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EYA4 EYA transcriptional coactivator and phosphatase 4 [ Homo sapiens (human) ]

Gene ID: 2070, updated on 3-Jun-2018
Official Symbol
EYA4provided by HGNC
Official Full Name
EYA transcriptional coactivator and phosphatase 4provided by HGNC
Primary source
HGNC:HGNC:3522
See related
Ensembl:ENSG00000112319 MIM:603550; Vega:OTTHUMG00000015602
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
Also known as
CMD1J; DFNA10
Summary
This gene encodes a member of the eyes absent (EYA) family of proteins. The encoded protein may act as a transcriptional activator through its protein phosphatase activity, and it may be important for eye development, and for continued function of the mature organ of Corti. Mutations in this gene are associated with postlingual, progressive, autosomal dominant hearing loss at the deafness, autosomal dominant non-syndromic sensorineural 10 locus. The encoded protein is also a putative oncogene that mediates DNA repair, apoptosis, and innate immunity following DNA damage, cellular damage, and viral attack. Defects in this gene are also associated with dilated cardiomyopathy 1J. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2014]
Expression
Broad expression in prostate (RPKM 1.8), kidney (RPKM 1.5) and 15 other tissues See more
Orthologs
See EYA4 in Genome Data Viewer
Location:
6q23.2
Exon count:
22
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (133240340..133532120)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (133561512..133853258)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 326 Neighboring gene MT-CYB pseudogene 4 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 21 Neighboring gene TCF21 antisense RNA inducing promoter demethylation Neighboring gene GATA motif-containing MPRA enhancer 179 Neighboring gene ferritin heavy chain 1 pseudogene 26

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-09-06)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-09-06)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
A genome-wide association study identifies protein quantitative trait loci (pQTLs).
NHGRI GWA Catalog
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
NHGRI GWA Catalog
Genomic association analysis identifies multiple loci influencing antihypertensive response to an angiotensin II receptor blocker.
NHGRI GWA Catalog
Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment.
NHGRI GWA Catalog
  • DNA Double Strand Break Response, organism-specific biosystem (from REACTOME)
    DNA Double Strand Break Response, organism-specific biosystemDNA double strand break (DSB) response involves sensing of DNA DSBs by the MRN complex which triggers ATM activation. ATM phosphorylates a number of proteins involved in DNA damage checkpoint signali...
  • DNA Double-Strand Break Repair, organism-specific biosystem (from REACTOME)
    DNA Double-Strand Break Repair, organism-specific biosystemNumerous types of DNA damage can occur within a cell due to the endogenous production of oxygen free radicals, normal alkylation reactions, or exposure to exogenous radiations and chemicals. Double-s...
  • DNA Repair, organism-specific biosystem (from REACTOME)
    DNA Repair, organism-specific biosystemDNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, enviro...
  • Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks, organism-specific biosystem (from REACTOME)
    Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks, organism-specific biosystemActivated ATM phosphorylates a number of proteins involved in the DNA damage checkpoint and DNA repair (Thompson and Schild 2002, Ciccia and Elledge 2010), thereby triggering and coordinating accumul...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein tyrosine phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
DNA repair IEA
Inferred from Electronic Annotation
more info
 
anatomical structure development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
anatomical structure morphogenesis TAS
Traceable Author Statement
more info
PubMed 
cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone dephosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of extrinsic apoptotic signaling pathway in absence of ligand IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
peptidyl-tyrosine dephosphorylation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of DNA repair IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
sensory perception of sound IEA
Inferred from Electronic Annotation
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
visual perception TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Preferred Names
eyes absent homolog 4
Names
dJ78N10.1 (eyes absent)
eyes absent-like protein 4
NP_001287941.1
NP_001287942.1
NP_004091.3
NP_742101.2
NP_742103.1
XP_005266908.1
XP_005266910.1
XP_016865857.1
XP_016865858.1
XP_016865859.1
XP_016865860.1
XP_016865861.1
XP_016865862.1
XP_016865863.1
XP_016865864.1

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.

Genomic

  1. NG_011596.1 RefSeqGene

    Range
    5001..295764
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001301012.1NP_001287941.1  eyes absent homolog 4 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) has multiple differences in its coding region, compared to variant 1. The resulting isoform (e) is shorter than isoform a.
    Source sequence(s)
    AK295798, AK301950, AL450270, AW613879
    Consensus CDS
    CCDS75523.1
    UniProtKB/Swiss-Prot
    O95677
    UniProtKB/TrEMBL
    A0A0S2Z3Q2, B4DIV6
    Related
    ENSP00000395916.2, OTTHUMP00000233943, ENST00000452339.6, OTTHUMT00000391009
    Conserved Domains (2) summary
    TIGR01658
    Location:314585
    EYA-cons_domain; eyes absent protein conserved domain
    pfam12533
    Location:153232
    Neuro_bHLH; Neuronal helix-loop-helix transcription factor
  2. NM_001301013.1NP_001287942.1  eyes absent homolog 4 isoform f

