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

    Gene ID: 8531, updated on 28-Oct-2024

    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; AllianceGenome:HGNC:2428
    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
    Summary
    Enables RNA binding activity. Involved in cellular hyperosmotic response; cellular response to tumor necrosis factor; and negative regulation of programmed cell death. Located in cytosol. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Broad expression in testis (RPKM 175.4), skin (RPKM 131.9) and 23 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See YBX3 in Genome Data Viewer
    Location:
    12p13.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (10699089..10723323, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (10572193..10596426, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (10851688..10875922, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene killer cell lectin like receptor A1, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr12:10765265-10766144 and GRCh37_chr12:10766145-10767022 Neighboring gene mago homolog B, exon junction complex subunit Neighboring gene serine/threonine/tyrosine kinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4238 Neighboring gene uncharacterized LOC124902876 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4239 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4240 Neighboring gene uncharacterized LOC112268104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5963 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4241 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 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 Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables mRNA 3'-UTR binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables nucleic acid binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables ribonucleoprotein complex binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables small GTPase binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    involved_in 3'-UTR-mediated mRNA stabilization IC
    Inferred by Curator
    more info
    PubMed 
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular hyperosmotic response IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cellular response to tumor necrosis factor IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in ectopic germ cell programmed cell death IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in fertilization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in in utero embryonic development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in male gonad development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of necroptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of reproductive process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of skeletal muscle tissue development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of cytoplasmic translation ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in positive regulation of organ growth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in spermatogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in bicellular tight junction ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    located_in cytoplasm TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    located_in perinuclear region of cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    located_in synapse IEA
    Inferred from Electronic Annotation
    more info
     

    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)

    NEW Try the new Transcript table

    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_001145426.2NP_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)
      AC021049
      Consensus CDS
      CCDS44831.1
      UniProtKB/TrEMBL
      Q96GD7
      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
      B2RBW6, P16989, Q14121, Q969N6, Q96B76
      UniProtKB/TrEMBL
      Q96GD7
      Related
      ENSP00000228251.4, ENST00000228251.9
      Conserved Domains (1) summary
      pfam00313
      Location:91160
      CSD; 'Cold-shock' DNA-binding domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      10699089..10723323 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017020123.3XP_016875612.1  Y-box-binding protein 3 isoform X3

      UniProtKB/TrEMBL
      Q96GD7
    2. XM_017020122.3XP_016875611.1  Y-box-binding protein 3 isoform X2

    3. XM_047429799.1XP_047285755.1  Y-box-binding protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B2RBW6, P16989, Q14121, Q969N6, Q96B76
    4. XM_011520871.4XP_011519173.1  Y-box-binding protein 3 isoform X4

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      10572193..10596426 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054373689.1XP_054229664.1  Y-box-binding protein 3 isoform X3

    2. XM_054373688.1XP_054229663.1  Y-box-binding protein 3 isoform X2

    3. XM_054373687.1XP_054229662.1  Y-box-binding protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B2RBW6, P16989, Q14121, Q969N6, Q96B76
    4. XM_054373690.1XP_054229665.1  Y-box-binding protein 3 isoform X4