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YBX3 (Y-box binding protein 3)

Identity

Alias_namesCSDA
cold shock domain protein A
Alias_symbol (synonym)dbpA
ZONAB
CSDA1
Other aliasDBPA
HGNC (Hugo) YBX3
LocusID (NCBI) 8531
Atlas_Id 45758
Location 12p13.2  [Link to chromosome band 12p13]
Location_base_pair Starts at 10699077 and ends at 10723354 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
CANX (5q35.3) / YBX3 (12p13.2)FOXJ2 (12p13.31) / YBX3 (12p13.2)MRC2 (17q23.2) / YBX3 (12p13.2)
P4HB (17q25.3) / YBX3 (12p13.2)TMEM8A (16p13.3) / YBX3 (12p13.2)YBX3 (12p13.2) / HIPK2 (7q34)
YBX3 (12p13.2) / PSMB1 (6q27)YBX3 (12p13.2) / TMEM8A (16p13.3)YBX3 (12p13.2) / VIPR1 (3p22.1)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)YBX3   2428
Cards
Entrez_Gene (NCBI)YBX3  8531  Y-box binding protein 3
AliasesCSDA; CSDA1; DBPA; ZONAB
GeneCards (Weizmann)YBX3
Ensembl hg19 (Hinxton)ENSG00000060138 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000060138 [Gene_View]  chr12:10699077-10723354 [Contig_View]  YBX3 [Vega]
ICGC DataPortalENSG00000060138
TCGA cBioPortalYBX3
AceView (NCBI)YBX3
Genatlas (Paris)YBX3
WikiGenes8531
SOURCE (Princeton)YBX3
Genetics Home Reference (NIH)YBX3
Genomic and cartography
GoldenPath hg38 (UCSC)YBX3  -     chr12:10699077-10723354 -  12p13.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)YBX3  -     12p13.2   [Description]    (hg19-Feb_2009)
EnsemblYBX3 - 12p13.2 [CytoView hg19]  YBX3 - 12p13.2 [CytoView hg38]
Mapping of homologs : NCBIYBX3 [Mapview hg19]  YBX3 [Mapview hg38]
OMIM603437   
Gene and transcription
Genbank (Entrez)AA621593 AB209896 AK314846 AU117252 BC008801
RefSeq transcript (Entrez)NM_001145426 NM_003651
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)YBX3
Cluster EST : UnigeneHs.221889 [ NCBI ]
CGAP (NCI)Hs.221889
Alternative Splicing GalleryENSG00000060138
Gene ExpressionYBX3 [ NCBI-GEO ]   YBX3 [ EBI - ARRAY_EXPRESS ]   YBX3 [ SEEK ]   YBX3 [ MEM ]
Gene Expression Viewer (FireBrowse)YBX3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)8531
GTEX Portal (Tissue expression)YBX3
Protein : pattern, domain, 3D structure
UniProt/SwissProtP16989   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP16989  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP16989
Splice isoforms : SwissVarP16989
PhosPhoSitePlusP16989
Domaine pattern : Prosite (Expaxy)COLD_SHOCK (PS00352)   
Domains : Interpro (EBI)Cold-shock_CS    CSD    CSP_DNA-bd    NA-bd_OB-fold   
Domain families : Pfam (Sanger)CSD (PF00313)   
Domain families : Pfam (NCBI)pfam00313   
Domain families : Smart (EMBL)CSP (SM00357)  
Conserved Domain (NCBI)YBX3
DMDM Disease mutations8531
Blocks (Seattle)YBX3
SuperfamilyP16989
Human Protein AtlasENSG00000060138
Peptide AtlasP16989
HPRD10347
IPIIPI00031801   IPI00219147   IPI00219148   IPI00555698   IPI01014994   
Protein Interaction databases
DIP (DOE-UCLA)P16989
IntAct (EBI)P16989
FunCoupENSG00000060138
BioGRIDYBX3
STRING (EMBL)YBX3
ZODIACYBX3
Ontologies - Pathways
QuickGOP16989
