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DENR (density-regulated protein)

Written2008-06Line S Reinert, Ronald B Gartenhaus
University of Maryland Greenebaum Cancer Center, 9-011 BRB, 655 West Baltimore Street, Baltimore, MD 21201, USA

(Note : for Links provided by Atlas : click)

Identity

Alias_namesdensity-regulated protein
Alias_symbol (synonym)DRP
DRP1
SMAP-3
Other alias
HGNC (Hugo) DENR
LocusID (NCBI) 8562
Atlas_Id 40295
Location 12q24.31  [Link to chromosome band 12q24]
Location_base_pair Starts at 122752821 and ends at 122771064 bp from pter ( according to hg19-Feb_2009)  [Mapping DENR.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
C14orf37 (14q23.1) / DENR (12q24.31)CD99L2 (Xq28) / DENR (12q24.31)DENR (12q24) / CCSER1 (4q22.1)
DENR (12q24.31) / CMBL (5p15.2)DENR (12q24.31) / KNTC1 (12q24.31)DENR (12q24.31) / RAB31 (18p11.22)
GBF1 (10q24.32) / DENR (12q24.31)KDM1B (6p22.3) / DENR (12q24.31)

DNA/RNA

Description The gene encompasses 18583 bp DNA and contains 8 exons (e.g. NCBI: NC_000012).
Transcription 2766 bp mRNA
The!3'-űntvanslated region (3'UTR) of DENR was found to have a high number of uracyl (U)- and adenine (A)-rich sequences (AREs) (Mazan-Mamczarz and Gartenhaus, 2007).

Protein

Description Size: 198 amino acids; 22092 Da.
Expression DENR is expressed in variety of tissues, with the highest quantity in skeletal and cardiac muscle. The protein level of DENR is up regulated in parallel with increasing cell density (Deyo et al., 1998). Very recently, it was found that this up regulation is controlled by the AUF-1 protein which binds to the 3'UTR of DENR mRNA and in a cell density-dependent manner (Mazan-Mamczarz and Gartenhaus, 2007). Furthermore, Oh JJ. et al. showed that DENR expression is increased in association with HER-2 overexpression in ovarian and breast cancers (Oh et al., 1999).
Localisation Predominantly in the cytoplasm of 3T3 cells.
Function Until recently there was little published data regarding DENR function. Reinert et al. showed that the oncogene MCT-1 interacts with DENR in vivo and in vitro. DENR contains a SUI1 domain which is also found in translation initiation factor eIF1, where the SUI1 domain is involved in recognition of the translation initiation codon (Yoon and Donahue, 1992). Interestingly, DENR together with MCT-1 sediment in the translation initiation complex fraction in both human embryonic kidney cell cultures and lymphoid cell lines. This complex was shown to interact with the cap complex and to alter the mRNA translational profile of a subset of cancer-related mRNAs. This supports a model where MCT-1 exerts it ongogenic function, at least in part by recruiting the SUI1 domain containing DENR to the translation initiation complex, thereby modulating the translational profile (Reinert et al., 2006).
Homology The SUI1 domain present in DENR is homologous to the SUI-1 domain found in eIF1. The SUI1 domain contains a secondary structure fold corresponding to that found in a number of ribosomal proteins and RNA-binding domains.

Implicated in

Note
  
Entity Lymphoma oncogene
Note The MCT-1 oncogene protein modifies mRNA translational profiles through its interaction with DENR which contains an SUI1 domain involved in recognition of the translation initiation codon (Reinert et.al., 2006) (Yoon and Donahue, 1992).
  
  
Entity Ovarian cancer and Breast cancer
Disease DENR expression is increased in association with HER-2 overexpression in ovarian and breast cancers (Oh. et al., 1999).
  

Bibliography

drp, a novel protein expressed at high cell density but not during growth arrest.
Deyo JE, Chiao PJ, Tainsky MA.
DNA Cell Biol. 1998 May;17(5):437-47.
PMID 9628587
 
Post-transcriptional control of the MCT-1-associated protein DENR/DRP by RNA-binding protein AUF1.
Mazan-Mamczarz K, Gartenhaus RB.
Cancer Genomics Proteomics. 2007 May-Jun;4(3):233-9.
PMID 17878526
 
Identification of differentially expressed genes associated with HER-2/neu overexpression in human breast cancer cells.
Oh JJ, Grosshans DR, Wong SG, Slamon DJ.
Nucleic Acids Res. 1999 Oct 15;27(20):4008-17.
PMID 10497265
 
MCT-1 protein interacts with the cap complex and modulates messenger RNA translational profiles.
Reinert LS, Shi B, Nandi S, Mazan-Mamczarz K, Vitolo M, Bachman KE, He H, Gartenhaus RB.
Cancer Res. 2006 Sep 15;66(18):8994-9001.
PMID 16982740
 
The suil suppressor locus in Saccharomyces cerevisiae encodes a translation factor that functions during tRNA(iMet) recognition of the start codon.
Yoon HJ, Donahue TF.
Mol Cell Biol. 1992 Jan;12(1):248-60.
PMID 1729602
 

Citation

This paper should be referenced as such :
Reinert, LS ; Gartenhaus, RB
DENR (density-regulated protein)
Atlas Genet Cytogenet Oncol Haematol. 2009;13(5):336-337.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/DENRID40295ch12q24.html


