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TARDBP (TAR DNA binding protein)

Identity

Alias_symbol (synonym)TDP-43
ALS10
HGNC (Hugo) TARDBP
LocusID (NCBI) 23435
Atlas_Id 51706
Location 1p36.22  [Link to chromosome band 1p36]
Location_base_pair Starts at 11072679 and ends at 11085549 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
C11orf80 (11q13.2) / TARDBP (1p36.22)GNB1 (1p36.33) / TARDBP (1p36.22)PDLIM5 (4q22.3) / TARDBP (1p36.22)
RUNX1 (21q22.12) / TARDBP (1p36.22)TARDBP (1p36.22) / LRCH3 (3q29)TARDBP (1p36.22) / XRN2 (20p11.23)

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)TARDBP   11571
LRG (Locus Reference Genomic)LRG_659
Cards
Entrez_Gene (NCBI)TARDBP  23435  TAR DNA binding protein
AliasesALS10; TDP-43
GeneCards (Weizmann)TARDBP
Ensembl hg19 (Hinxton)ENSG00000120948 [Gene_View]  chr1:11072679-11085549 [Contig_View]  TARDBP [Vega]
Ensembl hg38 (Hinxton)ENSG00000120948 [Gene_View]  chr1:11072679-11085549 [Contig_View]  TARDBP [Vega]
ICGC DataPortalENSG00000120948
TCGA cBioPortalTARDBP
AceView (NCBI)TARDBP
Genatlas (Paris)TARDBP
WikiGenes23435
SOURCE (Princeton)TARDBP
Genetics Home Reference (NIH)TARDBP
Genomic and cartography
GoldenPath hg19 (UCSC)TARDBP  -     chr1:11072679-11085549 +  1p36.22   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)TARDBP  -     1p36.22   [Description]    (hg38-Dec_2013)
EnsemblTARDBP - 1p36.22 [CytoView hg19]  TARDBP - 1p36.22 [CytoView hg38]
Mapping of homologs : NCBITARDBP [Mapview hg19]  TARDBP [Mapview hg38]
OMIM605078   612069   
Gene and transcription
Genbank (Entrez)AF311304 AK222754 AK295920 AK299454 AK312416
RefSeq transcript (Entrez)NM_007375
RefSeq genomic (Entrez)NC_000001 NC_018912 NG_008734 NT_032977 NW_004929289
Consensus coding sequences : CCDS (NCBI)TARDBP
Cluster EST : UnigeneHs.300624 [ NCBI ]
CGAP (NCI)Hs.300624
Alternative Splicing GalleryENSG00000120948
Gene ExpressionTARDBP [ NCBI-GEO ]   TARDBP [ EBI - ARRAY_EXPRESS ]   TARDBP [ SEEK ]   TARDBP [ MEM ]
Gene Expression Viewer (FireBrowse)TARDBP [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)23435
GTEX Portal (Tissue expression)TARDBP
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ13148   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ13148  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ13148
Splice isoforms : SwissVarQ13148
PhosPhoSitePlusQ13148
Domaine pattern : Prosite (Expaxy)RRM (PS50102)   
Domains : Interpro (EBI)Nucleotide-bd_a/b_plait    RRM_dom   
Domain families : Pfam (Sanger)RRM_1 (PF00076)   
Domain families : Pfam (NCBI)pfam00076   
Domain families : Smart (EMBL)RRM (SM00360)  
Conserved Domain (NCBI)TARDBP
DMDM Disease mutations23435
Blocks (Seattle)TARDBP
PDB (SRS)1WF0    2CQG    2N2C    2N4P    4BS2    4IUF   
PDB (PDBSum)1WF0    2CQG    2N2C    2N4P    4BS2    4IUF   
PDB (IMB)1WF0    2CQG    2N2C    2N4P    4BS2    4IUF   
PDB (RSDB)1WF0    2CQG    2N2C    2N4P    4BS2    4IUF   
Structural Biology KnowledgeBase1WF0    2CQG    2N2C    2N4P    4BS2    4IUF   
SCOP (Structural Classification of Proteins)1WF0    2CQG    2N2C    2N4P    4BS2    4IUF   
CATH (Classification of proteins structures)1WF0    2CQG    2N2C    2N4P    4BS2    4IUF   
SuperfamilyQ13148
Human Protein AtlasENSG00000120948
Peptide AtlasQ13148
HPRD05466
IPIIPI00971018   IPI00025815   IPI00844544   IPI00910355   IPI00009928   IPI00977115   IPI00639819   
Protein Interaction databases
DIP (DOE-UCLA)Q13148
IntAct (EBI)Q13148
FunCoupENSG00000120948
BioGRIDTARDBP
STRING (EMBL)TARDBP
ZODIACTARDBP
Ontologies - Pathways
QuickGOQ13148
