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Aliases for KDM2A Gene

Aliases for KDM2A Gene

  • Lysine (K)-Specific Demethylase 2A 2 3
  • F-Box And Leucine-Rich Repeat Protein 11 2 3 4
  • FBXL11 3 4 6
  • JmjC Domain-Containing Histone Demethylation Protein 1A 3 4
  • Jumonji C Domain-Containing Histone Demethylase 1A 2 3
  • [Histone-H3]-Lysine-36 Demethylase 1A 3 4
  • CXXC-Type Zinc Finger Protein 8 3 4
  • F-Box/LRR-Repeat Protein 11 3 4
  • EC 1.14.11.27 4 64
  • JHDM1A 3 4
  • FBL11 3 6
  • CXXC8 3 4
  • FBL7 3 4
  • Lysine-Specific Demethylase 2A 3
  • F-Box Protein Lilina 4
  • F-Box Protein FBL11 2
  • F-Box Protein FBL7 4
  • KIAA1004 4
  • LILINA 3

External Ids for KDM2A Gene

Previous Symbols for KDM2A Gene

  • FBXL11

Summaries for KDM2A Gene

Entrez Gene Summary for KDM2A Gene

  • This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbls class and, in addition to an F-box, contains at least six highly degenerated leucine-rich repeats. This family member plays a role in epigenetic silencing. It nucleates at CpG islands and specifically demethylates both mono- and di-methylated lysine-36 of histone H3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2012]

GeneCards Summary for KDM2A Gene

KDM2A (Lysine (K)-Specific Demethylase 2A) is a Protein Coding gene. GO annotations related to this gene include histone demethylase activity (H3-K36 specific) and unmethylated CpG binding. An important paralog of this gene is KDM2B.

UniProtKB/Swiss-Prot for KDM2A Gene

  • Histone demethylase that specifically demethylates Lys-36 of histone H3, thereby playing a central role in histone code. Preferentially demethylates dimethylated H3 Lys-36 residue while it has weak or no activity for mono- and tri-methylated H3 Lys-36. May also recognize and bind to some phosphorylated proteins and promote their ubiquitination and degradation. Required to maintain the heterochromatic state. Associates with centromeres and represses transcription of small non-coding RNAs that are encoded by the clusters of satellite repeats at the centromere. Required to sustain centromeric integrity and genomic stability, particularly during mitosis.

Gene Wiki entry for KDM2A Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KDM2A Gene

Genomics for KDM2A Gene

Genomic Location for KDM2A Gene

Start:
67,119,216 bp from pter
End:
67,258,087 bp from pter
Size:
138,872 bases
Orientation:
Plus strand

Genomic View for KDM2A Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for KDM2A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KDM2A Gene

Regulatory Elements for KDM2A Gene

Proteins for KDM2A Gene

  • Protein details for KDM2A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y2K7-KDM2A_HUMAN
    Recommended name:
    Lysine-specific demethylase 2A
    Protein Accession:
    Q9Y2K7
    Secondary Accessions:
    • D4QA03
    • E9PIL6
    • I3VM55
    • Q49A21
    • Q4G0M3
    • Q69YY8
    • Q9BVH5
    • Q9H7H5
    • Q9UK66

    Protein attributes for KDM2A Gene

    Size:
    1162 amino acids
    Molecular mass:
    132793 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Note=Binds 1 Fe(2+) ion per subunit.;
    Quaternary structure:
    • Part of a SCF (SKP1-cullin-F-box) protein ligase complex (By similarity). Interacts with CBX5/HP1A; the interaction promotes CBX5 localization to chromatin.
    SequenceCaution:
    • Sequence=AAD56012.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAA76848.2; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB15795.1; Type=Frameshift; Positions=410; Evidence={ECO:0000305}; Sequence=BAJ05817.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for KDM2A Gene

    Alternative splice isoforms for KDM2A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for KDM2A Gene

Proteomics data for KDM2A Gene at MOPED

Post-translational modifications for KDM2A Gene

  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys518

Other Protein References for KDM2A Gene

Domains for KDM2A Gene

Gene Families for KDM2A Gene

HGNC:
  • KDM :Chromatin-modifying enzymes / K-demethylases
  • FBXL :F-boxes / Leucine-rich repeats

UniProtKB/Swiss-Prot:

KDM2A_HUMAN
Domain:
  • The JmjC domain mediates demethylation activity and is required for satellite silencing:
    • Q9Y2K7
  • The CXXC zinc finger preferentially recognizes nonmethylated CpG DNA, and binding is blocked when the CpG DNA is methylated:
    • Q9Y2K7
  • Contains 1 F-box domain.:
    • Q9Y2K7
  • Contains 1 JmjC domain.:
    • Q9Y2K7
Family:
  • Belongs to the JHDM1 histone demethylase family.:
    • Q9Y2K7
Similarity:
  • Contains 1 CXXC-type zinc finger.:
    • Q9Y2K7
  • Contains 6 LRR (leucine-rich) repeats.:
    • Q9Y2K7
  • Contains 1 PHD-type zinc finger.:
    • Q9Y2K7
genes like me logo Genes that share domains with KDM2A: view

Function for KDM2A Gene

Molecular function for KDM2A Gene

UniProtKB/Swiss-Prot CatalyticActivity: Protein N(6),N(6)-dimethyl-L-lysine + 2-oxoglutarate + O(2) = protein N(6)-methyl-L-lysine + succinate + formaldehyde + CO(2).
UniProtKB/Swiss-Prot CatalyticActivity: Protein N(6)-methyl-L-lysine + 2-oxoglutarate + O(2) = protein L-lysine + succinate + formaldehyde + CO(2).
UniProtKB/Swiss-Prot Function: Histone demethylase that specifically demethylates Lys-36 of histone H3, thereby playing a central role in histone code. Preferentially demethylates dimethylated H3 Lys-36 residue while it has weak or no activity for mono- and tri-methylated H3 Lys-36. May also recognize and bind to some phosphorylated proteins and promote their ubiquitination and degradation. Required to maintain the heterochromatic state. Associates with centromeres and represses transcription of small non-coding RNAs that are encoded by the clusters of satellite repeats at the centromere. Required to sustain centromeric integrity and genomic stability, particularly during mitosis.

Enzyme Numbers (IUBMB) for KDM2A Gene

Gene Ontology (GO) - Molecular Function for KDM2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding --
GO:0005515 protein binding --
GO:0008270 zinc ion binding IEA --
GO:0045322 unmethylated CpG binding IEA --
GO:0051864 histone demethylase activity (H3-K36 specific) IEA --
genes like me logo Genes that share ontologies with KDM2A: view

Phenotypes for KDM2A Gene

GenomeRNAi human phenotypes for KDM2A:
genes like me logo Genes that share phenotypes with KDM2A: view

No data available for Animal Models , Transcription Factor Targeting and HOMER Transcription for KDM2A Gene

Localization for KDM2A Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM2A Gene

Nucleus, nucleoplasm. Note=Punctate expression throughout the nucleoplasm and enriched in the perinucleolar region. Specifically nucleates at CpG islands where its presence results in chromatin depleted in H3K36me2.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for KDM2A Gene COMPARTMENTS Subcellular localization image for KDM2A gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for KDM2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin IEA --
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IDA --
genes like me logo Genes that share ontologies with KDM2A: view

Pathways for KDM2A Gene

SuperPathways for KDM2A Gene

No Data Available

Gene Ontology (GO) - Biological Process for KDM2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006303 double-strand break repair via nonhomologous end joining IMP 21187428
GO:0006325 chromatin organization TAS --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with KDM2A: view

No data available for Pathways by source for KDM2A Gene

Compounds for KDM2A Gene

(2) HMDB Compounds for KDM2A Gene

Compound Synonyms Cas Number PubMed IDs
Formaldehyde
  • Aldeide formica
50-00-0
L-Lysine
  • (+)-S-Lysine
56-87-1
genes like me logo Genes that share compounds with KDM2A: view

Transcripts for KDM2A Gene

Unigene Clusters for KDM2A Gene

Lysine (K)-specific demethylase 2A:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for KDM2A Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16a · 16b · 16c ^ 17a ·
SP1: - - - - - - - - -
SP2: - -
SP3: - - - -
SP4: -
SP5: -
SP6:
SP7:
SP8:
SP9: -
SP10:
SP11:
SP12:

ExUns: 17b ^ 18 ^ 19 ^ 20a · 20b ^ 21 ^ 22a · 22b ^ 23 ^ 24 ^ 25
SP1: - - - -
SP2:
SP3:
SP4:
SP5: -
SP6: -
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for KDM2A Gene

GeneLoc Exon Structure for
KDM2A
ECgene alternative splicing isoforms for
KDM2A

Expression for KDM2A Gene

mRNA expression in normal human tissues for KDM2A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for KDM2A Gene

