Atlas of Genetics and Cytogenetics in Oncology and Haematology

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KDM5D (lysine demethylase 5D)

Identity

Alias_namesHYA
HY
SMCY
JARID1D
Jumonji, AT rich interactive domain 1D (RBP2-like)
Smcy homolog, Y-linked (mouse)
jumonji, AT rich interactive domain 1D
lysine (K)-specific demethylase 5D
Alias_symbol (synonym)KIAA0234
Other alias
HGNC (Hugo) KDM5D
LocusID (NCBI) 8284
Atlas_Id 56630
Location Yq11.223  [Link to chromosome band Yq11]
Location_base_pair Starts at 19705415 and ends at 19744939 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
KDM5D (Yq11.222) / PRDX5 (11q13.1)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 

External links

Nomenclature
HGNC (Hugo)KDM5D   11115
Cards
Entrez_Gene (NCBI)KDM5D  8284  lysine demethylase 5D
AliasesHY; HYA; JARID1D; SMCY
GeneCards (Weizmann)KDM5D
Ensembl hg19 (Hinxton)ENSG00000012817 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000012817 [Gene_View]  ENSG00000012817 [Sequence]  chrY:19705415-19744939 [Contig_View]  KDM5D [Vega]
ICGC DataPortalENSG00000012817
TCGA cBioPortalKDM5D
AceView (NCBI)KDM5D
Genatlas (Paris)KDM5D
WikiGenes8284
SOURCE (Princeton)KDM5D
Genetics Home Reference (NIH)KDM5D
Genomic and cartography
GoldenPath hg38 (UCSC)KDM5D  -     chrY:19705415-19744939 -  Yq11.223   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)KDM5D  -     Yq11.223   [Description]    (hg19-Feb_2009)
EnsemblKDM5D - Yq11.223 [CytoView hg19]  KDM5D - Yq11.223 [CytoView hg38]
Mapping of homologs : NCBIKDM5D [Mapview hg19]  KDM5D [Mapview hg38]
OMIM415000   426000   
Gene and transcription
Genbank (Entrez)AA864889 AK095923 AK127269 AK304027 BC011053
RefSeq transcript (Entrez)NM_001146705 NM_001146706 NM_004653
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)KDM5D
Cluster EST : UnigeneHs.80358 [ NCBI ]
CGAP (NCI)Hs.80358
Alternative Splicing GalleryENSG00000012817
Gene ExpressionKDM5D [ NCBI-GEO ]   KDM5D [ EBI - ARRAY_EXPRESS ]   KDM5D [ SEEK ]   KDM5D [ MEM ]
Gene Expression Viewer (FireBrowse)KDM5D [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)8284
GTEX Portal (Tissue expression)KDM5D
Human Protein AtlasENSG00000012817-KDM5D [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9BY66   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9BY66  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9BY66
Splice isoforms : SwissVarQ9BY66
Catalytic activity : Enzyme1.14.11.- [ Enzyme-Expasy ]   1.14.11.-1.14.11.- [ IntEnz-EBI ]   1.14.11.- [ BRENDA ]   1.14.11.- [ KEGG ]   
PhosPhoSitePlusQ9BY66
Domaine pattern : Prosite (Expaxy)ARID (PS51011)    JMJC (PS51184)    JMJN (PS51183)    ZF_PHD_1 (PS01359)    ZF_PHD_2 (PS50016)   
Domains : Interpro (EBI)ARID_dom    ARID_dom_sf    JmjC_dom    JmjN    Lys_sp_deMease-like_dom    Zinc_finger_PHD-type_CS    Znf_C5HC2    Znf_FYVE_PHD    Znf_PHD    Znf_PHD-finger    Znf_RING/FYVE/PHD   
Domain families : Pfam (Sanger)ARID (PF01388)    JmjC (PF02373)    JmjN (PF02375)    PHD (PF00628)    PLU-1 (PF08429)    zf-C5HC2 (PF02928)   
Domain families : Pfam (NCBI)pfam01388    pfam02373    pfam02375    pfam00628    pfam08429    pfam02928   
Domain families : Smart (EMBL)BRIGHT (SM00501)  JmjC (SM00558)  JmjN (SM00545)  PHD (SM00249)  
Conserved Domain (NCBI)KDM5D
DMDM Disease mutations8284
Blocks (Seattle)KDM5D
PDB (RSDB)2E6R    2YQE   
PDB Europe2E6R    2YQE   
PDB (PDBSum)2E6R    2YQE   
PDB (IMB)2E6R    2YQE   
Structural Biology KnowledgeBase2E6R    2YQE   
SCOP (Structural Classification of Proteins)2E6R    2YQE   
CATH (Classification of proteins structures)2E6R    2YQE   
SuperfamilyQ9BY66
Human Protein Atlas [tissue]ENSG00000012817-KDM5D [tissue]
Peptide AtlasQ9BY66
HPRD02464
IPIIPI00329577   IPI00219940   IPI01013623   IPI00922879   IPI00644852   IPI00644955   IPI00643783   
