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Aliases for KDM4D Gene

Aliases for KDM4D Gene

  • Lysine Demethylase 4D 2 3
  • Lysine (K)-Specific Demethylase 4D 2 3 5
  • JmjC Domain-Containing Histone Demethylation Protein 3D 3 4
  • Jumonji Domain-Containing Protein 2D 3 4
  • Jumonji Domain Containing 2D 2 3
  • JMJD2D 3 4
  • EC 1.14.11.- 4
  • EC 1.14.11 63
  • JHDM3D 4

External Ids for KDM4D Gene

Previous HGNC Symbols for KDM4D Gene

  • JMJD2D

Previous GeneCards Identifiers for KDM4D Gene

  • GC11P094347
  • GC11P094706
  • GC11P090771

Summaries for KDM4D Gene

GeneCards Summary for KDM4D Gene

KDM4D (Lysine Demethylase 4D) is a Protein Coding gene. Among its related pathways are Chromatin organization and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. GO annotations related to this gene include dioxygenase activity and histone demethylase activity (H3-K9 specific). An important paralog of this gene is KDM4B.

UniProtKB/Swiss-Prot for KDM4D Gene

  • Histone demethylase that specifically demethylates Lys-9 of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 Lys-4, H3 Lys-27, H3 Lys-36 nor H4 Lys-20. Demethylates both di- and trimethylated H3 Lys-9 residue, while it has no activity on monomethylated residues. Demethylation of Lys residue generates formaldehyde and succinate.

Gene Wiki entry for KDM4D Gene

No data available for Entrez Gene Summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KDM4D Gene

Genomics for KDM4D Gene

Regulatory Elements for KDM4D Gene

Enhancers for KDM4D Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around KDM4D on UCSC Golden Path with GeneCards custom track

Genomic Location for KDM4D Gene

Chromosome:
11
Start:
94,973,681 bp from pter
End:
94,999,518 bp from pter
Size:
25,838 bases
Orientation:
Plus strand

Genomic View for KDM4D Gene

Genes around KDM4D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KDM4D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KDM4D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KDM4D Gene

Proteins for KDM4D Gene

  • Protein details for KDM4D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6B0I6-KDM4D_HUMAN
    Recommended name:
    Lysine-specific demethylase 4D
    Protein Accession:
    Q6B0I6
    Secondary Accessions:
    • B3KPC4
    • Q0VF39
    • Q9NT41
    • Q9NW76

    Protein attributes for KDM4D Gene

    Size:
    523 amino acids
    Molecular mass:
    58603 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA91508.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for KDM4D Gene

neXtProt entry for KDM4D Gene

Proteomics data for KDM4D Gene at MOPED

Selected DME Specific Peptides for KDM4D Gene

Post-translational modifications for KDM4D Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for KDM4D Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for KDM4D Gene

Gene Families for KDM4D Gene

Protein Domains for KDM4D Gene

Suggested Antigen Peptide Sequences for KDM4D Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q6B0I6

UniProtKB/Swiss-Prot:

KDM4D_HUMAN :
  • Contains 1 JmjC domain.
  • Belongs to the JHDM3 histone demethylase family.
Domain:
  • Contains 1 JmjC domain.
  • Contains 1 JmjN domain.
Family:
  • Belongs to the JHDM3 histone demethylase family.
genes like me logo Genes that share domains with KDM4D: view

Function for KDM4D Gene

Molecular function for KDM4D Gene

UniProtKB/Swiss-Prot Function:
Histone demethylase that specifically demethylates Lys-9 of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 Lys-4, H3 Lys-27, H3 Lys-36 nor H4 Lys-20. Demethylates both di- and trimethylated H3 Lys-9 residue, while it has no activity on monomethylated residues. Demethylation of Lys residue generates formaldehyde and succinate.

Enzyme Numbers (IUBMB) for KDM4D Gene

genes like me logo Genes that share phenotypes with KDM4D: view

Animal Models for KDM4D Gene

MGI Knock Outs for KDM4D:

Animal Model Products

miRNA for KDM4D Gene

miRTarBase miRNAs that target KDM4D

No data available for Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for KDM4D Gene

Localization for KDM4D Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM4D Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for KDM4D Gene COMPARTMENTS Subcellular localization image for KDM4D gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 2

No data available for Gene Ontology (GO) - Cellular Components for KDM4D Gene

Pathways & Interactions for KDM4D Gene

genes like me logo Genes that share pathways with KDM4D: view

Pathways by source for KDM4D Gene

1 GeneTex pathway for KDM4D Gene

Gene Ontology (GO) - Biological Process for KDM4D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000724 double-strand break repair via homologous recombination IMP 24550317
GO:0006325 chromatin organization TAS --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0033169 histone H3-K9 demethylation IDA 25124442
genes like me logo Genes that share ontologies with KDM4D: view

No data available for SIGNOR curated interactions for KDM4D Gene

Drugs & Compounds for KDM4D Gene

(1) Drugs for KDM4D Gene - From: ApexBio

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
JIB-04 Pharma Jumonji histone demethylase inihibitor 0

