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Aliases for KDM4B Gene

Aliases for KDM4B Gene

  • Lysine Demethylase 4B 2 3 5
  • JmjC Domain-Containing Histone Demethylation Protein 3B 3 4
  • Jumonji Domain-Containing Protein 2B 3 4
  • Lysine (K)-Specific Demethylase 4B 2 3
  • Jumonji Domain Containing 2B 2 3
  • Tudor Domain Containing 14B 2 3
  • JMJD2B 3 4
  • Lysine-Specific Demethylase 4B 3
  • EC 1.14.11.- 4
  • KIAA0876 4
  • TDRD14B 3
  • JHDM3B 4

External Ids for KDM4B Gene

Previous HGNC Symbols for KDM4B Gene

  • JMJD2B

Previous GeneCards Identifiers for KDM4B Gene

  • GC19P004921
  • GC19P004730

Summaries for KDM4B Gene

GeneCards Summary for KDM4B Gene

KDM4B (Lysine Demethylase 4B) is a Protein Coding gene. Among its related pathways are Chromatin organization and DNA Double-Strand Break Repair. Gene Ontology (GO) annotations related to this gene include dioxygenase activity. An important paralog of this gene is KDM4C.

UniProtKB/Swiss-Prot for KDM4B Gene

  • Histone demethylase that specifically demethylates Lys-9 of histone H3, thereby playing a role in histone code. Does not demethylate histone H3 Lys-4, H3 Lys-27, H3 Lys-36 nor H4 Lys-20. Only able to demethylate trimethylated H3 Lys-9, with a weaker activity than KDM4A, KDM4C and KDM4D. Demethylation of Lys residue generates formaldehyde and succinate.

Gene Wiki entry for KDM4B Gene

Additional gene information for KDM4B Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KDM4B Gene

Genomics for KDM4B Gene

GeneHancer (GH) Regulatory Elements for KDM4B Gene

Promoters and enhancers for KDM4B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J004967 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 671.7 +1.7 1687 5.8 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 YY1 ZNF213 ZNF207 KDM4B PIR49056 DUS3L SAFB YJU2 SNRPEP4 ENSG00000267030 ENSG00000267769 SAFB2 HDGFL2
GH19J005689 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 58.1 +723.0 722990 5 ZFP64 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 ZNF548 SP3 ZC3H11A RPL36 DUS3L KHSRP SAFB ENSG00000267571 SNRPEP4 SAFB2 VMAC RANBP3 KDM4B
GH19J005717 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 30.8 +750.1 750143 4.4 CLOCK MLX FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 LONP1 CATSPERD DUS3L ENSG00000267571 SAFB KHSRP KDM4B VMAC RANBP3 RPL36
GH19J005679 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 31.5 +711.3 711327 2.5 HDGF PKNOX1 FOXA2 SMAD1 ARNT ARID4B SIN3A YBX1 DMAP1 ZNF2 HSD11B1L C19orf70 DUS3L SAFB KHSRP ENSG00000267571 KDM4B RANBP3 SAFB2 GTF2F1
GH19J004907 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 20.9 -56.4 -56429 9.5 HDGF PKNOX1 FOXA2 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 E2F8 UHRF1 ENSG00000267030 SAFB SAFB2 YJU2 ENSG00000267769 DUS3L KDM4B DPP9-AS1 PLIN3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around KDM4B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the KDM4B gene promoter:
  • Lmo2
  • AML1a
  • NF-E2 p45
  • NF-E2
  • Egr-2
  • MAZR
  • LCR-F1
  • C/EBPalpha
  • Nkx5-1
  • USF-1

Genomic Locations for KDM4B Gene

Genomic Locations for KDM4B Gene
chr19:4,969,112-5,153,598
(GRCh38/hg38)
Size:
184,487 bases
Orientation:
Plus strand
chr19:4,969,124-5,153,609
(GRCh37/hg19)
Size:
184,486 bases
Orientation:
Plus strand

Genomic View for KDM4B Gene

Genes around KDM4B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KDM4B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for KDM4B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KDM4B Gene

Proteins for KDM4B Gene

  • Protein details for KDM4B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O94953-KDM4B_HUMAN
    Recommended name:
    Lysine-specific demethylase 4B
    Protein Accession:
    O94953
    Secondary Accessions:
    • B9EGN8
    • D6W631
    • O75274
    • Q6P3R5
    • Q9P1V1
    • Q9UF40

    Protein attributes for KDM4B Gene

    Size:
    1096 amino acids
    Molecular mass:
    121897 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAC33799.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=BAA74899.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for KDM4B Gene

    Alternative splice isoforms for KDM4B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for KDM4B Gene

Post-translational modifications for KDM4B Gene

  • Ubiquitination at isoforms=1032 and Lys106
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for KDM4B Gene

