 10,713,798(+) CTGAG(C/T)GAAAC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for YBX3 Gene

Variant ID Type Subtype PubMed ID
esv3628543 CNV gain 21293372
esv3628544 CNV gain 21293372
nsv1118229 CNV deletion 24896259

Variation tolerance for YBX3 Gene

Residual Variation Intolerance Score: 89.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.14; 84.64% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for YBX3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
YBX3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for YBX3 Gene

Disorders for YBX3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for YBX3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
uterine inflammatory disease
  • inflammatory disease of the uterus
primary bacterial infectious disease
- elite association - COSMIC cancer census association via MalaCards
Search YBX3 in MalaCards View complete list of genes associated with diseases

Relevant External Links for YBX3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
YBX3
genes like me logo Genes that share disorders with YBX3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for YBX3 Gene

Publications for YBX3 Gene

  1. Cold shock domain proteins repress transcription from the GM-CSF promoter. (PMID: 8710501) Coles L.S. … Shannon M.F. (Nucleic Acids Res. 1996) 2 3 4 65
  2. Characterization of the gene for dbpA, a family member of the nucleic-acid-binding proteins containing a cold-shock domain. (PMID: 7628487) Kudo S. … Fukuda M. (Eur. J. Biochem. 1995) 3 4 22 65
  3. Two human genes isolated by a novel method encode DNA-binding proteins containing a common region of homology. (PMID: 2977358) Sakura H. … Ishii S. (Gene 1988) 2 3 4 65
  4. Upregulation of human DNA binding protein A (dbpA) in gastric cancer cells. (PMID: 19749785) Wang G.R. … He D.L. (Acta Pharmacol. Sin. 2009) 3 22 65
  5. Regulation of PCNA and cyclin D1 expression and epithelial morphogenesis by the ZO-1-regulated transcription factor ZONAB/DbpA. (PMID: 16508013) Sourisseau T. … Balda M.S. (Mol. Cell. Biol. 2006) 3 22 65

Products for YBX3 Gene

Sources for YBX3 Gene

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