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  RNA polymerase II regulatory region sequence-specific DNA binding  transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding  in utero embryonic development  double-stranded DNA binding  single-stranded DNA binding  transcription factor activity, sequence-specific DNA binding  transcription corepressor activity  RNA binding  mRNA 3'-UTR binding  nucleus  cytoplasm  cytosol  polysome  bicellular tight junction  transcription, DNA-templated  spermatogenesis  male gonad development  response to cold  fertilization  Rho GTPase binding  positive regulation of organ growth  perinuclear region of cytoplasm  negative regulation of skeletal muscle tissue development  negative regulation of necroptotic process  3'-UTR-mediated mRNA stabilization  cellular response to tumor necrosis factor  cellular hyperosmotic response  negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress  positive regulation of cytoplasmic translation  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  RNA polymerase II regulatory region sequence-specific DNA binding  transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding  in utero embryonic development  double-stranded DNA binding  single-stranded DNA binding  transcription factor activity, sequence-specific DNA binding  transcription corepressor activity  RNA binding  mRNA 3'-UTR binding  nucleus  cytoplasm  cytosol  polysome  bicellular tight junction  transcription, DNA-templated  spermatogenesis  male gonad development  response to cold  fertilization  Rho GTPase binding  positive regulation of organ growth  perinuclear region of cytoplasm  negative regulation of skeletal muscle tissue development  negative regulation of necroptotic process  3'-UTR-mediated mRNA stabilization  cellular response to tumor necrosis factor  cellular hyperosmotic response  negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress  positive regulation of cytoplasmic translation  
Pathways : KEGGTight junction   
NDEx NetworkYBX3
Atlas of Cancer Signalling NetworkYBX3
Wikipedia pathwaysYBX3
Orthology - Evolution
OrthoDB8531
GeneTree (enSembl)ENSG00000060138
Phylogenetic Trees/Animal Genes : TreeFamYBX3
HOVERGENP16989
HOGENOMP16989
Homologs : HomoloGeneYBX3
Homology/Alignments : Family Browser (UCSC)YBX3
Gene fusions - Rearrangements
Fusion : MitelmanP4HB/YBX3 [17q25.3/12p13.2]  [t(12;17)(p13;q25)]  
Fusion : MitelmanTMEM8A/YBX3 [16p13.3/12p13.2]  [t(12;16)(p13;p13)]  
Fusion : MitelmanYBX3/TMEM8A [12p13.2/16p13.3]  [t(12;16)(p13;p13)]  
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerYBX3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)YBX3
dbVarYBX3
ClinVarYBX3
1000_GenomesYBX3 
Exome Variant ServerYBX3
ExAC (Exome Aggregation Consortium)YBX3 (select the gene name)
Genetic variants : HAPMAP8531
Genomic Variants (DGV)YBX3 [DGVbeta]
DECIPHERYBX3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisYBX3 
Mutations
ICGC Data PortalYBX3 
TCGA Data PortalYBX3 
Broad Tumor PortalYBX3
OASIS PortalYBX3 [ Somatic mutations - Copy number]
Mutations and Diseases : HGMDYBX3
intOGen PortalCSDA
BioMutasearch YBX3
DgiDB (Drug Gene Interaction Database)YBX3
DoCM (Curated mutations)YBX3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)YBX3 (select a term)
intoGenYBX3
Cancer3DYBX3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM603437   
Orphanet
MedgenYBX3
Genetic Testing Registry YBX3
NextProtP16989 [Medical]
TSGene8531
GENETestsYBX3
Target ValidationYBX3
Huge Navigator YBX3 [HugePedia]
snp3D : Map Gene to Disease8531
BioCentury BCIQYBX3
ClinGenYBX3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD8531
Chemical/Pharm GKB GenePA26929
Clinical trialYBX3
Miscellaneous
canSAR (ICR)YBX3 (select the gene name)
Probes
Litterature
PubMed68 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineYBX3
EVEXYBX3
GoPubMedYBX3
iHOPYBX3
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Sep 25 19:38:36 CEST 2017

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