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Atxn3 ataxin 3 [ Rattus norvegicus (Norway rat) ]

Gene ID: 60331, updated on 2-Oct-2018

Summary

Official Symbol
Atxn3provided by RGD
Official Full Name
ataxin 3provided by RGD
Primary source
RGD:621567
See related
Ensembl:ENSRNOG00000005470
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
gene associated with spinocerebellar ataxia type 3 [RGD, Feb 2006]
Expression
Biased expression in Thymus (RPKM 100.1), Lung (RPKM 99.8) and 9 other tissues See more
Orthologs

Genomic context

See Atxn3 in Genome Data Viewer
Location:
6q32
Exon count:
13
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 6 NC_005105.4 (125817420..125853461, complement)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 6 NC_005105.3 (135029278..135065455, complement)

Chromosome 6 - NC_005105.4Genomic Context describing neighboring genes Neighboring gene fibulin 5 Neighboring gene thyroid hormone receptor interactor 11 Neighboring gene putative 60S ribosomal protein L37a-like Neighboring gene uncharacterized LOC103692691 Neighboring gene protein LLP homolog Neighboring gene NADH:ubiquinone oxidoreductase subunit B1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
ATPase binding ISO
Inferred from Sequence Orthology
more info
 
ATPase binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Lys48-specific deubiquitinase activity ISO
Inferred from Sequence Orthology
more info
 
Lys48-specific deubiquitinase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
Lys63-specific deubiquitinase activity ISO
Inferred from Sequence Orthology
more info
 
Lys63-specific deubiquitinase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
RNA polymerase II regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
contributes_to histone deacetylase activity IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding ISO
Inferred from Sequence Orthology
more info
 
identical protein binding ISS
Inferred from Sequence or Structural Similarity
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
thiol-dependent ubiquitin-specific protease activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
thiol-dependent ubiquitin-specific protease activity ISO
Inferred from Sequence Orthology
more info
 
thiol-dependent ubiquitin-specific protease activity ISS
Inferred from Sequence or Structural Similarity
more info
 
thiol-dependent ubiquitinyl hydrolase activity ISO
Inferred from Sequence Orthology
more info
 
thiol-dependent ubiquitinyl hydrolase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
ubiquitin protein ligase binding ISO
Inferred from Sequence Orthology
more info
 
ubiquitin protein ligase binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
actin cytoskeleton organization ISO
Inferred from Sequence Orthology
more info
 
actin cytoskeleton organization ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular response to heat IEA
Inferred from Electronic Annotation
more info
 
cellular response to heat ISO
Inferred from Sequence Orthology
more info
 
cellular response to misfolded protein ISO
Inferred from Sequence Orthology
more info
 
cellular response to misfolded protein ISS
Inferred from Sequence or Structural Similarity
more info
 
exploration behavior IEA
Inferred from Electronic Annotation
more info
 
exploration behavior ISO
Inferred from Sequence Orthology
more info
 
histone H3 deacetylation IEP
Inferred from Expression Pattern
more info
PubMed 
intermediate filament cytoskeleton organization ISO
Inferred from Sequence Orthology
more info
 
intermediate filament cytoskeleton organization ISS
Inferred from Sequence or Structural Similarity
more info
 
microtubule cytoskeleton organization ISO
Inferred from Sequence Orthology
more info
 
microtubule cytoskeleton organization ISS
Inferred from Sequence or Structural Similarity
more info
 
monoubiquitinated protein deubiquitination ISO
Inferred from Sequence Orthology
more info
 
monoubiquitinated protein deubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of ERAD pathway IEA
Inferred from Electronic Annotation
more info
 
positive regulation of ERAD pathway ISO
Inferred from Sequence Orthology
more info
 
proteasome-mediated ubiquitin-dependent protein catabolic process ISO
Inferred from Sequence Orthology
more info
 
proteasome-mediated ubiquitin-dependent protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
protein K48-linked deubiquitination ISO
Inferred from Sequence Orthology
more info
 
protein K48-linked deubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
 
protein K63-linked deubiquitination ISO
Inferred from Sequence Orthology
more info
 
