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    Kdm5c lysine demethylase 5C [ Mus musculus (house mouse) ]

    Gene ID: 20591, updated on 21-Apr-2024

    Summary

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    Official Symbol
    Kdm5cprovided by MGI
    Official Full Name
    lysine demethylase 5Cprovided by MGI
    Primary source
    MGI:MGI:99781
    See related
    Ensembl:ENSMUSG00000025332 AllianceGenome:MGI:99781
    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
    Smcx; Jarid1c; mKIAA0234; D930009K15Rik
    Summary
    Predicted to enable several functions, including histone H3-tri/di/monomethyl-lysine-4 demethylase activity; identical protein binding activity; and zinc ion binding activity. Involved in negative regulation of transcription, DNA-templated. Acts upstream of or within histone H3-K4 demethylation. Located in nucleus. Is expressed in several structures, including brain; early conceptus; gonad; limb; and metanephros. Used to study syndromic X-linked intellectual disability Claes-Jensen type. Human ortholog(s) of this gene implicated in syndromic X-linked intellectual disability Claes-Jensen type. Orthologous to human KDM5C (lysine demethylase 5C). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 13.0), ovary adult (RPKM 12.8) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    X F3; X 68.46 cM
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (151015698..151062098)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (152233198..152279102)

    Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene IQ motif and Sec7 domain 2 Neighboring gene predicted gene, 52480 Neighboring gene STARR-seq mESC enhancer starr_48090 Neighboring gene predicted gene, 52430 Neighboring gene STARR-seq mESC enhancer starr_48091 Neighboring gene STARR-seq mESC enhancer starr_48092 Neighboring gene STARR-seq mESC enhancer starr_48093 Neighboring gene Kdm5c adjacent non-coding transcript Neighboring gene STARR-positive B cell enhancer mm9_chrX:148771022-148771323 Neighboring gene TSPY-like 2

    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. Sexually Dimorphic Alterations in the Transcriptome and Behavior with Loss of Histone Demethylase KDM5C. Bonefas KM, et al. Cells, 2023 Feb 16. PMID 36831303, Free PMC Article
    2. X chromosome dosage of histone demethylase KDM5C determines sex differences in adiposity. Link JC, et al. J Clin Invest, 2020 Nov 2. PMID 32701509, Free PMC Article
    3. Loss of Kdm5c Causes Spurious Transcription and Prevents the Fine-Tuning of Activity-Regulated Enhancers in Neurons. Scandaglia M, et al. Cell Rep, 2017 Oct 3. PMID 28978483, Free PMC Article
    4. Patient Mutations of the Intellectual Disability Gene KDM5C Downregulate Netrin G2 and Suppress Neurite Growth in Neuro2a Cells. Wei G, et al. J Mol Neurosci, 2016 Sep. PMID 27421841, Free PMC Article
    5. A Mouse Model of X-linked Intellectual Disability Associated with Impaired Removal of Histone Methylation. Iwase S, et al. Cell Rep, 2016 Feb 9. PMID 26804915, Free PMC Article

    See all (85) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. WNT signalling control by KDM5C during development affects cognition.
      Title: WNT signalling control by KDM5C during development affects cognition.
    2. The X-linked histone demethylases KDM5C and KDM6A as regulators of T cell-driven autoimmunity in the central nervous system.
      Title: The X-linked histone demethylases KDM5C and KDM6A as regulators of T cell-driven autoimmunity in the central nervous system.
    3. The histone demethylase KDM5C controls female bone mass by promoting energy metabolism in osteoclasts.
      Title: The histone demethylase KDM5C controls female bone mass by promoting energy metabolism in osteoclasts.
    4. The histone demethylase KDM5C functions as a tumor suppressor in AML by repression of bivalently marked immature genes.
      Title: The histone demethylase KDM5C functions as a tumor suppressor in AML by repression of bivalently marked immature genes.
    5. Alcohol-associated fibrosis in females is mediated by female-specific activation of lysine demethylases KDM5B and KDM5C.
      Title: Alcohol-associated fibrosis in females is mediated by female-specific activation of lysine demethylases KDM5B and KDM5C.
    6. Activation of Xist by an evolutionarily conserved function of KDM5C demethylase.
      Title: Activation of Xist by an evolutionarily conserved function of KDM5C demethylase.
    7. Mutually suppressive roles of KMT2A and KDM5C in behaviour, neuronal structure, and histone H3K4 methylation.
      Title: Mutually suppressive roles of KMT2A and KDM5C in behaviour, neuronal structure, and histone H3K4 methylation.
    8. X chromosome dosage of histone demethylase KDM5C determines sex differences in adiposity.
      Title: X chromosome dosage of histone demethylase KDM5C determines sex differences in adiposity.
    9. Loss of Kdm5c causes spurious transcription and prevents the fine-tuning of activity-regulated enhancers in neurons.
      Title: Loss of Kdm5c Causes Spurious Transcription and Prevents the Fine-Tuning of Activity-Regulated Enhancers in Neurons.
    10. The results identify two key regulators, PCGF6 and JARID1c that temper dendritic cells (DC) activation and implicate active transcriptional silencing via histone demethylation as a previously unappreciated mechanism for regulating DC activation and quiescence.
      Title: The Transcriptional Repressor Polycomb Group Factor 6, PCGF6, Negatively Regulates Dendritic Cell Activation and Promotes Quiescence.
    Submit: New GeneRIF Correction See all GeneRIFs (16)

