| Nomenclature |
|---|
| HGNC (Hugo) | KDM5D 11115 |
| Cards |
|---|
| Entrez_Gene (NCBI) | KDM5D 8284 lysine demethylase 5D |
| Aliases | HY; 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 DataPortal | ENSG00000012817 |
| TCGA cBioPortal | KDM5D |
| AceView (NCBI) | KDM5D |
| Genatlas (Paris) | KDM5D |
| WikiGenes | 8284 |
| 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) |
| Ensembl | KDM5D - Yq11.223 [CytoView hg19] KDM5D - Yq11.223 [CytoView hg38] |
| Mapping of homologs : NCBI | KDM5D [Mapview hg19] KDM5D [Mapview hg38] |
| OMIM | 415000 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 : Unigene | Hs.80358 [ NCBI ] |
| CGAP (NCI) | Hs.80358 |
| Alternative Splicing Gallery | ENSG00000012817 |
| Gene Expression | KDM5D [ 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] |
| Genevestigator | Expression in : [tissues] [cell-lines] [cancer] [perturbations] |
| BioGPS (Tissue expression) | 8284 |
| GTEX Portal (Tissue expression) | KDM5D |
| Human Protein Atlas | ENSG00000012817-KDM5D [pathology] [cell] [tissue] |
| Protein : pattern, domain, 3D structure |
|---|
| UniProt/SwissProt | Q9BY66 [function] [subcellular_location] [family_and_domains] [pathology_and_biotech] [ptm_processing] [expression] [interaction] |
| NextProt | Q9BY66 [Sequence] [Exons] [Medical] [Publications] |
| With graphics : InterPro | Q9BY66 |
| Splice isoforms : SwissVar | Q9BY66 |
| Catalytic activity : Enzyme | 1.14.11.- [ Enzyme-Expasy ] 1.14.11.-1.14.11.- [ IntEnz-EBI ] 1.14.11.- [ BRENDA ] 1.14.11.- [ KEGG ] |
| PhosPhoSitePlus | Q9BY66 |
| 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 mutations | 8284 |
| Blocks (Seattle) | KDM5D |
| PDB (SRS) | 2E6R 2YQE |
| PDB (PDBSum) | 2E6R 2YQE |
| PDB (IMB) | 2E6R 2YQE |
| PDB (RSDB) | 2E6R 2YQE |
| Structural Biology KnowledgeBase | 2E6R 2YQE |
| SCOP (Structural Classification of Proteins) | 2E6R 2YQE |
| CATH (Classification of proteins structures) | 2E6R 2YQE |
| Superfamily | Q9BY66 |
| Human Protein Atlas [tissue] | ENSG00000012817-KDM5D [tissue] |
| Peptide Atlas | Q9BY66 |
| HPRD | 02464 |
| IPI | IPI00329577 IPI00219940 IPI01013623 IPI00922879 IPI00644852 IPI00644955 IPI00643783 |
| Protein Interaction databases |
|---|
| DIP (DOE-UCLA) | Q9BY66 |
| IntAct (EBI) | Q9BY66 |
| FunCoup | ENSG00000012817 |
| BioGRID | KDM5D |
| STRING (EMBL) | KDM5D |
| ZODIAC | KDM5D |
| Ontologies - Pathways |
|---|
| QuickGO | Q9BY66 |
| Ontology : AmiGO | RNA polymerase II transcription factor activity, sequence-specific DNA binding transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding fibrillar center T cell antigen processing and presentation DNA binding chromatin binding protein binding cellular_component nucleus nucleoplasm transcription, DNA-templated regulation of transcription by RNA polymerase II histone demethylase activity histone demethylase activity histone demethylase activity (H3-K4 specific) histone demethylase activity (H3-trimethyl-K4 specific) histone H3-K4 demethylation methylated histone binding histone methyltransferase complex metal ion binding androgen receptor binding dioxygenase activity oxidation-reduction process regulation of androgen receptor signaling pathway |
