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ELP3 elongator acetyltransferase complex subunit 3 [ Homo sapiens (human) ]

Gene ID: 55140, updated on 3-Apr-2024

Summary

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Official Symbol
ELP3provided by HGNC
Official Full Name
elongator acetyltransferase complex subunit 3provided by HGNC
Primary source
HGNC:HGNC:20696
See related
Ensembl:ENSG00000134014 MIM:612722; AllianceGenome:HGNC:20696
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
KAT9
Summary
Enables acetyltransferase activity and phosphorylase kinase regulator activity. Involved in regulation of transcription by RNA polymerase II and tRNA wobble uridine modification. Located in cytosol and nucleolus. Part of elongator holoenzyme complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in brain (RPKM 10.1), endometrium (RPKM 9.6) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
8p21.1
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (28090232..28191153)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (28368442..28469343)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (27947749..28048670)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene scavenger receptor class A member 5 Neighboring gene uncharacterized LOC105379342 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:27806885-27807386 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:27807387-27807886 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:27834121-27835005 Neighboring gene nuclear GTPase, germinal center associated Neighboring gene ReSE screen-validated silencer GRCh37_chr8:27918038-27918203 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:27920879-27921378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27160 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:27950237-27950790 Neighboring gene MPRA-validated peak6972 silencer Neighboring gene uncharacterized LOC105379343 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:28042753-28043255 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:28049121-28049873 Neighboring gene delta 4-desaturase, sphingolipid 1 pseudogene Neighboring gene PDZ and LIM domain 7 (enigma) pseudogene

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. Relation between the circular and linear form of the Elongator Acetyltransferase Complex Subunit 3 in the progression of triple-negative breast cancer. Barznegar M, et al. Cell Biochem Funct, 2022 Aug. PMID 35722999
  2. ELP3 Acetyltransferase is phosphorylated and regulated by the oncogenic anaplastic lymphoma kinase (ALK). Li MT, et al. Biochem J, 2019 Aug 15. PMID 31341009
  3. Structural insights into the function of Elongator. Dalwadi U, et al. Cell Mol Life Sci, 2018 May. PMID 29332244
  4. hElp3 directly modulates the expression of HSP70 gene in HeLa cells via HAT activity. Li F, et al. PLoS One, 2011. PMID 22216241, Free PMC Article
  5. Elongator - an emerging role in neurological disorders. Nguyen L, et al. Trends Mol Med, 2010 Jan. PMID 20036197

See all (88) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Amyloid pathology reduces ELP3 expression and tRNA modifications leading to impaired proteostasis.
    Title: Amyloid pathology reduces ELP3 expression and tRNA modifications leading to impaired proteostasis.
  2. Relation between the circular and linear form of the Elongator Acetyltransferase Complex Subunit 3 in the progression of triple-negative breast cancer.
    Title: Relation between the circular and linear form of the Elongator Acetyltransferase Complex Subunit 3 in the progression of triple-negative breast cancer.
  3. study reveals a novel regulatory mechanism for ELP3, provides an example that acetyltransferase itself can be regulated by PTM, and suggests a potential target for ALK-positive cancer therapies.
    Title: ELP3 Acetyltransferase is phosphorylated and regulated by the oncogenic anaplastic lymphoma kinase (ALK).
  4. 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.
  5. and CTU1/2, partner enzymes in U34 methoxycarbonylmethyl-2-thio tRNA modification, are up-regulated in human breast cancers and sustain metastasis.
    Title: Elp3 links tRNA modification to IRES-dependent translation of LEF1 to sustain metastasis in breast cancer.
  6. Promoter hypermethylation is an important mechanism of the transcriptional inactivation of ELP3 in invasive ductal breast carcinoma.
    Title: Promoter hypermethylation may be an important mechanism of the transcriptional inactivation of ARRDC3, GATA5, and ELP3 in invasive ductal breast carcinoma.
  7. Regulation of G6PD acetylation by SIRT2 and KAT9 modulates NADPH homeostasis and cell survival during oxidative stress.
    Title: Regulation of G6PD acetylation by SIRT2 and KAT9 modulates NADPH homeostasis and cell survival during oxidative stress.
  8. data suggest that hElp3 can regulate the transcription of HSP70 gene, and the HAT domain of hElp3 is essential for this function
    Title: hElp3 directly modulates the expression of HSP70 gene in HeLa cells via HAT activity.
  9. Observational study and genome-wide association study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Genome-wide association study of increasing suicidal ideation during antidepressant treatment in the GENDEP project.
  10. The results of this study uncover a novel role for Elp3 in the regulation of synaptic bouton expansion during neurogenesis that may be linked with a requirement for sleep.
    Title: The histone acetyltransferase Elp3 plays in active role in the control of synaptic bouton expansion and sleep in Drosophila.
Submit: New GeneRIF Correction See all GeneRIFs (15)

