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KDM4D Gene

protein-coding   GIFtS: 51
GCID: GC11P094706

Lysine (K)-Specific Demethylase 4D

(Previous name: jumonji domain containing 2D)
(Previous symbol: JMJD2D)
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(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 4D1 2     Lysine-Specific Demethylase 4D2
JMJD2D1 2 3 5     EC 1.14.11.-3
Jumonji Domain Containing 2D1 2     JHDM3D3
JmjC Domain-Containing Histone Demethylation Protein 3D2 3     EC 1.14.118
Jumonji Domain-Containing Protein 2D2 3     

External Ids:    HGNC: 254981   Entrez Gene: 556932   Ensembl: ENSG000001862807   OMIM: 6097665   UniProtKB: Q6B0I63   

Export aliases for KDM4D gene to outside databases

Previous GC identifers: GC11P094347 GC11P090771


(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 KDM4D Gene:
KDM4D (lysine (K)-specific demethylase 4D) is a protein-coding gene. GO annotations related to this gene include dioxygenase activity. An important paralog of this gene is KDM4A.

UniProtKB/Swiss-Prot: KDM4D_HUMAN, Q6B0I6
Function: Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role
in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Demethylates
both di- and trimethylated H3 'Lys-9' residue, while it has no activity on monomethylated residues. Demethylation
of Lys residue generates formaldehyde and succinate

Gene Wiki entry for KDM4D (JMJD2D) 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_000011.9  NC_018922.2  NT_033899.9  
Regulatory elements:
   Regulatory transcription factor binding sites in the KDM4D gene promoter:
         Sp1   AP-1   RREB-1   Nkx2-2   ATF-2   Nkx2-5   POU6F1 (c2)   S8   c-Jun   En-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidKDM4D promoter sequence
   Search Chromatin IP Primers for KDM4D

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat KDM4D


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

Entrez Gene cytogenetic band: 11q21   Ensembl cytogenetic band:  11q21   HGNC cytogenetic band: 11q21

KDM4D Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
KDM4D gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P094706:  view genomic region     (about GC identifiers)

Start:
94,706,845 bp from pter      End:
94,732,682 bp from pter
Size:
25,838 bases      Orientation:
plus 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: KDM4D_HUMAN, Q6B0I6 (See protein sequence)
Recommended Name: Lysine-specific demethylase 4D  
Size: 523 amino acids; 58603 Da
Cofactor: Binds 1 Fe(2+) ion per subunit (By similarity)
Caution: It is uncertain whether Met-1 or Met-4 is the initiator
Sequence caution: Sequence=BAA91508.1; Type=Erroneous initiation;
4 PDB 3D structures from and Proteopedia for KDM4D:
3DXT (3D)        3DXU (3D)        4HON (3D)        4HOO (3D)    
Secondary accessions: B3KPC4 Q0VF39 Q9NT41 Q9NW76

Explore the universe of human proteins at neXtProt for KDM4D: NX_Q6B0I6

Explore proteomics data for KDM4D at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for KDM4D (Q6B0I6) (see all 5)
     YSINYLH  GEPKTWY  LERKYWKN  EDMDLYSIN 


    See KDM4D Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_060509.2  
    ENSEMBL proteins: 
     ENSP00000334181   ENSP00000460897  

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    Cloud-Clone Corp. Proteins for KDM4D

     
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    (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

    2 InterPro protein domains:
     IPR003347 JmjC_dom
     IPR003349 TF_JmjN

    Graphical View of Domain Structure for InterPro Entry Q6B0I6

    ProtoNet protein and cluster: Q6B0I6

    1 Blocks protein domain: IPB003347 Transcription factor jumonji

    UniProtKB/Swiss-Prot: KDM4D_HUMAN, Q6B0I6
    Similarity: Belongs to the JHDM3 histone demethylase family
    Similarity: Contains 1 JmjC domain
    Similarity: Contains 1 JmjN domain


    Find genes that share domains with KDM4D           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: KDM4D_HUMAN, Q6B0I6
    Function: Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role
    in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Demethylates
    both di- and trimethylated H3 'Lys-9' residue, while it has no activity on monomethylated residues. Demethylation
    of Lys residue generates formaldehyde and succinate

         Enzyme Numbers (IUBMB): EC 1.14.11.-1 EC 1.14.112

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
    GO:0046872metal ion binding IEA--
    GO:0051213dioxygenase activity IEA--
         
