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

Gene ID: 20591, updated on 18-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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