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PRDM4 (PR/SET domain 4)

Identity

Alias_namesPR domain containing 4
PR domain 4
Alias_symbol (synonym)PFM1
Other alias
HGNC (Hugo) PRDM4
LocusID (NCBI) 11108
Atlas_Id 41835
Location 12q23.3  [Link to chromosome band 12q23]
Location_base_pair Starts at 107732866 and ends at 107761137 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)PRDM4   9348
Cards
Entrez_Gene (NCBI)PRDM4  11108  PR/SET domain 4
AliasesPFM1
GeneCards (Weizmann)PRDM4
Ensembl hg19 (Hinxton)ENSG00000110851 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000110851 [Gene_View]  chr12:107732866-107761137 [Contig_View]  PRDM4 [Vega]
ICGC DataPortalENSG00000110851
TCGA cBioPortalPRDM4
AceView (NCBI)PRDM4
Genatlas (Paris)PRDM4
WikiGenes11108
SOURCE (Princeton)PRDM4
Genetics Home Reference (NIH)PRDM4
Genomic and cartography
GoldenPath hg38 (UCSC)PRDM4  -     chr12:107732866-107761137 -  12q23.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PRDM4  -     12q23.3   [Description]    (hg19-Feb_2009)
EnsemblPRDM4 - 12q23.3 [CytoView hg19]  PRDM4 - 12q23.3 [CytoView hg38]
Mapping of homologs : NCBIPRDM4 [Mapview hg19]  PRDM4 [Mapview hg38]
OMIM605780   
Gene and transcription
Genbank (Entrez)AF144757 AK056378 AL133083 BC035581 BC068562
RefSeq transcript (Entrez)NM_012406
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PRDM4
Cluster EST : UnigeneHs.506655 [ NCBI ]
CGAP (NCI)Hs.506655
Alternative Splicing GalleryENSG00000110851
Gene ExpressionPRDM4 [ NCBI-GEO ]   PRDM4 [ EBI - ARRAY_EXPRESS ]   PRDM4 [ SEEK ]   PRDM4 [ MEM ]
Gene Expression Viewer (FireBrowse)PRDM4 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)11108
GTEX Portal (Tissue expression)PRDM4
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9UKN5   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9UKN5  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9UKN5
Splice isoforms : SwissVarQ9UKN5
Catalytic activity : Enzyme2.1.1.- [ Enzyme-Expasy ]   2.1.1.-2.1.1.- [ IntEnz-EBI ]   2.1.1.- [ BRENDA ]   2.1.1.- [ KEGG ]   
PhosPhoSitePlusQ9UKN5
Domaine pattern : Prosite (Expaxy)SET (PS50280)    ZINC_FINGER_C2H2_1 (PS00028)    ZINC_FINGER_C2H2_2 (PS50157)   
Domains : Interpro (EBI)PRDM4    SET_dom    Znf_C2H2    Znf_C2H2-like    Znf_C2H2/integrase_DNA-bd   
Domain families : Pfam (Sanger)zf-C2H2 (PF00096)   
Domain families : Pfam (NCBI)pfam00096   
Domain families : Smart (EMBL)ZnF_C2H2 (SM00355)  
Conserved Domain (NCBI)PRDM4
DMDM Disease mutations11108
Blocks (Seattle)PRDM4
PDB (SRS)2L9Z    3DB5   
PDB (PDBSum)2L9Z    3DB5   
PDB (IMB)2L9Z    3DB5   
PDB (RSDB)2L9Z    3DB5   
Structural Biology KnowledgeBase2L9Z    3DB5   
SCOP (Structural Classification of Proteins)2L9Z    3DB5   
CATH (Classification of proteins structures)2L9Z    3DB5   
SuperfamilyQ9UKN5
Human Protein AtlasENSG00000110851
Peptide AtlasQ9UKN5
HPRD10425
IPIIPI00296947   IPI00552860   IPI00432413   IPI01021695   IPI01022813   
Protein Interaction databases
DIP (DOE-UCLA)Q9UKN5
IntAct (EBI)Q9UKN5
FunCoupENSG00000110851
BioGRIDPRDM4
STRING (EMBL)PRDM4
ZODIACPRDM4
Ontologies - Pathways
QuickGOQ9UKN5
Ontology : AmiGODNA binding  protein binding  regulation of transcription, DNA-templated  transcription from RNA polymerase II promoter  signal transduction  methyltransferase activity  zinc ion binding  cell proliferation  histone methyltransferase complex  histone H4-R3 methylation  histone methyltransferase binding  
Ontology : EGO-EBIDNA binding  protein binding  regulation of transcription, DNA-templated  transcription from RNA polymerase II promoter  signal transduction  methyltransferase activity  zinc ion binding  cell proliferation  histone methyltransferase complex  histone H4-R3 methylation  histone methyltransferase binding  
Pathways : KEGGNeurotrophin signaling pathway   
NDEx NetworkPRDM4
Atlas of Cancer Signalling NetworkPRDM4
Wikipedia pathwaysPRDM4
Orthology - Evolution
OrthoDB11108
GeneTree (enSembl)ENSG00000110851
Phylogenetic Trees/Animal Genes : TreeFamPRDM4
HOVERGENQ9UKN5
HOGENOMQ9UKN5
Homologs : HomoloGenePRDM4
Homology/Alignments : Family Browser (UCSC)PRDM4
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPRDM4 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PRDM4
dbVarPRDM4
ClinVarPRDM4
1000_GenomesPRDM4 
Exome Variant ServerPRDM4
ExAC (Exome Aggregation Consortium)PRDM4 (select the gene name)
Genetic variants : HAPMAP11108
Genomic Variants (DGV)PRDM4 [DGVbeta]
DECIPHERPRDM4 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPRDM4 
Mutations
ICGC Data PortalPRDM4 
TCGA Data PortalPRDM4 
Broad Tumor PortalPRDM4
OASIS PortalPRDM4 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPRDM4  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPRDM4
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 PRDM4
DgiDB (Drug Gene Interaction Database)PRDM4
DoCM (Curated mutations)PRDM4 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PRDM4 (select a term)
intoGenPRDM4
Cancer3DPRDM4(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM605780   
Orphanet
MedgenPRDM4
Genetic Testing Registry PRDM4
NextProtQ9UKN5 [Medical]
TSGene11108
GENETestsPRDM4
Target ValidationPRDM4
Huge Navigator PRDM4 [HugePedia]
snp3D : Map Gene to Disease11108
BioCentury BCIQPRDM4
ClinGenPRDM4
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD11108
Chemical/Pharm GKB GenePA33716
Clinical trialPRDM4
Miscellaneous
canSAR (ICR)PRDM4 (select the gene name)
Probes
Litterature
PubMed15 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePRDM4
EVEXPRDM4
GoPubMedPRDM4
iHOPPRDM4
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Wed Jun 7 12:50:56 CEST 2017

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