ATXN3L Gene (Protein Coding)

Ataxin 3 Like

GC0XM013336
GIFtS:
34
This intronless gene may be a pseudogene (PMID:11450850). This gene is similar to the multi-exon gene which encodes ataxin 3 and contains a coding region which could encode a protein similar to ataxin 3. Mutations in the gene encoding ataxin 3 are associated with Machado-Joseph disease. [provided by RefSeq, Sep 2011] See more...

Aliases for ATXN3L Gene

Aliases for ATXN3L Gene

  • Ataxin 3 Like 2 3 5
  • MJDL 2 3 4
  • Machado-Joseph Disease Protein 1-Like 3 4
  • Ataxin-3-Like Protein 3 4
  • Putative Ataxin-3-Like Protein 3
  • Ataxin 3-Like 2
  • EC 3.4.19.12 4
  • EC 3.4.22 50
  • ATXN3L 5
  • ATX3L 4

External Ids for ATXN3L Gene

Previous GeneCards Identifiers for ATXN3L Gene

  • GC0XM013096
  • GC0XM013246
  • GC0XM011098

Summaries for ATXN3L Gene

Entrez Gene Summary for ATXN3L Gene

  • This intronless gene may be a pseudogene (PMID:11450850). This gene is similar to the multi-exon gene which encodes ataxin 3 and contains a coding region which could encode a protein similar to ataxin 3. Mutations in the gene encoding ataxin 3 are associated with Machado-Joseph disease. [provided by RefSeq, Sep 2011]

GeneCards Summary for ATXN3L Gene

ATXN3L (Ataxin 3 Like) is a Protein Coding gene. Diseases associated with ATXN3L include Machado-Joseph Disease and Autosomal Dominant Cerebellar Ataxia. Among its related pathways are Pathways of neurodegeneration - multiple diseases and Spinocerebellar ataxia. Gene Ontology (GO) annotations related to this gene include ubiquitin protein ligase binding and obsolete ubiquitin thiolesterase activity. An important paralog of this gene is ATXN3.

UniProtKB/Swiss-Prot Summary for ATXN3L Gene

  • Deubiquitinating enzyme that cleaves both 'Lys-48'-linked and 'Lys-63'-linked poly-ubiquitin chains (in vitro).

Additional gene information for ATXN3L Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ATXN3L Gene

Genomics for ATXN3L Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for ATXN3L Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH0XJ013687 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 3.4 -371.1 -371121 7.1 BCLAF1 IKZF1 ZNF600 ZNF580 ATF2 JUND POLR2A ZIC2 YY1 CEBPB OFD1 RAB9A TCEANC TRAPPC2 ATXN3L HSALNG0136723 HSALNG0136724
GH0XJ012945 Enhancer 1.5 FANTOM5 ENCODE dbSUPER 1.4 +368.0 368044 13.1 BCLAF1 SP1 ZNF207 NCOR1 MYC ZNF654 IKZF1 JUND ZNF592 POLR2A TLR8 TMSB4X OFD1 TLR8-AS1 TLR7 ATXN3L lnc-TMSB4X-5 HSALNG0136678-002
GH0XJ012841 Enhancer 0.2 FANTOM5 4.8 +478.6 478601 0 piR-43105-683 ATXN3L lnc-FAM9C-5 HSALNG0136681 HSALNG0136677 lnc-FAM9C-6 TLR7 HSALNG0136678-001 PRPS2 HSALNG0136678-002
GH0XJ013282 Enhancer 1.2 FANTOM5 Ensembl ENCODE 0.3 +34.9 34885 6.6 IKZF1 NCOR1 JUND ZNF592 NFIC CEBPB SIN3A ARNT IRF2 EP300 LINC02154 lnc-EGFL6-12 lnc-TMSB4X-8 ATXN3L lnc-TMSB4X-7 RF00017-7561 FAM9C
GH0XJ013303 Promoter/Enhancer 0.8 EPDnew Ensembl 0.4 +15.4 15398 3.6 SPI1 POLR2A SOX6 MNT LINC02154 HSALNG0136704 HSALNG0136705-001 ATXN3L lnc-ATXN3L-4 RF00017-7561 FAM9C
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ATXN3L on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ATXN3L

Top Transcription factor binding sites by QIAGEN in the ATXN3L gene promoter:
  • AP-1
  • c-Fos
  • c-Jun
  • Pax-2
  • Pax-2a
  • POU2F1a
  • POU2F2
  • POU2F2 (Oct-2.1)
  • POU2F2B
  • POU3F1