protein K63-linked deubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
 
protein deubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein deubiquitination ISO
Inferred from Sequence Orthology
more info
 
protein localization to cytosolic proteasome complex involved in ERAD pathway IEA
Inferred from Electronic Annotation
more info
 
protein localization to cytosolic proteasome complex involved in ERAD pathway ISO
Inferred from Sequence Orthology
more info
 
protein quality control for misfolded or incompletely synthesized proteins ISO
Inferred from Sequence Orthology
more info
 
protein quality control for misfolded or incompletely synthesized proteins ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cell-substrate adhesion ISO
Inferred from Sequence Orthology
more info
 
regulation of cell-substrate adhesion ISS
Inferred from Sequence or Structural Similarity
more info
 
ubiquitin-dependent protein catabolic process ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
cytoplasm ISO
Inferred from Sequence Orthology
more info
 
cytosol ISO
Inferred from Sequence Orthology
more info
 
cytosol ISS
Inferred from Sequence or Structural Similarity
more info
 
endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 
colocalizes_with endoplasmic reticulum membrane ISO
Inferred from Sequence Orthology
more info
 
mitochondrial matrix IEA
Inferred from Electronic Annotation
more info
 
mitochondrial matrix ISO
Inferred from Sequence Orthology
more info
 
mitochondrial membrane IEA
Inferred from Electronic Annotation
more info
 
mitochondrial membrane ISO
Inferred from Sequence Orthology
more info
 
nuclear inclusion body IEA
Inferred from Electronic Annotation
more info
 
nuclear inclusion body ISO
Inferred from Sequence Orthology
more info
 
nucleolus IEA
Inferred from Electronic Annotation
more info
 
nucleolus ISO
Inferred from Sequence Orthology
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus ISO
Inferred from Sequence Orthology
more info
 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane ISO
Inferred from Sequence Orthology
more info
 

General protein information

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_017449827.1

NCBI Reference Sequences (RefSeq)

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_021702.1NP_067734.1  ataxin-3

    See identical proteins and their annotated locations for NP_067734.1

    Status: PROVISIONAL

    Source sequence(s)
    Y12319
    UniProtKB/Swiss-Prot
    O35815
    Related
    ENSRNOP00000007505.1, ENSRNOT00000007505.2
    Conserved Domains (2) summary
    pfam02099
    Location:9163
    Josephin; Josephin
    pfam16619
    Location:264321
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

Reference Rnor_6.0 Primary Assembly

Genomic

  1. NC_005105.4 Reference Rnor_6.0 Primary Assembly

    Range
    125817420..125853461 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (2) summary
    pfam02099
    Location:9162
    Josephin; Josephin
    pfam16619
    Location:263320
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3
  2. XM_006240486.3XP_006240548.1  ataxin-3 isoform X3

    Conserved Domains (2) summary
    pfam02099
    Location:9189
    Josephin; Josephin
    pfam16619
    Location:290347
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3
  3. XM_006240493.3XP_006240555.1  ataxin-3 isoform X4

    Conserved Domains (2) summary
    pfam02099
    Location:9163
    Josephin; Josephin
    pfam16619
    Location:264321
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3
  4. XM_006240487.3XP_006240549.1  ataxin-3 isoform X2

    Conserved Domains (2) summary
    pfam02099
    Location:9190
    Josephin; Josephin
    pfam16619
    Location:291348
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3
  5. XM_006240485.3XP_006240547.1  ataxin-3 isoform X1

    Conserved Domains (2) summary
    pfam02099
    Location:9190
    Josephin; Josephin
    pfam16619
    Location:291348
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3
  6. XM_017594337.1XP_017449826.1  ataxin-3 isoform X6

  7. XM_006240490.1XP_006240552.1  ataxin-3 isoform X7

    Conserved Domains (3) summary
    pfam02099
    Location:13143
    Josephin; Josephin
    pfam02809
    Location:204219
    UIM; Ubiquitin interaction motif
    pfam16619
    Location:244301
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3
  8. XM_017594338.1XP_017449827.1  ataxin-3 isoform X8

Alternate Rn_Celera

Genomic

  1. AC_000074.1 Alternate Rn_Celera

    Range
    118571601..118605060 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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