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ATXN3L Gene

protein-coding   GIFtS: 47
GCID: GC0XM013336

Ataxin 3-Like

  See ATXN3L-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Ataxin 3-Like1 2     ATX3L3
Machado-Joseph Disease Protein 1-Like2 3     EC 3.4.19.123
MJDL2 3     EC 3.4.228
Putative Ataxin-3-Like Protein2     

External Ids:    HGNC: 241731   Entrez Gene: 925522   Ensembl: ENSG000001235947   UniProtKB: Q9H3M93   

Export aliases for ATXN3L gene to outside databases

Previous GC identifers: GC0XM013096 GC0XM013246 GC0XM011098


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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. GO annotations related to this gene include ubiquitin-specific protease activity and omega peptidase activity. An important paralog of this gene is ATXN3.

UniProtKB/Swiss-Prot: ATX3L_HUMAN, Q9H3M9
Function: Deubiquitinating enzyme that cleaves both 'Lys-48'-linked and 'Lys-63'-linked poly-ubiquitin chains (in
vitro)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000023.10  NC_018934.2  NT_167197.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the ATXN3L gene promoter:
         POU2F2 (Oct-2.1)   c-Fos   AP-1   POU3F1   Pax-2   Pax-2a   POU2F2   POU2F1a   c-Jun   POU2F2B   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for ATXN3L

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ATXN3L


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Xp22.2   Ensembl cytogenetic band:  Xp22.2   HGNC cytogenetic band: Xp22

ATXN3L Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ATXN3L gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM013336:  view genomic region     (about GC identifiers)

Start:
13,336,766 bp from pter      End:
13,338,518 bp from pter
Size:
1,753 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: ATX3L_HUMAN, Q9H3M9 (See protein sequence)
Recommended Name: Putative ataxin-3-like protein  
Size: 355 amino acids; 40747 Da
Caution: Could be the product of a pseudogene. Suggested by the absence of intron
1 PDB 3D structure from and Proteopedia for ATXN3L:
3O65 (3D)    
Secondary accessions: B2RNY8

Explore the universe of human proteins at neXtProt for ATXN3L: NX_Q9H3M9

Explore proteomics data for ATXN3L at MOPED

Selected DME Specific Peptides for ATXN3L (Q9H3M9) (see all 5)
 IFHEKQEG  WFNLNSLL  GPELISDT  FVVKGDLPDCEADQLLQ 


See ATXN3L Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001129467.1  
ENSEMBL proteins: 
 ENSP00000369996  

ATXN3L Human Recombinant Protein Products:

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antibodies-online proteins for ATXN3L 

 
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antibodies-online antibodies for ATXN3L (12 products) 

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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2 InterPro protein domains:
 IPR006155 Josephin
 IPR003903 Ubiquitin-int_motif

Graphical View of Domain Structure for InterPro Entry Q9H3M9

ProtoNet protein and cluster: Q9H3M9

2 Blocks protein domains:
IPB003903 Ubiquitin interacting motif
IPB006155 Josephin signature


UniProtKB/Swiss-Prot: ATX3L_HUMAN, Q9H3M9
Similarity: Contains 1 Josephin domain
Similarity: Contains 2 UIM (ubiquitin-interacting motif) repeats


Find genes that share domains with ATXN3L           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: ATX3L_HUMAN, Q9H3M9
Function: Deubiquitinating enzyme that cleaves both 'Lys-48'-linked and 'Lys-63'-linked poly-ubiquitin chains (in
vitro)
Catalytic activity: 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)

     Enzyme Numbers (IUBMB): EC 3.4.222 EC 3.4.19.121

     Gene Ontology (GO): 2 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0004843ubiquitin-specific protease activity IDA--
GO:0008242omega peptidase activity IEA--
     
Find genes that share ontologies with ATXN3L           About GenesLikeMe


Animal Models:
   genOway: Develop your customized and physiologically relevant rodent model for ATXN3L

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
ATX3L_HUMAN, Q9H3M9: Nucleus (By similarity)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus3
cytosol1
extracellular1

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus IEA--

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(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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SuperPaths for ATXN3L About    
See pathways by source

SuperPathContained pathways About
1Protein processing in endoplasmic reticulum
Protein processing in endoplasmic reticulum


Find genes that share SuperPaths with ATXN3L           About GenesLikeMe

Pathways by source                                                                                                                                                                 See SuperPaths
Show all pathways



1 Kegg Pathway  (Kegg details for ATXN3L):
    Protein processing in endoplasmic reticulum

    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for ATXN3L
Interactions:

    Search GeneGlobe Interaction Network for ATXN3L

STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

3 Interacting proteins for ATXN3L (Q9H3M93 ENSP000003699964) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
UBCP0CG483, ENSP000003448184I2D: score=1 STRING: ENSP00000344818
UBA52ENSP000003881074STRING: ENSP00000388107
HAAOENSP000002949734STRING: ENSP00000294973
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Gene Ontology (GO): 4 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006351transcription, DNA-templated IEA--
GO:0006355regulation of transcription, DNA-templated IEA--
GO:0006508proteolysis ----
GO:0016579protein deubiquitination IDA--

Find genes that share ontologies with ATXN3L           About GenesLikeMe



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for ATXN3L (ATX3L)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for ATXN3L gene: 
NM_001135995.1  

Unigene Cluster for ATXN3L:

Ataxin 3-like
Hs.382641  [show with all ESTs]
Unigene Representative Sequence: NM_001135995
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000380622(uc010ned.3)
miRNA
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  QuantiFast Probe-based Assays in human, mouse, rat ATXN3L

Additional mRNA sequence: 

AB050195.1 AK302365.1 BC137186.1 BC137187.1 

2 DOTS entries:

DT.40225272  DT.91811394 

3 AceView cDNA sequences:

AA411848 AB050195 AA402429 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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ATXN3L expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TGTAACTCCT
ATXN3L Expression
About this image

ATXN3L Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

ATXN3L Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.382641
    Custom PCR Arrays for ATXN3L
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ATXN3L

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of animals.

