Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

PRDM9 (PR/SET domain 9)

Identity

Alias_namesMSBP3
minisatellite binding protein 3, 115kDa
minisatellite binding protein 3 (115kD)
PR domain containing 9
PR domain 9
Alias_symbol (synonym)PFM6
ZNF899
Other aliasKMT8B
MEISETZ
HGNC (Hugo) PRDM9
LocusID (NCBI) 56979
Atlas_Id 53542
Location 5p14.2  [Link to chromosome band 5p14]
Location_base_pair Starts at 23507609 and ends at 23528597 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)

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)PRDM9   13994
Cards
Entrez_Gene (NCBI)PRDM9  56979  PR/SET domain 9
AliasesKMT8B; MEISETZ; MSBP3; PFM6; 
ZNF899
GeneCards (Weizmann)PRDM9
Ensembl hg19 (Hinxton)ENSG00000164256 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000164256 [Gene_View]  ENSG00000164256 [Sequence]  chr5:23507609-23528597 [Contig_View]  PRDM9 [Vega]
ICGC DataPortalENSG00000164256
TCGA cBioPortalPRDM9
AceView (NCBI)PRDM9
Genatlas (Paris)PRDM9
WikiGenes56979
SOURCE (Princeton)PRDM9
Genetics Home Reference (NIH)PRDM9
Genomic and cartography
GoldenPath hg38 (UCSC)PRDM9  -     chr5:23507609-23528597 +  5p14.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PRDM9  -     5p14.2   [Description]    (hg19-Feb_2009)
EnsemblPRDM9 - 5p14.2 [CytoView hg19]  PRDM9 - 5p14.2 [CytoView hg38]
Mapping of homologs : NCBIPRDM9 [Mapview hg19]  PRDM9 [Mapview hg38]
OMIM609760   
Gene and transcription
Genbank (Entrez)AF275816 AK301776 DB636359 DQ388610 GU216222
RefSeq transcript (Entrez)NM_001310214 NM_020227
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PRDM9
Cluster EST : UnigeneHs.283096 [ NCBI ]
CGAP (NCI)Hs.283096
Alternative Splicing GalleryENSG00000164256
Gene ExpressionPRDM9 [ NCBI-GEO ]   PRDM9 [ EBI - ARRAY_EXPRESS ]   PRDM9 [ SEEK ]   PRDM9 [ MEM ]
Gene Expression Viewer (FireBrowse)PRDM9 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)56979
GTEX Portal (Tissue expression)PRDM9
Human Protein AtlasENSG00000164256-PRDM9 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9NQV7   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9NQV7  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9NQV7
Splice isoforms : SwissVarQ9NQV7
Catalytic activity : Enzyme2.1.1.43 [ Enzyme-Expasy ]   2.1.1.432.1.1.43 [ IntEnz-EBI ]   2.1.1.43 [ BRENDA ]   2.1.1.43 [ KEGG ]   
PhosPhoSitePlusQ9NQV7
Domaine pattern : Prosite (Expaxy)KRAB_RELATED (PS50806)    SET (PS50280)    ZINC_FINGER_C2H2_1 (PS00028)    ZINC_FINGER_C2H2_2 (PS50157)   
Domains : Interpro (EBI)KRAB    KRAB_dom_sf    Krueppel-associated_box-rel    SET_dom    SSXRD_motif    Znf_C2H2_sf    Znf_C2H2_type   
Domain families : Pfam (Sanger)KRAB (PF01352)    SET (PF00856)    SSXRD (PF09514)   
Domain families : Pfam (NCBI)pfam01352    pfam00856    pfam09514   
Domain families : Smart (EMBL)KRAB (SM00349)  ZnF_C2H2 (SM00355)  
Conserved Domain (NCBI)PRDM9
DMDM Disease mutations56979
Blocks (Seattle)PRDM9
PDB (RSDB)4IJD    5EGB    5EH2    5EI9   
PDB Europe4IJD    5EGB    5EH2    5EI9   
PDB (PDBSum)4IJD    5EGB    5EH2    5EI9   
PDB (IMB)4IJD    5EGB    5EH2    5EI9   
Structural Biology KnowledgeBase4IJD    5EGB    5EH2    5EI9   
SCOP (Structural Classification of Proteins)4IJD    5EGB    5EH2    5EI9   
CATH (Classification of proteins structures)4IJD    5EGB    5EH2    5EI9   
SuperfamilyQ9NQV7
Human Protein Atlas [tissue]ENSG00000164256-PRDM9 [tissue]
Peptide AtlasQ9NQV7
HPRD17905
IPIIPI00847313   IPI00478898   IPI00954990   IPI00955029   IPI00967899   
Protein Interaction databases
DIP (DOE-UCLA)Q9NQV7
IntAct (EBI)Q9NQV7
