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    Atxn1 ataxin 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 25049, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Atxn1provided by RGD
    Official Full Name
    ataxin 1provided by RGD
    Primary source
    RGD:3624
    See related
    Ensembl:ENSRNOG00000016998 AllianceGenome:RGD:3624
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Sca1
    Summary
    Predicted to enable several functions, including identical protein binding activity; protein C-terminus binding activity; and single-stranded RNA binding activity. Predicted to be involved in several processes, including learning or memory; negative regulation of transcription by RNA polymerase II; and social behavior. Predicted to act upstream of or within several processes, including negative regulation of insulin-like growth factor receptor signaling pathway; positive regulation of glial cell proliferation; and visual learning. Predicted to be located in cytosol; nuclear inclusion body; and nuclear lumen. Predicted to be part of protein-containing complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in spinocerebellar ataxia type 1. Orthologous to human ATXN1 (ataxin 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Brain (RPKM 74.0), Muscle (RPKM 72.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Atxn1 in Genome Data Viewer
    Location:
    17p14
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 17 NC_086035.1 (18943397..19354751)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 17 NC_051352.1 (18737491..19142360)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 17 NC_005116.4 (19160986..19533814)

    Chromosome 17 - NC_086035.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120097858 Neighboring gene uncharacterized LOC108348532 Neighboring gene uncharacterized LOC120097815 Neighboring gene uncharacterized LOC120097816 Neighboring gene U6 spliceosomal RNA Neighboring gene guanosine monophosphate reductase

    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. Transplantation of cardiac Sca-1-positive cells rather than c-Kit-positive cells preserves mitochondrial oxygen consumption of the viable myocardium following myocardial infarction in rats. Marunouchi T, et al. J Pharmacol Sci, 2019 Jul. PMID 31375326
    2. Prominent expression of spinocerebellar ataxia type-1 (SCA1) gene encoding ataxin-1 in LH-producing cells, LbetaT2. Ogawa S, et al. J Reprod Dev, 2004 Oct. PMID 15514462
    3. cDNA cloning and expression of rsca1, the rat counterpart of the human spinocerebellar ataxia type 1 gene. Gossen M, et al. Hum Mol Genet, 1996 Mar. PMID 8852664
    4. The AXH domain adopts alternative folds the solution structure of HBP1 AXH. de Chiara C, et al. Structure, 2005 May. PMID 15893665
    5. The spinocerebellar ataxia type 1 protein, ataxin-1, has RNA-binding activity that is inversely affected by the length of its polyglutamine tract. Yue S, et al. Hum Mol Genet, 2001 Jan 1. PMID 11136710

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The possibility that CrCDC and Sca-1(+) cells rather than c-Kit(+) cells may be used therapeutically to preserve cardiac function and energy metabolism after myocardial infarction.
      Title: Transplantation of cardiac Sca-1-positive cells rather than c-Kit-positive cells preserves mitochondrial oxygen consumption of the viable myocardium following myocardial infarction in rats.
    2. CD24 and Sca-1 in the mammary glands were expressed at lower level in 6-week-old female rats than in 9-week-old female rats.
      Title: [Expressions of Sca-1, CD24 and Muc1 in quiescent mammary glands of female rats].
    3. expression of SCA1 gene is prominent in LH-producing cells and is not under direct control of gonadal factor(s) in both genders
      Title: Prominent expression of spinocerebellar ataxia type-1 (SCA1) gene encoding ataxin-1 in LH-producing cells, LbetaT2.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables POZ domain binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables poly(G) binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables poly(G) binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables poly(U) RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables poly(U) RNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within adult locomotory behavior ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in brain development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in brain development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within excitatory postsynaptic potential ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of insulin-like growth factor receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in learning ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in learning ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within lung alveolus development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in memory ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in memory ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within negative regulation of insulin-like growth factor receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of phosphorylation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nervous system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in nuclear export ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nuclear export ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of_or_within positive regulation of glial cell proliferation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in social behavior ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in social behavior ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    acts_upstream_of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within visual learning ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear inclusion body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear inclusion body ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nuclear matrix ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear matrix ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in postsynapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    ataxin-1
    Names
    spinocerebellar ataxia 1
    spinocerebellar ataxia type 1 protein homolog

    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_012726.3 → NP_036858.1  ataxin-1

      See identical proteins and their annotated locations for NP_036858.1

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000017
      UniProtKB/Swiss-Prot
      Q63540
      UniProtKB/TrEMBL
      A6J718
      Related
      ENSRNOP00000023140.2, ENSRNOT00000023140.5
      Conserved Domains (2) summary
      smart00536
      Location:547 → 662
      AXH; domain in Ataxins and HMG containing proteins
      PHA03247
      Location:79 → 241
      PHA03247; large tegument protein UL36; Provisional

    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_086035.1 Reference GRCr8

      Range
      18943397..19354751
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039095353.2 → XP_038951281.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      Q63540
      UniProtKB/TrEMBL
      A6J718
      Conserved Domains (2) summary
      smart00536
      Location:547 → 662
      AXH; domain in Ataxins and HMG containing proteins
      PHA03247
      Location:79 → 241
      PHA03247; large tegument protein UL36; Provisional