Domains & Families for KDM4B Gene

Gene Families for KDM4B Gene

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

Suggested Antigen Peptide Sequences for KDM4B Gene

Graphical View of Domain Structure for InterPro Entry

O94953

UniProtKB/Swiss-Prot:

KDM4B_HUMAN :
  • The 2 Tudor domains recognize and bind methylated histones. Double Tudor domain has an interdigitated structure and the unusual fold is required for its ability to bind methylated histone tails (By similarity).
  • Belongs to the JHDM3 histone demethylase family.
Domain:
  • The 2 Tudor domains recognize and bind methylated histones. Double Tudor domain has an interdigitated structure and the unusual fold is required for its ability to bind methylated histone tails (By similarity).
Family:
  • Belongs to the JHDM3 histone demethylase family.
genes like me logo Genes that share domains with KDM4B: view

Function for KDM4B Gene

Molecular function for KDM4B Gene

UniProtKB/Swiss-Prot Function:
Histone demethylase that specifically demethylates Lys-9 of histone H3, thereby playing a role in histone code. Does not demethylate histone H3 Lys-4, H3 Lys-27, H3 Lys-36 nor H4 Lys-20. Only able to demethylate trimethylated H3 Lys-9, with a weaker activity than KDM4A, KDM4C and KDM4D. Demethylation of Lys residue generates formaldehyde and succinate.

Enzyme Numbers (IUBMB) for KDM4B Gene

Phenotypes From GWAS Catalog for KDM4B Gene

Gene Ontology (GO) - Molecular Function for KDM4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016491 oxidoreductase activity IEA --
GO:0032452 histone demethylase activity TAS --
GO:0032454 histone demethylase activity (H3-K9 specific) IMP 28262558
GO:0046872 metal ion binding IEA --
GO:0051213 dioxygenase activity IEA --
genes like me logo Genes that share ontologies with KDM4B: view
genes like me logo Genes that share phenotypes with KDM4B: view

Animal Models for KDM4B Gene

MGI Knock Outs for KDM4B:
  • Kdm4b Kdm4b<tm1a(EUCOMM)Wtsi>
  • Kdm4b Kdm4b<tm1.2Okad>

Animal Model Products

Clone Products

  • Addgene plasmids for KDM4B

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for KDM4B Gene

Localization for KDM4B Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM4B 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 KDM4B gene
Compartment Confidence
nucleus 5
cytosol 2
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleus (3)
  • Cytosol (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for KDM4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm TAS --
GO:0005829 cytosol IDA --
GO:0031618 nuclear pericentric heterochromatin IEA --
genes like me logo Genes that share ontologies with KDM4B: view

Pathways & Interactions for KDM4B Gene

genes like me logo Genes that share pathways with KDM4B: view

Pathways by source for KDM4B Gene

1 Cell Signaling Technology pathway for KDM4B Gene

Gene Ontology (GO) - Biological Process for KDM4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0033169 histone H3-K9 demethylation IMP 28262558
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with KDM4B: view

No data available for SIGNOR curated interactions for KDM4B Gene

Drugs & Compounds for KDM4B Gene

(1) Drugs for KDM4B Gene - From:

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
JIB-04 Pharma Jumonji histone demethylase inihibitor 0
genes like me logo Genes that share compounds with KDM4B: view

Transcripts for KDM4B Gene

Unigene Clusters for KDM4B Gene

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

Clone Products

  • Addgene plasmids for KDM4B

Alternative Splicing Database (ASD) splice patterns (SP) for KDM4B Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21a · 21b ·
SP1: - - - - -
SP2:
SP3:
SP4: - - - -
SP5:
SP6:
SP7: - -
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:

ExUns: 21c ^ 22 ^ 23a · 23b ^ 24a · 24b ^ 25 ^ 26 ^ 27 ^ 28a · 28b ^ 29 ^ 30 ^ 31a · 31b ^ 32
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:

Relevant External Links for KDM4B Gene

GeneLoc Exon Structure for
KDM4B
ECgene alternative splicing isoforms for
KDM4B

Expression for KDM4B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for KDM4B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for KDM4B Gene

This gene is overexpressed in Whole Blood (x4.1).

