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    Kdm6b lysine demethylase 6B [ Rattus norvegicus (Norway rat) ]

    Gene ID: 363630, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Kdm6bprovided by RGD
    Official Full Name
    lysine demethylase 6Bprovided by RGD
    Primary source
    RGD:1307629
    See related
    EnsemblRapid:ENSRNOG00000037613 AllianceGenome:RGD:1307629
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Jmjd3
    Summary
    Enables chromatin binding activity. Involved in several processes, including hippocampus development; response to activity; and response to fungicide. Predicted to be located in nucleus. Predicted to be part of MLL3/4 complex. 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
    Biased expression in Spleen (RPKM 47.1), Thymus (RPKM 39.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Kdm6b in Genome Data Viewer
    Location:
    10q24
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (54619520..54641014, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (54120716..54142212, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (56000494..56009582, complement)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene N(alpha)-acetyltransferase 38, NatC auxiliary subunit Neighboring gene cytochrome b5 domain containing 1 Neighboring gene transmembrane protein 88 Neighboring gene dynein, axonemal, heavy chain 2 Neighboring gene uncharacterized LOC102557224 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TRPM7 Mediates BSCB Disruption After Spinal Cord Injury by Regulating the mTOR/JMJD3 Axis in Rats.
      Title: TRPM7 Mediates BSCB Disruption After Spinal Cord Injury by Regulating the mTOR/JMJD3 Axis in Rats.
    2. Upregulation of lysine-specific demethylase 6B aggravates inflammatory pain through H3K27me3 demethylation-dependent production of TNF-alpha in the dorsal root ganglia and spinal dorsal horn in rats.
      Title: Upregulation of lysine-specific demethylase 6B aggravates inflammatory pain through H3K27me3 demethylation-dependent production of TNF-α in the dorsal root ganglia and spinal dorsal horn in rats.
    3. KDM6B Negatively Regulates the Neurogenesis Potential of Apical Papilla Stem Cells via HES1.
      Title: KDM6B Negatively Regulates the Neurogenesis Potential of Apical Papilla Stem Cells via HES1.
    4. Lysine demethylase KDM6B regulates HIF-1alpha-mediated systemic and cellular responses to intermittent hypoxia.
      Title: Lysine demethylase KDM6B regulates HIF-1α-mediated systemic and cellular responses to intermittent hypoxia.
    5. Jmjd3 Mediates Neuropathic Pain by Inducing Macrophage Infiltration and Activation in Lumbar Spinal Stenosis Animal Model.
      Title: Jmjd3 Mediates Neuropathic Pain by Inducing Macrophage Infiltration and Activation in Lumbar Spinal Stenosis Animal Model.
    6. Polycomb represses a gene network controlling puberty via modulation of histone demethylase Kdm6b expression.
      Title: Polycomb represses a gene network controlling puberty via modulation of histone demethylase Kdm6b expression.
    7. Histone H3K27 methyltransferase EZH2 and demethylase JMJD3 regulate hepatic stellate cells activation and liver fibrosis.
      Title: Histone H3K27 methyltransferase EZH2 and demethylase JMJD3 regulate hepatic stellate cells activation and liver fibrosis.
    8. Histone demethylase JMJD3 protects against renal fibrosis by suppressing TGFbeta and Notch signaling and preserving PTEN expression.
      Title: Histone demethylase JMJD3 protects against renal fibrosis by suppressing TGFβ and Notch signaling and preserving PTEN expression.
    9. IL-4 Alleviates Ischaemia-Reperfusion Injury by Inducing Kupffer Cells M2 Polarization via STAT6-JMJD3 Pathway after Rat Liver Transplantation.
      Title: IL-4 Alleviates Ischaemia-Reperfusion Injury by Inducing Kupffer Cells M2 Polarization via STAT6-JMJD3 Pathway after Rat Liver Transplantation.
    10. Jmjd3 is involved in the susceptibility to depression induced by maternal separation via enhancing the neuroinflammation in the prefrontal cortex and hippocampus of male rats.
      Title: Jmjd3 is involved in the susceptibility to depression induced by maternal separation via enhancing the neuroinflammation in the prefrontal cortex and hippocampus of male rats.
    Submit: New GeneRIF Correction See all GeneRIFs (17)

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K27me2/H3K27me3 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in cardiac muscle cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cell fate commitment ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cellular response to hydrogen peroxide ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endothelial cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in heart development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in hippocampus development IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in inflammatory response to antigenic stimulus IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in mesodermal cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of cold-induced thermogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of cold-induced thermogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in response to activity IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in response to fungicide IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of MLL3/4 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    lysine-specific demethylase 6B
    Names
    jumonji domain-containing 3
    lysine (K)-specific demethylase 6B
    NP_001102299.2
    NP_001388879.1
    XP_038942397.1
    XP_038942398.1
    XP_038942399.1
    XP_038942400.1
    XP_038942401.1
    XP_038942402.1
    XP_038942403.1
    XP_038942404.1
    XP_038942405.1
    XP_038942406.1
    XP_038942407.1
    XP_038942408.1
    XP_038942409.1
    XP_038942411.1
    XP_063125586.1
    XP_063125587.1
    XP_063125588.1

    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_001108829.2 → NP_001102299.2  lysine-specific demethylase 6B isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/TrEMBL
      G3V9U4
      Related
      ENSRNOP00000060247.4, ENSRNOT00000067677.5

