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Aliases for SETX Gene

Aliases for SETX Gene

  • Senataxin 2 3 4 5
  • Amyotrophic Lateral Sclerosis 4 Protein 3 4
  • SEN1 Homolog 3 4
  • SCAR1 3 4
  • ALS4 3 4
  • Spinocerebellar Ataxia, Recessive, Non-Friedreich Type 1 2
  • Amyotrophic Lateral Sclerosis 4 2
  • BA479K20.2 3
  • EC 3.6.4.- 4
  • KIAA0625 4
  • EC 3.6.1 63
  • AOA2 3

External Ids for SETX Gene

Previous HGNC Symbols for SETX Gene

  • ALS4
  • SCAR1

Previous GeneCards Identifiers for SETX Gene

  • GC09M132170
  • GC09M134129
  • GC09M135136
  • GC09M104630

Summaries for SETX Gene

Entrez Gene Summary for SETX Gene

  • This gene encodes a protein named for its homology to the Sen1p protein of fungi which has RNA helicase activity encoded by a domain at the C-terminal end of the protein. The protein encoded by this gene contains a DNA/RNA helicase domain at its C-terminal end which suggests that it may be involved in both DNA and RNA processing. Mutations in this gene have been associated with ataxia-ocular apraxia-2 (AOA2) and an autosomal dominant form of juvenile amyotrophic lateral sclerosis (ALS4). [provided by RefSeq, Jul 2008]

GeneCards Summary for SETX Gene

SETX (Senataxin) is a Protein Coding gene. Diseases associated with SETX include spinocerebellar ataxia, autosomal recessive 1 and amyotrophic lateral sclerosis 4, juvenile. GO annotations related to this gene include identical protein binding and transcription termination site sequence-specific DNA binding.

UniProtKB/Swiss-Prot for SETX Gene

  • Probable RNA/DNA helicase involved in diverse aspects of RNA metabolism and genomic integrity. Plays a role in transcription regulation by its ability to modulate RNA Polymerase II (Pol II) binding to chromatin and through its interaction with proteins involved in transcription (PubMed:19515850, PubMed:21700224). Contributes to the mRNA splicing efficiency and splice site selection (PubMed:19515850). Required for the resolution of R-loop RNA-DNA hybrid formation at G-rich pause sites located downstream of the poly(A) site, allowing XRN2 recruitment and XRN2-mediated degradation of the downstream cleaved RNA and hence efficient RNA polymerase II (RNAp II) transcription termination (PubMed:19515850, PubMed:21700224, PubMed:26700805). Required for the 3 transcriptional termination of PER1 and CRY2, thus playing an important role in the circadian rhythm regulation (By similarity). Involved in DNA double-strand breaks damage response generated by oxidative stress (PubMed:17562789). In association with RRP45, targets the RNA exosome complex to sites of transcription-induced DNA damage (PubMed:24105744). Plays a role in the development and maturation of germ cells: essential for male meiosis, acting at the interface of transcription and meiotic recombination, and in the process of gene silencing during meiotic sex chromosome inactivation (MSCI) (By similarity). May be involved in telomeric stability through the regulation of telomere repeat-containing RNA (TERRA) transcription (PubMed:21112256). Plays a role in neurite outgrowth in hippocampal cells through FGF8-activated signaling pathways. Inhibits retinoic acid-induced apoptosis (PubMed:21576111).

Gene Wiki entry for SETX Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SETX Gene

Genomics for SETX Gene

Regulatory Elements for SETX Gene

Genomic Location for SETX Gene

Chromosome:
9
Start:
132,261,356 bp from pter
End:
132,356,726 bp from pter
Size:
95,371 bases
Orientation:
Minus strand

Genomic View for SETX Gene

Genes around SETX on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SETX Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SETX Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SETX Gene

Proteins for SETX Gene

  • Protein details for SETX Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7Z333-SETX_HUMAN
    Recommended name:
    Probable helicase senataxin
    Protein Accession:
    Q7Z333
    Secondary Accessions:
    • A2A396
    • B2RPB2
    • B5ME16
    • C9JQ10
    • O75120
    • Q3KQX4
    • Q5JUJ1
    • Q68DW5
    • Q6AZD7
    • Q7Z3J6
    • Q8WX33
    • Q9H9D1
    • Q9NVP9

