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KDM5B Gene

protein-coding   GIFtS: 57
GCID: GC01M202696

Lysine (K)-Specific Demethylase 5B

(Previous names: Jumonji, AT rich interactive domain 1B (RBP2-like), jumonji,...)
(Previous symbol: JARID1B)
  See KDM5B-related disease
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 5B1 2     RBP2-H12 3
JARID1B1 2 3 5     PUT12 5
Cancer/Testis Antigen 311 2 3     RBBP2H1A2 5
PLU12 3 5     Jumonji, AT Rich Interactive Domain 1B (RBP2-Like)1
Jumonji, AT Rich Interactive Domain 1B1 2     Lysine-Specific Demethylase 5B2
Histone Demethylase JARID1B2 3     Putative DNA/Chromatin Binding Motif2
Jumonji/ARID Domain-Containing Protein 1B2 3     Retinoblastoma-Binding Protein 2, Homolog 1A2
Retinoblastoma-Binding Protein 2 Homolog 12 3     EC 1.14.11.-3
CT312 3     RBBP2H13
PLU-12 3     EC 1.14.118

External Ids:    HGNC: 180391   Entrez Gene: 107652   Ensembl: ENSG000001171397   OMIM: 6053935   UniProtKB: Q9UGL13   

Export aliases for KDM5B gene to outside databases

Previous GC identifers: GC01M200965 GC01M173862


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for KDM5B Gene:
KDM5B (lysine (K)-specific demethylase 5B) is a protein-coding gene. Diseases associated with KDM5B include retinoblastoma. GO annotations related to this gene include oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is KDM5C.

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) Gene


(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 at NCBI GenBank:
NC_000001.10  NC_018912.2  NT_004487.20  
Regulatory elements:
   Regulatory transcription factor binding sites in the KDM5B gene promoter:
         NF-1   Elk-1   HSF1 (long)   NF-kappaB   LCR-F1   E2F-1   E2F   COMP1   HSF1short   NF-kappaB1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidKDM5B promoter sequence
   Search Chromatin IP Primers for KDM5B

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat KDM5B


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

Entrez Gene cytogenetic band: 1q32.1   Ensembl 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)
KDM5B gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M202696:  view genomic region     (about GC identifiers)

Start:
202,696,526 bp from pter      End:
202,778,598 bp from pter
Size:
82,073 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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: KDM5B_HUMAN, Q9UGL1 (See protein sequence)
Recommended Name: Lysine-specific demethylase 5B  
Size: 1544 amino acids; 175658 Da
Cofactor: Binds 1 Fe(2+) ion per subunit (By similarity)
Subunit: Interacts with FOXG1B, PAX9, MYC, MYCN and RB1. Interacts with HDAC1, HDAC4, HDAC5 and HDAC7 (By
similarity)
Sequence caution: Sequence=CAB63108.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
1 PDB 3D structure from and Proteopedia for KDM5B:
2MA5 (3D)    
Secondary accessions: O95811 Q15752 Q9Y3Q5
Alternative splicing: 2 isoforms:  Q9UGL1-1   Q9UGL1-2   

Explore the universe of human proteins at neXtProt for KDM5B: NX_Q9UGL1

Explore proteomics data for KDM5B at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys355, Lys363, Lys408, Lys821, Lys832, Lys956, Lys1011, Lys1136, Lys1166, Lys1276
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for KDM5B (Q9UGL1) (see all 28)
     RYCVFSH  DKEYKPH  GEPKTWY  KCKTTCF 


    See KDM5B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_006609.3  
    ENSEMBL proteins: 
     ENSP00000356234   ENSP00000356233   ENSP00000235790   ENSP00000473481  

    KDM5B Human Recombinant Protein Products:

    Browse Purified and Recombinant Proteins at EMD Millipore
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    OriGene Protein Over-expression Lysate for KDM5B
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    Novus Biologicals KDM5B Protein
    Novus Biologicals KDM5B Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for KDM5B

     
    Search eBioscience for Proteins for KDM5B 

    KDM5B Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of KDM5B
    R&D Systems Antibodies for KDM5B (Lysine (K)-specific Demethylase 5B/KDM5B)
    Cell Signaling Technology (CST) Antibodies for KDM5B  (JARID1B)
    OriGene Antibodies for KDM5B
    OriGene Custom Antibody Services for KDM5B
    Novus Biologicals KDM5B Antibodies
    Abcam antibodies for KDM5B
    Cloud-Clone Corp. Antibodies for KDM5B
    Search ThermoFisher Antibodies for KDM5B
    LSBio Antibodies in human, mouse, rat for KDM5B

    KDM5B Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    GenScript Custom Assay Services for KDM5B
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for KDM5B
    Cloud-Clone Corp. CLIAs for KDM5B
    Search eBioscience for ELISAs for KDM5B 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    KDM: Chromatin-modifying enzymes / K-demethylases
    PHF: Zinc fingers, PHD-type

