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
  • Y-Box-Binding Protein 3 3 4
  • 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 3
  • Cold Shock Domain Protein A 2
  • 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
  • GC12M012422
  • GC12M012641
  • GC12M012796
  • GC12M010842
  • GC12M011025
  • GC12M011330
  • GC12M011547
  • GC12M011738
  • GC12M011925
  • GC12M012111
  • GC12M012288

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 Lyme Disease and Uterine Inflammatory Disease. Among its related pathways are Sertoli-Sertoli Cell Junction Dynamics and Apoptosis-related network due to altered Notch3 in ovarian cancer. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and DNA-binding transcription factor activity. An important paralog of this gene is YBX1.

UniProtKB/Swiss-Prot Summary 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

Additional gene information for YBX3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for YBX3 Gene

Genomics for YBX3 Gene

GeneHancer (GH) Regulatory Elements for YBX3 Gene

Promoters and enhancers for YBX3 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
GH12J010715 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 511.1 +3.4 3354 8.8 ZBTB40 ZSCAN5C SIN3A TCF12 MYC ZNF300 POLR2G USF1 PHF8 JUND YBX3 KLRA1P TAS2R31 TAS2R14 TAS2R10 MAGOHB TAS2R15P TAS2R20 TAS2R19 TAS2R64P
GH12J010708 Enhancer 0.6 Ensembl ENCODE dbSUPER 10.5 +14.1 14145 1.7 RBM22 STYK1 YBX3 ENSG00000255958 GABARAPL1 MAGOHB KLRC1 lnc-STYK1-1 lnc-STYK1-2
GH12J010740 Enhancer 0.8 Ensembl ENCODE 5.6 -16.8 -16753 1.2 RELA CTBP1 TAF9B ZNF316 NBN NFE2 IRF1 NR2F1 ZNF189 ZFP91 KLRC1 YBX3 TAS2R14 RF00017-1089 piR-61514-048
GH12J010701 Enhancer 0.3 ENCODE 9.7 +22.0 21976 0.7 GATA1 PKNOX1 STYK1 ENSG00000255958 GABARAPL1 MAGOHB YBX3 KLRC1 lnc-STYK1-1
GH12J010707 Enhancer 0.3 dbSUPER 11.9 +15.8 15848 1.1 POLR2A YBX3 STYK1 ENSG00000255958 GABARAPL1 MAGOHB KLRC1 lnc-STYK1-1 lnc-STYK1-2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around YBX3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for YBX3

Genomic Locations for YBX3 Gene

Genomic Locations for YBX3 Gene
chr12:10,699,077-10,723,448
(GRCh38/hg38)
Size:
24,372 bases
Orientation:
Minus strand
chr12:10,851,676-10,875,953
(GRCh37/hg19)
Size:
24,278 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 (By similarity). Interacts with RRP1B (PubMed:19710015).
    SequenceCaution:
    • Sequence=AAA35749.1; Type=Erroneous initiation; Note=Extended N-terminus.; 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 Lys268
  • 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

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

Protein Domains for YBX3 Gene

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

Suggested Antigen Peptide Sequences for YBX3 Gene

GenScript: Design optimal peptide antigens:
  • Single-strand DNA-binding protein NF-GMB (DBPA_HUMAN)
genes like me logo Genes that share domains with YBX3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot 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).

Phenotypes From GWAS Catalog for YBX3 Gene

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:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific NAS 19274049
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific IEA --
GO:0003676 nucleic acid binding IEA --
GO:0003677 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

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for YBX3

Clone 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.

