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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 23507655 and ends at 23528084 bp from pter ( according to hg38-Dec_2013)

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]  chr5:23507655-23528084 [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  -     chr5:23507655-23528084 +  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]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)56979
GTEX Portal (Tissue expression)PRDM9
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    Krueppel-associated_box-rel    SET_dom    SSXRD_motif    Znf_C2H2    Znf_C2H2-like    Znf_C2H2/integrase_DNA-bd   
Domain families : Pfam (Sanger)KRAB (PF01352)    SET (PF00856)    SSXRD (PF09514)    zf-C2H2 (PF00096)    zf-C2H2_6 (PF13912)   
Domain families : Pfam (NCBI)pfam01352    pfam00856    pfam09514    pfam00096    pfam13912   
Domain families : Smart (EMBL)KRAB (SM00349)  ZnF_C2H2 (SM00355)  
Conserved Domain (NCBI)PRDM9
DMDM Disease mutations56979
Blocks (Seattle)PRDM9
PDB (SRS)4IJD    5EGB    5EH2    5EI9   
PDB (PDBSum)4IJD    5EGB    5EH2    5EI9   
PDB (IMB)4IJD    5EGB    5EH2    5EI9   
PDB (RSDB)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 AtlasENSG00000164256
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 : AmiGOnucleic acid binding  nucleoplasm  chromosome  meiotic gene conversion  transcription, DNA-templated  regulation of transcription, DNA-templated  positive regulation of reciprocal meiotic recombination  histone-lysine N-methyltransferase activity  histone lysine methylation  metal ion binding  
Ontology : EGO-EBInucleic acid binding  nucleoplasm  chromosome  meiotic gene conversion  transcription, DNA-templated  regulation of transcription, DNA-templated  positive regulation of reciprocal meiotic recombination  histone-lysine N-methyltransferase activity  histone lysine methylation  metal ion binding  
NDEx NetworkPRDM9
Atlas of Cancer Signalling NetworkPRDM9
Wikipedia pathwaysPRDM9
Orthology - Evolution
OrthoDB56979
GeneTree (enSembl)ENSG00000164256
Phylogenetic Trees/Animal Genes : TreeFamPRDM9
HOVERGENQ9NQV7
HOGENOMQ9NQV7
Homologs : HomoloGenePRDM9
Homology/Alignments : Family Browser (UCSC)PRDM9
Gene fusions - Rearrangements
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)PRDM9 (select the gene name)
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] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM609760   
Orphanet
MedgenPRDM9
Genetic Testing Registry PRDM9
NextProtQ9NQV7 [Medical]
TSGene56979
GENETestsPRDM9
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)
Probes
Litterature
PubMed28 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

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indexed on : Fri May 19 12:32:40 CEST 2017

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