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KDM6B lysine demethylase 6B [ Homo sapiens (human) ]

Gene ID: 23135, updated on 12-Aug-2018

Summary

Official Symbol
KDM6Bprovided by HGNC
Official Full Name
lysine demethylase 6Bprovided by HGNC
Primary source
HGNC:HGNC:29012
See related
Ensembl:ENSG00000132510 MIM:611577; Vega:OTTHUMG00000178021
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
JMJD3
Summary
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]
Expression
Ubiquitous expression in bone marrow (RPKM 9.0), appendix (RPKM 7.9) and 25 other tissues See more
Orthologs

Genomic context

See KDM6B in Genome Data Viewer
Location:
17p13.1
Exon count:
28
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 17 NC_000017.11 (7834210..7854796)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (7737521..7758118)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene dynein axonemal heavy chain 2 Neighboring gene ribosomal protein L29 pseudogene 2 Neighboring gene uncharacterized LOC105371516 Neighboring gene uncharacterized LOC107987244 Neighboring gene transmembrane protein 88 Neighboring gene cytochrome b5 domain containing 1 Neighboring gene N(alpha)-acetyltransferase 38, NatC auxiliary subunit

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120 upregulates the expression of lysine-specific demethylase 6B (KDM6B) in human B cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Cellular Senescence, organism-specific biosystem (from REACTOME)
    Cellular Senescence, organism-specific biosystemCellular senescence involves irreversible growth arrest accompanied by phenotypic changes such as enlarged morphology, reorganization of chromatin through formation of senescence-associated heterochr...
  • Cellular responses to stress, organism-specific biosystem (from REACTOME)
    Cellular responses to stress, organism-specific biosystemCells are subject to external molecular and physical stresses such as foreign molecules that perturb metabolic or signaling processes, and changes in temperature or pH. The ability of cells and tissu...
  • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
    Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
  • Chromatin organization, organism-specific biosystem (from REACTOME)
    Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
  • HDMs demethylate histones, organism-specific biosystem (from REACTOME)
    HDMs demethylate histones, organism-specific biosystemHistone lysine demethylases (KDMs) are able to reverse N-methylations of histones and probably other proteins. To date KDMs have been demonstrated to catalyse demethylation of N-epsilon methylated ly...
  • Oxidative Stress Induced Senescence, organism-specific biosystem (from REACTOME)
    Oxidative Stress Induced Senescence, organism-specific biosystemOxidative stress, caused by increased concentration of reactive oxygen species (ROS) in the cell, can happen as a consequence of mitochondrial dysfunction induced by the oncogenic RAS (Moiseeva et al...
  • Pathways Affected in Adenoid Cystic Carcinoma, organism-specific biosystem (from WikiPathways)
    Pathways Affected in Adenoid Cystic Carcinoma, organism-specific biosystemProtein pathways altered by mutations in adenoid cystic carcinoma. Pathways include epigentic modification, DNA damage checkpoint signals, MYB/MYC signalling pathway, FGF/IGF/PI3K signalling, and not...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Homology

Clone Names

  • KIAA0346

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA polymerase II proximal promoter sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
beta-catenin binding IEA
Inferred from Electronic Annotation
more info
 
chromatin DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
histone demethylase activity TAS
Traceable Author Statement
more info
 
histone demethylase activity (H3-K27 specific) EXP
Inferred from Experiment
more info
PubMed 
histone demethylase activity (H3-K27 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone demethylase activity (H3-K27 specific) IMP
Inferred from Mutant Phenotype
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cardiac muscle cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
cell fate commitment IEA
Inferred from Electronic Annotation
more info
 
cellular response to hydrogen peroxide IEA
Inferred from Electronic Annotation
more info
 
chromatin remodeling ISS
Inferred from Sequence or Structural Similarity
more info
 
endothelial cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
hippocampus development IEA
Inferred from Electronic Annotation
more info
 
histone H3-K27 demethylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
inflammatory response to antigenic stimulus IEA
Inferred from Electronic Annotation
more info
 
mesodermal cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
oxidation-reduction process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cold-induced thermogenesis ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
response to activity IEA
Inferred from Electronic Annotation
more info
 
response to fungicide IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
MLL3/4 complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 

General protein information

Preferred Names
lysine-specific demethylase 6B
Names
jmjC domain-containing protein 3
jumonji domain containing 3, histone lysine demethylase
jumonji domain-containing protein 3
lysine (K)-specific demethylase 6B

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_053032.1 RefSeqGene

    Range
    10718..25597
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001080424.2NP_001073893.1  lysine-specific demethylase 6B isoform 1

