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

Summary

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, Oct 2024]
Expression: Ubiquitous expression in brain (RPKM 10.1), endometrium (RPKM 9.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 8p21.1

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	8	NC_000008.11 (28090232..28191153)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	8	NC_060932.1 (28368442..28469343)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	8	NC_000008.10 (27947749..28048670)

Chromosome 8 - NC_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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).
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.
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.
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.
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.
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G19915 (e-PCR)
- UniSTS:56342

A002C05 (e-PCR)
- UniSTS:56343

D8S1820 (e-PCR), detects polymorphism
- UniSTS:14109

D8S2279 (e-PCR)
- UniSTS:473907

WI-19683 (e-PCR)
- UniSTS:65085

SHGC-2723 (e-PCR)
- UniSTS:16219

G04236 (e-PCR)
- UniSTS:72028

STS-H84776 (e-PCR)
- UniSTS:82538

D10S16 (e-PCR)
- UniSTS:155756

D15S1477 (e-PCR)
- UniSTS:474482

SHGC-144874 (e-PCR)
- UniSTS:172470

WI-11768 (e-PCR)
- UniSTS:78521

STS-D29223 (e-PCR)
- UniSTS:57021

RH16604 (e-PCR)
- UniSTS:1500

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

EC 2.3.1.311

NP_001271151.1

EC 2.3.1.311

NP_001271153.1

EC 2.3.1.311

NP_001271154.1

EC 2.3.1.311

NP_001271155.1

EC 2.3.1.311

NP_060561.3

EC 2.3.1.311

XP_024302952.1

EC 2.3.1.311

XP_054216724.1

EC 2.3.1.311

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)

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
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
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]
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]
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
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000008.11 Reference GRCh38.p14 Primary Assembly

Range

28090232..28191153

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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