Setx senataxin [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Setxprovided by MGI
Official Full Name: senataxinprovided by MGI
Primary source: MGI:MGI:2443480
See related: Ensembl:ENSMUSG00000043535 AllianceGenome:MGI:2443480
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: AOA2; Als4; Sen1; SCAR1; mKIAA0625; A130090N03; A930037J23Rik
Summary: Predicted to enable RNA binding activity; identical protein binding activity; and transcription termination site sequence-specific DNA binding activity. Acts upstream of or within circadian rhythm and termination of RNA polymerase II transcription. Predicted to be located in several cellular components, including growth cone; intercellular bridge; and nuclear lumen. Predicted to be active in nuclear body. Human ortholog(s) of this gene implicated in amyotrophic lateral sclerosis type 4 and ataxia with oculomotor apraxia type 2. Orthologous to human SETX (senataxin). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in testis adult (RPKM 26.8), CNS E11.5 (RPKM 4.6) and 19 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2; 2 A3- B

Exon count:: 30

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (29013600..29072483)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (29123588..29182471)

Chromosome 2 - NC_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Premature ovarian ageing following heterozygous loss of Senataxin.
Title: Premature ovarian ageing following heterozygous loss of Senataxin.
Oocytes mount a noncanonical DNA damage response involving APC-Cdh1-mediated proteolysis.
Title: Oocytes mount a noncanonical DNA damage response involving APC-Cdh1-mediated proteolysis.
SETX ALS4 mice thus recapitulated ALS disease phenotypes in association with TDP-43 mislocalization and provided insight into the basis for TDP-43 histopathology, linking SETX dysfunction to common pathways of ALS motor neuron degeneration.
Title: Senataxin mutations elicit motor neuron degeneration phenotypes and yield TDP-43 mislocalization in ALS4 mice and human patients.
Senataxin (SETX)-deficiency results in increased RNA-DNA hybrids (R-loops) and DNA double-strand breaks (DSBs), and deficiency of DNA-activated protein kinase-catalytic subunit (DNA-PKcs), which impairs DSB repair. SETX overexpression in SMA neurons reduces R-loops and DNA damage, and rescues neurodegeneration.
Title: Combined deficiency of Senataxin and DNA-PKcs causes DNA damage accumulation and neurodegeneration in spinal muscular atrophy.
Study report a previously uncharacterized protein, SAN1, the Fam120b gene product, as a 5' exonuclease that acts independently of the Fanconi anemia pathway in response to inter-strand DNA cross-links (ICLs). Deletion of SAN1 in HeLa cells and mouse embryonic fibroblasts causes sensitivity to ICLs. SAN1 binds to senataxin (SETX). SAN1-SETX binding is increased by ICLs and is required to prevent cross-link sensitivity.
Title: A senataxin-associated exonuclease SAN1 is required for resistance to DNA interstrand cross-links.
Results identify novel genes related to senataxin function in normal and disease states.
Title: Mutation of senataxin alters disease-specific transcriptional networks in patients with ataxia with oculomotor apraxia type 2.
These data support key roles for senataxin in coordinating meiotic crossing-over with transcription and in gene silencing to protect the integrity of the genome.
Title: Senataxin plays an essential role with DNA damage response proteins in meiotic recombination and gene silencing.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (4) 1 citation
Endonuclease-mediated (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Homologs of the Setx gene: The Setx gene is conserved in human, chimpanzee, Rhesus monkey, dog, cow, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 399 organisms have orthologs with human gene Setx
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
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	PubMed
enables transcription termination site sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA damage response	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within DNA recombination	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within DNA repair	IEA Inferred from Electronic Annotation more info
involved_in DNA-templated transcription termination	ISO Inferred from Sequence Orthology more info
involved_in MAPK cascade	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in cellular response to fibroblast growth factor stimulus	ISO Inferred from Sequence Orthology more info
involved_in cellular response to hydrogen peroxide	ISO Inferred from Sequence Orthology more info
involved_in cellular response to oxidative stress	ISO Inferred from Sequence Orthology more info
involved_in cellular response to retinoic acid	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in double-strand break repair	ISO Inferred from Sequence Orthology more info
involved_in fibroblast growth factor receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in mRNA splice site selection	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within nervous system development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription initiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of RNA splicing	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of neuron projection development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of termination of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in protein kinase B signaling	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within rhythmic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within 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	PubMed
acts_upstream_of_or_within termination of RNA polymerase II transcription	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in axon	ISO Inferred from Sequence Orthology more info
located_in cell projection	IEA Inferred from Electronic Annotation more info
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in chromosome, telomeric region	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in growth cone	ISO Inferred from Sequence Orthology more info
located_in intercellular bridge	ISO Inferred from Sequence Orthology more info
is_active_in nuclear body	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nuclear chromosome	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: probable helicase senataxin

