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    Atxn1 ataxin 1 [ Mus musculus (house mouse) ]

    Gene ID: 20238, updated on 9-Dec-2024

    Summary

    Official Symbol
    Atxn1provided by MGI
    Official Full Name
    ataxin 1provided by MGI
    Primary source
    MGI:MGI:104783
    See related
    Ensembl:ENSMUSG00000046876 AllianceGenome:MGI:104783
    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
    Atx1; Sca1; Gm10786; 2900016G23Rik
    Summary
    Enables POZ domain binding activity; RNA binding activity; and chromatin binding activity. Involved in brain development; learning or memory; and social behavior. Acts upstream of or within several processes, including negative regulation of insulin-like growth factor receptor signaling pathway; regulation of transcription by RNA polymerase II; and visual learning. Located in nuclear inclusion body. Part of protein-containing complex. Is expressed in several structures, including central nervous system; early conceptus; genitourinary system; liver; and skeleton. Used to study spinocerebellar ataxia type 1. Human ortholog(s) of this gene implicated in spinocerebellar ataxia type 1. Orthologous to human ATXN1 (ataxin 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in cortex adult (RPKM 5.7), frontal lobe adult (RPKM 4.8) and 28 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Atxn1 in Genome Data Viewer
    Location:
    13 A5; 13 21.98 cM
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 13 NC_000079.7 (45703231..46118467, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 13 NC_000079.6 (45549755..45964991, complement)

    Chromosome 13 - NC_000079.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E5392 Neighboring gene STARR-positive B cell enhancer ABC_E7232 Neighboring gene predicted gene, 53792 Neighboring gene STARR-seq mESC enhancer starr_34395 Neighboring gene predicted gene, 34582 Neighboring gene guanosine monophosphate reductase Neighboring gene STARR-positive B cell enhancer mm9_chr13:45744500-45744801 Neighboring gene CapStarr-seq enhancer MGSCv37_chr13:45789016-45789125 Neighboring gene STARR-seq mESC enhancer starr_34397 Neighboring gene STARR-seq mESC enhancer starr_34398 Neighboring gene STARR-positive B cell enhancer mm9_chr13:45980000-45980300 Neighboring gene STARR-seq mESC enhancer starr_34399 Neighboring gene STARR-positive B cell enhancer mm9_chr13:46017736-46018037 Neighboring gene RIKEN cDNA 5033430I15 gene Neighboring gene STARR-positive B cell enhancer mm9_chr13:46060268-46060569 Neighboring gene STARR-seq mESC enhancer starr_34400 Neighboring gene STARR-seq mESC enhancer starr_34402 Neighboring gene STARR-seq mESC enhancer starr_34403 Neighboring gene STARR-seq mESC enhancer starr_34404 Neighboring gene predicted gene, 34991

    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)

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables POZ domain binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    acts_upstream_of_or_within adult locomotory behavior IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in brain development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in brain development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within excitatory postsynaptic potential IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of insulin-like growth factor receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in learning IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within lung alveolus development IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in memory IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within negative regulation of phosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    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 phosphorylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of glial cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in social behavior IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within visual learning IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nuclear inclusion body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    ataxin-1
    Names
    spinocerebellar ataxia 1 homolog

    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_001199304.1NP_001186233.1  ataxin-1 isoform b

      See identical proteins and their annotated locations for NP_001186233.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice junction at the 3' end of an exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 2 and 3 both encode the same isoform (b).
      Source sequence(s)
      AC154817, AK048268, AK165114, BE993799
      Consensus CDS
      CCDS26483.1
      UniProtKB/Swiss-Prot
      P54254, Q8C866
      Related
      ENSMUSP00000129890.3, ENSMUST00000167708.4
      Conserved Domains (2) summary
      PHA03247
      Location:79280
      PHA03247; large tegument protein UL36; Provisional
      pfam08517
      Location:550661
      AXH; Ataxin-1 and HBP1 module (AXH)
    2. NM_001199305.1NP_001186234.1  ataxin-1 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
      Source sequence(s)
      AC154817, AK048268, AK165114, BE993799
      Consensus CDS
      CCDS56877.1
      UniProtKB/TrEMBL
      J3QPR1
      Related
      ENSMUSP00000137439.2, ENSMUST00000180110.9
      Conserved Domains (2) summary
      smart00536
      Location:549672
      AXH; domain in Ataxins and HMG containing proteins
      pfam12547
      Location:391421
      ATXN-1_C; Capicua transcriptional repressor modulator
    3. NM_009124.6NP_033150.2  ataxin-1 isoform b