External links

Nomenclature
HGNC (Hugo)DENR   2769
Cards
AtlasDENRID40295ch12q24
Entrez_Gene (NCBI)DENR  8562  density regulated re-initiation and release factor
AliasesDRP; DRP1; SMAP-3
GeneCards (Weizmann)DENR
Ensembl hg19 (Hinxton)ENSG00000139726 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000139726 [Gene_View]  chr12:122752821-122771064 [Contig_View]  DENR [Vega]
ICGC DataPortalENSG00000139726
TCGA cBioPortalDENR
AceView (NCBI)DENR
Genatlas (Paris)DENR
WikiGenes8562
SOURCE (Princeton)DENR
Genetics Home Reference (NIH)DENR
Genomic and cartography
GoldenPath hg38 (UCSC)DENR  -     chr12:122752821-122771064 +  12q24.31   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)DENR  -     12q24.31   [Description]    (hg19-Feb_2009)
EnsemblDENR - 12q24.31 [CytoView hg19]  DENR - 12q24.31 [CytoView hg38]
Mapping of homologs : NCBIDENR [Mapview hg19]  DENR [Mapview hg38]
OMIM604550   
Gene and transcription
Genbank (Entrez)AB014731 AF038554 AF103800 AI093093 AI093455
RefSeq transcript (Entrez)NM_003677
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)DENR
Cluster EST : UnigeneHs.22393 [ NCBI ]
CGAP (NCI)Hs.22393
Alternative Splicing GalleryENSG00000139726
Gene ExpressionDENR [ NCBI-GEO ]   DENR [ EBI - ARRAY_EXPRESS ]   DENR [ SEEK ]   DENR [ MEM ]
Gene Expression Viewer (FireBrowse)DENR [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)8562
GTEX Portal (Tissue expression)DENR
Human Protein AtlasENSG00000139726-DENR [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO43583   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO43583  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO43583
Splice isoforms : SwissVarO43583
PhosPhoSitePlusO43583
Domaine pattern : Prosite (Expaxy)SUI1 (PS50296)   
Domains : Interpro (EBI)Drp1    SUI1    SUI1_arc_bac   
Domain families : Pfam (Sanger)SUI1 (PF01253)   
Domain families : Pfam (NCBI)pfam01253   
Conserved Domain (NCBI)DENR
DMDM Disease mutations8562
Blocks (Seattle)DENR
SuperfamilyO43583
Human Protein Atlas [tissue]ENSG00000139726-DENR [tissue]
Peptide AtlasO43583
HPRD05182
IPIIPI00306280   IPI00940755   
Protein Interaction databases
DIP (DOE-UCLA)O43583
IntAct (EBI)O43583
FunCoupENSG00000139726
BioGRIDDENR
STRING (EMBL)DENR
ZODIACDENR
Ontologies - Pathways
QuickGOO43583
Ontology : AmiGOformation of translation preinitiation complex  translation reinitiation  IRES-dependent translational initiation  molecular_function  mRNA binding  translation initiation factor activity  protein binding  cellular_component  ribosome  ribosome disassembly  ribosome binding  translation initiation complex  
Ontology : EGO-EBIformation of translation preinitiation complex  translation reinitiation  IRES-dependent translational initiation  molecular_function  mRNA binding  translation initiation factor activity  protein binding  cellular_component  ribosome  ribosome disassembly  ribosome binding  translation initiation complex  
NDEx NetworkDENR
Atlas of Cancer Signalling NetworkDENR
Wikipedia pathwaysDENR
Orthology - Evolution
OrthoDB8562
GeneTree (enSembl)ENSG00000139726
Phylogenetic Trees/Animal Genes : TreeFamDENR
HOVERGENO43583
HOGENOMO43583
Homologs : HomoloGeneDENR
Homology/Alignments : Family Browser (UCSC)DENR
Gene fusions - Rearrangements
Fusion : MitelmanDENR/KNTC1 [12q24.31/12q24.31]  
Fusion: TCGA_MDACCDENR 12q24.31 KNTC1 12q24.31 LUAD
Tumor Fusion PortalDENR
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerDENR [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)DENR
dbVarDENR
ClinVarDENR
1000_GenomesDENR 
Exome Variant ServerDENR
ExAC (Exome Aggregation Consortium)ENSG00000139726
GNOMAD BrowserENSG00000139726
Genetic variants : HAPMAP8562
Genomic Variants (DGV)DENR [DGVbeta]
DECIPHERDENR [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisDENR 
Mutations
ICGC Data PortalDENR 
TCGA Data PortalDENR 
Broad Tumor PortalDENR
OASIS PortalDENR [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICDENR  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDDENR
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch DENR
DgiDB (Drug Gene Interaction Database)DENR
DoCM (Curated mutations)DENR (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)DENR (select a term)
intoGenDENR
NCG5 (London)DENR
Cancer3DDENR(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM604550   
Orphanet
DisGeNETDENR
MedgenDENR
Genetic Testing Registry DENR
NextProtO43583 [Medical]
TSGene8562
GENETestsDENR
Target ValidationDENR
Huge Navigator DENR [HugePedia]
snp3D : Map Gene to Disease8562
BioCentury BCIQDENR
ClinGenDENR
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD8562
Chemical/Pharm GKB GenePA27252
Clinical trialDENR
Miscellaneous
canSAR (ICR)DENR (select the gene name)
Probes
Litterature
PubMed22 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineDENR
EVEXDENR
GoPubMedDENR
iHOPDENR
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Nov 21 14:48:22 CET 2017

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