Names: SEN1 homolog; amyotrophic lateral sclerosis 4 homolog; amyotrophic lateral sclerosis 4 protein homolog

NP_932150.2

EC 3.6.1.-

XP_006498142.1

EC 3.6.1.-

XP_006498143.1

EC 3.6.1.-

XP_006498145.1

EC 3.6.1.-

XP_030107510.1

EC 3.6.1.-

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.

mRNA and Protein(s)

NM_198033.2 → NP_932150.2 probable helicase senataxin

See identical proteins and their annotated locations for NP_932150.2

Status: VALIDATED

Source sequence(s)

AL772379, AL845267, BC058109, BK001523

Consensus CDS

CCDS38090.1

UniProtKB/Swiss-Prot

A2AKX3, Q8C8P6

Related

ENSMUSP00000051492.3, ENSMUST00000061578.9

Conserved Domains (4) summary

pfam12726
Location:37 → 356

SEN1_N; SEN1 N terminal

pfam13086
Location:1909 → 2194

AAA_11; AAA domain

pfam13087
Location:2201 → 2400

AAA_12; AAA domain

pfam13245
Location:1933 → 1996

AAA_19; Part of AAA domain

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...

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

Reference GRCm39 C57BL/6J

Genomic

NC_000068.8 Reference GRCm39 C57BL/6J

Range

29013600..29072483

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030251650.2 → XP_030107510.1 probable helicase senataxin isoform X1

Conserved Domains (3) summary

cd18042
Location:1910 → 2235

DEXXQc_SETX; DEXXQ-box helicase domain of SETX

pfam12726
Location:37 → 334

SEN1_N; SEN1 N terminal

pfam13087
Location:2201 → 2455

AAA_12; AAA domain
XM_006498080.5 → XP_006498143.1 probable helicase senataxin isoform X1

See identical proteins and their annotated locations for XP_006498143.1

Conserved Domains (3) summary

cd18042
Location:1910 → 2235

DEXXQc_SETX; DEXXQ-box helicase domain of SETX

pfam12726
Location:37 → 334

SEN1_N; SEN1 N terminal

pfam13087
Location:2201 → 2455

AAA_12; AAA domain
XM_006498079.4 → XP_006498142.1 probable helicase senataxin isoform X1

See identical proteins and their annotated locations for XP_006498142.1

Conserved Domains (3) summary

cd18042
Location:1910 → 2235

DEXXQc_SETX; DEXXQ-box helicase domain of SETX

pfam12726
Location:37 → 334

SEN1_N; SEN1 N terminal

pfam13087
Location:2201 → 2455

AAA_12; AAA domain
XM_006498082.5 → XP_006498145.1 probable helicase senataxin isoform X1

See identical proteins and their annotated locations for XP_006498145.1

Conserved Domains (3) summary

cd18042
Location:1910 → 2235

DEXXQc_SETX; DEXXQ-box helicase domain of SETX

pfam12726
Location:37 → 334

SEN1_N; SEN1 N terminal

pfam13087
Location:2201 → 2455

AAA_12; AAA domain

RNA

XR_001782867.3 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_177365.2: Suppressed sequence

Description

NM_177365.2: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.