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

    Gene ID: 75605, updated on 9-Dec-2024

    Summary

    Official Symbol
    Kdm5bprovided by MGI
    Official Full Name
    lysine demethylase 5Bprovided by MGI
    Primary source
    MGI:MGI:1922855
    See related
    Ensembl:ENSMUSG00000042207 AllianceGenome:MGI:1922855
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    PUT1; Plu1; PLU-1; Rb-Bp2; Jarid1b; RBBP2H1A; mKIAA4034; D1Ertd202e; 2010009J12Rik; 2210016I17Rik
    Summary
    This gene encodes a lysine-specific histone demethylase that belongs to the jumonji/ARID domain-containing family of histone demethylases. The encoded protein is capable of demethylating tri-, di- and monomethylated lysine 4 of histone H3. This protein plays a role in the transcriptional repression or certain tumor suppressor genes and is upregulated in certain cancer cells. This protein may also play a role in genome stability and DNA repair. Homozygous mutant mice display decreased body weight, decreased female fertility, lower uterine weight, and a delay in mammary development. Knockout of this gene has also been associated with embryonic lethality. [provided by RefSeq, Dec 2016]
    Expression
    Ubiquitous expression in testis adult (RPKM 14.9), CNS E11.5 (RPKM 13.4) and 28 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Kdm5b in Genome Data Viewer
    Location:
    1 E4; 1 58.24 cM
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (134487916..134560621)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (134560178..134632878)

    Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_02337 Neighboring gene STARR-seq mESC enhancer starr_02338 Neighboring gene STARR-positive B cell enhancer ABC_E10037 Neighboring gene predicted gene, 46159 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:136456618-136456805 Neighboring gene STARR-seq mESC enhancer starr_02340 Neighboring gene predicted gene, 46160 Neighboring gene MGAT4 family, member E Neighboring gene STARR-seq mESC enhancer starr_02343 Neighboring gene STARR-seq mESC enhancer starr_02345 Neighboring gene synaptotagmin II Neighboring gene protein phosphatase 1, regulatory subunit 12B Neighboring gene predicted gene, 32670

    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)

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA4034

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables histone H3K4 demethylase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone H3K4 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables histone binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables histone binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables nucleic acid binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sequence-specific double-stranded DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables transcription corepressor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables transcription corepressor activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables zinc ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of_or_within branching involved in mammary gland duct morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cellular response to fibroblast growth factor stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within cellular response to leukemia inhibitory factor IEP
    Inferred from Expression Pattern
    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 lens fiber cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within mammary duct terminal end bud growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of gene expression IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of mammary gland epithelial cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within post-embryonic development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of circadian rhythm NAS
    Non-traceable Author Statement
    more info
    PubMed 
    acts_upstream_of_or_within regulation of estradiol secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to fungicide IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in rhythmic process IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within single fertilization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within uterus morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    lysine-specific demethylase 5B
    Names
    [histone H3]-trimethyl-L-lysine(4) demethylase 5B
    histone demethylase JARID1B
    jumonji, AT rich interactive domain 1B (Rbp2 like)
    jumonji/ARID domain-containing protein 1B
    lysine (K)-specific demethylase 5B
    putative DNA/chromatin binding motif 1
    NP_690855.2
    XP_011246392.1
    XP_017168105.1
    XP_017168106.1

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

      See identical proteins and their annotated locations for NP_690855.2

      Status: REVIEWED

      Source sequence(s)
      AK076888, BC048180, CX206086, CX567343, W35764
      Consensus CDS
      CCDS35716.1
      UniProtKB/Swiss-Prot
      Q5DTR9, Q80Y84, Q8BLU1, Q8JZL8
      Related
      ENSMUSP00000038138.8, ENSMUST00000047714.14
      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: 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_000067.7 Reference GRCm39 C57BL/6J

      Range
      134487916..134560621
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011248090.4XP_011246392.1  lysine-specific demethylase 5B isoform X1

      Conserved Domains (7) summary
      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)
      pfam02373
      Location:328444
      JmjC; JmjC domain, hydroxylase
      cl28902
      Location:125
      ARID; ARID/BRIGHT DNA binding domain family
      pfam02928
      Location:534586
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:599928
      PLU-1; PLU-1-like protein
    2. XM_017312617.3XP_017168106.1  lysine-specific demethylase 5B isoform X2

      Conserved Domains (7) summary
      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)
      pfam02373
      Location:328444
      JmjC; JmjC domain, hydroxylase
      cl28902
      Location:125
      ARID; ARID/BRIGHT DNA binding domain family
      pfam02928
      Location:534586
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:599928
      PLU-1; PLU-1-like protein
      cl22851
      Location:13281345
      PHD_SF; PHD finger superfamily
    3. XM_017312616.3XP_017168105.1  lysine-specific demethylase 5B isoform X1

      Conserved Domains (7) summary
      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)
      pfam02373
      Location:328444
      JmjC; JmjC domain, hydroxylase
      cl28902
      Location:125
      ARID; ARID/BRIGHT DNA binding domain family
      pfam02928
      Location:534586
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:599928
      PLU-1; PLU-1-like protein