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KDM5B Gene

protein-coding   GIFtS: 46

GC01M200965
lysine (K)-specific demethylase 5B
(Previous names: Jumonji, AT rich interactive domain 1B (RBP2-like), jumonji, AT rich interactive domain 1B )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: JARID1B)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
CT31 1, 2, 3
EC 1.14.11.- 3
FLJ10538 2
FLJ12459 2
FLJ12491 2
FLJ16281 2
FLJ23670 2
JARID1B 2, 3
OTTHUMP00000038815 2
PLU-1 1, 2, 3
PLU1 3
PUT1 2
RBBP2H1 3
RBBP2H1A 1, 2
RBP2-H1 3
RBP2-like 2
Descriptions
Cancer/testis antigen 31 2, 3
Histone demethylase JARID1B 3
Jumonji, AT rich interactive domain 1B (RBP2-like) 1
Jumonji/ARID domain-containing protein 1B 3
Retinoblastoma-binding protein 2 homolog 1 3
jumonji, AT rich interactive domain 1B 1, 2
lysine (K)-specific demethylase 5B 2
lysine-specific demethylase 5B 1
putative DNA/chromatin binding motif 2
retinoblastoma-binding protein 2, homolog 1A 2
External Ids
HGNC: 180391
Entrez Gene: 107652
UniProtKB: Q9UGL13
Search outside databases for aliases for KDM5B gene

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

UniProtKB/Swiss-Prot: KDM5B_HUMAN, Q9UGL1
Function: Histone demethylase that demethylates 'Lys-4' of histone H3, thereby playing a central
role in histone code. Does not demethylate histone H3 'Lys-9' or H3 'Lys-27'. Demethylates
trimethylated, dimethylated and monomethylated H3 'Lys-4'. Acts as a transcriptional corepressor
for FOXG1B and PAX9. Favors the proliferation of breast cancer cells by repressing tumor
suppressor genes such as BRCA1 and HOXA5. In contrast, may act as a tumor suppressor for melanoma

Gene Wiki entry for KDM5B (JARID1B)

(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: 1q32.1   HGNC cytogenetic band: 1q32.1

KDM5B 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 1         GeneLoc Exon Structure

GeneLoc location for GC01M200965:     (about GC identifiers)

Start:
200,963,155 bp from pter
End:
201,044,172 bp from pter
Size:
81,018 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000001.9  NT_004487.18  
(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)
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UniProtKB/Swiss-Prot: KDM5B_HUMAN, Q9UGL1 (See protein sequence)
Recommended Name: Lysine-specific demethylase 5B  
Size: 1544 amino acids; 175645 Da
Cofactor: Fe(2+) (By similarity)
Subunit: Interacts with FOXG1B, PAX9, MYC, MYCN and RB1. Interacts with HDAC1, HDAC4, HDAC5 and
HDAC7 (By similarity)
Subcellular location: Nucleus
Secondary accessions: O95811 Q15752 Q9Y3Q5
Alternative splicing: 2 isoforms:  Q9UGL1-1   Q9UGL1-2   

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_006609.3  
    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 (KDM5B / PLU1 / Jarid1B)
    Human Recombinant Proteins from Abnova (JARID1B)
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    2 Gene Ontology (GO) cellular component terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622 intracellular IEA--
    GO:0005634 nucleus TAS10336460 12657635
    About this table

    Antibodies for KDM5B: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Sigma-Aldrich Antibodies for KDM5B
    Browse R&D Systems for Antibodies
    Cell Signaling Technology (CST) Antibodies for KDM5B  (JARID1B)
    Antibodies from Abcam (KDM5B / PLU1 / Jarid1B), each with their AbpromiseSM
    Monoclonal and Polyclonal Antibodies from Abnova (JARID1B)
    Novus Biologicals Antibodies for JARID1B

    Assays for KDM5B: 
    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

    5/9 InterPro domains/families (see all 9 ):
     IPR001965 Znf_PHD
     IPR013129 TF_JmjC
     IPR013637 PLU-1
     IPR003347 TF_JmjC_AAH
     IPR019786 Zinc_finger_PHD-type_CS


       GeneDecks  KDM5B for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q9UGL1

    ProtoNet protein and cluster: Q9UGL1

    5 Blocks protein families:
    IPB001606 ARID (AT-rich interaction domain) protein
    IPB003347 Transcription factor jumonji
    IPB003349 Transcription factor jumonji
    IPB004198 Zn-finger
    IPB013637 PLU-1-like


    UniProtKB/Swiss-Prot: KDM5B_HUMAN, Q9UGL1
    Domain: Both the JmjC domain and the JmjN domain are required for enzymatic activity
    Domain: The 2 first PHD-type zinc finger domains are required for transcription repression activity
    Similarity: Belongs to the JARID1 histone demethylase family
    Similarity: Contains 1 ARID domain
    Similarity: Contains 1 JmjC domain
    Similarity: Contains 1 JmjN domain
    Similarity: Contains 3 PHD-type zinc fingers

