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

Gene ID: 8531, updated on 11-Apr-2024

Summary

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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, Apr 2022]
Expression
Broad expression in testis (RPKM 175.4), skin (RPKM 131.9) and 23 other tissues See more
Orthologs
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Genomic context

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See YBX3 in Genome Data Viewer
Location:
12p13.2
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (10699089..10723323, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (10572193..10596426, complement)
105.20220307 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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Identification of RNA-binding protein YBX3 as an oncogene in clear cell renal cell carcinoma. Wang C, et al. Funct Integr Genomics, 2023 Jul 7. PMID 37418046, Free PMC Article
  2. Knockdown of DNA-binding protein A enhances the chemotherapy sensitivity of colorectal cancer via suppressing the Wnt/β-catenin/Chk1 pathway. Tong C, et al. Cell Biol Int, 2020 Oct. PMID 32652867
  3. Y-Box-Binding Protein 3 (YBX3) Restricts Influenza A Virus by Interacting with Viral Ribonucleoprotein Complex and Imparing its Function. Qin Z, et al. J Gen Virol, 2020 Apr. PMID 32553055
  4. The RNA-Binding Protein YBX3 Controls Amino Acid Levels by Regulating SLC mRNA Abundance. Cooke A, et al. Cell Rep, 2019 Jun 11. PMID 31189097
  5. Zonula occludens-1 associated nucleic acid binding protein plays an invasion-promoting role in bladder cancer. Xu X, et al. Neoplasma, 2019 May 23. PMID 30784285

See all (181) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The YBX3 RNA-binding protein posttranscriptionally controls SLC1A5 mRNA in proliferating and differentiating skeletal muscle cells.
    Title: The YBX3 RNA-binding protein posttranscriptionally controls SLC1A5 mRNA in proliferating and differentiating skeletal muscle cells.
  2. M6A-mediated-upregulation of lncRNA BLACAT3 promotes bladder cancer angiogenesis and hematogenous metastasis through YBX3 nuclear shuttling and enhancing NCF2 transcription.
    Title: M6A-mediated-upregulation of lncRNA BLACAT3 promotes bladder cancer angiogenesis and hematogenous metastasis through YBX3 nuclear shuttling and enhancing NCF2 transcription.
  3. Identification of RNA-binding protein YBX3 as an oncogene in clear cell renal cell carcinoma.
    Title: Identification of RNA-binding protein YBX3 as an oncogene in clear cell renal cell carcinoma.
  4. Identification and verification of YBX3 and its regulatory gene HEIH as an oncogenic system: A multidimensional analysis in colon cancer.
    Title: Identification and verification of YBX3 and its regulatory gene HEIH as an oncogenic system: A multidimensional analysis in colon cancer.
  5. Knockdown of DNA-binding protein A enhances the chemotherapy sensitivity of colorectal cancer via suppressing the Wnt/beta-catenin/Chk1 pathway.
    Title: Knockdown of DNA-binding protein A enhances the chemotherapy sensitivity of colorectal cancer via suppressing the Wnt/β-catenin/Chk1 pathway.
  6. YB-3 substitutes YB-1 in global mRNA binding.
    Title: YB-3 substitutes YB-1 in global mRNA binding.
  7. Y-Box-Binding Protein 3 (YBX3) Restricts Influenza A Virus by Interacting with Viral Ribonucleoprotein Complex and Imparing its Function.
    Title: Y-Box-Binding Protein 3 (YBX3) Restricts Influenza A Virus by Interacting with Viral Ribonucleoprotein Complex and Imparing its Function.
  8. YBX3 binds within the 3' UTR of SLC7A5 to stabilize the transcript.
    Title: The RNA-Binding Protein YBX3 Controls Amino Acid Levels by Regulating SLC mRNA Abundance.
  9. ZONAB is up-regulated in bladder cancer cell lines, which promotes invasion, demonstrating the important role it plays in tumorogenesis and cancer progression
    Title: Zonula occludens-1 associated nucleic acid binding protein plays an invasion-promoting role in bladder cancer.
  10. Authors examined, for the first time in a Turkish population, the association between protamine gene alleles (PRM1 c.-190C>A, PRM1 c.197G>T, and PRM2 c.248C>T), and YBX2 (c.187T>C and c.1095 + 16A>G) and male infertility.
    Title: Genetic Polymorphisms in PRM1, PRM2, and YBX2 Genes are Associated with Male Factor Infertility.
Submit: New GeneRIF Correction See all GeneRIFs (24)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 ribosome 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

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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)

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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_001145426.2 → NP_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:91 → 160
    CSD; 'Cold-shock' DNA-binding domain

  2. NM_003651.5 → NP_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:91 → 160
    CSD; 'Cold-shock' DNA-binding domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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_017020123.3 → XP_016875612.1  Y-box-binding protein 3 isoform X3

    UniProtKB/TrEMBL
    Q96GD7

  2. XM_017020122.3 → XP_016875611.1  Y-box-binding protein 3 isoform X2

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

    UniProtKB/Swiss-Prot
    B2RBW6, P16989, Q14121, Q969N6, Q96B76

  4. XM_011520871.4 → XP_011519173.1  Y-box-binding protein 3 isoform X4

    Conserved Domains (1) summary
    pfam00313
    Location:91 → 160
    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_054373689.1 → XP_054229664.1  Y-box-binding protein 3 isoform X3

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

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

    UniProtKB/Swiss-Prot
    B2RBW6, P16989, Q14121, Q969N6, Q96B76

  4. XM_054373690.1 → XP_054229665.1  Y-box-binding protein 3 isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P16989.4 GenPept UniProtKB/Swiss-Prot:P16989

Gene LinkOut

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