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SETX senataxin [ Homo sapiens (human) ]

Gene ID: 23064, updated on 28-Oct-2024

Summary

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Official Symbol
SETXprovided by HGNC
Official Full Name
senataxinprovided by HGNC
Primary source
HGNC:HGNC:445
See related
Ensembl:ENSG00000107290 MIM:608465; AllianceGenome:HGNC:445
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ALS4; AOA2; STEX; Sen1; SCAN2; SCAR1; bA479K20.2
Summary
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]
Expression
Ubiquitous expression in thyroid (RPKM 20.6), testis (RPKM 18.7) and 24 other tissues See more
Orthologs
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Genomic context

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See SETX in Genome Data Viewer
Location:
9q34.13
Exon count:
33
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (132261356..132356744, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (144475833..144571334, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (135136743..135230373, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135004636-135005136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135005137-135005637 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135011939-135012452 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135029860-135030360 Neighboring gene uncharacterized LOC124902291 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135044919-135045676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135045677-135046434 Neighboring gene Sharpr-MPRA regulatory region 1592 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135061794-135062407 Neighboring gene netrin G2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135082729-135083404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135083405-135084080 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:135089048-135089792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135115111-135115628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20426 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20428 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20427 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135120407-135120912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135120913-135121418 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:135144739-135145938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135171222-135171722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135171723-135172223 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29217 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:135229958-135231157 Neighboring gene Sharpr-MPRA regulatory region 6614 Neighboring gene uncharacterized LOC124902292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29218 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29219 Neighboring gene uncharacterized LOC105376304 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20431 Neighboring gene transcription termination factor 1 Neighboring gene cilia and flagella associated protein 77

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Ataxia with oculomotor apraxia type 2: a clinical and genetic study of 19 patients. Tazir M, et al. J Neurol Sci, 2009 Mar 15. PMID 19141356
  2. Integrated genome and transcriptome analyses reveal the mechanism of genome instability in ataxia with oculomotor apraxia 2. Kanagaraj R, et al. Proc Natl Acad Sci U S A, 2022 Jan 25. PMID 35042798, Free PMC Article
  3. SETX mutations are a frequent genetic cause of juvenile and adult onset cerebellar ataxia with neuropathy and elevated serum alpha-fetoprotein. Nanetti L, et al. Orphanet J Rare Dis, 2013 Aug 14. PMID 23941260, Free PMC Article
  4. Association of genetic variants in senataxin and Alzheimer's disease in a Chinese Han population in Taiwan. Shen CP, et al. Chin J Physiol, 2014 Apr 30. PMID 24694197
  5. Hypoxia-induced SETX links replication stress with the unfolded protein response. Ramachandran S, et al. Nat Commun, 2021 Jun 17. PMID 34140498, Free PMC Article

See all (136) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. R-loops and impaired autophagy trigger cGAS-dependent inflammation via micronuclei formation in Senataxin-deficient cells.
    Title: R-loops and impaired autophagy trigger cGAS-dependent inflammation via micronuclei formation in Senataxin-deficient cells.
  2. Senataxin deficiency disrupts proteostasis through nucleolar ncRNA-driven protein aggregation.
    Title: Senataxin deficiency disrupts proteostasis through nucleolar ncRNA-driven protein aggregation.
  3. Genetic heterogeneity within a consanguineous family involving TTPA and SETX genes.
    Title: Genetic heterogeneity within a consanguineous family involving TTPA and SETX genes.
  4. Sen1 architecture: RNA-DNA hybrid resolution, autoregulation, and insights into SETX inactivation in AOA2.
    Title: Sen1 architecture: RNA-DNA hybrid resolution, autoregulation, and insights into SETX inactivation in AOA2.
  5. Human senataxin is a bona fide R-loop resolving enzyme and transcription termination factor.
    Title: Human senataxin is a bona fide R-loop resolving enzyme and transcription termination factor.
  6. FANCD2 promotes mitotic rescue from transcription-mediated replication stress in SETX-deficient cancer cells.
    Title: FANCD2 promotes mitotic rescue from transcription-mediated replication stress in SETX-deficient cancer cells.
  7. Transcriptional targets of senataxin and E2 promoter binding factors are associated with neuro-degenerative pathways during increased autophagic flux.
    Title: Transcriptional targets of senataxin and E2 promoter binding factors are associated with neuro-degenerative pathways during increased autophagic flux.
  8. Mutation in senataxin alters the mechanism of R-loop resolution in amyotrophic lateral sclerosis 4.
    Title: Mutation in senataxin alters the mechanism of R-loop resolution in amyotrophic lateral sclerosis 4.
  9. DeltaNp63-Senataxin circuit controls keratinocyte differentiation by promoting the transcriptional termination of epidermal genes.
    Title: ΔNp63-Senataxin circuit controls keratinocyte differentiation by promoting the transcriptional termination of epidermal genes.
  10. Integrated genome and transcriptome analyses reveal the mechanism of genome instability in ataxia with oculomotor apraxia 2.
    Title: Integrated genome and transcriptome analyses reveal the mechanism of genome instability in ataxia with oculomotor apraxia 2.
Submit: New GeneRIF Correction See all GeneRIFs (66)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ12840, FLJ43459, KIAA0625, DKFZp781B151

