Free for academic non-profit institutions. Other users need a Commercial license

Aliases for KDM2B Gene

Aliases for KDM2B Gene

  • Lysine Demethylase 2B 2 3
  • F-Box And Leucine-Rich Repeat Protein 10 2 3 4
  • Lysine (K)-Specific Demethylase 2B 2 3 5
  • 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
  • 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 Demethylase 2B) is a Protein Coding gene. Diseases associated with KDM2B include exencephaly and dravet syndrome. Among its related pathways are Chromatin Regulation / Acetylation and Chromatin organization. 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

Enhancers for KDM2B Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around KDM2B on UCSC Golden Path with GeneCards custom track

Promoters for KDM2B Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around KDM2B on UCSC Golden Path with GeneCards custom track

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

Genomic Location for KDM2B Gene

Chromosome:
12
Start:
121,402,501 bp from pter
End:
121,581,113 bp from pter
Size:
178,613 bases
Orientation:
Minus strand

Genomic View for KDM2B Gene

Genes around KDM2B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KDM2B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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;
    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 Lys 147
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for KDM2B (FBXL10)

Domains & Families for KDM2B Gene

Graphical View of Domain Structure for InterPro Entry

Q8NHM5

UniProtKB/Swiss-Prot:

KDM2B_HUMAN :
  • The JmjC domain mediates demethylation activity (By similarity). It is also required for repression of ribosomal RNA genes.
  • Belongs to the JHDM1 histone demethylase family.
  • Contains 1 CXXC-type zinc finger.
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:0005515 protein binding IPI 16943429
GO:0019843 rRNA binding IEA --
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

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets 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

No data available for Gene Ontology (GO) - Cellular Components for KDM2B Gene

Pathways & Interactions for KDM2B Gene

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

Pathways by source for KDM2B Gene

1 GeneTex pathway for KDM2B Gene
1 Cell Signaling Technology pathway for KDM2B Gene

Gene Ontology (GO) - Biological Process for KDM2B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0007283 spermatogenesis ISS --
GO:0021555 midbrain-hindbrain boundary morphogenesis ISS --
GO:0021592 fourth ventricle development ISS --
GO:0021670 lateral ventricle development ISS --
genes like me logo Genes that share ontologies with KDM2B: view

No data available for SIGNOR curated interactions for KDM2B Gene

Drugs & Compounds for KDM2B Gene

(7) Drugs for KDM2B Gene - From: ApexBio and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
L-Lysine Approved Nutra Full agonist, Agonist 0
Succinic acid Approved Nutra Full agonist, Agonist 0
Formaldehyde Experimental Pharma 78
IOX 1 Pharma Histone demethylase inhibitor; cell permeable 0
ML324 Pharma JMJD2 demethylase inhibitor, potent and cell-permeable 0

(3) Additional Compounds for KDM2B Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
carbon dioxide
  • Carbon oxide
  • Carbon-12 dioxide
  • Carbonic acid anhydride
  • Carbonic acid gas
  • Carbonic anhydride
124-38-9
Oxoglutaric acid
  • 2-Ketoglutarate
  • 2-Ketoglutaric acid
  • 2-Oxo-1,5-pentanedioate
  • 2-Oxo-1,5-pentanedioic acid
  • 2-Oxoglutarate
328-50-7
oxygen
  • Dioxygen
  • Molecular oxygen
  • O2
  • Oxygen
  • Oxygen molecule
7782-44-7

(4) ApexBio Compounds for KDM2B Gene

Compound Action Cas Number
IOX 1 5852-78-8
ML324 JMJD2 demethylase inhibitor, potent and cell-permeable 1222800-79-4
SP2509 Demethylase 1 (LSD1) antagonist, novel Lysine-specific 1423715-09-6
Tranylcypromine hydrochloride 1986-47-6
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:

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

Protein differential expression in normal tissues from HIPED for KDM2B Gene

This gene is overexpressed in Ovary (20.9), Testis (17.9), Spleen (14.7), and Liver (9.5).

Integrated Proteomics: protein expression in normal tissues and cell lines 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 expression patterns with KDM2B: view

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners 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
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
chimpanzee
(Pan troglodytes)
Mammalia KDM2B 35
  • 99.53 (n)
  • 99.85 (a)
KDM2B 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Kdm2b 35
  • 90.13 (n)
  • 95.44 (a)
oppossum
(Monodelphis domestica)
Mammalia -- 36
  • 79 (a)
OneToMany
-- 36
  • 86 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia KDM2B 36
  • 76 (a)
OneToOne
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
tropical clawed frog
(Silurana tropicalis)
Amphibia kdm2b 35
  • 71.49 (n)
  • 82.58 (a)
Str.8397 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.7069 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
rs2037763 -- 121,470,013(+) aatca(A/C)ttgaa intron-variant
rs7134248 -- 121,459,249(+) tttaa(C/T)aagga intron-variant
rs13754 -- 121,429,454(-) GGAGG(G/T)TCTGC intron-variant, utr-variant-3-prime
rs15876 -- 121,429,689(-) TTCAT(C/T)GACAC intron-variant, utr-variant-3-prime
rs7139144 -- 121,454,784(+) TGTCA(C/T)ACTTG 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

Variation tolerance for KDM2B Gene

Residual Variation Intolerance Score: 2.02% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.17; 39.33% of all genes are more intolerant (likely to be disease-causing)

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

MalaCards: The human disease database

(2) MalaCards diseases for KDM2B Gene - From: GeneCards

Disorder Aliases PubMed IDs
exencephaly
dravet syndrome
  • dravet syndrome, modifier of
- elite association - COSMIC cancer census association via MalaCards
Search KDM2B in MalaCards View complete list of genes associated with diseases

Relevant External Links for KDM2B

Genetic Association Database (GAD)
KDM2B
Human Genome Epidemiology (HuGE) Navigator
KDM2B
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
KDM2B
genes like me logo Genes that share disorders with KDM2B: view

No data available for UniProtKB/Swiss-Prot and Genatlas 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 67
  2. 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
  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. 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
  5. The FBXL10/KDM2B scaffolding protein associates with novel polycomb repressive complex-1 to regulate adipogenesis. (PMID: 25533466) Inagaki T. … Sakai J. (J. Biol. Chem. 2015) 3

Products for KDM2B Gene

Sources for KDM2B Gene

Content