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ATXN3 ataxin 3 [ Homo sapiens (human) ]

Gene ID: 4287, updated on 12-Aug-2018

Summary

Official Symbol
ATXN3provided by HGNC
Official Full Name
ataxin 3provided by HGNC
Primary source
HGNC:HGNC:7106
See related
Ensembl:ENSG00000066427 MIM:607047; Vega:OTTHUMG00000162212
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
AT3; JOS; MJD; ATX3; MJD1; SCA3
Summary
Machado-Joseph disease, also known as spinocerebellar ataxia-3, is an autosomal dominant neurologic disorder. The protein encoded by this gene contains (CAG)n repeats in the coding region, and the expansion of these repeats from the normal 12-44 to 52-86 is one cause of Machado-Joseph disease. There is a negative correlation between the age of onset and CAG repeat numbers. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2016]
Expression
Ubiquitous expression in skin (RPKM 4.6), testis (RPKM 3.0) and 25 other tissues See more
Orthologs

Genomic context

See ATXN3 in Genome Data Viewer
Location:
14q32.12
Exon count:
13
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 14 NC_000014.9 (92058552..92106621, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (92524896..92572965, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene fibulin 5 Neighboring gene thyroid hormone receptor interactor 11 Neighboring gene prothymosin alpha pseudogene 7 Neighboring gene ataxin 3 repeat instability region Neighboring gene NADH:ubiquinone oxidoreductase subunit B1 Neighboring gene cleavage and polyadenylation specific factor 2

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Azorean disease Compare labs

NHGRI GWAS Catalog

Description
Genetics of coronary artery calcification among African Americans, a meta-analysis.
NHGRI GWA Catalog
Genome wide study of maternal and parent-of-origin effects on the etiology of orofacial clefts.
NHGRI GWA Catalog
Identification of ten loci associated with height highlights new biological pathways in human growth.
NHGRI GWA Catalog
Many sequence variants affecting diversity of adult human height.
NHGRI GWA Catalog

Pathways from BioSystems

  • Deubiquitination, organism-specific biosystem (from REACTOME)
    Deubiquitination, organism-specific biosystemUbiquitination, the modification of proteins by the covalent attachment of ubiquitin (Ub), is a key regulatory mechanism for many many cellular processes, including protein degradation by the 26S pro...
  • Josephin domain DUBs, organism-specific biosystem (from REACTOME)
    Josephin domain DUBs, organism-specific biosystemThe Josephin domain is present in four human DUBs: Ataxin-3 (ATXN3), ATXN3L, Josephin-1 (JOSD1) and JOSD2. All have been shown to possess DUB activity (Tzveltkov & Breuer 2007, Weeks et al. 2011). Jo...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • Protein processing in endoplasmic reticulum, organism-specific biosystem (from KEGG)
    Protein processing in endoplasmic reticulum, organism-specific biosystemThe endoplasmic reticulum (ER) is a subcellular organelle where proteins are folded with the help of lumenal chaperones. Newly synthesized peptides enter the ER via the sec61 pore and are glycosylate...
  • Protein processing in endoplasmic reticulum, conserved biosystem (from KEGG)
    Protein processing in endoplasmic reticulum, conserved biosystemThe endoplasmic reticulum (ER) is a subcellular organelle where proteins are folded with the help of lumenal chaperones. Newly synthesized peptides enter the ER via the sec61 pore and are glycosylate...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATPase binding IPI
Inferred from Physical Interaction
more info
PubMed 
Lys48-specific deubiquitinase activity IDA
Inferred from Direct Assay
more info
PubMed 
Lys63-specific deubiquitinase activity IDA
Inferred from Direct Assay
more info
PubMed 
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 ISS
Inferred from Sequence or Structural Similarity
more info
 
thiol-dependent ubiquitinyl hydrolase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
thiol-dependent ubiquitinyl hydrolase activity TAS
Traceable Author Statement
more info
 
ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin protein ligase binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
actin cytoskeleton organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to heat ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular response to misfolded protein ISS
Inferred from Sequence or Structural Similarity
more info
 
chemical synaptic transmission TAS
Traceable Author Statement
more info
PubMed 
intermediate filament cytoskeleton organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
microtubule cytoskeleton organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
monoubiquitinated protein deubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
 
nervous system development TAS
Traceable Author Statement
more info
PubMed 
nucleotide-excision repair TAS
Traceable Author Statement
more info
PubMed 
positive regulation of ERAD pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
proteasome-mediated ubiquitin-dependent protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
protein K48-linked deubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein K63-linked deubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein deubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein deubiquitination IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein deubiquitination TAS
Traceable Author Statement
more info
 
