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Aliases for KDM5C Gene

Aliases for KDM5C Gene

  • Lysine (K)-Specific Demethylase 5C 2 3
  • DXS1272E 3 4 6
  • JARID1C 3 4 6
  • XE169 3 4 6
  • SMCX 3 4 6
  • Jumonji, AT Rich Interactive Domain 1C (RBP2-Like) 2 3
  • Jumonji/ARID Domain-Containing Protein 1C 3 4
  • Histone Demethylase JARID1C 3 4
  • MRXSCJ 3 6
  • Jumonji, AT Rich Interactive Domain 1C 2
  • JmjC Domain-Containing Protein SMCX 3
  • Mental Retardation, X-Linked 13 2
  • Smcy Homolog, X-Linked (Mouse) 2
  • Lysine-Specific Demethylase 5C 3
  • Smcx Homolog, X Chromosome 3
  • Smcy Homolog, X-Linked 3
  • Protein Xe169 4
  • Protein SmcX 4
  • EC 1.14.11.- 4
  • EC 1.14.11 63
  • MRXSJ 3
  • MRX13 3
  • MRXJ 3

External Ids for KDM5C Gene

Previous HGNC Symbols for KDM5C Gene

  • SMCX
  • JARID1C
  • MRX13

Previous GeneCards Identifiers for KDM5C Gene

  • GC0XM053237
  • GC0XM050285
  • GC0XM053220

Summaries for KDM5C Gene

Entrez Gene Summary for KDM5C Gene

  • This gene is a member of the SMCY homolog family and encodes a protein with one ARID domain, one JmjC domain, one JmjN domain and two PHD-type zinc fingers. The DNA-binding motifs suggest this protein is involved in the regulation of transcription and chromatin remodeling. Mutations in this gene have been associated with X-linked mental retardation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]

GeneCards Summary for KDM5C Gene

KDM5C (Lysine (K)-Specific Demethylase 5C) is a Protein Coding gene. Diseases associated with KDM5C include mental retardation, x-linked, syndromic, claes-jensen type and syndromic x-linked intellectual disability due to jarid1c mutation. Among its related pathways are Chromatin Regulation / Acetylation. GO annotations related to this gene include oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors and histone demethylase activity (H3-K4 specific). An important paralog of this gene is KDM5D.

UniProtKB/Swiss-Prot for KDM5C Gene

  • Histone demethylase that specifically demethylates Lys-4 of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 Lys-9, H3 Lys-27, H3 Lys-36, H3 Lys-79 or H4 Lys-20. Demethylates trimethylated and dimethylated but not monomethylated H3 Lys-4. Participates in transcriptional repression of neuronal genes by recruiting histone deacetylases and REST at neuron-restrictive silencer elements. Represses the CLOCK-ARNTL/BMAL1 heterodimer-mediated transcriptional activation of the core clock component PER2 (By similarity).

Gene Wiki entry for KDM5C Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for KDM5C Gene

Genomics for KDM5C Gene

Regulatory Elements for KDM5C Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for KDM5C Gene

Start:
53,191,321 bp from pter
End:
53,225,422 bp from pter
Size:
34,102 bases
Orientation:
Minus strand

Genomic View for KDM5C Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for KDM5C Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for KDM5C Gene

Proteins for KDM5C Gene

  • Protein details for KDM5C Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P41229-KDM5C_HUMAN
    Recommended name:
    Lysine-specific demethylase 5C
    Protein Accession:
    P41229
    Secondary Accessions:
    • B0QZ44
    • B4E3I2
    • F5H3T1
    • Q5JUX3
    • Q5JUX4
    • Q5JUX5
    • Q7Z5S5

    Protein attributes for KDM5C Gene

    Size:
    1560 amino acids
    Molecular mass:
    175720 Da
    Cofactor:
    Name=2-oxoglutarate; Xref=ChEBI:CHEBI:16810;
    Cofactor:
    Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Note=Binds 1 Fe(2+) ion per subunit.;
    Quaternary structure:
    • Part of two distinct complexes, one containing E2F6, and the other containing REST.
    Miscellaneous:
    • Escapes X-inactivation

    Three dimensional structures from OCA and Proteopedia for KDM5C Gene

    Alternative splice isoforms for KDM5C Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for KDM5C Gene

Proteomics data for KDM5C Gene at MOPED

Post-translational modifications for KDM5C Gene

  • Ubiquitination at Lys91, Lys101, Lys377, Lys739, Lys776, Lys1114, and Lys1121
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for KDM5C (JARID1C)

Domains for KDM5C Gene

Gene Families for KDM5C Gene

HGNC:
  • KDM :Chromatin-modifying enzymes / K-demethylases
  • PHF :Zinc fingers, PHD-type

