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Atxn3 ataxin 3 [ Rattus norvegicus (Norway rat) ]

Gene ID: 60331, updated on 10-Jul-2024

Summary

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Official Symbol
Atxn3provided by RGD
Official Full Name
ataxin 3provided by RGD
Primary source
RGD:621567
See related
EnsemblRapid:ENSRNOG00000005470 AllianceGenome:RGD:621567
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
MJD1; Rsca3
Summary
Enables RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Contributes to histone deacetylase activity. Involved in histone H3 deacetylation. Located in nucleus. Human ortholog(s) of this gene implicated in Machado-Joseph disease. Orthologous to several human genes including ATXN3 (ataxin 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Thymus (RPKM 100.1), Lung (RPKM 99.8) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Atxn3 in Genome Data Viewer
Location:
6q32
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 6 NC_086024.1 (126837107..126872919, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 6 NC_051341.1 (121072228..121107902, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 6 NC_005105.4 (125817420..125853461, complement)

Chromosome 6 - NC_086024.1Genomic Context describing neighboring genes Neighboring gene fibulin 5 Neighboring gene thyroid hormone receptor interactor 11 Neighboring gene uncharacterized LOC120103604 Neighboring gene ribosomal protein L37A, pseudogene 6 Neighboring gene uncharacterized LOC134479251 Neighboring gene LLP homolog, long-term synaptic facilitation factor, pseudogene 1 Neighboring gene NADH:ubiquinone oxidoreductase subunit B1

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. Silencing ataxin-3 mitigates degeneration in a rat model of Machado-Joseph disease: no role for wild-type ataxin-3? Alves S, et al. Hum Mol Genet, 2010 Jun 15. PMID 20308049
  2. Allele-specific RNA silencing of mutant ataxin-3 mediates neuroprotection in a rat model of Machado-Joseph disease. Alves S, et al. PLoS One, 2008 Oct 8. PMID 18841197, Free PMC Article
  3. Characterization of the rat spinocerebellar ataxia type 3 gene. Schmitt I, et al. Neurogenetics, 1997 Sep. PMID 10732811
  4. An isoform of ataxin-3 accumulates in the nucleus of neuronal cells in affected brain regions of SCA3 patients. Schmidt T, et al. Brain Pathol, 1998 Oct. PMID 9804376, Free PMC Article
  5. The role of the central flexible region on the aggregation and conformational properties of human ataxin-3. Santambrogio C, et al. FEBS J, 2012 Feb. PMID 22129356

See all (31) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Ataxin-3 phosphorylation decreases neuronal defects in spinocerebellar ataxia type 3 models.
    Title: Ataxin-3 phosphorylation decreases neuronal defects in spinocerebellar ataxia type 3 models.
  2. Data support the importance of ATXN3 in neuronal cells and indicate that an expanded polyQ tract leads to a partial loss of the cellular function of ATXN3 that may be relevant to neurodegeneration.
    Title: Dominant negative effect of polyglutamine expansion perturbs normal function of ataxin-3 in neuronal cells.
  3. CK2-dependent phosphorylation controls the nuclear localization, aggregation and stability of ataxin-3.
    Title: CK2-dependent phosphorylation determines cellular localization and stability of ataxin-3.
Submit: New GeneRIF Correction

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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Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables ATPase binding ISO
Inferred from Sequence Orthology
more info
  
enables ATPase binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables K48-linked deubiquitinase activity ISO
Inferred from Sequence Orthology
more info
  
enables K48-linked deubiquitinase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables K63-linked deubiquitinase activity ISO
Inferred from Sequence Orthology
more info
  
enables K63-linked deubiquitinase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables cysteine-type deubiquitinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables cysteine-type deubiquitinase activity IEA
Inferred from Electronic Annotation
more info
  
enables cysteine-type deubiquitinase activity ISO
Inferred from Sequence Orthology
more info
  
enables cysteine-type deubiquitinase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
contributes_to histone deacetylase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone deacetylase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
  
enables identical protein binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables transcription corepressor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin protein ligase binding IEA
Inferred from Electronic Annotation
more info
  
enables ubiquitin protein ligase binding ISO
Inferred from Sequence Orthology
more info
  
