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    Kdm5d lysine demethylase 5D [ Mus musculus (house mouse) ]

    Gene ID: 20592, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Kdm5dprovided by MGI
    Official Full Name
    lysine demethylase 5Dprovided by MGI
    Primary source
    MGI:MGI:99780
    See related
    Ensembl:ENSMUSG00000056673 AllianceGenome:MGI:99780
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    HY; H-Y; Smcy; Jarid1d
    Summary
    Predicted to enable histone H3K4me/H3K4me2/H3K4me3 demethylase activity and nuclear androgen receptor binding activity. Acts upstream of or within T cell antigen processing and presentation. Predicted to be located in chromatin and fibrillar center. Predicted to be active in nucleus. Is expressed in several structures, including central nervous system; genitourinary system; heart; liver; and lung. Orthologous to human KDM5D (lysine demethylase 5D). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in CNS E18 (RPKM 4.0), CNS E14 (RPKM 3.8) and 21 other tissues See more
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    Genomic context

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    See Kdm5d in Genome Data Viewer
    Location:
    Y; Ypter
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) Y NC_000087.8 (897566..946316)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) Y NC_000087.7 (897566..943813)

    Chromosome Y - NC_000087.8Genomic Context describing neighboring genes Neighboring gene ubiquitin-activating enzyme, Chr Y Neighboring gene ras homolog A translocated to the Y, pseudogene 3 Neighboring gene STARR-seq mESC enhancer starr_48294 Neighboring gene STARR-seq mESC enhancer starr_48295 Neighboring gene STARR-seq mESC enhancer starr_48296 Neighboring gene nuclear encoded rRNA 5S 1 Neighboring gene eukaryotic translation initiation factor 2, subunit 3, structural gene Y-linked

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. KDM5D-mediated H3K4 demethylation is required for sexually dimorphic gene expression in mouse embryonic fibroblasts. Mizukami H, et al. J Biochem, 2019 Apr 1. PMID 30541083
    2. Histone demethylase KDM5D upregulation drives sex differences in colon cancer. Li J, et al. Nature, 2023 Jul. PMID 37344599, Free PMC Article
    3. Spermatogenic failure in male mice lacking H-Y antigen. Burgoyne PS, et al. Nature, 1986 Mar 13-19. PMID 3951555
    4. Mutations of histone demethylase genes encoded by X and Y chromosomes, Kdm5c and Kdm5d, lead to noncompaction cardiomyopathy in mice. Kosugi M, et al. Biochem Biophys Res Commun, 2020 Feb 17. PMID 32081420
    5. Isolation of sex-specific cDNAs from fetal mouse brain using mRNA differential display and representational difference analysis. Eriksson A, et al. Brain Res Mol Brain Res, 1999 Dec 10. PMID 10640679

    See all (48) 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. these data not only suggest an importance of KDM5D-mediated demethylation of H3K4 involved in the sexually dimorphic gene expression in male MEFs, but also may provide information regarding sex-dependent changes in gene expression when MEFs are used for experiments.
      Title: KDM5D-mediated H3K4 demethylation is required for sexually dimorphic gene expression in mouse embryonic fibroblasts.
    3. Immunohistochemical analysis revealed the co-localization of SMCY with MSH5 at a specific stage of meiotic prophase progression during murine spermatogenesis.
      Title: Spermatogenesis-specific association of SMCY and MSH5.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K4 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone H3K4me/H3K4me2/H3K4me3 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nuclear androgen receptor binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nuclear androgen receptor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within T cell antigen processing and presentation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of androgen receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in fibrillar center IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in fibrillar center ISO
    Inferred from Sequence Orthology
    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
    [histone H3]-trimethyl-L-lysine(4) demethylase 5D
    histocompatibility Y antigen
    histone demethylase JARID1D
    jumonji, AT rich interactive domain 1D (Rbp2 like)
    jumonji/ARID domain-containing protein 1D
    lysine (K)-specific demethylase 5D
    protein SmcY
    selected mouse cDNA on the Y
    NP_035549.1
    XP_006531641.1
    XP_011246882.1
    XP_017174173.1
    XP_030107422.1
    XP_036018080.1

    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.

    mRNA and Protein(s)

    1. NM_011419.4 → NP_035549.1  lysine-specific demethylase 5D

      See identical proteins and their annotated locations for NP_035549.1

      Status: VALIDATED

      Source sequence(s)
      AC134433, AC145392
      Consensus CDS
      CCDS30541.1
      UniProtKB/Swiss-Prot
      Q3US03, Q62240, Q6PCX3, Q9QVR9, Q9R040
      Related
      ENSMUSP00000061095.8, ENSMUST00000055032.14
      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:500 → 616
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:325 → 370
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:706 → 758
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:771 → 1094
      PLU-1; PLU-1-like protein
      cl22851
      Location:1182 → 1242
      PHD_SF; PHD finger superfamily

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000087.8 Reference GRCm39 C57BL/6J

      Range
      897566..946316
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017318684.3 → XP_017174173.1  lysine-specific demethylase 5D isoform X5

      Related
      ENSMUSP00000140663.2, ENSMUST00000186696.7
      Conserved Domains (4) summary
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:325 → 370
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02373
      Location:500 → 616
      JmjC; JmjC domain, hydroxylase
      cd16875
      Location:79 → 170
      ARID_KDM5C_5D; ARID/BRIGHT DNA binding domain of lysine-specific demethylase KDM5C and KDM5D

    2. XM_011248580.3 → XP_011246882.1  lysine-specific demethylase 5D isoform X1

      Conserved Domains (7) summary
      smart00545
      Location:13 → 50
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:299 → 344
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02373
      Location:474 → 590
      JmjC; JmjC domain, hydroxylase
      cd16875
      Location:53 → 144
      ARID_KDM5C_5D; ARID/BRIGHT DNA binding domain of lysine-specific demethylase KDM5C and KDM5D
      pfam02928
      Location:680 → 732
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:745 → 1068
      PLU-1; PLU-1-like protein
      cl22851
      Location:1156 → 1216
      PHD_SF; PHD finger superfamily

    3. XM_030251562.2 → XP_030107422.1  lysine-specific demethylase 5D isoform X2

      Conserved Domains (5) summary
      cd15604
      Location:21 → 66
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02373
      Location:196 → 312
      JmjC; JmjC domain, hydroxylase
      pfam02928
      Location:402 → 454
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:467 → 790
      PLU-1; PLU-1-like protein
      cl22851
      Location:878 → 938
      PHD_SF; PHD finger superfamily

    4. XM_006531578.4 → XP_006531641.1  lysine-specific demethylase 5D isoform X4

      Conserved Domains (3) summary
      pfam02928
      Location:27 → 79
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:92 → 415
      PLU-1; PLU-1-like protein
      cl22851
      Location:503 → 563
      PHD_SF; PHD finger superfamily

    5. XM_036162187.1 → XP_036018080.1  lysine-specific demethylase 5D isoform X3

      Conserved Domains (3) summary
      pfam02928
      Location:57 → 109
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:122 → 445
      PLU-1; PLU-1-like protein
      cl22851
      Location:533 → 593
      PHD_SF; PHD finger superfamily

    RNA

    1. XR_003953250.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q62240.2 GenPept UniProtKB/Swiss-Prot:Q62240

    Gene LinkOut

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