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

Gene ID: 225876, updated on 9-May-2024

Summary

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Official Symbol
Kdm2aprovided by MGI
Official Full Name
lysine (K)-specific demethylase 2Aprovided by MGI
Primary source
MGI:MGI:1354736
See related
Ensembl:ENSMUSG00000054611 AllianceGenome:MGI:1354736
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
Fbl7; Cxxc8; Fbl11; Jhdm1; Fbxl11; Gm4560; Jhdm1a; lalina; 100043628; 5530401A10Rik
Summary
Enables unmethylated CpG binding activity. Acts upstream of or within several processes, including chordate embryonic development; heart looping; and positive regulation of macromolecule metabolic process. Located in chromatin. Is expressed in embryo; forebrain; and limb. Human ortholog(s) of this gene implicated in lung non-small cell carcinoma. Orthologous to human KDM2A (lysine demethylase 2A). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thymus adult (RPKM 17.5), limb E14.5 (RPKM 16.0) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
19 A; 19 4.01 cM
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2024_02 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)

Chromosome 19 - NC_000085.7Genomic Context describing neighboring genes Neighboring gene ankyrin repeat domain 13 family, member D Neighboring gene STARR-positive B cell enhancer ABC_E5677 Neighboring gene CapStarr-seq enhancer MGSCv37_chr19:4294334-4294632 Neighboring gene STARR-positive B cell enhancer ABC_E7626 Neighboring gene CapStarr-seq enhancer MGSCv37_chr19:4302085-4302194 Neighboring gene CapStarr-seq enhancer MGSCv37_chr19:4302330-4302483 Neighboring gene STARR-positive B cell enhancer ABC_E9988 Neighboring gene G protein-coupled receptor kinase 2 Neighboring gene STARR-seq mESC enhancer starr_45347 Neighboring gene RIKEN cDNA 9430078G10 gene Neighboring gene STARR-positive B cell enhancer ABC_E1521 Neighboring gene STARR-seq mESC enhancer starr_45348 Neighboring gene RIKEN cDNA A930001C03 gene Neighboring gene STARR-seq mESC enhancer starr_45349 Neighboring gene ras homolog family member D Neighboring gene synaptotagmin XII

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. The histone H3K36 demethylase Fbxl11 plays pivotal roles in the development of retinal late-born cell types. Iwagawa T, et al. Genes Cells, 2023 Jul. PMID 37073980
  2. Oocyte-Specific Knockout of Histone Lysine Demethylase KDM2a Compromises Fertility by Blocking the Development of Follicles and Oocytes. Xiong X, et al. Int J Mol Sci, 2022 Oct 9. PMID 36233308, Free PMC Article
  3. Ablation of KDM2A Inhibits Preadipocyte Proliferation and Promotes Adipogenic Differentiation. Hua Y, et al. Int J Mol Sci, 2021 Sep 9. PMID 34575926, Free PMC Article
  4. Spatial and temporal expression of histone demethylase, Kdm2a, during murine molar development. Yi Q, et al. Biotech Histochem, 2016. PMID 26720400
  5. MiR-134-5p Regulates Myocardial Apoptosis and Angiogenesis by Directly Targeting KDM2A After Myocardial Infarction. Li X, et al. Int Heart J, 2020 Jul 30. PMID 32684588

See all (39) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Testis-specific knockout of Kdm2a reveals nonessential roles in male fertility but partially compromises spermatogenesis.
    Title: Testis-specific knockout of Kdm2a reveals nonessential roles in male fertility but partially compromises spermatogenesis.
  2. Maternal Kdm2a-mediated PI3K/Akt signaling and E-cadherin stimulate the morula-to-blastocyst transition revealing crucial roles in early embryonic development.
    Title: Maternal Kdm2a-mediated PI3K/Akt signaling and E-cadherin stimulate the morula-to-blastocyst transition revealing crucial roles in early embryonic development.
  3. Targeting KDM2A Enhances T-cell Infiltration in NSD1-Deficient Head and Neck Squamous Cell Carcinoma.
    Title: Targeting KDM2A Enhances T-cell Infiltration in NSD1-Deficient Head and Neck Squamous Cell Carcinoma.
  4. The histone H3K36 demethylase Fbxl11 plays pivotal roles in the development of retinal late-born cell types.
    Title: The histone H3K36 demethylase Fbxl11 plays pivotal roles in the development of retinal late-born cell types.
  5. Oocyte-Specific Knockout of Histone Lysine Demethylase KDM2a Compromises Fertility by Blocking the Development of Follicles and Oocytes.
    Title: Oocyte-Specific Knockout of Histone Lysine Demethylase KDM2a Compromises Fertility by Blocking the Development of Follicles and Oocytes.
  6. Ablation of KDM2A Inhibits Preadipocyte Proliferation and Promotes Adipogenic Differentiation.
    Title: Ablation of KDM2A Inhibits Preadipocyte Proliferation and Promotes Adipogenic Differentiation.
  7. SIRT6 mono-ADP ribosylates KDM2A to locally increase H3K36me2 at DNA damage sites to inhibit transcription and promote repair.
    Title: SIRT6 mono-ADP ribosylates KDM2A to locally increase H3K36me2 at DNA damage sites to inhibit transcription and promote repair.
  8. MiR-134-5p Regulates Myocardial Apoptosis and Angiogenesis by Directly Targeting KDM2A After Myocardial Infarction.
    Title: MiR-134-5p Regulates Myocardial Apoptosis and Angiogenesis by Directly Targeting KDM2A After Myocardial Infarction.
  9. KDM2 proteins play a widespread and demethylase-independent role in constraining gene expression from CpG islands CGI)-associated gene promoters. KDM2 proteins shape RNA Polymerase II occupancy but not chromatin accessibility at CGI-associated promoters.
    Title: KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity.
  10. Kdm2a expression may be closely related to cell proliferation
    Title: Spatial and temporal expression of histone demethylase, Kdm2a, during murine molar development.
Submit: New GeneRIF Correction See all GeneRIFs (13)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (6)  1 citation
  • Endonuclease-mediated (2) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables catalytic activity IEA
Inferred from Electronic Annotation
more info
  
