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    Kdm4b lysine demethylase 4B [ Rattus norvegicus (Norway rat) ]

    Gene ID: 301128, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Kdm4bprovided by RGD
    Official Full Name
    lysine demethylase 4Bprovided by RGD
    Primary source
    RGD:1588576
    See related
    EnsemblRapid:ENSRNOG00000049221 AllianceGenome:RGD:1588576
    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
    Summary
    Predicted to enable histone H3K36 demethylase activity and histone H3K9me2/H3K9me3 demethylase activity. Predicted to be involved in brain development; chromatin remodeling; and regulation of gene expression. Predicted to be located in cytosol; nucleoplasm; and pericentric heterochromatin. Predicted to be active in nucleus. 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, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 97.0), Brain (RPKM 96.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Kdm4b in Genome Data Viewer
    Location:
    9q11
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (1245885..1324384)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (1158737..1237233)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (10656035..10734127, complement)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene arrestin domain containing 5 Neighboring gene ubiquitin-like with PHD and ring finger domains 1 Neighboring gene ribosomal protein S27 like 3 Neighboring gene transfer RNA lysine (anticodon CUU) 11 Neighboring gene protein tyrosine phosphatase, receptor type, S Neighboring gene zinc and ring finger 4

    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
    • 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. Osmolarity controls the differentiation of adipose-derived stem cells into nucleus pulposus cells via histone demethylase KDM4B. Zhang Y, et al. Mol Cell Biochem, 2020 Sep. PMID 32594337
    2. Microarray comparative genomic hybridization detection of copy number changes in desmoplastic melanoma and malignant peripheral nerve sheath tumor. Pryor JG, et al. Am J Dermatopathol, 2011 Dec. PMID 21785329
    3. JMJD2B promotes epithelial-mesenchymal transition by cooperating with β-catenin and enhances gastric cancer metastasis. Zhao L, et al. Clin Cancer Res, 2013 Dec 1. PMID 24077348
    4. Histone demethylase JMJD2B is required for tumor cell proliferation and survival and is overexpressed in gastric cancer. Li W, et al. Biochem Biophys Res Commun, 2011 Dec 16. PMID 22133676
    5. The histone demethylase JMJD2B plays an essential role in human carcinogenesis through positive regulation of cyclin-dependent kinase 6. Toyokawa G, et al. Cancer Prev Res (Phila), 2011 Dec. PMID 21930796

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Osmolarity controls the differentiation of adipose-derived stem cells into nucleus pulposus cells via histone demethylase KDM4B.
      Title: Osmolarity controls the differentiation of adipose-derived stem cells into nucleus pulposus cells via histone demethylase KDM4B.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K9me2/H3K9me3 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone demethylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in brain development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    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 cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in pericentric heterochromatin ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    lysine-specific demethylase 4B
    Names
    lysine (K)-specific demethylase 4B
    NP_001037701.2
    NP_001382562.1
    XP_006244381.1
    XP_006244382.1
    XP_038939071.1
    XP_038939072.1
    XP_063122897.1
    XP_063122898.1
    XP_063122899.1

    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_001044236.3 → NP_001037701.2  lysine-specific demethylase 4B isoform 1

      See identical proteins and their annotated locations for NP_001037701.2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/TrEMBL
      A0A0G2JXG2, A6KQY4, M0RB75
      Related
      ENSRNOP00000066803.1, ENSRNOT00000071199.4
      Conserved Domains (7) summary
      smart00545
      Location:15 → 56
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15714
      Location:798 → 907
      ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
      pfam11725
      Location:475 → 671
      AvrE; Pathogenicity factor
      pfam02373
      Location:176 → 292
      JmjC; JmjC domain, hydroxylase
      cd20464
      Location:920 → 973
      Tudor_JMJD2B_rpt1; first Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins
      cl02573
      Location:977 → 1032
      Tudor_SF; Tudor domain superfamily
      cl22851
      Location:686 → 789
      PHD_SF; PHD finger superfamily