FunCoupENSG00000164256
BioGRIDPRDM9
STRING (EMBL)PRDM9
ZODIACPRDM9
Ontologies - Pathways
QuickGOQ9NQV7
Ontology : AmiGORNA polymerase II regulatory region sequence-specific DNA binding  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity  nucleus  nucleoplasm  chromosome  meiotic gene conversion  regulation of transcription by RNA polymerase II  recombination hotspot binding  positive regulation of reciprocal meiotic recombination  positive regulation of reciprocal meiotic recombination  nucleosome positioning  histone-lysine N-methyltransferase activity  histone-lysine N-methyltransferase activity  chromatin DNA binding  histone methyltransferase activity (H3-K4 specific)  sequence-specific DNA binding  sequence-specific DNA binding  transcription regulatory region DNA binding  metal ion binding  histone H3-K4 methylation  
Ontology : EGO-EBIRNA polymerase II regulatory region sequence-specific DNA binding  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity  nucleus  nucleoplasm  chromosome  meiotic gene conversion  regulation of transcription by RNA polymerase II  recombination hotspot binding  positive regulation of reciprocal meiotic recombination  positive regulation of reciprocal meiotic recombination  nucleosome positioning  histone-lysine N-methyltransferase activity  histone-lysine N-methyltransferase activity  chromatin DNA binding  histone methyltransferase activity (H3-K4 specific)  sequence-specific DNA binding  sequence-specific DNA binding  transcription regulatory region DNA binding  metal ion binding  histone H3-K4 methylation  
NDEx NetworkPRDM9
Atlas of Cancer Signalling NetworkPRDM9
Wikipedia pathwaysPRDM9
Orthology - Evolution
OrthoDB56979
GeneTree (enSembl)ENSG00000164256
Phylogenetic Trees/Animal Genes : TreeFamPRDM9
HOGENOMQ9NQV7
Homologs : HomoloGenePRDM9
Homology/Alignments : Family Browser (UCSC)PRDM9
Gene fusions - Rearrangements
Fusion : QuiverPRDM9
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPRDM9 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PRDM9
dbVarPRDM9
ClinVarPRDM9
1000_GenomesPRDM9 
Exome Variant ServerPRDM9
ExAC (Exome Aggregation Consortium)ENSG00000164256
GNOMAD BrowserENSG00000164256
Varsome BrowserPRDM9
Genetic variants : HAPMAP56979
Genomic Variants (DGV)PRDM9 [DGVbeta]
DECIPHERPRDM9 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPRDM9 
Mutations
ICGC Data PortalPRDM9 
TCGA Data PortalPRDM9 
Broad Tumor PortalPRDM9
OASIS PortalPRDM9 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPRDM9  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPRDM9
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 PRDM9
DgiDB (Drug Gene Interaction Database)PRDM9
DoCM (Curated mutations)PRDM9 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PRDM9 (select a term)
intoGenPRDM9
Cancer3DPRDM9(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM609760   
Orphanet
DisGeNETPRDM9
MedgenPRDM9
Genetic Testing Registry PRDM9
NextProtQ9NQV7 [Medical]
TSGene56979
GENETestsPRDM9
Target ValidationPRDM9
Huge Navigator PRDM9 [HugePedia]
snp3D : Map Gene to Disease56979
BioCentury BCIQPRDM9
ClinGenPRDM9
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD56979
Chemical/Pharm GKB GenePA33721
Clinical trialPRDM9
Miscellaneous
canSAR (ICR)PRDM9 (select the gene name)
DataMed IndexPRDM9
Probes
Litterature
PubMed32 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePRDM9
EVEXPRDM9
GoPubMedPRDM9
iHOPPRDM9
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Thu Jan 17 18:32:35 CET 2019

Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.