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

Gene ID: 8284, updated on 3-Apr-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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Location:
Yq11.223
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (19703865..19744726, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (20610415..20651276, complement)
105.20220307 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
  • 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. 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
  2. Down-Regulation of a Male-Specific H3K4 Demethylase, KDM5D, Impairs Cardiomyocyte Differentiation. Meyfour A, et al. J Proteome Res, 2019 Dec 6. PMID 31560558
  3. Proteomics based identification of KDM5 histone demethylases associated with cardiovascular disease. Mokou M, et al. EBioMedicine, 2019 Mar. PMID 30826357, Free PMC Article
  4. ATR inhibition controls aggressive prostate tumors deficient in Y-linked histone demethylase KDM5D. Komura K, et al. J Clin Invest, 2018 Jul 2. PMID 29863497, Free PMC Article
  5. JARID1D Is a Suppressor and Prognostic Marker of Prostate Cancer Invasion and Metastasis. Li N, et al. Cancer Res, 2016 Feb 15. PMID 26747897, Free PMC Article

See all (41) 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
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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
part_of 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_2023_10

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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