Genomic Locations for ATXN3L Gene

Latest Assembly
chrX:13,318,236-13,320,399
(GRCh38/hg38)
Size:
2,164 bases
Orientation:
Minus strand

Previous Assembly
chrX:13,336,766-13,338,172
(GRCh37/hg19 by Entrez Gene)
Size:
1,407 bases
Orientation:
Minus strand

chrX:13,336,770-13,338,518
(GRCh37/hg19 by Ensembl)
Size:
1,749 bases
Orientation:
Minus strand

Genomic View for ATXN3L Gene

Genes around ATXN3L on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATXN3L Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATXN3L Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for ATXN3L Gene

Proteins for ATXN3L Gene

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  3. Assay products for research

  • Protein details for ATXN3L Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H3M9-ATX3L_HUMAN
    Recommended name:
    Ataxin-3-like protein
    Protein Accession:
    Q9H3M9
    Secondary Accessions:
    • B2RNY8

    Protein attributes for ATXN3L Gene

    Size:
    355 amino acids
    Molecular mass:
    40747 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for ATXN3L Gene

neXtProt entry for ATXN3L Gene

Protein Expression for ATXN3L Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for ATXN3L Gene

Q9H3M9:
  • LCAQHCLNNLLQGEYFSPVEL
  • FVVKGDLPDCEADQLLQ
  • IFHEKQEG
  • GPELISDT
  • WFNLNSLL

Post-translational modifications for ATXN3L Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ATXN3L Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for ATXN3L Gene

Gene Families for ATXN3L Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for ATXN3L Gene

InterPro:
Blocks:
  • Ubiquitin interacting motif
  • Josephin signature

Suggested Antigen Peptide Sequences for ATXN3L Gene

GenScript: Design optimal peptide antigens:
  • Machado-Joseph disease protein 1-like (ATX3L_HUMAN)
genes like me logo Genes that share domains with ATXN3L: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for ATXN3L Gene

Function for ATXN3L Gene

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  6. Cell Lines for research

Molecular function for ATXN3L Gene

UniProtKB/Swiss-Prot Function:
Deubiquitinating enzyme that cleaves both 'Lys-48'-linked and 'Lys-63'-linked poly-ubiquitin chains (in vitro).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).; EC=3.4.19.12; Evidence={ECO:0000269|PubMed:21118805};.

Enzyme Numbers (IUBMB) for ATXN3L Gene

Phenotypes From GWAS Catalog for ATXN3L Gene

Gene Ontology (GO) - Molecular Function for ATXN3L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004843 thiol-dependent ubiquitin-specific protease activity IEA,IDA 21118805
GO:0008233 peptidase activity IEA --
GO:0008234 cysteine-type peptidase activity IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with ATXN3L: view

Phenotypes for ATXN3L Gene

GenomeRNAi human phenotypes for ATXN3L:
genes like me logo Genes that share phenotypes with ATXN3L: view

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATXN3L

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ATXN3L Gene

Localization for ATXN3L Gene

Subcellular locations from UniProtKB/Swiss-Prot for ATXN3L Gene

Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ATXN3L gene
Compartment Confidence
nucleus 4
cytosol 4
extracellular 0

Gene Ontology (GO) - Cellular Components for ATXN3L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IBA 21873635
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with ATXN3L: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for ATXN3L Gene

Pathways & Interactions for ATXN3L Gene

genes like me logo Genes that share pathways with ATXN3L: view

Gene Ontology (GO) - Biological Process for ATXN3L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IEA --
GO:0016579 protein deubiquitination IEA,TAS --
GO:0018215 protein phosphopantetheinylation IEA --
genes like me logo Genes that share ontologies with ATXN3L: view

No data available for SIGNOR curated interactions for ATXN3L Gene

Drugs & Compounds for ATXN3L Gene

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  1. Drug products for research
No Compound Related Data Available

Transcripts for ATXN3L Gene

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mRNA/cDNA for ATXN3L Gene

2 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ATXN3L

Alternative Splicing Database (ASD) splice patterns (SP) for ATXN3L Gene

No ASD Table

Relevant External Links for ATXN3L Gene

GeneLoc Exon Structure for
ATXN3L

Expression for ATXN3L Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ATXN3L Gene

mRNA expression in normal human tissues for ATXN3L Gene
mRNA expression by BioGPS for ATXN3L GenemRNA expression by GTEx for ATXN3L Gene

mRNA differential expression in normal tissues according to GTEx for ATXN3L Gene

This gene is overexpressed in Testis (x50.7).

