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KDM4B Gene

protein-coding   GIFtS: 54

GC19P004921
lysine (K)-specific demethylase 4B
(Previous name: jumonji domain containing 2B )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: JMJD2B)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
EC 1.14.11.- 3
FLJ44906 2
JHDM3B 3
JMJD2B 2, 3
KIAA0876 1, 2, 3
Descriptions
JmjC domain-containing histone demethylation protein 3B 3
Jumonji domain-containing protein 2B 3
jumonji domain containing 2B 1, 2
lysine (K)-specific demethylase 4B 2
lysine-specific demethylase 4B 1
External Ids
HGNC: 291361
Entrez Gene: 230302
UniProtKB: O949533
Ensembl: ENSG000001276637
Search outside databases for aliases for KDM4B gene

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: KDM4B_HUMAN, O94953
Function: Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing
a role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4
'Lys-20'. Only able to demethylate trimethylated H3 'Lys-9', with a weaker activity than KDM4A,
KDM4C and KDM4D. Demethylation of Lys residue generates formaldehyde and succinate

Gene Wiki entry for KDM4B (JMJD2B)

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19p13.3   Ensembl cytogenetic band:  19p13.3   HGNC cytogenetic band: 19p13.3

KDM4B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P004921:     (about GC identifiers)

Start:
4,920,132 bp from pter
End:
5,104,606 bp from pter
Size:
184,475 bases
Orientation:
plus strand
RefSeq DNA sequence:
NC_000019.8  NT_011255.14  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

UniProtKB/Swiss-Prot: KDM4B_HUMAN, O94953 (See protein sequence)
Recommended Name: Lysine-specific demethylase 4B  
Size: 1096 amino acids; 121897 Da
Cofactor: Binds 1 Fe(2+) ion per subunit (By similarity)
Subcellular location: Nucleus
Sequence caution: Sequence=AAC33799.1; Type=Erroneous gene model prediction;
Secondary accessions: O75274 Q6P3R5 Q9P1V1 Q9UF40
Alternative splicing: 2 isoforms:  O94953-1   O94953-2   

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_055830.1  

    ENSEMBL proteins: 
    ENSP00000371178 ENSP00000159111 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
    Browse Human Recombinant Proteins at Sigma-Aldrich  
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Recombinant Proteins from Abcam (KDM4B / JMJD2B)
    Human Recombinant Proteins from Abnova (JMJD2B)
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    1 Gene Ontology (GO) cellular component term (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634 nucleus IEA--
    About this table

    Antibodies for KDM4B: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Browse Antibodies at Sigma-Aldrich
    Browse R&D Systems for Antibodies
    Cell Signaling Technology (CST) Antibodies for KDM4B  (JMJD2B)
    Antibodies from Abcam (KDM4B / JMJD2B), each with their AbpromiseSM
    Monoclonal and Polyclonal Antibodies from Abnova (JMJD2B)
    Novus Biologicals Antibodies for JMJD2B

    Assays for KDM4B: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    5/8 InterPro domains/families (see all 8 ):
     IPR001965 Znf_PHD
     IPR013129 TF_JmjC
     IPR003347 TF_JmjC_AAH
     IPR019786 Zinc_finger_PHD-type_CS
     IPR003349 TF_JmjN


       GeneDecks  KDM4B for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry O94953

    ProtoNet protein and cluster: O94953

    3 Blocks protein families:
    IPB001965 Zn-finger-like
    IPB003347 Transcription factor jumonji
    IPB003349 Transcription factor jumonji


    UniProtKB/Swiss-Prot: KDM4B_HUMAN, O94953
    Domain: The 2 Tudor domains recognize and bind methylated histones. Double Tudor domain has an
    interdigitated structure and the unusual fold is required for its ability to bind methylated
    histone tails (By similarity)
    Similarity: Belongs to the JHDM3 histone demethylase family
    Similarity: Contains 1 JmjC domain
    Similarity: Contains 1 JmjN domain
    Similarity: Contains 2 PHD-type zinc fingers
    Similarity: Contains 2 Tudor domains

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (KDM4B)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (JMJD2B)
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_015015

                  Applied Biosystems Silencer® siRNAs for KDM4B

                  Sigma-Aldrich siRNA and siRNA Panels for KDM4B  
                         Sigma-Aldrich shRNA for KDM4B  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Invitrogen Clones for KDM4B
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_015015
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_015015
                                     untagged cDNA clone in CMV expression vector: NM_015015 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_015015