    2. NM_001395633.1 → NP_001382562.1  lysine-specific demethylase 4B isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/TrEMBL
      A0A0G2JXG2
      Conserved Domains (7) summary
      smart00545
      Location:15 → 56
      JmjN; Small domain found in the jumonji family of transcription factors
      PHA03247
      Location:327 → 739
      PHA03247; large tegument protein UL36; Provisional
      cd15714
      Location:792 → 901
      ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
      pfam02373
      Location:176 → 292
      JmjC; JmjC domain, hydroxylase
      cd20464
      Location:914 → 967
      Tudor_JMJD2B_rpt1; first Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins
      cl02573
      Location:971 → 1026
      Tudor_SF; Tudor domain superfamily
      cl22851
      Location:680 → 783
      PHD_SF; PHD finger superfamily

    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_086027.1 Reference GRCr8

      Range
      1245885..1324384
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063266828.1 → XP_063122898.1  lysine-specific demethylase 4B isoform X6

    2. XM_063266829.1 → XP_063122899.1  lysine-specific demethylase 4B isoform X7

    3. XM_039083143.2 → XP_038939071.1  lysine-specific demethylase 4B isoform X1

      UniProtKB/TrEMBL
      A0A0G2JXG2, A6KQY4, M0RB75
      Conserved Domains (7) summary
      smart00545
      Location:15 → 56
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15714
      Location:798 → 907
      ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
      pfam11725
      Location:475 → 671
      AvrE; Pathogenicity factor
      pfam02373
      Location:176 → 292
      JmjC; JmjC domain, hydroxylase
      cd20464
      Location:920 → 973
      Tudor_JMJD2B_rpt1; first Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins
      cl02573
      Location:977 → 1032
      Tudor_SF; Tudor domain superfamily
      cl22851
      Location:686 → 789
      PHD_SF; PHD finger superfamily

    4. XM_006244320.5 → XP_006244382.1  lysine-specific demethylase 4B isoform X4

      UniProtKB/TrEMBL
      A0A8I5ZWQ3
      Conserved Domains (4) summary
      smart00545
      Location:15 → 56
      JmjN; Small domain found in the jumonji family of transcription factors
      smart00333
      Location:922 → 972
      TUDOR; Tudor domain
      pfam02373
      Location:176 → 292
      JmjC; JmjC domain, hydroxylase
      cl22851
      Location:798 → 907
      PHD_SF; PHD finger superfamily

    5. XM_006244319.5 → XP_006244381.1  lysine-specific demethylase 4B isoform X2

      UniProtKB/TrEMBL
      A0A0G2JXG2
      Related
      ENSRNOP00000070258.3, ENSRNOT00000089374.3
      Conserved Domains (5) summary
      smart00545
      Location:15 → 56
      JmjN; Small domain found in the jumonji family of transcription factors
      smart00333
      Location:888 → 938
      TUDOR; Tudor domain
      pfam02373
      Location:176 → 292
      JmjC; JmjC domain, hydroxylase
      cd15714
      Location:764 → 873
      ePHD_JMJD2B; Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
      cl22851
      Location:652 → 755
      PHD_SF; PHD finger superfamily

    6. XM_063266827.1 → XP_063122897.1  lysine-specific demethylase 4B isoform X3

      UniProtKB/TrEMBL
      A0A0G2JXG2

    7. XM_039083144.2 → XP_038939072.1  lysine-specific demethylase 4B isoform X5

      Conserved Domains (5) summary
      pfam11725
      Location:233 → 429
      AvrE; Pathogenicity factor
      cd20464
      Location:678 → 731
      Tudor_JMJD2B_rpt1; first Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins
      cl02573
      Location:735 → 790
      Tudor_SF; Tudor domain superfamily
      cl22851
      Location:556 → 665
      PHD_SF; PHD finger superfamily
      cl40423
      Location:1 → 50
      cupin_RmlC-like; RmlC-like cupin superfamily

    RNA

    1. XR_010054572.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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