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KDM2B Gene

protein-coding   GIFtS: 56
GCID: GC12M121866

Lysine (K)-Specific Demethylase 2B

(Previous name: F-box and leucine-rich repeat protein 10)
(Previous symbol: FBXL10)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Lysine (K)-Specific Demethylase 2B1 2     CXXC-Type Zinc Finger Protein 22 3
FBXL101 2 3     F-Box Protein FBL102 3
F-Box And Leucine-Rich Repeat Protein 101 2 3     F-Box/LRR-Repeat Protein 102 3
Jumonji C Domain-Containing Histone Demethylase 1B1 2     EC 1.14.11.273 8
JmjC Domain-Containing Histone Demethylation Protein 1B2 3     Fbl102
Protein-Containing CXXC Domain 22 3     JEMMA (Jumonji Domain, EMSY-Interactor, Methyltransferase Motif) Protein2
CXXC22 3     Lysine-Specific Demethylase 2B2
JHDM1B2 3     FBL103
PCCX22 3     Jumonji Domain-Containing EMSY-Interactor Methyltransferase Motif Protein3
[Histone-H3]-Lysine-36 Demethylase 1B2 3     Protein JEMMA3

External Ids:    HGNC: 136101   Entrez Gene: 846782   Ensembl: ENSG000000890947   OMIM: 6090785   UniProtKB: Q8NHM53   

Export aliases for KDM2B gene to outside databases

Previous GC identifers: GC12M120351 GC12M118876


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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. Diseases associated with KDM2B include coloboma, and acute myeloid leukemia. GO annotations related to this gene include rRNA binding and histone demethylase activity. An important paralog of this gene is PHF2.

UniProtKB/Swiss-Prot: KDM2B_HUMAN, Q8NHM5
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




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000012.12  NT_029419.13  NC_018923.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the KDM2B gene promoter:
         AP-1   ATF-2   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): KDM2B promoter sequence
   Search Chromatin IP Primers for KDM2B

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat KDM2B


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 12q24.31   Ensembl cytogenetic band:  12q24.31   HGNC cytogenetic band: 12q24.31

KDM2B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
KDM2B gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12M121866:  view genomic region     (about GC identifiers)

Start:
121,866,899 bp from pter      End:
122,018,920 bp from pter
Size:
152,022 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: KDM2B_HUMAN, Q8NHM5 (See protein sequence)
Recommended Name: Lysine-specific demethylase 2B  
Size: 1336 amino acids; 152615 Da
Cofactor: Binds 1 Fe(2+) ion per subunit (By similarity)
Subunit: Directly interacts with SKP1 and CUL1 (By similarity)
Sequence caution: Sequence=AAH08735.2; Type=Erroneous initiation; Sequence=BAB55112.1; Type=Erroneous initiation;
Sequence=BAB55301.1; Type=Erroneous initiation; Sequence=BAC11159.1; Type=Erroneous initiation;
Secondary accessions: A8MRS1 Q8NCI2 Q96HC7 Q96SL0 Q96T03 Q9NS96 Q9UF75
Alternative splicing: 4 isoforms:  Q8NHM5-1   Q8NHM5-2   Q8NHM5-3   Q8NHM5-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for KDM2B: NX_Q8NHM5

Explore proteomics data for KDM2B at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys147
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for KDM2B (Q8NHM5) (see all 11)
     IHAVYTP  TDFHIDF  GLGIKMP  GTSVWYH 


    See KDM2B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001005366.1  NP_115979.3  

    ENSEMBL proteins: 
     ENSP00000366269   ENSP00000437821   ENSP00000366271   ENSP00000438138   ENSP00000474307  
     ENSP00000398279   ENSP00000444846   ENSP00000445102   ENSP00000437497   ENSP00000443052  
     ENSP00000440942   ENSP00000442293   ENSP00000440373   ENSP00000445196  

    KDM2B Human Recombinant Protein Products:

    Browse Purified and Recombinant Proteins at EMD Millipore
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    Browse OriGene Protein Over-expression Lysates
    OriGene Custom MassSpec
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    Novus Biologicals KDM2B Protein
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for KDM2B

    KDM2B Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of KDM2B
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    Abcam antibodies for KDM2B
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    ThermoFisher Antibodies for KDM2B
    LSBio Antibodies in human, mouse, rat for KDM2B

    KDM2B Assay Products:

    EMD Millipore Kits and Assays for the Analysis of KDM2B
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    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for KDM2B
    Cloud-Clone Corp. CLIAs for KDM2B


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    FBXL: F-boxes / Leucine-rich repeats
    KDM: Chromatin-modifying enzymes / K-demethylases

