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Aliases for KDM5C Gene

Aliases for KDM5C Gene

  • Lysine Demethylase 5C 2 3
  • Lysine (K)-Specific Demethylase 5C 2 3 5
  • Jumonji, AT Rich Interactive Domain 1C (RBP2-Like) 2 3
  • Jumonji/ARID Domain-Containing Protein 1C 3 4
  • Histone Demethylase JARID1C 3 4
  • DXS1272E 3 4
  • JARID1C 3 4
  • XE169 3 4
  • SMCX 3 4
  • 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
  • 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
  • MRXSCJ 3
  • 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
  • GC0XM053192

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 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 organization and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. 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

Promoters for KDM5C Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around KDM5C on UCSC Golden Path with GeneCards custom track

Genomic Location for KDM5C Gene

Chromosome:
X
Start:
53,158,726 bp from pter
End:
53,225,422 bp from pter
Size:
66,697 bases
Orientation:
Minus strand

Genomic View for KDM5C Gene

Genes around KDM5C on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
KDM5C Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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;
    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 Lys 377 and Lys 1121
  • Modification sites at PhosphoSitePlus

Antibody Products

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

Domains & Families for KDM5C Gene

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 :
  • The first PHD-type zinc finger domain recognizes and binds H3-K9Me3.
  • Belongs to the JARID1 histone demethylase family.
  • Contains 2 PHD-type zinc fingers.
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:0005515 protein binding IEA --
GO:0032452 histone demethylase activity TAS --
genes like me logo Genes that share ontologies with KDM5C: view
genes like me logo Genes that share phenotypes with KDM5C: view

Human Phenotype Ontology for KDM5C Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

No data available for Animal Models , Transcription Factor Targets 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

No data available for Gene Ontology (GO) - Cellular Components for KDM5C Gene

Pathways & Interactions for KDM5C Gene

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

Pathways by source for KDM5C Gene

1 GeneTex pathway for KDM5C Gene

Gene Ontology (GO) - Biological Process for KDM5C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with KDM5C: view

No data available for SIGNOR curated interactions for KDM5C Gene

Drugs & Compounds for KDM5C Gene

(1) Drugs for KDM5C Gene - From: DGIdb

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
PBIT Pharma 0
genes like me logo Genes that share compounds with KDM5C: view

Transcripts for KDM5C Gene

Unigene Clusters for KDM5C Gene

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

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

Protein differential expression in normal tissues from HIPED for KDM5C Gene

This gene is overexpressed in Retina (19.4), Placenta (17.6), Heart (17.1), and Adipocyte (8.4).

Integrated Proteomics: protein expression in normal tissues and cell lines 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 expression patterns with KDM5C: view

Protein tissue co-expression partners for KDM5C Gene

Primer Products

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 36
  • 97 (a)
OneToOne
KDM5C 35
  • 92.76 (n)
  • 97.35 (a)
mouse
(Mus musculus)
Mammalia Kdm5c 16
Kdm5c 35
  • 90.22 (n)
  • 95.52 (a)
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 36
  • 61 (a)
OneToMany
kdm5c 35
  • 65.82 (n)
  • 69.16 (a)
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

(9) 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
VAR_022730 Mental retardation, X-linked, syndromic, Claes-Jensen type (MRXSCJ)
VAR_022731 Mental retardation, X-linked, syndromic, Claes-Jensen type (MRXSCJ)
VAR_022732 Mental retardation, X-linked, syndromic, Claes-Jensen type (MRXSCJ)
VAR_022733 Mental retardation, X-linked, syndromic, Claes-Jensen type (MRXSCJ)
VAR_032986 Mental retardation, X-linked, syndromic, Claes-Jensen type (MRXSCJ)

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

Variation tolerance for KDM5C Gene

Residual Variation Intolerance Score: 1.18% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.59; 12.72% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for KDM5C Gene

HapMap Linkage Disequilibrium report
KDM5C
Human Gene Mutation Database (HGMD)
KDM5C

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

Disorders for KDM5C Gene

MalaCards: The human disease database

(9) MalaCards diseases for KDM5C Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, and GeneCards

Disorder Aliases PubMed IDs
mental retardation, x-linked, syndromic, claes-jensen type
  • x-linked syndromic mental retardation, claes-jensen type
syndromic x-linked intellectual disability due to jarid1c mutation
spastic paraplegia 43, autosomal recessive
  • autosomal recessive spastic paraplegia type 43
mental retardation, autosomal recessive 48
  • mrt48
ewing sarcoma
  • neuroepithelioma
- elite association - COSMIC cancer census association via MalaCards
Search KDM5C in MalaCards View complete list of genes associated with diseases

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, ECO:0000269 PubMed:23356856, ECO:0000269 PubMed:25666439}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for KDM5C

Genetic Association Database (GAD)
KDM5C
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
KDM5C
genes like me logo Genes that share disorders with KDM5C: view

No data available for Genatlas for KDM5C Gene

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 67
  2. 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
  3. Repression of Smad3 activity by histone demethylase SMCX/JARID1C. (PMID: 18078810) Kim T.D. … Janknecht R. (Biochem. Biophys. Res. Commun. 2008) 3 23
  4. Mutations in JARID1C are associated with X-linked mental retardation, short stature and hyperreflexia. (PMID: 18697827) Abidi F.E. … Schwartz C.E. (J. Med. Genet. 2008) 3 23
  5. A novel mutation in JARID1C gene associated with mental retardation. (PMID: 16538222) Santos C. … Mila M. (Eur. J. Hum. Genet. 2006) 3 23

Products for KDM5C Gene

Sources for KDM5C Gene

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