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) contains an alternate in-frame segment of the 5' coding region, compared to variant 1. The resulting isoform (f) is longer than isoform a.
    Source sequence(s)
    AK299378, AK301950, AL450270, AW613879, Y17114
    Consensus CDS
    CCDS75521.1
    UniProtKB/Swiss-Prot
    O95677
    UniProtKB/TrEMBL
    B4DRQ6, F2Z2Y1
    Related
    ENSP00000432770.1, OTTHUMP00000233946, ENST00000531901.5, OTTHUMT00000391012
    Conserved Domains (3) summary
    TIGR01658
    Location:374645
    EYA-cons_domain; eyes absent protein conserved domain
    pfam00702
    Location:376621
    Hydrolase; haloacid dehalogenase-like hydrolase
    pfam12533
    Location:207286
    Neuro_bHLH; Neuronal helix-loop-helix transcription factor
  3. NM_004100.4NP_004091.3  eyes absent homolog 4 isoform a

    See identical proteins and their annotated locations for NP_004091.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform a, which is more abundant in adult brain.
    Source sequence(s)
    AL450270, AW613879, BC014193, BX490250, DA760903, Y17114
    Consensus CDS
    CCDS5165.1
    UniProtKB/Swiss-Prot
    O95677
    UniProtKB/TrEMBL
    Q96CJ7
    Related
    ENSP00000347434.7, OTTHUMP00000017235, ENST00000355286.11, OTTHUMT00000042282
    Conserved Domains (3) summary
    TIGR01658
    Location:368639
    EYA-cons_domain; eyes absent protein conserved domain
    pfam00702
    Location:370615
    Hydrolase; haloacid dehalogenase-like hydrolase
    pfam12533
    Location:207286
    Neuro_bHLH; Neuronal helix-loop-helix transcription factor
  4. NM_172103.3NP_742101.2  eyes absent homolog 4 isoform b

    See identical proteins and their annotated locations for NP_742101.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame segment of the 5' coding region, compared to variant 1. The resulting isoform (b) is shorter than isoform a.
    Source sequence(s)
    AL450270, AW613879, BC014193, BC041063, BX490250, Y17114
    Consensus CDS
    CCDS43506.1
    UniProtKB/Swiss-Prot
    O95677
    UniProtKB/TrEMBL
    A0A0S2Z3V9, Q96CJ7
    Related
    ENSP00000404558.3, OTTHUMP00000233945, ENST00000431403.3, OTTHUMT00000391011
    Conserved Domains (2) summary
    cd02601
    Location:345616
    HAD_Eya; protein tyrosine phosphatase domain of the nuclear transcription factor of Eyes absent (Eya) and related phosphatase domains
    cl25764
    Location:109260
    PAT1; Topoisomerase II-associated protein PAT1
  5. NM_172105.3NP_742103.1  eyes absent homolog 4 isoform d

    See identical proteins and their annotated locations for NP_742103.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an alternate in-frame exon in the 3' coding region, compared to variant 1. The resulting isoform (d) is the same size but has a region of difference in the C-terminal, compared to isoform a.
    Source sequence(s)
    AJ007994, AL450270, AW613879, BC014193, BX490250, DA760903, Y17114
    Consensus CDS
    CCDS5166.1
    UniProtKB/Swiss-Prot
    O95677
    UniProtKB/TrEMBL
    Q96CJ7
    Related
    ENSP00000347294.3, ENST00000355167.7
    Conserved Domains (2) summary
    TIGR01658
    Location:368639
    EYA-cons_domain; eyes absent protein conserved domain
    pfam12533
    Location:207286
    Neuro_bHLH; Neuronal helix-loop-helix transcription factor

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p12 Primary Assembly

    Range
    133240340..133532120
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017010368.2XP_016865857.1  eyes absent homolog 4 isoform X1

  2. XM_017010374.2XP_016865863.1  eyes absent homolog 4 isoform X9

    Related
    ENSP00000388670.2, OTTHUMP00000233944, ENST00000430974.6
  3. XM_017010375.1XP_016865864.1  eyes absent homolog 4 isoform X10

  4. XM_005266851.5XP_005266908.1  eyes absent homolog 4 isoform X3

    Conserved Domains (2) summary
    TIGR01658
    Location:374645
    EYA-cons_domain; eyes absent protein conserved domain
    pfam12533
    Location:207286
    Neuro_bHLH; Neuronal helix-loop-helix transcription factor
  5. XM_017010369.2XP_016865858.1  eyes absent homolog 4 isoform X2

  6. XM_017010370.2XP_016865859.1  eyes absent homolog 4 isoform X4

  7. XM_005266853.5XP_005266910.1  eyes absent homolog 4 isoform X6

    UniProtKB/TrEMBL
    E9PLN6
    Related
    ENSP00000433219.1, OTTHUMP00000017236, ENST00000525849.6
    Conserved Domains (2) summary
    TIGR01658
    Location:345616
    EYA-cons_domain; eyes absent protein conserved domain
    pfam12533
    Location:184263
    Neuro_bHLH; Neuronal helix-loop-helix transcription factor
  8. XM_017010371.2XP_016865860.1  eyes absent homolog 4 isoform X5

  9. XM_017010372.2XP_016865861.1  eyes absent homolog 4 isoform X7

  10. XM_017010373.2XP_016865862.1  eyes absent homolog 4 isoform X8

RNA

  1. XR_001743220.2 RNA Sequence

  2. XR_001743219.2 RNA Sequence

    Related
    ENST00000531861.5

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_172104.1: Suppressed sequence

    Description
    NM_172104.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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