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 YBX3 gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 2
extracellular 2
cytoskeleton 2
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for YBX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS,IEA 22711822
GO:0005737 cytoplasm TAS 7628487
GO:0005829 cytosol IDA --
GO:0005923 bicellular tight junction ISS 22711822
GO:0048471 perinuclear region of cytoplasm ISS 22711822
genes like me logo Genes that share ontologies with YBX3: view

Pathways & Interactions 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
  • Cell adhesion Tight junctions
2 Qiagen pathways for YBX3 Gene
  • Epithelial Tight Junctions
  • Sertoli-Sertoli Cell Junction Dynamics

Gene Ontology (GO) - Biological Process for YBX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0001701 in utero embryonic development IEA --
GO:0007283 spermatogenesis IEA --
GO:0008584 male gonad development IEA --
GO:0009409 response to cold TAS 8710501
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

(2) Drugs for YBX3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) 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

mRNA/cDNA for YBX3 Gene

2 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
18 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 YBX3

Clone 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

Expression for YBX3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE 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, MaxQB, and MOPED for YBX3 Gene



Protein tissue co-expression partners for YBX3 Gene

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

Evidence on tissue expression from TISSUES for YBX3 Gene

  • Muscle(4.8)
  • Blood(4.7)
  • Lung(4.7)
  • Kidney(4.5)
  • Eye(4)
  • Heart(3.6)
  • Skin(3.3)
  • Nervous system(3.3)
  • Intestine(2.5)
  • Pancreas(2.4)
  • Spleen(2.3)
  • Bone marrow(2.1)
  • Liver(2.1)
  • Gall bladder(2)
genes like me logo Genes that share expression patterns with YBX3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer 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 30
  • 100 (n)
YBX3 31
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CSDA 31 30
  • 91.4 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CSDA 31 30
  • 87.9 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ybx3 30
  • 87.9 (n)
mouse
(Mus musculus)
Mammalia Ybx3 17 31 30
  • 86.89 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia YBX3 31
  • 83 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia YBX3 31
  • 81 (a)
OneToOne
chicken
(Gallus gallus)
Aves CSDA 30
  • 74.26 (n)
YBX3 31
  • 63 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ybx3 30
  • 62.31 (n)
fruit fly
(Drosophila melanogaster)
Insecta yps 31
  • 34 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea cey-1 31
  • 44 (a)
ManyToMany
cey-4 31
  • 31 (a)
ManyToMany
cey-3 31
  • 28 (a)
ManyToMany
cey-2 31
  • 28 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10127 31
  • 40 (a)
OneToMany
Cin.5400 30
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5400 30
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)
Aminode:
Evolutionary constrained regions (ECRs) for YBX3: view image

Paralogs for YBX3 Gene

Paralogs for YBX3 Gene

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

  • YBOX3_HUMAN
  • H0YG22_HUMAN

Pseudogenes.org Pseudogenes for YBX3 Gene

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

Variants for YBX3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for YBX3 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
rs1126501 - p.Thr75Ala

Additional dbSNP identifiers (rs#s) for YBX3 Gene

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)

Additional Variant Information for YBX3 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for YBX3 Gene

MalaCards: The human disease database

(7) MalaCards diseases for YBX3 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
lyme disease
  • bannwarth syndrome
uterine inflammatory disease
  • inflammatory disease of the uterus
mixed germ cell cancer
  • mixed germ cell neoplasm
leukodystrophy, hypomyelinating, 2
  • hld2
tick infestation
  • tick infestations
- elite association - COSMIC cancer census association via MalaCards
Search YBX3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for 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 LS … Shannon MF (Nucleic acids research 1996) 2 3 4 54
  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 (European journal of biochemistry 1995) 3 4 23 54
  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 54
  4. The metastasis efficiency modifier ribosomal RNA processing 1 homolog B (RRP1B) is a chromatin-associated factor. (PMID: 19710015) Crawford NP … Hunter KW (The Journal of biological chemistry 2009) 3 4 54
  5. Upregulation of human DNA binding protein A (dbpA) in gastric cancer cells. (PMID: 19749785) Wang GR … He DL (Acta pharmacologica Sinica 2009) 3 23 54

Products for YBX3 Gene

Sources for YBX3 Gene