protein localization to cytosolic proteasome complex involved in ERAD pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein quality control for misfolded or incompletely synthesized proteins ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cell-substrate adhesion IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
ubiquitin-dependent protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
cytoplasm TAS
Traceable Author Statement
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
colocalizes_with endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
PubMed 
mitochondrial matrix ISS
Inferred from Sequence or Structural Similarity
more info
 
mitochondrial membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
nuclear inclusion body ISS
Inferred from Sequence or Structural Similarity
more info
 
nuclear matrix IEA
Inferred from Electronic Annotation
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
ataxin-3
Names
Machado-Joseph disease protein 1
josephin
olivopontocerebellar ataxia 3
spinocerebellar ataxia type 3 protein
NP_001121168.1
NP_001121169.2
NP_001158246.1
NP_001158248.1
NP_001158249.1
NP_001158250.1
NP_001158251.1
NP_001158252.1
NP_001158253.1
NP_001158254.1
NP_004984.2
NP_109376.1

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.

Genomic

  1. NG_008198.2 RefSeqGene

    Range
    5001..53070
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001127696.1NP_001121168.1  ataxin-3 isoform ad

    Status: REVIEWED

    Description
    Transcript Variant: This variant (ad, also known as variant 3) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant encodes isoform ad (also known as isoform 3).
    Source sequence(s)
    AB050194, AL049872, BU190081, DA827537
    Consensus CDS
    CCDS45154.1
    UniProtKB/Swiss-Prot
    P54252
    Related
    ENSP00000426697.1, OTTHUMP00000221587, ENST00000503767.5, OTTHUMT00000367926
    Conserved Domains (2) summary
    pfam02099
    Location:9148
    Josephin; Josephin
    pfam16619
    Location:249313
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3
  2. NM_001127697.2NP_001121169.2  ataxin-3 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (e, also known as variant 4) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant encodes isoform e (also known as isoform 4).
    Source sequence(s)
    AL049872, AL121773
    UniProtKB/TrEMBL
    A0A0A0MS38
    Related
    ENSP00000376965.6, ENST00000393287.9
    Conserved Domains (2) summary
    pfam02099
    Location:9112
    Josephin; Josephin
    pfam16619
    Location:213277
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3
  3. NM_001164774.1NP_001158246.1  ataxin-3 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (b) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant encodes isoform b.
    Source sequence(s)
    AL049872, AL121773
    Conserved Domains (1) summary
    pfam02099
    Location:956
    Josephin; Josephin
  4. NM_001164776.1NP_001158248.1  ataxin-3 isoform g

    Status: REVIEWED

    Description
    Transcript Variant: This variant (g) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant encodes isoform g.
    Source sequence(s)
    AL049872, AL121773
    Conserved Domains (1) summary
    pfam02099
    Location:978
    Josephin; Josephin
  5. NM_001164777.1NP_001158249.1  ataxin-3 isoform j

    Status: REVIEWED

    Description
    Transcript Variant: This variant (j) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant encodes isoform j.
    Source sequence(s)
    AL049872, AL121773
    Conserved Domains (1) summary
    pfam02099
    Location:1023
    Josephin; Josephin
  6. NM_001164778.1NP_001158250.1  ataxin-3 isoform o

    Status: REVIEWED

    Description
    Transcript Variant: This variant (o) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant encodes isoform o.
    Source sequence(s)
    AL049872, AL121773
    Conserved Domains (1) summary
    pfam02099
    Location:9129
    Josephin; Josephin
  7. NM_001164779.1NP_001158251.1  ataxin-3 isoform r

    Status: REVIEWED

    Description
    Transcript Variant: This variant (r) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant encodes isoform r.
    Source sequence(s)
    AL049872, AL121773
    Related
    ENSP00000450641.1, OTTHUMP00000245332, ENST00000556220.5, OTTHUMT00000412092
    Conserved Domains (2) summary
    pfam02099
    Location:542
    Josephin; Josephin
    pfam16619
    Location:143207
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3
  8. NM_001164780.1NP_001158252.1  ataxin-3 isoform u

    Status: REVIEWED

    Description
    Transcript Variant: This variant (u) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant encodes isoform u. PMID:19714377 predicts that this is a noncoding transcript, but there is a downstream orf that may encode a protein identical to the C-terminus of the reference isoform.
    Source sequence(s)
    AL049872, AL121773
    Consensus CDS
    CCDS53908.1
    UniProtKB/Swiss-Prot
    P54252
    Related
    ENSP00000425322.1, OTTHUMP00000221586, ENST00000502250.5, OTTHUMT00000367925
    Conserved Domains (1) summary
    pfam16619
    Location:85149
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3
  9. NM_001164781.1NP_001158253.1  ataxin-3 isoform y