Suggested Antigen Peptide Sequences for KDM5C Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P41229

UniProtKB/Swiss-Prot:

KDM5C_HUMAN :
  • P41229
Domain:
  • The first PHD-type zinc finger domain recognizes and binds H3-K9Me3
  • Both the JmjC domain and the JmjN domain are required for enzymatic activity
  • Contains 1 ARID domain.
  • Contains 1 JmjC domain.
  • Contains 1 JmjN domain.
Family:
  • Belongs to the JARID1 histone demethylase family.
Similarity:
  • Contains 2 PHD-type zinc fingers.
genes like me logo Genes that share domains with KDM5C: view

Function for KDM5C Gene

Molecular function for KDM5C Gene

UniProtKB/Swiss-Prot Function: Histone demethylase that specifically demethylates Lys-4 of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 Lys-9, H3 Lys-27, H3 Lys-36, H3 Lys-79 or H4 Lys-20. Demethylates trimethylated and dimethylated but not monomethylated H3 Lys-4. Participates in transcriptional repression of neuronal genes by recruiting histone deacetylases and REST at neuron-restrictive silencer elements. Represses the CLOCK-ARNTL/BMAL1 heterodimer-mediated transcriptional activation of the core clock component PER2 (By similarity).

Enzyme Numbers (IUBMB) for KDM5C Gene

Gene Ontology (GO) - Molecular Function for KDM5C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding --
GO:0008270 zinc ion binding IEA --
GO:0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors IEA --
GO:0032453 histone demethylase activity (H3-K4 specific) IDA 17320160
genes like me logo Genes that share ontologies with KDM5C: view
genes like me logo Genes that share phenotypes with KDM5C: view

Animal Model Products

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for KDM5C

In Situ Assay Products

Flow Cytometry Products

No data available for Animal Models , Transcription Factor Targeting and HOMER Transcription for KDM5C Gene

Localization for KDM5C Gene

Subcellular locations from UniProtKB/Swiss-Prot for KDM5C Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for KDM5C Gene COMPARTMENTS Subcellular localization image for KDM5C gene
Compartment Confidence
nucleus 5
cytosol 2
mitochondrion 1

Gene Ontology (GO) - Cellular Components for KDM5C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular --
GO:0005634 nucleus IDA 18078810
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with KDM5C: view

Pathways for KDM5C Gene

genes like me logo Genes that share pathways with KDM5C: view

Pathways by source for KDM5C Gene

1 Cell Signaling Technology pathway for KDM5C Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays
    • Epigenetic Chromatin Modification Enzymes in human,mouse,rat

Gene Ontology (GO) - Biological Process for KDM5C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization TAS --
GO:0006351 transcription, DNA-templated IEA --
GO:0034720 histone H3-K4 demethylation IDA 17320160
GO:0045892 negative regulation of transcription, DNA-templated ISS --
GO:0048511 rhythmic process IEA --
genes like me logo Genes that share ontologies with KDM5C: view

Transcripts for KDM5C Gene

Unigene Clusters for KDM5C Gene

Lysine (K)-specific demethylase 5C:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for KDM5C

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for KDM5C Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^
SP1: - - - - - - -
SP2: - - - - - - -
SP3: - - - -
SP4: - -
SP5:
SP6:
SP7:
SP8: - - - -
SP9:
SP10:
SP11:
SP12:

ExUns: 16a · 16b ^ 17 ^ 18a · 18b ^ 19a · 19b ^ 20a · 20b ^ 21 ^ 22a · 22b ^ 23a · 23b ^ 24 ^ 25a · 25b · 25c ^ 26a · 26b ^ 27 ^ 28
SP1: - -
SP2: - -
SP3:
SP4:
SP5: -
SP6: -
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for KDM5C Gene

GeneLoc Exon Structure for
KDM5C
ECgene alternative splicing isoforms for
KDM5C

Expression for KDM5C Gene

mRNA expression in normal human tissues for KDM5C Gene

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for KDM5C Gene

SOURCE GeneReport for Unigene cluster for KDM5C Gene Hs.631768

mRNA Expression by UniProt/SwissProt for KDM5C Gene

P41229-KDM5C_HUMAN
Tissue specificity: Expressed in all tissues examined. Highest levels found in brain and skeletal muscle.
genes like me logo Genes that share expressions with KDM5C: view