Protein differential expression in normal tissues from HIPED for KDM4B Gene

This gene is overexpressed in Nasal epithelium (63.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for KDM4B Gene



NURSA nuclear receptor signaling pathways regulating expression of KDM4B Gene:

KDM4B

SOURCE GeneReport for Unigene cluster for KDM4B Gene:

Hs.654816

Evidence on tissue expression from TISSUES for KDM4B Gene

  • Nervous system(4.7)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with KDM4B: view

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for KDM4B Gene

Orthologs for KDM4B Gene

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

Orthologs for KDM4B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia KDM4B 34 33
  • 99.24 (n)
OneToOne
cow
(Bos Taurus)
Mammalia KDM4B 34 33
  • 86.61 (n)
OneToOne
dog
(Canis familiaris)
Mammalia KDM4B 34 33
  • 86.32 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Kdm4b 33
  • 80.9 (n)
mouse
(Mus musculus)
Mammalia Kdm4b 16 34 33
  • 80.81 (n)
oppossum
(Monodelphis domestica)
Mammalia KDM4B 34
  • 69 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia KDM4B 34
  • 61 (a)
OneToOne
chicken
(Gallus gallus)
Aves KDM4B 34 33
  • 69.52 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia KDM4B 34
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia kdm4b 33
  • 63.93 (n)
zebrafish
(Danio rerio)
Actinopterygii kdm4b 34 33
  • 68.39 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006770 33
  • 66.87 (n)
fruit fly
(Drosophila melanogaster)
Insecta Kdm4A 34 33
  • 65.86 (n)
ManyToMany
Kdm4B 34
  • 39 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea jmjd-2 34
  • 32 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RPH1 36 34
  • 26 (a)
GIS1 34
  • 18 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10508 34
  • 40 (a)
OneToMany
Species where no ortholog for KDM4B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • 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 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)
  • wheat (Triticum aestivum)

Evolution for KDM4B Gene

ENSEMBL:
Gene Tree for KDM4B (if available)
TreeFam:
Gene Tree for KDM4B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for KDM4B: view image

Paralogs for KDM4B Gene

Paralogs for KDM4B Gene

(6) SIMAP similar genes for KDM4B Gene using alignment to 4 proteins:

  • KDM4B_HUMAN
  • F5GX28_HUMAN
  • K7EQ54_HUMAN
  • K7ES23_HUMAN

Pseudogenes.org Pseudogenes for KDM4B Gene

genes like me logo Genes that share paralogs with KDM4B: view

Variants for KDM4B Gene

Sequence variations from dbSNP and Humsavar for KDM4B Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1000005316 -- 5,005,904(+) G/A genic_upstream_transcript_variant, intron_variant
rs1000048463 -- 5,102,163(+) C/T genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant
rs1000073382 -- 5,093,696(+) G/C genic_downstream_transcript_variant, genic_upstream_transcript_variant, intron_variant
rs1000080693 -- 5,040,841(+) AA/ genic_upstream_transcript_variant, intron_variant
rs1000155721 -- 5,148,544(+) C/T genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for KDM4B Gene

Variant ID Type Subtype PubMed ID
dgv616e199 CNV deletion 23128226
esv1001351 CNV deletion 20482838
esv1201127 CNV insertion 17803354
esv1690767 CNV insertion 17803354
esv2013056 CNV deletion 18987734
esv2105827 CNV deletion 18987734
esv26165 CNV gain 19812545
esv2718037 CNV deletion 23290073
esv2718038 CNV deletion 23290073
esv2718039 CNV deletion 23290073
esv27574 CNV gain 19812545
esv3335016 CNV duplication 20981092
esv3643520 CNV loss 21293372
esv3643521 CNV gain 21293372
nsv1057373 CNV gain 25217958
nsv1063881 CNV gain 25217958
nsv1071898 CNV deletion 25765185
nsv1072850 CNV deletion 25765185
nsv1129616 CNV tandem duplication 24896259
nsv1143906 CNV deletion 24896259
nsv510750 CNV deletion 20534489
nsv525126 CNV loss 19592680
nsv828407 CNV loss 20364138
nsv833722 CNV loss 17160897
nsv833723 CNV loss 17160897
nsv953951 CNV deletion 24416366

Variation tolerance for KDM4B Gene

Residual Variation Intolerance Score: 4.86% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.19; 24.00% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for KDM4B Gene

Human Gene Mutation Database (HGMD)
KDM4B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
KDM4B

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KDM4B Gene

Disorders for KDM4B Gene

Additional Disease Information for KDM4B

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

No disorders were found for KDM4B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for KDM4B Gene

Publications for KDM4B Gene

  1. Functional characterization of JMJD2A, a histone deacetylase- and retinoblastoma-binding protein. (PMID: 15927959) Gray SG … Dangond F (The Journal of biological chemistry 2005) 3 4 22 58
  2. Identification and characterization of JMJD2 family genes in silico. (PMID: 15138608) Katoh M … Katoh M (International journal of oncology 2004) 2 3 22 58
  3. Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10048485) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 2 3 4 58
  4. Potent and Selective KDM5 Inhibitor Stops Cellular Demethylation of H3K4me3 at Transcription Start Sites and Proliferation of MM1S Myeloma Cells. (PMID: 28262558) Tumber A … Brennan PE (Cell chemical biology 2017) 3 4 58
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58

Products for KDM4B Gene

Sources for KDM4B Gene

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