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    SETX senataxin [ Homo sapiens (human) ]

    Gene ID: 23064, updated on 17-Mar-2024

    Summary

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    Official Symbol
    SETXprovided by HGNC
    Official Full Name
    senataxinprovided by HGNC
    Primary source
    HGNC:HGNC:445
    See related
    Ensembl:ENSG00000107290 MIM:608465; AllianceGenome:HGNC:445
    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; STEX; Sen1; SCAN2; 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]
    Expression
    Ubiquitous expression in thyroid (RPKM 20.6), testis (RPKM 18.7) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    9q34.13
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (132261356..132356744, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (144475833..144571334, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (135136743..135230373, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135004636-135005136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135005137-135005637 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135011939-135012452 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135029860-135030360 Neighboring gene uncharacterized LOC124902291 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135044919-135045676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135045677-135046434 Neighboring gene Sharpr-MPRA regulatory region 1592 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135061794-135062407 Neighboring gene netrin G2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135082729-135083404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135083405-135084080 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:135089048-135089792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135115111-135115628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20426 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20428 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20427 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135120407-135120912 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135120913-135121418 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:135144739-135145938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135171222-135171722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135171723-135172223 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29217 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:135229958-135231157 Neighboring gene Sharpr-MPRA regulatory region 6614 Neighboring gene uncharacterized LOC124902292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29218 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29219 Neighboring gene uncharacterized LOC105376304 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20431 Neighboring gene transcription termination factor 1 Neighboring gene cilia and flagella associated protein 77

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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 Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Human senataxin is a bona fide R-loop resolving enzyme and transcription termination factor. Hasanova Z, et al. Nucleic Acids Res, 2023 Apr 11. PMID 36864660, Free PMC Article
    2. Transcriptional targets of senataxin and E2 promoter binding factors are associated with neuro-degenerative pathways during increased autophagic flux. Casey AE, et al. Sci Rep, 2022 Oct 21. PMID 36271102, Free PMC Article
    3. Mutation in senataxin alters the mechanism of R-loop resolution in amyotrophic lateral sclerosis 4. Kannan A, et al. Brain, 2022 Sep 14. PMID 35045161, Free PMC Article
    4. Integrated genome and transcriptome analyses reveal the mechanism of genome instability in ataxia with oculomotor apraxia 2. Kanagaraj R, et al. Proc Natl Acad Sci U S A, 2022 Jan 25. PMID 35042798, Free PMC Article
    5. Hypoxia-induced SETX links replication stress with the unfolded protein response. Ramachandran S, et al. Nat Commun, 2021 Jun 17. PMID 34140498, Free PMC Article

    See all (124) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Genetic heterogeneity within a consanguineous family involving TTPA and SETX genes.
      Title: Genetic heterogeneity within a consanguineous family involving TTPA and SETX genes.
    2. Sen1 architecture: RNA-DNA hybrid resolution, autoregulation, and insights into SETX inactivation in AOA2.
      Title: Sen1 architecture: RNA-DNA hybrid resolution, autoregulation, and insights into SETX inactivation in AOA2.
    3. Human senataxin is a bona fide R-loop resolving enzyme and transcription termination factor.
      Title: Human senataxin is a bona fide R-loop resolving enzyme and transcription termination factor.
    4. FANCD2 promotes mitotic rescue from transcription-mediated replication stress in SETX-deficient cancer cells.
      Title: FANCD2 promotes mitotic rescue from transcription-mediated replication stress in SETX-deficient cancer cells.
    5. Transcriptional targets of senataxin and E2 promoter binding factors are associated with neuro-degenerative pathways during increased autophagic flux.
      Title: Transcriptional targets of senataxin and E2 promoter binding factors are associated with neuro-degenerative pathways during increased autophagic flux.
    6. Mutation in senataxin alters the mechanism of R-loop resolution in amyotrophic lateral sclerosis 4.
      Title: Mutation in senataxin alters the mechanism of R-loop resolution in amyotrophic lateral sclerosis 4.
    7. DeltaNp63-Senataxin circuit controls keratinocyte differentiation by promoting the transcriptional termination of epidermal genes.
      Title: ΔNp63-Senataxin circuit controls keratinocyte differentiation by promoting the transcriptional termination of epidermal genes.
    8. Integrated genome and transcriptome analyses reveal the mechanism of genome instability in ataxia with oculomotor apraxia 2.
      Title: Integrated genome and transcriptome analyses reveal the mechanism of genome instability in ataxia with oculomotor apraxia 2.
    9. USP11 controls R-loops by regulating senataxin proteostasis.
      Title: USP11 controls R-loops by regulating senataxin proteostasis.
    10. Evidence of synergism among three genetic variants in a patient with LMNA-related lipodystrophy and amyotrophic lateral sclerosis leading to a remarkable nuclear phenotype.
      Title: Evidence of synergism among three genetic variants in a patient with LMNA-related lipodystrophy and amyotrophic lateral sclerosis leading to a remarkable nuclear phenotype.
    Submit: New GeneRIF Correction See all GeneRIFs (64)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ12840, FLJ43459, KIAA0625, DKFZp781B151

