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

Gene ID: 2140, updated on 5-Mar-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (27970344..28088610, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (27812178..27930443, complement)
105.20220307 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
  • 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. 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
  2. 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
  3. Circular RNA CircEYA3 induces energy production to promote pancreatic ductal adenocarcinoma progression through the miR-1294/c-Myc axis. Rong Z, et al. Mol Cancer, 2021 Aug 21. PMID 34419070, Free PMC Article
  4. A recurrent missense variant in EYA3 gene is associated with oculo-auriculo-vertebral spectrum. Tingaud-Sequeira A, et al. Hum Genet, 2021 Jun. PMID 33475861
  5. WDR1 is a novel EYA3 substrate and its dephosphorylation induces modifications of the cellular actin cytoskeleton. Mentel M, et al. Sci Rep, 2018 Feb 13. PMID 29440662, Free PMC Article

See all (41) 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_2023_10

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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