    Status: REVIEWED

    Description
    Transcript Variant: This variant (y) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant encodes isoform y.
    Source sequence(s)
    AL049872, AL121773
    Consensus CDS
    CCDS73680.1
    UniProtKB/TrEMBL
    C9JQV6
    Related
    ENSP00000389376.3, ENST00000429774.6
    Conserved Domains (2) summary
    pfam02099
    Location:993
    Josephin; Josephin
    pfam16619
    Location:194258
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3
  10. NM_001164782.1NP_001158254.1  ataxin-3 isoform ae

    Status: REVIEWED

    Description
    Transcript Variant: This variant (ae) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant encodes isoform ae.
    Source sequence(s)
    AL049872, AL121773
  11. NM_004993.5NP_004984.2  ataxin-3 reference isoform

    See identical proteins and their annotated locations for NP_004984.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (reference, also known as variant 1) encodes the longest isoform (reference isoform, also known as isoform 1).
    Source sequence(s)
    AB050194, AL049872, DA827537
    Consensus CDS
    CCDS9900.1
    UniProtKB/Swiss-Prot
    P54252
    Related
    ENSP00000478320.1, OTTHUMP00000221583, ENST00000558190.6, OTTHUMT00000367922
    Conserved Domains (2) summary
    pfam02099
    Location:11163
    Josephin; Josephin
    pfam16619
    Location:264328
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3
  12. NM_030660.4NP_109376.1  ataxin-3 isoform h

    See identical proteins and their annotated locations for NP_109376.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (h, also known as variant 2) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant encodes isoform h (also known as isoform 2).
    Source sequence(s)
    AB050194, AL049872, DA827537
    Consensus CDS
    CCDS32143.1
    UniProtKB/Swiss-Prot
    P54252
    Related
    ENSP00000339110.6, OTTHUMP00000221585, ENST00000340660.10, OTTHUMT00000367924
    Conserved Domains (2) summary
    pfam02099
    Location:10108
    Josephin; Josephin
    pfam16619
    Location:209273
    SUIM_assoc; Unstructured region C-term to UIM in Ataxin3

RNA

  1. NR_028453.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (a) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant is not thought to be protein-coding.
    Source sequence(s)
    AL049872, AL121773
  2. NR_028454.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (d) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant is not thought to be protein-coding.
    Source sequence(s)
    AL049872, AL121773
  3. NR_028455.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (f) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant is not thought to be protein-coding.
    Source sequence(s)
    AL049872, AL121773
  4. NR_028456.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (i) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant is not thought to be protein-coding.
    Source sequence(s)
    AL049872, AL121773
  5. NR_028457.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (k) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant is not thought to be protein-coding.
    Source sequence(s)
    AL049872, AL121773
  6. NR_028458.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (l) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant is not thought to be protein-coding.
    Source sequence(s)
    AL049872, AL121773
  7. NR_028459.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (m) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant is a nonsense-mediated mRNA decay candidate and is not thought to be protein-coding, although PMID:19714377 predicts that it is protein-coding.
    Source sequence(s)
    AL049872, AL121773
  8. NR_028460.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (n) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant is not thought to be protein-coding.
    Source sequence(s)
    AL049872, AL121773
  9. NR_028461.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (p) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant is not thought to be protein-coding.
    Source sequence(s)
    AL049872, AL121773
  10. NR_028462.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (q) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant is a nonsense-mediated mRNA decay candidate and is not thought to be protein-coding, although PMID:19714377 predicts that it is protein-coding.
    Source sequence(s)
    AL049872, AL121773
  11. NR_028463.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (t) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant is not thought to be protein-coding.
    Source sequence(s)
    AL049872, AL121773
  12. NR_028464.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (v) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant is a nonsense-mediated mRNA decay candidate and is not thought to be protein-coding, although PMID:19714377 predicts that it is protein-coding.
    Source sequence(s)
    AL049872, AL121773
  13. NR_028465.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (w) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant is not thought to be protein-coding.
    Source sequence(s)
    AL049872, AL121773
  14. NR_028466.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (x) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant is not thought to be protein-coding.
    Source sequence(s)
    AL049872, AL121773
  15. NR_028467.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (z) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant is not thought to be protein-coding.
    Source sequence(s)
    AL049872, AL121773
  16. NR_028468.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (ac) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant is not thought to be protein-coding.
    Source sequence(s)
    AL049872, AL121773
  17. NR_028469.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (af) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant is not thought to be protein-coding.
    Source sequence(s)
    AL049872, AL121773
  18. NR_028470.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (am) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant is not thought to be protein-coding.
    Source sequence(s)
    AL049872, AL121773
  19. NR_031765.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (c) is one of several transcript variants described in figure 2 of Bettencourt et al. (PMID: 19714377). This variant is not thought to be protein-coding.
    Source sequence(s)
    AL049872, AL121773

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p12 Primary Assembly

    Range
    92058552..92106621 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001024631.1: Suppressed sequence

    Description
    NM_001024631.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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