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Kdm4b lysine (K)-specific demethylase 4B [ Mus musculus (house mouse) ]

Gene ID: 193796, updated on 2-Nov-2024

Summary

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Official Symbol
Kdm4bprovided by MGI
Official Full Name
lysine (K)-specific demethylase 4Bprovided by MGI
Primary source
MGI:MGI:2442355
See related
Ensembl:ENSMUSG00000024201 AllianceGenome:MGI:2442355
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
Jmjd2b; 4732474L06Rik
Summary
Enables histone H3K36 demethylase activity and histone H3K9 demethylase activity. Involved in brain development. Located in pericentric heterochromatin. Is expressed in several structures, including central nervous system; peripheral nervous system ganglion; reproductive system; sensory organ; and urinary system. Human ortholog(s) of this gene implicated in autosomal dominant intellectual developmental disorder; breast cancer; colorectal cancer; malignant peripheral nerve sheath tumor; and stomach cancer. Orthologous to human KDM4B (lysine demethylase 4B). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in thymus adult (RPKM 19.4), ovary adult (RPKM 19.2) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Kdm4b in Genome Data Viewer
Location:
17 D; 17 29.27 cM
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (56632975..56710774)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (56325970..56403774)

Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E3208 Neighboring gene STARR-positive B cell enhancer ABC_E3209 Neighboring gene arrestin domain containing 5 Neighboring gene ubiquitin-like, containing PHD and RING finger domains, 1 Neighboring gene STARR-positive B cell enhancer ABC_E141 Neighboring gene STARR-positive B cell enhancer ABC_E8923 Neighboring gene predicted gene, 32715 Neighboring gene protein tyrosine phosphatase receptor type S Neighboring gene microRNA 6977 Neighboring gene STARR-positive B cell enhancer ABC_E5622 Neighboring gene STARR-positive B cell enhancer mm9_chr17:56601992-56602293 Neighboring gene predicted gene, 32822 Neighboring gene predicted gene 9258

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. Super-enhancer-driven LncRNA PPARα-seRNA exacerbates glucolipid metabolism and diabetic cardiomyopathy via recruiting KDM4B. Ma X, et al. Mol Metab, 2024 Aug. PMID 38950776, Free PMC Article
  2. Novel insights into the angiogenic function of JMJD2B in diabetic hind limb ischemia: involvement of activating Wnt/β-catenin pathway. Wang Z, et al. Hum Cell, 2023 May. PMID 36773117
  3. Transient JMJD2B-mediated reduction of H3K9me3 levels improves reprogramming of embryonic stem cells into cloned embryos. Antony J, et al. Mol Cell Biol, 2013 Mar. PMID 23263990, Free PMC Article
  4. KDM4B-mediated reduction of H3K9me3 and H3K36me3 levels improves somatic cell reprogramming into pluripotency. Wei J, et al. Sci Rep, 2017 Aug 8. PMID 28790329, Free PMC Article
  5. Mutations inhibiting KDM4B drive ALT activation in ATRX-mutated glioblastomas. Udugama M, et al. Nat Commun, 2021 May 10. PMID 33972520, Free PMC Article