    UniProtKB/Swiss-Prot: KDM4B_HUMAN, O94953
    Function: Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing
    a role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4
    'Lys-20'. Only able to demethylate trimethylated H3 'Lys-9', with a weaker activity than KDM4A,
    KDM4C and KDM4D. Demethylation of Lys residue generates formaldehyde and succinate
    Enzyme Number (IUBMB): EC 1.14.11.- 

    5/7 Gene Ontology (GO) molecular function terms (links to tree view) (see all 7 ):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676 nucleic acid binding IEA--
    GO:0005506 iron ion binding IEA--
    GO:0005515 protein binding IEA--
    GO:0008270 zinc ion binding IEA--
    GO:0016491 oxidoreductase activity IEA--
    About this table

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section



    5 Interacting proteins for KDM4B (ENSP000001591113 O949532) via UniProtKB, MINT, and/or STRING
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MED10Q9BTT42MINT-65334
    JMJD1CENSP000003359293STRING (score=.953)
    PDCENSP000003420333STRING (score=.895)
    MBD2ENSP000002564293STRING (score=.803)
    --ENSP000003491943STRING (score=.728)
    About this table

    4 Gene Ontology (GO) biological process terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006350 transcription IEA--
    GO:0006355 regulation of transcription, DNA-dependent IEA--
    GO:0016568 chromatin modification IEA--
    GO:0055114 oxidation reduction IEA--
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for KDM4B

    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (KDM4B)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (JMJD2B)
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_015015

                  Sigma-Aldrich siRNA and siRNA Panels for KDM4B  
                         Sigma-Aldrich shRNA for KDM4B  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_015015  

    REFSEQ mRNAs for KDM4B gene: 

    NM_015015.2   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_015015  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_015015
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_015015
                                     untagged cDNA clone in CMV expression vector: NM_015015 

    Additional cDNA sequence: 

    AB020683.2 AF052144.1 AK026040.1 AK090405.1 AK126854.1 AL133622.1 AL831872.1 BC015378.1 
    BC040014.1 BC046167.1 BC063889.1 BC136611.1 BC144292.1 CR592462.1 

    14 DOTS entries:

    DT.95268131  DT.100673094  DT.91736535  DT.100782044  DT.75166336  DT.97842572  DT.99929060  DT.91736528 
    DT.91894949  DT.100025963  DT.92010446  DT.101967033  DT.121459830  DT.97798143 

    24/63 AceView cDNA sequences (see all 63 ):

    BC063889 BM992894 BQ219578 BF868628 AW450344 AA884638 CB158429 AL831872 
    BM801857 AI939571 BG236071 BU844833 CA307451 AI658783 AI362737 BI020470 
    BE672463 AA326284 AI684636 BM703561 BF313933 BE261870 BQ225977 BM703553 

    Unigene Cluster for KDM4B:

    Lysine (K)-specific demethylase 4B
    Hs.654816  [show with all ESTs]
    Unigene Representative Sequence: NM_015015


    GeneLoc Exon Structure

    5/13 Alternative Splicing Database (ASD) splice patterns (SP) for KDM4B (see all 13 )

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21a · 21b ·
    SP1:        -     -                             -           -                       -                                                                           
    SP2:                                                                                                                                                            
    SP3:                                                                                                                                                            
    SP4:                                                                                -                             -     -     -                                 
    SP5:                                                                                                                                                            

    ExUns: 21c ^ 22 ^ 23a · 23b ^ 24a · 24b ^ 25 ^ 26 ^ 27 ^ 28a · 28b ^ 29 ^ 30 ^ 31a · 31b ^ 32
    SP1:                                                                                                
    SP2:                                                                                                
    SP3:                                                                                                
    SP4:                                                                                                
    SP5:                                                                                                

    About this scheme

    ECgene alternative splicing isoforms for KDM4B

    2 Ensembl transcripts including schematic representations:
    ENST00000381759  ENST00000159111  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    KDM4B expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for KDM4B

    1 / 2

    13 probe-sets matching KDM4B gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
    33226_at2 U95-A 1 1.00 1.00 0.87 0.83 -- -- -- -- --

