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    SETX senataxin [ Homo sapiens (human) ]

    Gene ID: 23064, updated on 9-Jul-2017
    Official Symbol
    SETXprovided by HGNC
    Official Full Name
    senataxinprovided by HGNC
    Primary source
    HGNC:HGNC:445
    See related
    Ensembl:ENSG00000107290 MIM:608465; Vega:OTTHUMG00000020834
    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; Sen1; 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]
    Orthologs
    Location:
    9q34.13
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 9 NC_000009.12 (132261440..132356726, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (135136827..135232113, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376302 Neighboring gene netrin G2 Neighboring gene uncharacterized LOC105376304 Neighboring gene transcription termination factor 1 Neighboring gene cilia and flagella associated protein 77

    • Project title: 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ12840, FLJ43459, KIAA0625, DKFZp781B151

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    DNA binding IC
    Inferred by Curator
    more info
    PubMed 
    DNA helicase activity TAS
    Traceable Author Statement
    more info
    PubMed 
    identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    transcription termination site sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    DNA duplex unwinding IEA
    Inferred from Electronic Annotation
    more info
     
    DNA recombination IEA
    Inferred from Electronic Annotation
    more info
     
    DNA-templated transcription, termination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    MAPK cascade IDA
    Inferred from Direct Assay
    more info
    PubMed 
    RNA processing TAS
    Traceable Author Statement
    more info
    PubMed 
    cellular response to DNA damage stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cellular response to fibroblast growth factor stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cellular response to hydrogen peroxide IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cellular response to oxidative stress IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cellular response to retinoic acid IDA
    Inferred from Direct Assay
    more info
    PubMed 
    circadian rhythm IEA
    Inferred from Electronic Annotation
    more info
     
    double-strand break repair IDA
    Inferred from Direct Assay
    more info
    PubMed 
    fibroblast growth factor receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    mRNA splice site selection IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of DNA-templated transcription, initiation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of DNA-templated transcription, termination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of RNA splicing IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of neuron projection development IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of transcription from RNA polymerase II promoter IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein kinase B signaling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    spermatogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    termination of RNA polymerase II transcription IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    axon IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chromosome, telomeric region IEA
    Inferred from Electronic Annotation
    more info
     
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    growth cone IDA
    Inferred from Direct Assay
    more info
    PubMed 
    intercellular bridge IDA
    Inferred from Direct Assay
    more info
     
    nuclear body IDA
    Inferred from Direct Assay
    more info
     
    nuclear chromosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleolus IEA
    Inferred from Electronic Annotation
    more info
     
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    probable helicase senataxin
    Names
    SEN1 homolog
    amyotrophic lateral sclerosis 4 protein
    NP_055861.3
    XP_005272228.1
    XP_005272229.1
    XP_005272230.1
    XP_011516706.1
    XP_011516707.1
    XP_011516708.1
    XP_011516709.1
    XP_011516710.1
    XP_016869984.1
    XP_016869985.1
    XP_016869986.1

    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_001351527.1NP_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
    2. NM_001351528.1NP_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
    3. NM_015046.6NP_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
      Q7Z333
      Related
      ENSP00000224140.5, OTTHUMP00000022428, ENST00000224140.5
      Conserved Domains (4) summary
      pfam12726
      Location:37356
      SEN1_N; SEN1 N terminal
      pfam13086
      Location:19332218
      AAA_11; AAA domain
      pfam13087
      Location:22252424
      AAA_12; AAA domain
      pfam13245
      Location:19572020
      AAA_19; Part of AAA domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p7 Primary Assembly

      Range
      132261440..132356726 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005272171.1XP_005272228.1  probable helicase senataxin isoform X1

      UniProtKB/Swiss-Prot
      Q7Z333
      Conserved Domains (4) summary
      pfam12726
      Location:37356
      SEN1_N; SEN1 N terminal
      pfam13086
      Location:19332218
      AAA_11; AAA domain
      pfam13087
      Location:22252424
      AAA_12; AAA domain
      pfam13245
      Location:19572020
      AAA_19; Part of AAA domain
    2. XM_017014496.1XP_016869985.1  probable helicase senataxin isoform X6

      Related
      ENSP00000409143.1, OTTHUMP00000022429, ENST00000436441.5, OTTHUMT00000054775
    3. XM_017014495.1XP_016869984.1  probable helicase senataxin isoform X2