    (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 (KDM5B)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (JARID1B)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_006618

                  Applied Biosystems Silencer® siRNAs for KDM5B

                  Sigma-Aldrich siRNA and siRNA Panels for KDM5B  
                         Sigma-Aldrich shRNA for KDM5B  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Browse Clone Ranger at Invitrogen for clones
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_006618
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_006618
                                     untagged cDNA clone in CMV expression vector: NM_006618 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_006618

    UniProtKB/Swiss-Prot: KDM5B_HUMAN, Q9UGL1
    Function: Histone demethylase that demethylates 'Lys-4' of histone H3, thereby playing a central
    role in histone code. Does not demethylate histone H3 'Lys-9' or H3 'Lys-27'. Demethylates
    trimethylated, dimethylated and monomethylated H3 'Lys-4'. Acts as a transcriptional corepressor
    for FOXG1B and PAX9. Favors the proliferation of breast cancer cells by repressing tumor
    suppressor genes such as BRCA1 and HOXA5. In contrast, may act as a tumor suppressor for melanoma
    Enzyme Number (IUBMB): EC 1.14.11.- 

    5/8 Gene Ontology (GO) molecular function terms (links to tree view) (see all 8 ):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003700 transcription factor activity TAS10336460
    GO:0005506 iron ion binding IEA--
    GO:0005515 protein binding IPI12657635
    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


    1 Sigma-Aldrich "Your Favorite Gene" Pathway for  KDM5B  (Your Favorite Gene powered by Ingenuity) 
     Role of Oct4 in Mammalian Embryonic Stem Cell Pluripotency

       GeneDecks  KDM5B for the pathways selected above  
    About GeneDecksing

     Gene Network CentralTM Interacting Genes and Proteins Network for  KDM5B 

      --

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006350 transcription IEA--
    GO:0016568 chromatin modification IEA--
    GO:0045892 negative regulation of transcription, DNA-dependent IDA12657635
    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 KDM5B

    (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 (KDM5B)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (JARID1B)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_006618

                  Sigma-Aldrich siRNA and siRNA Panels for KDM5B  
                         Sigma-Aldrich shRNA for KDM5B  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_006618  

    REFSEQ mRNAs for KDM5B gene: 

    NM_006618.3   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_006618  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_006618
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_006618
                                     untagged cDNA clone in CMV expression vector: NM_006618 

    Additional cDNA sequence: 

    AB015348.1 AF087481.1 AJ132440.1 AJ243706.1 AK001400.1 AK022521.1 AK022553.1 AK074250.1 
    AK122752.1 AK125746.1 AL133040.1 AL133048.1 AL133072.1 AL137622.1 AL833515.1 CR610637.1 

    18 DOTS entries:

    DT.97857065  DT.449384  DT.101963351  DT.97770938  DT.121434552  DT.101967997  DT.97810559  DT.91804138 
    DT.121434559  DT.121434585  DT.92008652  DT.120304  DT.121434525  DT.121434554  DT.121434565  DT.121434582 
    DT.92384997  DT.95200889 

    24/359 AceView cDNA sequences (see all 359 ):

    BM702957 BQ637269 AI026894 AL704530 W72258 BX104183 BF000575 BM985272 
    AU149588 AU132575 BM998212 AI352104 AW151255 Z39493 BF901260 AI005463 
    AA948108 AA630339 CB133686 CA450574 AI751550 BF594529 BQ222747 BE550346 

    Unigene Cluster for KDM5B:

    Lysine (K)-specific demethylase 5B
    Hs.443650  [show with all ESTs]
    Unigene Representative Sequence: AJ243706


    GeneLoc Exon Structure

    (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

    KDM5B expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for KDM5B

    1 / 2

    9 probe-sets matching KDM5B gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
    39713_at2 U95-A 2 1.00 0.50 1.00 1.00 -- -- -- -- --

    201548_s_at2 U133-A 2 1.00 0.50 -- -- -- -- -- -- --

    211202_s_at2 U133-A 2 1.00 0.50 -- -- -- -- -- -- --

    201547_at2 U133-A 2 1.00 0.50 -- -- -- -- -- -- --

    201549_x_at2 U133-A 2 1.00 0.50 -- -- -- -- -- -- --

    201548_s_at2 U133Plus2 2 1.00 0.50 -- -- -- -- -- -- --

    211202_s_at2 U133Plus2 2 1.00 0.50 -- -- -- -- -- -- --

    201547_at2 U133Plus2 2 1.00 0.50 -- -- -- -- -- -- --

    201549_x_at2 U133Plus2 2 1.00 0.50 -- -- -- -- -- -- --
    GeneDecks  KDM5B 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: TACAGCATTA

