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Aliases for KDM6B Gene

Aliases for KDM6B Gene

  • Lysine Demethylase 6B 2 3 4 5
  • Jumonji Domain Containing 3, Histone Lysine Demethylase 2 3
  • Jumonji Domain-Containing Protein 3 3 4
  • Lysine (K)-Specific Demethylase 6B 2 3
  • JmjC Domain-Containing Protein 3 3 4
  • JMJD3 3 4
  • Lysine-Specific Demethylase 6B 3
  • Jumonji Domain Containing 3 2
  • EC 1.14.11.- 4
  • EC 1.14.11 58
  • KIAA0346 4

External Ids for KDM6B Gene

Previous HGNC Symbols for KDM6B Gene

  • JMJD3

Previous GeneCards Identifiers for KDM6B Gene

  • GC17P007686

Summaries for KDM6B Gene

Entrez Gene Summary for KDM6B Gene

  • The protein encoded by this gene is a lysine-specific demethylase that specifically demethylates di- or tri-methylated lysine 27 of histone H3 (H3K27me2 or H3K27me3). H3K27 trimethylation is a repressive epigenetic mark controlling chromatin organization and gene silencing. This protein can also demethylate non-histone proteins such as retinoblastoma protein. Through its demethylation actvity this gene influences cellular differentiation and development, tumorigenesis, inflammatory diseases, and neurodegenerative diseases. This protein has two classical nuclear localization signals at its N-terminus. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Feb 2017]

GeneCards Summary for KDM6B Gene

KDM6B (Lysine Demethylase 6B) is a Protein Coding gene. Among its related pathways are Chromatin organization and Cellular Senescence (REACTOME). 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 (PubMed:17825402, PubMed:17851529, PubMed:17713478, PubMed:18003914). Demethylates trimethylated and dimethylated H3 Lys-27 (PubMed:17825402, PubMed:17851529, PubMed:17713478, PubMed:18003914). Plays a central role in regulation of posterior development, by regulating HOX gene expression (PubMed:17851529). Involved in inflammatory response by participating in macrophage differentiation in case of inflammation by regulating gene expression and macrophage differentiation (PubMed:17825402).

Tocris Summary for KDM6B Gene

  • Histone demethylases (KDMs) 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.

Additional gene information for KDM6B Gene

No data available for CIViC 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

Enhancers for KDM6B Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH17H007833 1.9 FANTOM5 ENCODE dbSUPER 48.6 +5.5 5530 12 MLX ZFP64 FEZF1 DMAP1 YY1 ZNF416 ZNF143 ZNF548 SP3 NFYC DVL2 PFAS CTC1 WRAP53 POLR2A CNTROB SNORD10 ENSG00000265749 NLGN2 KDM6B
GH17H008172 1.5 ENCODE dbSUPER 49.4 +340.8 340767 5 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF416 ZNF143 SP3 ZC3H11A DVL2 POLR2A CNTROB CTC1 WRAP53 PFAS SNORD10 ENSG00000265749 KDM6B PER1
GH17H007882 1.7 FANTOM5 ENCODE dbSUPER 27.9 +52.4 52412 7 HDGF PKNOX1 FOXA2 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF207 KDM6B WRAP53 CYB5D1 TMEM88 GPS2 PER1 KCNAB3 TRAPPC1 CNTROB GUCY2D
GH17H007474 1.8 FANTOM5 ENCODE dbSUPER 21.9 -353.6 -353611 12 FEZF1 DMAP1 YBX1 YY1 SLC30A9 ZNF143 SP3 NFYC ZFP41 SSRP1 DVL2 PFAS SNORD10 POLR2A SNORA48 CTC1 KCTD11 NEURL4 CHRNB1 CNTROB
GH17H007233 1.5 ENCODE dbSUPER 22 -595.5 -595520 11 MLX ZFP64 FEZF1 DMAP1 YY1 ZNF416 ZNF143 SP3 NFYC MEF2D DVL2 CNTROB SNORD10 SNORA48 WRAP53 POLR2A NEURL4 KCTD11 NLGN2 PLSCR3
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around KDM6B on UCSC Golden Path with GeneCards custom track

