KDM4A lysine demethylase 4A [Homo sapiens (human)] - Gene

Summary

Official Symbol: KDM4Aprovided by HGNC
Official Full Name: lysine demethylase 4Aprovided by HGNC
Primary source: HGNC:HGNC:22978
See related: Ensembl:ENSG00000066135 MIM:609764; AllianceGenome:HGNC:22978
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: JMJD2; JHDM3A; JMJD2A; TDRD14A
Summary: This gene is a member of the Jumonji domain 2 (JMJD2) family and encodes a protein containing a JmjN domain, a JmjC domain, a JD2H domain, two TUDOR domains, and two PHD-type zinc fingers. This nuclear protein functions as a trimethylation-specific demethylase, converting specific trimethylated histone residues to the dimethylated form, and as a transcriptional repressor. [provided by RefSeq, Apr 2009]
Expression: Ubiquitous expression in duodenum (RPKM 11.5), thyroid (RPKM 10.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p34.2-p34.1

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (43650149..43705518)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (43520658..43576010)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (44115820..44171189)

Chromosome 1 - NC_000001.11 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
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?

The role of KDM4A-mediated histone methylation on temozolomide resistance in glioma cells through the HUWE1/ROCK2 axis.
Title: The role of KDM4A-mediated histone methylation on temozolomide resistance in glioma cells through the HUWE1/ROCK2 axis.
SET7/9-mediated methylation affects oncogenic functions of histone demethylase JMJD2A.
Title: SET7/9-mediated methylation affects oncogenic functions of histone demethylase JMJD2A.
Carcinogenesis promotion in oral squamous cell carcinoma: KDM4A complex-mediated gene transcriptional suppression by LEF1.
Title: Carcinogenesis promotion in oral squamous cell carcinoma: KDM4A complex-mediated gene transcriptional suppression by LEF1.
JMJD2A participates in cytoskeletal remodeling to regulate castration-resistant prostate cancer docetaxel resistance.
Title: JMJD2A participates in cytoskeletal remodeling to regulate castration-resistant prostate cancer docetaxel resistance.
SUMO Modification of Histone Demethylase KDM4A in Kaposi's Sarcoma-Associated Herpesvirus-Induced Primary Effusion Lymphoma.
Title: SUMO Modification of Histone Demethylase KDM4A in Kaposi's Sarcoma-Associated Herpesvirus-Induced Primary Effusion Lymphoma.
Investigation of the Mechanism of hsa_circ_000 1429 Adsorbed miR-205 to Regulate KDM4A and Promote Breast Cancer Metastasis.
Title: Investigation of the Mechanism of hsa_circ_000 1429 Adsorbed miR-205 to Regulate KDM4A and Promote Breast Cancer Metastasis.
Histone demethylase KDM4A plays an oncogenic role in nasopharyngeal carcinoma by promoting cell migration and invasion.
Title: Histone demethylase KDM4A plays an oncogenic role in nasopharyngeal carcinoma by promoting cell migration and invasion.
Mechanistic insights into KDM4A driven genomic instability.
Title: Mechanistic insights into KDM4A driven genomic instability.
Essential role of the histone lysine demethylase KDM4A in the biology of malignant pleural mesothelioma (MPM).
Title: Essential role of the histone lysine demethylase KDM4A in the biology of malignant pleural mesothelioma (MPM).
Histone demethylase KDM4A overexpression improved the efficiency of corrected human tripronuclear zygote development.
Title: Histone demethylase KDM4A overexpression improved the efficiency of corrected human tripronuclear zygote development.

Submit: New GeneRIF Correction See all GeneRIFs (82)

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

EBI GWAS Catalog

Description
Age of onset of amyotrophic lateral sclerosis is modulated by a locus on 1p34.1. EBI GWAS Catalog EBI GWAS CatalogPubMed
Biological insights from 108 schizophrenia-associated genetic loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic association of short sleep duration with hypertension incidence--a 6-year follow-up in the Korean genome and epidemiology study. EBI GWAS Catalog EBI GWAS CatalogPubMed
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

SGC34395 (e-PCR)
- UniSTS:16664

RH79804 (e-PCR)
- UniSTS:92013

RH123656 (e-PCR)
- UniSTS:136078

RH35886 (e-PCR)
- UniSTS:56722

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables histone H3K36 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K36 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K36me2/H3K36me3 demethylase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K9 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K9me2/H3K9me3 demethylase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables histone demethylase activity	TAS Traceable Author Statement more info
enables methylated histone binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in apoptotic chromosome condensation	IEA Inferred from Electronic Annotation more info
involved_in cardiac muscle hypertrophy in response to stress	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of astrocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of autophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of neuron differentiation	IEA Inferred from Electronic Annotation more info
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to nutrient levels	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in fibrillar center	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
part_of pericentric heterochromatin	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: lysine-specific demethylase 4A

Names: [histone H3]-trimethyl-L-lysine(36) demethylase 4A; [histone H3]-trimethyl-L-lysine(9) demethylase 4A; jmjC domain-containing histone demethylation protein 3A; jumonji C domain-containing histone demethylase 3A; jumonji domain containing 2; jumonji domain containing 2A; jumonji domain-containing protein 2A; lysine (K)-specific demethylase 4A; tudor domain containing 14A

NP_055478.2

EC 1.14.11.66

EC 1.14.11.69

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_014663.3 → NP_055478.2 lysine-specific demethylase 4A

See identical proteins and their annotated locations for NP_055478.2

Status: REVIEWED

Source sequence(s)

AB014577, BP198064, CA944984, CN361683

Consensus CDS

CCDS491.1

UniProtKB/Swiss-Prot

O75164, Q5VVB1

Related

ENSP00000361473.3, ENST00000372396.4

Conserved Domains (5) summary

smart00545
Location:13 → 55

JmjN; Small domain found in the jumonji family of transcription factors

smart00333
Location:955 → 1010

TUDOR; Tudor domain

pfam02373
Location:175 → 291

JmjC; JmjC domain, hydroxylase

cd15575
Location:667 → 766

PHD_JMJD2A; PHD finger found in Jumonji domain-containing protein 2A (JMJD2A)

cd15713
Location:775 → 884

ePHD_JMJD2A; Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A)