    2. XM_039095354.2 → XP_038951282.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      Q63540
      UniProtKB/TrEMBL
      A6J718
      Conserved Domains (2) summary
      smart00536
      Location:547 → 662
      AXH; domain in Ataxins and HMG containing proteins
      PHA03247
      Location:79 → 241
      PHA03247; large tegument protein UL36; Provisional

    3. XM_039095351.2 → XP_038951279.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      Q63540
      UniProtKB/TrEMBL
      A6J718
      Conserved Domains (2) summary
      smart00536
      Location:547 → 662
      AXH; domain in Ataxins and HMG containing proteins
      PHA03247
      Location:79 → 241
      PHA03247; large tegument protein UL36; Provisional

    4. XM_063276067.1 → XP_063132137.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      Q63540
      UniProtKB/TrEMBL
      A6J718

    5. XM_039095363.2 → XP_038951291.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      Q63540
      UniProtKB/TrEMBL
      A6J718
      Conserved Domains (2) summary
      smart00536
      Location:547 → 662
      AXH; domain in Ataxins and HMG containing proteins
      PHA03247
      Location:79 → 241
      PHA03247; large tegument protein UL36; Provisional

    6. XM_039095352.2 → XP_038951280.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      Q63540
      UniProtKB/TrEMBL
      A6J718
      Conserved Domains (2) summary
      smart00536
      Location:547 → 662
      AXH; domain in Ataxins and HMG containing proteins
      PHA03247
      Location:79 → 241
      PHA03247; large tegument protein UL36; Provisional

    7. XM_039095364.2 → XP_038951292.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      Q63540
      UniProtKB/TrEMBL
      A6J718
      Conserved Domains (2) summary
      smart00536
      Location:547 → 662
      AXH; domain in Ataxins and HMG containing proteins
      PHA03247
      Location:79 → 241
      PHA03247; large tegument protein UL36; Provisional

    8. XM_063276064.1 → XP_063132134.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      Q63540
      UniProtKB/TrEMBL
      A6J718

    9. XM_063276066.1 → XP_063132136.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      Q63540
      UniProtKB/TrEMBL
      A6J718

    10. XM_039095356.2 → XP_038951284.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      Q63540
      UniProtKB/TrEMBL
      A6J718
      Conserved Domains (2) summary
      smart00536
      Location:547 → 662
      AXH; domain in Ataxins and HMG containing proteins
      PHA03247
      Location:79 → 241
      PHA03247; large tegument protein UL36; Provisional

    11. XM_063276065.1 → XP_063132135.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      Q63540
      UniProtKB/TrEMBL
      A6J718

    12. XM_039095361.2 → XP_038951289.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      Q63540
      UniProtKB/TrEMBL
      A6J718
      Conserved Domains (2) summary
      smart00536
      Location:547 → 662
      AXH; domain in Ataxins and HMG containing proteins
      PHA03247
      Location:79 → 241
      PHA03247; large tegument protein UL36; Provisional

    13. XM_039095357.2 → XP_038951285.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      Q63540
      UniProtKB/TrEMBL
      A6J718
      Conserved Domains (2) summary
      smart00536
      Location:547 → 662
      AXH; domain in Ataxins and HMG containing proteins
      PHA03247
      Location:79 → 241
      PHA03247; large tegument protein UL36; Provisional

    14. XM_039095366.2 → XP_038951294.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      Q63540
      UniProtKB/TrEMBL
      A6J718
      Conserved Domains (2) summary
      smart00536
      Location:547 → 662
      AXH; domain in Ataxins and HMG containing proteins
      PHA03247
      Location:79 → 241
      PHA03247; large tegument protein UL36; Provisional

    15. XM_063276068.1 → XP_063132138.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      Q63540
      UniProtKB/TrEMBL
      A6J718

    16. XM_039095365.2 → XP_038951293.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      Q63540
      UniProtKB/TrEMBL
      A6J718
      Conserved Domains (2) summary
      smart00536
      Location:547 → 662
      AXH; domain in Ataxins and HMG containing proteins
      PHA03247
      Location:79 → 241
      PHA03247; large tegument protein UL36; Provisional

    17. XM_039095368.2 → XP_038951296.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      Q63540
      UniProtKB/TrEMBL
      A6J718
      Conserved Domains (2) summary
      smart00536
      Location:547 → 662
      AXH; domain in Ataxins and HMG containing proteins
      PHA03247
      Location:79 → 241
      PHA03247; large tegument protein UL36; Provisional

    18. XM_039095367.2 → XP_038951295.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      Q63540
      UniProtKB/TrEMBL
      A6J718
      Conserved Domains (2) summary
      smart00536
      Location:547 → 662
      AXH; domain in Ataxins and HMG containing proteins
      PHA03247
      Location:79 → 241
      PHA03247; large tegument protein UL36; Provisional
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q63540.1 GenPept UniProtKB/Swiss-Prot:Q63540

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