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KDM5D Gene

protein-coding   GIFtS: 57
GCID: GC0YM021865

Lysine (K)-Specific Demethylase 5D

(Previous names: Jumonji, AT rich interactive domain 1D (RBP2-like), Smcy...)
(Previous symbols: HYA, HY, SMCY, JARID1D)
  See related diseases
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 5D1 2     H-Y2 3
HYA1 2 3 5     Jumonji, AT Rich Interactive Domain 1D1
JARID1D1 2 3 5     Smcy Homolog, Y-Linked (Mouse)1
SMCY1 2 3 5     Lysine-Specific Demethylase 5D2
HY1 2 3     Selected Mouse CDNA On Y, Human Homolog Of2
Jumonji, AT Rich Interactive Domain 1D (RBP2-Like)1 2     SMC Homolog, Y Chromosome2
Histocompatibility Y Antigen2 3     Smcy Homolog, Y-Linked2
Histone Demethylase JARID1D2 3     EC 1.14.11.-3
Jumonji/ARID Domain-Containing Protein 1D2 3     KIAA02343
Protein SmcY2 3     EC 1.14.118

External Ids:    HGNC: 111151   Entrez Gene: 82842   Ensembl: ENSG000000128177   OMIM: 4260005   UniProtKB: Q9BY663   

Export aliases for KDM5D gene to outside databases

Previous GC identifers: GC0YM020326 GC0YM015577


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for KDM5D Gene:
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, Apr 2009)

GeneCards Summary for KDM5D Gene:
KDM5D (lysine (K)-specific demethylase 5D) is a protein-coding gene. Diseases associated with KDM5D include chronic graft versus host disease, and y chromosome infertility. 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 histone demethylase activity (H3-K4 specific). An important paralog of this gene is KDM5C.

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) 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:
NC_000024.10  NT_011875.13  
Regulatory elements:
   Regulatory transcription factor binding sites in the KDM5D gene promoter:
         Egr-3   GR   AML1a   GR-beta   AP-2gamma   SRY   AP-2beta   STAT3   SEF-1 (1)   GR-alpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidKDM5D promoter sequence
   Search Chromatin IP Primers for KDM5D

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat KDM5D


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

Entrez Gene cytogenetic band: 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)
KDM5D gene location

GeneLoc information about chromosome Y         GeneLoc Exon Structure

GeneLoc location for GC0YM021865:  view genomic region     (about GC identifiers)

Start:
21,865,751 bp from pter      End:
21,906,825 bp from pter
Size:
41,075 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: KDM5D_HUMAN, Q9BY66 (See protein sequence)
Recommended Name: Lysine-specific demethylase 5D  
Size: 1539 amino acids; 174073 Da
Cofactor: Ascorbate
Cofactor: Binds 1 Fe(2+) ion per subunit
Subunit: Interacts with PCGF6 and MSH5
Sequence caution: Sequence=BAA13241.2; Type=Erroneous initiation;
2 PDB 3D structures from and Proteopedia for KDM5D:
2E6R (3D)        2YQE (3D)    
Secondary accessions: A2RU19 A6H8V7 B7ZLX1 Q92509 Q92809 Q9HCU1
Alternative splicing: 3 isoforms:  Q9BY66-1   Q9BY66-2   Q9BY66-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for KDM5D: NX_Q9BY66

Explore proteomics data for KDM5D at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys91, Lys101, Lys413, Lys729, Lys752, Lys766, Lys1101, Lys1281
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for KDM5D (Q9BY66) (see all 54)
     DKEYKPH  STKRSRW  LLEVLCP  TFLKKNS 


    See KDM5D Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

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

    ENSEMBL proteins: 
     ENSP00000322408   ENSP00000372256   ENSP00000398543   ENSP00000389433   ENSP00000416377  
     ENSP00000444293  

    KDM5D Human Recombinant Protein Products:

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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
    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 Q9BY66

    ProtoNet protein and cluster: Q9BY66

    Selected Blocks protein domains (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


    KDM5D for domains           About GeneDecksing


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

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

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0005515protein binding ----
    GO:0008270zinc ion binding IEA--
    GO:0016706oxidoreductase 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 IEA--
    GO:0032453histone demethylase activity (H3-K4 specific) IDA17320160
         
    KDM5D for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for KDM5D:
     Decreased viability of wild-ty  Synthetic lethal with c-Myc af 

    Animal Models:
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    hsa-mir-26b-5p (MIRT029979), hsa-mir-335-5p (MIRT018612)

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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
    KDM5D_HUMAN, Q9BY66: Nucleus (Probable)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus4
    cytosol2
    mitochondrion1