See all (70) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Super-enhancer-driven LncRNA PPARalpha-seRNA exacerbates glucolipid metabolism and diabetic cardiomyopathy via recruiting KDM4B.
    Title: Super-enhancer-driven LncRNA PPARα-seRNA exacerbates glucolipid metabolism and diabetic cardiomyopathy via recruiting KDM4B.
  2. Novel insights into the angiogenic function of JMJD2B in diabetic hind limb ischemia: involvement of activating Wnt/beta-catenin pathway.
    Title: Novel insights into the angiogenic function of JMJD2B in diabetic hind limb ischemia: involvement of activating Wnt/β-catenin pathway.
  3. Histone H3.3 phosphorylation promotes heterochromatin formation by inhibiting H3K9/K36 histone demethylase.
    Title: Histone H3.3 phosphorylation promotes heterochromatin formation by inhibiting H3K9/K36 histone demethylase.
  4. Enterotoxigenic Bacteroides fragilis induces the stemness in colorectal cancer via upregulating histone demethylase JMJD2B.
    Title: Enterotoxigenic Bacteroides fragilis induces the stemness in colorectal cancer via upregulating histone demethylase JMJD2B.
  5. Histone demethylase JMJD2B/KDM4B regulates transcriptional program via distinctive epigenetic targets and protein interactors for the maintenance of trophoblast stem cells.
    Title: Histone demethylase JMJD2B/KDM4B regulates transcriptional program via distinctive epigenetic targets and protein interactors for the maintenance of trophoblast stem cells.
  6. Mutations inhibiting KDM4B drive ALT activation in ATRX-mutated glioblastomas.
    Title: Mutations inhibiting KDM4B drive ALT activation in ATRX-mutated glioblastomas.
  7. Histone H3K9 Demethylase JMJD2B Plays a Role in LXRalpha-Dependent Lipogenesis.
    Title: Histone H3K9 Demethylase JMJD2B Plays a Role in LXRα-Dependent Lipogenesis.
  8. Heterozygous Variants in KDM4B Lead to Global Developmental Delay and Neuroanatomical Defects.
    Title: Heterozygous Variants in KDM4B Lead to Global Developmental Delay and Neuroanatomical Defects.
  9. KDM4 knockdown resulted in the down-regulation of miR-29 expression.
    Title: The histone demethylase Kdm4 suppresses activation of hepatic stellate cell by inducing MiR-29 transcription.
  10. The JMJD2B-dependent upregulation of PPARgamma2 was associated with the removal of di- and trimethylation of histone H3 lysine 9 on the promoter of PPARgamma2. Furthermore, exogeneous expression of JMJD2B using adenovirus in mice resulted in hepatic steatosis when fed a HFD, which was accompanied with increased expression of hepatic PPARgamma2 and its steatosis target genes.
    Title: Histone H3K9 demethylase JMJD2B induces hepatic steatosis through upregulation of PPARγ2.
Submit: New GeneRIF Correction See all GeneRIFs (22)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (3) 
  • Targeted (5)  1 citation

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

  • MGC6349

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables histone H3K36 demethylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H3K36 demethylase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables histone H3K36 demethylase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone H3K9 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone H3K9 demethylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H3K9 demethylase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables histone H3K9 demethylase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone H3K9me2/H3K9me3 demethylase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H3K9me2/H3K9me3 demethylase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone demethylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in brain development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in pericentric heterochromatin IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
lysine-specific demethylase 4B
Names
[histone H3]-trimethyl-L-lysine(9) demethylase 4B
jmjC domain-containing histone demethylation protein 3B
jumonji domain-containing protein 2B
NP_001344838.1
NP_742144.1
XP_006523957.1
XP_006523958.1
XP_006523959.1
XP_006523960.1
XP_006523961.1
XP_017172842.1
XP_017172843.1
XP_017172844.1
XP_017172845.1
XP_030105461.1
XP_030105462.1
XP_030105463.1
XP_030105464.1
XP_030105465.1
XP_030105466.1

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_001357909.1 → NP_001344838.1  lysine-specific demethylase 4B isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC026385, BP762845, CT009637
    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    smart00333
    Location:881 → 931
    TUDOR; Tudor domain
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    cl22851
    Location:757 → 866
    PHD_SF; PHD finger superfamily

  2. NM_172132.3 → NP_742144.1  lysine-specific demethylase 4B isoform 1

    See identical proteins and their annotated locations for NP_742144.1

    Status: VALIDATED

    Source sequence(s)
    AK141879, BP762845, CA324771, CJ093438, CT009637
    Consensus CDS
    CCDS28904.1
    UniProtKB/Swiss-Prot
    Q3UR22, Q6ZQ30, Q91VY5, Q99K42
    UniProtKB/TrEMBL
    B0V2M9
    Related
    ENSMUSP00000025036.5, ENSMUST00000025036.11
    Conserved Domains (4) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:910 → 944
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:785 → 894
    PHD_SF; PHD finger superfamily

