Atxn3 ataxin 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Atxn3provided by RGD
Official Full Name: ataxin 3provided by RGD
Primary source: RGD:621567
See related: Ensembl: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

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_086024.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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 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

EC 3.4.19.12

XP_006240547.1

EC 3.4.19.12

XP_006240548.1

EC 3.4.19.12

XP_006240549.1

EC 3.4.19.12

XP_006240550.1

EC 3.4.19.12

XP_006240552.1

EC 3.4.19.12

XP_006240555.1

EC 3.4.19.12

XP_017449826.1

EC 3.4.19.12

XP_038968739.1

EC 3.4.19.12

XP_063118464.1

EC 3.4.19.12

XP_063118465.1

EC 3.4.19.12

XP_063118466.1

EC 3.4.19.12

XP_063118467.1

EC 3.4.19.12

XP_063118468.1

EC 3.4.19.12

XP_063118469.1

EC 3.4.19.12

XP_063118470.1

EC 3.4.19.12

XP_063118471.1

EC 3.4.19.12

XP_063118472.1

EC 3.4.19.12

XP_063118473.1

EC 3.4.19.12

XP_063118474.1

EC 3.4.19.12

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)

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, ENSRNOT00000007505.3

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

NC_086024.1 Reference GRCr8

Range

126837107..126872919 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A8I6A6D3
XM_063262395.1 → XP_063118465.1 ataxin-3 isoform X7

UniProtKB/TrEMBL

A0A8I6A6D3
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
XM_063262399.1 → XP_063118469.1 ataxin-3 isoform X11

UniProtKB/TrEMBL

A0A8I6A6D3
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
XM_063262396.1 → XP_063118466.1 ataxin-3 isoform X9

UniProtKB/TrEMBL

A0A8I6A6D3
XM_063262394.1 → XP_063118464.1 ataxin-3 isoform X4

UniProtKB/TrEMBL

A0A8I6A6D3
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
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
XM_006240485.5 → XP_006240547.1 ataxin-3 isoform X1

UniProtKB/TrEMBL

A0A8I6A6D3, A0A8I6GJ61

Related

ENSRNOP00000091691.1

Conserved Domains (2) summary

pfam02099
Location:9 → 190

Josephin; Josephin

pfam16619
Location:291 → 348

SUIM_assoc; Unstructured region C-term to UIM in Ataxin3
XM_017594337.3 → XP_017449826.1 ataxin-3 isoform X8

UniProtKB/TrEMBL

A0A8I6A6D3
XM_063262397.1 → XP_063118467.1 ataxin-3 isoform X10

UniProtKB/TrEMBL

A0A8I6A6D3
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
XM_063262398.1 → XP_063118468.1 ataxin-3 isoform X11

UniProtKB/TrEMBL

A0A8I6A6D3
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
XM_063262401.1 → XP_063118471.1 ataxin-3 isoform X13
XM_063262404.1 → XP_063118474.1 ataxin-3 isoform X16
XM_063262403.1 → XP_063118473.1 ataxin-3 isoform X15
XM_063262402.1 → XP_063118472.1 ataxin-3 isoform X14