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Aliases for KDM4A Gene

Aliases for KDM4A Gene

  • Lysine Demethylase 4A 2 3 5
  • JmjC Domain-Containing Histone Demethylation Protein 3A 3 4
  • Jumonji C Domain-Containing Histone Demethylase 3A 2 3
  • Jumonji Domain-Containing Protein 2A 3 4
  • Lysine (K)-Specific Demethylase 4A 2 3
  • Jumonji Domain Containing 2A 2 3
  • Jumonji Domain Containing 2 2 3
  • Tudor Domain Containing 14A 2 3
  • JMJD2A 3 4
  • JHDM3A 3 4
  • JMJD2 3 4
  • Lysine-Specific Demethylase 4A 3
  • EC 1.14.11.- 4
  • KIAA0677 4
  • TDRD14A 3

External Ids for KDM4A Gene

Previous HGNC Symbols for KDM4A Gene

  • JMJD2
  • JMJD2A

Previous GeneCards Identifiers for KDM4A Gene

  • GC01P043889
  • GC01P044115
  • GC01P042237

Summaries for KDM4A Gene

Entrez Gene Summary for KDM4A Gene

  • 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]

GeneCards Summary for KDM4A Gene

KDM4A (Lysine Demethylase 4A) is a Protein Coding gene. Among its related pathways are Chromatin organization and DNA Double-Strand Break Repair. Gene Ontology (GO) annotations related to this gene include ubiquitin protein ligase binding and histone demethylase activity (H3-K36 specific). An important paralog of this gene is KDM4C.

UniProtKB/Swiss-Prot for KDM4A Gene

  • Histone demethylase that specifically demethylates Lys-9 and Lys-36 residues of histone H3, thereby playing a central role in histone code (PubMed:26741168). Does not demethylate histone H3 Lys-4, H3 Lys-27 nor H4 Lys-20. Demethylates trimethylated H3 Lys-9 and H3 Lys-36 residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. Participates in transcriptional repression of ASCL2 and E2F-responsive promoters via the recruitment of histone deacetylases and NCOR1, respectively.

  • Isoform 2: Crucial for muscle differentiation, promotes transcriptional activation of the Myog gene by directing the removal of repressive chromatin marks at its promoter. Lacks the N-terminal demethylase domain.

Gene Wiki entry for KDM4A Gene

Additional gene information for KDM4A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KDM4A Gene

Genomics for KDM4A Gene

GeneHancer (GH) Regulatory Elements for KDM4A Gene

Promoters and enhancers for KDM4A Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J043648 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 +0.2 249 4.6 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF213 ENSG00000284989 KDM4A DMAP1 MKRN8P SZT2 ZNF691 KDM4A-AS1 PPIH MED8 ATP6V0B
GH01J043706 Promoter 0.6 EPDnew 650.2 +55.2 55231 0.1 CTCF PIR59454 ST3GAL3 KDM4A KDM4A-AS1 GC01M043702 ENSG00000284989
GH01J044212 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE 22.7 +563.4 563356 2.3 MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 DMAP1 SZT2 KDM4A-AS1 HYI ARTN RPS8 MED8 HECTD3 PTCH2 KDM4A
GH01J043522 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 19.9 -126.1 -126092 3.4 HDGF PKNOX1 SMAD1 FOXA2 ARNT SIN3A YBX1 ZNF766 E2F8 FOS PTPRF SZT2 P3H1 MED8 KDM4A HYI PPIH ZNF691 KDM4A-AS1 DMAP1
GH01J042657 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 20.2 -991.8 -991762 2.4 HDGF PKNOX1 SMAD1 FOXA2 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 PPIH SZT2 P3H1 KDM4A MED8 SVBP ZNF691 HYI CCDC30 ENSG00000234917
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around KDM4A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the KDM4A gene promoter:
  • IRF-7A
  • C/EBPalpha
  • MAZR
  • Spz1
  • Hlf
  • STAT1beta
  • STAT1alpha
  • STAT1
  • AP-4
  • LCR-F1

