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

DDX43 (DEAD (Asp-Glu-Ala-Asp) box polypeptide 43)

Written2007-01Etienne De Plaen
Ludwig Institute for Cancer Research- Brussels branch, Avenue Hippocrate 74 - UCL 7459, B-1200 Brussels, Belgium

(Note : for Links provided by Atlas : click)

Identity

Alias_namesDEAD (Asp-Glu-Ala-Asp) box polypeptide 43
Alias_symbol (synonym)HAGE
DKFZp434H2114
CT13
Other aliasHAGE (for Helicase AntiGEn)
HGNC (Hugo) DDX43
LocusID (NCBI) 55510
Atlas_Id 40288
Location 6q13  [Link to chromosome band 6q13]
Location_base_pair Starts at 73394562 and ends at 73417566 bp from pter ( according to hg19-Feb_2009)  [Mapping DDX43.png]
Local_order between markers GATA11B08 and D6S284
 
  Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
DDX43 (6q13) / NUDCD3 (7p13)
Note This gene was isolated as a cDNA by applying a subtraction approach named representational difference analysis (RDA). Rhabdomyosarcoma LB23-SAR was used as the source of tester cDNA that was subtracted with driver cDNA, a mixture of human uterus, breast, heart, and colon cDNA.

DNA/RNA

Transcription The transcript is about 2.2 kb. Gene HAGE is weakly transcribed in normal tissues: the level of expression was estimated to represent only 0.2% of the level found in the LB23-SAR reference cell line. The only exception is testis, which shows a level of expression comparable to that of LB23-SAR. Gene HAGE was found to be expressed in 90 out of 383 tumor samples of different histological types, well above the level in normal tissues; about 5% of the positive samples showed a level of expression above 10% of the level of LB23-SAR, and 7% showed a level of expression between 1-10%. Expression of HAGE was induced in fibroblasts after treatment with the demethylating agent, 5-aza-2'-deoxycytidine.

Protein

Description The largest open reading frame comprises 1,944 nucleotides and encodes a protein of 648 amino acids (72,871 Da). The pKi of the protein is 9.29.
Function Comparison with databases revealed that HAGE shows 55% similarity with the human p68 protein, an ATP-dependent RNA helicase that is a member of the DEAD-box proteins. Four motifs that are present in members of the DEAD box family are conserved in the HAGE protein. However, ATPase and helicase activities of HAGE were not demonstrated.

Mutations

Note No mutation was observed in the HAGE cDNA isolated from LB23-SAR.

Implicated in

Note
  
Entity Tumors
Note HAGE expression can be induced by demethylating agent 5-azadeoxycytidine, suggesting that demethylation plays a role in the activation of these genes in tumors. Activation of HAGE in tumor cells most likely results therefore from the genome-wide demethylation process that is known to occur in these cells.
Oncogenesis HAGE is not the first case of a DEAD-box protein that is overexpressed in tumors. Moreover, it worth noting that one out of 42 discovered mutated human tumor antigens is produced by a point mutation in a gene named MUM-3. This gene encodes a protein with homology with members of the RNA helicase family. These observations suggest that mutated or overexpressed helicases may contribute to tumoral transformation or progression.
  

Bibliography

Frequent expression of HAGE in presentation chronic myeloid leukaemias.
Adams SP, Sahota SS, Mijovic A, Czepulkowski B, Padua RA, Mufti GJ, Guinn BA
Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, U.K. 2002 ; 16 (11) : 2238-2242.
PMID 12399967
 
High frequency of autologous anti-melanoma CTL directed against an antigen generated by a point mutation in a new helicase gene.
Baurain JF, Colau D, van Baren N, Landry C, Martelange V, Vikkula M, Boon T, Coulie PG
Journal of immunology (Baltimore, Md. : 1950). 2000 ; 164 (11) : 6057-6066.
PMID 10820291
 
Identification on a human sarcoma of two new genes with tumor-specific expression.
Martelange V, De Smet C, De Plaen E, Lurquin C, Boon T
Cancer research. 2000 ; 60 (14) : 3848-3855.
PMID 10919659
 
Analysis of the tumour suppressor genes, FHIT and WT-1, and the tumour rejection genes, BAGE, GAGE-1/2, HAGE, MAGE-1, and MAGE-3, in benign and malignant neoplasms of the salivary glands.
Nagel H, Laskawi R, Eiffert H, Schlott T
Molecular pathology : MP. 2003 ; 56 (4) : 226-231.
PMID 12890744
 

Citation

This paper should be referenced as such :
De Plaen, E
DDX43 (DEAD (Asp-Glu-Ala-Asp) box polypeptide 43)
Atlas Genet Cytogenet Oncol Haematol. 2007;11(2):119-120.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/DDX43ID40288ch6q13.html