Genomic Location for KDM6B Gene

Chromosome:
17
Start:
7,834,200 bp from pter
End:
7,854,800 bp from pter
Size:
20,601 bases
Orientation:
Plus strand

Genomic View for KDM6B Gene

Genes around KDM6B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KDM6B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

Selected DME Specific Peptides for KDM6B Gene

O15054:
  • QRPGDLVWINAGTVHWVQA
  • GWCNNIAWNVGPLTA
  • KLNPPTPSIYLE
  • IKFGTNIDLSD
  • SHTTIAKYAQYQA

Post-translational modifications for KDM6B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

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

Domains & Families for KDM6B Gene

Gene Families for KDM6B Gene

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

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 :
  • Belongs to the UTX family.
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 (PubMed:17825402, PubMed:17851529, PubMed:17713478, PubMed:18003914). Demethylates trimethylated and dimethylated H3 Lys-27 (PubMed:17825402, PubMed:17851529, PubMed:17713478, PubMed:18003914). Plays a central role in regulation of posterior development, by regulating HOX gene expression (PubMed:17851529). Involved in inflammatory response by participating in macrophage differentiation in case of inflammation by regulating gene expression and macrophage differentiation (PubMed:17825402).
UniProtKB/Swiss-Prot Induction:
By 12-O-tetradecanoylphorbol-13-acetate (TPA) in myeloid leukemia cells.

Enzyme Numbers (IUBMB) for KDM6B Gene

Phenotypes From GWAS Catalog for KDM6B Gene

Gene Ontology (GO) - Molecular Function for KDM6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding IEA --
GO:0005515 protein binding IPI 21841772
GO:0008013 beta-catenin binding IEA --
GO:0016491 oxidoreductase activity IEA --
GO:0032452 histone demethylase activity TAS --
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

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for KDM6B
  • Applied Biological Materials Clones for KDM6B
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for KDM6B Gene

Localization for KDM6B Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM6B 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 KDM6B gene
Compartment Confidence
nucleus 5
extracellular 2
mitochondrion 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for KDM6B Gene

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

Pathways & Interactions for KDM6B Gene

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

Pathways by source for KDM6B Gene

1 GeneTex pathway for KDM6B Gene
1 Cell Signaling Technology pathway for KDM6B Gene

Gene Ontology (GO) - Biological Process for KDM6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002437 inflammatory response to antigenic stimulus IEA --
GO:0006954 inflammatory response IEA --
GO:0010468 regulation of gene expression IEA --
GO:0014823 response to activity IEA --
GO:0016569 covalent chromatin modification IEA --
genes like me logo Genes that share ontologies with KDM6B: view

No data available for SIGNOR curated interactions for KDM6B Gene

Drugs & Compounds for KDM6B Gene

(9) Drugs for KDM6B Gene - From: ApexBio, DGIdb, and Tocris

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
JIB-04 Pharma Jumonji histone demethylase inihibitor, Pan Jumonji inhibitor; active in vivo 0
Daminozide Pharma KDM2A inhibitor 7
GSK J1 Pharma H3K27 demethylase JMJD3 inhibitor 0
GSK J4 free base Pharma 0
GSK J4 HCl Pharma Inhibitor of H3K27 demethylase JMJD3,potent and cell-permeable 0

(1) Additional Compounds for KDM6B Gene - From: Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
GSK J4
1373423-53-0

(5) Tocris Compounds for KDM6B Gene

Compound Action Cas Number
GSK J4 Histone 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 inhibitor; active in vivo 199596-05-9
RN 1 dihydrochloride LSD1 inhibitor 1781835-13-9
TC-E 5002 Selective KDM2/7 inhibitor 1453071-47-0

(5) ApexBio Compounds for KDM6B Gene

Compound Action Cas Number
Daminozide KDM2A inhibitor 1596-84-5
GSK J1 H3K27 demethylase JMJD3 inhibitor 1373422-53-7
GSK J4 free base
GSK J4 HCl Inhibitor of H3K27 demethylase JMJD3,potent and cell-permeable 1373423-53-0
JIB-04 Jumonji histone demethylase inihibitor 199596-05-9
genes like me logo Genes that share compounds with KDM6B: view

Drug Products

Transcripts for KDM6B Gene

Unigene Clusters for KDM6B Gene

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

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for KDM6B
  • Applied Biological Materials Clones for KDM6B
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 from GTEx, Illumina, BioGPS, and CGAP SAGE for KDM6B Gene

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

This gene is overexpressed in Whole Blood (x7.8).