    Gene Ontology (GO): 3 cellular component terms:    About this table

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

    KDM5D for ontologies           About GeneDecksing


    (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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        Pathway & Disease-focused RT2 Profiler PCR Array including KDM5D: 
              Polycomb & Trithorax Complexes in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for KDM5D

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

    Selected Interacting proteins for KDM5D (Q9BY663 ENSP000003224084) via UniProtKB, MINT, STRING, and/or I2D (see all 37)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PCGF6Q9BYE73, ENSP000003588624I2D: score=1 STRING: ENSP00000358862
    HIST3H3ENSP000003556574STRING: ENSP00000355657
    CHEK1ENSP000002789164STRING: ENSP00000278916
    ACTR6ENSP000001883124STRING: ENSP00000188312
    DMAP1ENSP000003126974STRING: ENSP00000312697
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007283spermatogenesis ----
    GO:0034720histone H3-K4 demethylation IDA17320160
    GO:0055114oxidation-reduction process ----

    KDM5D for ontologies           About GeneDecksing



    (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 KDM5D

    1 DrugBank Compound for KDM5D    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Vitamin CAscorbate (see all 6)50-81-7target--17139284 17016423



    (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,
    Conferences by KenesGroup, 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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for KDM5D gene (3 alternative transcripts): 
    NM_001146705.1  NM_001146706.1  NM_004653.4  

    Unigene Cluster for KDM5D:

    Lysine (K)-specific demethylase 5D
    Hs.80358  [show with all ESTs]
    Unigene Representative Sequence: NM_001146705
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000469599 ENST00000317961(uc004fuf.3) ENST00000382806 ENST00000492117
    ENST00000440077 ENST00000415360 ENST00000485154 ENST00000478891 ENST00000447300
    ENST00000541639(uc011naz.2 uc004fug.3 uc010nwy.3 uc011nba.1 uc004fuh.2)

    miRNA
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      QuantiFast Probe-based Assays in human, mouse, rat KDM5D

    Additional mRNA 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 

    Selected AceView cDNA sequences (see all 87):

    BQ651915 AA846126 AA465521 BM052719 AA262767 CF552345 AI341366 AA215375 
    BI025365 U52365 D87072 AA113921 NM_004653 BX648643 BQ053814 CD652272 
    AV763928 AI660371 AA377435 AA864889 BP367589 AL043711 BP382487 BM053001 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for KDM5D (see all 10)    About this scheme

    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:        -                                                                                                   


    ECgene alternative splicing isoforms for KDM5D

    (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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    KDM5D expression in normal human tissues (normalized intensities)      KDM5D embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ACTCTACCTG
    KDM5D Expression
    About this image


    KDM5D expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 4) fully expand
     
     Testis (Reproductive System)    fully expand to see all 4 entries
             Testicular Interstitial Cells Testis Interstitium
     
     Gonad (Reproductive System)    fully expand to see all 2 entries
             Testis Somatic Cells Primitive Gonad
     
     Peripheral Nervous System (Nervous System)
             Schwann Precursor Cells Peripheral Nerve Domain
     
     Brain (Nervous System)
             Choroid Plexus Progenitor Cells Choroid Plexus
    KDM5D Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    KDM5D Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.80358
        Pathway & Disease-focused RT2 Profiler PCR Array including KDM5D: 
              Polycomb & Trithorax Complexes in human mouse rat

    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for KDM5D

    (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 KDM5D gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Kdm5d1 , 5 lysine (K)-specific demethylase 5D1, 5 80.33(n)1
    80.94(a)1
      Y5
    205921  NM_011419.31  NP_035549.11 
     8977885 
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    74(a)
    1 → many
    1(204862436-204882164)
    zebrafish
    (Danio rerio)
    Actinopterygii kdm5c6
    lysine (K)-specific demethylase 5C
    58(a)
    1 → many
    8(38095710-38138758) ENSDARG00000006124
    fruit fly
    (Drosophila melanogaster)
    Insecta lid6
    little imaginal discs
    34(a)
    1 → many
    2L(5989463-5999501)
    worm
    (Caenorhabditis elegans)
    Secernentea rbr-26
    Protein RBR-2 (rbr-2) mRNA, complete cds
    27(a)
    1 → many
    IV(10920107-10926797) WBGene00004319
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes JHD2(YJR119C)4 JmjC domain family histone demethylase specific for more   --   10(646490-644304) 853583  NP_012653.1 


    ENSEMBL Gene Tree for KDM5D (if available)
    TreeFam Gene Tree for KDM5D (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for KDM5D gene
    KDM5C2  JARID22  KDM5B2  KDM5A2  
    12 SIMAP similar genes for KDM5D using alignment to 4 protein entries:     KDM5D_HUMAN (see all proteins):
    JARID1C    KDM5C    PLU-1    PHF8    KDM5A    JARID1B
    KDM5B    DKFZp434N0335    DKFZp434D0815    DKFZp434I0617    AIRE    DKFZp434I2412