    See identical proteins and their annotated locations for NP_001073893.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) retains an intron in the 3' coding region, compared to variant 2, and encodes a longer protein (isoform 1), compared to isoform 2.
    Source sequence(s)
    AB002344, AC104581, BC035897
    Consensus CDS
    CCDS32552.1
    UniProtKB/Swiss-Prot
    O15054
    Related
    ENSP00000254846.5, OTTHUMP00000258343, ENST00000254846.9, OTTHUMT00000440247
    Conserved Domains (3) summary
    pfam02373
    Location:13771485
    JmjC; JmjC domain, hydroxylase
    smart00558
    Location:13431407
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam05308
    Location:566640
    Mito_fiss_reg; Mitochondrial fission regulator
  2. NM_001348716.1NP_001335645.1  lysine-specific demethylase 6B isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) encodes the shorter isoform (2).
    Source sequence(s)
    AC104581, BC009994, BC035897
    Consensus CDS
    CCDS86569.1
    UniProtKB/Swiss-Prot
    O15054
    Related
    ENSP00000412513.2, ENST00000448097.6
    Conserved Domains (3) summary
    pfam02373
    Location:13771485
    JmjC; JmjC domain, hydroxylase
    smart00558
    Location:13431407
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    cl26247
    Location:572718
    DNA_pol3_delta2; DNA polymerase III, delta subunit

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p12 Primary Assembly

    Range
    7834210..7854796
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005256549.3XP_005256606.1  lysine-specific demethylase 6B isoform X1

    See identical proteins and their annotated locations for XP_005256606.1

    UniProtKB/Swiss-Prot
    O15054
    Conserved Domains (3) summary
    pfam02373
    Location:13771485
    JmjC; JmjC domain, hydroxylase
    smart00558
    Location:13431407
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam05308
    Location:566640
    Mito_fiss_reg; Mitochondrial fission regulator
  2. XM_005256551.3XP_005256608.1  lysine-specific demethylase 6B isoform X1

    See identical proteins and their annotated locations for XP_005256608.1

    UniProtKB/Swiss-Prot
    O15054
    Conserved Domains (3) summary
    pfam02373
    Location:13771485
    JmjC; JmjC domain, hydroxylase
    smart00558
    Location:13431407
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam05308
    Location:566640
    Mito_fiss_reg; Mitochondrial fission regulator
  3. XM_006721483.3XP_006721546.1  lysine-specific demethylase 6B isoform X1

    See identical proteins and their annotated locations for XP_006721546.1

    UniProtKB/Swiss-Prot
    O15054
    Conserved Domains (3) summary
    pfam02373
    Location:13771485
    JmjC; JmjC domain, hydroxylase
    smart00558
    Location:13431407
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam05308
    Location:566640
    Mito_fiss_reg; Mitochondrial fission regulator
  4. XM_011523750.2XP_011522052.1  lysine-specific demethylase 6B isoform X1

    See identical proteins and their annotated locations for XP_011522052.1

    UniProtKB/Swiss-Prot
    O15054
    Conserved Domains (3) summary
    pfam02373
    Location:13771485
    JmjC; JmjC domain, hydroxylase
    smart00558
    Location:13431407
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam05308
    Location:566640
    Mito_fiss_reg; Mitochondrial fission regulator
  5. XM_011523752.3XP_011522054.1  lysine-specific demethylase 6B isoform X1

    See identical proteins and their annotated locations for XP_011522054.1

    UniProtKB/Swiss-Prot
    O15054
    Conserved Domains (3) summary
    pfam02373
    Location:13771485
    JmjC; JmjC domain, hydroxylase
    smart00558
    Location:13431407
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam05308
    Location:566640
    Mito_fiss_reg; Mitochondrial fission regulator
  6. XM_005256552.5XP_005256609.1  lysine-specific demethylase 6B isoform X1

    See identical proteins and their annotated locations for XP_005256609.1

    UniProtKB/Swiss-Prot
    O15054
    Conserved Domains (3) summary
    pfam02373
    Location:13771485
    JmjC; JmjC domain, hydroxylase
    smart00558
    Location:13431407
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam05308
    Location:566640
    Mito_fiss_reg; Mitochondrial fission regulator
  7. XM_005256550.4XP_005256607.1  lysine-specific demethylase 6B isoform X1

    See identical proteins and their annotated locations for XP_005256607.1

    UniProtKB/Swiss-Prot
    O15054
    Conserved Domains (3) summary
    pfam02373
    Location:13771485
    JmjC; JmjC domain, hydroxylase
    smart00558
    Location:13431407
    JmjC; A domain family that is part of the cupin metalloenzyme superfamily
    pfam05308
    Location:566640
    Mito_fiss_reg; Mitochondrial fission regulator
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