| Ontology : EGO-EBI | RNA polymerase II transcription factor activity, sequence-specific DNA binding transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding fibrillar center T cell antigen processing and presentation DNA binding chromatin binding protein binding cellular_component nucleus nucleoplasm transcription, DNA-templated regulation of transcription by RNA polymerase II histone demethylase activity histone demethylase activity histone demethylase activity (H3-K4 specific) histone demethylase activity (H3-trimethyl-K4 specific) histone H3-K4 demethylation methylated histone binding histone methyltransferase complex metal ion binding androgen receptor binding dioxygenase activity oxidation-reduction process regulation of androgen receptor signaling pathway |
| NDEx Network | KDM5D |
| Atlas of Cancer Signalling Network | KDM5D |
| Wikipedia pathways | KDM5D |
| Orthology - Evolution |
|---|
| OrthoDB | 8284 |
| GeneTree (enSembl) | ENSG00000012817 |
| Phylogenetic Trees/Animal Genes : TreeFam | KDM5D |
| HOVERGEN | Q9BY66 |
| HOGENOM | Q9BY66 |
| Homologs : HomoloGene | KDM5D |
| Homology/Alignments : Family Browser (UCSC) | KDM5D |
| Gene fusions - Rearrangements |
|---|
| Fusion : Quiver | KDM5D |
| Polymorphisms : SNP and Copy number variants |
|---|
| NCBI Variation Viewer | KDM5D [hg38] |
| dbSNP Single Nucleotide Polymorphism (NCBI) | KDM5D |
| dbVar | KDM5D |
| ClinVar | KDM5D |
| 1000_Genomes | KDM5D |
| Exome Variant Server | KDM5D |
| ExAC (Exome Aggregation Consortium) | ENSG00000012817 |
| GNOMAD Browser | ENSG00000012817 |
| Varsome Browser | KDM5D |
| Genetic variants : HAPMAP | 8284 |
| Genomic Variants (DGV) | KDM5D [DGVbeta] |
| DECIPHER | KDM5D [patients] [syndromes] [variants] [genes] |
| CONAN: Copy Number Analysis | KDM5D |
| Mutations |
|---|
| ICGC Data Portal | KDM5D |
| TCGA Data Portal | KDM5D |
| Broad Tumor Portal | KDM5D |
| OASIS Portal | KDM5D [ Somatic mutations - Copy number] |
| Somatic Mutations in Cancer : COSMIC | KDM5D [overview] [genome browser] [tissue] [distribution] |
| Mutations and Diseases : HGMD | KDM5D |
| LOVD (Leiden Open Variation Database) | Whole genome datasets |
| LOVD (Leiden Open Variation Database) | LOVD 3.0 shared installation |
| BioMuta | search 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) |
| intoGen | KDM5D |
| Cancer3D | KDM5D(select the gene name) |
| Impact of mutations | [PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser] |
| Diseases |
|---|
| OMIM | 415000 426000 |
| Orphanet | |
| DisGeNET | KDM5D |
| Medgen | KDM5D |
| Genetic Testing Registry | KDM5D
|
| NextProt | Q9BY66 [Medical] |
| TSGene | 8284 |
| GENETests | KDM5D |
| Target Validation | KDM5D |
| Huge Navigator |
KDM5D [HugePedia] |
| snp3D : Map Gene to Disease | 8284 |
| BioCentury BCIQ | KDM5D |
| ClinGen | KDM5D |
| Clinical trials, drugs, therapy |
|---|
| Chemical/Protein Interactions : CTD | 8284 |
| Chemical/Pharm GKB Gene | PA35965 |
| Clinical trial | KDM5D |
| Miscellaneous |
|---|
| canSAR (ICR) | KDM5D (select the gene name) |
| Probes |
|---|
| Litterature |
|---|
| PubMed | 29 Pubmed reference(s) in Entrez |
| GeneRIFs | Gene References Into Functions (Entrez) |
| CoreMine | KDM5D |
| EVEX | KDM5D |
| GoPubMed | KDM5D |
| iHOP | KDM5D |