Protein differential expression in normal tissues from HIPED for ATXN3L Gene

This gene is overexpressed in Brain (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for ATXN3L Gene



Protein tissue co-expression partners for ATXN3L Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ATXN3L

SOURCE GeneReport for Unigene cluster for ATXN3L Gene:

Hs.382641
genes like me logo Genes that share expression patterns with ATXN3L: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for ATXN3L Gene

Orthologs for ATXN3L Gene

This gene was present in the common ancestor of animals.

Orthologs for ATXN3L Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia ATXN3L 29 30
  • 92.39 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia -- 30
  • 69 (a)
 ManyToMany
-- 30
  • 66 (a)
 ManyToMany
-- 30
  • 62 (a)
 ManyToMany
Mouse
(Mus musculus)
 Mammalia Atxn3 30
  • 66 (a)
 OneToMany
Oppossum
(Monodelphis domestica)
 Mammalia -- 30
  • 65 (a)
 OneToMany
Cow
(Bos Taurus)
 Mammalia ATXN3 30
  • 65 (a)
 OneToMany
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 30
  • 61 (a)
 OneToMany
Chicken
(Gallus gallus)
 Aves ATXN3 30
  • 60 (a)
 OneToMany
Lizard
(Anolis carolinensis)
 Reptilia -- 30
  • 56 (a)
 OneToMany
Zebrafish
(Danio rerio)
 Actinopterygii ATXN3 30
  • 48 (a)
 OneToMany
Worm
(Caenorhabditis elegans)
 Secernentea atx-3 30
  • 31 (a)
 OneToMany
Species where no ortholog for ATXN3L was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)

Evolution for ATXN3L Gene

ENSEMBL:
Gene Tree for ATXN3L (if available)
TreeFam:
Gene Tree for ATXN3L (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ATXN3L: view image
Alliance of Genome Resources:
Additional Orthologs for ATXN3L

Paralogs for ATXN3L Gene

Paralogs for ATXN3L Gene

(1) SIMAP similar genes for ATXN3L Gene using alignment to 1 proteins:

  • ATX3L_HUMAN
genes like me logo Genes that share paralogs with ATXN3L: view

Variants for ATXN3L Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ATXN3L Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
973116 Likely Benign: Intellectual disability 13,319,070(-) T/A
NM_001135995.1(ATXN3L):c.865A>T (p.Lys289Ter) 		NONSENSE,NON_CODING_TRANSCRIPT
rs16999010 -- p.Leu266Phe
rs4830842 -- p.Gly332Asp

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for ATXN3L Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for ATXN3L Gene

Variant ID Type Subtype PubMed ID
esv3576773 CNV gain 25503493

Variation tolerance for ATXN3L Gene

Residual Variation Intolerance Score: 97.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.20; 39.77% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ATXN3L Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ATXN3L
Leiden Open Variation Database (LOVD)
ATXN3L

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ATXN3L Gene

Disorders for ATXN3L Gene

MalaCards: The human disease database

(2) MalaCards diseases for ATXN3L Gene - From: COP and GCD

Disorder Aliases PubMed IDs
machado-joseph disease
  • mjd
autosomal dominant cerebellar ataxia
  • spinocerebellar ataxia
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for ATXN3L

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with ATXN3L: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ATXN3L Gene

Publications for ATXN3L Gene

  1. Crystal structure of a Josephin-ubiquitin complex: evolutionary restraints on ataxin-3 deubiquitinating activity. (PMID: 21118805) Weeks SD … Loll PJ (The Journal of biological chemistry 2011) 3 4
  2. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross MT … Bentley DR (Nature 2005) 3 4
  3. The genomic structure and expression of MJD, the Machado-Joseph disease gene. (PMID: 11450850) Ichikawa Y … Kanazawa I (Journal of human genetics 2001) 3 4
  4. Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. (PMID: 30021884) Fasci D … Heck AJR (Molecular & cellular proteomics : MCP 2018) 3
  5. Ataxin-3 like (ATXN3L), a member of the Josephin family of deubiquitinating enzymes, promotes breast cancer proliferation by deubiquitinating Krüppel-like factor 5 (KLF5). (PMID: 26079537) Ge F … Chen C (Oncotarget 2015) 3

ExternalLinks

View latest publications for ATXN3L gene in Mastermind

Products for ATXN3L Gene

Sources for ATXN3L Gene