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KDM4C (Gene amplified in squamous cell carcinoma 1)

Written2002-12Zeng-Quan Yang
University of Michigan, Department of Radiation Oncology, RM. 7121 CCGC, 1500 E Med Ctr. Dr., Ann Arbor, MI 48109-0948, USA

(Note : for Links provided by Atlas : click)

Identity

Other namesGASC1
JHDM3C
JMJD2C
TDRD14C
HGNC (Hugo) KDM4C
LocusID (NCBI) 23081
Atlas_Id 432
Location 9p24.1
Location_base_pair Starts at 6757641 and ends at 7077264 bp from pter ( according to hg19-Feb_2009)  [Mapping]
Fusion genes
(updated 2015)
IGH (14q32.33) / KDM4C (9p24.1)KDM4C (9p24.1) / ARMC2 (6q21)KDM4C (9p24.1) / JAK2 (9p24.1)
KDM4C (9p24.1) / KLK7 (19q13.41)KDM4C (9p24.1) / PTPRD (9p24.1)KDM4C (9p24.1) / RFX3 (9p24.2)
PGPEP1 (19p13.11) / KDM4C (9p24.1)

DNA/RNA

Note At least 22 exons spanning approximately 417194 bps. 4239 bp mRNA; coding sequence: 3171 bp

Protein

Description 1056 ammino acid; possesses PHD domain

Implicated in

Note
Entity amplification and overexpression in cell lines derived from esophageal squamous cell carcinomas
  

Bibliography

Identification of a novel gene, GASC1, within an amplicon at 9p23-24 frequently detected in esophageal cancer cell lines.
Yang ZQ, Imoto I, Fukuda Y, Pimkhaokham A, Shimada Y, Imamura M, Sugano S, Nakamura Y, Inazawa J
Cancer research. 2000 ; 60 (17) : 4735-4739.
PMID 10987278
 
A novel amplicon at 9p23 - 24 in squamous cell carcinoma of the esophagus that lies proximal to GASC1 and harbors NFIB.
Yang ZQ, Imoto I, Pimkhaokham A, Shimada Y, Sasaki K, Oka M, Inazawa J
Japanese journal of cancer research : Gann. 2001 ; 92 (4) : 423-428.
PMID 11346465
 

Citation

This paper should be referenced as such :
Yang, ZQ
GASC1 (gene amplified in squamous cell carcinoma 1)
Atlas Genet Cytogenet Oncol Haematol. 2003;7(1):21-21.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/GASC1ID432.html