    Variation

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    Alleles

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

    Pathways from PubChem

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    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 RNA polymerase II-specific DNA-binding transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K4 demethylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    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 negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of circadian rhythm NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within rhythmic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    lysine-specific demethylase 5C
    Names
    [histone H3]-trimethyl-L-lysine(4) demethylase 5C
    histone demethylase JARID1C
    jumonji, AT rich interactive domain 1C (Rbp2 like)
    jumonji/ARID domain-containing protein 1C
    lysine (K)-specific demethylase 5C
    selected mouse cDNA on the X
    NP_001390000.1
    NP_001390001.1
    NP_001390002.1
    NP_001390003.1
    NP_001390004.1
    NP_001390005.1
    NP_001406705.1
    NP_001406706.1
    NP_038696.2
    XP_006528834.1
    XP_030107134.1

    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_001403071.1 → NP_001390000.1  lysine-specific demethylase 5C isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC083816
      UniProtKB/Swiss-Prot
      O54995, P41230, Q3TYU8, Q3U1X6, Q3U282, Q6ZQF8, Q80XQ9, Q9CVI4, Q9D0C3, Q9QVR8, Q9R039
      Related
      ENSMUSP00000108203.2, ENSMUST00000112584.8

    2. NM_001403072.1 → NP_001390001.1  lysine-specific demethylase 5C isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC083816

    3. NM_001403073.1 → NP_001390002.1  lysine-specific demethylase 5C isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC083816
      Related
      ENSMUSP00000080814.7, ENSMUST00000082177.13

    4. NM_001403074.1 → NP_001390003.1  lysine-specific demethylase 5C isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC083816

    5. NM_001403075.1 → NP_001390004.1  lysine-specific demethylase 5C isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC083816

    6. NM_001403076.1 → NP_001390005.1  lysine-specific demethylase 5C isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC083816

    7. NM_001419776.1 → NP_001406705.1  lysine-specific demethylase 5C isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC083816

    8. NM_001419777.1 → NP_001406706.1  lysine-specific demethylase 5C isoform 9

      Status: VALIDATED

      Source sequence(s)
      AC083816

    9. NM_013668.5 → NP_038696.2  lysine-specific demethylase 5C isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC083816
      Consensus CDS
      CCDS41178.1
      UniProtKB/Swiss-Prot
      P41230
      Related
      ENSMUSP00000108207.3, ENSMUST00000112588.9
      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:501 → 617
      JmjC; JmjC domain, hydroxylase
      cd15604
      Location:326 → 371
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02928
      Location:707 → 759
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:772 → 1098
      PLU-1; PLU-1-like protein
      cl22851
      Location:1187 → 1247
      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_000086.8 Reference GRCm39 C57BL/6J

      Range
      151015698..151062098
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006528771.5 → XP_006528834.1  lysine-specific demethylase 5C isoform X4

      Conserved Domains (7) summary
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:285 → 330
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02373
      Location:460 → 576
      JmjC; JmjC domain, hydroxylase
      cl28902
      Location:68 → 129
      ARID; ARID/BRIGHT DNA binding domain family
      pfam02928
      Location:666 → 718
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:731 → 1057
      PLU-1; PLU-1-like protein
      cl22851
      Location:1146 → 1206
      PHD_SF; PHD finger superfamily

    2. XM_030251274.2 → XP_030107134.1  lysine-specific demethylase 5C isoform X5

      Conserved Domains (7) summary
      smart00545
      Location:13 → 54
      JmjN; Small domain found in the jumonji family of transcription factors
      cd15604
      Location:284 → 329
      PHD1_KDM5C_5D; PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D)
      pfam02373
      Location:459 → 575
      JmjC; JmjC domain, hydroxylase
      cl28902
      Location:68 → 129
      ARID; ARID/BRIGHT DNA binding domain family
      pfam02928
      Location:665 → 717
      zf-C5HC2; C5HC2 zinc finger
      pfam08429
      Location:730 → 1056
      PLU-1; PLU-1-like protein
      cl22851
      Location:1145 → 1205
      PHD_SF; PHD finger superfamily

    RNA

    1. XR_003953003.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P41230.4 GenPept UniProtKB/Swiss-Prot:P41230

    Gene LinkOut

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