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

Gene ID: 363630, updated on 17-Aug-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. Located in nucleus. Orthologous to human KDM6B (lysine demethylase 6B). [provided by Alliance of Genome Resources, Apr 2022]
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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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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Related articles in PubMed

  1. Jmjd3 Mediates Neuropathic Pain by Inducing Macrophage Infiltration and Activation in Lumbar Spinal Stenosis Animal Model. Lee J, et al. Int J Mol Sci, 2021 Dec 14. PMID 34948220, Free PMC Article
  2. Lysine demethylase KDM6B regulates HIF-1α-mediated systemic and cellular responses to intermittent hypoxia. Nanduri J, et al. Physiol Genomics, 2021 Sep 1. PMID 34297635, Free PMC Article
  3. 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. Wang R, et al. Exp Neurol, 2020 Jun. PMID 32084453
  4. Decreased Methylation Level of H3K27me3 Increases Seizure Susceptibility. Wang Z, et al. Mol Neurobiol, 2017 Nov. PMID 27815838
  5. High-intensity training induces EIB in rats through neuron transdifferentiation of adrenal medulla chromaffin cells. He R, et al. Am J Physiol Lung Cell Mol Physiol, 2013 May 1. PMID 23418092

See all (31) citations in PubMed

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
    A6HFR1, 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, A6HFR1

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, A6HFR1

  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, A6HFR1

  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, A6HFR1
    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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