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Tchem
KDM4A
Lysine-specific demethylase 4A

Protein Summary
Description
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. 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 func ...more
Uniprot Accession IDs
Gene Name
Ensembl ID
  • ENST00000372396
  • ENSP00000361473
  • ENSG00000066135

Symbol
  • JHDM3A
  • JMJD2
  • JMJD2A
  • KIAA0677
  • JMJD2
  • JHDM3A
  • JMJD2A
  • TDRD14A
Illumination Graph
Knowledge Table
Most Knowledge About
Knowledge Value (0 to 1 scale)
protein domain
0.85
cell type or tissue
0.78
transcription factor binding site profile
0.76
biological process
0.75
molecular function
0.73


Related Tools
Target Illumination GWAS Analytics (TIGA)
TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.
GENEVA
GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.
GlyGen
GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.
ARCHS4
ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.
IDG Development Level Summary
Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 170.58   (req: < 5)
Gene RIFs: 55   (req: <= 3)
Antibodies: 387   (req: <= 50)
Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 170.58   (req: >= 5)
Gene RIFs: 55   (req: > 3)
Antibodies: 387   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 23
Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligands: 49
Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0
Active Ligands (49)
1 – 10 of 49
CHEMBL316034
chemical structure image
CHEMBL3774692
chemical structure image
CHEMBL3769724
chemical structure image
CHEMBL3771198,CHEMBL3771180
chemical structure image
CHEMBL3770740
chemical structure image
CHEMBL3775889
chemical structure image
CHEMBL3775237
chemical structure image
CHEMBL3774747
chemical structure image
CHEMBL3775933
chemical structure image
CHEMBL3774922
chemical structure image
GWAS Traits (4)
GWAS Trait
EFO ID
Study Count
SNP Count
Beta Count
Odds Ratio
Evidence (Mean Rank Score)
Provenance
mathematical ability
4
2
4
98.8
self reported educational attainment
1
1
1
94.5
age at menarche
1
1
1
36.8
household income
1
1
1
19.1
GWAS Trait
EFO ID
Beta Count
Odds Ratio
Evidence (Mean Rank Score)
Provenance
mathematical ability
4
98.8
self reported educational attainment
1
94.5
age at menarche
1
36.8
household income
1
19.1
Orthologs (11)
1 – 5 of 11
Species
Name
Source ID
Gene ID
OMA
EggNOG
Inparanoid
Chimp
lysine demethylase 4A
VGNC:8061
456829
Macaque
lysine demethylase 4A
701272
Mouse
MGI:2446210
230674
Rat
RGD:1306378
313539
Dog
lysine demethylase 4A
VGNC:42324
482530
Species
Name
OMA
EggNOG
Inparanoid
Chimp
lysine demethylase 4A
Macaque
lysine demethylase 4A
Mouse
Rat
Dog
lysine demethylase 4A
Protein Structure (68 Structures, 1 AlphaFold Model)
RepresentationColor Scheme

Click on a row in the table to change the structure displayed.
More information can be found at RCSB PDB

AF-O75164-F1-model_v1

AlphaFold Structures Developed by DeepMind and EMBL-EBI

1 – 5 of 68
PDB Structure Id
Ligand
Method
Resolution (Å)
Residues
Fraction of Total Protein
Pub Year
Title
PDB Structure Id
Fraction of Total Protein
Resolution
Pub Year
Pathways (8)
Chromatin modifying enzymes (R-HSA-3247509)

Click on a row in the table to change the structure displayed.

Items per page:
1 – 5 of 7
Data Source
Name
Explore in Pharos
Explore in Source
Reactome
Chromatin modifying enzymes
Reactome
Chromatin organization
Reactome
DNA Double Strand Break Response
Reactome
DNA Double-Strand Break Repair
Reactome
DNA Repair
Name
Explore in Pharos
Explore in Source
Chromatin modifying enzymes
Chromatin organization
DNA Double Strand Break Response
DNA Double-Strand Break Repair
DNA Repair
Gene Ontology Terms (29)
Items per page:
10
1 – 9 of 9
GO Term
Evidence
Assigned by
Inferred from Direct Assay (IDA)
UniProtKB
Inferred from Direct Assay (IDA)
UniProtKB
Inferred from Direct Assay (IDA)
UniProtKB
Inferred from Physical Interaction (IPI)
UniProtKB
Inferred from Mutant Phenotype (IMP)
UniProtKB
Inferred from Biological aspect of Ancestor (IBA)
GO_Central
Inferred from Biological aspect of Ancestor (IBA)
GO_Central
Inferred from Biological aspect of Ancestor (IBA)
GO_Central
Inferred from Biological aspect of Ancestor (IBA)
GO_Central
Protein-Protein Interactions (163)
1 – 10 of 163
ZNF414
Tdark
Novelty: 1.29024829
p_int: 0.999999501
p_ni: 4.95e-7
p_wrong: 4e-9
Score: 0.58
Data Source: BioPlex,STRINGDB
CCL19
Tbio
Novelty: 0.00169711
p_int: 0.999999406
p_ni: 5.77e-7
p_wrong: 1.7e-8
Data Source: BioPlex
CCL22
Tbio
Novelty: 0.00245992
p_int: 0.99999937
p_ni: 3.2e-8
p_wrong: 5.97e-7
Score: 0.169
Data Source: BioPlex,STRINGDB
STK11
Tchem
Family: Kinase
Novelty: 0.00073247
p_int: 0.999998658
p_ni: 0.000001342
p_wrong: 1e-9
Score: 0.246
Data Source: BioPlex,STRINGDB
KDM4B
Tchem
Family: Epigenetic
Novelty: 0.01615072
p_int: 0.999896731
p_ni: 1.1e-8
p_wrong: 0.000103259
Score: 0.968
Data Source: BioPlex,STRINGDB
AFAP1L1
Tbio
Novelty: 0.2636613
p_int: 0.999406597
p_ni: 0.000252683
p_wrong: 0.00034072
Data Source: BioPlex
ABHD5
Tbio
Family: Enzyme
Novelty: 0.00806614
p_int: 0.757873857
p_ni: 0.000169951
p_wrong: 0.241956192
Score: 0.232
Data Source: BioPlex,STRINGDB
HIST3H3
Tbio
Novelty: 0.04915012
Score: 0.992
Data Source: Reactome,STRINGDB
RNF8
Tbio
Family: Enzyme
Novelty: 0.01189548
Score: 0.967
Data Source: Reactome,STRINGDB
RNF168
Tbio
Family: Enzyme
Novelty: 0.01827754
Score: 0.967
Data Source: Reactome,STRINGDB
Publication Statistics
PubMed Score  170.58

PubMed score by year
PubTator Score  105.69

PubTator score by year
Amino Acid Sequence
Residue Counts
Protein Sequence
ProtVista Viewer
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