    58501_at2 U95-B 1 0.88 1.00 0.79 1.49 -- -- -- -- --

    68886_r_at*2 U95-D 1 0.81 1.00 0.89 0.69 -- -- -- -- --

    216023_at2 U133-A 1 1.00 1.00 -- -- -- -- -- -- --

    215616_s_at2 U133-A 1 1.00 1.00 -- -- -- -- -- -- --

    212492_s_at2 U133-A 1 1.00 1.00 -- -- -- -- -- -- --

    212495_at2 U133-A 1 1.00 1.00 -- -- -- -- -- -- --

    212496_s_at2 U133-A 1 1.00 1.00 -- -- -- -- -- -- --

    216023_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    215616_s_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    212492_s_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    212495_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    212496_s_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    GeneDecks  KDM4B for binary patterns associated with the probe-sets selected above  
    About GeneDecksing
    About this table    
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: AACGCTGCGA

    SOURCE GeneReport for Unigene cluster: Hs.654816
    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for KDM4B gene from 5/9 species (see all 9 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    JMJD2B1   -- jumonji domain containing 2B 87.15(n)
    89.42(a)
    476741  XM_533946.2  XP_533946.2 
    chimpanzee
    (Pan troglodytes)
    JMJD2B1   -- jumonji domain containing 2B 99.3(n)
    99.45(a)
    455614  XM_001140426.1  XP_001140426.1 
    cow
    (Bos taurus)
    JMJD2B1   -- jumonji domain containing 2B 86.57(n)
    89.32(a)
    508141  XM_584880.3  XP_584880.3 
    mouse
    (Mus musculus)
    Kdm4b5
    Jmjd2b1
    175
    lysine (K)-specific demethylase 4B5
    jumonji domain containing 2B1
    80.87(n)1
    83.71(a)1
    1937961  NM_172132.11  NP_742144.11 
     AK0289625  AK0436785  (see all 22)
    zebrafish
    (Danio rerio)
    si:ch211-124a3.41   -- si:ch211-124a3.4 65.19(n)
    62.24(a)
    556504  NM_001082805.1  NP_001076274.1 
    About this table        Species with no ortholog for KDM4B

    ENSEMBL Gene Tree for KDM4B
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for KDM4B gene
    KDM4D2  KDM4A2  JARID22  KDM4C2  

    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/1160 NCBI SNPs in KDM4B are shown (see all 1160 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 336)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 19 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs26138041,2
    A,C,F,H5103445(+) CCTCCC/TATGGC 1 -- ut31 ese34Minor allele frequency- T:0.37EU EA WA 404
    --
    rs115141,2
    A,C,F,H5104606(-) GGTTTC/TGCAGC 1 -- ut316Minor allele frequency- T:0.19EA MN EU WA 2082
    --
    rs65108321,2
    A,C,F,H4918954(+) TAAGCT/GCCAGA 1 -- ng51 tfbs33Minor allele frequency- G:0.01EU EA 300
    rs26208281,2
    A,C,F,H5103387(-) CTCTCG/AGGTGA 1 -- ut31 ese34Minor allele frequency- A:0.37EU EA WA 406
    rs1971471,2
    C,F,H4918407(-) AAACCG/AGTATC 1 -- ng515Minor allele frequency- A:0.01MN EU EA WA 602
    rs26208271,2
    A,C5104793(-) AGCTGC/TCCCTG 1 -- ng310--------
    rs1971461,2
    C4918946(-) TTACAC/TAATTC 1 -- ng511Minor allele frequency- T:0.00MN 184
    rs116672061,2
    H4983987(+) CTTCAA/CCAAAT 1 N/T mis1 ese34Minor allele frequency- C:0.00EU EA WA 406
    --
    rs106891,2
    F5104604(-) TTTCGC/TAGCGT 1 -- ut31 ese31Minor allele frequency- T:0.01MN 184
    rs26208361,2
    C5086392(-) GCCCTC/TTCCGA 1 E/K mis10--------
    About this table

    HapMap Linkage Disequilibrium images for KDM4B (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 609765

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/17 PubMed articles for KDM4B gene (see all 17 ):
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     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, and/or H-InvDB)
    About This Section

    Entrez Gene: 23030 HGNC: 29136 AceView: JMJD2B Ensembl:ENSG00000127663 euGenes: HUgn23030
    ECgene: KDM4B H-InvDB: KDM4B
    (According to HUGE)
    About This Section

    HUGE: KIAA0876
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

      --
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for KDM4B:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



      Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
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     Predesigned and custom siRNAs for KDM4B Browse antibodies at Sigma-Aldrich
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for KDM4B Browse small molecules at Sigma-Aldrich
     "Your Favorite Gene" Pathwaysfeedback


      
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     Recombinant & Natural Proteins  

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     Recombinant Proteins
    (KDM4B / JMJD2B)
     Antibodies (KDM4B / JMJD2B)
     Search OriGene for KDM4B
     Search Tocris compounds for KDM4B




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