    Selected InterPro protein domains (see all 6):
     IPR001965 Znf_PHD
     IPR002857 Znf_CXXC
     IPR001810 F-box_dom
     IPR003347 JmjC_dom
     IPR011011 Znf_FYVE_PHD

    Graphical View of Domain Structure for InterPro Entry Q8NHM5

    ProtoNet protein and cluster: Q8NHM5

    2 Blocks protein domains:
    IPB002857 Zn-finger
    IPB003347 Transcription factor jumonji


    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
    Similarity: Belongs to the JHDM1 histone demethylase family
    Similarity: Contains 1 CXXC-type zinc finger
    Similarity: Contains 1 F-box domain
    Similarity: Contains 1 JmjC domain
    Similarity: Contains 7 LRR (leucine-rich) repeats
    Similarity: Contains 1 PHD-type zinc finger


    KDM2B for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: KDM2B_HUMAN, Q8NHM5
    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
    Catalytic activity: Protein N(6),N(6)-dimethyl-L-lysine + 2-oxoglutarate + O(2) = protein N(6)-methyl-L-lysine +
    succinate + formaldehyde + CO(2)
    Catalytic activity: Protein N(6)-methyl-L-lysine + 2-oxoglutarate + O(2) = protein L-lysine + succinate +
    formaldehyde + CO(2)

         Enzyme Number (IUBMB): EC 1.14.11.271 2

         Gene Ontology (GO): Selected molecular function terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding NAS10799292
    GO:0005515protein binding IPI16943429
    GO:0008270zinc ion binding IEA--
    GO:0019843rRNA binding IEA--
    GO:0032452histone demethylase activity TAS--
         
    KDM2B for ontologies           About GeneDecksing


    Phenotypes:
         4 GenomeRNAi human phenotypes for KDM2B:
     Decreased nuclei size in G2M  Increased cell death HMECs cel  Synthetic lethal with Ras  Upregulation of Wnt/beta-caten 

         9 MGI mutant phenotypes (inferred from 1 allele(MGI details for Kdm2b):
     cardiovascular system  cellular  embryogenesis  growth/size/body  limbs/digits/tail 
     mortality/aging  nervous system  reproductive system  vision/eye 

    KDM2B for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for KDM2B
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for KDM2B

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for KDM2B
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for KDM2B

    miRNA
    Products:
        
    miRTarBase miRNAs that target KDM2B:
    hsa-mir-324-3p (MIRT042973), hsa-mir-1 (MIRT024040)

    Block miRNA regulation of human, mouse, rat KDM2B using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate KDM2B (see all 16):
    hsa-miR-411* hsa-miR-148b* hsa-miR-379* hsa-miR-146a hsa-miR-586 hsa-miR-3065-5p hsa-miR-183 hsa-miR-200a
    SwitchGear 3'UTR luciferase reporter plasmidKDM2B 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for KDM2B
    Predesigned siRNA for gene silencing in human, mouse, rat KDM2B

    Gene Editing
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    Clone
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    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): KDM2B (NM_001005366)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for KDM2B
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat KDM2B

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    Browse ESI BIO Cell Lines and PureStem Progenitors for KDM2B 
    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for KDM2B


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    KDM2B_HUMAN, Q8NHM5: Nucleus, nucleolus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus NAS10799292
    GO:0005730nucleolus IEA--
    GO:0031519colocalizes with PcG protein complex IDA16943429

    KDM2B for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Pathway & Disease-focused RT2 Profiler PCR Arrays including KDM2B: 
              Polycomb & Trithorax Complexes in human mouse rat
              Ubiquitin Ligases in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for KDM2B

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for KDM2B (Q8NHM51, 3 ENSP000003662714) via UniProtKB, MINT, STRING, and/or I2D (see all 65)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ENSG00000235107Q065873, ENSP000003964394I2D: score=2 STRING: ENSP00000396439
    ENSG00000206287Q065873I2D: score=2 
    ENSG00000226788Q065873I2D: score=2 
    ENSG00000228520Q065873I2D: score=2 
    ENSG00000231115Q065873I2D: score=2 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 16):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter ISS--
    GO:0006351transcription, DNA-templated IEA--
    GO:0007283spermatogenesis ISS--
    GO:0016577histone demethylation TAS--
    GO:0021555midbrain-hindbrain boundary morphogenesis ISS--

    KDM2B for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for KDM2B

    2 HMDB Compounds for KDM2B    About this table
    CompoundSynonyms CAS #PubMed Ids
    FormaldehydeAldeide formica (see all 16)50-00-0--
    L-Lysine(+)-S-Lysine (see all 25)56-87-1--



