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Aliases for KDM6B Gene

Aliases for KDM6B Gene

  • Lysine (K)-Specific Demethylase 6B 2 3
  • JMJD3 3 4 6
  • Jumonji Domain Containing 3, Histone Lysine Demethylase 2 3
  • Jumonji Domain-Containing Protein 3 3 4
  • JmjC Domain-Containing Protein 3 3 4
  • Lysine Demethylase 6B 3 4
  • KIAA0346 4 6
  • Lysine-Specific Demethylase 6B 3
  • Jumonji Domain Containing 3 2
  • EC 1.14.11.- 4
  • EC 1.14.11 63

External Ids for KDM6B Gene

Previous HGNC Symbols for KDM6B Gene

  • JMJD3

Previous GeneCards Identifiers for KDM6B Gene

  • GC17P007686

Summaries for KDM6B Gene

GeneCards Summary for KDM6B Gene

KDM6B (Lysine (K)-Specific Demethylase 6B) is a Protein Coding gene. Among its related pathways are Cellular Senescence and Chromatin Regulation / Acetylation. GO annotations related to this gene include sequence-specific DNA binding and dioxygenase activity. An important paralog of this gene is KDM6A.

UniProtKB/Swiss-Prot for KDM6B Gene

  • Histone demethylase that specifically demethylates Lys-27 of histone H3, thereby playing a central role in histone code. Demethylates trimethylated and dimethylated H3 Lys-27. Plays a central role in regulation of posterior development, by regulating HOX gene expression. Involved in inflammatory response by participating in macrophage differentiation in case of inflammation by regulating gene expression and macrophage differentiation.

Tocris Summary for KDM6B Gene

  • Histone demethylases are a family of enzymes that catalyze the removal of methyl groups from lysine and arginine residues on histone tails. They reverse the methylation of lysine and arginine residues that is catalyzed by histone methyltransferases

No data available for Entrez Gene Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KDM6B Gene

Genomics for KDM6B Gene

Regulatory Elements for KDM6B Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for KDM6B Gene

Start:
7,834,203 bp from pter
End:
7,854,800 bp from pter
Size:
20,598 bases
Orientation:
Plus strand

Genomic View for KDM6B Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for KDM6B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KDM6B Gene

Proteins for KDM6B Gene

  • Protein details for KDM6B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O15054-KDM6B_HUMAN
    Recommended name:
    Lysine-specific demethylase 6B
    Protein Accession:
    O15054
    Secondary Accessions:
    • C9IZ40
    • Q96G33

    Protein attributes for KDM6B Gene

    Size:
    1643 amino acids
    Molecular mass:
    176632 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
    Cofactor:
    Name=L-ascorbate; Xref=ChEBI:CHEBI:38290;
    Quaternary structure:
    • Interacts with TLE1 (By similarity). Component of the MLL4 complex, at least composed of KMT2B/MLL4, ASH2L, RBBP5, WDR5, and KDM6B.
    SequenceCaution:
    • Sequence=BAA21572.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for KDM6B Gene

    Alternative splice isoforms for KDM6B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for KDM6B Gene

Proteomics data for KDM6B Gene at MOPED

Selected DME Specific Peptides for KDM6B Gene

Post-translational modifications for KDM6B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for KDM6B Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

Antibody Products

  • R&D Systems Antibodies for KDM6B (Lysine (K)-specific Demethylase 6B/KDM6B)
  • Cell Signaling Technology (CST) Antibodies for KDM6B (JMJD3)

Domains for KDM6B Gene

Gene Families for KDM6B Gene

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

Protein Domains for KDM6B Gene

Suggested Antigen Peptide Sequences for KDM6B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O15054

UniProtKB/Swiss-Prot:

KDM6B_HUMAN :
  • O15054
Domain:
  • Contains 1 JmjC domain.
Family:
  • Belongs to the UTX family.
genes like me logo Genes that share domains with KDM6B: view