Ontology : AmiGOnucleotide binding  transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific binding  negative regulation of protein phosphorylation  double-stranded DNA binding  transcription factor activity, sequence-specific DNA binding  RNA binding  mRNA 3'-UTR binding  protein binding  nucleus  nucleoplasm  perichromatin fibrils  cytoplasm  transcription from RNA polymerase II promoter  mRNA processing  RNA splicing  negative regulation of gene expression  nuclear speck  nuclear fragmentation involved in apoptotic nuclear change  positive regulation of insulin secretion  response to endoplasmic reticulum stress  interchromatin granule  identical protein binding  negative regulation by host of viral transcription  poly(A) RNA binding  positive regulation of transcription from RNA polymerase II promoter  regulation of cell cycle  3'-UTR-mediated mRNA stabilization  nuclear inner membrane organization  
Ontology : EGO-EBInucleotide binding  transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific binding  negative regulation of protein phosphorylation  double-stranded DNA binding  transcription factor activity, sequence-specific DNA binding  RNA binding  mRNA 3'-UTR binding  protein binding  nucleus  nucleoplasm  perichromatin fibrils  cytoplasm  transcription from RNA polymerase II promoter  mRNA processing  RNA splicing  negative regulation of gene expression  nuclear speck  nuclear fragmentation involved in apoptotic nuclear change  positive regulation of insulin secretion  response to endoplasmic reticulum stress  interchromatin granule  identical protein binding  negative regulation by host of viral transcription  poly(A) RNA binding  positive regulation of transcription from RNA polymerase II promoter  regulation of cell cycle  3'-UTR-mediated mRNA stabilization  nuclear inner membrane organization  
NDEx NetworkTARDBP
Atlas of Cancer Signalling NetworkTARDBP
Wikipedia pathwaysTARDBP
Orthology - Evolution
OrthoDB23435
GeneTree (enSembl)ENSG00000120948
Phylogenetic Trees/Animal Genes : TreeFamTARDBP
HOVERGENQ13148
HOGENOMQ13148
Homologs : HomoloGeneTARDBP
Homology/Alignments : Family Browser (UCSC)TARDBP
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerTARDBP [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)TARDBP
dbVarTARDBP
ClinVarTARDBP
1000_GenomesTARDBP 
Exome Variant ServerTARDBP
ExAC (Exome Aggregation Consortium)TARDBP (select the gene name)
Genetic variants : HAPMAP23435
Genomic Variants (DGV)TARDBP [DGVbeta]
DECIPHER (Syndromes)1:11072679-11085549  ENSG00000120948
CONAN: Copy Number AnalysisTARDBP 
Mutations
ICGC Data PortalTARDBP 
TCGA Data PortalTARDBP 
Broad Tumor PortalTARDBP
OASIS PortalTARDBP [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICTARDBP  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDTARDBP
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
LOVD (Leiden Open Variation Database)Mendelian genes
BioMutasearch TARDBP
DgiDB (Drug Gene Interaction Database)TARDBP
DoCM (Curated mutations)TARDBP (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)TARDBP (select a term)
intoGenTARDBP
Cancer3DTARDBP(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM605078    612069   
Orphanet106    20341   
MedgenTARDBP
Genetic Testing Registry TARDBP
NextProtQ13148 [Medical]
TSGene23435
GENETestsTARDBP
Huge Navigator TARDBP [HugePedia]
snp3D : Map Gene to Disease23435
BioCentury BCIQTARDBP
ClinGenTARDBP
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD23435
Chemical/Pharm GKB GenePA36336
Clinical trialTARDBP
Miscellaneous
canSAR (ICR)TARDBP (select the gene name)
Probes
Litterature
PubMed437 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineTARDBP
EVEXTARDBP
GoPubMedTARDBP
iHOPTARDBP
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 : Fri Nov 18 19:53:17 CET 2016

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