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA binding IC
Inferred by Curator
more info
 PubMed 
enables DNA helicase activity TAS
Traceable Author Statement
more info
 PubMed 
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription termination site sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables transcription termination site sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA damage response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in DNA duplex unwinding IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA recombination IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA-templated transcription termination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in RNA processing TAS
Traceable Author Statement
more info
 PubMed 
involved_in cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in cellular response to hydrogen peroxide IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to oxidative stress IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in circadian rhythm IEA
Inferred from Electronic Annotation
more info
  
involved_in double-strand break repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA splice site recognition IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in nervous system development IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of DNA-templated transcription initiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of RNA splicing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of neuron projection development IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of termination of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in spermatogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in termination of RNA polymerase II transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in axon IDA
Inferred from Direct Assay
more info
 PubMed 
located_in chromosome, telomeric region IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in growth cone IDA
Inferred from Direct Assay
more info
 PubMed 
located_in intercellular bridge IDA
Inferred from Direct Assay
more info
  
is_active_in nuclear body IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nuclear body IDA
Inferred from Direct Assay
more info
  
located_in nuclear chromosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleolus IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
probable helicase senataxin
Names
SEN1 homolog
amyotrophic lateral sclerosis 4 protein
NP_001338456.1
NP_001338457.1
NP_055861.3
XP_005272229.1
XP_005272230.1
XP_011516706.1
XP_011516707.1
XP_011516708.1
XP_011516709.1
XP_011516710.1
XP_047278979.1
XP_047278980.1
XP_047278981.1
XP_054218404.1
XP_054218405.1
XP_054218406.1
XP_054218407.1
XP_054218408.1
XP_054218409.1
XP_054218410.1
XP_054218411.1
XP_054218412.1
XP_054218413.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_007946.1 RefSeqGene

    Range
    5001..98546
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_268

mRNA and Protein(s)

  1. NM_001351527.2 → NP_001338456.1  probable helicase senataxin isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AA609547, AB014525, AI123313, AL353701, AY362728, BX538166, DA794966, DA989674
    Consensus CDS
    CCDS6947.1
    UniProtKB/Swiss-Prot
    A2A396, B2RPB2, B5ME16, C9JQ10, O75120, Q3KQX4, Q5JUJ1, Q68DW5, Q6AZD7, Q7Z333, Q7Z3J6, Q8WX33, Q9H9D1, Q9NVP9
    Conserved Domains (3) summary
    pfam12726
    Location:37 → 351
    SEN1_N; SEN1 N terminal
    pfam13086
    Location:1933 → 2218
    AAA_11; AAA domain
    pfam13087
    Location:2225 → 2424
    AAA_12; AAA domain

  2. NM_001351528.2 → NP_001338457.1  probable helicase senataxin isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (2) has the same N- and C-terimini, but is longer than isoform 1.
    Source sequence(s)
    AA609547, AB014525, AI123313, AK302394, AY362728, BX538166, DA989674
    Conserved Domains (3) summary
    pfam12726
    Location:37 → 351
    SEN1_N; SEN1 N terminal
    pfam13086
    Location:1933 → 2218
    AAA_11; AAA domain
    pfam13087
    Location:2225 → 2424
    AAA_12; AAA domain

  3. NM_015046.7 → NP_055861.3  probable helicase senataxin isoform 1

    See identical proteins and their annotated locations for NP_055861.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shortest transcript and encodes the shorter isoform (1). Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AA609547, AB014525, AI123313, AY362728, BX538166, DA989674
    Consensus CDS
    CCDS6947.1
    UniProtKB/Swiss-Prot
    A2A396, B2RPB2, B5ME16, C9JQ10, O75120, Q3KQX4, Q5JUJ1, Q68DW5, Q6AZD7, Q7Z333, Q7Z3J6, Q8WX33, Q9H9D1, Q9NVP9
    Related
    ENSP00000224140.5, ENST00000224140.6
    Conserved Domains (3) summary
    pfam12726
    Location:37 → 351
    SEN1_N; SEN1 N terminal
    pfam13086
    Location:1933 → 2218
    AAA_11; AAA domain
    pfam13087
    Location:2225 → 2424
    AAA_12; AAA domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    132261356..132356744 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005272172.4 → XP_005272229.1  probable helicase senataxin isoform X1