Protein differential expression in normal tissues from HIPED for KDM6B Gene

This gene is overexpressed in Serum (36.7) and Cervix (21.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for KDM6B Gene



Protein tissue co-expression partners for KDM6B Gene

NURSA nuclear receptor signaling pathways regulating expression of KDM6B Gene:

KDM6B

SOURCE GeneReport for Unigene cluster for KDM6B Gene:

Hs.223678

Evidence on tissue expression from TISSUES for KDM6B Gene

  • Nervous system(4.5)
  • Lung(2.1)
genes like me logo Genes that share expression patterns with KDM6B: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 33 34
  • 99.58 (n)
cow
(Bos Taurus)
Mammalia KDM6B 33 34
  • 90.63 (n)
dog
(Canis familiaris)
Mammalia KDM6B 33 34
  • 90.43 (n)
mouse
(Mus musculus)
Mammalia Kdm6b 33 16 34
  • 88.36 (n)
rat
(Rattus norvegicus)
Mammalia Kdm6b 33
  • 87.6 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia KDM6B 34
  • 50 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia KDM6B 34
  • 57 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii KDM6B (2 of 2) 34
  • 32 (a)
OneToMany
kdm6bb 34
  • 30 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea jmjd-3.3 34
  • 20 (a)
OneToMany
jmjd-3.1 34
  • 18 (a)
OneToMany
jmjd-3.2 34
  • 17 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CYC8 34
  • 10 (a)
OneToMany
Species where no ortholog for KDM6B was found in the sources mined by GeneCards:
  • 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

(5) 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
rs59627144 Likely benign 7,848,568(+) ACCAC(-/CACCAC)GGCCA cds-indel
rs148641957 Uncertain significance 7,846,654(+) AGCCT(G/T)TGCCT reference, missense
rs199964822 Uncertain significance 7,848,258(+) TGTGC(C/T)GCCCG reference, missense
rs768799563 Uncertain significance 7,846,875(+) CACCA(-/CCACCA/CCACCC)CCACC cds-indel
rs879255353 Uncertain significance 7,848,479(+) TTGCA(G/T)CTCTG reference, missense

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

Variant ID Type Subtype PubMed ID
dgv172e215 CNV deletion 23714750
dgv510n67 CNV gain 20364138
esv2715604 CNV deletion 23290073
esv2715605 CNV deletion 23290073
esv2715606 CNV deletion 23290073
esv3204242 CNV deletion 24192839
esv989512 CNV deletion 20482838
nsv1070804 CNV deletion 25765185
nsv833351 CNV loss 17160897

Variation tolerance for KDM6B Gene

Residual Variation Intolerance Score: 22% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 15.69; 97.30% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for KDM6B Gene

Human Gene Mutation Database (HGMD)
KDM6B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
KDM6B

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

Disorders for KDM6B Gene

Relevant External Links for KDM6B

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
KDM6B

No disorders were found for KDM6B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas 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 research : an international journal for rapid publication of reports on genes and genomes 1997) 2 3 4 60
  2. 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 60
  3. UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development. (PMID: 17713478) Agger K … Helin K (Nature 2007) 3 4 60
  4. 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 60
  5. Identification of JmjC domain-containing UTX and JMJD3 as histone H3 lysine 27 demethylases. (PMID: 18003914) Hong S … Ge K (Proceedings of the National Academy of Sciences of the United States of America 2007) 3 4 60

Products for KDM6B Gene

Sources for KDM6B Gene

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