      UniProtKB/Swiss-Prot
      Q7Z333
      Conserved Domains (4) summary
      pfam12726
      Location:37356
      SEN1_N; SEN1 N terminal
      pfam13086
      Location:19332218
      AAA_11; AAA domain
      pfam13087
      Location:22252424
      AAA_12; AAA domain
      pfam13245
      Location:19572020
      AAA_19; Part of AAA domain
    4. XM_017014497.1XP_016869986.1  probable helicase senataxin isoform X7

      UniProtKB/Swiss-Prot
      Q7Z333
      UniProtKB/TrEMBL
      A0A0S2Z550
      Conserved Domains (4) summary
      pfam13086
      Location:84369
      AAA_11; AAA domain
      pfam13087
      Location:376575
      AAA_12; AAA domain
      pfam13245
      Location:108171
      AAA_19; Part of AAA domain
      cl21455
      Location:329364
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases
    5. XM_005272172.2XP_005272229.1  probable helicase senataxin isoform X1

      See identical proteins and their annotated locations for XP_005272229.1

      UniProtKB/Swiss-Prot
      Q7Z333
      Conserved Domains (4) summary
      pfam12726
      Location:37356
      SEN1_N; SEN1 N terminal
      pfam13086
      Location:19332218
      AAA_11; AAA domain
      pfam13087
      Location:22252424
      AAA_12; AAA domain
      pfam13245
      Location:19572020
      AAA_19; Part of AAA domain
    6. XM_011518404.2XP_011516706.1  probable helicase senataxin isoform X1

      See identical proteins and their annotated locations for XP_011516706.1

      UniProtKB/Swiss-Prot
      Q7Z333
      Conserved Domains (4) summary
      pfam12726
      Location:37356
      SEN1_N; SEN1 N terminal
      pfam13086
      Location:19332218
      AAA_11; AAA domain
      pfam13087
      Location:22252424
      AAA_12; AAA domain
      pfam13245
      Location:19572020
      AAA_19; Part of AAA domain
    7. XM_011518405.2XP_011516707.1  probable helicase senataxin isoform X1

      See identical proteins and their annotated locations for XP_011516707.1

      UniProtKB/Swiss-Prot
      Q7Z333
      Conserved Domains (4) summary
      pfam12726
      Location:37356
      SEN1_N; SEN1 N terminal
      pfam13086
      Location:19332218
      AAA_11; AAA domain
      pfam13087
      Location:22252424
      AAA_12; AAA domain
      pfam13245
      Location:19572020
      AAA_19; Part of AAA domain
    8. XM_005272173.2XP_005272230.1  probable helicase senataxin isoform X1

      See identical proteins and their annotated locations for XP_005272230.1

      UniProtKB/Swiss-Prot
      Q7Z333
      Conserved Domains (4) summary
      pfam12726
      Location:37356
      SEN1_N; SEN1 N terminal
      pfam13086
      Location:19332218
      AAA_11; AAA domain
      pfam13087
      Location:22252424
      AAA_12; AAA domain
      pfam13245
      Location:19572020
      AAA_19; Part of AAA domain
    9. XM_011518406.2XP_011516708.1  probable helicase senataxin isoform X3

      Conserved Domains (4) summary
      pfam12726
      Location:37356
      SEN1_N; SEN1 N terminal
      pfam13086
      Location:19332218
      AAA_11; AAA domain
      pfam13087
      Location:22252400
      AAA_12; AAA domain
      pfam13245
      Location:19572020
      AAA_19; Part of AAA domain
    10. XM_011518407.1XP_011516709.1  probable helicase senataxin isoform X4

      Conserved Domains (4) summary
      pfam12726
      Location:37356
      SEN1_N; SEN1 N terminal
      pfam13086
      Location:19332218
      AAA_11; AAA domain
      pfam13245
      Location:19572020
      AAA_19; Part of AAA domain
      cl22977
      Location:22252366
      UvrD_C_2; UvrD-like helicase C-terminal domain
    11. XM_011518408.2XP_011516710.1  probable helicase senataxin isoform X5

      Conserved Domains (3) summary
      pfam12726
      Location:37356
      SEN1_N; SEN1 N terminal
      pfam13086
      Location:19332182
      AAA_11; AAA domain
      pfam13245
      Location:19572020
      AAA_19; Part of AAA domain

    RNA

    1. XR_001746251.1 RNA Sequence

    2. XR_929739.2 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018920.2 Alternate CHM1_1.1

      Range
      135286879..135380398 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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