SOURCE GeneReport for Unigene cluster for KDM2A Gene Hs.124147

mRNA Expression by UniProt/SwissProt for KDM2A Gene

Q9Y2K7-KDM2A_HUMAN
Tissue specificity: Widely expressed, with highest levels in brain, testis and ovary, followed by lung.
genes like me logo Genes that share expressions with KDM2A: view

Orthologs for KDM2A Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for KDM2A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia KDM2A 36
  • 99.89 (n)
  • 100 (a)
KDM2A 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia KDM2A 36
  • 94.83 (n)
  • 98.02 (a)
KDM2A 37
  • 87 (a)
OneToOne
dog
(Canis familiaris)
Mammalia KDM2A 36
  • 95.81 (n)
  • 99.48 (a)
KDM2A 37
  • 99 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Kdm2a 36
  • 92.08 (n)
  • 96.9 (a)
Kdm2a 16
Kdm2a 37
  • 97 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia KDM2A 37
  • 96 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia KDM2A 37
  • 82 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Kdm2a 36
  • 92.28 (n)
  • 97.33 (a)
chicken
(Gallus gallus)
Aves KDM2A 36
  • 79.37 (n)
  • 87.33 (a)
KDM2A 37
  • 87 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia KDM2A 37
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia kdm2a 36
  • 65.66 (n)
  • 70.93 (a)
Str.10470 36
zebrafish
(Danio rerio)
Actinopterygii CT955967.1 37
  • 50 (a)
OneToMany
kdm2a 36
  • 63.93 (n)
  • 65.86 (a)
kdm2aa 37
  • 48 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Kdm2 36
  • 52.46 (n)
  • 50.44 (a)
Kdm2 37
  • 32 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea jhdm-1 37
  • 23 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes JHD1 37
  • 26 (a)
OneToMany
JHD1 39
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.8451 36
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 45 (a)
OneToMany
Species with no ortholog for KDM2A:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for KDM2A Gene

ENSEMBL:
Gene Tree for KDM2A (if available)
TreeFam:
Gene Tree for KDM2A (if available)

Paralogs for KDM2A Gene

Paralogs for KDM2A Gene

Selected SIMAP similar genes for KDM2A Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with KDM2A: view

Variants for KDM2A Gene

Sequence variations from dbSNP and Humsavar for KDM2A Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type MAF
rs3624 -- 67,213,707(-) atctc(A/G)gctca intron-variant
rs608273 -- 67,158,297(-) aaaca(C/T)ccata intron-variant
rs629570 -- 67,183,640(-) TGGAG(A/C)AGCTG intron-variant
rs645387 -- 67,192,921(-) ctctc(A/C)tactt intron-variant
rs646834 -- 67,165,282(+) CACAC(A/C)TGGCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for KDM2A Gene

Variant ID Type Subtype PubMed ID
esv2661599 CNV Deletion 23128226
esv23935 CNV Loss 19812545
esv2669621 CNV Deletion 23128226
esv2744644 CNV Deletion 23290073
nsv825958 CNV Gain 20364138
nsv509419 CNV Insertion 20534489
nsv513322 CNV Insertion 21212237
nsv436787 CNV Insertion 17901297
esv1081118 CNV Insertion 17803354
nsv825959 CNV Gain 20364138
nsv897796 CNV Loss 21882294
nsv897797 CNV Loss 21882294
dgv1192n71 CNV Loss 21882294
nsv897800 CNV Loss 21882294

Relevant External Links for KDM2A Gene

HapMap Linkage Disequilibrium report
KDM2A

Disorders for KDM2A Gene

No disorders were found for KDM2A Gene.

No data available for UniProtKB/Swiss-Prot for KDM2A Gene

Publications for KDM2A Gene

  1. Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10231032) Nagase T. … Ohara O. (DNA Res. 1999) 2 3 4
  2. Validation-based insertional mutagenesis identifies lysine demethylase FBXL11 as a negative regulator of NFkappaB. (PMID: 19805303) Lu T. … Stark G.R. (Proc. Natl. Acad. Sci. U.S.A. 2009) 3 23
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4
  4. Histone demethylation by a family of JmjC domain-containing proteins. (PMID: 16362057) Tsukada Y. … Zhang Y. (Nature 2006) 3 4
  5. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen J.V. … Mann M. (Cell 2006) 3 4

Products for KDM2A Gene

Sources for KDM2A Gene

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