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KDM5D Gene

protein-coding   GIFtS: 53

GC0YM020326
lysine (K)-specific demethylase 5D
(Previous names: Jumonji, AT rich interactive domain 1D (RBP2-like), Smcy homolog, Y-linked (mouse), jumonji, AT rich interactive domain 1D )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbols: HYA, HY, SMCY, JARID1D)
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
H-Y 3
HY 2, 3
HYA 2, 3
JARID1D 2, 3
KIAA0234 1, 2, 3
SMCY 2, 3
Descriptions
Histocompatibility Y antigen 2, 3
Histone demethylase JARID1D 3
Jumonji, AT rich interactive domain 1D (RBP2-like) 1, 2
Jumonji/ARID domain-containing protein 1D 3
Protein SmcY 3
SMC homolog, Y chromosome 2
Smcy homolog, Y chromosome 2
Smcy homolog, Y-linked 2
Smcy homolog, Y-linked (mouse) 1
jumonji, AT rich interactive domain 1D 1, 2
lysine (K)-specific demethylase 5D 2
lysine-specific demethylase 5D 1
selected mouse cDNA on Y, human homolog of 2
External Ids
HGNC: 111151
Entrez Gene: 82842
UniProtKB: Q9BY663
Ensembl: ENSG000000128177
Search outside databases for aliases for KDM5D gene

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

EntrezGene summary for KDM5D:
This gene encodes a protein containing zinc finger domains. A short peptide derived from this
protein is a minor histocompatibility antigen which can lead to graft rejection of male donor
cells in a female recipient. Alternative splicing results in multiple transcript variants.
[provided by RefSeq]

UniProtKB/Swiss-Prot: KDM5D_HUMAN, Q9BY66
Function: Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing
a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36',
H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3
'Lys-4'. May play a role in spermatogenesis

Gene Wiki entry for KDM5D (JARID1D)

(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: Yq11|Yq11   Ensembl cytogenetic band:  Yq11.222   HGNC cytogenetic band: Yq11

KDM5D 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 Y         GeneLoc Exon Structure

GeneLoc location for GC0YM020326:     (about GC identifiers)

Start:
20,326,689 bp from pter
End:
20,366,212 bp from pter
Size:
39,524 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000024.8  NT_011875.11  
(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: KDM5D_HUMAN, Q9BY66 (See protein sequence)
Recommended Name: Lysine-specific demethylase 5D  
Size: 1539 amino acids; 174073 Da
Cofactor: Ascorbate
Cofactor: Fe(2+)
Subunit: Interacts with PCGF6
Subcellular location: Nucleus (Probable)
PDB structure from and Proteopedia :
2E6R (3D)    2YQE (3D)    
Secondary accessions: A2RU19 Q92509 Q92809 Q9HCU1
Alternative splicing: 2 isoforms:  Q9BY66-1   Q9BY66-2   (Additional isoforms seem to exist)

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins (3 alternative transcripts): 
    NP_001140177.1  NP_001140178.1  NP_004644.2  


    ENSEMBL proteins: 
    ENSP00000322408 ENSP00000372256 


    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 (KDM5D / Jarid1D / SMCY)
    Browse Abnova for Human Recombinant Proteins
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575 cellular_component ND--
    GO:0005622 intracellular IEA--
    GO:0005634 nucleus IEA--
    About this table

    Antibodies for KDM5D: 
    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
    Antibodies from Abcam (KDM5D / Jarid1D / SMCY), each with their AbpromiseSM
    Monoclonal and Polyclonal Antibodies from Abnova (JARID1D)
    Novus Biologicals Antibodies for JARID1D

    Assays for KDM5D: 
    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  KDM5D for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q9BY66

    ProtoNet protein and cluster: Q9BY66

    5/6 Blocks protein families (see all 6 ):
    IPB001606 ARID (AT-rich interaction domain) protein
    IPB001965 Zn-finger-like
    IPB003347 Transcription factor jumonji
    IPB003349 Transcription factor jumonji
    IPB004198 Zn-finger


    UniProtKB/Swiss-Prot: KDM5D_HUMAN, Q9BY66
    Domain: The JmjC domain is required for enzymatic 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 2 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 (KDM5D)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (JARID1D)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_004653

                  Applied Biosystems Silencer® siRNAs for KDM5D

                  Sigma-Aldrich siRNA and siRNA Panels for KDM5D  
                         Sigma-Aldrich shRNA for KDM5D  
                         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_004653
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_004653
                                     untagged cDNA clone in CMV expression vector: NM_004653 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_004653

    UniProtKB/Swiss-Prot: KDM5D_HUMAN, Q9BY66
    Function: Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing
    a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36',
    H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3
    'Lys-4'. May play a role in spermatogenesis
    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:0003674 molecular_function ND--
    GO:0003677 DNA binding IEA--
    GO:0005506 iron ion binding IEA--
    GO:0005515 protein binding IPI17320160
    GO:0008270 zinc ion binding 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


