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    Kdm6b KDM1 lysine (K)-specific demethylase 6B [ Mus musculus (house mouse) ]

    Gene ID: 216850, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Kdm6bprovided by MGI
    Official Full Name
    KDM1 lysine (K)-specific demethylase 6Bprovided by MGI
    Primary source
    MGI:MGI:2448492
    See related
    Ensembl:ENSMUSG00000018476 AllianceGenome:MGI:2448492
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Jmjd3; 1700064E03Rik
    Summary
    Enables beta-catenin binding activity; histone H3K27me2/H3K27me3 demethylase activity; and sequence-specific DNA binding activity. Involved in several processes, including cardiac muscle cell differentiation; mesodermal cell differentiation; and positive regulation of cold-induced thermogenesis. Acts upstream of or within cell fate commitment; cellular response to hydrogen peroxide; and positive regulation of transcription by RNA polymerase II. Located in nucleus. Is expressed in several structures, including 1st branchial arch ectoderm; brain; genitourinary system; olfactory epithelium; and palatal shelf. Human ortholog(s) of this gene implicated in Stolerman neurodevelopmental syndrome. Orthologous to human KDM6B (lysine demethylase 6B). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in thymus adult (RPKM 16.9), duodenum adult (RPKM 10.2) and 25 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Kdm6b in Genome Data Viewer
    Location:
    11 B3; 11 42.6 cM
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (69289334..69311188, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (69398508..69420367, complement)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E7004 Neighboring gene STARR-positive B cell enhancer ABC_E5241 Neighboring gene cytochrome b5 domain containing 1 Neighboring gene STARR-positive B cell enhancer ABC_E2996 Neighboring gene STARR-positive B cell enhancer ABC_E5242 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:69223376-69223485 Neighboring gene transmembrane protein 88 Neighboring gene N(alpha)-acetyltransferase 38, NatC auxiliary subunit Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:69231989-69232098 Neighboring gene predicted gene, 51903 Neighboring gene dynein, axonemal, heavy chain 2 Neighboring gene STARR-seq mESC enhancer starr_29847 Neighboring gene STARR-seq mESC enhancer starr_29849 Neighboring gene ephrin B3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Histone demethylase JMJD3 is required for osteoblast differentiation in mice. Zhang F, et al. Sci Rep, 2015 Aug 25. PMID 26302868, Free PMC Article
    2. The histone lysine demethylase Kdm6b is required for activity-dependent preconditioning of hippocampal neuronal survival. Wijayatunge R, et al. Mol Cell Neurosci, 2014 Jul. PMID 24983519, Free PMC Article
    3. JMJD3/H3K27me3 epigenetic modification regulates Th17/Treg cell differentiation in ulcerative colitis. Leng XY, et al. Int Immunopharmacol, 2022 Sep. PMID 35777266
    4. Critical role of histone demethylase Jmjd3 in the regulation of CD4+ T-cell differentiation. Li Q, et al. Nat Commun, 2014 Dec 22. PMID 25531312, Free PMC Article
    5. KDM6B-dependent chromatin remodeling underpins effective virus-specific CD8(+) T cell differentiation. Li J, et al. Cell Rep, 2021 Mar 16. PMID 33730567

    See all (183) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Understanding the Role of the SMN Complex Component GEMIN5 and Its Functional Relationship with Demethylase KDM6B in the Flunarizine-Mediated Neuroprotection of Motor Neuron Disease Spinal Muscular Atrophy.
      Title: Understanding the Role of the SMN Complex Component GEMIN5 and Its Functional Relationship with Demethylase KDM6B in the Flunarizine-Mediated Neuroprotection of Motor Neuron Disease Spinal Muscular Atrophy.
    2. Diabetic Wound Keratinocytes Induce Macrophage JMJD3-Mediated Nlrp3 Expression via IL-1R Signaling.
      Title: Diabetic Wound Keratinocytes Induce Macrophage JMJD3-Mediated Nlrp3 Expression via IL-1R Signaling.
    3. High-intensity interval training ameliorates postnatal immune activation-induced mood disorders through KDM6B-regulated glial activation.
      Title: High-intensity interval training ameliorates postnatal immune activation-induced mood disorders through KDM6B-regulated glial activation.
    4. YAP represses intestinal inflammation through epigenetic silencing of JMJD3.
      Title: YAP represses intestinal inflammation through epigenetic silencing of JMJD3.
    5. KDM6B drives epigenetic reprogramming associated with lymphoid stromal cell early commitment and immune properties.
      Title: KDM6B drives epigenetic reprogramming associated with lymphoid stromal cell early commitment and immune properties.
    6. Osteoblast Jmjd3 regulates osteoclastogenesis via EphB4 and RANKL signalling.
      Title: Osteoblast Jmjd3 regulates osteoclastogenesis via EphB4 and RANKL signalling.
    7. Lineage commitment of dermal fibroblast progenitors is controlled by Kdm6b-mediated chromatin demethylation.
      Title: Lineage commitment of dermal fibroblast progenitors is controlled by Kdm6b-mediated chromatin demethylation.
    8. Integrative bioinformatics and validation studies reveal KDM6B and its associated molecules as crucial modulators in Idiopathic Pulmonary Fibrosis.
      Title: Integrative bioinformatics and validation studies reveal KDM6B and its associated molecules as crucial modulators in Idiopathic Pulmonary Fibrosis.
    9. KDM6B protects T-ALL cells from NOTCH1-induced oncogenic stress.
      Title: KDM6B protects T-ALL cells from NOTCH1-induced oncogenic stress.
    10. JMJD3 downregulates IL4i1 aggravating lipopolysaccharide-induced acute lung injury via H3K27 and H3K4 demethylation.
      Title: JMJD3 downregulates IL4i1 aggravating lipopolysaccharide-induced acute lung injury via H3K27 and H3K4 demethylation.
    Submit: New GeneRIF Correction See all GeneRIFs (126)

