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

    Gene ID: 193796, updated on 9-Dec-2024

    Summary

    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, Dec 2024]
    Expression
    Ubiquitous expression in thymus adult (RPKM 19.4), ovary adult (RPKM 19.2) and 28 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    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

    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)

    NEW Try the new Transcript table

    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_001357909.1NP_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:1556
      JmjN; Small domain found in the jumonji family of transcription factors
      smart00333
      Location:881931
      TUDOR; Tudor domain
      pfam02373
      Location:176292
      JmjC; JmjC domain, hydroxylase
      cl22851
      Location:757866
      PHD_SF; PHD finger superfamily
    2. NM_172132.3NP_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:1556
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:176292
      JmjC; JmjC domain, hydroxylase
      pfam18104
      Location:910944
      Tudor_2; Jumonji domain-containing protein 2A Tudor domain
      cl22851
      Location:785894
      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_006523896.3XP_006523959.1  lysine-specific demethylase 4B isoform X6

      UniProtKB/TrEMBL
      B0V2M9
      Related
      ENSMUSP00000084045.6, ENSMUST00000086835.12
      Conserved Domains (4) summary
      smart00545
      Location:1556
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:176292
      JmjC; JmjC domain, hydroxylase
      pfam18104
      Location:903937
      Tudor_2; Jumonji domain-containing protein 2A Tudor domain
      cl22851
      Location:778887
      PHD_SF; PHD finger superfamily
    2. XM_030249601.1XP_030105461.1  lysine-specific demethylase 4B isoform X1

      UniProtKB/TrEMBL
      B0V2M9
      Conserved Domains (4) summary
      smart00545
      Location:1556
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:176292
      JmjC; JmjC domain, hydroxylase
      pfam18104
      Location:948982
      Tudor_2; Jumonji domain-containing protein 2A Tudor domain
      cl22851
      Location:823932
      PHD_SF; PHD finger superfamily
    3. XM_006523894.3XP_006523957.1  lysine-specific demethylase 4B isoform X4

      UniProtKB/TrEMBL
      B0V2M9
      Conserved Domains (4) summary
      smart00545
      Location:1556
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:176292
      JmjC; JmjC domain, hydroxylase
      pfam18104
      Location:910944
      Tudor_2; Jumonji domain-containing protein 2A Tudor domain
      cl22851
      Location:785894
      PHD_SF; PHD finger superfamily
    4. XM_006523895.3XP_006523958.1  lysine-specific demethylase 4B isoform X5

      UniProtKB/TrEMBL
      B0V2M9
      Conserved Domains (4) summary
      smart00545
      Location:1556
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:176292
      JmjC; JmjC domain, hydroxylase
      pfam18104
      Location:904938
      Tudor_2; Jumonji domain-containing protein 2A Tudor domain
      cl22851
      Location:779888
      PHD_SF; PHD finger superfamily
    5. XM_006523898.3XP_006523961.1  lysine-specific demethylase 4B isoform X8

      UniProtKB/TrEMBL
      B0V2M9
      Conserved Domains (4) summary
      smart00545
      Location:1556
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:176292
      JmjC; JmjC domain, hydroxylase
      pfam18104
      Location:897931
      Tudor_2; Jumonji domain-containing protein 2A Tudor domain
      cl22851
      Location:772881
      PHD_SF; PHD finger superfamily
    6. XM_006523897.3XP_006523960.1  lysine-specific demethylase 4B isoform X7

      UniProtKB/TrEMBL
      B0V2M9
      Conserved Domains (4) summary
      smart00545
      Location:1556
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:176292
      JmjC; JmjC domain, hydroxylase
      pfam18104
      Location:901935
      Tudor_2; Jumonji domain-containing protein 2A Tudor domain
      cl22851
      Location:776885
      PHD_SF; PHD finger superfamily
    7. XM_030249602.1XP_030105462.1  lysine-specific demethylase 4B isoform X1

