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    KDM5D lysine demethylase 5D [ Homo sapiens (human) ]

    Gene ID: 8284, updated on 2-Nov-2024

    Summary

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    Official Symbol
    KDM5Dprovided by HGNC
    Official Full Name
    lysine demethylase 5Dprovided by HGNC
    Primary source
    HGNC:HGNC:11115
    See related
    Ensembl:ENSG00000012817 MIM:426000; AllianceGenome:HGNC:11115
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HY; HYA; SMCY; JARID1D
    Summary
    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]
    Expression
    Broad expression in small intestine (RPKM 5.6), prostate (RPKM 3.5) and 20 other tissues See more
    Orthologs
    all
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    Genomic context

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    See KDM5D in Genome Data Viewer
    Location:
    Yq11.223
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (19703865..19744726, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (20610415..20651276, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (21865751..21906612, complement)

    Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377223 Neighboring gene taxilin gamma Y-linked (pseudogene) Neighboring gene uncharacterized LOC105377224 Neighboring gene regulator of chromosome condensation 2 pseudogene 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Functional HY-specific CD8+ T cells are found in a high proportion of women following pregnancy with a male fetus. Piper KP, et al. Biol Reprod, 2007 Jan. PMID 16988213
    2. Human H-Y: a male-specific histocompatibility antigen derived from the SMCY protein. Wang W, et al. Science, 1995 Sep 15. PMID 7667640
    3. Gene sequence and evolutionary conservation of human SMCY. Kent-First MG, et al. Nat Genet, 1996 Oct. PMID 8841177
    4. H-Y incompatibility predicts short-term outcomes for kidney transplant recipients. Kim SJ, et al. J Am Soc Nephrol, 2009 Sep. PMID 19541808, Free PMC Article
    5. Y disruption, autosomal hypomethylation and poor male lung cancer survival. Willis-Owen SAG, et al. Sci Rep, 2021 Jun 14. PMID 34127738, Free PMC Article

    See all (44) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Histone demethylase KDM5D upregulation drives sex differences in colon cancer.
      Title: Histone demethylase KDM5D upregulation drives sex differences in colon cancer.
    2. KDM5D inhibits the transcriptional activation of FKBP4 by suppressing the expression of E2F1 in colorectal cancer in males.
      Title: KDM5D inhibits the transcriptional activation of FKBP4 by suppressing the expression of E2F1 in colorectal cancer in males.
    3. X- and Y-Linked Chromatin-Modifying Genes as Regulators of Sex-Specific Cancer Incidence and Prognosis.
      Title: X- and Y-Linked Chromatin-Modifying Genes as Regulators of Sex-Specific Cancer Incidence and Prognosis.
    4. Y disruption, autosomal hypomethylation and poor male lung cancer survival.
      Title: Y disruption, autosomal hypomethylation and poor male lung cancer survival.
    5. Increased Expression of Y-Encoded Demethylases During Differentiation of Human Male Neural Stem Cells.
      Title: Increased Expression of Y-Encoded Demethylases During Differentiation of Human Male Neural Stem Cells.
    6. ETV4 promotes the progression of gastric cancer through regulating KDM5D.
      Title: ETV4 promotes the progression of gastric cancer through regulating KDM5D.
    7. Down-Regulation of a Male-Specific H3K4 Demethylase, KDM5D, Impairs Cardiomyocyte Differentiation.
      Title: Down-Regulation of a Male-Specific H3K4 Demethylase, KDM5D, Impairs Cardiomyocyte Differentiation.
    8. KDM5D inhibit epithelial-mesenchymal transition of gastric cancer through demethylation in the promoter of Cul4A in male.
      Title: KDM5D inhibit epithelial-mesenchymal transition of gastric cancer through demethylation in the promoter of Cul4A in male.
    9. loss of the male-specific histone demethylase lysine-specific demethylase 5D (KDM5D) encoded on the Y chromosome epigenetically modifies histone methylation marks and alters gene expression, resulting in aggressive prostate cancer
      Title: ATR inhibition controls aggressive prostate tumors deficient in Y-linked histone demethylase KDM5D.
    10. KDM5D exhibited pronounced overexpression in blood vessels with cardiovascular disease.
      Title: Proteomics based identification of KDM5 histone demethylases associated with cardiovascular disease.
    Submit: New GeneRIF Correction See all GeneRIFs (20)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Spermatogenic failure, Y-linked, 2
    MedGen: C1839071 OMIM: 415000 GeneReviews: Y Chromosome Infertility
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0234