External links

Nomenclature
HGNC (Hugo)KDM4C   17071
Cards
AtlasGASC1ID432
Entrez_Gene (NCBI)KDM4C  23081  lysine (K)-specific demethylase 4C
GeneCards (Weizmann)KDM4C
Ensembl hg19 (Hinxton)ENSG00000107077 [Gene_View]  chr9:6757641-7077264 [Contig_View]  KDM4C [Vega]
Ensembl hg38 (Hinxton)ENSG00000107077 [Gene_View]  chr9:6757641-7077264 [Contig_View]  KDM4C [Vega]
ICGC DataPortalENSG00000107077
TCGA cBioPortalKDM4C
AceView (NCBI)KDM4C
Genatlas (Paris)KDM4C
WikiGenes23081
SOURCE (Princeton)KDM4C
Genomic and cartography
GoldenPath hg19 (UCSC)KDM4C  -     chr9:6757641-7077264 +  9p24.1   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)KDM4C  -     9p24.1   [Description]    (hg38-Dec_2013)
EnsemblKDM4C - 9p24.1 [CytoView hg19]  KDM4C - 9p24.1 [CytoView hg38]
Mapping of homologs : NCBIKDM4C [Mapview hg19]  KDM4C [Mapview hg38]
OMIM605469   
Gene and transcription
Genbank (Entrez)AB018323 AB037901 AF085959 AI017056 AI969877
RefSeq transcript (Entrez)NM_001146694 NM_001146695 NM_001146696 NM_001304339 NM_001304340 NM_001304341 NM_015061
RefSeq genomic (Entrez)NC_000009 NC_018920 NT_008413 NW_004929342
Consensus coding sequences : CCDS (NCBI)KDM4C
Cluster EST : UnigeneHs.709425 [ NCBI ]
CGAP (NCI)Hs.709425
Alternative Splicing : Fast-db (Paris)GSHG0030014
Alternative Splicing GalleryENSG00000107077
Gene ExpressionKDM4C [ NCBI-GEO ]     KDM4C [ SEEK ]   KDM4C [ MEM ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
BioGPS (Tissue expression)23081
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9H3R0 (Uniprot)
NextProtQ9H3R0  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9H3R0
Splice isoforms : SwissVarQ9H3R0 (Swissvar)
Catalytic activity : Enzyme1.14.11.- [ Enzyme-Expasy ]   1.14.11.-1.14.11.- [ IntEnz-EBI ]   1.14.11.- [ BRENDA ]   1.14.11.- [ KEGG ]   
PhosPhoSitePlusQ9H3R0
Domaine pattern : Prosite (Expaxy)JMJC (PS51184)    JMJN (PS51183)   
Domains : Interpro (EBI)JmjC_dom    JmjN    Tudor    Znf_FYVE_PHD    Znf_PHD   
Domain families : Pfam (Sanger)JmjC (PF02373)    JmjN (PF02375)   
Domain families : Pfam (NCBI)pfam02373    pfam02375   
Domain families : Smart (EMBL)JmjC (SM00558)  JmjN (SM00545)  PHD (SM00249)  TUDOR (SM00333)  
DMDM Disease mutations23081
Blocks (Seattle)KDM4C
PDB (SRS)2XDP    2XML    4XDO    4XDP   
PDB (PDBSum)2XDP    2XML    4XDO    4XDP   
PDB (IMB)2XDP    2XML    4XDO    4XDP   
PDB (RSDB)2XDP    2XML    4XDO    4XDP   
Structural Biology KnowledgeBase2XDP    2XML    4XDO    4XDP   
SCOP (Structural Classification of Proteins)2XDP    2XML    4XDO    4XDP   
CATH (Classification of proteins structures)2XDP    2XML    4XDO    4XDP   
Human Protein AtlasENSG00000107077
Peptide AtlasQ9H3R0
HPRD12016
IPIIPI00027642   IPI00645825   IPI01018984   IPI00910024   IPI01010286   IPI00878778   IPI00929542   IPI00552718   IPI00878239   
Protein Interaction databases
DIP (DOE-UCLA)Q9H3R0
IntAct (EBI)Q9H3R0
FunCoupENSG00000107077
BioGRIDKDM4C
IntegromeDBKDM4C
STRING (EMBL)KDM4C
ZODIACKDM4C
Ontologies - Pathways
QuickGOQ9H3R0
Ontology : AmiGOnuclear chromatin  nucleoplasm  chromatin organization  transcription, DNA-templated  regulation of transcription from RNA polymerase II promoter  small GTPase mediated signal transduction  zinc ion binding  positive regulation of cell proliferation  enzyme binding  histone demethylase activity  histone demethylase activity (H3-K9 specific)  histone demethylase activity (H3-K9 specific)  histone H3-K9 demethylation  histone H3-K9 demethylation  androgen receptor binding  dioxygenase activity  oxidation-reduction process  