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA binding IC
    Inferred by Curator
    more info
    		 PubMed 
    enables DNA helicase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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
    		  
    enables transcription termination site sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA damage response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in DNA duplex unwinding IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA recombination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in DNA-templated transcription termination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in MAPK cascade IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in RNA processing TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cellular response to fibroblast growth factor stimulus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cellular response to hydrogen peroxide IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cellular response to oxidative stress IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cellular response to retinoic acid IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in circadian rhythm IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in double-strand break repair IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in fibroblast growth factor receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mRNA splice site recognition IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of apoptotic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phosphatidylinositol 3-kinase/protein kinase B signal transduction IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription initiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of RNA splicing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of neuron projection development IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of termination of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in 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
    		  
    Component Evidence Code Pubs
    located_in axon IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chromosome, telomeric region IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in growth cone IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in intercellular bridge IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nuclear body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nuclear chromosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    probable helicase senataxin
    Names
    SEN1 homolog
    amyotrophic lateral sclerosis 4 protein
    NP_001338456.1
    NP_001338457.1
    NP_055861.3
    XP_005272229.1
    XP_005272230.1
    XP_011516706.1
    XP_011516707.1
    XP_011516708.1
    XP_011516709.1
    XP_011516710.1
    XP_047278979.1
    XP_047278980.1
    XP_047278981.1
    XP_054218404.1
    XP_054218405.1
    XP_054218406.1
    XP_054218407.1
    XP_054218408.1
    XP_054218409.1
    XP_054218410.1
    XP_054218411.1
    XP_054218412.1
    XP_054218413.1

    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.

    Genomic

    1. NG_007946.1 RefSeqGene

      Range
      5001..98546
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_268

    mRNA and Protein(s)

    1. NM_001351527.2 → NP_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
      Consensus CDS
      CCDS6947.1
      UniProtKB/Swiss-Prot
      A2A396, B2RPB2, B5ME16, C9JQ10, O75120, Q3KQX4, Q5JUJ1, Q68DW5, Q6AZD7, Q7Z333, Q7Z3J6, Q8WX33, Q9H9D1, Q9NVP9
      Conserved Domains (3) summary
      pfam12726
      Location:37 → 351
      SEN1_N; SEN1 N terminal
      pfam13086
      Location:1933 → 2218
      AAA_11; AAA domain
      pfam13087
      Location:2225 → 2424
      AAA_12; AAA domain

    2. NM_001351528.2 → NP_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
      Conserved Domains (3) summary
      pfam12726
      Location:37 → 351
      SEN1_N; SEN1 N terminal
      pfam13086
      Location:1933 → 2218
      AAA_11; AAA domain
      pfam13087
      Location:2225 → 2424
      AAA_12; AAA domain

    3. NM_015046.7 → NP_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
      A2A396, B2RPB2, B5ME16, C9JQ10, O75120, Q3KQX4, Q5JUJ1, Q68DW5, Q6AZD7, Q7Z333, Q7Z3J6, Q8WX33, Q9H9D1, Q9NVP9
      Related
      ENSP00000224140.5, ENST00000224140.6
      Conserved Domains (3) summary
      pfam12726
      Location:37 → 351
      SEN1_N; SEN1 N terminal
      pfam13086
      Location:1933 → 2218
      AAA_11; AAA domain
      pfam13087
      Location:2225 → 2424
      AAA_12; AAA domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      132261356..132356744 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005272172.4 → XP_005272229.1  probable helicase senataxin isoform X1

      See identical proteins and their annotated locations for XP_005272229.1

      UniProtKB/Swiss-Prot
      Q7Z333
      Conserved Domains (3) summary
      pfam12726
      Location:37 → 351
      SEN1_N; SEN1 N terminal
      pfam13086
      Location:1933 → 2218
      AAA_11; AAA domain
      pfam13087
      Location:2225 → 2424
      AAA_12; AAA domain