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K4 demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone demethylase activity TAS
    Traceable Author Statement
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nuclear androgen receptor binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in T cell antigen processing and presentation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of androgen receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in fibrillar center IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    lysine-specific demethylase 5D
    Names
    H-Y
    Jumonji, AT rich interactive domain 1D (RBP2-like)
    SMC homolog, Y chromosome
    Smcy homolog, Y-linked
    [histone H3]-trimethyl-L-lysine(4) demethylase 5D
    epididymis secretory sperm binding protein
    histocompatibility Y antigen
    histone demethylase JARID1D
    jumonji/ARID domain-containing protein 1D
    lysine (K)-specific demethylase 5D
    protein SmcY
    selected mouse cDNA on Y, human homolog of
    NP_001140177.1
    NP_001140178.1
    NP_004644.2
    XP_005262617.1
    XP_005262618.1
    XP_011529770.1
    XP_047298719.1
    XP_047298720.1
    XP_047298721.1
    XP_047298722.1
    XP_047298723.1
    XP_047298724.1
    XP_047298725.1
    XP_047298726.1
    XP_054184341.1
    XP_054184342.1
    XP_054184343.1
    XP_054184344.1
    XP_054184345.1
    XP_054184346.1
    XP_054184347.1
    XP_054184348.1
    XP_054184349.1
    XP_054184350.1
    XP_054184351.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_032920.1 RefSeqGene

      Range
      5214..46075
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001146705.2 → NP_001140177.1  lysine-specific demethylase 5D isoform 1

      See identical proteins and their annotated locations for NP_001140177.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AA864889, AC010889, BC144102, BC146767
      Consensus CDS
      CCDS55555.1
      UniProtKB/TrEMBL
      E9PFH2
      Related
      ENSP00000444293.1, ENST00000541639.5
      Conserved Domains (7) summary
      smart00501
      Location:80 → 170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:522 → 638
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:316 → 361
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd15608
      Location:1205 → 1265
      PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:728 → 780
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:793 → 1116
      PLU-1; PLU-1-like protein

    2. NM_001146706.2 → NP_001140178.1  lysine-specific demethylase 5D isoform 3

      See identical proteins and their annotated locations for NP_001140178.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks two alternate exons in the coding region, compared to variant 1. This results in a shorter protein (isoform 3), compared to isoform 1.
      Source sequence(s)
      AA864889, AC010889, BC132721, BC146767
      Consensus CDS
      CCDS55554.1
      UniProtKB/TrEMBL
      E9PFH2
      Related
      ENSP00000372256.2, ENST00000382806.6
      Conserved Domains (7) summary
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:434 → 550
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:259 → 304
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd15608
      Location:1117 → 1177
      PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:640 → 692
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:705 → 1028
      PLU-1; PLU-1-like protein
      cl02633
      Location:80 → 117
      ARID; ARID/BRIGHT DNA binding domain

    3. NM_004653.5 → NP_004644.2  lysine-specific demethylase 5D isoform 2

      See identical proteins and their annotated locations for NP_004644.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AA864889, AC010889, BC132721, BC146767, U52191
      Consensus CDS
      CCDS14794.1
      UniProtKB/Swiss-Prot
      A2RU19, A6H8V7, B7ZLX1, Q92509, Q92809, Q9BY66, Q9HCU1
      UniProtKB/TrEMBL
      A0A384MR42, E9PFH2
      Related
      ENSP00000322408.4, ENST00000317961.9
      Conserved Domains (7) summary
      smart00501
      Location:80 → 170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:491 → 607
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:316 → 361
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd15608
      Location:1174 → 1234
      PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:697 → 749
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:762 → 1085
      PLU-1; PLU-1-like protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000024.10 Reference GRCh38.p14 Primary Assembly