Genomic Locations for KDM4A Gene

Genomic Locations for KDM4A Gene
chr1:43,650,126-43,705,518
(GRCh38/hg38)
Size:
55,393 bases
Orientation:
Plus strand
chr1:44,115,797-44,171,189
(GRCh37/hg19)
Size:
55,393 bases
Orientation:
Plus strand

Genomic View for KDM4A Gene

Genes around KDM4A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KDM4A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KDM4A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KDM4A Gene

Proteins for KDM4A Gene

  • Protein details for KDM4A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75164-KDM4A_HUMAN
    Recommended name:
    Lysine-specific demethylase 4A
    Protein Accession:
    O75164
    Secondary Accessions:
    • Q5VVB1

    Protein attributes for KDM4A Gene

    Size:
    1064 amino acids
    Molecular mass:
    120662 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Quaternary structure:
    • Interacts with histone deacetylase proteins HDAC1, HDAC2 and HDAC3. Interacts with RB and NCOR1.
    • (Microbial infection) Interacts with HTLV-1 Tax protein.
    SequenceCaution:
    • Sequence=BAA31652.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for KDM4A Gene

    Alternative splice isoforms for KDM4A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for KDM4A Gene

Post-translational modifications for KDM4A Gene

  • Ubiquitinated by RNF8 and RNF168 following DNA damage, leading to its degradation. Degradation promotes accessibility of H4K20me2 mark for DNA repair protein TP53BP1, which is then recruited.
  • Ubiquitination at isoforms=224
  • Modification sites at PhosphoSitePlus

Other Protein References for KDM4A Gene

Antibody Products

  • R&D Systems Antibodies for KDM4A (Lysine (K)-specific Demethylase 4A/KDM4A)

No data available for DME Specific Peptides for KDM4A Gene

Domains & Families for KDM4A Gene

Gene Families for KDM4A Gene

Graphical View of Domain Structure for InterPro Entry

O75164

UniProtKB/Swiss-Prot:

KDM4A_HUMAN :
  • The 2 Tudor domains recognize and bind methylated histone H3 Lys-4 residue (H3K4me). Double Tudor domain has an interdigitated structure and the unusual fold is required for its ability to bind methylated histone tails. Trimethylated H3 Lys-4 (H3K4me3) is bound in a cage of 3 aromatic residues, 2 of which are from the Tudor domain 2, while the binding specificity is determined by side-chain interactions involving residues from the Tudor domain 1. The Tudor domains are also able to bind trimethylated histone H3 Lys-9 (H3K9me3), di- and trimethylated H4 Lys-20 (H4K20me2 and H4K20me3). Has high affinity for H4K20me2, blocking recruitment of proteins such as TP53BP1.
  • Belongs to the JHDM3 histone demethylase family.
Domain:
  • The 2 Tudor domains recognize and bind methylated histone H3 Lys-4 residue (H3K4me). Double Tudor domain has an interdigitated structure and the unusual fold is required for its ability to bind methylated histone tails. Trimethylated H3 Lys-4 (H3K4me3) is bound in a cage of 3 aromatic residues, 2 of which are from the Tudor domain 2, while the binding specificity is determined by side-chain interactions involving residues from the Tudor domain 1. The Tudor domains are also able to bind trimethylated histone H3 Lys-9 (H3K9me3), di- and trimethylated H4 Lys-20 (H4K20me2 and H4K20me3). Has high affinity for H4K20me2, blocking recruitment of proteins such as TP53BP1.
Family:
  • Belongs to the JHDM3 histone demethylase family.
genes like me logo Genes that share domains with KDM4A: view