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_000083.7 Reference GRCm39 C57BL/6J

    Range
    56632975..56710774
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006523896.3 → XP_006523959.1  lysine-specific demethylase 4B isoform X6

    UniProtKB/TrEMBL
    B0V2M9
    Related
    ENSMUSP00000084045.6, ENSMUST00000086835.12
    Conserved Domains (4) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:903 → 937
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:778 → 887
    PHD_SF; PHD finger superfamily

  2. XM_030249601.1 → XP_030105461.1  lysine-specific demethylase 4B isoform X1

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:948 → 982
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:823 → 932
    PHD_SF; PHD finger superfamily

  3. XM_006523894.3 → XP_006523957.1  lysine-specific demethylase 4B isoform X4

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:910 → 944
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:785 → 894
    PHD_SF; PHD finger superfamily

  4. XM_006523895.3 → XP_006523958.1  lysine-specific demethylase 4B isoform X5

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:904 → 938
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:779 → 888
    PHD_SF; PHD finger superfamily

  5. XM_006523898.3 → XP_006523961.1  lysine-specific demethylase 4B isoform X8

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:897 → 931
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:772 → 881
    PHD_SF; PHD finger superfamily

  6. XM_006523897.3 → XP_006523960.1  lysine-specific demethylase 4B isoform X7

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:901 → 935
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:776 → 885
    PHD_SF; PHD finger superfamily

  7. XM_030249602.1 → XP_030105462.1  lysine-specific demethylase 4B isoform X1

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:948 → 982
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:823 → 932
    PHD_SF; PHD finger superfamily

  8. XM_030249603.2 → XP_030105463.1  lysine-specific demethylase 4B isoform X3

    UniProtKB/Swiss-Prot
    Q3UR22, Q6ZQ30, Q91VY5, Q99K42
    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:910 → 944
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:785 → 894
    PHD_SF; PHD finger superfamily

  9. XM_030249604.1 → XP_030105464.1  lysine-specific demethylase 4B isoform X6

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:903 → 937
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:778 → 887
    PHD_SF; PHD finger superfamily

  10. XM_030249605.1 → XP_030105465.1  lysine-specific demethylase 4B isoform X7

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:901 → 935
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:776 → 885
    PHD_SF; PHD finger superfamily

  11. XM_017317354.2 → XP_017172843.1  lysine-specific demethylase 4B isoform X2

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:920 → 954
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:795 → 904
    PHD_SF; PHD finger superfamily

  12. XM_017317353.2 → XP_017172842.1  lysine-specific demethylase 4B isoform X2

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:920 → 954
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:795 → 904
    PHD_SF; PHD finger superfamily

  13. XM_017317355.2 → XP_017172844.1  lysine-specific demethylase 4B isoform X9

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:882 → 916
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:757 → 866
    PHD_SF; PHD finger superfamily

  14. XM_017317356.2 → XP_017172845.1  lysine-specific demethylase 4B isoform X10

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:876 → 910
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:751 → 860
    PHD_SF; PHD finger superfamily

  15. XM_030249606.2 → XP_030105466.1  lysine-specific demethylase 4B isoform X11

    UniProtKB/TrEMBL
    B0V2M9
    Conserved Domains (4) summary
    smart00545
    Location:15 → 56
    JmjN; Small domain found in the jumonji family of transcription factors
    pfam02373
    Location:176 → 292
    JmjC; JmjC domain, hydroxylase
    pfam18104
    Location:875 → 909
    Tudor_2; Jumonji domain-containing protein 2A Tudor domain
    cl22851
    Location:750 → 859
    PHD_SF; PHD finger superfamily
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q91VY5.1 GenPept UniProtKB/Swiss-Prot:Q91VY5

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