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PRDM5 (PR domain 5)

Identity

Other namesBCS2
PFM2
HGNC (Hugo) PRDM5
LocusID (NCBI) 11107
Atlas_Id 41836
Location 4q27  [Link to chromosome band 4q27]
Location_base_pair Starts at 121613068 and ends at 121844021 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
RBM39 (20q11.22) / PRDM5 (4q27)RBM39 20q11.22 / PRDM5 4q27

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)PRDM5   9349
Cards
Entrez_Gene (NCBI)PRDM5  11107  PR domain 5
AliasesBCS2; PFM2
GeneCards (Weizmann)PRDM5
Ensembl hg19 (Hinxton)ENSG00000138738 [Gene_View]  chr4:121613068-121844021 [Contig_View]  PRDM5 [Vega]
Ensembl hg38 (Hinxton)ENSG00000138738 [Gene_View]  chr4:121613068-121844021 [Contig_View]  PRDM5 [Vega]
ICGC DataPortalENSG00000138738
TCGA cBioPortalPRDM5
AceView (NCBI)PRDM5
Genatlas (Paris)PRDM5
WikiGenes11107
SOURCE (Princeton)PRDM5
Genomic and cartography
GoldenPath hg19 (UCSC)PRDM5  -     chr4:121613068-121844021 -  4q27   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)PRDM5  -     4q27   [Description]    (hg38-Dec_2013)
EnsemblPRDM5 - 4q27 [CytoView hg19]  PRDM5 - 4q27 [CytoView hg38]
Mapping of homologs : NCBIPRDM5 [Mapview hg19]  PRDM5 [Mapview hg38]
OMIM614161   614170   
Gene and transcription
Genbank (Entrez)AF272897 AK056352 AK310958 AK314293 AW341546
RefSeq transcript (Entrez)NM_001300823 NM_001300824 NM_018699
RefSeq genomic (Entrez)NC_000004 NC_018915 NG_031862 NT_016354 NW_004929320
Consensus coding sequences : CCDS (NCBI)PRDM5
Cluster EST : UnigeneHs.666782 [ NCBI ]
CGAP (NCI)Hs.666782
Alternative Splicing GalleryENSG00000138738
Gene ExpressionPRDM5 [ NCBI-GEO ]   PRDM5 [ EBI - ARRAY_EXPRESS ]   PRDM5 [ SEEK ]   PRDM5 [ MEM ]
Gene Expression Viewer (FireBrowse)PRDM5 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)11107
GTEX Portal (Tissue expression)PRDM5
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9NQX1 (Uniprot)
NextProtQ9NQX1  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9NQX1
Splice isoforms : SwissVarQ9NQX1 (Swissvar)
Catalytic activity : Enzyme2.1.1.- [ Enzyme-Expasy ]   2.1.1.-2.1.1.- [ IntEnz-EBI ]   2.1.1.- [ BRENDA ]   2.1.1.- [ KEGG ]   
PhosPhoSitePlusQ9NQX1
Domaine pattern : Prosite (Expaxy)SET (PS50280)    ZINC_FINGER_C2H2_1 (PS00028)    ZINC_FINGER_C2H2_2 (PS50157)   
Domains : Interpro (EBI)SET_dom    Znf_C2H2    Znf_C2H2-like    Znf_C2H2/integrase_DNA-bd    Znf_C2H2_jaz    Znf_PRDM5   
Domain families : Pfam (Sanger)zf-C2H2 (PF00096)    zf-C2H2_6 (PF13912)    zf-C2H2_jaz (PF12171)   
Domain families : Pfam (NCBI)pfam00096    pfam13912    pfam12171   
Domain families : Smart (EMBL)SET (SM00317)  ZnF_C2H2 (SM00355)  
DMDM Disease mutations11107
Blocks (Seattle)PRDM5
SuperfamilyQ9NQX1
Human Protein AtlasENSG00000138738
Peptide AtlasQ9NQX1
HPRD17902
IPIIPI00032997   IPI00914659   IPI00744738   IPI00744612   IPI00981059   IPI00968109   IPI00967335   
Protein Interaction databases
DIP (DOE-UCLA)Q9NQX1
IntAct (EBI)Q9NQX1
FunCoupENSG00000138738
BioGRIDPRDM5
STRING (EMBL)PRDM5
ZODIACPRDM5
Ontologies - Pathways
QuickGOQ9NQX1
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  mitotic cell cycle  RNA polymerase II core promoter proximal region sequence-specific DNA binding  transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding  protein binding  nucleus  transcription, DNA-templated  methyltransferase activity  histone deacetylation  sequence-specific DNA binding  transcription regulatory region DNA binding  negative regulation of transcription, DNA-templated  metal ion binding  histone H3-K9 methylation  repressing transcription factor binding  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  mitotic cell cycle  RNA polymerase II core promoter proximal region sequence-specific DNA binding  transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding  protein binding  nucleus  transcription, DNA-templated  methyltransferase activity  histone deacetylation  sequence-specific DNA binding  transcription regulatory region DNA binding  negative regulation of transcription, DNA-templated  metal ion binding  histone H3-K9 methylation  repressing transcription factor binding  
NDEx Network
Atlas of Cancer Signalling NetworkPRDM5
Wikipedia pathwaysPRDM5
Orthology - Evolution
OrthoDB11107
GeneTree (enSembl)ENSG00000138738
Phylogenetic Trees/Animal Genes : TreeFamPRDM5
Homologs : HomoloGenePRDM5
Homology/Alignments : Family Browser (UCSC)PRDM5
Gene fusions - Rearrangements
Fusion: TCGARBM39 20q11.22 PRDM5 4q27 BLCA
Polymorphisms : SNP, variants
NCBI Variation ViewerPRDM5 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PRDM5
dbVarPRDM5
ClinVarPRDM5
1000_GenomesPRDM5 
Exome Variant ServerPRDM5
ExAC (Exome Aggregation Consortium)PRDM5 (select the gene name)
Genetic variants : HAPMAP11107
Genomic Variants (DGV)PRDM5 [DGVbeta]
Mutations
ICGC Data PortalPRDM5 
TCGA Data PortalPRDM5 
Broad Tumor PortalPRDM5
OASIS PortalPRDM5 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPRDM5 
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 PRDM5
DgiDB (Drug Gene Interaction Database)PRDM5
DoCM (Curated mutations)PRDM5 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PRDM5 (select a term)
intoGenPRDM5
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)4:121613068-121844021  ENSG00000138738
CONAN: Copy Number AnalysisPRDM5 
Mutations and Diseases : HGMDPRDM5
OMIM614161    614170   
MedgenPRDM5
Genetic Testing Registry PRDM5
NextProtQ9NQX1 [Medical]
TSGene11107
GENETestsPRDM5
Huge Navigator PRDM5 [HugePedia]
snp3D : Map Gene to Disease11107
BioCentury BCIQPRDM5
ClinGenPRDM5
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD11107
Chemical/Pharm GKB GenePA33717
Clinical trialPRDM5
Miscellaneous
canSAR (ICR)PRDM5 (select the gene name)
Probes
Litterature
PubMed20 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePRDM5
EVEXPRDM5
GoPubMedPRDM5
iHOPPRDM5
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Aug 9 19:17:14 CEST 2016

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