Function for KDM4A Gene

Molecular function for KDM4A Gene

UniProtKB/Swiss-Prot Function:
Histone demethylase that specifically demethylates Lys-9 and Lys-36 residues of histone H3, thereby playing a central role in histone code (PubMed:26741168). Does not demethylate histone H3 Lys-4, H3 Lys-27 nor H4 Lys-20. Demethylates trimethylated H3 Lys-9 and H3 Lys-36 residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. Participates in transcriptional repression of ASCL2 and E2F-responsive promoters via the recruitment of histone deacetylases and NCOR1, respectively.
UniProtKB/Swiss-Prot Function:
Isoform 2: Crucial for muscle differentiation, promotes transcriptional activation of the Myog gene by directing the removal of repressive chromatin marks at its promoter. Lacks the N-terminal demethylase domain.
UniProtKB/Swiss-Prot EnzymeRegulation:
Several specific inhibitors are being developed and tested.

Enzyme Numbers (IUBMB) for KDM4A Gene

Phenotypes From GWAS Catalog for KDM4A Gene

Gene Ontology (GO) - Molecular Function for KDM4A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16415788
GO:0008270 zinc ion binding IDA 27214403
GO:0016491 oxidoreductase activity IEA --
GO:0031625 ubiquitin protein ligase binding IPI 22373579
GO:0032452 histone demethylase activity TAS --
genes like me logo Genes that share ontologies with KDM4A: view
genes like me logo Genes that share phenotypes with KDM4A: view

Animal Model Products

Clone Products

  • Addgene plasmids for KDM4A

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for KDM4A Gene

Localization for KDM4A Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM4A Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for KDM4A gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli fibrillar center (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for KDM4A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001650 fibrillar center IDA --
GO:0005634 nucleus IMP 21914792
GO:0005654 nucleoplasm TAS --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with KDM4A: view

Pathways & Interactions for KDM4A Gene

genes like me logo Genes that share pathways with KDM4A: view

Pathways by source for KDM4A Gene

1 GeneTex pathway for KDM4A Gene
1 BioSystems pathway for KDM4A Gene

Gene Ontology (GO) - Biological Process for KDM4A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0010507 negative regulation of autophagy IMP 25660547
GO:0010629 negative regulation of gene expression IMP 25660547
genes like me logo Genes that share ontologies with KDM4A: view

No data available for SIGNOR curated interactions for KDM4A Gene

Drugs & Compounds for KDM4A Gene

(6) Drugs for KDM4A Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
IOX 1 Pharma Histone demethylase inhibitor; cell permeable 0
JIB-04 Pharma Jumonji histone demethylase inihibitor 0
ML324 Pharma JMJD2 demethylase inhibitor, potent and cell-permeable 0
SP2509 Pharma Demethylase 1 (LSD1) antagonist, novel Lysine-specific 0
Tranylcypromine hydrochloride Pharma Irreversible inhibitor of LSD1; also inhibits MAO 0
genes like me logo Genes that share compounds with KDM4A: view

Transcripts for KDM4A Gene

mRNA/cDNA for KDM4A Gene

Unigene Clusters for KDM4A Gene

Lysine (K)-specific demethylase 4A:
Representative Sequences:

Clone Products

  • Addgene plasmids for KDM4A

Alternative Splicing Database (ASD) splice patterns (SP) for KDM4A Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18a · 18b ^ 19 ^ 20 ^ 21 ^
SP1: - - - - - -
SP2: -
SP3:
SP4: - -
SP5: -
SP6:
SP7:
SP8:

ExUns: 22a · 22b ^ 23a · 23b · 23c ^ 24a · 24b
SP1: - - -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7: -
SP8: -

Relevant External Links for KDM4A Gene

GeneLoc Exon Structure for
KDM4A
ECgene alternative splicing isoforms for
KDM4A

Expression for KDM4A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for KDM4A Gene

Protein differential expression in normal tissues from HIPED for KDM4A Gene

This gene is overexpressed in Peripheral blood mononuclear cells (52.0) and Blymphocyte (10.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for KDM4A Gene



Protein tissue co-expression partners for KDM4A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of KDM4A Gene:

