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    Setx senataxin [ Rattus norvegicus (Norway rat) ]

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

    Summary

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    Official Symbol
    Setxprovided by RGD
    Official Full Name
    senataxinprovided by RGD
    Primary source
    RGD:1565575
    See related
    Ensembl: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 intracellular signal transduction; nucleic acid metabolic process; and positive regulation of RNA metabolic 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 ataxia with oculomotor apraxia type 2. Orthologous to human SETX (senataxin). [provided by Alliance of Genome Resources, Apr 2022]
    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
    • 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

    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
      Related
      ENSRNOP00000082851.1
      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
      ENSRNOP00000083466.1
      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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