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    Kdm5b lysine (K)-specific demethylase 5B [ Mus musculus (house mouse) ]

    Gene ID: 75605, updated on 25-Sep-2016
    Official Symbol
    Kdm5bprovided by MGI
    Official Full Name
    lysine (K)-specific demethylase 5Bprovided by MGI
    Primary source
    MGI:MGI:1922855
    See related
    Ensembl:ENSMUSG00000042207 Vega:OTTMUSG00000017092
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    PUT1; Plu1; PLU-1; Rb-Bp2; Jarid1b; AW556288; RBBP2H1A; mKIAA4034; D1Ertd202e; 2010009J12Rik; 2210016I17Rik
    Orthologs
    Location:
    1 E4; 1 58.24 cM
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 1 NC_000067.6 (134560178..134632878)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 1 NC_000067.5 (136456755..136529455)

    Chromosome 1 - NC_000067.6Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108167729 Neighboring gene uncharacterized LOC108167730 Neighboring gene MGAT4 family, member E Neighboring gene synaptotagmin II Neighboring gene protein phosphatase 1, regulatory (inhibitor) subunit 12B Neighboring gene predicted gene, 32670

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • KIAA4034

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    2,4-dichlorophenoxyacetate alpha-ketoglutarate dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
     
    C-19 gibberellin 2-beta-dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
     
    C-20 gibberellin 2-beta-dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
     
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    DNA-N1-methyladenine dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
     
    dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
     
    histone demethylase activity (H3-K4 specific) IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone demethylase activity (H3-K4 specific) ISO
    Inferred from Sequence Orthology
    more info
     
    histone demethylase activity (H3-dimethyl-K4 specific) ISO
    Inferred from Sequence Orthology
    more info
     
    histone demethylase activity (H3-trimethyl-K4 specific) ISO
    Inferred from Sequence Orthology
    more info
     
    hypophosphite dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
     
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
     
    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors IEA
    Inferred from Electronic Annotation
    more info
     
    procollagen-proline dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    sulfonate dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
     
    transcription corepressor activity ISO
    Inferred from Sequence Orthology
    more info
     
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    branching involved in mammary gland duct morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    chromatin modification IEA
    Inferred from Electronic Annotation
    more info
     
    histone H3-K4 demethylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone H3-K4 demethylation ISO
    Inferred from Sequence Orthology
    more info
     
    mammary duct terminal end bud growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    oxidation-reduction process IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of gene expression IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of mammary gland epithelial cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    post-embryonic development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of circadian rhythm NAS
    Non-traceable Author Statement
    more info
    PubMed 
    regulation of estradiol secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    rhythmic process IEA
    Inferred from Electronic Annotation
    more info
     
    single fertilization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    uterus morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    Preferred Names
    lysine-specific demethylase 5B
    Names
    histone demethylase JARID1B
    jumonji, AT rich interactive domain 1B (Rbp2 like)
    jumonji/ARID domain-containing protein 1B
    putative DNA/chromatin binding motif 1

    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_152895.2NP_690855.2  lysine-specific demethylase 5B

      See identical proteins and their annotated locations for NP_690855.2

      Status: VALIDATED

      Source sequence(s)
      AK076888, BC048180, CX206086, CX567343, W35764
      Consensus CDS
      CCDS35716.1
      UniProtKB/Swiss-Prot
      Q80Y84
      Related
      ENSMUSP00000038138, OTTMUSP00000018570, ENSMUST00000047714, OTTMUST00000041390
      Conserved Domains (8) summary
      smart00501
      Location:98188
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:3172
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:486602
      JmjC; JmjC domain, hydroxylase
      cd15603
      Location:311356
      PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)
      cd15687
      Location:14861535
      PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)
      pfam02928
      Location:692744
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7571086
      PLU-1; PLU-1-like protein
      cl22851
      Location:11781221
      PHD_SF; PHD finger superfamily

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000067.6 Reference GRCm38.p4 C57BL/6J

      Range
      134560178..134632878
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011248090.2XP_011246392.1  

      Conserved Domains (6) summary
      pfam02373
      Location:328444
      JmjC; JmjC domain, hydroxylase
      cd15603
      Location:153198
      PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)
      cd15607
      Location:10201063
      PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)
      cd15687
      Location:13281377
      PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)
      pfam02928
      Location:534586
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:599928
      PLU-1; PLU-1-like protein
    2. XM_017312617.1XP_017168106.1  

    3. XM_017312616.1XP_017168105.1  

      Conserved Domains (6) summary
      pfam02373
      Location:328444
      JmjC; JmjC domain, hydroxylase
      cd15603
      Location:153198
      PHD1_KDM5B; PHD finger 1 found in lysine-specific demethylase 5B (KDM5B)
      cd15607
      Location:10201063
      PHD2_KDM5B; PHD finger 2 found in lysine-specific demethylase 5B (KDM5B)
      cd15687
      Location:13281377
      PHD3_KDM5B; PHD finger 3 found in lysine-specific demethylase 5B (KDM5B)
      pfam02928
      Location:534586
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:599928
      PLU-1; PLU-1-like protein
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