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

Gene ID: 216850, updated on 2-Nov-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, Nov 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 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. Downregulation of the endothelial histone demethylase JMJD3 is associated with neointimal hyperplasia of arteriovenous fistulas in kidney failure. Feng S, et al. J Biol Chem, 2022 May. PMID 35278430, Free PMC Article

See all (182) 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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