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

    Gene ID: 8284, updated on 28-Oct-2024

    Summary

    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
    NEW
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    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    NEW Try the new Transcript table

    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_001146705.2NP_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:80170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:522638
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:316361
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd15608
      Location:12051265
      PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:728780
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7931116
      PLU-1; PLU-1-like protein
    2. NM_001146706.2NP_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:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:434550
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:259304
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd15608
      Location:11171177
      PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:640692
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7051028
      PLU-1; PLU-1-like protein
      cl02633
      Location:80117
      ARID; ARID/BRIGHT DNA binding domain
    3. NM_004653.5NP_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:80170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:491607
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:316361
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd15608
      Location:11741234
      PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:697749
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7621085
      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_047442766.1XP_047298722.1  lysine-specific demethylase 5D isoform X7

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

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

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

      UniProtKB/TrEMBL
      E9PFH2
      Conserved Domains (7) summary
      smart00501
      Location:80170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:446562
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:271316
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd15608
      Location:11291189
      PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:652704
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7171040
      PLU-1; PLU-1-like protein
    5. XM_047442764.1XP_047298720.1  lysine-specific demethylase 5D isoform X5

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

      UniProtKB/TrEMBL
      E9PFH2
      Conserved Domains (7) summary
      smart00501
      Location:80170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:491607
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:316361
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd15608
      Location:10971157
      PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:697749
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7621008
      PLU-1; PLU-1-like protein
    7. XM_011531468.4XP_011529770.1  lysine-specific demethylase 5D isoform X1

      UniProtKB/TrEMBL
      E9PFH2
      Conserved Domains (7) summary
      smart00501
      Location:80170
      BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain
      smart00545
      Location:1354
      JmjN; Small domain found in the jumonji family of transcription factors
      pfam02373
      Location:491607
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:316361
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      cd15608
      Location:11481208
      PHD2_KDM5C_5D; PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:697749
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:7621083
      PLU-1; PLU-1-like protein
    8. XM_047442767.1XP_047298723.1  lysine-specific demethylase 5D isoform X8

      Related
      ENSP00000398543.1, ENST00000440077.5
    9. XM_047442768.1XP_047298724.1  lysine-specific demethylase 5D isoform X9

      UniProtKB/TrEMBL
      B4E1Y0
    10. XM_047442769.1XP_047298725.1  lysine-specific demethylase 5D isoform X10

    11. XM_047442770.1XP_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_054328372.1XP_054184347.1  lysine-specific demethylase 5D isoform X7

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

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

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

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

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

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

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

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

      UniProtKB/TrEMBL
      B4E1Y0
    10. XM_054328375.1XP_054184350.1  lysine-specific demethylase 5D isoform X10

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