Orthologs for ATXN3L gene from Selected species (see all 10)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chicken
(Gallus gallus)
Aves ATXN36
Gallus gallus ataxin 3 (ATXN3), mRNA.
60(a)
1 → many
5(43832919-43844552)
lizard
(Anolis carolinensis)
Reptilia --
Uncharacterized protein
56(a)
1 → many
1(11651929-11674005)
zebrafish
(Danio rerio)
Actinopterygii ATXN36
ataxin 3
48(a)
1 → many
17(53814584-53817190) ENSDARG00000009264
worm
(Caenorhabditis elegans)
Secernentea atx-36
Protein ATX-3 (atx-3) mRNA, complete cds
31(a)
1 → many
V(15575499-15577043) WBGene00006446
        Species with no ortholog for ATXN3L

ENSEMBL Gene Tree for ATXN3L (if available)
TreeFam Gene Tree for ATXN3L (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for ATXN3L gene
ATXN32  
1 SIMAP similar gene for ATXN3L using alignment to 1 protein entry:     ATX3L_HUMAN:
ATXN3

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(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for ATXN3L (see all 70)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr X posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1931605851,2
--13251804(+) CTGGGA/CGACAG 1 -- int10--------
rs1827939651,2
--13251847(+) CAAAGA/CAAGAG 1 -- int10--------
rs1497824031,2
--13251991(+) GAAATA/GACATA 1 -- int10--------
rs1456824151,2
--13252076(+) CACAGA/GCAAGA 1 -- int10--------
rs412972911,2
C--13252251(+) AGATAC/TTGCAG 1 -- int10--------
rs588787371,2
C,F--13252350(+) TTTAGG/TCCCAC 1 -- ut311Minor allele frequency- T:0.00WA 2
rs2008214601,2
C--13252539(+) ATTTCG/TAAAAT 2 L F mis10--------
rs1878263311,2
C--13252551(+) GTGTCA/GACAGC 2 V syn10--------
rs1999685591,2
C--13252562(+) GGCCTA/GTACTG 2 Q * stg10--------
rs48308421,2,,4
C,F,A,H--13252570(+) CTGTGT/CCTTCA 2 /D /G mis128Minor allele frequency- C:0.29NS EA NA WA CSA 2682

HapMap Linkage Disequilibrium report for ATXN3L (13336766 - 13338518 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for ATXN3L: --
Human Gene Mutation Database (HGMD): ATXN3L
Locus Specific Mutation Databases (LSDB): ATXN3L

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing ATXN3L
DNA2.0 Custom Variant and Variant Library Synthesis for ATXN3L

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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1 disease for ATXN3L:    
About MalaCards
machado-joseph disease

1 disease from the University of Copenhagen DISEASES database for ATXN3L:
Machado-Joseph disease

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Genetic Association Database (GAD): ATXN3L

Export disorders for ATXN3L gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for ATXN3L gene integrated from 10 sources:
(articles sorted by number of sources associating them with ATXN3L)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Crystal structure of a Josephin-ubiquitin complex: evolutionary restraints on ataxin-3 deubiquitinating activity. (PubMed id 21118805)1, 2 Weeks S.D.... Loll P.J. (J. Biol. Chem. 2011)
  2. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 2005)
  3. The genomic structure and expression of MJD, the Machado-Joseph disease gene. (PubMed id 11450850)1, 2 Ichikawa Y.... Kanazawa I. (J. Hum. Genet. 2001)
  4. A microarray of ubiquitylated proteins for profiling deubiquitylase activity reveals the critical roles of both chain and substrate. (PubMed id 22626734)1 Loch C.M. and Strickler J.E. (Biochim. Biophys. Acta 2012)
  5. Genome-wide association with bone mass and geometry in the Framingham Heart Study. (PubMed id 17903296)4 Kiel D.P....Karasik D. (BMC Med. Genet. 2007)
  6. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. (PubMed id 17903299)4 Kathiresan S....Cupples L.A. (BMC Med. Genet. 2007)
  7. Genome-wide association and linkage analyses of hemostatic factors and hematological phenotypes in the Framingham Heart Study. (PubMed id 17903294)4 Yang Q....O'Donnell C.J. (BMC Med. Genet. 2007)
  8. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
  9. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 92552 HGNC: 24173 AceView: ATXN3L Ensembl:ENSG00000123594 euGenes: HUgn92552
ECgene: ATXN3L Kegg: 92552 H-InvDB: ATXN3L

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for ATXN3L Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for ATXN3L gene:
Search GeneIP for patents involving ATXN3L

GeneCards and IP:
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(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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