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Aliases for KDM4D Gene

Aliases for KDM4D Gene

  • Lysine Demethylase 4D 2 3 5
  • JmjC Domain-Containing Histone Demethylation Protein 3D 3 4
  • Jumonji Domain-Containing Protein 2D 3 4
  • Lysine (K)-Specific Demethylase 4D 2 3
  • Jumonji Domain Containing 2D 2 3
  • JMJD2D 3 4
  • Lysine-Specific Demethylase 4D 3
  • EC 1.14.11.- 4
  • EC 1.14.11 61
  • 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 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 and Chromatin organization. GO annotations related to this gene include dioxygenase activity and histone demethylase activity (H3-K9 specific). An important paralog of this gene is KDM4F.

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 , CIViC 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 Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11G095106 1.9 FANTOM5 Ensembl ENCODE dbSUPER 9.3 +134.3 134260 3.9 PKNOX1 ATF1 ARNT FEZF1 ZNF2 TCF12 GATA2 FOS JUNB REST LOC101929295 CWC15 KDM4D ENDOD1 GC11M095076 GC11P095138
GH11G095066 1.4 ENCODE dbSUPER 10.6 +94.2 94217 3.2 HDGF PKNOX1 FOXA2 CREB3L1 ARNT AGO1 WRNIP1 ARID4B SIN3A FEZF1 ENDOD1 SRSF8 LOC101929295 KDM4E KDM4D CWC15 GC11P095067
GH11G095095 1.3 Ensembl ENCODE dbSUPER 10 +122.6 122564 1.7 PKNOX1 MXI1 TBL1XR1 ZBTB40 ARID3A CBX5 EED FOS RELB ETV6 LOC101929295 ENDOD1 CWC15 KDM4D KDM4E GC11P095093 GC11M095076
GH11G095133 1.2 Ensembl ENCODE dbSUPER 10.4 +160.9 160852 2.9 ZMYM3 SIN3A RAD21 ZIC2 ZFHX2 ZNF316 POLR2A ZNF600 RELB PRDM10 ENDOD1 CWC15 KDM4D KDM4E SRSF8 LOC105369435 GC11P095138 GC11M095076
GH11G094948 1.1 Ensembl ENCODE 11.2 -25.1 -25091 1.0 BCOR ESRRA CBX3 ZMYM3 CEBPG ZKSCAN1 FOSL1 ZNF664 ZSCAN5C ADNP CWC15 ENSG00000256469 KDM4D LOC105369438 KDM4E GC11P094966
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around KDM4D on UCSC Golden Path with GeneCards custom track

Promoters for KDM4D Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000043544 -181 1801 PKNOX1 WRNIP1 ARID4B SIN3A DMAP1 FEZF1 YY1 ZNF766 ZNF416 ZNF143

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

Selected DME Specific Peptides for KDM4D Gene

Q6B0I6:
  • LERKYWKN
  • EDMDLYSIN
  • IEGVNTPYLYFGMWKT
  • GEPKTWY
  • YSINYLH

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 :
  • Belongs to the JHDM3 histone demethylase family.
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

Gene Ontology (GO) - Molecular Function for KDM4D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003684 damaged DNA binding IEA --
GO:0016491 oxidoreductase activity IEA --
GO:0031490 chromatin DNA binding IEA --
GO:0032452 histone demethylase activity TAS --
GO:0032454 histone demethylase activity (H3-K9 specific) IDA 21914792
genes like me logo Genes that share ontologies with KDM4D: view
genes like me logo Genes that share phenotypes with KDM4D: view

Animal Models for KDM4D Gene

MGI Knock Outs for KDM4D:

Animal Model Products

CRISPR Products

miRNA for KDM4D Gene

miRTarBase miRNAs that target KDM4D

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for KDM4D

Flow Cytometry Products

No data available for 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
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 KDM4D gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for KDM4D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005721 pericentric heterochromatin IEA --
GO:0035861 site of double-strand break IDA 24550317
GO:0072562 blood microparticle IDA 22516433
genes like me logo Genes that share ontologies with KDM4D: view

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:0001932 regulation of protein phosphorylation IMP 24550317
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006974 cellular response to DNA damage stimulus IEA --
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, Pan Jumonji inhibitor; active in vivo 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:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for KDM4D

Flow Cytometry Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE for KDM4D Gene

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

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

NURSA nuclear receptor signaling pathways regulating expression of KDM4D Gene:

KDM4D

SOURCE GeneReport for Unigene cluster for KDM4D Gene:

Hs.503598

Evidence on tissue expression from TISSUES for KDM4D Gene

  • Nervous system(4.1)
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 , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia KDM4D 35
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LOC524768 34
  • 80.59 (n)
-- 35
  • 71 (a)
OneToMany
dog
(Canis familiaris)
Mammalia KDM4D 34
  • 78.27 (n)
-- 35
  • 73 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Kdm4d 34 16 35
  • 74.97 (n)
rat
(Rattus norvegicus)
Mammalia LOC100909834 34
  • 74.17 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 62 (a)
ManyToMany
-- 35
  • 41 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta Kdm4A 35
  • 39 (a)
ManyToMany
Kdm4B 35
  • 29 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RPH1 35
  • 19 (a)
ManyToMany
GIS1 35
  • 13 (a)
ManyToMany
Species where no ortholog for KDM4D 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)
  • 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

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
rs1000166412 -- 94,981,747(+) TTCAC(C/T)AGTCT intron-variant
rs1000201931 -- 94,972,040(+) AAAAA(A/G)GAAAG intron-variant, upstream-variant-2KB
rs1000341126 -- 94,979,039(+) AGTTA(C/T)ATGTG intron-variant
rs1000548414 -- 94,985,747(+) AGAAT(C/T)GAAAG intron-variant
rs1000714570 -- 94,993,024(+) ATACA(C/T)ATGCA intron-variant

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

Variant ID Type Subtype PubMed ID
nsv446 CNV deletion 18451855
nsv518887 CNV gain 19592680
nsv975972 CNV duplication 23825009

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)

Relevant External Links for KDM4D Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
KDM4D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot 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 22 64
  2. Human chromosome 11 DNA sequence and analysis including novel gene identification. (PMID: 16554811) Taylor T.D. … Sakaki Y. (Nature 2006) 3 4 64
  3. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. (PMID: 16603238) Whetstine J.R. … Shi Y. (Cell 2006) 3 4 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for KDM4D Gene

Sources for KDM4D Gene

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