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

Gene ID: 20592, updated on 11-Apr-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 androgen receptor binding activity and histone H3-tri/di/monomethyl-lysine-4 demethylase activity. Acts upstream of or within T cell antigen processing and presentation. Predicted to be located in fibrillar center. Predicted to be active in nucleus. Is expressed in several structures, including early conceptus; genitourinary system; heart; liver; and lung. Orthologous to human KDM5D (lysine demethylase 5D). [provided by Alliance of Genome Resources, Apr 2022]
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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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. 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
  3. Inefficient purifying selection: the mammalian Y chromosome in the rodent genus Mus. Sandstedt SA, et al. Mamm Genome, 2006 Jan. PMID 16416087
  4. 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
  5. Mouse H-Y encoding Smcy gene and its X chromosomal homolog Smcx. Agulnik AI, et al. Mamm Genome, 1999 Sep. PMID 10441747

See all (45) 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 dioxygenase activity 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 metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables nuclear androgen receptor binding ISO
Inferred from Sequence Orthology
more info
  
enables oxidoreductase activity IEA
Inferred from Electronic Annotation
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 
acts_upstream_of_or_within chromatin organization 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 ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
part_of chromatin IBA
Inferred from Biological aspect of Ancestor
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

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