      See identical proteins and their annotated locations for NP_033150.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 3' end of an exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Variants 2 and 3 both encode the same isoform (b).
      Source sequence(s)
      AC154817, AK048268, AK165114, BE993799
      Consensus CDS
      CCDS26483.1
      UniProtKB/Swiss-Prot
      P54254, Q8C866
      Related
      ENSMUSP00000089217.4, ENSMUST00000091628.11
      Conserved Domains (2) summary
      PHA03247
      Location:79280
      PHA03247; large tegument protein UL36; Provisional
      pfam08517
      Location:550661
      AXH; Ataxin-1 and HBP1 module (AXH)

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000079.7 Reference GRCm39 C57BL/6J

      Range
      45703231..46118467 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011244386.4XP_011242688.1  ataxin-1 isoform X1

      See identical proteins and their annotated locations for XP_011242688.1

      UniProtKB/Swiss-Prot
      P54254, Q8C866
      Conserved Domains (2) summary
      PHA03247
      Location:79280
      PHA03247; large tegument protein UL36; Provisional
      pfam08517
      Location:550661
      AXH; Ataxin-1 and HBP1 module (AXH)
    2. XM_011244385.4XP_011242687.1  ataxin-1 isoform X1

      See identical proteins and their annotated locations for XP_011242687.1

      UniProtKB/Swiss-Prot
      P54254, Q8C866
      Conserved Domains (2) summary
      PHA03247
      Location:79280
      PHA03247; large tegument protein UL36; Provisional
      pfam08517
      Location:550661
      AXH; Ataxin-1 and HBP1 module (AXH)
    3. XM_030247210.2XP_030103070.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      P54254, Q8C866
      Conserved Domains (2) summary
      PHA03247
      Location:79280
      PHA03247; large tegument protein UL36; Provisional
      pfam08517
      Location:550661
      AXH; Ataxin-1 and HBP1 module (AXH)
    4. XM_011244383.4XP_011242685.1  ataxin-1 isoform X1

      See identical proteins and their annotated locations for XP_011242685.1

      UniProtKB/Swiss-Prot
      P54254, Q8C866
      Conserved Domains (2) summary
      PHA03247
      Location:79280
      PHA03247; large tegument protein UL36; Provisional
      pfam08517
      Location:550661
      AXH; Ataxin-1 and HBP1 module (AXH)
    5. XM_011244381.4XP_011242683.1  ataxin-1 isoform X1

      See identical proteins and their annotated locations for XP_011242683.1

      UniProtKB/Swiss-Prot
      P54254, Q8C866
      Conserved Domains (2) summary
      PHA03247
      Location:79280
      PHA03247; large tegument protein UL36; Provisional
      pfam08517
      Location:550661
      AXH; Ataxin-1 and HBP1 module (AXH)
    6. XM_011244390.4XP_011242692.1  ataxin-1 isoform X1

      See identical proteins and their annotated locations for XP_011242692.1

      UniProtKB/Swiss-Prot
      P54254, Q8C866
      Conserved Domains (2) summary
      PHA03247
      Location:79280
      PHA03247; large tegument protein UL36; Provisional
      pfam08517
      Location:550661
      AXH; Ataxin-1 and HBP1 module (AXH)
    7. XM_011244389.4XP_011242691.1  ataxin-1 isoform X1

