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    EYA3 EYA transcriptional coactivator and phosphatase 3 [ Homo sapiens (human) ]

    Gene ID: 2140, updated on 28-Oct-2024

    Summary

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    Official Symbol
    EYA3provided by HGNC
    Official Full Name
    EYA transcriptional coactivator and phosphatase 3provided by HGNC
    Primary source
    HGNC:HGNC:3521
    See related
    Ensembl:ENSG00000158161 MIM:601655; AllianceGenome:HGNC:3521
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This gene encodes a member of the eyes absent (EYA) family of proteins. The encoded protein may act as a transcriptional activator and have a role during development. It can act as a mediator of chemoresistance and cell survival in Ewing sarcoma cells, where this gene is up-regulated via a micro-RNA that binds to the 3' UTR of the transcript. A similar protein in mice acts as a transcriptional activator. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Sep 2013]
    Expression
    Ubiquitous expression in testis (RPKM 6.3), kidney (RPKM 5.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See EYA3 in Genome Data Viewer
    Location:
    1p35.3
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (27970344..28088610, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (27812178..27930443, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (28296855..28415121, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:28261145-28262046 Neighboring gene Sharpr-MPRA regulatory region 12823 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:28269804-28270304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:28270305-28270805 Neighboring gene sphingomyelin phosphodiesterase acid like 3B Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:28286425-28286988 Neighboring gene XK related 8 Neighboring gene MPRA-validated peak136 silencer Neighboring gene RNA, 7SL, cytoplasmic 559, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 581 Neighboring gene signal peptidase complex subunit 2 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 582 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 583 Neighboring gene ARL8B pseudogene 2

    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 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. Structure-activity relationships of benzbromarone metabolites and derivatives as EYA inhibitory anti-angiogenic agents. Pandey RN, et al. PLoS One, 2013. PMID 24367676, Free PMC Article
    2. Analysis of EYA3 Phosphorylation by Src Kinase Identifies Residues Involved in Cell Proliferation. Ionescu AE, et al. Int J Mol Sci, 2019 Dec 13. PMID 31847183, Free PMC Article
    3. Identification of novel mutations in EYA3 and EFTUD2 in a family with craniofacial microsomia: evidence of digenic inheritance. Si N, et al. Front Med, 2023 Oct. PMID 37507637
    4. EWS/FLI1 regulates EYA3 in Ewing sarcoma via modulation of miRNA-708, resulting in increased cell survival and chemoresistance. Robin TP, et al. Mol Cancer Res, 2012 Aug. PMID 22723308, Free PMC Article
    5. The Eyes Absent proteins in development and disease. Tadjuidje E, et al. Cell Mol Life Sci, 2013 Jun. PMID 22971774, Free PMC Article

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of novel mutations in EYA3 and EFTUD2 in a family with craniofacial microsomia: evidence of digenic inheritance.
      Title: Identification of novel mutations in EYA3 and EFTUD2 in a family with craniofacial microsomia: evidence of digenic inheritance.
    2. Circular RNA CircEYA3 induces energy production to promote pancreatic ductal adenocarcinoma progression through the miR-1294/c-Myc axis.
      Title: Circular RNA CircEYA3 induces energy production to promote pancreatic ductal adenocarcinoma progression through the miR-1294/c-Myc axis.
    3. A recurrent missense variant in EYA3 gene is associated with oculo-auriculo-vertebral spectrum.
      Title: A recurrent missense variant in EYA3 gene is associated with oculo-auriculo-vertebral spectrum.
    4. These findings suggest that EYA3's tyrosine phosphorylation sites are non-equivalent with their phosphorylation levels being under the control of Src-kinase activity and of EYA3's autodephosphorylation.
      Title: Analysis of EYA3 Phosphorylation by Src Kinase Identifies Residues Involved in Cell Proliferation.
    5. WDR1 is an EYA3-specific substrate, which implies that EYA3 is a key modulator of the cytoskeletal reorganization
      Title: WDR1 is a novel EYA3 substrate and its dephosphorylation induces modifications of the cellular actin cytoskeleton.
    6. Study identifies Eya3 as a regulator of PP2A, a major cellular Ser/Thr phosphatase, and uncovers a mechanism of controlling the stability of a critical oncogene, c-Myc.
      Title: Eya3 partners with PP2A to induce c-Myc stabilization and tumor progression.
    7. Benzbromarone metabolites and derivatives function as EYA3 inhibitory anti-angiogenic agents.
      Title: Structure-activity relationships of benzbromarone metabolites and derivatives as EYA inhibitory anti-angiogenic agents.
    8. These studies identify EYA3 as a novel mediator of chemoresistance in Ewing sarcoma and define the molecular mechanisms of both EYA3 overexpression and of EYA3-mediated chemoresistance
      Title: EWS/FLI1 regulates EYA3 in Ewing sarcoma via modulation of miRNA-708, resulting in increased cell survival and chemoresistance.
    9. EYA2 and EYA3 displayed specificity for Tyr-142 of H2A.X
      Title: Dephosphorylation of the C-terminal tyrosyl residue of the DNA damage-related histone H2A.X is mediated by the protein phosphatase eyes absent.
    Submit: New GeneRIF Correction

