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YBX3 Y-box binding protein 3 [ Homo sapiens (human) ]

Gene ID: 8531, updated on 6-Jan-2019

Summary

Official Symbol
YBX3provided by HGNC
Official Full Name
Y-box binding protein 3provided by HGNC
Primary source
HGNC:HGNC:2428
See related
Ensembl:ENSG00000060138 MIM:603437
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CSDA; DBPA; CSDA1; ZONAB
Expression
Broad expression in testis (RPKM 175.4), skin (RPKM 131.9) and 23 other tissues See more
Orthologs

Genomic context

See YBX3 in Genome Data Viewer
Location:
12p13.2
Exon count:
11
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (10699077..10723442, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (10851676..10876047, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene mago homolog B, exon junction complex subunit Neighboring gene serine/threonine/tyrosine kinase 1 Neighboring gene uncharacterized LOC112268104 Neighboring gene long intergenic non-protein coding RNA 2366 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 12

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Apoptosis-related network due to altered Notch3 in ovarian cancer, organism-specific biosystem (from WikiPathways)
    Apoptosis-related network due to altered Notch3 in ovarian cancer, organism-specific biosystemResults of pathway analysis of apoptosis-related genes in OVCAR3 cells treated with Notch3 siRNA or control siRNA.
  • RalA downstream regulated genes, organism-specific biosystem (from WikiPathways)
    RalA downstream regulated genes, organism-specific biosystemDownstream genes of RalA signaling pathways, including the Rac-family GTPase-activating protein RLIP (also known as RLIP76 and ralA binding protein 1 (RALBP1)), CDC42(cell division cycle 42), RAC1 (r...
  • Tight junction, organism-specific biosystem (from KEGG)
    Tight junction, organism-specific biosystemTight junctions (TJs) are essential for establishing a selectively permeable barrier to diffusion through the paracellular space between neighboring cells. TJs are composed of at least three types of...
  • Tight junction, conserved biosystem (from KEGG)
    Tight junction, conserved biosystemTight junctions (TJs) are essential for establishing a selectively permeable barrier to diffusion through the paracellular space between neighboring cells. TJs are composed of at least three types of...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription factor activity NAS
Non-traceable Author Statement
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific NAS
Non-traceable Author Statement
more info
PubMed 
DNA-binding transcription repressor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
 
RNA binding HDA PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
Rho GTPase binding ISS
Inferred from Sequence or Structural Similarity
more info
 
double-stranded DNA binding TAS
Traceable Author Statement
more info
PubMed 
mRNA 3'-UTR binding ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
polysome binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription corepressor activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
3'-UTR-mediated mRNA stabilization IC
Inferred by Curator
more info
PubMed 
cellular hyperosmotic response IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to tumor necrosis factor IMP
Inferred from Mutant Phenotype
more info
PubMed 
fertilization IEA
Inferred from Electronic Annotation
more info
 
in utero embryonic development IEA
Inferred from Electronic Annotation
more info
 
male gonad development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of necroptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of skeletal muscle tissue development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cytoplasmic translation ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
positive regulation of organ growth IEA
Inferred from Electronic Annotation
more info
 
response to cold TAS
Traceable Author Statement
more info
PubMed 
spermatogenesis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
bicellular tight junction ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
cytoplasm TAS
Traceable Author Statement
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
nucleus ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
perinuclear region of cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 

General protein information

Preferred Names
Y-box-binding protein 3
Names
DNA-binding protein A
ZO-1-associated nucleic acid-binding protein
cold shock domain-containing protein A
cold-shock domain containing A1
cold-shock domain protein A
single-strand DNA-binding protein NF-GMB

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001145426.1NP_001138898.1  Y-box-binding protein 3 isoform b

    See identical proteins and their annotated locations for NP_001138898.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting protein (isoform b) is shorter compared to isoform a.
    Source sequence(s)
    AA621593, AC021049, AU117252, BC015913
    Consensus CDS
    CCDS44831.1
    UniProtKB/Swiss-Prot
    P16989
    UniProtKB/TrEMBL
    A0A024RAV4
    Related
    ENSP00000279550.7, ENST00000279550.11
    Conserved Domains (1) summary
    pfam00313
    Location:91160
    CSD; 'Cold-shock' DNA-binding domain
  2. NM_003651.5NP_003642.3  Y-box-binding protein 3 isoform a

    See identical proteins and their annotated locations for NP_003642.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AC021049
    Consensus CDS
    CCDS8630.1
    UniProtKB/Swiss-Prot
    P16989
    UniProtKB/TrEMBL
    A0A024RAQ1
    Related
    ENSP00000228251.4, ENST00000228251.8
    Conserved Domains (1) summary
    pfam00313
    Location:91160
    CSD; 'Cold-shock' DNA-binding domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    10699077..10723442 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017020123.2XP_016875612.1  Y-box-binding protein 3 isoform X2

  2. XM_017020122.2XP_016875611.1  Y-box-binding protein 3 isoform X1

  3. XM_011520871.3XP_011519173.1  Y-box-binding protein 3 isoform X3

    Conserved Domains (1) summary
    pfam00313
    Location:91160
    CSD; 'Cold-shock' DNA-binding domain

RNA

  1. XR_001748906.2 RNA Sequence

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