Aliases for KDM4D Gene

Aliases for KDM4D Gene

  • Lysine Demethylase 4D 2 3 5
  • JmjC Domain-Containing Histone Demethylation Protein 3D 3 4
  • [Histone H3]-Trimethyl-L-Lysine(9) Demethylase 4D 3 4
  • Jumonji Domain-Containing Protein 2D 3 4
  • Lysine (K)-Specific Demethylase 4D 2 3
  • Lysine-Specific Demethylase 4D 3 4
  • Jumonji Domain Containing 2D 2 3
  • JMJD2D 3 4
  • EC 1.14.11'); 51
  • EC 1.14.11.66 4
  • EC 1.14.11 51
  • FLJ10251 2
  • JHDM3D 4
  • KDM4D 5

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. Diseases associated with KDM4D include Osteogenesis Imperfecta, Type Xvi and Patulous Eustachian Tube. Among its related pathways are Chromatin organization and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. Gene Ontology (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 Summary 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 , Rfam classification and piRNA Summary for KDM4D Gene

Genomics for KDM4D Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for KDM4D Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around KDM4D on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for KDM4D

Top Transcription factor binding sites by QIAGEN in the KDM4D gene promoter:
  • AP-1
  • ATF-2
  • c-Jun
  • En-1
  • Nkx2-2
  • Nkx2-5
  • POU6F1 (c2)
  • RREB-1
  • S8
  • Sp1

Genomic Locations for KDM4D Gene

Genomic Locations for KDM4D Gene
chr11:94,973,709-94,999,519
(GRCh38/hg38)
Size:
25,811 bases
Orientation:
Plus strand
chr11:94,706,845-94,732,682
(GRCh37/hg19)
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; Note=Truncated N-terminus.; 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

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for KDM4D Gene

InterPro:
Blocks:
  • Transcription factor jumonji, jmjC
ProtoNet:

Suggested Antigen Peptide Sequences for KDM4D Gene

GenScript: Design optimal peptide antigens:
  • Jumonji domain-containing protein 2D (KDM4D_HUMAN)

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.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=2 2-oxoglutarate + N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3] + 2 O2 = 2 CO2 + 2 formaldehyde + N(6)-methyl-L-lysyl(9)-[histone H3] + 2 succinate; Xref=Rhea:RHEA:60200, Rhea:RHEA-COMP:15538, Rhea:RHEA-COMP:15542, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810, ChEBI:CHEBI:16842, ChEBI:CHEBI:30031, ChEBI:CHEBI:61929, ChEBI:CHEBI:61961; EC=1.14.11.66; Evidence={ECO:0000269|PubMed:16603238};.

Enzyme Numbers (IUBMB) for KDM4D Gene

Phenotypes From GWAS Catalog 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 IBA 21873635
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

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for KDM4D

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
nucleus 5
extracellular 4
cytosol 3
plasma membrane 2
cytoskeleton 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for KDM4D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005654 nucleoplasm TAS --
GO:0005721 pericentric heterochromatin IEA --
GO:0035097 histone methyltransferase complex IBA 21873635
GO:0035861 site of double-strand break IDA 24550317
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:0006325 chromatin organization IEA --
GO:0006338 chromatin remodeling IBA 21873635
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 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

Drug Products

Transcripts for KDM4D Gene

mRNA/cDNA for KDM4D Gene

1 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for KDM4D

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

No ASD Table

Relevant External Links for KDM4D Gene

GeneLoc Exon Structure for
KDM4D

Expression for KDM4D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for KDM4D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Testis (Reproductive System)

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

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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for KDM4D

SOURCE GeneReport for Unigene cluster for KDM4D Gene:

Hs.503598

Evidence on tissue expression from TISSUES for KDM4D Gene

  • Nervous system(4.5)
  • Kidney(2.6)
  • Skin(2.5)
  • Blood(2.4)
genes like me logo Genes that share expression patterns with KDM4D: view

No data available for 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 31
  • 99 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia LOC524768 30
  • 80.59 (n)
-- 31
  • 71 (a)
OneToMany
Dog
(Canis familiaris)
Mammalia KDM4D 30
  • 78.27 (n)
-- 31
  • 73 (a)
OneToMany
Mouse
(Mus musculus)
Mammalia Kdm4d 30 17 31
  • 74.97 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Kdm4d 30
  • 74.17 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 62 (a)
ManyToMany
-- 31
  • 41 (a)
ManyToMany
Fruit Fly
(Drosophila melanogaster)
Insecta Kdm4A 31
  • 39 (a)
ManyToMany
Kdm4B 31
  • 29 (a)
ManyToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RPH1 31
  • 19 (a)
ManyToMany
GIS1 31
  • 13 (a)
ManyToMany
Species where no ortholog for KDM4D was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)
Aminode:
Evolutionary constrained regions (ECRs) for KDM4D: view image

Paralogs for KDM4D Gene

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

  • KDM4D_HUMAN

Pseudogenes.org Pseudogenes for KDM4D Gene

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

Variants for KDM4D Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for KDM4D Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
775297 Benign: not provided 94,998,437(+) C/G MISSENSE_VARIANT
775298 Benign: not provided 94,998,783(+) G/T MISSENSE_VARIANT
rs34366036 - p.Ala471Ser
rs35631512 - p.Ser355Arg
rs3740853 - p.Arg408Gln

Additional dbSNP identifiers (rs#s) for KDM4D Gene

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)

Additional Variant Information for KDM4D Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KDM4D Gene

Disorders for KDM4D Gene

MalaCards: The human disease database

(5) MalaCards diseases for KDM4D Gene - From: DISEASES and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search KDM4D in MalaCards View complete list of genes associated with diseases

Additional Disease Information for KDM4D

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with KDM4D: view

No data available for 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 (International journal of oncology 2004) 2 3 4 23
  2. Human chromosome 11 DNA sequence and analysis including novel gene identification. (PMID: 16554811) Taylor TD … Sakaki Y (Nature 2006) 3 4
  3. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. (PMID: 16603238) Whetstine JR … Shi Y (Cell 2006) 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

Products for KDM4D Gene

  • Signalway Proteins for KDM4D

Sources for KDM4D Gene