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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
  • Tudor Domain Containing 14A 2 3
  • Jumonji Domain Containing 2 2 3
  • JMJD2A 3 4
  • JHDM3A 3 4
  • JMJD2 3 4
  • Lysine-Specific Demethylase 4A 3
  • EC 1.14.11.- 4
  • EC 1.14.11 56
  • 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 DNA Double-Strand Break Repair and DNA Double Strand Break Response. 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
GH01I043648 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.8 +0.2 249 4.6 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF213 KDM4A DMAP1 SZT2 ZNF691 KDM4A-AS1 PPIH MED8 ATP6V0B ARTN HYI
GH01I044212 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 HYI KDM4A-AS1 ARTN LOC101929609 RPS8 HECTD3 PTCH2 KDM4A
GH01I042657 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
GH01I044628 Promoter/Enhancer 1.8 Ensembl ENCODE dbSUPER 23.3 +981.4 981353 6.6 HDGF PKNOX1 SMAD1 MLX ARNT ARID4B SIN3A DMAP1 YY1 POLR2B PIR47647 TOE1 DMAP1 KDM4A C1orf228 HECTD3 RPS8 MUTYH CCDC17 ARTN
GH01I043705 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 19.3 +57.5 57469 3.8 HDGF FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 KDM4A-AS1 ST3GAL3 SZT2 DMAP1 P3H1 KDM4A HYI MED8 ARTN ZNF691
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around KDM4A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the KDM4A gene promoter:

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)

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. 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

Selected DME Specific Peptides for KDM4A Gene

O75164:
  • RWIEYGK
  • EDMDLYSIN
  • VTGQSGLFTQYNIQKKAMTV
  • YTLDEELPKRVK
  • IEGVNTPYLYFGMWKT
  • PPEHGKRLERLA
  • LERKYWKN
  • VHASCYG
  • YSINYLH
  • AESTNFA
  • LRHKMTLISP
  • DMVKISM
  • AYIESQGAHRAGLAK

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

Other Protein References for KDM4A Gene

Antibody Products

  • R&D Systems Antibodies for KDM4A (Lysine (K)-specific Demethylase 4A/KDM4A)
  • Cell Signaling Technology (CST) Antibodies for KDM4A (JMJD2A)

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 EnzymeRegulation:
Several specific inhibitors are being developed and tested.
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.

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 IEA,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:0005721 pericentric heterochromatin IEA --
GO:0005737 cytoplasm IEA --
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 Cell Signaling Technology pathway for KDM4A Gene

Gene Ontology (GO) - Biological Process for KDM4A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0010507 negative regulation of autophagy IMP 25660547
GO:0010628 positive regulation of gene expression IEA --
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: ApexBio and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
IOX 1 Pharma 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 0

(5) ApexBio Compounds for KDM4A Gene

Compound Action Cas Number
IOX 1 5852-78-8
JIB-04 Jumonji histone demethylase inihibitor 199596-05-9
ML324 JMJD2 demethylase inhibitor, potent and cell-permeable 1222800-79-4
SP2509 Demethylase 1 (LSD1) antagonist, novel Lysine-specific 1423715-09-6
Tranylcypromine hydrochloride 1986-47-6
genes like me logo Genes that share compounds with KDM4A: view

Drug Products

Transcripts 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, PaxDb, 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(2.2)
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 33 34
  • 96.69 (n)
dog
(Canis familiaris)
Mammalia KDM4A 33 34
  • 91.94 (n)
cow
(Bos Taurus)
Mammalia KDM4A 33 34
  • 89.81 (n)
rat
(Rattus norvegicus)
Mammalia Kdm4a 33
  • 86.99 (n)
mouse
(Mus musculus)
Mammalia Kdm4a 33 16 34
  • 86.89 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia KDM4A 34
  • 83 (a)
OneToOne
chicken
(Gallus gallus)
Aves KDM4A 33 34
  • 74.13 (n)
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 33 34
  • 50.25 (n)
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)

Paralogs for KDM4A Gene

Paralogs for KDM4A Gene

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

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

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. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. (PMID: 16603238) Whetstine JR … Shi Y (Cell 2006) 3 4 22 58
  2. 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
  3. Structural insights into histone demethylation by JMJD2 family members. (PMID: 16677698) Chen Z … Zhang G (Cell 2006) 3 4 22 58
  4. 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
  5. 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

Products for KDM4A Gene

Sources for KDM4A Gene

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