enables ubiquitin protein ligase binding ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within actin cytoskeleton organization ISO
Inferred from Sequence Orthology
more info
  
involved_in actin cytoskeleton organization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cellular response to amino acid starvation ISO
Inferred from Sequence Orthology
more info
  
involved_in cellular response to amino acid starvation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cellular response to heat IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within cellular response to heat ISO
Inferred from Sequence Orthology
more info
  
involved_in cellular response to misfolded protein IEA
Inferred from Electronic Annotation
more info
  
involved_in cellular response to misfolded protein ISO
Inferred from Sequence Orthology
more info
  
involved_in cellular response to misfolded protein ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
involved_in exploration behavior IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within exploration behavior ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within intermediate filament cytoskeleton organization ISO
Inferred from Sequence Orthology
more info
  
involved_in intermediate filament cytoskeleton organization ISS
Inferred from Sequence or Structural Similarity
more info
  
acts_upstream_of_or_within microtubule cytoskeleton organization ISO
Inferred from Sequence Orthology
more info
  
involved_in microtubule cytoskeleton organization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in monoubiquitinated protein deubiquitination IEA
Inferred from Electronic Annotation
more info
  
involved_in monoubiquitinated protein deubiquitination ISO
Inferred from Sequence Orthology
more info
  
involved_in monoubiquitinated protein deubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of TORC1 signaling ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of TORC1 signaling ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of ERAD pathway ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of ubiquitin-dependent protein catabolic process ISO
Inferred from Sequence Orthology
more info
  
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process ISO
Inferred from Sequence Orthology
more info
  
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein K48-linked deubiquitination ISO
Inferred from Sequence Orthology
more info
  
involved_in protein K48-linked deubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein K63-linked deubiquitination ISO
Inferred from Sequence Orthology
more info
  
involved_in protein K63-linked deubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein deubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein localization to cytosolic proteasome complex ISO
Inferred from Sequence Orthology
more info
  
involved_in protein modification process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein quality control for misfolded or incompletely synthesized proteins IEA
Inferred from Electronic Annotation
more info
  
involved_in protein quality control for misfolded or incompletely synthesized proteins ISO
Inferred from Sequence Orthology
more info
  
involved_in protein quality control for misfolded or incompletely synthesized proteins ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in proteolysis IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of cell-substrate adhesion IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within regulation of cell-substrate adhesion ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of cell-substrate adhesion ISS
Inferred from Sequence or Structural Similarity
more info
  
acts_upstream_of_or_within ubiquitin-dependent protein catabolic process ISO
Inferred from Sequence Orthology
more info
  
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 cytosol ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in endoplasmic reticulum membrane ISO
Inferred from Sequence Orthology
more info
  
is_active_in lysosomal membrane ISO
Inferred from Sequence Orthology
more info
  
is_active_in lysosomal membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in mitochondrial matrix IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrial matrix ISO
Inferred from Sequence Orthology
more info
  
located_in mitochondrial membrane IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrial membrane ISO
Inferred from Sequence Orthology
more info
  
located_in nuclear inclusion body IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear inclusion body ISO
Inferred from Sequence Orthology
more info
  
located_in nuclear matrix 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
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
ataxin-3
Names
machado-Joseph disease protein 1 homolog
NP_067734.1
XP_006240547.1
XP_006240548.1
XP_006240549.1
XP_006240550.1
XP_006240552.1
XP_006240555.1
XP_017449826.1
XP_038968739.1
XP_063118464.1
XP_063118465.1
XP_063118466.1
XP_063118467.1
XP_063118468.1
XP_063118469.1
XP_063118470.1
XP_063118471.1
XP_063118472.1
XP_063118473.1
XP_063118474.1

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.

mRNA and Protein(s)

  1. NM_021702.2 → NP_067734.1  ataxin-3

    See identical proteins and their annotated locations for NP_067734.1

    Status: PROVISIONAL

    Source sequence(s)
    JAXUCZ010000006
    UniProtKB/Swiss-Prot
    O35815
    UniProtKB/TrEMBL
    A0A8I6A6D3, A6JEJ5
    Related
    ENSRNOP00000007505.1, ENSRNOT00000007505.4
    Conserved Domains (2) summary
    pfam02099
    Location:9 → 163
    Josephin; Josephin
    pfam16619
    Location:264 → 321
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3