    KDM5D for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for KDM5D
    PGOHUM00000233789


    (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)
    About This Section

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    Selected SNPs for KDM5D (see all 419)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr Y posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs20326301,2
    C,F,H--21866840(+) AAAGCT/AACTAC 3 -- ds50012Minor allele frequency- A:0.03NS 114
    rs134473771,2
    C--21867718(+) CTTTAC/TGAACC 3 -- ut31 ese30--------
    rs20326311,2
    C,F,H--21867787(+) AGATAG/AGCAAA 3 -- ut31 ese312Minor allele frequency- A:0.37MN NA NS WA CSA 432
    rs356815231,2
    C--21868068(-) GGGCCG/AAGAAG 6 /Q /R mis12Minor allele frequency- A:0.02MN NA 48
    rs20326321,2
    C,H--21868672(+) ACACCT/CGTCTT 3 -- int16Minor allele frequency- C:0.00NS EA NA 264
    rs20326331,2
    C,F--21868726(+) CTGTCT/CCCATT 6 /G syn15Minor allele frequency- C:0.15MN NA CSA 286
    rs340787681,2
    C,F--21868863(-) GAAGCC/TTGTGT 3 -- int13Minor allele frequency- T:0.04MN NA CSA 48
    rs20326201,2
    C,H--21869264(+) CGCACG/AGGCAG 6 /P syn1 ese37Minor allele frequency- A:0.00MN NS EA NA 446
    rs3716461831,2
    C--21869519(+) GAAGTC/TGGAGA 6 P syn10--------
    rs1995724511,2
    C--21869856(+) GACAGC/TCCCAG 6 G syn10--------

    HapMap Linkage Disequilibrium report for KDM5D (21865751 - 21906825 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for KDM5D:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv10025CNV Gain18304495

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing KDM5D
    DNA2.0 Custom Variant and Variant Library Synthesis for KDM5D

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 426000    OMIM disorders: --

    11 diseases for KDM5D:    About MalaCards
    chronic graft versus host disease    y chromosome infertility    acute graft versus host disease    graft versus host disease
    azoospermia    infertility    retinoblastoma    choroiditis
    mental retardation    prostate cancer    prostatitis


    KDM5D for disorders           About GeneDecksing


    Export disorders for KDM5D 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 KDM5D gene, integrated from 10 sources (see all 45):
    (articles sorted by number of sources associating them with KDM5D)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Gene sequence and evolutionary conservation of human SMCY. (PubMed id 8841177)1, 2, 3 Kent-First M.G.... Vandeberg J. (Nat. Genet. 1996)
    2. Spermatogenesis-specific association of SMCY and MSH5. (PubMed id 18459961)1, 2 Akimoto C.... Kato S. (Genes Cells 2008)
    3. Physical and functional association of a trimethyl H3K4 demethylase and Ring6a/MBLR, a polycomb-like protein. (PubMed id 17320162)1, 2 Lee M.G.... Shiekhattar R. (Cell 2007)
    4. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. (PubMed id 17320160)1, 2 Iwase S.... Shi Y. (Cell 2007)
    5. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. (PubMed id 12815422)1, 2 Skaletsky H.... Page D.C. (Nature 2003)
    6. Population genetic implications from sequence variation in four Y chromosome genes. (PubMed id 10861003)1, 2 Shen P.... Oefner P.J. (Proc. Natl. Acad. Sci. U.S.A. 2000)
    7. Analysis of mutation rates in the SMCY/SMCX genes shows that mammalian evolution is male driven. (PubMed id 9060413)1, 2 Agulnik A.I.... Solovyev V.V. (Mamm. Genome 1997)
    8. Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain. (PubMed id 9039502)1, 2 Nagase T.... Nomura N. (DNA Res. 1996)
    9. Human H-Y: a male-specific histocompatibility antigen derived from the SMCY protein. (PubMed id 7667640)1, 9 Wang W....Bishop C.E. (Science 1995)
    10. Antibody responses to H-Y minor histocompatibility antigens correlate with chronic graft-versus-host disease and disease remission. (PubMed id 15613541)1, 9 Miklos D.B....Ritz J. (Blood 2005)

    (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: 8284 HGNC: 11115 AceView: JARID1D Ensembl:ENSG00000012817 euGenes: HUgn8284
    ECgene: KDM5D H-InvDB: KDM5D

    (According to HUGE)
    About This Section

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    HUGE: KIAA0234

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for KDM5D 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 KDM5D gene:
    Search GeneIP for patents involving KDM5D

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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