    2. NM_001401950.1 → NP_001388879.1  lysine-specific demethylase 6B isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/TrEMBL
      A0A8I6AFH2

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086028.1 Reference GRCr8

      Range
      54619520..54641014 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063269518.1 → XP_063125588.1  lysine-specific demethylase 6B isoform X2

      UniProtKB/TrEMBL
      A0A8I6AFH2

    2. XM_039086478.2 → XP_038942406.1  lysine-specific demethylase 6B isoform X1

      UniProtKB/TrEMBL
      A6HFR1
      Conserved Domains (3) summary
      smart00558
      Location:1336 → 1400
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1370 → 1478
      JmjC; JmjC domain, hydroxylase

    3. XM_039086483.2 → XP_038942411.1  lysine-specific demethylase 6B isoform X3

      UniProtKB/TrEMBL
      A6HFR1
      Conserved Domains (3) summary
      smart00558
      Location:1270 → 1334
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1304 → 1412
      JmjC; JmjC domain, hydroxylase

    4. XM_039086469.2 → XP_038942397.1  lysine-specific demethylase 6B isoform X1

      UniProtKB/TrEMBL
      A6HFR1
      Conserved Domains (3) summary
      smart00558
      Location:1336 → 1400
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1370 → 1478
      JmjC; JmjC domain, hydroxylase

    5. XM_063269516.1 → XP_063125586.1  lysine-specific demethylase 6B isoform X2

      UniProtKB/TrEMBL
      A0A8I6AFH2

    6. XM_039086479.2 → XP_038942407.1  lysine-specific demethylase 6B isoform X1

      UniProtKB/TrEMBL
      A6HFR1
      Conserved Domains (3) summary
      smart00558
      Location:1336 → 1400
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1370 → 1478
      JmjC; JmjC domain, hydroxylase

    7. XM_039086470.2 → XP_038942398.1  lysine-specific demethylase 6B isoform X1

      UniProtKB/TrEMBL
      A6HFR1
      Conserved Domains (3) summary
      smart00558
      Location:1336 → 1400
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1370 → 1478
      JmjC; JmjC domain, hydroxylase

    8. XM_039086471.2 → XP_038942399.1  lysine-specific demethylase 6B isoform X1

      UniProtKB/TrEMBL
      A6HFR1
      Conserved Domains (3) summary
      smart00558
      Location:1336 → 1400
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1370 → 1478
      JmjC; JmjC domain, hydroxylase

    9. XM_039086480.2 → XP_038942408.1  lysine-specific demethylase 6B isoform X1

      UniProtKB/TrEMBL
      A6HFR1
      Conserved Domains (3) summary
      smart00558
      Location:1336 → 1400
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1370 → 1478
      JmjC; JmjC domain, hydroxylase

    10. XM_039086481.2 → XP_038942409.1  lysine-specific demethylase 6B isoform X1

      UniProtKB/TrEMBL
      A6HFR1
      Conserved Domains (3) summary
      smart00558
      Location:1336 → 1400
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1370 → 1478
      JmjC; JmjC domain, hydroxylase

    11. XM_039086472.2 → XP_038942400.1  lysine-specific demethylase 6B isoform X1

      UniProtKB/TrEMBL
      A6HFR1
      Conserved Domains (3) summary
      smart00558
      Location:1336 → 1400
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1370 → 1478
      JmjC; JmjC domain, hydroxylase

    12. XM_039086477.2 → XP_038942405.1  lysine-specific demethylase 6B isoform X1

      UniProtKB/TrEMBL
      A6HFR1
      Conserved Domains (3) summary
      smart00558
      Location:1336 → 1400
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1370 → 1478
      JmjC; JmjC domain, hydroxylase

    13. XM_039086476.2 → XP_038942404.1  lysine-specific demethylase 6B isoform X1

      UniProtKB/TrEMBL
      A6HFR1
      Conserved Domains (3) summary
      smart00558
      Location:1336 → 1400
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1370 → 1478
      JmjC; JmjC domain, hydroxylase

    14. XM_039086475.2 → XP_038942403.1  lysine-specific demethylase 6B isoform X1

      UniProtKB/TrEMBL
      A6HFR1
      Conserved Domains (3) summary
      smart00558
      Location:1336 → 1400
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1370 → 1478
      JmjC; JmjC domain, hydroxylase

    15. XM_063269517.1 → XP_063125587.1  lysine-specific demethylase 6B isoform X2

      UniProtKB/TrEMBL
      A0A8I6AFH2
      Related
      ENSRNOP00000091469.1, ENSRNOT00000116399.2

    16. XM_039086474.2 → XP_038942402.1  lysine-specific demethylase 6B isoform X1

      UniProtKB/TrEMBL
      A6HFR1
      Conserved Domains (3) summary
      smart00558
      Location:1336 → 1400
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1370 → 1478
      JmjC; JmjC domain, hydroxylase

    17. XM_039086473.2 → XP_038942401.1  lysine-specific demethylase 6B isoform X1

      UniProtKB/TrEMBL
      A6HFR1
      Conserved Domains (3) summary
      smart00558
      Location:1336 → 1400
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      sd00006
      Location:106 → 136
      TPR; TPR repeat [structural motif]
      pfam02373
      Location:1370 → 1478
      JmjC; JmjC domain, hydroxylase
    Nucleotide Protein Strain
    Heading Accession and Version

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