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Aliases for YBX3 Gene

Aliases for YBX3 Gene

  • Y Box Binding Protein 3 2 3
  • CSDA 3 4 6
  • DBPA 3 4 6
  • Single-Strand DNA-Binding Protein NF-GMB 3 4
  • Cold Shock Domain-Containing Protein A 3 4
  • Cold-Shock Domain Containing A1 2 3
  • Cold Shock Domain Protein A 2 3
  • DNA-Binding Protein A 3 4
  • ZO-1-Associated Nucleic Acid-Binding Protein 3
  • Cold-Shock Domain Protein A 3
  • Y-Box-Binding Protein 3 3
  • CSDA1 3
  • ZONAB 3

External Ids for YBX3 Gene

Previous Symbols for YBX3 Gene

  • CSDA

Summaries for YBX3 Gene

GeneCards Summary for YBX3 Gene

YBX3 (Y Box Binding Protein 3) is a Protein Coding gene. Among its related pathways are Sertoli-Sertoli Cell Junction Dynamics and Sertoli-Sertoli Cell Junction Dynamics. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and double-stranded DNA binding. An important paralog of this gene is YBX2.

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

Genomic Location for YBX3 Gene

Start:
10,699,077 bp from pter
End:
10,723,354 bp from pter
Size:
24,278 bases
Orientation:
Minus strand

Genomic View for YBX3 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for YBX3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for YBX3 Gene

No data available for Regulatory Elements 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

Proteomics data for YBX3 Gene at MOPED

Post-translational modifications for YBX3 Gene

  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys90, Lys96, Lys113, Lys124, Lys125, and Lys268

Other Protein References for YBX3 Gene

No data available for DME Specific Peptides for YBX3 Gene

Domains for YBX3 Gene

Graphical View of Domain Structure for InterPro Entry

P16989

UniProtKB/Swiss-Prot:

YBOX3_HUMAN
Domain:
  • Contains 1 CSD (cold-shock) domain.:
    • P16989
genes like me logo Genes that share domains with YBX3: view

No data available for Gene Families and Suggested Antigen Peptide Sequences for YBX3 Gene

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 RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription IEA --
GO:0003676 nucleic acid binding --
GO:0003677 DNA binding --
GO:0003690 double-stranded DNA binding TAS 2977358
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:

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting 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 ISS 22711822
GO:0005737 cytoplasm IDA --
GO:0005844 polysome IEA --
GO:0005923 bicellular tight junction ISS 22711822
GO:0030529 ribonucleoprotein complex --
genes like me logo Genes that share ontologies with YBX3: view

No data available for Subcellular locations from COMPARTMENTS for YBX3 Gene

Pathways for YBX3 Gene

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

Pathways by source for YBX3 Gene

1 GeneGo (Thomson Reuters) pathway for YBX3 Gene
1 BioSystems pathway for YBX3 Gene
1 KEGG 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:0006355 regulation of transcription, DNA-templated --
GO:0007283 spermatogenesis IEA --
genes like me logo Genes that share ontologies with YBX3: view

Compounds for YBX3 Gene

(4) Novoseek inferred chemical compound relationships for YBX3 Gene

Compound -log(P) Hits PubMed IDs
dbpa 99 134
hydrogen 26.5 4
lysine 5.42 3
vegf 0 4
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:

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 differential expression in normal tissues according to GTEx for YBX3 Gene

This gene is overexpressed in Muscle - Skeletal (19.6).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for YBX3 Gene

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 expressions with YBX3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for YBX3 Gene

Orthologs for YBX3 Gene

This gene was present in the common ancestor of animals.

Orthologs for YBX3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CSDA 35
  • 100 (n)
  • 100 (a)
YBX3 36
  • 94 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CSDA 35
  • 87.9 (n)
  • 87.81 (a)
CSDA 36
  • 85 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CSDA 35
  • 91.4 (n)
  • 89.75 (a)
CSDA 36
  • 79 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Csda 16
Ybx3 35
  • 86.89 (n)
  • 86.43 (a)
Ybx3 36
  • 89 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia YBX3 36
  • 81 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia YBX3 36
  • 83 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ybx3 35
  • 87.9 (n)
  • 87.53 (a)
chicken
(Gallus gallus)
Aves CSDA 35
  • 74.26 (n)
  • 76.24 (a)
YBX3 36
  • 63 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ybx3 35
  • 62.31 (n)
  • 64.86 (a)
fruit fly
(Drosophila melanogaster)
Insecta yps 36
  • 34 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea cey-1 36
  • 44 (a)
ManyToMany
cey-2 36
  • 28 (a)
ManyToMany
cey-3 36
  • 28 (a)
ManyToMany
cey-4 36
  • 31 (a)
ManyToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5400 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10127 36
  • 40 (a)
OneToMany
Species with no ortholog for YBX3:
  • 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

Selected 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 MAF
rs7270 -- 10,699,173(+) ATGTT(A/T)TCCTC utr-variant-3-prime
rs11788 -- 10,699,281(+) CGGAA(A/G)AAAAA utr-variant-3-prime
rs15223 -- 10,699,234(-) AGTGT(C/T)ATGAT utr-variant-3-prime
rs15224 -- 10,699,397(-) TTTCT(A/G)TTTTT utr-variant-3-prime
rs17629 -- 10,699,507(-) AAACA(A/G/T)CTACA utr-variant-3-prime

Relevant External Links for YBX3 Gene

HapMap Linkage Disequilibrium report
YBX3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for YBX3 Gene

Disorders for YBX3 Gene

(6) Novoseek inferred disease relationships for YBX3 Gene

Disease -log(P) Hits PubMed IDs
lyme neuroborreliosis 79.6 1
lyme disease 72.4 4
lyme arthritis 66.8 2
shock 48.2 15
hepatocellular carcinoma 17 9
genes like me logo Genes that share disorders with YBX3: view

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

Publications for YBX3 Gene

  1. 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 23
  2. 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
  3. 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
  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 23
  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 23

Products for YBX3 Gene

Sources for YBX3 Gene

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