    Find genes that share ontologies with KDM4D           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for KDM4D:
     Decreased p24 protein expressi 

         6 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Kdm4d):
     cellular  endocrine/exocrine gland  growth/size/body  pigmentation  reproductive system 
     vision/eye 

    Find genes that share phenotypes with KDM4D           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Kdm4dtm1Zuk for KDM4D

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for KDM4D
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    miRNA
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    miRTarBase miRNAs that target KDM4D:
    hsa-mir-20a-5p (MIRT050602), hsa-mir-192-5p (MIRT026730), hsa-mir-215-5p (MIRT024726)

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    1 qRT-PCR Assays for microRNA that regulate KDM4D:
    hsa-miR-889
    SwitchGear 3'UTR luciferase reporter plasmidKDM4D 3' UTR sequence
    Inhib. RNA
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    (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
    KDM4D_HUMAN, Q6B0I6: Nucleus (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol2

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0072562blood microparticle IDA--

    Find genes that share ontologies with KDM4D           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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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for KDM4D
    Interactions:

        GeneGlobe Interaction Network for KDM4D

    STRING Interaction Network Preview (showing 5 interactants - click image to see 19)

    Selected Interacting proteins for KDM4D (Q6B0I63 ENSP000003341814) via UniProtKB, MINT, STRING, and/or I2D (see all 19)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ARP102753, ENSP000003638224I2D: score=1 STRING: ENSP00000363822
    TP53ENSP000002693054STRING: ENSP00000269305
    SOD1ENSP000002701424STRING: ENSP00000270142
    SOD2ENSP000003371274STRING: ENSP00000337127
    TADA2AENSP000002253964STRING: ENSP00000225396
    About this table

    Gene Ontology (GO): 3 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-templated IEA--
    GO:0006355regulation of transcription, DNA-templated IEA--
    GO:0033169histone H3-K9 demethylation IEA--

    Find genes that share ontologies with KDM4D           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 KDM4D



    (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 KDM4D gene: 
    NM_018039.2  

    Unigene Cluster for KDM4D:

    Lysine (K)-specific demethylase 4D
    Hs.503598  [show with all ESTs]
    Unigene Representative Sequence: NM_018039
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000335080(uc001pfe.3) ENST00000536741
    miRNA
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    1 qRT-PCR Assays for microRNA that regulate KDM4D:
    hsa-miR-889
    SwitchGear 3'UTR luciferase reporter plasmidKDM4D 3' UTR sequence
    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat KDM4D
      QuantiFast Probe-based Assays in human, mouse, rat KDM4D

    Additional mRNA sequence: 

    AK001113.1 AK056162.1 AL137545.1 BC031862.1 BC074739.2 BC119010.1 BC122858.1 

    1 DOTS entry:

    DT.106378 

    Selected AceView cDNA sequences (see all 26):

    AW339850 BC074739 AU149055 NM_018039 AK056162 AW593120 AU120493 AA732856 
    BC031862 AK001113 BQ006169 AA236569 CA311555 AI467798 AL137545 AA758505 
    AA435771 AA234602 BG719158 BE719807 BE719813 AU153509 BX283998 AI350395 

    GeneLoc Exon Structure


    (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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    KDM4D expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTAGTTTTCA
    KDM4D Expression
    About this image

    KDM4D Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    KDM4D Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.503598
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    In Situ
    Assay Products:
     

     
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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 animals and fungi.

    Orthologs for KDM4D gene from Selected species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Kdm4d1 , 5 lysine (K)-specific demethylase 4D1, 5 74.97(n)1
    72.31(a)1
      9 (4.05 cM)5
    2446941  NM_173433.21  NP_775609.21 
     144625485 
    fruit fly
    (Drosophila melanogaster)
    Insecta Kdm4A6
    Kdm4B6
    Histone demethylase 4B
    39(a)
    29(a)
    many ↔ many
    many ↔ many
    2R(3810280-3812488)
    2R(9063599-9085869)
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes RPH16
    GIS16
    JmjC domain-containing histone demethylase; specif...
    JmjC domain-containing histone demethylase and tra...
    19(a)
    13(a)
    many ↔ many
    many ↔ many
    V(523369-525759) YER169W
    IV(637139-639823) YDR096W