(1) ApexBio Compounds for KDM4D Gene

Compound Action Cas Number
JIB-04 Jumonji histone demethylase inihibitor 199596-05-9
genes like me logo Genes that share compounds with KDM4D: view

Transcripts for KDM4D Gene

mRNA/cDNA for KDM4D Gene

Unigene Clusters for KDM4D Gene

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

Alternative Splicing Database (ASD) splice patterns (SP) for KDM4D Gene

No ASD Table

Relevant External Links for KDM4D Gene

GeneLoc Exon Structure for
KDM4D
ECgene alternative splicing isoforms for
KDM4D

Expression for KDM4D Gene

mRNA expression in normal human tissues for KDM4D Gene

mRNA differential expression in normal tissues according to GTEx for KDM4D Gene

This gene is overexpressed in Testis (x25.9).

SOURCE GeneReport for Unigene cluster for KDM4D Gene Hs.503598

genes like me logo Genes that share expression patterns with KDM4D: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners for KDM4D Gene

Orthologs for KDM4D Gene

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

Orthologs for KDM4D Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia LOC524768 35
  • 80.59 (n)
  • 82.42 (a)
-- 36
  • 71 (a)
OneToMany
dog
(Canis familiaris)
Mammalia KDM4D 35
  • 78.27 (n)
  • 73.61 (a)
-- 36
  • 73 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Kdm4d 35
  • 74.97 (n)
  • 72.31 (a)
Kdm4d 16
Kdm4d 36
  • 70 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia LOC100909834 35
  • 74.17 (n)
  • 70.72 (a)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 62 (a)
ManyToMany
-- 36
  • 41 (a)
ManyToMany
chimpanzee
(Pan troglodytes)
Mammalia KDM4D 36
  • 99 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Kdm4A 36
  • 39 (a)
ManyToMany
Kdm4B 36
  • 29 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GIS1 36
  • 13 (a)
ManyToMany
RPH1 36
  • 19 (a)
ManyToMany
Species with no ortholog for KDM4D:
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • lizard (Anolis carolinensis)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for KDM4D Gene

ENSEMBL:
Gene Tree for KDM4D (if available)
TreeFam:
Gene Tree for KDM4D (if available)

Paralogs for KDM4D Gene

(5) SIMAP similar genes for KDM4D Gene using alignment to 1 proteins:

Pseudogenes.org Pseudogenes for KDM4D Gene

genes like me logo Genes that share paralogs with KDM4D: view

Variants for KDM4D Gene

Sequence variations from dbSNP and Humsavar for KDM4D Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs3740853 - 94,998,595(+) ACGCC(A/G/T)ATCTG reference, missense
rs35631512 - 94,998,437(+) GCCAG(C/G)CAAGA reference, missense
rs34366036 - 94,998,783(+) CTCCA(G/T)CCAAG reference, missense
rs906530 -- 94,978,574(-) CCCAG(C/T)CTGGA intron-variant
rs968193 -- 94,976,391(-) tttaa(A/G)agctt intron-variant

Structural Variations from Database of Genomic Variants (DGV) for KDM4D Gene

Variant ID Type Subtype PubMed ID
nsv446 CNV Loss 18451855
nsv518887 CNV Gain 19592680

Variation tolerance for KDM4D Gene

Residual Variation Intolerance Score: 41.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.74; 57.68% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for KDM4D Gene

Disorders for KDM4D Gene

Relevant External Links for KDM4D

Genetic Association Database (GAD)
KDM4D
Human Genome Epidemiology (HuGE) Navigator
KDM4D
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
KDM4D

No disorders were found for KDM4D Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for KDM4D Gene

Publications for KDM4D Gene

  1. Identification and characterization of JMJD2 family genes in silico. (PMID: 15138608) Katoh M. … Katoh M. (Int. J. Oncol. 2004) 2 3 4 23 67
  2. The emerging role of lysine demethylases in DNA damage response: dissecting the recruitment mode of KDM4D/JMJD2D to DNA damage sites. (PMID: 25714495) Khoury-Haddad H. … Ayoub N. (Cell Cycle 2015) 3
  3. PARP1-dependent recruitment of KDM4D histone demethylase to DNA damage sites promotes double-strand break repair. (PMID: 24550317) Khoury-Haddad H. … Ayoub N. (Proc. Natl. Acad. Sci. U.S.A. 2014) 3
  4. Transdifferentiation. Sequential histone-modifying activities determine the robustness of transdifferentiation. (PMID: 25124442) Zuryn S. … Jarriault S. (Science 2014) 3
  5. Structural and functional analysis of JMJD2D reveals molecular basis for site-specific demethylation among JMJD2 demethylases. (PMID: 23219879) Krishnan S. … Trievel R.C. (Structure 2013) 3

Products for KDM4D Gene

Sources for KDM4D Gene

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