    SOURCE GeneReport for Unigene cluster: Hs.443650

    UniProtKB/Swiss-Prot: KDM5B_HUMAN, Q9UGL1
    Tissue specificity: Ubiquitously expressed, with highest levels in testis. Down-regulated in
    melanoma and gllioblastoma. Up-regulated in breast cancer (at protein level)

    (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 KDM5B gene from 5/11 species (see all 11 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    JARID1B1   -- jumonji, AT rich interactive domain 1B 93.03(n)
    96.49(a)
    479999  XM_537122.2  XP_537122.2 
    chimpanzee
    (Pan troglodytes)
    JARID1B1   -- jumonji, AT rich interactive domain 1B 99.37(n)
    99.59(a)
    457630  XM_514104.2  XP_514104.2 
    cow
    (Bos taurus)
    JARID1B1   -- jumonji, AT rich interactive domain 1B 87.29(n)
    91.94(a)
    540633  XM_612405.3  XP_612405.3 
    rat
    (Rattus norvegicus)
    Jarid1b1   -- jumonji, AT rich interactive domain 1B 88.56(n)
    93.98(a)
    304809  XM_239761.4  XP_239761.3 
    mouse
    (Mus musculus)
    Kdm5b5
    Jarid1b1
    1 (72.00 cM)5
    lysine (K)-specific demethylase 5B5
    jumonji, AT rich interactive domain 1B (Rbp2 like)1
    88.88(n)1
    94.11(a)1
    756051  NM_152895.11  NP_690855.11 
     AA2204275  AA6455195  (see all 32)
    About this table        Species with no ortholog for KDM5B
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

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


    10/498 NCBI SNPs in KDM5B are shown (see all 498 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 121)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 1 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs43487781,2
    A,C,F,H200962870(+) TTGTGC/TTTACT 1 -- ng514Minor allele frequency- T:0.49EU EA WA 418
    rs109204641,2
    A,C,F,H200964170(+) ACACAC/GTGTTT 1 -- ut314Minor allele frequency- G:0.08EU EA WA 420
    rs42457131,2
    C,F,H201044884(+) GGGGCA/GAAAGA 1 -- ng3112Minor allele frequency- G:0.22EU EA WA 1256
    rs104948371,2
    C,F,H200963958(+) TGTTAG/AGACGA 1 -- ut3112Minor allele frequency- A:0.03NS NA EU EA WA 666
    rs104948361,2
    C,F,H200963501(+) ATTCAC/TAAGTC 1 -- ut3112Minor allele frequency- T:0.11NS NA EU EA WA 666
    rs121265391,2
    H200964256(+) AGTCTA/CCCAGG 1 -- ut314Minor allele frequency- C:0.00EU EA WA 420
    rs18921641,2
    A,C,F,H,O200984825(+) TCATCA/GTGGGA 1 H/H syn18Minor allele frequency- G:0.40MN NA EU EA WA 736
    rs31966691,2
    A,C,F,H,O200999861(-) ACAACA/GGAAGC 1 T/T syn17Minor allele frequency- G:0.37EU EA WA NA 558
    rs11411081,2
    A,C,F,H200981907(-) CCTTAT/CAAATA 1 Y/Y syn15Minor allele frequency- C:0.37MN EU EA WA 596
    rs11411091,2
    C,F,H200972078(-) ATCCCG/CGTACA 1 P/P syn18Minor allele frequency- C:0.40EU EA WA 838
    About this table

    HapMap Linkage Disequilibrium images for KDM5B (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: 605393

    (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

    10/23 PubMed articles for KDM5B gene (see all 23 ):
    (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: 10765 HGNC: 18039 AceView: JARID1B euGenes: HUgn10765 ECgene: KDM5B
    H-InvDB: KDM5B
    (According to HUGE)
    About This Section

      --
    (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 KDM5B:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



      Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
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      Invitrogen Proteins / Assays / Screening Services  Search Invitrogen catalog for KDM5B-related products

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     Predesigned and custom siRNAs for KDM5B Antibodies for KDM5B
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for KDM5B Browse small molecules at Sigma-Aldrich
     "Your Favorite Gene" Pathwaysfeedback


      
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     Recombinant & Natural Proteins  

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     Custom Service for Mouse Mab
     Custom Service for Rabbit Pab from Full-length Protein
      
     Antibodies & Assays for KDM5B  (JARID1B)

     Recombinant Proteins
    (KDM5B / PLU1 / Jarid1B)
     Antibodies (KDM5B / PLU1 / Jarid1B)
     Search OriGene for KDM5B
     Search Tocris compounds for KDM5B




     Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies
     Antibodies for JARID1B

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