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for KDM2B gene (2 alternative transcripts): 
    NM_001005366.1  NM_032590.4  

    Unigene Cluster for KDM2B:

    Lysine (K)-specific demethylase 2B
    Hs.524800  [show with all ESTs]
    Unigene Representative Sequence: NM_032590
    18 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000377069(uc001uas.3 uc021rfd.1) ENST00000542973(uc001uap.3 uc001uaq.3)
    ENST00000538503(uc001uao.3 uc010szx.2 uc010szy.2 uc001uar.3)
    ENST00000377071(uc001uat.3 uc001uau.3 uc021rfe.1) ENST00000543025
    ENST00000536036 ENST00000538243 ENST00000538046(uc001uav.4) ENST00000446152
    ENST00000542030 ENST00000538379 ENST00000545022 ENST00000541318 ENST00000543852
    ENST00000541511 ENST00000539394 ENST00000540191 ENST00000536437
    miRNA
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    Block miRNA regulation of human, mouse, rat KDM2B using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate KDM2B (see all 16):
    hsa-miR-411* hsa-miR-148b* hsa-miR-379* hsa-miR-146a hsa-miR-586 hsa-miR-3065-5p hsa-miR-183 hsa-miR-200a
    SwitchGear 3'UTR luciferase reporter plasmidKDM2B 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat KDM2B
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    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): KDM2B (NM_001005366)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat KDM2B
    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat KDM2B
      QuantiFast Probe-based Assays in human, mouse, rat KDM2B

    Additional mRNA sequence: 

    AB031230.1 AJ459424.1 AK027440.1 AK027692.1 AK055282.1 AK074718.1 AK127328.1 AK299827.1 
    AK316470.1 BC008735.2 BC028612.1 BC115379.1 BC115380.1 BX648928.1 

    23 DOTS entries:

    DT.100779771  DT.95167649  DT.100731611  DT.100779773  DT.100779774  DT.75150484  DT.99954855  DT.100779777 
    DT.101983427  DT.402976  DT.95241592  DT.100655267  DT.100689945  DT.121128640  DT.121128677  DT.95208361 
    DT.97836402  DT.100697037  DT.121128657  DT.121128658  DT.121128720  DT.95262506  DT.86840697 

    Selected AceView cDNA sequences (see all 205):

    BM783782 CR622952 AW118403 BU623219 AK027440 BX331388 NM_032590 BM473316 
    AK027692 R43337 BM718141 AJ459424 N75007 CB240717 BM701125 AI470559 
    BC028612 T35255 AW514897 AA070843 BM759660 AA907525 AW196603 BM740439 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for KDM2B (see all 15)    About this scheme

    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:                    -                 -           -                             -     -                                                                     

    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:                                                                                                                                                


    ECgene alternative splicing isoforms for KDM2B

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    KDM2B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCTATTTCCT
    KDM2B Expression
    About this image


    KDM2B expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Kidney (Urinary System)
             Metanephros
    KDM2B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    KDM2B Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.524800
        Pathway & Disease-focused RT2 Profiler PCR Arrays including KDM2B: 
              Polycomb & Trithorax Complexes in human mouse rat
              Ubiquitin Ligases in human mouse rat

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for KDM2B

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for KDM2B gene from Selected species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Kdm2b1 , 5 lysine (K)-specific demethylase 2B1, 5 89.31(n)1
    94.67(a)1
      5 (62.63 cM)5
    308411  NM_001003953.11  NP_001003953.11 
     1228706685 
    chicken
    (Gallus gallus)
    Aves KDM2B1 lysine (K)-specific demethylase 2B 78.71(n)
    87.9(a)
      416844  XM_415137.4  XP_415137.3 
    lizard
    (Anolis carolinensis)
    Reptilia KDM2B6
    lysine (K)-specific demethylase 2B
    79(a)
    1 ↔ 1
    GL343550.1(44269-117133)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.70692 Xenopus laevis transcribed sequence with moderate similarity more 76.61(n)    BX852634.1 
    zebrafish
    (Danio rerio)
    Actinopterygii kdm2bb6
    kdm2ba6
    lysine (K)-specific demethylase 2Ba
    74(a)
    59(a)
    1 ↔ many
    1 ↔ many
    10(43194428-43202258) ENSDARG00000046010
    8(42291602-42314330) ENSDARG00000036593
    fruit fly
    (Drosophila melanogaster)
    Insecta Kdm26
    Lysine (K)-specific demethylase 2
    33(a)
    1 → many
    3R(4878240-4888967)
    worm
    (Caenorhabditis elegans)
    Secernentea jhdm-16
    Protein JHDM-1, isoform a
    25(a)
    1 → many
    III(6454483-6460010) WBGene00020821
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes JHD16
    JmjC domain family histone demethylase specific fo...
    27(a)
    1 → many
    V(254656-256134) YER051W


