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Aliases for KDM2B Gene

Aliases for KDM2B Gene

  • Lysine (K)-Specific Demethylase 2B 2 3
  • F-Box And Leucine-Rich Repeat Protein 10 2 3 4
  • JmjC Domain-Containing Histone Demethylation Protein 1B 3 4
  • Jumonji C Domain-Containing Histone Demethylase 1B 2 3
  • [Histone-H3]-Lysine-36 Demethylase 1B 3 4
  • Protein-Containing CXXC Domain 2 3 4
  • CXXC-Type Zinc Finger Protein 2 3 4
  • F-Box/LRR-Repeat Protein 10 3 4
  • F-Box Protein FBL10 3 4
  • EC 1.14.11.27 4 63
  • FBXL10 3 4
  • JHDM1B 3 4
  • Fbl10 3 4
  • CXXC2 3 4
  • PCCX2 3 4
  • Jumonji Domain-Containing EMSY-Interactor Methyltransferase Motif Protein 4
  • JEMMA (Jumonji Domain, EMSY-Interactor, Methyltransferase Motif) Protein 3
  • Lysine-Specific Demethylase 2B 3
  • Protein JEMMA 4

External Ids for KDM2B Gene

Previous HGNC Symbols for KDM2B Gene

  • FBXL10

Previous GeneCards Identifiers for KDM2B Gene

  • GC12M120351
  • GC12M121866
  • GC12M118876

Summaries for KDM2B Gene

Entrez Gene Summary for KDM2B 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. Multiple alternatively spliced transcript variants have been found for this gene, but the full-length nature of some variants has not been determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for KDM2B Gene

KDM2B (Lysine (K)-Specific Demethylase 2B) is a Protein Coding gene. GO annotations related to this gene include rRNA binding and histone demethylase activity. An important paralog of this gene is PHF2.

UniProtKB/Swiss-Prot for KDM2B Gene

  • Histone demethylase that demethylates Lys-4 and Lys-36 of histone H3, thereby playing a central role in histone code. Preferentially demethylates trimethylated H3 Lys-4 and dimethylated H3 Lys-36 residue while it has weak or no activity for mono- and tri-methylated H3 Lys-36. Preferentially binds the transcribed region of ribosomal RNA and represses the transcription of ribosomal RNA genes which inhibits cell growth and proliferation. May also serve as a substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KDM2B Gene

Genomics for KDM2B Gene

Regulatory Elements for KDM2B Gene

Transcription factor binding sites by QIAGEN in the KDM2B gene promoter:

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for KDM2B Gene

Start:
121,429,096 bp from pter
End:
121,581,015 bp from pter
Size:
151,920 bases
Orientation:
Minus strand

Genomic View for KDM2B Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for KDM2B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KDM2B Gene

Proteins for KDM2B Gene

  • Protein details for KDM2B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NHM5-KDM2B_HUMAN
    Recommended name:
    Lysine-specific demethylase 2B
    Protein Accession:
    Q8NHM5
    Secondary Accessions:
    • A8MRS1
    • Q1RLM7
    • Q8NCI2
    • Q96HC7
    • Q96SL0
    • Q96T03
    • Q9NS96
    • Q9UF75

    Protein attributes for KDM2B Gene

    Size:
    1336 amino acids
    Molecular mass:
    152615 Da
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Note=Binds 1 Fe(2+) ion per subunit.;
    Quaternary structure:
    • Directly interacts with SKP1 and CUL1.
    SequenceCaution:
    • Sequence=AAH08735.2; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB55112.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB55301.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAC11159.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for KDM2B Gene

    Alternative splice isoforms for KDM2B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for KDM2B Gene

Proteomics data for KDM2B Gene at MOPED

Post-translational modifications for KDM2B Gene

  • Ubiquitination at Lys147
  • Modification sites at PhosphoSitePlus

Domains for KDM2B Gene

Gene Families for KDM2B Gene

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

Graphical View of Domain Structure for InterPro Entry

Q8NHM5

UniProtKB/Swiss-Prot:

KDM2B_HUMAN :
  • Q8NHM5
Domain:
  • The JmjC domain mediates demethylation activity (By similarity). It is also required for repression of ribosomal RNA genes.
  • Contains 1 F-box domain.
  • Contains 1 JmjC domain.
Family:
  • Belongs to the JHDM1 histone demethylase family.
Similarity:
  • Contains 1 CXXC-type zinc finger.
  • Contains 7 LRR (leucine-rich) repeats.
  • Contains 1 PHD-type zinc finger.
genes like me logo Genes that share domains with KDM2B: view

Function for KDM2B Gene

Molecular function for KDM2B 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 demethylates Lys-4 and Lys-36 of histone H3, thereby playing a central role in histone code. Preferentially demethylates trimethylated H3 Lys-4 and dimethylated H3 Lys-36 residue while it has weak or no activity for mono- and tri-methylated H3 Lys-36. Preferentially binds the transcribed region of ribosomal RNA and represses the transcription of ribosomal RNA genes which inhibits cell growth and proliferation. May also serve as a substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex.

Enzyme Numbers (IUBMB) for KDM2B Gene

Gene Ontology (GO) - Molecular Function for KDM2B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding NAS 10799292
GO:0005515 protein binding IPI 16943429
GO:0008270 zinc ion binding IEA --
GO:0019843 rRNA binding IEA --
GO:0032452 histone demethylase activity TAS 21220025
genes like me logo Genes that share ontologies with KDM2B: view
genes like me logo Genes that share phenotypes with KDM2B: view

Animal Model Products

CRISPR Products

miRNA for KDM2B Gene

miRTarBase miRNAs that target KDM2B

No data available for Animal Models , Transcription Factor Targeting and HOMER Transcription for KDM2B Gene

Localization for KDM2B Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM2B Gene

Nucleus, nucleolus.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for KDM2B Gene COMPARTMENTS Subcellular localization image for KDM2B gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for KDM2B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus NAS 10799292
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IEA --
GO:0031519 colocalizes_with PcG protein complex IDA 16943429
genes like me logo Genes that share ontologies with KDM2B: view

Pathways for KDM2B Gene

SuperPathways for KDM2B Gene

No Data Available

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays
    • Polycomb & Trithorax Complexes in human,mouse,rat
    • Ubiquitin Ligases in human,mouse,rat

Gene Ontology (GO) - Biological Process for KDM2B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter ISS --
GO:0006325 chromatin organization TAS --
GO:0006351 transcription, DNA-templated IEA --
GO:0007283 spermatogenesis ISS --
GO:0016577 histone demethylation TAS 21220025
genes like me logo Genes that share ontologies with KDM2B: view

No data available for Pathways by source for KDM2B Gene

Compounds for KDM2B Gene

(2) HMDB Compounds for KDM2B 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 KDM2B: view

Transcripts for KDM2B Gene

Unigene Clusters for KDM2B Gene

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

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for KDM2B

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for KDM2B

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for KDM2B Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b · 8c ^ 9 ^ 10 ^ 11a · 11b ^ 12a · 12b ^ 13a · 13b · 13c ^ 14 ^ 15 ^ 16 ^ 17a ·
SP1:
SP2:
SP3:
SP4:
SP5: - - - - -
SP6: - - - -
SP7: -
SP8: - - -
SP9:
SP10:
SP11: -
SP12:
SP13:
SP14: -
SP15: -

ExUns: 17b ^ 18 ^ 19 ^ 20 ^ 21a · 21b ^ 22 ^ 23a · 23b · 23c ^ 24 ^ 25 ^ 26 ^ 27a · 27b ^ 28 ^ 29 ^ 30 ^ 31a · 31b ^ 32a · 32b · 32c · 32d
SP1: - -
SP2: - - -
SP3: - -
SP4: -
SP5:
SP6:
SP7:
SP8:
SP9: -
SP10: - -
SP11:
SP12:
SP13:
SP14:
SP15:

Relevant External Links for KDM2B Gene

GeneLoc Exon Structure for
KDM2B
ECgene alternative splicing isoforms for
KDM2B

Expression for KDM2B Gene

mRNA expression in normal human tissues for KDM2B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for KDM2B Gene