    Selected InterPro protein domains (see all 10):
     IPR001965 Znf_PHD
     IPR013083 Znf_RING/FYVE/PHD
     IPR003347 JmjC_dom
     IPR013637 Lys_sp_deMease_like_dom
     IPR019786 Zinc_finger_PHD-type_CS

    Graphical View of Domain Structure for InterPro Entry Q9UGL1

    ProtoNet protein and cluster: Q9UGL1

    5 Blocks protein domains:
    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


    Find genes that share domains with KDM5B           About GenesLikeMe


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: 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 Numbers (IUBMB): EC 1.14.11.-1 EC 1.14.112

         Gene Ontology (GO): Selected molecular function terms (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0003700sequence-specific DNA binding transcription factor activity TAS10336460
    GO:0003714transcription corepressor activity IDA12657635
    GO:0005515protein binding IPI12657635
    GO:0008270zinc ion binding IEA--
         
    Find genes that share ontologies with KDM5B           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for KDM5B:
     Increased cell death HMECs cel  Synthetic lethal with Ras 

         1 MGI mutant phenotype (inferred from 2 alleles(MGI details for Kdm5b):
     no phenotypic analysis 

    Find genes that share phenotypes with KDM5B           About GenesLikeMe

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for KDM5B
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for KDM5B
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for KDM5B

    miRNA
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    miRTarBase miRNAs that target KDM5B:
    hsa-mir-296-3p (MIRT038506), hsa-mir-335-5p (MIRT016728), hsa-mir-29c-3p (MIRT020412), hsa-let-7i-5p (MIRT046553)

    Block miRNA regulation of human, mouse, rat KDM5B using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate KDM5B (see all 49):
    hsa-miR-607 hsa-miR-300 hsa-miR-605 hsa-miR-29a hsa-miR-183* hsa-miR-4330 hsa-miR-155 hsa-miR-532-5p
    SwitchGear 3'UTR luciferase reporter plasmidKDM5B 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for KDM5B
    Predesigned siRNA for gene silencing in human, mouse, rat KDM5B

    Gene Editing
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    Clone
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    GenScript: all cDNA clones in your preferred vector: KDM5B (NM_006618)
    Browse Sino Biological Human cDNA Clones
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat KDM5B

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    Browse ESI BIO Cell Lines and PureStem Progenitors for KDM5B 
    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for KDM5B


    (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
    KDM5B_HUMAN, Q9UGL1: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular ----
    GO:0005634nucleus IEA--
    GO:0005730nucleolus ----
    GO:0043231intracellular membrane-bounded organelle ----

    Find genes that share ontologies with KDM5B           About GenesLikeMe


    (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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    SuperPaths for KDM5B About    
    See pathways by source

    SuperPathContained pathways About
    1Chromatin Regulation / Acetylation
    Chromatin Regulation / Acetylation


    Find genes that share SuperPaths with KDM5B           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Cell Signaling Technology (CST) Pathway for KDM5B
        Chromatin Regulation / Acetylation


        Pathway & Disease-focused RT2 Profiler PCR Array including KDM5B: 
              Epigenetic Chromatin Modification Enzymes in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for KDM5B

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

    Selected Interacting proteins for KDM5B (Q9UGL13 ENSP000003562344) via UniProtKB, MINT, STRING, and/or I2D (see all 106)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PAX9P557713, ENSP000003552454I2D: score=3 STRING: ENSP00000355245
    FOXG1P553163, ENSP000003390044I2D: score=2 STRING: ENSP00000339004
    PRPF4O431723, ENSP000003633134I2D: score=2 STRING: ENSP00000363313
    ARP102753, ENSP000003638224I2D: score=1 STRING: ENSP00000363822
    AXIN2Q9Y2T13, ENSP000003026254I2D: score=1 STRING: ENSP00000302625
    About this table

    Gene Ontology (GO): 5 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-templated IEA--
    GO:0034720histone H3-K4 demethylation IDA--
    GO:0034721histone H3-K4 demethylation, trimethyl-H3-K4-specific IDA--
    GO:0045892negative regulation of transcription, DNA-templated IDA12657635
    GO:0055114oxidation-reduction process ----

    Find genes that share ontologies with KDM5B           About GenesLikeMe



    (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 KDM5B



    (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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for KDM5B gene: 
    NM_006618.3  

    Unigene Cluster for KDM5B:

    Lysine (K)-specific demethylase 5B
    Hs.443650  [show with all ESTs]
    Unigene Representative Sequence: AJ243706
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000367265(uc001gyf.3) ENST00000367264(uc009xag.3) ENST00000472822
    ENST00000491153 ENST00000235790(uc001gyg.1) ENST00000498276 ENST00000456180
    ENST00000602511 ENST00000470573 ENST00000467487
    miRNA
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    Block miRNA regulation of human, mouse, rat KDM5B using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate KDM5B (see all 49):
    hsa-miR-607 hsa-miR-300 hsa-miR-605 hsa-miR-29a hsa-miR-183* hsa-miR-4330 hsa-miR-155 hsa-miR-532-5p
    SwitchGear 3'UTR luciferase reporter plasmidKDM5B 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for KDM5B
    Predesigned siRNA for gene silencing in human, mouse, rat KDM5B
    Clone
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    GenScript: all cDNA clones in your preferred vector: KDM5B (NM_006618)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat KDM5B
    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat KDM5B
      QuantiFast Probe-based Assays in human, mouse, rat KDM5B

    Additional mRNA 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 

    16 DOTS entries:

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

    Selected AceView cDNA sequences (see all 359):

    AI262935 CB139966 AW613260 AL597692 AU124063 AW137683 AA868065 CR610637 
    AA854560 AI026894 AI308132 AI824976 AL137622 BF594529 AL133048 BX422693 
    CF541414 F03403 T30187 AI681251 BM702957 BF000575 BM998212 AI090308 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for KDM5B (see all 8)    About this scheme

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

    ExUns: 19b ^ 20a · 20b ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28a · 28b ^ 29 ^ 30a · 30b ^ 31
    SP1:                                                              -                                 
    SP2:                                                              -                                 
    SP3:                                                                                                
    SP4:                                                                                                
    SP5:                                                                                                


    ECgene alternative splicing isoforms for KDM5B

    (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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    KDM5B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TACAGCATTA
    KDM5B Expression
    About this image


    KDM5B expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 8) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Testis (Reproductive System)    fully expand to see all 3 entries
             XY Germ Cells Testis Cord
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Ovarian Mesenchymal Stroma Cells Ovary Interstitium
             Oviduct
     
     Endoderm (Gastrulation Derivatives)    fully expand to see all 2 entries
             Definitive Endoderm Cells Definitive Endoderm
             Definitive Endoderm
     
     Gonad (Reproductive System)    fully expand to see all 2 entries
             Testis Somatic Cells Primitive Gonad
    KDM5B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    KDM5B Protein Expression

    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
    glioblastoma. Up-regulated in breast cancer (at protein level)

        Pathway & Disease-focused RT2 Profiler PCR Array including KDM5B: 
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    (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 eukaryotes.

    Orthologs for KDM5B gene from Selected species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Kdm5b1 , 5 lysine (K)-specific demethylase 5B1, 5 88.97(n)1
    94.24(a)1
      1 (58.24 cM)5
    756051  NM_152895.21  NP_690855.21 
     1345601715 
    chicken
    (Gallus gallus)
    Aves KDM5B1 lysine (K)-specific demethylase 5B 76.07(n)
    84.11(a)
      421168  NM_001031029.1  NP_001026200.1 
    lizard
    (Anolis carolinensis)
    Reptilia KDM5B6
    lysine (K)-specific demethylase 5B
    81(a)
    1 ↔ 1
    4(133781884-133846309)
    African clawed frog
    (Xenopus laevis)
    Amphibia BJ070037.12   -- 74.8(n)    BJ070037.1 
    zebrafish
    (Danio rerio)
    Actinopterygii idibd50502 Danio rerio cDNA clone IMAGE5603807, partial cds 74.2(n)    BC061452.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta lid6
    little imaginal discs
    36(a)
    1 → many
    2L(5989463-5999501)
    worm
    (Caenorhabditis elegans)
    Secernentea rbr-21 rbr-2 45.94(n)
    33.74(a)
      177985  NM_069631.6  NP_502032.2 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes JHD26
    JmjC domain family histone demethylase specific fo...
    29(a)
    1 → many
    X(644304-646490) YJR119C
    rice
    (Oryza sativa)
    Liliopsida Os.108682 Oryza sativa (japonica cultivar-group) cDNA cloneJ more 76(n)    AK121381.1 


    ENSEMBL Gene Tree for KDM5B (if available)
    TreeFam Gene Tree for KDM5B (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for KDM5B gene
    KDM5C2  JARID22  KDM5A2  KDM5D2  
    Selected SIMAP similar genes for KDM5B using alignment to 2 protein entries:     KDM5B_HUMAN (see all proteins) (see all similar genes):
    DKFZp434D0815    DKFZp434I0617    DKFZp434I2412    DKFZp434N0335    JARID1B    HRIHFB2060
    CRCP    AURA2    TNFRSF17    ZNF20    HKR1    LYRM4
    APOD    SHANK2    ZNF547    ZNF585B    ZNF738    EIF3L