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for KDM2B gene
    PHF22  PHF82  KDM2A2  KDM7A2  FBXL192  
    4 SIMAP similar genes for KDM2B using alignment to 11 protein entries:     KDM2B_HUMAN (see all proteins):
    FBXL10    KDM2A    PHF8    FBXL19

    KDM2B for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for KDM2B (see all 3214)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs3716144061,2
    C--121782835(+) TGCCT-/TTTTTTT 2 -- int10--------
    rs795639861,2
    C,F--121866736(+) GAGCAG/ACTCTT 2 -- ds50015Minor allele frequency- A:0.13NA CSA WA 244
    rs1471723091,2
    C--121866762(+) GTGTC-/TTAATT 2 -- ds50010--------
    rs1424115721,2
    --121866768(+) TAATTC/TCTACG 2 -- ds50010--------
    rs1839806251,2
    --121866774(+) CTACGC/TGTGGC 2 -- ds50010--------
    rs1512924551,2
    --121866846(+) CTGAAA/GAAAGA 2 -- ds50010--------
    rs1406106781,2
    --121866861(+) TGACGC/TACCAC 2 -- ds50010--------
    rs1176825491,2
    F--121866905(+) TTGGAC/TTTCAA 2 -- ut311Minor allele frequency- T:0.01NA 120
    rs1442475301,2
    --121866948(+) TAGTCC/TACTCC 2 -- ut310--------
    rs1465600421,2
    --121866985(+) AGTGGG/TTTTTT 2 -- ut310--------

    HapMap Linkage Disequilibrium report for KDM2B (121866899 - 122018920 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for KDM2B:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv509483CNV Insertion20534489
    esv1005622CNV Insertion20482838
    nsv909CNV Insertion18451855
    esv1005547CNV Loss20482838

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing KDM2B
    DNA2.0 Custom Variant and Variant Library Synthesis for KDM2B

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 609078    OMIM disorders: --

    8 diseases for KDM2B:    
    About MalaCards
    coloboma    acute myeloid leukemia    insulin resistance    myeloid leukemia
    pancreatic cancer    leukemia    pancreatitis    neuronitis


    KDM2B for disorders           About GeneDecksing

    Genetic Association Database (GAD): KDM2B
    Human Genome Epidemiology (HuGE) Navigator: KDM2B (1 document)

    Export disorders for KDM2B gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for KDM2B gene, integrated from 10 sources (see all 35):
    (articles sorted by number of sources associating them with KDM2B)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. JHDM1B/FBXL10 is a nucleolar protein that represses transcription of ribosomal RNA genes. (PubMed id 17994099)1, 2, 9 Frescas D....Pagano M. (Nature 2007)
    2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    3. Histone demethylation by a family of JmjC domain-containing proteins. (PubMed id 16362057)1, 2 Tsukada Y.... Zhang Y. (Nature 2006)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    6. PCCX1, a novel DNA-binding protein with PHD finger and CXXC domain, is regulated by proteolysis. (PubMed id 10799292)1, 3 Fujino T.... Takano T. (Biochem. Biophys. Res. Commun. 2000)
    7. The F-box protein Fbl10 is a novel transcriptional repressor of c-Jun. (PubMed id 17704768)1, 9 Koyama-Nasu R....Tanese N. (Nat. Cell Biol. 2007)
    8. Polycomb group and SCF ubiquitin ligases are found in a novel BCOR complex that is recruited to BCL6 targets. (PubMed id 16943429)1, 9 Gearhart M.D.... Bardwell V.J. (Mol. Cell. Biol. 2006)
    9. Fbxl10/Kdm2b recruits polycomb repressive complex 1 to CpG islands and regulates H2A ubiquitylation. (PubMed id 23395003)1 Wu X....Helin K. (Mol. Cell 2013)
    10. KDM2B promotes pancreatic cancer via Polycomb-dependent and -independent transcriptional programs. (PubMed id 23321669)1 Tzatsos A....Bardeesy N. (J. Clin. Invest. 2013)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 84678 HGNC: 13610 AceView: FBXL10 Ensembl:ENSG00000089094 euGenes: HUgn84678
    ECgene: KDM2B H-InvDB: KDM2B

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for KDM2B Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for KDM2B gene:
    Search GeneIP for patents involving KDM2B

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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