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

    Gene ID: 193796, updated on 21-Apr-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 H3-methyl-lysine-9 demethylase activity. Acts upstream of or within histone H3-K36 demethylation; histone H3-K9 demethylation; and negative regulation of histone H3-K9 trimethylation. Located in pericentric heterochromatin. Is expressed in several structures, including early conceptus; genitourinary system; heart; nervous system; and sensory organ. Human ortholog(s) of this gene implicated in autosomal dominant non-syndromic intellectual disability; 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, Apr 2022]
    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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    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
    • 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. 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
    2. Mutations inhibiting KDM4B drive ALT activation in ATRX-mutated glioblastomas. Udugama M, et al. Nat Commun, 2021 May 10. PMID 33972520, Free PMC Article
    3. Histone demethylase JMJD2B/KDM4B regulates transcriptional program via distinctive epigenetic targets and protein interactors for the maintenance of trophoblast stem cells. Mak KH, et al. Sci Rep, 2021 Jan 13. PMID 33441614, Free PMC Article
    4. Enterotoxigenic Bacteroides fragilis induces the stemness in colorectal cancer via upregulating histone demethylase JMJD2B. Liu QQ, et al. Gut Microbes, 2020 Nov 9. PMID 32684087, Free PMC Article
    5. JMJD2B/KDM4B inactivation in adipose tissues accelerates obesity and systemic metabolic abnormalities. Kang C, et al. Genes Cells, 2018 Sep. PMID 30073721

    See all (64) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. 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.
    3. 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.
    4. 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.
    5. Mutations inhibiting KDM4B drive ALT activation in ATRX-mutated glioblastomas.
      Title: Mutations inhibiting KDM4B drive ALT activation in ATRX-mutated glioblastomas.
    6. Histone H3K9 Demethylase JMJD2B Plays a Role in LXRalpha-Dependent Lipogenesis.
      Title: Histone H3K9 Demethylase JMJD2B Plays a Role in LXRα-Dependent Lipogenesis.
    7. 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.
    8. 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.
    9. 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.
    10. KDM4B-mediated reduction of H3K9me3 and H3K36me3 levels improves somatic cell reprogramming into pluripotency.
      Title: KDM4B-mediated reduction of H3K9me3 and H3K36me3 levels improves somatic cell reprogramming into pluripotency.
    Submit: New GeneRIF Correction See all GeneRIFs (21)

    Variation

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    Alleles

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

    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 dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 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
    		  
    enables oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in brain development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within chromatin remodeling IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of 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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