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    Setx senataxin [ Mus musculus (house mouse) ]

    Gene ID: 269254, updated on 16-Jul-2021

    Summary

    Official Symbol
    Setxprovided by MGI
    Official Full Name
    senataxinprovided by MGI
    Primary source
    MGI:MGI:2443480
    See related
    Ensembl:ENSMUSG00000043535
    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
    A; AOA2; Als4; Sen1; SCAR1; AW060766; mKIAA0625; A130090N03; A930037J23Rik
    Expression
    Broad expression in testis adult (RPKM 26.8), CNS E11.5 (RPKM 4.6) and 19 other tissues See more
    Orthologs
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    Genomic context

    See Setx in Genome Data Viewer
    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)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (28980512..29037991)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene transcription termination factor, RNA polymerase I Neighboring gene ring finger and WD repeat domain 2 pseudogene Neighboring gene RIKEN cDNA 6530402F18 gene Neighboring gene netrin G2 Neighboring gene mediator complex subunit 27 Neighboring gene microRNA 133c

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    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
    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 DNA damage stimulus ISO
    Inferred from Sequence Orthology
    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 DNA-templated transcription, termination 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 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

    Preferred Names
    probable helicase senataxin
    Names
    SEN1 homolog
    amyotrophic lateral sclerosis 4 homolog
    amyotrophic lateral sclerosis 4 protein homolog
    NP_932150.2
    XP_006498142.1
    XP_006498143.1
    XP_006498145.1
    XP_030107510.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_198033.2NP_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
      Related
      ENSMUSP00000051492.3, ENSMUST00000061578.9
      Conserved Domains (4) summary
      pfam12726
      Location:37356
      SEN1_N; SEN1 N terminal
      pfam13086
      Location:19092194
      AAA_11; AAA domain
      pfam13087
      Location:22012400
      AAA_12; AAA domain
      pfam13245
      Location:19331996
      AAA_19; Part of AAA domain

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000068.8 Reference GRCm39 C57BL/6J

      Range
      29013600..29072483
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

      Conserved Domains (3) summary
      cd18042
      Location:19102235
      DEXXQc_SETX; DEXXQ-box helicase domain of SETX
      pfam12726
      Location:37334
      SEN1_N; SEN1 N terminal
      pfam13087
      Location:22012455
      AAA_12; AAA domain
    2. XM_006498080.5XP_006498143.1  probable helicase senataxin isoform X1

      See identical proteins and their annotated locations for XP_006498143.1

      Conserved Domains (3) summary
      cd18042
      Location:19102235
      DEXXQc_SETX; DEXXQ-box helicase domain of SETX
      pfam12726
      Location:37334
      SEN1_N; SEN1 N terminal
      pfam13087
      Location:22012455
      AAA_12; AAA domain
    3. XM_006498079.4XP_006498142.1  probable helicase senataxin isoform X1

      See identical proteins and their annotated locations for XP_006498142.1

      Conserved Domains (3) summary
      cd18042
      Location:19102235
      DEXXQc_SETX; DEXXQ-box helicase domain of SETX
      pfam12726
      Location:37334
      SEN1_N; SEN1 N terminal
      pfam13087
      Location:22012455
      AAA_12; AAA domain
    4. XM_006498082.5XP_006498145.1  probable helicase senataxin isoform X1

      See identical proteins and their annotated locations for XP_006498145.1

      Conserved Domains (3) summary
      cd18042
      Location:19102235
      DEXXQc_SETX; DEXXQ-box helicase domain of SETX
      pfam12726
      Location:37334
      SEN1_N; SEN1 N terminal
      pfam13087
      Location:22012455
      AAA_12; AAA domain

    RNA

    1. XR_001782867.3 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. 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.
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