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    Kdm2a lysine (K)-specific demethylase 2A [ Mus musculus (house mouse) ]

    Gene ID: 225876, updated on 5-Sep-2021

    Summary

    Official Symbol
    Kdm2aprovided by MGI
    Official Full Name
    lysine (K)-specific demethylase 2Aprovided by MGI
    Primary source
    MGI:MGI:1354736
    See related
    Ensembl:ENSMUSG00000054611
    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
    Fbl; Fbl7; Cxxc8; Fbl11; Fbxl1; Jhdm1; Fbxl11; Gm4560; Jhdm1a; lalina; AA589516; AW536790; 100043628; 5530401A10Rik
    Expression
    Ubiquitous expression in thymus adult (RPKM 17.5), limb E14.5 (RPKM 16.0) and 28 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Kdm2a in Genome Data Viewer
    Location:
    19; 19 A
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    109 current GRCm39 (GCF_000001635.27) 19 NC_000085.7 (4366172..4448749, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (4316144..4398721, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 19 NC_000085.5 (4316144..4397077, complement)

    Chromosome 19 - NC_000085.7Genomic Context describing neighboring genes Neighboring gene ankyrin repeat domain 13 family, member D Neighboring gene G protein-coupled receptor kinase 2 Neighboring gene RIKEN cDNA 9430078G10 gene Neighboring gene RIKEN cDNA A930001C03 gene Neighboring gene ras homolog family member D Neighboring gene synaptotagmin XII

    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)

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3-di/monomethyl-lysine-36 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3-methyl-lysine-36 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables histone demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables unmethylated CpG binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables unmethylated CpG binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of_or_within chromatin organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in circadian regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in double-strand break repair via nonhomologous end joining ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within heart looping IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within histone H3-K36 demethylation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within in utero embryonic development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within multicellular organism growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of transcription by competitive promoter binding ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within neural tube closure IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within neuroepithelial cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within neuron differentiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of histone ubiquitination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein demethylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in regulation of circadian rhythm ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    acts_upstream_of_or_within rhythmic process IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    lysine-specific demethylase 2A
    Names
    F-box and leucine-rich repeat protein 11
    F-box protein containing leucine repeats
    F-box/LRR-repeat protein 11
    [Histone-H3]-lysine-36 demethylase 1A
    jmjC domain-containing histone demethylation protein 1A
    NP_001001984.2
    XP_006531785.1
    XP_006531786.1

    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_001001984.2NP_001001984.2  lysine-specific demethylase 2A

      See identical proteins and their annotated locations for NP_001001984.2

      Status: VALIDATED

      Source sequence(s)
      AC140073, AK173084, BC076576, CB246224
      Consensus CDS
      CCDS37886.1
      UniProtKB/Swiss-Prot
      P59997
      UniProtKB/TrEMBL
      F6YRW4
      Related
      ENSMUSP00000076698.5, ENSMUST00000075856.11
      Conserved Domains (7) summary
      cd09293
      Location:9311137
      AMN1; Antagonist of mitotic exit network protein 1
      sd00034
      Location:929953
      LRR_AMN1; leucine-rich repeat [structural motif]
      cd15643
      Location:619675
      PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)
      pfam02008
      Location:576609
      zf-CXXC; CXXC zinc finger domain
      pfam12937
      Location:895933
      F-box-like
      pfam17811
      Location:304339
      JHD; Jumonji helical domain
      cl21464
      Location:199299
      cupin_like; Conserved domain found in cupin and related proteins

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000085.7 Reference GRCm39 C57BL/6J

      Range
      4366172..4448749 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006531722.4XP_006531785.1  lysine-specific demethylase 2A isoform X1

      See identical proteins and their annotated locations for XP_006531785.1

      UniProtKB/TrEMBL
      F6YRW4
      Related
      ENSMUSP00000047683.8, ENSMUST00000047898.14
      Conserved Domains (7) summary
      cd09293
      Location:9311137
      AMN1; Antagonist of mitotic exit network protein 1
      sd00034
      Location:929953
      LRR_AMN1; leucine-rich repeat [structural motif]
      cd15643
      Location:619675
      PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)
      pfam02008
      Location:576609
      zf-CXXC; CXXC zinc finger domain
      pfam12937
      Location:895933
      F-box-like
      pfam17811
      Location:304339
      JHD; Jumonji helical domain
      cl21464
      Location:199299
      cupin_like; Conserved domain found in cupin and related proteins
    2. XM_006531723.4XP_006531786.1  lysine-specific demethylase 2A isoform X2

      Conserved Domains (5) summary
      cd09293
      Location:491697
      AMN1; Antagonist of mitotic exit network protein 1
      sd00034
      Location:489513
      LRR_AMN1; leucine-rich repeat [structural motif]
      cd15643
      Location:179235
      PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)
      pfam02008
      Location:136169
      zf-CXXC; CXXC zinc finger domain
      pfam12937
      Location:455493
      F-box-like
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