      UniProtKB/TrEMBL
      B0V2M9
      Conserved Domains (4) summary
      smart00545
      Location:1556
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:176292
      JmjC; JmjC domain, hydroxylase
      pfam18104
      Location:948982
      Tudor_2; Jumonji domain-containing protein 2A Tudor domain
      cl22851
      Location:823932
      PHD_SF; PHD finger superfamily
    8. XM_030249603.2XP_030105463.1  lysine-specific demethylase 4B isoform X3

      UniProtKB/Swiss-Prot
      Q3UR22, Q6ZQ30, Q91VY5, Q99K42
      UniProtKB/TrEMBL
      B0V2M9
      Conserved Domains (4) summary
      smart00545
      Location:1556
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:176292
      JmjC; JmjC domain, hydroxylase
      pfam18104
      Location:910944
      Tudor_2; Jumonji domain-containing protein 2A Tudor domain
      cl22851
      Location:785894
      PHD_SF; PHD finger superfamily
    9. XM_030249604.1XP_030105464.1  lysine-specific demethylase 4B isoform X6

      UniProtKB/TrEMBL
      B0V2M9
      Conserved Domains (4) summary
      smart00545
      Location:1556
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:176292
      JmjC; JmjC domain, hydroxylase
      pfam18104
      Location:903937
      Tudor_2; Jumonji domain-containing protein 2A Tudor domain
      cl22851
      Location:778887
      PHD_SF; PHD finger superfamily
    10. XM_030249605.1XP_030105465.1  lysine-specific demethylase 4B isoform X7

      UniProtKB/TrEMBL
      B0V2M9
      Conserved Domains (4) summary
      smart00545
      Location:1556
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:176292
      JmjC; JmjC domain, hydroxylase
      pfam18104
      Location:901935
      Tudor_2; Jumonji domain-containing protein 2A Tudor domain
      cl22851
      Location:776885
      PHD_SF; PHD finger superfamily
    11. XM_017317354.2XP_017172843.1  lysine-specific demethylase 4B isoform X2

      UniProtKB/TrEMBL
      B0V2M9
      Conserved Domains (4) summary
      smart00545
      Location:1556
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:176292
      JmjC; JmjC domain, hydroxylase
      pfam18104
      Location:920954
      Tudor_2; Jumonji domain-containing protein 2A Tudor domain
      cl22851
      Location:795904
      PHD_SF; PHD finger superfamily
    12. XM_017317353.2XP_017172842.1  lysine-specific demethylase 4B isoform X2

      UniProtKB/TrEMBL
      B0V2M9
      Conserved Domains (4) summary
      smart00545
      Location:1556
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:176292
      JmjC; JmjC domain, hydroxylase
      pfam18104
      Location:920954
      Tudor_2; Jumonji domain-containing protein 2A Tudor domain
      cl22851
      Location:795904
      PHD_SF; PHD finger superfamily
    13. XM_017317355.2XP_017172844.1  lysine-specific demethylase 4B isoform X9

      UniProtKB/TrEMBL
      B0V2M9
      Conserved Domains (4) summary
      smart00545
      Location:1556
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:176292
      JmjC; JmjC domain, hydroxylase
      pfam18104
      Location:882916
      Tudor_2; Jumonji domain-containing protein 2A Tudor domain
      cl22851
      Location:757866
      PHD_SF; PHD finger superfamily
    14. XM_017317356.2XP_017172845.1  lysine-specific demethylase 4B isoform X10

      UniProtKB/TrEMBL
      B0V2M9
      Conserved Domains (4) summary
      smart00545
      Location:1556
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:176292
      JmjC; JmjC domain, hydroxylase
      pfam18104
      Location:876910
      Tudor_2; Jumonji domain-containing protein 2A Tudor domain
      cl22851
      Location:751860
      PHD_SF; PHD finger superfamily
    15. XM_030249606.2XP_030105466.1  lysine-specific demethylase 4B isoform X11

      UniProtKB/TrEMBL
      B0V2M9
      Conserved Domains (4) summary
      smart00545
      Location:1556
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:176292
      JmjC; JmjC domain, hydroxylase
      pfam18104
      Location:875909
      Tudor_2; Jumonji domain-containing protein 2A Tudor domain
      cl22851
      Location:750859
      PHD_SF; PHD finger superfamily