enables dioxygenase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H3K36 demethylase activity ISO
Inferred from Sequence Orthology
more info
  
enables histone H3K36me/H3K36me2 demethylase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
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
  
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 in utero embryonic development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within metabolic process IEA
Inferred from Electronic Annotation
more info
  
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 
involved_in protein demethylation IBA
Inferred from Biological aspect of Ancestor
more info
  
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
  
acts_upstream_of_or_within rhythmic process IEA
Inferred from Electronic Annotation
more info
  
involved_in transcription initiation-coupled chromatin remodeling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of chromatin IDA
Inferred from Direct Assay
more info
 PubMed 
located_in chromosome IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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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)

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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_001001984.2 → NP_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, Q3U1M5, Q3UR56, Q3V3Q1, Q69ZT4
    UniProtKB/TrEMBL
    F6YRW4
    Related
    ENSMUSP00000076698.5, ENSMUST00000075856.11
    Conserved Domains (7) summary
    cd09293
    Location:931 → 1137
    AMN1; Antagonist of mitotic exit network protein 1
    sd00034
    Location:929 → 953
    LRR_AMN1; leucine-rich repeat [structural motif]
    cd15643
    Location:619 → 675
    PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)
    pfam02008
    Location:576 → 609
    zf-CXXC; CXXC zinc finger domain
    pfam12937
    Location:895 → 933
    F-box-like
    pfam17811
    Location:304 → 339
    JHD; Jumonji helical domain
    cl21464
    Location:199 → 299
    cupin_like; Conserved domain found in cupin and related proteins

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_000085.7 Reference GRCm39 C57BL/6J

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

mRNA and Protein(s)

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

    See identical proteins and their annotated locations for XP_006531785.1

    UniProtKB/Swiss-Prot
    P59997, Q3U1M5, Q3UR56, Q3V3Q1, Q69ZT4
    UniProtKB/TrEMBL
    F6YRW4
    Related
    ENSMUSP00000047683.8, ENSMUST00000047898.14
    Conserved Domains (7) summary
    cd09293
    Location:931 → 1137
    AMN1; Antagonist of mitotic exit network protein 1
    sd00034
    Location:929 → 953
    LRR_AMN1; leucine-rich repeat [structural motif]
    cd15643
    Location:619 → 675
    PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)
    pfam02008
    Location:576 → 609
    zf-CXXC; CXXC zinc finger domain
    pfam12937
    Location:895 → 933
    F-box-like
    pfam17811
    Location:304 → 339
    JHD; Jumonji helical domain
    cl21464
    Location:199 → 299
    cupin_like; Conserved domain found in cupin and related proteins

  2. XM_006531723.4 → XP_006531786.1  lysine-specific demethylase 2A isoform X2

    Conserved Domains (5) summary
    cd09293
    Location:491 → 697
    AMN1; Antagonist of mitotic exit network protein 1
    sd00034
    Location:489 → 513
    LRR_AMN1; leucine-rich repeat [structural motif]
    cd15643
    Location:179 → 235
    PHD_KDM2A; PHD finger found in Lysine-specific demethylase 2A (KDM2A)
    pfam02008
    Location:136 → 169
    zf-CXXC; CXXC zinc finger domain
    pfam12937
    Location:455 → 493
    F-box-like
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P59997.2 GenPept UniProtKB/Swiss-Prot:P59997

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