    Protein attributes for SETX Gene

    Size:
    2677 amino acids
    Molecular mass:
    302880 Da
    Quaternary structure:
    • Homodimer (PubMed:24244371). Interacts with PER2; the interaction inhibits termination of circadian target genes (By similarity). Interacts with CHD4, POLR2A, PRKDC and TRIM28 (PubMed:23149945). Does not interact with C14orf178 (PubMed:24244371). Interacts with UBE2I (PubMed:24105744). Interacts (via N-terminus domain) with EXOSC9 (via C-terminus region); the interaction enhances SETX sumoylation (PubMed:24105744). Interacts with NCL (via N-terminus domain) (PubMed:19515850). Interacts with PABPN1, PABPC1 and SF3B1 (PubMed:19515850). Interacts with SMN1/SMN2 and POLR2A; SMN1/SMN2 recruits SETX to POLR2A (PubMed:19515850, PubMed:26700805).
    SequenceCaution:
    • Sequence=BAA91701.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB14299.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAD97857.1; Type=Frameshift; Positions=1626; Evidence={ECO:0000305};

    Alternative splice isoforms for SETX Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SETX Gene

Proteomics data for SETX Gene at MOPED

Selected DME Specific Peptides for SETX Gene

Post-translational modifications for SETX Gene

Other Protein References for SETX Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

Domains & Families for SETX Gene

Gene Families for SETX Gene

Protein Domains for SETX Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SETX Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q7Z333

UniProtKB/Swiss-Prot:

SETX_HUMAN :
  • The N-terminus domain is necessary for S/G2 nuclear foci localization (PubMed:23149945).
  • Belongs to the DNA2/NAM7 helicase family.
Domain:
  • The N-terminus domain is necessary for S/G2 nuclear foci localization (PubMed:23149945).
Family:
  • Belongs to the DNA2/NAM7 helicase family.
genes like me logo Genes that share domains with SETX: view

Function for SETX Gene

Molecular function for SETX Gene

UniProtKB/Swiss-Prot Function:
Probable RNA/DNA helicase involved in diverse aspects of RNA metabolism and genomic integrity. Plays a role in transcription regulation by its ability to modulate RNA Polymerase II (Pol II) binding to chromatin and through its interaction with proteins involved in transcription (PubMed:19515850, PubMed:21700224). Contributes to the mRNA splicing efficiency and splice site selection (PubMed:19515850). Required for the resolution of R-loop RNA-DNA hybrid formation at G-rich pause sites located downstream of the poly(A) site, allowing XRN2 recruitment and XRN2-mediated degradation of the downstream cleaved RNA and hence efficient RNA polymerase II (RNAp II) transcription termination (PubMed:19515850, PubMed:21700224, PubMed:26700805). Required for the 3 transcriptional termination of PER1 and CRY2, thus playing an important role in the circadian rhythm regulation (By similarity). Involved in DNA double-strand breaks damage response generated by oxidative stress (PubMed:17562789). In association with RRP45, targets the RNA exosome complex to sites of transcription-induced DNA damage (PubMed:24105744). Plays a role in the development and maturation of germ cells: essential for male meiosis, acting at the interface of transcription and meiotic recombination, and in the process of gene silencing during meiotic sex chromosome inactivation (MSCI) (By similarity). May be involved in telomeric stability through the regulation of telomere repeat-containing RNA (TERRA) transcription (PubMed:21112256). Plays a role in neurite outgrowth in hippocampal cells through FGF8-activated signaling pathways. Inhibits retinoic acid-induced apoptosis (PubMed:21576111).

Enzyme Numbers (IUBMB) for SETX Gene

Gene Ontology (GO) - Molecular Function for SETX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IC 17562789
genes like me logo Genes that share ontologies with SETX: view
genes like me logo Genes that share phenotypes with SETX: view

Human Phenotype Ontology for SETX Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SETX Gene

MGI Knock Outs for SETX:

Animal Model Products

  • Taconic Biosciences Mouse Models for SETX

No data available for Transcription Factor Targets and HOMER Transcription for SETX Gene

Localization for SETX Gene

Subcellular locations from UniProtKB/Swiss-Prot for SETX Gene

Nucleus. Nucleus, nucleoplasm. Nucleus, nucleolus. Cytoplasm. Chromosome. Chromosome, telomere. Cell projection, axon. Cell projection, growth cone. Note=May be detected in the nucleolus only in cycling cells. At pachytene stage, colocalizes predominantly to the heterochromatic XY-body of sex chromosomes with DNA damage response proteins in a BRCA1-dependent manner (By similarity). Localizes with telomeric DNA in a transcription-dependent manner (PubMed:21112256). Under replication stress, colocalizes with a variety of DNA damage signaling and repair response proteins at distinct nuclear foci in mitotic S/G2- and G1-phase cells in a transcription- and RNA/DNA hybrid-dependent manner (PubMed:23149945). Localizes at limited number of nuclear foci (PubMed:24105744). Colocalizes with EXOSC9 in nuclear foci upon induction of transcription-related DNA damage at the S phase (PubMed:24105744). Most abundant in the nucleus. Detected in granules. Colocalized in cycling cells with FBL in the nucleolus. {ECO:0000250 UniProtKB:A2AKX3, ECO:0000269 PubMed:17562789, ECO:0000269 PubMed:21112256, ECO:0000269 PubMed:21576111, ECO:0000269 PubMed:23149945, ECO:0000269 PubMed:24105744}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SETX Gene COMPARTMENTS Subcellular localization image for SETX gene
Compartment Confidence
nucleus 5
cytosol 2
mitochondrion 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for SETX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA 17562789
genes like me logo Genes that share ontologies with SETX: view