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

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

  • FLJ10422

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 4 iron, 4 sulfur cluster binding IEA
Inferred from Electronic Annotation
more info
  
enables acetyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables phosphorylase kinase regulator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables tRNA binding IEA
Inferred from Electronic Annotation
more info
  
enables tRNA uridine(34) acetyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in central nervous system development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in neuron migration ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of cell migration ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of translation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation TAS
Traceable Author Statement
more info
 PubMed 
involved_in tRNA wobble uridine modification IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in tRNA wobble uridine modification NAS
Non-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 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
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 nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
elongator complex protein 3
Names
elongation protein 3 homolog
protein lysine acetyltransferase ELP3
tRNA uridine(34) acetyltransferase
NP_001271149.1
NP_001271151.1
NP_001271153.1
NP_001271154.1
NP_001271155.1
NP_060561.3
XP_024302952.1
XP_054216724.1

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_001284220.2 → NP_001271149.1  elongator complex protein 3 isoform 2

    See identical proteins and their annotated locations for NP_001271149.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and lacks an in-frame portion of the 5' coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC019031, AC021678, AK296475, BU683531
    Consensus CDS
    CCDS75718.1
    UniProtKB/TrEMBL
    B4DKA4, B4DPB7
    Related
    ENSP00000429180.1, ENST00000524103.5
    Conserved Domains (3) summary
    cd01335
    Location:24 → 268
    Radical_SAM; Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. ...
    COG1243
    Location:1 → 474
    ELP3; Histone acetyltransferase, component of the RNA polymerase elongator complex [Transcription, Chromatin structure and dynamics]
    pfam16199
    Location:242 → 320
    Radical_SAM_C; Radical_SAM C-terminal domain

  2. NM_001284222.2 → NP_001271151.1  elongator complex protein 3 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains a distinct 5' UTR and lacks an in-frame portion of the 5' coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (3) with a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC019031, AC021678, BU683531, BX648011, DA877844
    Consensus CDS
    CCDS75717.1
    UniProtKB/TrEMBL
    B4DPB7
    Related
    ENSP00000428449.1, ENST00000521015.5
    Conserved Domains (1) summary
    cl25699
    Location:22 → 532
    Radical_SAM_C; Radical_SAM C-terminal domain

  3. NM_001284224.2 → NP_001271153.1  elongator complex protein 3 isoform 4

    See identical proteins and their annotated locations for NP_001271153.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and lacks a portion of the 5' coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (4) with a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC019031, AC021678, AK302140, BU683531
    Consensus CDS
    CCDS64861.1
    UniProtKB/TrEMBL
    B4DXV1
    Conserved Domains (1) summary
    COG1243
    Location:13 → 427
    ELP3; Histone acetyltransferase, component of the RNA polymerase elongator complex [Transcription, Chromatin structure and dynamics]

  4. NM_001284225.2 → NP_001271154.1  elongator complex protein 3 isoform 4

    See identical proteins and their annotated locations for NP_001271154.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and lacks a portion of the 5' coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (4) with a shorter N-terminus, compared to isoform 1. Variants 4 and 5 encode the same isoform (5).
    Source sequence(s)
    AC019031, AC021678, AK293424, BU683531
    Consensus CDS
    CCDS64861.1
    UniProtKB/TrEMBL
    B4DXV1
    Related
    ENSP00000445558.1, ENST00000537665.2
    Conserved Domains (1) summary
    COG1243
    Location:13 → 427
    ELP3; Histone acetyltransferase, component of the RNA polymerase elongator complex [Transcription, Chromatin structure and dynamics]

  5. NM_001284226.2 → NP_001271155.1  elongator complex protein 3 isoform 5

    See identical proteins and their annotated locations for NP_001271155.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and lacks a portion of the 5' coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (6) with a shorter N-terminus, compared to isoform 1
    Source sequence(s)
    AC021678, AK295574, BU683531
    Consensus CDS
    CCDS64860.1
    UniProtKB/TrEMBL
    B4DPB7
    Related
    ENSP00000369711.4, ENST00000380353.8
    Conserved Domains (1) summary
    cl25699
    Location:1 → 454
    Radical_SAM_C; Radical_SAM C-terminal domain

  6. NM_018091.6 → NP_060561.3  elongator complex protein 3 isoform 1

    See identical proteins and their annotated locations for NP_060561.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AL834273, BM663362, DA150994
    Consensus CDS
    CCDS6065.1
    UniProtKB/Swiss-Prot
    B4DE19, B4DIG1, E2QRI5, Q53G84, Q6AWB0, Q9BVF7, Q9H9T3, Q9NVZ1
    UniProtKB/TrEMBL
    B4DPB7
    Related
    ENSP00000256398.8, ENST00000256398.13
    Conserved Domains (1) summary
    TIGR01211
    Location:36 → 546
    ELP3; radical SAM enzyme/protein acetyltransferase, ELP3 family

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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    28090232..28191153
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024447184.2 → XP_024302952.1  elongator complex protein 3 isoform X1

    UniProtKB/TrEMBL
    B4DPB7
    Conserved Domains (1) summary
    cl25699
    Location:22 → 532
    Radical_SAM_C; Radical_SAM C-terminal domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    28368442..28469343
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054360749.1 → XP_054216724.1  elongator complex protein 3 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H9T3.2 GenPept UniProtKB/Swiss-Prot:Q9H9T3

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