KDM4A

SOURCE GeneReport for Unigene cluster for KDM4A Gene:

Hs.155983

mRNA Expression by UniProt/SwissProt for KDM4A Gene:

O75164-KDM4A_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for KDM4A Gene

  • Nervous system(4.5)
  • Liver(2.8)
  • Intestine(2.1)
genes like me logo Genes that share expression patterns with KDM4A: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for KDM4A Gene

Orthologs for KDM4A Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for KDM4A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia KDM4A 34 33
  • 96.69 (n)
OneToOne
dog
(Canis familiaris)
Mammalia KDM4A 34 33
  • 91.94 (n)
OneToOne
cow
(Bos Taurus)
Mammalia KDM4A 34 33
  • 89.81 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Kdm4a 33
  • 86.99 (n)
mouse
(Mus musculus)
Mammalia Kdm4a 16 34 33
  • 86.89 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia KDM4A 34
  • 83 (a)
OneToOne
chicken
(Gallus gallus)
Aves KDM4A 34 33
  • 74.13 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia KDM4A 34
  • 79 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia kdm4a 33
  • 69.95 (n)
zebrafish
(Danio rerio)
Actinopterygii si:ch211-215f22.3 33
  • 70.03 (n)
kdm4ab 34
  • 59 (a)
OneToMany
KDM4A (1 of 2) 34
  • 32 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Kdm4A 34
  • 48 (a)
ManyToMany
Kdm4B 34
  • 39 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea jmjd-2 34 33
  • 50.25 (n)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RPH1 34
  • 24 (a)
ManyToMany
GIS1 34
  • 17 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10508 34
  • 39 (a)
OneToMany
Species where no ortholog for KDM4A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for KDM4A Gene

ENSEMBL:
Gene Tree for KDM4A (if available)
TreeFam:
Gene Tree for KDM4A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for KDM4A: view image

Paralogs for KDM4A Gene

Paralogs for KDM4A Gene

(5) SIMAP similar genes for KDM4A Gene using alignment to 2 proteins:

  • KDM4A_HUMAN
  • L8ECF0_HUMAN
genes like me logo Genes that share paralogs with KDM4A: view

Variants for KDM4A Gene

Sequence variations from dbSNP and Humsavar for KDM4A Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000045358 -- 43,678,663(+) C/G intron_variant
rs1000077562 -- 43,681,091(+) A/G intron_variant
rs1000082462 -- 43,699,794(+) A/C intron_variant
rs1000107486 -- 43,673,824(+) C/T intron_variant
rs1000190051 -- 43,693,619(+) G/A intron_variant

Variation tolerance for KDM4A Gene

Residual Variation Intolerance Score: 28.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.53; 44.13% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for KDM4A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
KDM4A

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for KDM4A Gene

Disorders for KDM4A Gene

Additional Disease Information for KDM4A

No disorders were found for KDM4A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for KDM4A Gene

Publications for KDM4A Gene

  1. Structural insights into histone demethylation by JMJD2 family members. (PMID: 16677698) Chen Z … Zhang G (Cell 2006) 3 4 22 58
  2. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. (PMID: 16603238) Whetstine JR … Shi Y (Cell 2006) 3 4 22 58
  3. Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A. (PMID: 16601153) Huang Y … Xu RM (Science (New York, N.Y.) 2006) 3 4 22 58
  4. JMJD2A is a novel N-CoR-interacting protein and is involved in repression of the human transcription factor achaete scute-like homologue 2 (ASCL2/Hash2). (PMID: 16024779) Zhang D … Wong J (Molecular and cellular biology 2005) 3 4 22 58
  5. Functional characterization of JMJD2A, a histone deacetylase- and retinoblastoma-binding protein. (PMID: 15927959) Gray SG … Dangond F (The Journal of biological chemistry 2005) 3 4 22 58

Products for KDM4A Gene

Sources for KDM4A Gene

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