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp686C132

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables histone H2AXY142 phosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein tyrosine phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein tyrosine phosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein tyrosine phosphatase activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in anatomical structure development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in anatomical structure morphogenesis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in double-strand break repair IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in double-strand break repair TAS
    Traceable Author Statement
    more info
    		  
    involved_in negative regulation of extrinsic apoptotic signaling pathway in absence of ligand IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of DNA repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of DNA repair IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to ionizing radiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in visual perception TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    eyes absent homolog 3
    Names
    eyes absent 3
    NP_001269489.1
    NP_001269490.1
    NP_001269491.1
    NP_001981.2
    XP_006710512.1
    XP_011539301.1
    XP_011539303.1
    XP_011539305.1
    XP_011539306.1
    XP_024309755.1
    XP_024309763.1
    XP_047305372.1
    XP_047305373.1
    XP_047305375.1
    XP_047305376.1
    XP_054191089.1
    XP_054191090.1
    XP_054191091.1
    XP_054191092.1
    XP_054191093.1
    XP_054191094.1
    XP_054191095.1
    XP_054191096.1
    XP_054191097.1
    XP_054191098.1
    XP_054191099.1

    NCBI Reference Sequences (RefSeq)

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    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_001282560.2 → NP_001269489.1  eyes absent homolog 3 isoform b

      See identical proteins and their annotated locations for NP_001269489.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, and contains an alternate 3' terminal exon and thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (b) has a distinct C-terminus and is shorter than isoform a.
      Source sequence(s)
      AL512288, BC041667, DC416048
      Consensus CDS
      CCDS60052.1
      UniProtKB/Swiss-Prot
      Q99504
      Related
      ENSP00000362970.3, ENST00000373863.3
      Conserved Domains (1) summary
      cd02601
      Location:256 → 501
      HAD_Eya; protein tyrosine phosphatase domain of the nuclear transcription factor of Eyes absent (Eya) and related phosphatase domains

    2. NM_001282561.2 → NP_001269490.1  eyes absent homolog 3 isoform c

      See identical proteins and their annotated locations for NP_001269490.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (c) that is shorter than isoform a.
      Source sequence(s)
      AK295745, AL512288, CA434977
      Consensus CDS
      CCDS60051.1
      UniProtKB/Swiss-Prot
      Q99504
      Related
      ENSP00000442558.1, ENST00000540618.5
      Conserved Domains (1) summary
      TIGR01658
      Location:256 → 527
      EYA-cons_domain; eyes absent protein conserved domain

    3. NM_001282562.2 → NP_001269491.1  eyes absent homolog 3 isoform d

      See identical proteins and their annotated locations for NP_001269491.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate exon in the 5' region which results in the use of a downstream in-frame start codon, compared to variant 1. The encoded isoform (d) is shorter at the N-terminus, compared to isoform a.
      Source sequence(s)
      AK298129, AL512288, CA434977
      Consensus CDS
      CCDS60050.1
      UniProtKB/Swiss-Prot
      Q99504
      Related
      ENSP00000405587.3, ENST00000436342.6
      Conserved Domains (1) summary
      TIGR01658
      Location:249 → 520
      EYA-cons_domain; eyes absent protein conserved domain

    4. NM_001990.4 → NP_001981.2  eyes absent homolog 3 isoform a

      See identical proteins and their annotated locations for NP_001981.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AK289805, AL512288, CR748247, DC416048
      Consensus CDS
      CCDS316.1
      UniProtKB/Swiss-Prot
      A8K190, B4DIR7, B4DNZ7, O95463, Q8IVX7, Q99504, Q99813
      Related
      ENSP00000362978.3, ENST00000373871.8
      Conserved Domains (1) summary
      TIGR01658
      Location:302 → 573
      EYA-cons_domain; eyes absent protein conserved domain

