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Aliases for KDM6B Gene

Aliases for KDM6B Gene

  • Lysine Demethylase 6B 2 3 4
  • Lysine (K)-Specific Demethylase 6B 2 3 5
  • Jumonji Domain Containing 3, Histone Lysine Demethylase 2 3
  • Jumonji Domain-Containing Protein 3 3 4
  • JmjC Domain-Containing Protein 3 3 4
  • JMJD3 3 4
  • Jumonji Domain Containing 3 2
  • EC 1.14.11.- 4
  • EC 1.14.11 63
  • 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

GeneCards Summary for KDM6B Gene

KDM6B (Lysine Demethylase 6B) is a Protein Coding gene. Among its related pathways are Cellular Senescence and Chromatin organization. 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 (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.

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

Promoters for KDM6B Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs 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

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:
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 & Families for KDM6B Gene

Gene Families for KDM6B Gene

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 :
  • Contains 1 JmjC domain.
  • Belongs to the UTX family.
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:0008013 beta-catenin 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

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
Jensen Localization Image for KDM6B Gene COMPARTMENTS Subcellular localization image for KDM6B gene
Compartment Confidence
nucleus 5
extracellular 2
cytosol 1
mitochondrion 1

No data available for Gene Ontology (GO) - Cellular Components for KDM6B Gene

Pathways & Interactions for KDM6B Gene

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

Pathways by source 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:0010468 regulation of gene expression IEA --
GO:0014823 response to activity IEA --
GO:0021766 hippocampus development IEA --
GO:0045446 endothelial cell differentiation ISS 23856522
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

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
JIB-04 Pharma Jumonji histone demethylase inihibitor 0
GSK-J1 Pharma 0
Daminozide Pharma Selective KDM2/7 inhibitor 0
IOX 1 Pharma Histone demethylase inhibitor; cell permeable 0
Tranylcypromine hydrochloride Pharma Irreversible inhibitor of LSD1; also inhibits MAO 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
GSK J1
1373422-53-7
GSK J4
1373423-53-0
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:

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 (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



SOURCE GeneReport for Unigene cluster for KDM6B Gene Hs.223678

genes like me logo Genes that share expression patterns with KDM6B: view

Protein tissue co-expression partners for KDM6B Gene

Primer Products

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
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
chimpanzee
(Pan troglodytes)
Mammalia KDM6B 35
  • 99.58 (n)
  • 99.52 (a)
KDM6B 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Kdm6b 35
  • 87.6 (n)
  • 91.31 (a)
platypus
(Ornithorhynchus anatinus)
Mammalia KDM6B 36
  • 50 (a)
OneToOne
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

(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
rs2270516 - 7,847,118(+) GCACT(C/T)GCTGC reference, missense
rs60738318 - 7,846,636(+) CTGAA(C/G/T)CCCCA reference, missense
rs1389613 -- 7,848,262(-) ACCCC(A/G)GGCGG reference, synonymous-codon
rs2270517 -- 7,847,529(+) CCACC(C/T)GCTTC intron-variant
rs3736305 -- 7,852,414(-) GCTGG(C/T)GGCTC intron-variant

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

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

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

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 Res. 1997) 2 3 4 67
  2. Physical map of 17p13 and the genes adjacent to p53. (PMID: 10662545) Cousin P. … Shaw P. (Genomics 2000) 2 3
  3. Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci. (PMID: 25429064) He M. … Qi L. (Hum. Mol. Genet. 2015) 3
  4. Histone demethylase Jmjd3 is required for the development of subsets of retinal bipolar cells. (PMID: 24572572) Iida A. … Watanabe S. (Proc. Natl. Acad. Sci. U.S.A. 2014) 3
  5. The localization of histone H3K27me3 demethylase Jmjd3 is dynamically regulated. (PMID: 24646476) Kamikawa Y.F. … Donohoe M.E. (Epigenetics 2014) 3

Products for KDM6B Gene

Sources for KDM6B Gene

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