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Clone Names

    • KIAA0346, mKIAA0346

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables beta-catenin binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables chromatin DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chromatin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K27me2/H3K27me3 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone H3K27me2/H3K27me3 demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K27me2/H3K27me3 demethylase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables histone H3K27me2/H3K27me3 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cardiac muscle cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within cell fate commitment IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within cellular response to hydrogen peroxide IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in chromatin remodeling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in endothelial cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in heart development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in hippocampus development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in hippocampus development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in inflammatory response to antigenic stimulus IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mesodermal cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of cold-induced thermogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to fungicide IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of MLL3/4 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    lysine-specific demethylase 6B
    Names
    [histone H3]-trimethyl-L-lysine(27) demethylase 6B
    jmjC domain-containing protein 3
    jumonji domain containing 3
    jumonji domain-containing protein 3
    NP_001017426.1
    XP_030101676.1
    XP_030101677.1
    XP_030101678.1
    XP_030101679.1
    XP_030101680.1
    XP_030101681.1
    XP_030101682.1
    XP_030101683.1
    XP_030101684.1
    XP_030101685.1
    XP_030101686.1
    XP_036012463.1
    XP_036012464.1

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_001017426.2 → NP_001017426.1  lysine-specific demethylase 6B

      See identical proteins and their annotated locations for NP_001017426.1

      Status: VALIDATED

      Source sequence(s)
      AL596125
      Consensus CDS
      CCDS24895.1
      UniProtKB/Swiss-Prot
      Q3UWY9, Q4VC26, Q5NCY0, Q6ZQD3
      Related
      ENSMUSP00000091620.5, ENSMUST00000094077.5
      Conserved Domains (3) summary
      pfam02373
      Location:1375 → 1483
      JmjC; JmjC domain, hydroxylase
      smart00558
      Location:1341 → 1405
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000077.7 Reference GRCm39 C57BL/6J

      Range
      69289334..69311188 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030245817.2 → XP_030101677.1  lysine-specific demethylase 6B isoform X1

      Conserved Domains (3) summary
      smart00558
      Location:1342 → 1406
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1376 → 1484
      JmjC; JmjC domain, hydroxylase

    2. XM_030245818.2 → XP_030101678.1  lysine-specific demethylase 6B isoform X1

      Conserved Domains (3) summary
      smart00558
      Location:1342 → 1406
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1376 → 1484
      JmjC; JmjC domain, hydroxylase

    3. XM_030245816.2 → XP_030101676.1  lysine-specific demethylase 6B isoform X1

      Conserved Domains (3) summary
      smart00558
      Location:1342 → 1406
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1376 → 1484
      JmjC; JmjC domain, hydroxylase

    4. XM_036156570.1 → XP_036012463.1  lysine-specific demethylase 6B isoform X1

      Conserved Domains (3) summary
      smart00558
      Location:1342 → 1406
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1376 → 1484
      JmjC; JmjC domain, hydroxylase

    5. XM_030245819.2 → XP_030101679.1  lysine-specific demethylase 6B isoform X1

      Conserved Domains (3) summary
      smart00558
      Location:1342 → 1406
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1376 → 1484
      JmjC; JmjC domain, hydroxylase

    6. XM_030245826.2 → XP_030101686.1  lysine-specific demethylase 6B isoform X1

      Conserved Domains (3) summary
      smart00558
      Location:1342 → 1406
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1376 → 1484
      JmjC; JmjC domain, hydroxylase

    7. XM_030245823.2 → XP_030101683.1  lysine-specific demethylase 6B isoform X1

      Conserved Domains (3) summary
      smart00558
      Location:1342 → 1406
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1376 → 1484
      JmjC; JmjC domain, hydroxylase

    8. XM_036156571.1 → XP_036012464.1  lysine-specific demethylase 6B isoform X1

      Conserved Domains (3) summary
      smart00558
      Location:1342 → 1406
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1376 → 1484
      JmjC; JmjC domain, hydroxylase

    9. XM_030245824.2 → XP_030101684.1  lysine-specific demethylase 6B isoform X1

      Conserved Domains (3) summary
      smart00558
      Location:1342 → 1406
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1376 → 1484
      JmjC; JmjC domain, hydroxylase

    10. XM_030245820.2 → XP_030101680.1  lysine-specific demethylase 6B isoform X1

      Conserved Domains (3) summary
      smart00558
      Location:1342 → 1406
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1376 → 1484
      JmjC; JmjC domain, hydroxylase

    11. XM_030245825.2 → XP_030101685.1  lysine-specific demethylase 6B isoform X1

      Conserved Domains (3) summary
      smart00558
      Location:1342 → 1406
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1376 → 1484
      JmjC; JmjC domain, hydroxylase

    12. XM_030245822.2 → XP_030101682.1  lysine-specific demethylase 6B isoform X1

      Conserved Domains (3) summary
      smart00558
      Location:1342 → 1406
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1376 → 1484
      JmjC; JmjC domain, hydroxylase

    13. XM_030245821.2 → XP_030101681.1  lysine-specific demethylase 6B isoform X1

      Conserved Domains (3) summary
      smart00558
      Location:1342 → 1406
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1376 → 1484
      JmjC; JmjC domain, hydroxylase
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5NCY0.1 GenPept UniProtKB/Swiss-Prot:Q5NCY0

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