      See identical proteins and their annotated locations for XP_011242691.1

      UniProtKB/Swiss-Prot
      P54254, Q8C866
      Conserved Domains (2) summary
      PHA03247
      Location:79280
      PHA03247; large tegument protein UL36; Provisional
      pfam08517
      Location:550661
      AXH; Ataxin-1 and HBP1 module (AXH)
    8. XM_030247213.2XP_030103073.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      P54254, Q8C866
      Conserved Domains (2) summary
      PHA03247
      Location:79280
      PHA03247; large tegument protein UL36; Provisional
      pfam08517
      Location:550661
      AXH; Ataxin-1 and HBP1 module (AXH)
    9. XM_036157943.1XP_036013836.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      P54254, Q8C866
      Conserved Domains (2) summary
      PHA03247
      Location:79280
      PHA03247; large tegument protein UL36; Provisional
      pfam08517
      Location:550661
      AXH; Ataxin-1 and HBP1 module (AXH)
    10. XM_011244387.4XP_011242689.1  ataxin-1 isoform X1

      See identical proteins and their annotated locations for XP_011242689.1

      UniProtKB/Swiss-Prot
      P54254, Q8C866
      Conserved Domains (2) summary
      PHA03247
      Location:79280
      PHA03247; large tegument protein UL36; Provisional
      pfam08517
      Location:550661
      AXH; Ataxin-1 and HBP1 module (AXH)
    11. XM_036157944.1XP_036013837.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      P54254, Q8C866
      Conserved Domains (2) summary
      PHA03247
      Location:79280
      PHA03247; large tegument protein UL36; Provisional
      pfam08517
      Location:550661
      AXH; Ataxin-1 and HBP1 module (AXH)
    12. XM_011244388.3XP_011242690.1  ataxin-1 isoform X1

      See identical proteins and their annotated locations for XP_011242690.1

      UniProtKB/Swiss-Prot
      P54254, Q8C866
      Conserved Domains (2) summary
      PHA03247
      Location:79280
      PHA03247; large tegument protein UL36; Provisional
      pfam08517
      Location:550661
      AXH; Ataxin-1 and HBP1 module (AXH)
    13. XM_030247212.2XP_030103072.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      P54254, Q8C866
      Conserved Domains (2) summary
      PHA03247
      Location:79280
      PHA03247; large tegument protein UL36; Provisional
      pfam08517
      Location:550661
      AXH; Ataxin-1 and HBP1 module (AXH)
    14. XM_030247211.2XP_030103071.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      P54254, Q8C866
      Conserved Domains (2) summary
      PHA03247
      Location:79280
      PHA03247; large tegument protein UL36; Provisional
      pfam08517
      Location:550661
      AXH; Ataxin-1 and HBP1 module (AXH)
    15. XM_011244392.3XP_011242694.1  ataxin-1 isoform X1

      See identical proteins and their annotated locations for XP_011242694.1

      UniProtKB/Swiss-Prot
      P54254, Q8C866
      Conserved Domains (2) summary
      PHA03247
      Location:79280
      PHA03247; large tegument protein UL36; Provisional
      pfam08517
      Location:550661
      AXH; Ataxin-1 and HBP1 module (AXH)
    16. XM_011244391.4XP_011242693.1  ataxin-1 isoform X1

      See identical proteins and their annotated locations for XP_011242693.1

      UniProtKB/Swiss-Prot
      P54254, Q8C866
      Conserved Domains (2) summary
      PHA03247
      Location:79280
      PHA03247; large tegument protein UL36; Provisional
      pfam08517
      Location:550661
      AXH; Ataxin-1 and HBP1 module (AXH)
    17. XM_017315463.3XP_017170952.1  ataxin-1 isoform X1

      UniProtKB/Swiss-Prot
      P54254, Q8C866
      Conserved Domains (2) summary
      PHA03247
      Location:79280
      PHA03247; large tegument protein UL36; Provisional
      pfam08517
      Location:550661
      AXH; Ataxin-1 and HBP1 module (AXH)