Atlas of Genetics and Cytogenetics in Oncology and Haematology


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SETX (senataxin)

Identity

Alias_namesALS4
SCAR1
amyotrophic lateral sclerosis 4
spinocerebellar ataxia, recessive, non-Friedreich type 1
Alias_symbol (synonym)KIAA0625
AOA2
Other aliasbA479K20.2
HGNC (Hugo) SETX
LocusID (NCBI) 23064
Atlas_Id 47714
Location 9q34.13  [Link to chromosome band 9q34]
Location_base_pair Starts at 132261440 and ends at 132354985 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
MYO10 (5p15.1) / SETX (9q34.13)PIK3R2 (19p13.11) / SETX (9q34.13)SETX (9q34.13) / FAM172A (5q15)
SETX (9q34.13) / PATJ (1p31.3)SETX (9q34.13) / PDE1C (7p14.3)SETX (9q34.13) / SETX (9q34.13)
SETX (9q34.13) / TNRC6A (16p12.1)SETX (9q34.13) / TTF1 (9q34.13)SETX 9q34.13 / TTF1 9q34.13

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)SETX   445
LRG (Locus Reference Genomic)LRG_268
Cards
Entrez_Gene (NCBI)SETX  23064  senataxin
AliasesALS4; AOA2; SCAR1; bA479K20.2
GeneCards (Weizmann)SETX
Ensembl hg19 (Hinxton)ENSG00000107290 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000107290 [Gene_View]  chr9:132261440-132354985 [Contig_View]  SETX [Vega]
ICGC DataPortalENSG00000107290
TCGA cBioPortalSETX
AceView (NCBI)SETX
Genatlas (Paris)SETX
WikiGenes23064
SOURCE (Princeton)SETX
Genetics Home Reference (NIH)SETX
Genomic and cartography
GoldenPath hg38 (UCSC)SETX  -     chr9:132261440-132354985 -  9q34.13   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SETX  -     9q34.13   [Description]    (hg19-Feb_2009)
EnsemblSETX - 9q34.13 [CytoView hg19]  SETX - 9q34.13 [CytoView hg38]
Mapping of homologs : NCBISETX [Mapview hg19]  SETX [Mapview hg38]
OMIM602433   606002   608465   
Gene and transcription
Genbank (Entrez)AB014525 AK001456 AK022902 AK024331 AK025601
RefSeq transcript (Entrez)NM_015046
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SETX
Cluster EST : UnigeneHs.460317 [ NCBI ]
CGAP (NCI)Hs.460317
Alternative Splicing GalleryENSG00000107290
Gene ExpressionSETX [ NCBI-GEO ]   SETX [ EBI - ARRAY_EXPRESS ]   SETX [ SEEK ]   SETX [ MEM ]
Gene Expression Viewer (FireBrowse)SETX [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)23064
GTEX Portal (Tissue expression)SETX
Human Protein AtlasENSG00000107290-SETX [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ7Z333   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ7Z333  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ7Z333
Splice isoforms : SwissVarQ7Z333
Catalytic activity : Enzyme3.6.4.- [ Enzyme-Expasy ]   3.6.4.-3.6.4.- [ IntEnz-EBI ]   3.6.4.- [ BRENDA ]   3.6.4.- [ KEGG ]   
PhosPhoSitePlusQ7Z333
Domains : Interpro (EBI)P-loop_NTPase    Senataxin   
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Conserved Domain (NCBI)SETX
DMDM Disease mutations23064
Blocks (Seattle)SETX
SuperfamilyQ7Z333
Human Protein Atlas [tissue]ENSG00000107290-SETX [tissue]
Peptide AtlasQ7Z333
HPRD07622
IPIIPI00142538   IPI00719643   IPI00646645   
Protein Interaction databases
DIP (DOE-UCLA)Q7Z333
IntAct (EBI)Q7Z333
FunCoupENSG00000107290
BioGRIDSETX
STRING (EMBL)SETX
ZODIACSETX
Ontologies - Pathways
QuickGOQ7Z333
Ontology : AmiGOMAPK cascade  nuclear chromosome  chromosome, telomeric region  transcription termination site sequence-specific DNA binding  DNA binding  DNA helicase activity  protein binding  ATP binding  nucleus  nucleoplasm  nucleolus  cytoplasm  double-strand break repair  DNA recombination  DNA-templated transcription, termination  termination of RNA polymerase II transcription  mRNA splice site selection  RNA processing  cellular response to DNA damage stimulus  spermatogenesis  circadian rhythm  fibroblast growth factor receptor signaling pathway  positive regulation of neuron projection development  nuclear body  axon  growth cone  DNA duplex unwinding  positive regulation of RNA splicing  cellular response to oxidative stress  identical protein binding  negative regulation of apoptotic process  protein kinase B signaling  cellular response to fibroblast growth factor stimulus  intercellular bridge  positive regulation of transcription from RNA polymerase II promoter  positive regulation of DNA-templated transcription, termination  cellular response to hydrogen peroxide  cellular response to retinoic acid  positive regulation of DNA-templated transcription, initiation  positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled  
