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Aliases for KDM4D Gene

Aliases for KDM4D Gene

  • Lysine (K)-Specific Demethylase 4D 2 3
  • JMJD2D 3 4 6
  • JmjC Domain-Containing Histone Demethylation Protein 3D 3 4
  • Jumonji Domain-Containing Protein 2D 3 4
  • Jumonji Domain Containing 2D 2 3
  • Lysine-Specific Demethylase 4D 3
  • EC 1.14.11.- 4
  • EC 1.14.11 64
  • JHDM3D 4

External Ids for KDM4D Gene

Previous Symbols for KDM4D Gene

  • JMJD2D

Summaries for KDM4D Gene

GeneCards Summary for KDM4D Gene

KDM4D (Lysine (K)-Specific Demethylase 4D) is a Protein Coding gene. GO annotations related to this gene include dioxygenase activity. 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

Genomic Location for KDM4D Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for KDM4D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KDM4D Gene

Regulatory Elements 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; Note=Binds 1 Fe(2+) ion per subunit.;
    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 for KDM4D Gene

Gene Families for KDM4D Gene

HGNC:
  • KDM :Chromatin-modifying enzymes / K-demethylases

Protein Domains for KDM4D Gene

UniProtKB/Swiss-Prot:

KDM4D_HUMAN
Domain:
  • Contains 1 JmjC domain.:
    • Q6B0I6
  • Contains 1 JmjN domain.:
    • Q6B0I6
Family:
  • Belongs to the JHDM3 histone demethylase family.:
    • Q6B0I6
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:0032454 histone demethylase activity (H3-K9 specific) IDA 25124442
GO:0046872 metal ion binding IEA --
GO:0051213 dioxygenase activity IEA --
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:

miRNA for KDM4D Gene

miRTarBase miRNAs that target KDM4D

No data available for Transcription Factor Targeting 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
nucleus 3
cytosol 2

Gene Ontology (GO) - Cellular Components for KDM4D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus --
GO:0005654 nucleoplasm TAS --
GO:0072562 blood microparticle IDA 22516433
genes like me logo Genes that share ontologies with KDM4D: view

Pathways for KDM4D Gene

SuperPathways for KDM4D Gene

No Data Available

Gene Ontology (GO) - Biological Process for KDM4D Gene

GO ID Qualified GO term Evidence PubMed IDs
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
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with KDM4D: view

No data available for Pathways by source for KDM4D Gene

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 (25.9).

SOURCE GeneReport for Unigene cluster for KDM4D Gene Hs.503598

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

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 37
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia -- 37
  • 71 (a)
OneToMany
LOC524768 36
  • 80.59 (n)
  • 82.42 (a)
dog
(Canis familiaris)
Mammalia -- 37
  • 73 (a)
OneToMany
KDM4D 36
  • 78.27 (n)
  • 73.61 (a)
mouse
(Mus musculus)
Mammalia Kdm4d 36
  • 74.97 (n)
  • 72.31 (a)
Kdm4d 16
Kdm4d 37
  • 70 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 37
  • 62 (a)
ManyToMany
-- 37
  • 41 (a)
ManyToMany
rat
(Rattus norvegicus)
Mammalia LOC100909834 36
  • 74.17 (n)
  • 70.72 (a)
fruit fly
(Drosophila melanogaster)
Insecta Kdm4A 37
  • 39 (a)
ManyToMany
Kdm4B 37
  • 29 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GIS1 37
  • 13 (a)
ManyToMany
RPH1 37
  • 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

Paralogs for KDM4D Gene

Selected 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 MAF
rs906530 -- 94,978,574(-) CCCAG(C/T)CTGGA intron-variant
rs968193 -- 94,976,391(-) tttaa(A/C/G/T)agctt intron-variant
rs1054532 -- 94,999,243(+) TTAGC(A/G)TAACC utr-variant-3-prime
rs1385967 -- 94,991,836(+) ACTTC(A/G)TTTTT intron-variant
rs2063171 -- 94,984,310(-) GCCAT(G/T)TTGCC 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

Relevant External Links for KDM4D Gene

HapMap Linkage Disequilibrium report
KDM4D

Disorders for KDM4D Gene

Relevant External Links for KDM4D

Genetic Association Database (GAD)
KDM4D
Human Genome Epidemiology (HuGE) Navigator
KDM4D
genes like me logo Genes that share disorders with KDM4D: view

No data available for UniProtKB/Swiss-Prot 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
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  3. 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
  4. Human chromosome 11 DNA sequence and analysis including novel gene identification. (PMID: 16554811) Taylor T.D. … Sakaki Y. (Nature 2006) 3 4
  5. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. (PMID: 16603238) Whetstine J.R. … Shi Y. (Cell 2006) 3 4

Products for KDM4D Gene

Sources for KDM4D Gene

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