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Aliases for KDM4B Gene

Aliases for KDM4B Gene

  • Lysine (K)-Specific Demethylase 4B 2 3
  • JMJD2B 3 4 6
  • JmjC Domain-Containing Histone Demethylation Protein 3B 3 4
  • Jumonji Domain-Containing Protein 2B 3 4
  • Jumonji Domain Containing 2B 2 3
  • Tudor Domain Containing 14B 2 3
  • KIAA0876 4 6
  • Lysine-Specific Demethylase 4B 3
  • EC 1.14.11.- 4
  • EC 1.14.11 64
  • TDRD14B 3
  • JHDM3B 4

External Ids for KDM4B Gene

Previous Symbols for KDM4B Gene

  • JMJD2B

Summaries for KDM4B Gene

GeneCards Summary for KDM4B Gene

KDM4B (Lysine (K)-Specific Demethylase 4B) is a Protein Coding gene. Among its related pathways are Chromatin Regulation / Acetylation. GO annotations related to this gene include dioxygenase activity. An important paralog of this gene is KDM4D.

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

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

Genomics for KDM4B Gene

Genomic Location for KDM4B Gene

Start:
4,969,112 bp from pter
End:
5,153,598 bp from pter
Size:
184,487 bases
Orientation:
Plus strand

Genomic View for KDM4B Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for KDM4B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KDM4B Gene

Regulatory Elements 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; Note=Binds 1 Fe(2+) ion per subunit.;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAC33799.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=BAA74899.2; Type=Erroneous initiation; 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

Proteomics data for KDM4B Gene at MOPED

Post-translational modifications for KDM4B Gene

  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys106 and Lys1032

Other Protein References for KDM4B Gene

Domains for KDM4B Gene

Gene Families for KDM4B Gene

HGNC:
  • KDM :Chromatin-modifying enzymes / K-demethylases
  • TDRD :Tudor domain containing

UniProtKB/Swiss-Prot:

KDM4B_HUMAN
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).:
    • O94953
  • Contains 1 JmjC domain.:
    • O94953
  • Contains 1 JmjN domain.:
    • O94953
  • Contains 2 Tudor domains.:
    • O94953
Family:
  • Belongs to the JHDM3 histone demethylase family.:
    • O94953
Similarity:
  • Contains 2 PHD-type zinc fingers.:
    • O94953
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

Gene Ontology (GO) - Molecular Function for KDM4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding --
GO:0008270 zinc 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

miRNA for KDM4B Gene

No data available for Animal Models , Transcription Factor Targeting and HOMER Transcription for KDM4B Gene

Localization for KDM4B Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM4B Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for KDM4B Gene COMPARTMENTS Subcellular localization image for KDM4B gene
Compartment Confidence
nucleus 5
cytosol 2
mitochondrion 1

Gene Ontology (GO) - Cellular Components for KDM4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm TAS --
GO:0005925 focal adhesion IDA --
GO:0030054 cell junction IDA --
genes like me logo Genes that share ontologies with KDM4B: view

Pathways 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 TAS --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0016568 chromatin modification IEA --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with KDM4B: view

Transcripts for KDM4B Gene

Unigene Clusters for KDM4B Gene

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

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 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 (4.1).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for KDM4B Gene