Pathways & Interactions for SETX Gene

SuperPathways for SETX Gene

No Data Available

Gene Ontology (GO) - Biological Process for SETX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000165 MAPK cascade IDA 21576111
GO:0006353 DNA-templated transcription, termination IMP 26700805
GO:0006369 termination of RNA polymerase II transcription IEA --
GO:0006376 mRNA splice site selection IMP 19515850
GO:0006974 cellular response to DNA damage stimulus IDA 17562789
genes like me logo Genes that share ontologies with SETX: view

No data available for Pathways by source and SIGNOR curated interactions for SETX Gene

Drugs & Compounds for SETX Gene

(2) Additional Compounds for SETX Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SETX: view

Transcripts for SETX Gene

Unigene Clusters for SETX Gene

Senataxin:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SETX Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b · 13c ^ 14 ^ 15a · 15b ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^
SP1:
SP2:
SP3:
SP4: -
SP5: - - -
SP6: -
SP7:
SP8:

ExUns: 22a · 22b ^ 23 ^ 24a · 24b ^ 25a · 25b ^ 26a · 26b ^ 27 ^ 28 ^ 29 ^ 30a · 30b
SP1: - - -
SP2:
SP3: -
SP4:
SP5:
SP6:
SP7:
SP8:

Relevant External Links for SETX Gene

GeneLoc Exon Structure for
SETX
ECgene alternative splicing isoforms for
SETX

Expression for SETX Gene

mRNA expression in normal human tissues for SETX Gene

Protein differential expression in normal tissues from HIPED for SETX Gene

This gene is overexpressed in Platelet (22.3), Liver (11.3), and Placenta (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for SETX Gene



SOURCE GeneReport for Unigene cluster for SETX Gene Hs.460317

mRNA Expression by UniProt/SwissProt for SETX Gene

Q7Z333-SETX_HUMAN
Tissue specificity: Highly expressed in skeletal muscle. Expressed in heart, fibroblast, placenta and liver. Weakly expressed in brain and lung. Expressed in the cortex of the kidney (highly expressed in tubular epithelial cells but low expression in the glomerulus).
genes like me logo Genes that share expression patterns with SETX: view

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Protein tissue co-expression partners for SETX Gene

Orthologs for SETX Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SETX Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia SETX 35
  • 83.53 (n)
  • 78.06 (a)
SETX 36
  • 77 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SETX 35
  • 85.74 (n)
  • 81.14 (a)
SETX 36
  • 81 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Setx 35
  • 80.01 (n)
  • 73.57 (a)
Setx 16
Setx 36
  • 73 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SETX 35
  • 99.19 (n)
  • 98.61 (a)
SETX 36
  • 98 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Setx 35
  • 79.5 (n)
  • 72.69 (a)
oppossum
(Monodelphis domestica)
Mammalia SETX 36
  • 61 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SETX 36
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves SETX 35
  • 63.42 (n)
  • 56.13 (a)
SETX 36
  • 49 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SETX 36
  • 39 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia setx 35
  • 56.86 (n)
  • 50.64 (a)
zebrafish
(Danio rerio)
Actinopterygii setx 35
  • 50.32 (n)
  • 40.72 (a)
setx 36
  • 36 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG7504 36
  • 20 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SEN1 36
  • 17 (a)
OneToMany
SEN1 38
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 3 (a)
OneToOne
Species with no ortholog for SETX:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SETX Gene

ENSEMBL:
Gene Tree for SETX (if available)
TreeFam:
Gene Tree for SETX (if available)

Paralogs for SETX Gene

No data available for Paralogs for SETX Gene

Variants for SETX Gene

Sequence variations from dbSNP and Humsavar for SETX Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs28941475 Amyotrophic lateral sclerosis 4 (ALS4) 132,349,421(-) GAGCA(C/T)ATGTT nc-transcript-variant, reference, missense
VAR_018777 Spinocerebellar ataxia, autosomal recessive, 1 (SCAR1)
rs29001665 Spinocerebellar ataxia, autosomal recessive, 1 (SCAR1) 132,331,293(-) ATATA(C/T)GGAAC nc-transcript-variant, reference, missense
rs29001584 Amyotrophic lateral sclerosis 4 (ALS4) 132,330,432(-) AACAT(C/T)AGCCA nc-transcript-variant, reference, missense
VAR_018780 Spinocerebellar ataxia, autosomal recessive, 1 (SCAR1)