    RNA

    1. NR_104214.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) contains an additional exon in the central region, and lacks two exons in the 3' region but includes a different 3' terminal exon, compared to variant 1. This variant is represented as non-coding because the use of the expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC029500, BQ018346, DC416048
      Related
      ENST00000471498.5

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      27970344..28088610 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011541004.3 → XP_011539306.1  eyes absent homolog 3 isoform X7

      See identical proteins and their annotated locations for XP_011539306.1

      Conserved Domains (1) summary
      TIGR01658
      Location:258 → 529
      EYA-cons_domain; eyes absent protein conserved domain

    2. XM_006710449.4 → XP_006710512.1  eyes absent homolog 3 isoform X3

      See identical proteins and their annotated locations for XP_006710512.1

      Conserved Domains (1) summary
      TIGR01658
      Location:304 → 575
      EYA-cons_domain; eyes absent protein conserved domain

    3. XM_047449420.1 → XP_047305376.1  eyes absent homolog 3 isoform X9

    4. XM_047449416.1 → XP_047305372.1  eyes absent homolog 3 isoform X4

      UniProtKB/Swiss-Prot
      A8K190, B4DIR7, B4DNZ7, O95463, Q8IVX7, Q99504, Q99813

    5. XM_011541001.4 → XP_011539303.1  eyes absent homolog 3 isoform X2

      See identical proteins and their annotated locations for XP_011539303.1

      Conserved Domains (1) summary
      cd02601
      Location:302 → 547
      HAD_Eya; protein tyrosine phosphatase domain of the nuclear transcription factor of Eyes absent (Eya) and related phosphatase domains

    6. XM_011541003.3 → XP_011539305.1  eyes absent homolog 3 isoform X5

      Conserved Domains (1) summary
      TIGR01658
      Location:258 → 503
      EYA-cons_domain; eyes absent protein conserved domain

    7. XM_011540999.3 → XP_011539301.1  eyes absent homolog 3 isoform X1

      See identical proteins and their annotated locations for XP_011539301.1

      Conserved Domains (1) summary
      cd02601
      Location:304 → 549
      HAD_Eya; protein tyrosine phosphatase domain of the nuclear transcription factor of Eyes absent (Eya) and related phosphatase domains

    8. XM_047449417.1 → XP_047305373.1  eyes absent homolog 3 isoform X6

    9. XM_024453995.2 → XP_024309763.1  eyes absent homolog 3 isoform X2

      Conserved Domains (1) summary
      cd02601
      Location:302 → 547
      HAD_Eya; protein tyrosine phosphatase domain of the nuclear transcription factor of Eyes absent (Eya) and related phosphatase domains

    10. XM_024453987.2 → XP_024309755.1  eyes absent homolog 3 isoform X1

      Conserved Domains (1) summary
      cd02601
      Location:304 → 549
      HAD_Eya; protein tyrosine phosphatase domain of the nuclear transcription factor of Eyes absent (Eya) and related phosphatase domains

    11. XM_047449419.1 → XP_047305375.1  eyes absent homolog 3 isoform X8

    RNA

    1. XR_007096080.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      27812178..27930443 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335122.1 → XP_054191097.1  eyes absent homolog 3 isoform X7

    2. XM_054335118.1 → XP_054191093.1  eyes absent homolog 3 isoform X3

    3. XM_054335124.1 → XP_054191099.1  eyes absent homolog 3 isoform X9

    4. XM_054335119.1 → XP_054191094.1  eyes absent homolog 3 isoform X4

      UniProtKB/Swiss-Prot
      A8K190, B4DIR7, B4DNZ7, O95463, Q8IVX7, Q99504, Q99813

    5. XM_054335116.1 → XP_054191091.1  eyes absent homolog 3 isoform X2

    6. XM_054335120.1 → XP_054191095.1  eyes absent homolog 3 isoform X5

    7. XM_054335114.1 → XP_054191089.1  eyes absent homolog 3 isoform X1

    8. XM_054335121.1 → XP_054191096.1  eyes absent homolog 3 isoform X6

    9. XM_054335117.1 → XP_054191092.1  eyes absent homolog 3 isoform X2

    10. XM_054335115.1 → XP_054191090.1  eyes absent homolog 3 isoform X1

    11. XM_054335123.1 → XP_054191098.1  eyes absent homolog 3 isoform X8

    RNA

    1. XR_008485962.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_172098.1: Suppressed sequence

      Description
      NM_172098.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q99504.3 GenPept UniProtKB/Swiss-Prot:Q99504

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