    2. XM_011518404.4 → XP_011516706.1  probable helicase senataxin isoform X1

      See identical proteins and their annotated locations for XP_011516706.1

      UniProtKB/Swiss-Prot
      Q7Z333
      Conserved Domains (3) summary
      pfam12726
      Location:37 → 351
      SEN1_N; SEN1 N terminal
      pfam13086
      Location:1933 → 2218
      AAA_11; AAA domain
      pfam13087
      Location:2225 → 2424
      AAA_12; AAA domain

    3. XM_047423023.1 → XP_047278979.1  probable helicase senataxin isoform X2

      UniProtKB/Swiss-Prot
      A2A396, B2RPB2, B5ME16, C9JQ10, O75120, Q3KQX4, Q5JUJ1, Q68DW5, Q6AZD7, Q7Z333, Q7Z3J6, Q8WX33, Q9H9D1, Q9NVP9

    4. XM_011518405.4 → XP_011516707.1  probable helicase senataxin isoform X1

      See identical proteins and their annotated locations for XP_011516707.1

      UniProtKB/Swiss-Prot
      Q7Z333
      Conserved Domains (3) summary
      pfam12726
      Location:37 → 351
      SEN1_N; SEN1 N terminal
      pfam13086
      Location:1933 → 2218
      AAA_11; AAA domain
      pfam13087
      Location:2225 → 2424
      AAA_12; AAA domain

    5. XM_005272173.4 → XP_005272230.1  probable helicase senataxin isoform X1

      See identical proteins and their annotated locations for XP_005272230.1

      UniProtKB/Swiss-Prot
      Q7Z333
      Conserved Domains (3) summary
      pfam12726
      Location:37 → 351
      SEN1_N; SEN1 N terminal
      pfam13086
      Location:1933 → 2218
      AAA_11; AAA domain
      pfam13087
      Location:2225 → 2424
      AAA_12; AAA domain

    6. XM_011518406.3 → XP_011516708.1  probable helicase senataxin isoform X3

      Conserved Domains (4) summary
      pfam12726
      Location:37 → 356
      SEN1_N; SEN1 N terminal
      pfam13086
      Location:1933 → 2218
      AAA_11; AAA domain
      pfam13087
      Location:2225 → 2400
      AAA_12; AAA domain
      pfam13245
      Location:1957 → 2020
      AAA_19; Part of AAA domain

    7. XM_011518407.2 → XP_011516709.1  probable helicase senataxin isoform X4

      Conserved Domains (4) summary
      pfam12726
      Location:37 → 356
      SEN1_N; SEN1 N terminal
      pfam13086
      Location:1933 → 2218
      AAA_11; AAA domain
      pfam13245
      Location:1957 → 2020
      AAA_19; Part of AAA domain
      cl22977
      Location:2225 → 2366
      UvrD_C_2; UvrD-like helicase C-terminal domain

    8. XM_011518408.4 → XP_011516710.1  probable helicase senataxin isoform X5

      Conserved Domains (3) summary
      pfam12726
      Location:37 → 356
      SEN1_N; SEN1 N terminal
      pfam13086
      Location:1933 → 2182
      AAA_11; AAA domain
      pfam13245
      Location:1957 → 2020
      AAA_19; Part of AAA domain

    9. XM_047423025.1 → XP_047278981.1  probable helicase senataxin isoform X7

    10. XM_047423024.1 → XP_047278980.1  probable helicase senataxin isoform X6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      144475833..144571334 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054362431.1 → XP_054218406.1  probable helicase senataxin isoform X1

    2. XM_054362432.1 → XP_054218407.1  probable helicase senataxin isoform X1

    3. XM_054362430.1 → XP_054218405.1  probable helicase senataxin isoform X1

    4. XM_054362433.1 → XP_054218408.1  probable helicase senataxin isoform X2

    5. XM_054362429.1 → XP_054218404.1  probable helicase senataxin isoform X1

    6. XM_054362434.1 → XP_054218409.1  probable helicase senataxin isoform X3

    7. XM_054362435.1 → XP_054218410.1  probable helicase senataxin isoform X4

    8. XM_054362436.1 → XP_054218411.1  probable helicase senataxin isoform X5

    9. XM_054362438.1 → XP_054218413.1  probable helicase senataxin isoform X7

    10. XM_054362437.1 → XP_054218412.1  probable helicase senataxin isoform X6

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z333.4 GenPept UniProtKB/Swiss-Prot:Q7Z333

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