Structural Variations from Database of Genomic Variants (DGV) for SETX Gene

Variant ID Type Subtype PubMed ID
nsv509328 CNV Insertion 20534489
dgv8318n71 CNV Loss 21882294
nsv433506 CNV Loss 18776910
esv989756 CNV Deletion 20482838
esv2739126 CNV Deletion 23290073
esv1132189 CNV Deletion 17803354
nsv894020 CNV Gain 21882294
nsv894021 CNV Gain 21882294

Variation tolerance for SETX Gene

Residual Variation Intolerance Score: 7.08% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.44; 81.98% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SETX Gene

HapMap Linkage Disequilibrium report
SETX
Human Gene Mutation Database (HGMD)
SETX

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SETX Gene

Disorders for SETX Gene

MalaCards: The human disease database

(19) MalaCards diseases for SETX Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
spinocerebellar ataxia, autosomal recessive 1
  • ataxia with oculomotor apraxia type 2
amyotrophic lateral sclerosis 4, juvenile
  • amyotrophic lateral sclerosis 4
amyotrophic lateral sclerosis type 4
  • amyotrophic lateral sclerosis 4, juvenile
setx-related amyotrophic lateral sclerosis
  • amyotrophic lateral sclerosis 4, juvenile
apraxia
  • dyspraxia
- elite association - COSMIC cancer census association via MalaCards
Search SETX in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SETX_HUMAN
  • Amyotrophic lateral sclerosis 4 (ALS4) [MIM:602433]: A form of amyotrophic lateral sclerosis with childhood- or adolescent-onset, and characterized by slow disease progression and the sparing of bulbar and respiratory muscles. Amyotrophic lateral sclerosis is a neurodegenerative disorder affecting upper motor neurons in the brain and lower motor neurons in the brain stem and spinal cord, resulting in fatal paralysis. Sensory abnormalities are absent. The pathologic hallmarks of the disease include pallor of the corticospinal tract due to loss of motor neurons, presence of ubiquitin-positive inclusions within surviving motor neurons, and deposition of pathologic aggregates. The etiology of amyotrophic lateral sclerosis is likely to be multifactorial, involving both genetic and environmental factors. The disease is inherited in 5-10% of the cases. {ECO:0000269 PubMed:14770181, ECO:0000269 PubMed:15106121, ECO:0000269 PubMed:21190393, ECO:0000269 PubMed:24105744, ECO:0000269 PubMed:24244371}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Spinocerebellar ataxia, autosomal recessive, 1 (SCAR1) [MIM:606002]: Spinocerebellar ataxia is a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCAR1 is an autosomal recessive form associated with peripheral neuropathy and elevated serum alpha-fetoprotein, immunoglobulins and, less commonly, creatine kinase levels. Some SCAR1 patients manifest oculomotor apraxia. {ECO:0000269 PubMed:14770181, ECO:0000269 PubMed:16644229, ECO:0000269 PubMed:16717225, ECO:0000269 PubMed:17096168, ECO:0000269 PubMed:23566282, ECO:0000269 PubMed:23786967, ECO:0000269 PubMed:23941260, ECO:0000269 PubMed:24105744}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SETX

Genetic Association Database (GAD)
SETX
Human Genome Epidemiology (HuGE) Navigator
SETX
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SETX
genes like me logo Genes that share disorders with SETX: view

No data available for Genatlas for SETX Gene

Publications for SETX Gene

  1. In cis autosomal dominant mutation of Senataxin associated with tremor/ataxia syndrome. (PMID: 17096168) Bassuk A.G. … Bennett C.L. (Neurogenetics 2007) 3 4 23 67
  2. Characterization of two novel SETX mutations in AOA2 patients reveals aspects of the pathophysiological role of senataxin. (PMID: 19593598) Airoldi G. … Bassi M.T. (Neurogenetics 2010) 3 23
  3. A novel mutation in the senataxin gene identified in a Chinese patient with sporadic amyotrophic lateral sclerosis. (PMID: 19058054) Zhao Z.H. … Murong S.X. (Amyotroph Lateral Scler 2009) 3 23
  4. Ataxia with oculomotor apraxia type 2: a clinical and genetic study of 19 patients. (PMID: 19141356) Tazir M. … Koenig M. (J. Neurol. Sci. 2009) 3 23
  5. Exon deletions and intragenic insertions are not rare in ataxia with oculomotor apraxia 2. (PMID: 19744353) Bernard V. … ZA1hlke C. (BMC Med. Genet. 2009) 3 23

Products for SETX Gene

Sources for SETX Gene

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