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    Kdm3b KDM3B lysine (K)-specific demethylase 3B [ Mus musculus (house mouse) ]

    Gene ID: 277250, updated on 18-Sep-2024

    Summary

    Official Symbol
    Kdm3bprovided by MGI
    Official Full Name
    KDM3B lysine (K)-specific demethylase 3Bprovided by MGI
    Primary source
    MGI:MGI:1923356
    See related
    Ensembl:ENSMUSG00000038773 AllianceGenome:MGI:1923356
    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
    JHDM2B; Jmjd1b; mKIAA1082; 5830462I21Rik
    Summary
    Predicted to enable chromatin DNA binding activity; histone H3-methyl-lysine-9 demethylase activity; and transcription coregulator activity. Predicted to be involved in histone H3-K9 demethylation and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within chromatin organization. Predicted to be located in nucleoplasm. Predicted to be part of histone deacetylase complex. Predicted to be active in chromatin. Is expressed in central nervous system; early conceptus; oocyte; and retina nuclear layer. Orthologous to human KDM3B (lysine demethylase 3B). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 12.5), thymus adult (RPKM 11.7) and 28 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Kdm3b in Genome Data Viewer
    Location:
    18 B1; 18 18.73 cM
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 18 NC_000084.7 (34910061..34972423)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 18 NC_000084.6 (34777008..34839370)

    Chromosome 18 - NC_000084.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 2010110K18 gene Neighboring gene STARR-positive B cell enhancer ABC_E7575 Neighboring gene microRNA 12191 Neighboring gene family with sequence similarity 53, member C Neighboring gene predicted gene 3561 Neighboring gene STARR-positive B cell enhancer ABC_E7576 Neighboring gene STARR-seq mESC enhancer starr_44212 Neighboring gene STARR-seq mESC enhancer starr_44215 Neighboring gene receptor accessory protein 2 Neighboring gene STARR-positive B cell enhancer ABC_E5650 Neighboring gene STARR-positive B cell enhancer ABC_E8958 Neighboring gene CapStarr-seq enhancer MGSCv37_chr18:35020809-35020992 Neighboring gene early growth response 1

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables antioxidant activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables antioxidant activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables chromatin DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone H3K9 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone H3K9me/H3K9me2 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Process Evidence Code Pubs
    involved_in cellular oxidant detoxification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of transcription by RNA polymerase II 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
     
    part_of histone deacetylase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    lysine-specific demethylase 3B
    Names
    [histone H3]-dimethyl-L-lysine(9) demethylase 3B
    jmjC domain-containing histone demethylation protein 2B
    jumonji domain containing 1B
    jumonji domain-containing protein 1B
    NP_001074725.1

    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_001081256.1NP_001074725.1  lysine-specific demethylase 3B

      See identical proteins and their annotated locations for NP_001074725.1

      Status: VALIDATED

      Source sequence(s)
      AC114820
      Consensus CDS
      CCDS37761.1
      UniProtKB/Swiss-Prot
      B9EKS2, Q2VPQ5, Q5U5V7, Q6P9K3, Q6ZPY7, Q8CCE2, Q8K2A5, Q9CU57
      Related
      ENSMUSP00000037628.8, ENSMUST00000043775.9
      Conserved Domains (2) summary
      smart00558
      Location:15031575
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl40423
      Location:16001705
      cupin_RmlC-like; RmlC-like cupin 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_000084.7 Reference GRCm39 C57BL/6J

      Range
      34910061..34972423
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_029518.1: Suppressed sequence

      Description
      NM_029518.1: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.