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Setx senataxin [ Rattus norvegicus (Norway rat) ]

Gene ID: 362096, updated on 2-Nov-2024

Summary

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Official Symbol
Setxprovided by RGD
Official Full Name
senataxinprovided by RGD
Primary source
RGD:1565575
See related
EnsemblRapid:ENSRNOG00000013491 AllianceGenome:RGD:1565575
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
RGD1565575
Summary
Predicted to enable RNA binding activity; identical protein binding activity; and transcription termination site sequence-specific DNA binding activity. Predicted to be involved in several processes, including RNA metabolic process; cellular response to hydrogen peroxide; and positive regulation of macromolecule biosynthetic process. Predicted to act upstream of or within circadian rhythm. 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 spinocerebellar ataxia with axonal neuropathy 2. Orthologous to human SETX (senataxin). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Thymus (RPKM 501.6), Spleen (RPKM 376.6) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Setx in Genome Data Viewer
Location:
3p12
Exon count:
30
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (32825771..32878740)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (12428091..12480801)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (7680430..7731815)

Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene cilia and flagella associated protein 77 Neighboring gene uncharacterized LOC108350345 Neighboring gene transcription termination factor 1 Neighboring gene netrin G2 Neighboring gene mediator complex subunit 27

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Senataxin modulates neurite growth through fibroblast growth factor 8 signalling. Vantaggiato C, et al. Brain, 2011 Jun. PMID 21576111
  2. Senataxin, defective in ataxia oculomotor apraxia type 2, is involved in the defense against oxidative DNA damage. Suraweera A, et al. J Cell Biol, 2007 Jun 18. PMID 17562789, Free PMC Article
  3. DNA/RNA helicase gene mutations in a form of juvenile amyotrophic lateral sclerosis (ALS4). Chen YZ, et al. Am J Hum Genet, 2004 Jun. PMID 15106121, Free PMC Article
  4. Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2-dependent termination. Skourti-Stathaki K, et al. Mol Cell, 2011 Jun 24. PMID 21700224, Free PMC Article
  5. Functional role for senataxin, defective in ataxia oculomotor apraxia type 2, in transcriptional regulation. Suraweera A, et al. Hum Mol Genet, 2009 Sep 15. PMID 19515850

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables helicase activity IEA
Inferred from Electronic Annotation
more info
  
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
  
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 ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in DNA damage response ISO
Inferred from Sequence Orthology
more info
  
involved_in DNA-templated transcription termination ISO
Inferred from Sequence Orthology
more info
  
involved_in biological_process ND
No biological Data available
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
  
acts_upstream_of_or_within circadian rhythm ISO
Inferred from Sequence Orthology
more info
  
involved_in double-strand break repair ISO
Inferred from Sequence Orthology
more info
  
involved_in mRNA splice site recognition ISO
Inferred from Sequence Orthology
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 termination of RNA polymerase II transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within termination of RNA polymerase II transcription ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in axon ISO
Inferred from Sequence Orthology
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 IEA
Inferred from Electronic Annotation
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
  
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
DEAxQ-box helicase
tRNA splicing endonuclease regulator 1
NP_001414209.1
XP_006233948.1
XP_006233949.1
XP_038962080.1

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)

  1. NM_001427280.2 → NP_001414209.1  probable helicase senataxin

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000003
    UniProtKB/TrEMBL
    D4AEB3
    Related
    ENSRNOP00000017984.4, ENSRNOT00000017984.7

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086021.1 Reference GRCr8

    Range
    32825771..32878740
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006233887.5 → XP_006233949.1  probable helicase senataxin isoform X1

    See identical proteins and their annotated locations for XP_006233949.1

    UniProtKB/TrEMBL
    A0A8I5ZVF7, A0A8I5ZYQ6
    Conserved Domains (4) summary
    pfam12726
    Location:37 → 356
    SEN1_N; SEN1 N terminal
    pfam13086
    Location:1910 → 2195
    AAA_11; AAA domain
    pfam13087
    Location:2202 → 2456
    AAA_12; AAA domain
    pfam13245
    Location:1934 → 1997
    AAA_19; Part of AAA domain

  2. XM_039106152.2 → XP_038962080.1  probable helicase senataxin isoform X2

    UniProtKB/TrEMBL
    A0A8I5ZVF7
    Conserved Domains (3) summary
    COG1112
    Location:1641 → 2256
    DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]
    cd18042
    Location:1911 → 2236
    DEXXQc_SETX; DEXXQ-box helicase domain of SETX
    pfam12726
    Location:37 → 334
    SEN1_N; SEN1 N terminal

  3. XM_006233886.5 → XP_006233948.1  probable helicase senataxin isoform X1

    See identical proteins and their annotated locations for XP_006233948.1

    UniProtKB/TrEMBL
    A0A8I5ZVF7, A0A8I5ZYQ6
    Related
    ENSRNOP00000082851.1, ENSRNOT00000101235.2
    Conserved Domains (4) summary
    pfam12726
    Location:37 → 356
    SEN1_N; SEN1 N terminal
    pfam13086
    Location:1910 → 2195
    AAA_11; AAA domain
    pfam13087
    Location:2202 → 2456
    AAA_12; AAA domain
    pfam13245
    Location:1934 → 1997
    AAA_19; Part of AAA domain

RNA

  1. XR_005502066.2 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version

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