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_086024.1 Reference GRCr8

    Range
    126837107..126872919 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063262400.1 → XP_063118470.1  ataxin-3 isoform X12

    UniProtKB/TrEMBL
    A0A8I6A6D3

  2. XM_063262395.1 → XP_063118465.1  ataxin-3 isoform X7

    UniProtKB/TrEMBL
    A0A8I6A6D3

  3. XM_006240488.5 → XP_006240550.1  ataxin-3 isoform X5

    UniProtKB/TrEMBL
    A0A8I6A6D3
    Conserved Domains (2) summary
    pfam02099
    Location:9 → 162
    Josephin; Josephin
    pfam16619
    Location:263 → 320
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3

  4. XM_063262399.1 → XP_063118469.1  ataxin-3 isoform X11

    UniProtKB/TrEMBL
    A0A8I6A6D3

  5. XM_006240493.5 → XP_006240555.1  ataxin-3 isoform X6

    UniProtKB/TrEMBL
    A0A8I6A6D3
    Conserved Domains (2) summary
    pfam02099
    Location:9 → 163
    Josephin; Josephin
    pfam16619
    Location:264 → 321
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3

  6. XM_063262396.1 → XP_063118466.1  ataxin-3 isoform X9

    UniProtKB/TrEMBL
    A0A8I6A6D3

  7. XM_063262394.1 → XP_063118464.1  ataxin-3 isoform X4

    UniProtKB/TrEMBL
    A0A8I6A6D3

  8. XM_006240486.5 → XP_006240548.1  ataxin-3 isoform X3

    UniProtKB/TrEMBL
    A0A8I6A6D3
    Conserved Domains (2) summary
    pfam02099
    Location:9 → 189
    Josephin; Josephin
    pfam16619
    Location:290 → 347
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3

  9. XM_006240487.5 → XP_006240549.1  ataxin-3 isoform X2

    UniProtKB/TrEMBL
    A0A8I6A6D3
    Conserved Domains (2) summary
    pfam02099
    Location:9 → 190
    Josephin; Josephin
    pfam16619
    Location:291 → 348
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3

  10. XM_006240485.5 → XP_006240547.1  ataxin-3 isoform X1

    UniProtKB/TrEMBL
    A0A8I6A6D3, A0A8I6GJ61
    Related
    ENSRNOP00000091691.1, ENSRNOT00000099444.2
    Conserved Domains (2) summary
    pfam02099
    Location:9 → 190
    Josephin; Josephin
    pfam16619
    Location:291 → 348
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3

  11. XM_017594337.3 → XP_017449826.1  ataxin-3 isoform X8

    UniProtKB/TrEMBL
    A0A8I6A6D3

  12. XM_063262397.1 → XP_063118467.1  ataxin-3 isoform X10

    UniProtKB/TrEMBL
    A0A8I6A6D3

  13. XM_006240490.3 → XP_006240552.1  ataxin-3 isoform X11

    UniProtKB/TrEMBL
    A0A8I6A6D3
    Conserved Domains (2) summary
    pfam02099
    Location:1 → 143
    Josephin
    pfam16619
    Location:244 → 302
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3

  14. XM_063262398.1 → XP_063118468.1  ataxin-3 isoform X11

    UniProtKB/TrEMBL
    A0A8I6A6D3

  15. XM_039112811.2 → XP_038968739.1  ataxin-3 isoform X11

    UniProtKB/TrEMBL
    A0A8I6A6D3
    Conserved Domains (2) summary
    pfam02099
    Location:1 → 143
    Josephin
    pfam16619
    Location:244 → 302
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3

  16. XM_063262401.1 → XP_063118471.1  ataxin-3 isoform X13

    Related
    ENSRNOP00000108385.1, ENSRNOT00000151556.1

  17. XM_063262404.1 → XP_063118474.1  ataxin-3 isoform X16

  18. XM_063262403.1 → XP_063118473.1  ataxin-3 isoform X15

  19. XM_063262402.1 → XP_063118472.1  ataxin-3 isoform X14

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O35815.1 GenPept UniProtKB/Swiss-Prot:O35815

Gene LinkOut

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