External links

Nomenclature
HGNC (Hugo)DDX43   18677
Cards
AtlasDDX43ID40288ch6q13
Entrez_Gene (NCBI)DDX43  55510  DEAD-box helicase 43
AliasesCT13; HAGE
GeneCards (Weizmann)DDX43
Ensembl hg19 (Hinxton)ENSG00000080007 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000080007 [Gene_View]  chr6:73394562-73417566 [Contig_View]  DDX43 [Vega]
ICGC DataPortalENSG00000080007
TCGA cBioPortalDDX43
AceView (NCBI)DDX43
Genatlas (Paris)DDX43
WikiGenes55510
SOURCE (Princeton)DDX43
Genetics Home Reference (NIH)DDX43
Genomic and cartography
GoldenPath hg38 (UCSC)DDX43  -     chr6:73394562-73417566 +  6q13   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)DDX43  -     6q13   [Description]    (hg19-Feb_2009)
EnsemblDDX43 - 6q13 [CytoView hg19]  DDX43 - 6q13 [CytoView hg38]
Mapping of homologs : NCBIDDX43 [Mapview hg19]  DDX43 [Mapview hg38]
OMIM606286   
Gene and transcription
Genbank (Entrez)AJ278110 AK303324 AK313686 AL136751 AM393499
RefSeq transcript (Entrez)NM_018665
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)DDX43
Cluster EST : UnigeneHs.125507 [ NCBI ]
CGAP (NCI)Hs.125507
Alternative Splicing GalleryENSG00000080007
Gene ExpressionDDX43 [ NCBI-GEO ]   DDX43 [ EBI - ARRAY_EXPRESS ]   DDX43 [ SEEK ]   DDX43 [ MEM ]
Gene Expression Viewer (FireBrowse)DDX43 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)55510
GTEX Portal (Tissue expression)DDX43
Human Protein AtlasENSG00000080007-DDX43 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9NXZ2   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9NXZ2  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9NXZ2
Splice isoforms : SwissVarQ9NXZ2
Catalytic activity : Enzyme3.6.4.13 [ Enzyme-Expasy ]   3.6.4.133.6.4.13 [ IntEnz-EBI ]   3.6.4.13 [ BRENDA ]   3.6.4.13 [ KEGG ]   
PhosPhoSitePlusQ9NXZ2
Domaine pattern : Prosite (Expaxy)DEAD_ATP_HELICASE (PS00039)    HELICASE_ATP_BIND_1 (PS51192)    HELICASE_CTER (PS51194)    KH_TYPE_1 (PS50084)    Q_MOTIF (PS51195)   
Domains : Interpro (EBI)DEAD/DEAH_box_helicase_dom    Helicase_ATP-bd    Helicase_C    KH_dom    KH_dom_type_1    P-loop_NTPase    RNA-helicase_DEAD-box_CS    RNA_helicase_DEAD_Q_motif   
Domain families : Pfam (Sanger)DEAD (PF00270)    Helicase_C (PF00271)    KH_1 (PF00013)   
Domain families : Pfam (NCBI)pfam00270    pfam00271    pfam00013   
Domain families : Smart (EMBL)DEXDc (SM00487)  HELICc (SM00490)  KH (SM00322)  
Conserved Domain (NCBI)DDX43
DMDM Disease mutations55510
Blocks (Seattle)DDX43
SuperfamilyQ9NXZ2
Human Protein Atlas [tissue]ENSG00000080007-DDX43 [tissue]
Peptide AtlasQ9NXZ2
HPRD10448
IPIIPI00032899   IPI01010634   
Protein Interaction databases
DIP (DOE-UCLA)Q9NXZ2
IntAct (EBI)Q9NXZ2
FunCoupENSG00000080007
BioGRIDDDX43
STRING (EMBL)DDX43
ZODIACDDX43
Ontologies - Pathways
QuickGOQ9NXZ2
Ontology : AmiGORNA binding  ATP-dependent RNA helicase activity  ATP binding  intracellular  RNA secondary structure unwinding  
Ontology : EGO-EBIRNA binding  ATP-dependent RNA helicase activity  ATP binding  intracellular  RNA secondary structure unwinding  
NDEx NetworkDDX43
Atlas of Cancer Signalling NetworkDDX43
Wikipedia pathwaysDDX43
Orthology - Evolution
OrthoDB55510
GeneTree (enSembl)ENSG00000080007
Phylogenetic Trees/Animal Genes : TreeFamDDX43
HOVERGENQ9NXZ2
HOGENOMQ9NXZ2
Homologs : HomoloGeneDDX43
Homology/Alignments : Family Browser (UCSC)DDX43
Gene fusions - Rearrangements
Tumor Fusion PortalDDX43
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerDDX43 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)DDX43
dbVarDDX43
ClinVarDDX43
1000_GenomesDDX43 
Exome Variant ServerDDX43
ExAC (Exome Aggregation Consortium)ENSG00000080007
GNOMAD BrowserENSG00000080007
Genetic variants : HAPMAP55510
Genomic Variants (DGV)DDX43 [DGVbeta]
DECIPHERDDX43 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisDDX43 
Mutations
ICGC Data PortalDDX43 
TCGA Data PortalDDX43 
Broad Tumor PortalDDX43
OASIS PortalDDX43 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICDDX43  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDDDX43
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 DDX43
DgiDB (Drug Gene Interaction Database)DDX43
DoCM (Curated mutations)DDX43 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)DDX43 (select a term)
intoGenDDX43
NCG5 (London)DDX43
Cancer3DDDX43(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM606286   
Orphanet
DisGeNETDDX43
MedgenDDX43
Genetic Testing Registry DDX43
NextProtQ9NXZ2 [Medical]
TSGene55510
GENETestsDDX43
Target ValidationDDX43
Huge Navigator DDX43 [HugePedia]
snp3D : Map Gene to Disease55510
BioCentury BCIQDDX43
ClinGenDDX43
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD55510
Chemical/Pharm GKB GenePA134988734
Clinical trialDDX43
Miscellaneous
canSAR (ICR)DDX43 (select the gene name)
Probes
Litterature
PubMed25 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineDDX43
EVEXDDX43
GoPubMedDDX43
iHOPDDX43
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 : Tue Nov 21 14:48:18 CET 2017

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.