    See identical proteins and their annotated locations for XP_005272229.1

    UniProtKB/Swiss-Prot
    Q7Z333
    Conserved Domains (3) summary
    pfam12726
    Location:37 → 351
    SEN1_N; SEN1 N terminal
    pfam13086
    Location:1933 → 2218
    AAA_11; AAA domain
    pfam13087
    Location:2225 → 2424
    AAA_12; AAA domain

  2. XM_011518404.4 → XP_011516706.1  probable helicase senataxin isoform X1

    See identical proteins and their annotated locations for XP_011516706.1

    UniProtKB/Swiss-Prot
    Q7Z333
    Conserved Domains (3) summary
    pfam12726
    Location:37 → 351
    SEN1_N; SEN1 N terminal
    pfam13086
    Location:1933 → 2218
    AAA_11; AAA domain
    pfam13087
    Location:2225 → 2424
    AAA_12; AAA domain

  3. XM_047423023.1 → XP_047278979.1  probable helicase senataxin isoform X2

    UniProtKB/Swiss-Prot
    A2A396, B2RPB2, B5ME16, C9JQ10, O75120, Q3KQX4, Q5JUJ1, Q68DW5, Q6AZD7, Q7Z333, Q7Z3J6, Q8WX33, Q9H9D1, Q9NVP9

  4. XM_011518405.4 → XP_011516707.1  probable helicase senataxin isoform X1

    See identical proteins and their annotated locations for XP_011516707.1

    UniProtKB/Swiss-Prot
    Q7Z333
    Conserved Domains (3) summary
    pfam12726
    Location:37 → 351
    SEN1_N; SEN1 N terminal
    pfam13086
    Location:1933 → 2218
    AAA_11; AAA domain
    pfam13087
    Location:2225 → 2424
    AAA_12; AAA domain

  5. XM_005272173.4 → XP_005272230.1  probable helicase senataxin isoform X1

    See identical proteins and their annotated locations for XP_005272230.1

    UniProtKB/Swiss-Prot
    Q7Z333
    Conserved Domains (3) summary
    pfam12726
    Location:37 → 351
    SEN1_N; SEN1 N terminal
    pfam13086
    Location:1933 → 2218
    AAA_11; AAA domain
    pfam13087
    Location:2225 → 2424
    AAA_12; AAA domain

  6. XM_011518406.3 → XP_011516708.1  probable helicase senataxin isoform X3

    Conserved Domains (4) summary
    pfam12726
    Location:37 → 356
    SEN1_N; SEN1 N terminal
    pfam13086
    Location:1933 → 2218
    AAA_11; AAA domain
    pfam13087
    Location:2225 → 2400
    AAA_12; AAA domain
    pfam13245
    Location:1957 → 2020
    AAA_19; Part of AAA domain

  7. XM_011518407.2 → XP_011516709.1  probable helicase senataxin isoform X4

    Conserved Domains (4) summary
    pfam12726
    Location:37 → 356
    SEN1_N; SEN1 N terminal
    pfam13086
    Location:1933 → 2218
    AAA_11; AAA domain
    pfam13245
    Location:1957 → 2020
    AAA_19; Part of AAA domain
    cl22977
    Location:2225 → 2366
    UvrD_C_2; UvrD-like helicase C-terminal domain

  8. XM_011518408.4 → XP_011516710.1  probable helicase senataxin isoform X5

    Conserved Domains (3) summary
    pfam12726
    Location:37 → 356
    SEN1_N; SEN1 N terminal
    pfam13086
    Location:1933 → 2182
    AAA_11; AAA domain
    pfam13245
    Location:1957 → 2020
    AAA_19; Part of AAA domain

  9. XM_047423025.1 → XP_047278981.1  probable helicase senataxin isoform X7

  10. XM_047423024.1 → XP_047278980.1  probable helicase senataxin isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    144475833..144571334 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054362431.1 → XP_054218406.1  probable helicase senataxin isoform X1

  2. XM_054362432.1 → XP_054218407.1  probable helicase senataxin isoform X1

  3. XM_054362430.1 → XP_054218405.1  probable helicase senataxin isoform X1

  4. XM_054362433.1 → XP_054218408.1  probable helicase senataxin isoform X2

  5. XM_054362429.1 → XP_054218404.1  probable helicase senataxin isoform X1

  6. XM_054362434.1 → XP_054218409.1  probable helicase senataxin isoform X3

  7. XM_054362435.1 → XP_054218410.1  probable helicase senataxin isoform X4

  8. XM_054362436.1 → XP_054218411.1  probable helicase senataxin isoform X5

  9. XM_054362438.1 → XP_054218413.1  probable helicase senataxin isoform X7

  10. XM_054362437.1 → XP_054218412.1  probable helicase senataxin isoform X6

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7Z333.4 GenPept UniProtKB/Swiss-Prot:Q7Z333

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