SOURCE GeneReport for Unigene cluster for KDM2B Gene Hs.524800

genes like me logo Genes that share expressions with KDM2B: view

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for KDM2B Gene

Orthologs for KDM2B Gene

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

Orthologs for KDM2B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia KDM2B 35
  • 99.53 (n)
  • 99.85 (a)
KDM2B 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia KDM2B 35
  • 92.97 (n)
  • 96.6 (a)
KDM2B 36
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia KDM2B 35
  • 92.71 (n)
  • 97.06 (a)
KDM2B 36
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Kdm2b 35
  • 89.31 (n)
  • 94.67 (a)
Kdm2b 16
Kdm2b 36
  • 94 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 36
  • 79 (a)
OneToMany
-- 36
  • 86 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia KDM2B 36
  • 76 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Kdm2b 35
  • 90.13 (n)
  • 95.44 (a)
chicken
(Gallus gallus)
Aves KDM2B 35
  • 78.71 (n)
  • 87.9 (a)
KDM2B 36
  • 85 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia KDM2B 36
  • 79 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.7069 35
tropical clawed frog
(Silurana tropicalis)
Amphibia kdm2b 35
  • 71.49 (n)
  • 82.58 (a)
Str.8397 35
zebrafish
(Danio rerio)
Actinopterygii kdm2ba 36
  • 59 (a)
OneToMany
kdm2bb 36
  • 74 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Kdm2 36
  • 33 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea jhdm-1 36
  • 25 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes JHD1 36
  • 27 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 45 (a)
OneToMany
Species with no ortholog for KDM2B:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 KDM2B Gene

ENSEMBL:
Gene Tree for KDM2B (if available)
TreeFam:
Gene Tree for KDM2B (if available)

Paralogs for KDM2B Gene

Paralogs for KDM2B Gene

genes like me logo Genes that share paralogs with KDM2B: view

Variants for KDM2B Gene

Sequence variations from dbSNP and Humsavar for KDM2B Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type MAF
rs13754 -- 121,429,454(-) GGAGG(G/T)TCTGC utr-variant-3-prime
rs15876 -- 121,429,689(-) TTCAT(C/T)GACAC utr-variant-3-prime
rs792601 -- 121,479,733(+) tctcc(C/T)gcctc intron-variant
rs812078 -- 121,479,741(+) ctcag(C/T)ctccc intron-variant
rs967757 -- 121,513,467(+) GGAGA(A/G)AAGTG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for KDM2B Gene

Variant ID Type Subtype PubMed ID
nsv509483 CNV Insertion 20534489
esv1005622 CNV Insertion 20482838
nsv909 CNV Insertion 18451855
esv1005547 CNV Loss 20482838

Relevant External Links for KDM2B Gene

HapMap Linkage Disequilibrium report
KDM2B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KDM2B Gene

Disorders for KDM2B Gene

Relevant External Links for KDM2B

Genetic Association Database (GAD)
KDM2B
Human Genome Epidemiology (HuGE) Navigator
KDM2B
genes like me logo Genes that share disorders with KDM2B: view

No data available for UniProtKB/Swiss-Prot for KDM2B Gene

Publications for KDM2B Gene

  1. JHDM1B/FBXL10 is a nucleolar protein that represses transcription of ribosomal RNA genes. (PMID: 17994099) Frescas D. … Pagano M. (Nature 2007) 3 4 23
  2. PCCX1, a novel DNA-binding protein with PHD finger and CXXC domain, is regulated by proteolysis. (PMID: 10799292) Fujino T. … Takano T. (Biochem. Biophys. Res. Commun. 2000) 2 3
  3. Polycomb group and SCF ubiquitin ligases are found in a novel BCOR complex that is recruited to BCL6 targets. (PMID: 16943429) Gearhart M.D. … Bardwell V.J. (Mol. Cell. Biol. 2006) 3 23
  4. The F-box protein Fbl10 is a novel transcriptional repressor of c-Jun. (PMID: 17704768) Koyama-Nasu R. … Tanese N. (Nat. Cell Biol. 2007) 3 23
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4

Products for KDM2B Gene

  • Addgene plasmids for KDM2B

Sources for KDM2B Gene

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