    Find genes that share paralogs with KDM5B           About GenesLikeMe



    (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 KDM5B (see all 1713)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1889353101,2
    --202696033(+) GGCAAC/GTGACA 1 -- ds50010--------
    rs1908853511,2
    --202696136(+) TAACTC/TACTCA 1 -- ds50010--------
    rs1827663381,2
    --202696164(+) CTTCCC/TCAAAG 1 -- ds50010--------
    rs720474591,2
    C--202696192(+) TGTGT-/ACCACCAC 1 -- ds50010--------
    rs1503657541,2
    --202696236(+) GGGGGC/TAGGGG 1 -- ds50010--------
    rs43487781,2
    C,F,A,H--202696247(+) TTGTGC/TTTACT 1 -- ds500122Minor allele frequency- T:0.50NS EA NA CSA WA 2347
    rs1450958421,2
    --202696266(+) AAAAGC/GTCTCT 1 -- ds50010--------
    rs1147668571,2
    C,F--202696276(+) TAAAGG/ACAGTG 1 -- ds50011Minor allele frequency- A:0.05WA 118
    rs1421435581,2
    --202696349(+) GACAGG/TTGGCA 1 -- ds50010--------
    rs1871639571,2
    --202696421(+) AACCAC/TGATGA 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for KDM5B (202696526 - 202778598 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for KDM5B:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv1740431CNV Deletion17803354
    nsv4110CNV Insertion18451855
    esv2490406CNV Insertion19546169
    nsv832359CNV Loss17160897
    nsv832348CNV Loss17160897
    dgv173e1CNV Complex17122850

    Human Gene Mutation Database (HGMD): KDM5B
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing KDM5B
    DNA2.0 Custom Variant and Variant Library Synthesis for KDM5B

    (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: 605393    OMIM disorders: --

    1 disease for KDM5B:    
    About MalaCards
    retinoblastoma


    Find genes that share disorders with KDM5B           About GenesLikeMe

    Human Genome Epidemiology (HuGE) Navigator: KDM5B (1 document)

    Export disorders for KDM5B 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 KDM5B gene, integrated from 10 sources (see all 60):
    (articles sorted by number of sources associating them with KDM5B)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. PLU-1 is an H3K4 demethylase involved in transcriptional repression and breast cancer cell proliferation. (PubMed id 17363312)1, 2 Yamane K.... Zhang Y. (Mol. Cell 2007)
    2. Breast cancer associated transcriptional repressor PLU-1/JARID1B interacts directly with histone deacetylases. (PubMed id 17373667)1, 2 Barrett A.... Taylor-Papadimitriou J. (Int. J. Cancer 2007)
    3. Re-expression of the retinoblastoma-binding protein 2-homolog 1 reveals tumor-suppressive functions in highly metastatic melanoma cells. (PubMed id 16645588)1, 2 Roesch A....Vogt T. (J. Invest. Dermatol. 2006)
    4. Retinoblastoma-binding protein 2-homolog 1: a retinoblastoma-binding protein downregulated in malignant melanomas. (PubMed id 15803180)1, 2 Roesch A....Vogt T. (Mod. Pathol. 2005)
    5. Human PLU-1 has transcriptional repression properties and interacts with the developmental transcription factors BF-1 and PAX9. (PubMed id 12657635)1, 2 Tan K....Freemont P.S. (J. Biol. Chem. 2003)
    6. PLU-1 nuclear protein, which is upregulated in breast cancer, shows restricted expression in normal human adult tissues: a new cancer/testis antigen? (PubMed id 12237901)1, 2 Barrett A.... Taylor-Papadimitriou J. (Int. J. Cancer 2002)
    7. Gene targeting of Desrt, a novel ARID class DNA-binding protein, causes growth retardation and abnormal development of reproductive organs. (PubMed id 11483573)1, 3 Lahoud M.H....Kola I. (Genome Res. 2001)
    8. Dynamics of the Mrf-2 DNA-binding domain free and in complex with DNA. (PubMed id 11478881)1, 3 Zhu L.... Chen Y. (Biochemistry 2001)
    9. Isolation and chromosomal localization of a new human retinoblastoma binding protein 2 homologue 1a (RBBP2H1A). (PubMed id 10878660)1, 2 Kashuba V.... Zabarovsky E. (Eur. J. Hum. Genet. 2000)
    10. A novel gene (PLU-1) containing highly conserved putative DNA/chromatin binding motifs is specifically up-regulated in breast cancer. (PubMed id 10336460)1, 2 Lu P.J....Taylor-Papadimitriou J. (J. Biol. Chem. 1999)

    (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: 10765 HGNC: 18039 AceView: JARID1B Ensembl:ENSG00000117139 euGenes: HUgn10765
    ECgene: KDM5B H-InvDB: KDM5B

    (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 KDM5B Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for KDM5B gene:
    Search GeneIP for patents involving KDM5B

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



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