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ELP4 elongator acetyltransferase complex subunit 4 [ Homo sapiens (human) ]

Gene ID: 26610, updated on 5-Mar-2024

Summary

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Official Symbol
ELP4provided by HGNC
Official Full Name
elongator acetyltransferase complex subunit 4provided by HGNC
Primary source
HGNC:HGNC:1171
See related
Ensembl:ENSG00000109911 MIM:606985; AllianceGenome:HGNC:1171
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
AN; AN2; hELP4; PAXNEB; PAX6NEB; C11orf19; dJ68P15A.1
Summary
This gene encodes a component of the six subunit elongator complex, a histone acetyltransferase complex that associates directly with RNA polymerase II during transcriptional elongation. The human gene can partially complement sensitivity phenotypes of yeast ELP4 deletion mutants. This gene has also been associated with Rolandic epilepsy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]
Expression
Ubiquitous expression in kidney (RPKM 4.9), brain (RPKM 4.9) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
11p13
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (31509767..31790324)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (31645605..31926139)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (31531314..31811872)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene doublecortin domain containing 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:31326823-31328022 Neighboring gene CYCS pseudogene 25 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4556 Neighboring gene MPRA-validated peak1237 silencer Neighboring gene MPRA-validated peak1238 silencer Neighboring gene DnaJ heat shock protein family (Hsp40) member C24 Neighboring gene MPRA-validated peak1240 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:31531307-31532196 Neighboring gene inner mitochondrial membrane peptidase subunit 1 Neighboring gene HCNE8 enhancer downstream of PAX6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:31565420-31566029 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:31566030-31566638 Neighboring gene RB enhancer downstream of PAX6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4558 Neighboring gene E100 enhancer downstream of PAX6 Neighboring gene PAX6 downstream regulatory region Neighboring gene E60 enhancer downstream of PAX6 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:31800787-31801986 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:31814755-31814968 Neighboring gene enhancer region in intron 7 of PAX6 Neighboring gene regulatory region in intron 4 of PAX6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:31827075-31827744 Neighboring gene PAX6 upstream regulatory region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3219 Neighboring gene VISTA enhancer hs1531 Neighboring gene PAX6 antisense RNA 1 Neighboring gene paired box 6 Neighboring gene PAX6 upstream antisense RNA Neighboring gene ReSE screen-validated silencer GRCh37_chr11:31960853-31961050 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4559 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4560 Neighboring gene VISTA enhancer hs855 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:32008494-32008994 Neighboring gene uncharacterized LOC107984420

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. Association between ELP4 rs986527 polymorphism and the occurrence and development of intracranial arachnoid cyst. Li K, et al. Brain Behav, 2019 Dec. PMID 31743616, Free PMC Article
  2. Microdeletions of ELP4 Are Associated with Language Impairment, Autism Spectrum Disorder, and Mental Retardation. Addis L, et al. Hum Mutat, 2015 Sep. PMID 26010655
  3. Major Susceptibility Genes for Common Idiopathic Epilepsies: ELP4 in Rolandic Epilepsy and BRD2 in Juvenile Myoclonic Epilepsy. Noebels JL, et al. , 2012. PMID 22787611
  4. Human Elongator complex is involved in cell cycle and suppresses cell growth in 293T human embryonic kidney cells. Gu J, et al. Acta Biochim Biophys Sin (Shanghai), 2009 Oct. PMID 19779648
  5. From rolandic epilepsy to continuous spike-and-waves during sleep and Landau-Kleffner syndromes: insights into possible genetic factors. Rudolf G, et al. Epilepsia, 2009 Aug. PMID 19682046