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for KDM5C Gene

Orthologs for KDM5C Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for KDM5C Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia KDM5C 36
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia KDM5C 35
  • 92.57 (n)
  • 97.02 (a)
SMCX 36
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia KDM5C 35
  • 92.76 (n)
  • 97.35 (a)
KDM5C 36
  • 97 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Kdm5c 35
  • 90.22 (n)
  • 95.52 (a)
Kdm5c 16
Kdm5c 36
  • 95 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 36
  • 79 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 87 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Kdm5c 35
  • 88.41 (n)
  • 92.58 (a)
lizard
(Anolis carolinensis)
Reptilia -- 36
  • 80 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia kdm5c 35
  • 68.75 (n)
  • 72.46 (a)
zebrafish
(Danio rerio)
Actinopterygii kdm5c 35
  • 65.82 (n)
  • 69.16 (a)
kdm5c 36
  • 61 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta lid 36
  • 35 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea rbr-2 36
  • 27 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes JHD2 36
  • 29 (a)
OneToMany
JHD2 38
rice
(Oryza sativa)
Liliopsida Os.7130 35
bread mold
(Neurospora crassa)
Ascomycetes NCU01238 35
  • 46.22 (n)
  • 34.01 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes lid2 35
  • 38.31 (n)
  • 25.6 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 42 (a)
OneToMany
Species with no ortholog for KDM5C:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for KDM5C Gene

ENSEMBL:
Gene Tree for KDM5C (if available)
TreeFam:
Gene Tree for KDM5C (if available)

Paralogs for KDM5C Gene

Paralogs for KDM5C Gene

Selected SIMAP similar genes for KDM5C Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with KDM5C: view

Variants for KDM5C Gene

Sequence variations from dbSNP and Humsavar for KDM5C Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type MAF
rs942925 -- 53,221,955(+) TGCAG(A/T)CCTCT intron-variant
rs942926 -- 53,227,029(+) ATTAC(C/T)TTGAA upstream-variant-2KB
rs1886889 -- 53,191,654(+) CAGTA(G/T)ATGGG utr-variant-3-prime, downstream-variant-500B
rs2025662 -- 53,207,753(-) CAGGA(C/T)GGTCT intron-variant
rs2025663 -- 53,207,608(-) AGTTC(A/G)CCCCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for KDM5C Gene

Variant ID Type Subtype PubMed ID
nsv435891 CNV Deletion 17901297
esv2740175 CNV Deletion 23290073

Relevant External Links for KDM5C Gene

HapMap Linkage Disequilibrium report
KDM5C
Human Gene Mutation Database (HGMD)
KDM5C
Locus Specific Mutation Databases (LSDB)
KDM5C

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for KDM5C Gene

Disorders for KDM5C Gene

(1) OMIM Diseases for KDM5C Gene (314690)

UniProtKB/Swiss-Prot

KDM5C_HUMAN
  • Mental retardation, X-linked, syndromic, Claes-Jensen type (MRXSCJ) [MIM:300534]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRXSCJ patients manifest mental retardation associated with variable features such as slowly progressive spastic paraplegia, seizures, facial dysmorphism. {ECO:0000269 PubMed:15586325, ECO:0000269 PubMed:16538222, ECO:0000269 PubMed:16541399}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(1) University of Copenhagen DISEASES for KDM5C Gene

(1) Novoseek inferred disease relationships for KDM5C Gene

Disease -log(P) Hits PubMed IDs
mental retardation 59.6 6

Relevant External Links for KDM5C

Genetic Association Database (GAD)
KDM5C
genes like me logo Genes that share disorders with KDM5C: view

Publications for KDM5C Gene

  1. Isolation and characterization of XE169, a novel human gene that escapes X-inactivation. (PMID: 8162017) Wu J. … Shapiro L.J. (Hum. Mol. Genet. 1994) 2 3 4 23
  2. Mutations in the JARID1C gene, which is involved in transcriptional regulation and chromatin remodeling, cause X-linked mental retardation. (PMID: 15586325) Jensen L.R. … Lenzner S. (Am. J. Hum. Genet. 2005) 3 4 23
  3. A novel mutation in JARID1C gene associated with mental retardation. (PMID: 16538222) Santos C. … Mila M. (Eur. J. Hum. Genet. 2006) 3 4 23
  4. A novel X gene with a widely transcribed Y-linked homologue escapes X-inactivation in mouse and human. (PMID: 7951230) Agulnik A.I. … Bishop C.E. (Hum. Mol. Genet. 1994) 2 3 4
  5. Identification and characterization of two novel JARID1C mutations: suggestion of an emerging genotype-phenotype correlation. (PMID: 19826449) Rujirabanjerd S. … Gecz J. (Eur. J. Hum. Genet. 2010) 2 3 23

Products for KDM5C Gene

  • Addgene plasmids for KDM5C

Sources for KDM5C Gene

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