Function for KDM6B Gene

Molecular function for KDM6B Gene

UniProtKB/Swiss-Prot Function: Histone demethylase that specifically demethylates Lys-27 of histone H3, thereby playing a central role in histone code. Demethylates trimethylated and dimethylated H3 Lys-27. Plays a central role in regulation of posterior development, by regulating HOX gene expression. Involved in inflammatory response by participating in macrophage differentiation in case of inflammation by regulating gene expression and macrophage differentiation.
UniProtKB/Swiss-Prot Induction: By 12-O-tetradecanoylphorbol-13-acetate (TPA) in myeloid leukemia cells.

Enzyme Numbers (IUBMB) for KDM6B Gene

Gene Ontology (GO) - Molecular Function for KDM6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21841772
GO:0008013 beta-catenin binding IEA --
GO:0043565 sequence-specific DNA binding IEA --
GO:0046872 metal ion binding IEA --
GO:0051213 dioxygenase activity IEA --
genes like me logo Genes that share ontologies with KDM6B: view
genes like me logo Genes that share phenotypes with KDM6B: view

Animal Models for KDM6B Gene

MGI Knock Outs for KDM6B:

Animal Model Products

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for KDM6B

In Situ Assay Products

Flow Cytometry Products

No data available for Transcription Factor Targeting and HOMER Transcription for KDM6B Gene

Localization for KDM6B Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM6B Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for KDM6B Gene COMPARTMENTS Subcellular localization image for KDM6B gene
Compartment Confidence
nucleus 4
extracellular 2
cytosol 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for KDM6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS 23856522
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with KDM6B: view

Pathways for KDM6B Gene

genes like me logo Genes that share pathways with KDM6B: view

Pathways by source for KDM6B Gene

1 Cell Signaling Technology pathway for KDM6B Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays
    • Epigenetic Chromatin Modification Enzymes in human,mouse,rat

Gene Ontology (GO) - Biological Process for KDM6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization TAS --
GO:0006954 inflammatory response IEA --
GO:0016577 histone demethylation --
GO:0045446 endothelial cell differentiation ISS 23856522
GO:0045944 positive regulation of transcription from RNA polymerase II promoter ISS 23856522
genes like me logo Genes that share ontologies with KDM6B: view

Compounds for KDM6B Gene

(5) Tocris Compounds for KDM6B Gene

Compound Action Cas Number
GSK J1 Potent histone demethylase JMJD3/UTX inhibitor [1373422-53-7]
GSK J4 Histone lysine demethylase (KDM) inhibitor; cell permeable [1373423-53-0]
GSK J5 Inactive isomer of GSK J4 (Cat. No. 4594); cell permeable [1394854-51-3]
JIB 04 Pan Jumonji histone demethylase inhibitor; active in vivo [199596-05-9]
RN 1 dihydrochloride LSD1 inhibitor
genes like me logo Genes that share compounds with KDM6B: view

Transcripts for KDM6B Gene

Unigene Clusters for KDM6B Gene

Lysine (K)-specific demethylase 6B:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for KDM6B

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for KDM6B

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for KDM6B Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^ 20a · 20b
SP1: -
SP2:
SP3:
SP4:
SP5:

Relevant External Links for KDM6B Gene

GeneLoc Exon Structure for
KDM6B
ECgene alternative splicing isoforms for
KDM6B

Expression for KDM6B Gene

mRNA expression in normal human tissues for KDM6B Gene

mRNA differential expression in normal tissues according to GTEx for KDM6B Gene

This gene is overexpressed in Whole Blood (7.8).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for KDM6B Gene

SOURCE GeneReport for Unigene cluster for KDM6B Gene Hs.223678

genes like me logo Genes that share expressions with KDM6B: view

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA Expression by UniProt/SwissProt for KDM6B Gene