See all (57) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ELP4 rs986527 polymorphism affected the incidence of clinical symptoms and the levels of TNF-alpha and IL-1beta in patients with intracranial Arachnoid Cysts.
    Title: Association between ELP4 rs986527 polymorphism and the occurrence and development of intracranial arachnoid cyst.
  2. Elongator activated migration and invasion of hepatocellular carcinoma cells by promoting the expression of MMP-2 and MMP-9 through the PI3K/AKT signaling pathway
    Title: Elongator promotes the migration and invasion of hepatocellular carcinoma cell by the phosphorylation of AKT.
  3. Our results suggest that ELP4 deletions are highly likely to be pathogenic, predisposing to a range of neurodevelopmental phenotypes from ASD to language impairment and epilepsy.
    Title: Microdeletions of ELP4 Are Associated with Language Impairment, Autism Spectrum Disorder, and Mental Retardation.
  4. Results show no difference in BDNF and ELP4 genotype frequencies between benign epilepsy with centrotemporal spikes patients and controls; haplotype analysis also revealed no statistical difference
    Title: Association of brain-derived neurotrophic factor (BDNF) and elongator protein complex 4 (ELP4) polymorphisms with benign epilepsy with centrotemporal spikes in a Greek population.
  5. No association of SNPs in the ELP4 gene was detected in rolandic epilepsy patients.
    Title: Analysis of ELP4, SRPX2, and interacting genes in typical and atypical rolandic epilepsy.
  6. Data suggest that a non-coding mutation in ELP4 impairs brain-specific Elongator-mediated interaction of genes implicated in brain development, resulting in susceptibility to seizures and neurodevelopmental disorders.
    Title: Centrotemporal sharp wave EEG trait in rolandic epilepsy maps to Elongator Protein Complex 4 (ELP4).
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

Associated conditions

Description Tests
Aniridia 2
MedGen: C0344543 OMIM: 617141 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Genome-wide association and admixture analysis of glaucoma in the Women's Health Initiative.
EBI GWAS Catalog

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

Clone Names

  • FLJ20498

Gene Ontology Provided by GOA

Function Evidence Code Pubs
contributes_to RNA polymerase II complex binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables phosphorylase kinase regulator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 PubMed 
involved_in regulation of translation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in tRNA wobble uridine modification IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in tRNA wobble uridine modification NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in transcription elongation by RNA polymerase II TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
part_of elongator holoenzyme complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of elongator holoenzyme complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of elongator holoenzyme complex IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
part_of transcription elongation factor complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of transcription elongation factor complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
elongator complex protein 4
Names
PAX6 neighbor gene protein
elongation protein 4 homolog

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.

Genomic

  1. NG_034086.2 RefSeqGene

    Range
    5002..285559
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001288725.2 → NP_001275654.1  elongator complex protein 4 isoform 2

    See identical proteins and their annotated locations for NP_001275654.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate exon in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (2) has a longer and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK000505, AK304885, AL136677, BF969161, BM680240, BQ083338, D59285, Z83307
    Consensus CDS
    CCDS73271.1
    UniProtKB/TrEMBL
    A0A1W2PRF5
    Related
    ENSP00000368461.5, ENST00000379163.10
    Conserved Domains (1) summary
    pfam05625
    Location:28 → 382
    PAXNEB; PAXNEB protein

  2. NM_001288726.2 → NP_001275655.1  elongator complex protein 4 isoform 3

    See identical proteins and their annotated locations for NP_001275655.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains two alternate exon in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (3) has a longer and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC131571, AK000505, BC012514, BF969161, BM680240, BQ083338, D59285, Z83307
    Consensus CDS
    CCDS73272.1
    UniProtKB/TrEMBL
    B1B1I7, G5E9D4
    Related
    ENSP00000379267.2, ENST00000395934.2
    Conserved Domains (1) summary
    pfam05625
    Location:28 → 416
    PAXNEB; PAXNEB protein

  3. NM_019040.5 → NP_061913.3  elongator complex protein 4 isoform 1

    See identical proteins and their annotated locations for NP_061913.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shortest transcript and encodes the shortest protein.
    Source sequence(s)
    AK000505, BF969161, BM680240, BQ083338, D59285, Z83307
    Consensus CDS
    CCDS7875.2
    UniProtKB/Swiss-Prot
    B4E3W0, E7EPZ6, Q96EB1, Q9H4E8, Q9NX11
    UniProtKB/TrEMBL
    A0A1X7SBS0
    Related
    ENSP00000492152.1, ENST00000640961.2
    Conserved Domains (1) summary
    pfam05625
    Location:28 → 423
    PAXNEB; PAXNEB protein

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    31509767..31790324
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    31645605..31926139
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96EB1.2 GenPept UniProtKB/Swiss-Prot:Q96EB1

Gene LinkOut

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