SOURCE GeneReport for Unigene cluster for KDM4B Gene Hs.654816

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

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 36
  • 99.24 (n)
  • 99.45 (a)
KDM4B 37
  • 96 (a)
OneToOne
cow
(Bos Taurus)
Mammalia KDM4B 36
  • 86.61 (n)
  • 88.87 (a)
KDM4B 37
  • 86 (a)
OneToOne
dog
(Canis familiaris)
Mammalia KDM4B 36
  • 86.32 (n)
  • 87.91 (a)
KDM4B 37
  • 86 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Kdm4b 36
  • 80.81 (n)
  • 83.52 (a)
Kdm4b 16
Kdm4b 37
  • 81 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia KDM4B 37
  • 69 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia KDM4B 37
  • 61 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Kdm4b 36
  • 80.9 (n)
  • 83.63 (a)
chicken
(Gallus gallus)
Aves KDM4B 36
  • 69.52 (n)
  • 74.79 (a)
KDM4B 37
  • 69 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia KDM4B 37
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia kdm4b 36
  • 63.93 (n)
  • 67.95 (a)
zebrafish
(Danio rerio)
Actinopterygii kdm4b 36
  • 68.39 (n)
  • 66.9 (a)
kdm4b 37
  • 51 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006770 36
  • 66.87 (n)
  • 64.62 (a)
fruit fly
(Drosophila melanogaster)
Insecta Kdm4A 36
  • 65.86 (n)
  • 64.05 (a)
Kdm4A 37
  • 47 (a)
ManyToMany
Kdm4B 37
  • 39 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea jmjd-2 37
  • 32 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GIS1 37
  • 18 (a)
ManyToMany
RPH1 37
  • 26 (a)
ManyToMany
RPH1 39
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10508 37
  • 40 (a)
OneToMany
Species with no ortholog for KDM4B:
  • 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)

Paralogs for KDM4B Gene

Paralogs for KDM4B Gene

Selected SIMAP similar genes for KDM4B Gene using alignment to 4 proteins:

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 Sequence Context AA Info Type MAF
rs10689 -- 5,153,593(-) TTTCG(C/T)AGCGT utr-variant-3-prime
rs11514 -- 5,153,595(-) GGTTT(C/T)GCAGC utr-variant-3-prime
rs14948 -- 5,153,475(+) GTGCA(A/G)AGACG utr-variant-3-prime
rs169080 -- 4,980,853(-) GCCAC(A/G)GACTG intron-variant
rs174654 -- 4,990,130(-) aattt(G/T)tttgt intron-variant

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

Variant ID Type Subtype PubMed ID
nsv910862 CNV Loss 21882294
dgv3682n71 CNV Loss 21882294
dgv616e199 CNV Deletion 23128226
nsv910866 CNV Loss 21882294
esv2718037 CNV Deletion 23290073
esv27574 CNV Gain 19812545
nsv833722 CNV Loss 17160897
dgv3683n71 CNV Loss 21882294
dgv3684n71 CNV Loss 21882294
dgv3685n71 CNV Loss 21882294
nsv910875 CNV Loss 21882294
esv2105827 CNV Deletion 18987734
nsv525126 CNV Loss 19592680
dgv3686n71 CNV Loss 21882294
esv2013056 CNV Deletion 18987734
esv2718038 CNV Deletion 23290073
esv26165 CNV Gain 19812545
esv2718039 CNV Deletion 23290073
esv1001351 CNV Deletion 20482838
esv1201127 CNV Insertion 17803354
dgv3687n71 CNV Loss 21882294
dgv3688n71 CNV Loss 21882294
nsv833723 CNV Loss 17160897
nsv828407 CNV Loss 20364138
nsv510750 CNV Loss 20534489
esv1690767 CNV Insertion 17803354

Relevant External Links for KDM4B Gene

HapMap Linkage Disequilibrium report
KDM4B

Disorders for KDM4B Gene

Relevant External Links for KDM4B

Genetic Association Database (GAD)
KDM4B
Human Genome Epidemiology (HuGE) Navigator
KDM4B
genes like me logo Genes that share disorders with KDM4B: view

No data available for UniProtKB/Swiss-Prot for KDM4B Gene

Publications for KDM4B Gene

  1. Identification and characterization of JMJD2 family genes in silico. (PMID: 15138608) Katoh M. … Katoh M. (Int. J. Oncol. 2004) 2 3 23
  2. Functional characterization of JMJD2A, a histone deacetylase- and retinoblastoma-binding protein. (PMID: 15927959) Gray S.G. … Dangond F. (J. Biol. Chem. 2005) 3 4 23
  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 Res. 1998) 2 3 4
  4. Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones. (PMID: 12168954) Nakajima D. … Nagase T. (DNA Res. 2002) 3 4
  5. Comparative integromics on JMJD2A, JMJD2B and JMJD2C: preferential expression of JMJD2C in undifferentiated ES cells. (PMID: 17611647) Katoh Y. … Katoh M. (Int. J. Mol. Med. 2007) 3 23

Products for KDM4B Gene

  • Addgene plasmids for KDM4B

Sources for KDM4B Gene

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