      Range
      19703865..19744726 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047442766.1 → XP_047298722.1  lysine-specific demethylase 5D isoform X7

    2. XM_047442765.1 → XP_047298721.1  lysine-specific demethylase 5D isoform X6

    3. XM_047442763.1 → XP_047298719.1  lysine-specific demethylase 5D isoform X3

    4. XM_005262560.4 → XP_005262617.1  lysine-specific demethylase 5D isoform X2

      UniProtKB/TrEMBL
      E9PFH2
      Conserved Domains (7) summary
      smart00501
      Location:80 → 170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:446 → 562
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:271 → 316
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd15608
      Location:1129 → 1189
      PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:652 → 704
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:717 → 1040
      PLU-1; PLU-1-like protein

    5. XM_047442764.1 → XP_047298720.1  lysine-specific demethylase 5D isoform X5

    6. XM_005262561.4 → XP_005262618.1  lysine-specific demethylase 5D isoform X4

      UniProtKB/TrEMBL
      E9PFH2
      Conserved Domains (7) summary
      smart00501
      Location:80 → 170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:491 → 607
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:316 → 361
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd15608
      Location:1097 → 1157
      PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:697 → 749
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:762 → 1008
      PLU-1; PLU-1-like protein

    7. XM_011531468.4 → XP_011529770.1  lysine-specific demethylase 5D isoform X1

      UniProtKB/TrEMBL
      E9PFH2
      Conserved Domains (7) summary
      smart00501
      Location:80 → 170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:491 → 607
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:316 → 361
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd15608
      Location:1148 → 1208
      PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:697 → 749
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:762 → 1083
      PLU-1; PLU-1-like protein

    8. XM_047442767.1 → XP_047298723.1  lysine-specific demethylase 5D isoform X8

      Related
      ENSP00000398543.1, ENST00000440077.5

    9. XM_047442768.1 → XP_047298724.1  lysine-specific demethylase 5D isoform X9

      UniProtKB/TrEMBL
      B4E1Y0

    10. XM_047442769.1 → XP_047298725.1  lysine-specific demethylase 5D isoform X10

    11. XM_047442770.1 → XP_047298726.1  lysine-specific demethylase 5D isoform X11

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060948.1 Alternate T2T-CHM13v2.0

      Range
      20610415..20651276 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054328372.1 → XP_054184347.1  lysine-specific demethylase 5D isoform X7

    2. XM_054328371.1 → XP_054184346.1  lysine-specific demethylase 5D isoform X6

    3. XM_054328368.1 → XP_054184343.1  lysine-specific demethylase 5D isoform X3

    4. XM_054328367.1 → XP_054184342.1  lysine-specific demethylase 5D isoform X2

    5. XM_054328370.1 → XP_054184345.1  lysine-specific demethylase 5D isoform X5

    6. XM_054328369.1 → XP_054184344.1  lysine-specific demethylase 5D isoform X4

    7. XM_054328366.1 → XP_054184341.1  lysine-specific demethylase 5D isoform X1

    8. XM_054328373.1 → XP_054184348.1  lysine-specific demethylase 5D isoform X8

    9. XM_054328374.1 → XP_054184349.1  lysine-specific demethylase 5D isoform X9

      UniProtKB/TrEMBL
      B4E1Y0

    10. XM_054328375.1 → XP_054184350.1  lysine-specific demethylase 5D isoform X10

    11. XM_054328376.1 → XP_054184351.1  lysine-specific demethylase 5D isoform X11

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BY66.2 GenPept UniProtKB/Swiss-Prot:Q9BY66

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