Orthologs for KDM6B Gene

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

Orthologs for KDM6B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia KDM6B 35
  • 99.58 (n)
  • 99.52 (a)
KDM6B 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia KDM6B 35
  • 90.63 (n)
  • 92.49 (a)
KDM6B 36
  • 92 (a)
OneToOne
dog
(Canis familiaris)
Mammalia KDM6B 35
  • 90.43 (n)
  • 93.02 (a)
KDM6B 36
  • 92 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Kdm6b 35
  • 88.36 (n)
  • 92.44 (a)
Kdm6b 16
Kdm6b 36
  • 90 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia KDM6B 36
  • 50 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Kdm6b 35
  • 87.6 (n)
  • 91.31 (a)
lizard
(Anolis carolinensis)
Reptilia KDM6B 36
  • 57 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii KDM6B (2 of 2) 36
  • 32 (a)
OneToMany
kdm6bb 36
  • 30 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea jmjd-3.1 36
  • 18 (a)
OneToMany
jmjd-3.2 36
  • 17 (a)
OneToMany
jmjd-3.3 36
  • 20 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CYC8 36
  • 10 (a)
OneToMany
Species with no ortholog for KDM6B:
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • 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)

Evolution for KDM6B Gene

ENSEMBL:
Gene Tree for KDM6B (if available)
TreeFam:
Gene Tree for KDM6B (if available)

Paralogs for KDM6B Gene

Paralogs for KDM6B Gene

Selected SIMAP similar genes for KDM6B Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with KDM6B: view

Variants for KDM6B Gene

Sequence variations from dbSNP and Humsavar for KDM6B Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type MAF
rs1389613 -- 7,848,262(-) ACCCC(A/G)GGCGG reference, synonymous-codon
rs2270516 - 7,847,118(+) GCACT(C/T)GCTGC reference, missense
rs2270517 -- 7,847,529(+) CCACC(C/T)GCTTC intron-variant
rs3736305 -- 7,852,414(-) GCTGG(C/T)GGCTC intron-variant
rs3736306 -- 7,851,142(-) GGCCA(G/T)ATCTG synonymous-codon, reference

Structural Variations from Database of Genomic Variants (DGV) for KDM6B Gene

Variant ID Type Subtype PubMed ID
nsv833351 CNV Loss 17160897
nsv907653 CNV Loss 21882294
esv2715604 CNV Deletion 23290073
esv2715605 CNV Deletion 23290073
esv2715606 CNV Deletion 23290073
esv989512 CNV Deletion 20482838
dgv510n67 CNV Gain 20364138

Relevant External Links for KDM6B Gene

HapMap Linkage Disequilibrium report
KDM6B
Human Gene Mutation Database (HGMD)
KDM6B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KDM6B Gene

Disorders for KDM6B Gene

No disorders were found for KDM6B Gene.

No data available for UniProtKB/Swiss-Prot for KDM6B Gene

Publications for KDM6B Gene

  1. Prediction of the coding sequences of unidentified human genes. VII. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9205841) Nagase T. … Ohara O. (DNA Res. 1997) 2 3 4
  2. Physical map of 17p13 and the genes adjacent to p53. (PMID: 10662545) Cousin P. … Shaw P. (Genomics 2000) 2 3
  3. The histone H3 lysine-27 demethylase Jmjd3 links inflammation to inhibition of polycomb-mediated gene silencing. (PMID: 17825402) De Santa F. … Natoli G. (Cell 2007) 3 4
  4. Identification of JmjC domain-containing UTX and JMJD3 as histone H3 lysine 27 demethylases. (PMID: 18003914) Hong S. … Ge K. (Proc. Natl. Acad. Sci. U.S.A. 2007) 3 4
  5. Control of differentiation in a self-renewing mammalian tissue by the histone demethylase JMJD3. (PMID: 18628393) Sen G.L. … Khavari P.A. (Genes Dev. 2008) 3

Products for KDM6B Gene

Sources for KDM6B Gene

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