Ontology : EGO-EBIMAPK cascade  nuclear chromosome  chromosome, telomeric region  transcription termination site sequence-specific DNA binding  DNA binding  DNA helicase activity  protein binding  ATP binding  nucleus  nucleoplasm  nucleolus  cytoplasm  double-strand break repair  DNA recombination  DNA-templated transcription, termination  termination of RNA polymerase II transcription  mRNA splice site selection  RNA processing  cellular response to DNA damage stimulus  spermatogenesis  circadian rhythm  fibroblast growth factor receptor signaling pathway  positive regulation of neuron projection development  nuclear body  axon  growth cone  DNA duplex unwinding  positive regulation of RNA splicing  cellular response to oxidative stress  identical protein binding  negative regulation of apoptotic process  protein kinase B signaling  cellular response to fibroblast growth factor stimulus  intercellular bridge  positive regulation of transcription from RNA polymerase II promoter  positive regulation of DNA-templated transcription, termination  cellular response to hydrogen peroxide  cellular response to retinoic acid  positive regulation of DNA-templated transcription, initiation  positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled  
NDEx NetworkSETX
Atlas of Cancer Signalling NetworkSETX
Wikipedia pathwaysSETX
Orthology - Evolution
OrthoDB23064
GeneTree (enSembl)ENSG00000107290
Phylogenetic Trees/Animal Genes : TreeFamSETX
HOVERGENQ7Z333
HOGENOMQ7Z333
Homologs : HomoloGeneSETX
Homology/Alignments : Family Browser (UCSC)SETX
Gene fusions - Rearrangements
Fusion : MitelmanSETX/TTF1 [9q34.13/9q34.13]  
Fusion: TCGA_MDACCSETX 9q34.13 TTF1 9q34.13 HNSC
Tumor Fusion PortalSETX
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSETX [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SETX
dbVarSETX
ClinVarSETX
1000_GenomesSETX 
Exome Variant ServerSETX
ExAC (Exome Aggregation Consortium)ENSG00000107290
GNOMAD BrowserENSG00000107290
Genetic variants : HAPMAP23064
Genomic Variants (DGV)SETX [DGVbeta]
DECIPHERSETX [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSETX 
Mutations
ICGC Data PortalSETX 
TCGA Data PortalSETX 
Broad Tumor PortalSETX
OASIS PortalSETX [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSETX  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSETX
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)Leiden Muscular Dystrophy pages
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)Mendelian genes
BioMutasearch SETX
DgiDB (Drug Gene Interaction Database)SETX
DoCM (Curated mutations)SETX (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SETX (select a term)
intoGenSETX
Cancer3DSETX(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM602433    606002    608465   
Orphanet22199    10857   
DisGeNETSETX
MedgenSETX
Genetic Testing Registry SETX
NextProtQ7Z333 [Medical]
TSGene23064
GENETestsSETX
Target ValidationSETX
Huge Navigator SETX [HugePedia]
snp3D : Map Gene to Disease23064
BioCentury BCIQSETX
ClinGenSETX
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD23064
Chemical/Pharm GKB GenePA24751
Clinical trialSETX
Miscellaneous
canSAR (ICR)SETX (select the gene name)
Probes
Litterature
PubMed64 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSETX
EVEXSETX
GoPubMedSETX
iHOPSETX
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 : Tue Nov 21 14:34:17 CET 2017

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