     Gene Network CentralTM Interacting Genes and Proteins Network for  KDM5D 


    5/23 Interacting proteins for KDM5D (ENSP000003224083 Q9BY661) via UniProtKB, MINT, and/or STRING (see all 23 )
    InteractantInteraction Details
    GeneCardExternal ID(s)
    - - (xeno)P684321EBI-1246860, EBI-79764
    TMSB4YENSP000002848563STRING (score=.897)
    ENSG00000147050ENSP000003672033STRING (score=.868)
    SRYENSP000003725473STRING (score=.844)
    FASENSP000003609423STRING (score=.841)
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007283 spermatogenesis NAS--
    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 KDM5D

    (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 (KDM5D)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (JARID1D)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_004653

                  Sigma-Aldrich siRNA and siRNA Panels for KDM5D  
                         Sigma-Aldrich shRNA for KDM5D  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_004653  

    REFSEQ mRNAs for KDM5D gene (3 alternative transcripts): 

    NM_001146705.1   NM_001146706.1   NM_004653.4   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_004653  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_004653
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_004653
                                     untagged cDNA clone in CMV expression vector: NM_004653 

    Additional cDNA sequence: 

    AK095923.1 AK304027.1 BC011053.1 BC132721.1 BC144101.1 BC144102.1 BC146767.1 BX648643.1 
    D87072.1 U52191.1 U52365.1 

    12 DOTS entries:

    DT.95159961  DT.40233810  DT.92046785  DT.100691331  DT.40131582  DT.120654025  DT.101957266  DT.120654022 
    DT.120654028  DT.120654029  DT.91978680  DT.95322478 

    24/87 AceView cDNA sequences (see all 87 ):

    CD652272 AA262767 D87072 BI025365 AA215375 BM052719 BQ651915 BP367589 
    AA465521 U52365 CF552345 AI341366 AA377435 BX648643 BQ053814 AL043711 
    AA113921 NM_004653 AI660371 AV763928 AA846126 AA864889 CK903936 BU664887 

    Unigene Cluster for KDM5D:

    Lysine (K)-specific demethylase 5D
    Hs.80358  [show with all ESTs]
    Unigene Representative Sequence: BX648643


    GeneLoc Exon Structure

    5/10 Alternative Splicing Database (ASD) splice patterns (SP) for KDM5D (see all 10 )

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

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

    About this scheme

    ECgene alternative splicing isoforms for KDM5D

    2 Ensembl transcripts including schematic representations:
    ENST00000317961  ENST00000382806  
    (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

    KDM5D expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for KDM5D

    1 / 2

    4 probe-sets matching KDM5D gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

    37583_at2 U95-A 1 1.00 1.00 0.96 1.25 -- -- -- -- --

    51528_at2 U95-C 1 0.94 1.00 0.96 0.75 -- -- -- -- --

    206700_s_at2 U133-A 1 1.00 1.00 -- -- -- -- -- -- --

    206700_s_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    About this table
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: ACTCTACCTG

    SOURCE GeneReport for Unigene cluster: Hs.80358
    (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 KDM5D gene from 4 species
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    chimpanzee
    (Pan troglodytes)
    JARID1D1   -- jumonji, AT rich interactive domain 1D 99.35(n)
    99.02(a)
    449032  NM_001008975.1  NP_001008975.1 
    mouse
    (Mus musculus)
    Kdm5d5
    Jarid1d1
    Y5
    lysine (K)-specific demethylase 5D5
    jumonji, AT rich interactive domain 1D (Rbp2 like)1
    80.48(n)1
    81.27(a)1
    205921  NM_011419.31  NP_035549.11 
     AB2216065  AB2216075  (see all 17)
    baker's yeast
    (Saccharomyces cerevisiae)
    JHD2(YJR119C)4 10(646480-644294) JmjC domain family histone demethylase specific for more   -- 853583  NP_012653.1 
    sea squirt
    (Ciona intestinalis)
    Cin.99382   -- Ciona intestinalis transcribed sequence with moderate more 76.58(n)  BW123343.1 
    About this table        Species with no ortholog for KDM5D

    ENSEMBL Gene Tree for KDM5D
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for KDM5D gene
    KDM5C2  ENSG000001171392  KDM5A2  

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

      --
    (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: 426000

    (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

    10/36 PubMed articles for KDM5D gene (see all 36 ):
    (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: 8284 HGNC: 11115 AceView: JARID1D Ensembl:ENSG00000012817 euGenes: HUgn8284
    ECgene: KDM5D H-InvDB: KDM5D
    (According to HUGE)
    About This Section

    HUGE: KIAA0234
    (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 KDM5D:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Predesigned and custom siRNAs for KDM5D Browse antibodies at Sigma-Aldrich
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for KDM5D Browse small molecules at Sigma-Aldrich
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     Search OriGene for KDM5D
     Search Tocris compounds for KDM5D




     Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies
     Antibodies for JARID1D

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