Ontology : EGO-EBInuclear chromatin  nucleoplasm  chromatin organization  transcription, DNA-templated  regulation of transcription from RNA polymerase II promoter  small GTPase mediated signal transduction  zinc ion binding  positive regulation of cell proliferation  enzyme binding  histone demethylase activity  histone demethylase activity (H3-K9 specific)  histone demethylase activity (H3-K9 specific)  histone H3-K9 demethylation  histone H3-K9 demethylation  androgen receptor binding  dioxygenase activity  oxidation-reduction process  
REACTOMEQ9H3R0 [protein]
REACTOME PathwaysR-HSA-3214842 HDMs demethylate histones [pathway]
REACTOME PathwaysR-HSA-5625886 Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 [pathway]
Protein Interaction DatabaseKDM4C
Atlas of Cancer Signalling NetworkKDM4C
Wikipedia pathwaysKDM4C
Orthology - Evolution
OrthoDB23081
GeneTree (enSembl)ENSG00000107077
Phylogenetic Trees/Animal Genes : TreeFamKDM4C
Gene fusions - Rearrangements
Fusion : MitelmanIGH/KDM4C [14q32.33/9p24.1]  [t(9;14)(p24;q32)]  
Fusion : MitelmanKDM4C/ARMC2 [9p24.1/6q21]  [t(6;9)(q21;p24)]  
Fusion : MitelmanKDM4C/JAK2 [9p24.1/9p24.1]  [t(9;9)(p24;p24)]  
Fusion : MitelmanKDM4C/KLK7 [9p24.1/19q13.41]  [t(9;19)(p24;q13)]  
Fusion : MitelmanKDM4C/PTPRD [9p24.1/9p24.1]  [t(9;9)(p23;p24)]  
Fusion : MitelmanKDM4C/RFX3 [9p24.1/9p24.2]  [t(9;9)(p24;p24)]  
Fusion : MitelmanPGPEP1/KDM4C [19p13.11/9p24.1]  [t(9;19)(p24;p13)]  
Fusion: TCGAKDM4C 9p24.1 ARMC2 6q21 BRCA
Fusion: TCGAKDM4C 9p24.1 JAK2 9p24.1 BRCA
Fusion: TCGAKDM4C 9p24.1 KLK7 19q13.41 LUAD
Fusion: TCGAKDM4C 9p24.1 PTPRD 9p24.1 PRAD
Fusion: TCGAKDM4C 9p24.1 RFX3 9p24.2 KIRC
Fusion: TCGAPGPEP1 19p13.11 KDM4C 9p24.1 BRCA
Polymorphisms : SNP, variants
NCBI Variation ViewerKDM4C [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)KDM4C
dbVarKDM4C
ClinVarKDM4C
1000_GenomesKDM4C 
Exome Variant ServerKDM4C
SNP (GeneSNP Utah)KDM4C
SNP : HGBaseKDM4C
Genetic variants : HAPMAPKDM4C
Genomic Variants (DGV)KDM4C [DGVbeta]
Mutations
ICGC Data PortalKDM4C 
TCGA Data PortalKDM4C 
Tumor PortalKDM4C
TCGA Copy Number PortalKDM4C
Somatic Mutations in Cancer : COSMICKDM4C 
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch KDM4C
DgiDB (Drug Gene Interaction Database)KDM4C
DoCM (Curated mutations)KDM4C (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)KDM4C (select a term)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)9:6757641-7077264
CONAN: Copy Number AnalysisKDM4C 
Mutations and Diseases : HGMDKDM4C
OMIM605469   
MedgenKDM4C
NextProtQ9H3R0 [Medical]
TSGene23081
GENETestsKDM4C
Huge Navigator KDM4C [HugePedia]  KDM4C [HugeCancerGEM]
snp3D : Map Gene to Disease23081
BioCentury BCIQKDM4C
General knowledge
Homologs : HomoloGeneKDM4C
Homology/Alignments : Family Browser (UCSC)KDM4C
Chemical/Protein Interactions : CTD23081
Chemical/Pharm GKB GenePA164721503
Clinical trialKDM4C
Other databases
Probes
Litterature
PubMed47 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineKDM4C
GoPubMedKDM4C
iHOPKDM4C
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri Jan 29 18:39:17 CET 2016

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