    ENSEMBL Gene Tree for KDM4D (if available)
    TreeFam Gene Tree for KDM4D (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for KDM4D gene
    KDM4A2  KDM4C2  KDM4E2  KDM4B2  
    5 SIMAP similar genes for KDM4D using alignment to 1 protein entry:     KDM4D_HUMAN:
    KDM4A    KDM4E    KDM4C    KDM4B    JMJD2B

    Find genes that share paralogs with KDM4D           About GenesLikeMe


    3 Pseudogenes.org Pseudogenes for KDM4D
    PGOHUM00000242864 PGOHUM00000242865 PGOHUM00000242869


    (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 KDM4D (see all 513)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1871523841,2
    --94705065(+) TAAAAC/TCACAG 1 -- us2k10--------
    rs1915842881,2
    --94705118(+) GAAAAC/TAGATA 1 -- us2k10--------
    rs729777271,2
    C,F--94705163(+) CCATGC/TCATTT 1 -- us2k12Minor allele frequency- T:0.08WA NA 238
    rs771747271,2
    C,F--94705436(+) ATACTG/AGTAAA 1 -- us2k11Minor allele frequency- A:0.03WA 118
    rs789467511,2
    C,F--94705472(+) AACCTG/ACTTAA 1 -- us2k11Minor allele frequency- A:0.03WA 118
    rs1160992171,2
    F--94705492(+) ACAAAA/TGTTTT 1 -- us2k11Minor allele frequency- T:0.01WA 118
    rs110209901,2
    C,F,H--94705612(+) TTCTGA/TCTATA 1 -- us2k112Minor allele frequency- T:0.35NA NS EA WA 918
    rs714606211,2
    C,F--94705677(+) CCTCAT/CAGATT 1 -- us2k14Minor allele frequency- C:0.15NA CSA 126
    rs1454722981,2
    --94705779(+) TACCAA/GACTCT 1 -- us2k10--------
    rs1156520871,2
    C,F--94705863(+) AAAAAT/CATCAC 1 -- us2k11Minor allele frequency- C:0.02WA 118

    HapMap Linkage Disequilibrium report for KDM4D (94706845 - 94732682 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for KDM4D:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv446CNV Loss18451855
    nsv518887CNV Gain19592680

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing KDM4D
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    (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: 609766    OMIM disorders: --


    Find genes that share disorders with KDM4D           About GenesLikeMe

    Genetic Association Database (GAD): KDM4D
    Human Genome Epidemiology (HuGE) Navigator: KDM4D (1 document)

    Export disorders for KDM4D 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 KDM4D gene, integrated from 10 sources (see all 19):
    (articles sorted by number of sources associating them with KDM4D)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification and characterization of JMJD2 family genes in silico. (PubMed id 15138608)1, 2, 3, 9 Katoh M. and Katoh M. (Int. J. Oncol. 2004)
    2. Human chromosome 11 DNA sequence and analysis including novel gene identification. (PubMed id 16554811)1, 2 Taylor T.D....Sakaki Y. (Nature 2006)
    3. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. (PubMed id 16603238)1, 2 Whetstine J.R.... Shi Y. (Cell 2006)
    4. 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)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    6. Structural and functional analysis of JMJD2D reveals molecular basis for site-specific demethylation among JMJD2 demethylases. (PubMed id 23219879)1 Krishnan S. and Trievel R.C. (Structure 2013)
    7. The HECT type ubiquitin ligase NEDL2 is degraded by anaphase-promoting complex/cyclosome (APC/C)-Cdh1, and its tight regulation maintains the metaphase to anaphase transition. (PubMed id 24163370)1 Lu L....Zhang L. (J. Biol. Chem. 2013)
    8. Poly (ADP-ribose) glycohydrolase regulates retinoic acid receptor- mediated gene expression. (PubMed id 23102699)2 Le May N.... Coin F. (Mol. Cell 2012)
    9. Regulation of tumor suppressor p53 and HCT116 cell physiology by histone demethylase JMJD2D/KDM4D. (PubMed id 22514644)1 Kim T.D....Janknecht R. (PLoS ONE 2012)
    10. Identification of the human testis protein phosphatase 1 interactome. (PubMed id 21382349)1 Fardilha M....da Cruz e Silva E.F. (Biochem. Pharmacol. 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 55693 HGNC: 25498 AceView: JMJD2D Ensembl:ENSG00000186280 euGenes: HUgn55693
    ECgene: KDM4D H-InvDB: KDM4D

    (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 KDM4D 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 KDM4D gene:
    Search GeneIP for patents involving KDM4D

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



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