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Atxn1 ataxin 1 [ Mus musculus (house mouse) ]

Gene ID: 20238, updated on 8-Feb-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 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, Apr 2022]
Expression
Ubiquitous expression in cortex adult (RPKM 5.7), frontal lobe adult (RPKM 4.8) and 28 other tissues See more
Orthologs
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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 IDA
Inferred from Direct Assay
more info
PubMed 
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(U) RNA binding ISO
Inferred from Sequence Orthology
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein self-association ISO
Inferred from Sequence Orthology
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 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
 
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 nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in nuclear export ISO
Inferred from Sequence Orthology
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 regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
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 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 matrix ISO
Inferred from Sequence Orthology
more info
 
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
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
 
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)