Protein Interaction databases
DIP (DOE-UCLA)Q9BY66
IntAct (EBI)Q9BY66
FunCoupENSG00000012817
BioGRIDKDM5D
STRING (EMBL)KDM5D
ZODIACKDM5D
Ontologies - Pathways
QuickGOQ9BY66
Ontology : AmiGOnegative regulation of transcription by RNA polymerase II  DNA-binding transcription factor activity, RNA polymerase II-specific  fibrillar center  T cell antigen processing and presentation  DNA binding  protein binding  cellular_component  nucleus  nucleoplasm  chromatin remodeling  histone demethylase activity  histone demethylase activity  histone demethylase activity (H3-K4 specific)  histone demethylase activity (H3-trimethyl-K4 specific)  histone H3-K4 demethylation  histone H3-K4 demethylation, trimethyl-H3-K4-specific  histone methyltransferase complex  metal ion binding  androgen receptor binding  dioxygenase activity  oxidation-reduction process  regulation of androgen receptor signaling pathway  regulation of androgen receptor signaling pathway  
Ontology : EGO-EBInegative regulation of transcription by RNA polymerase II  DNA-binding transcription factor activity, RNA polymerase II-specific  fibrillar center  T cell antigen processing and presentation  DNA binding  protein binding  cellular_component  nucleus  nucleoplasm  chromatin remodeling  histone demethylase activity  histone demethylase activity  histone demethylase activity (H3-K4 specific)  histone demethylase activity (H3-trimethyl-K4 specific)  histone H3-K4 demethylation  histone H3-K4 demethylation, trimethyl-H3-K4-specific  histone methyltransferase complex  metal ion binding  androgen receptor binding  dioxygenase activity  oxidation-reduction process  regulation of androgen receptor signaling pathway  regulation of androgen receptor signaling pathway  
NDEx NetworkKDM5D
Atlas of Cancer Signalling NetworkKDM5D
Wikipedia pathwaysKDM5D
Orthology - Evolution
OrthoDB8284
GeneTree (enSembl)ENSG00000012817
Phylogenetic Trees/Animal Genes : TreeFamKDM5D
HOGENOMQ9BY66
Homologs : HomoloGeneKDM5D
Homology/Alignments : Family Browser (UCSC)KDM5D
Gene fusions - Rearrangements
Fusion : QuiverKDM5D
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerKDM5D [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)KDM5D
dbVarKDM5D
ClinVarKDM5D
1000_GenomesKDM5D 
Exome Variant ServerKDM5D
ExAC (Exome Aggregation Consortium)ENSG00000012817
GNOMAD BrowserENSG00000012817
Varsome BrowserKDM5D
Genetic variants : HAPMAP8284
Genomic Variants (DGV)KDM5D [DGVbeta]
DECIPHERKDM5D [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisKDM5D 
Mutations
ICGC Data PortalKDM5D 
TCGA Data PortalKDM5D 
Broad Tumor PortalKDM5D
OASIS PortalKDM5D [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICKDM5D  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDKDM5D
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch KDM5D
DgiDB (Drug Gene Interaction Database)KDM5D
DoCM (Curated mutations)KDM5D (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)KDM5D (select a term)
intoGenKDM5D
Cancer3DKDM5D(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM415000    426000   
Orphanet
DisGeNETKDM5D
MedgenKDM5D
Genetic Testing Registry KDM5D
NextProtQ9BY66 [Medical]
TSGene8284
GENETestsKDM5D
Target ValidationKDM5D
Huge Navigator KDM5D [HugePedia]
snp3D : Map Gene to Disease8284
BioCentury BCIQKDM5D
ClinGenKDM5D
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD8284
Chemical/Pharm GKB GenePA35965
Clinical trialKDM5D
Miscellaneous
canSAR (ICR)KDM5D (select the gene name)
DataMed IndexKDM5D
Probes
Litterature
PubMed30 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineKDM5D
EVEXKDM5D
GoPubMedKDM5D
iHOPKDM5D
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Thu Feb 14 16:37:23 CET 2019
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