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

    Gene ID: 26610, updated on 3-Nov-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
    mouse all
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    Genomic context

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    See ELP4 in Genome Data Viewer
    Location:
    11p13
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (31509767..31790324)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (31645605..31926139)
    RS_2024_09 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 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. 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
    2. 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
    3. Microdeletions of ELP4 Are Associated with Language Impairment, Autism Spectrum Disorder, and Mental Retardation. Addis L, et al. Hum Mutat, 2015 Sep. PMID 26010655
    4. Major Susceptibility Genes for Common Idiopathic Epilepsies: ELP4 in Rolandic Epilepsy and BRD2 in Juvenile Myoclonic Epilepsy. Noebels JL, et al. , 2012. PMID 22787611
    5. Centrotemporal sharp wave EEG trait in rolandic epilepsy maps to Elongator Protein Complex 4 (ELP4). Strug LJ, et al. Eur J Hum Genet, 2009 Sep. PMID 19172991, Free PMC Article

    See all (62) 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)

    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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