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Aliases for SETX Gene

Aliases for SETX Gene

  • Senataxin 2 3 4
  • SCAR1 3 4 6
  • ALS4 3 4 6
  • Amyotrophic Lateral Sclerosis 4 Protein 3 4
  • SEN1 Homolog 3 4
  • AOA2 3 6
  • Spinocerebellar Ataxia, Recessive, Non-Friedreich Type 1 2
  • Amyotrophic Lateral Sclerosis 4 2
  • Probable Helicase Senataxin 3
  • BA479K20.2 3
  • EC 3.6.4.- 4
  • KIAA0625 4
  • EC 3.6.1 64

External Ids for SETX Gene

Previous Symbols for SETX Gene

  • ALS4
  • SCAR1

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 ataxia-ocular apraxia-2 and amyotrophic lateral sclerosis type 4. GO annotations related to this gene include DNA helicase activity. An important paralog of this gene is ZNFX1.

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). 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

Genomic Location for SETX Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SETX Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SETX Gene

Regulatory Elements 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, SF3B1 and SMN1 (PubMed:19515850). Interacts with the RNA polymerase II large subunit (PubMed:19515850).
    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:

Domains for SETX Gene

Protein Domains for SETX Gene

InterPro:
ProtoNet:

UniProtKB/Swiss-Prot:

SETX_HUMAN
Domain:
  • The N-terminus domain is necessary for S/G2 nuclear foci localization (PubMed:23149945).:
    • Q7Z333
Family:
  • Belongs to the DNA2/NAM7 helicase family.:
    • Q7Z333
genes like me logo Genes that share domains with SETX: view

No data available for Gene Families for SETX Gene

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). 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:0001147 transcription termination site sequence-specific DNA binding IDA 21700224
GO:0003677 DNA binding IC 17562789
GO:0003678 DNA helicase activity TAS 17562789
GO:0005515 protein binding IPI 19515850
GO:0005524 ATP binding IEA --
genes like me logo Genes that share ontologies with SETX: view

Phenotypes for SETX Gene

GenomeRNAi human phenotypes for SETX:
genes like me logo Genes that share phenotypes with SETX: view

miRNA for SETX Gene

miRTarBase miRNAs that target SETX

No data available for Animal Models , Transcription Factor Targeting 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:0000228 nuclear chromosome IDA 24105744
GO:0000781 chromosome, telomeric region IEA --
GO:0005634 nucleus IDA 17562789
GO:0005654 nucleoplasm IDA 17562789
GO:0005730 nucleolus IEA --
genes like me logo Genes that share ontologies with SETX: view

Pathways 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:0006302 double-strand break repair IDA 17562789
GO:0006310 DNA recombination IEA --
GO:0006369 termination of RNA polymerase II transcription IEA --
GO:0006376 mRNA splice site selection IMP 19515850
genes like me logo Genes that share ontologies with SETX: view

No data available for Pathways by source for SETX Gene

Compounds for SETX Gene

(2) Novoseek inferred chemical compound relationships for SETX Gene

Compound -log(P) Hits PubMed IDs
vitamin-e 31.4 3
alpha tocopherol 26 2
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

Integrated Proteomics: protein expression 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 expressions with SETX: view

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
chimpanzee
(Pan troglodytes)
Mammalia SETX 36
  • 99.19 (n)
  • 98.61 (a)
SETX 37
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SETX 36
  • 83.53 (n)
  • 78.06 (a)
SETX 37
  • 77 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SETX 36
  • 85.74 (n)
  • 81.14 (a)
SETX 37
  • 81 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Setx 36
  • 80.01 (n)
  • 73.57 (a)
Setx 16
Setx 37
  • 73 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SETX 37
  • 61 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SETX 37
  • 82 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Setx 36
  • 79.5 (n)
  • 72.69 (a)
chicken
(Gallus gallus)
Aves SETX 36
  • 63.42 (n)
  • 56.13 (a)
SETX 37
  • 49 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SETX 37
  • 39 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia setx 36
  • 56.86 (n)
  • 50.64 (a)
zebrafish
(Danio rerio)
Actinopterygii setx 36
  • 50.32 (n)
  • 40.72 (a)
setx 37
  • 36 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG7504 37
  • 20 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SEN1 37
  • 17 (a)
OneToMany
SEN1 39
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 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

Paralogs for SETX Gene

genes like me logo Genes that share paralogs with SETX: view

Variants for SETX Gene

Sequence variations from dbSNP and Humsavar for SETX Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type MAF
rs7025 -- 132,262,871(-) CTGTA(A/G)TGAAT utr-variant-3-prime
rs12507 -- 132,261,838(-) TTCAA(A/T)ATTAG utr-variant-3-prime
rs14973 -- 132,262,884(-) AAAAA(A/C)TAGGG utr-variant-3-prime
rs472052 -- 132,322,701(-) tactc(A/C)cattt intron-variant
rs472270 -- 132,322,620(+) caact(C/G)acaca intron-variant

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

Relevant External Links for SETX Gene

HapMap Linkage Disequilibrium report
SETX
Human Gene Mutation Database (HGMD)
SETX
Locus Specific Mutation Databases (LSDB)
SETX

Disorders for SETX Gene

(2) OMIM Diseases for SETX Gene (608465)

UniProtKB/Swiss-Prot

SETX_HUMAN
  • 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.
  • 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.

(8) Novoseek inferred disease relationships for SETX Gene

Disease -log(P) Hits PubMed IDs
third-nerve palsy 93 1
cerebellar ataxia early onset 92.1 1
apraxias 91.5 15
vitamin e deficiency 70.6 3
friedreich ataxia 69.5 4

Relevant External Links for SETX

GeneTests
SETX
GeneReviews
SETX
Genetic Association Database (GAD)
SETX
Human Genome Epidemiology (HuGE) Navigator
SETX
genes like me logo Genes that share disorders with SETX: view

Publications for SETX Gene

  1. Senataxin, the ortholog of a yeast RNA helicase, is mutant in ataxia- ocular apraxia 2. (PMID: 14770181) Moreira M.-C. … Koenig M. (Nat. Genet. 2004) 3 4 23
  2. DNA/RNA helicase gene mutations in a form of juvenile amyotrophic lateral sclerosis (ALS4). (PMID: 15106121) Chen Y.-Z. … Chance P.F. (Am. J. Hum. Genet. 2004) 3 4 23
  3. Autosomal recessive ataxia with peripheral neuropathy and elevated AFP: novel mutations in SETX. (PMID: 16717225) Asaka T. … Matsushima A. (Neurology 2006) 3 4 23
  4. Senataxin, defective in ataxia oculomotor apraxia type 2, is involved in the defense against oxidative DNA damage. (PMID: 17562789) Suraweera A. … Lavin M.F. (J. Cell Biol. 2007) 3 4 23
  5. 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

Products for SETX Gene

Sources for SETX Gene

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