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ATXN8OS Gene

RNA gene   GIFtS: 28
GCID: GC13P070681

ATXN8 Opposite Strand (Non-Protein Coding)

(Previous names: spinocerebellar ataxia 8, kelch-like 1 antisense (Drosophila))
(Previous symbols: SCA8, KLHL1AS)
  See ATXN8OS-related diseases
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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Subcategory (RNA class): antisense

Quality score for this RNA gene is 3.4

Aliases
ATXN8 Opposite Strand (Non-Protein Coding)1 2     Non-Protein Coding RNA 31
KLHL1AS1 2 5     Spinocerebellar Ataxia 81
SCA81 2 5     NCRNA000032
Kelch-Like 1 Antisense (Drosophila)1     

External Ids:    HGNC: 105611   Entrez Gene: 63152   Ensembl: ENSG000002302237   OMIM: 6036805   
ORGUL members:    fRNAdb10:FR388608 FR160065 FR002839 FR019374 FR313543      
NONCODE14:n1175    
RNAdb15:EVF39732 EVF11110 RNZ10209 EVF10316 EVF9214    

Export aliases for ATXN8OS gene to outside databases

Previous GC identifers: GC13P069579 GC13P051383


(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 ATXN8OS Gene:
This gene is an antisense transcript to the KLHL1 gene (homolog to the Drosophila KELCH gene); it does not itself
appear to be protein coding. A TAC/TGC trinucleotide repeat expansion that is incorporated into this gene
transcript, but not the KLHL1 transcript, causes spinocerebellar ataxia type 8. Presumably the expansion
interferes with normal antisense function of this transcript. (provided by RefSeq, Oct 2008)

GeneCards Summary for ATXN8OS Gene:
ATXN8OS (ATXN8 opposite strand (non-protein coding)) is an RNA gene, and is affiliated with the antisense RNA class. Diseases associated with ATXN8OS include spinocerebellar ataxia type 8, and infantile onset spinocerebellar ataxia.

Gene Wiki entry for ATXN8OS Gene

fRNAdb sequence ontology for ATXN8OS:
nc_conserved_region - Non-coding region of sequence similarity by descent from a common ancestor.

View fRNAdb secondary structures for ATXN8OS

(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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Regulatory elements:
   Regulatory transcription factor binding sites in the ATXN8OS gene promoter:
         TBP   TFIID   Nkx2-5   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for ATXN8OS

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ATXN8OS


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

Entrez Gene cytogenetic band: 13q21   Ensembl cytogenetic band:  13q21.33   HGNC cytogenetic band: 13q21

ATXN8OS Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ATXN8OS gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13P070681:  view genomic region     (about GC identifiers)

Start:
70,681,345 bp from pter      End:
70,713,885 bp from pter
Size:
32,541 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for ATXN8OS

(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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
LNCRNA: Long non-coding RNAs

  --

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, 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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Phenotypes:
     2 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Atxn8os):
 behavior/neurological  nervous system 

Find genes that share phenotypes with ATXN8OS           About GenesLikeMe

Animal Models:
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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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  --

(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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Interactions:

    Search GeneGlobe Interaction Network for ATXN8OS

(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 ATXN8OS



(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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3 fRNAdb Secondary structures:


2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000414504(antisense) ENST00000424524(antisense)
miRNA
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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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Expression evidence for ATXN8OS:none

ATXN8OS expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GCAGAAGAGC
ATXN8OS Expression
About this image

ATXN8OS Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
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(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 human and mouse.

Orthologs for ATXN8OS gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Atxn8os5 ATXN8 opposite strand   --   14 96556570 


ENSEMBL Gene Tree for ATXN8OS (if available)
TreeFam Gene Tree for ATXN8OS (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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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 ATXN8OS (see all 810)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 13 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs349765511,2
C,F--51405014(+) CCACC-/T/TT  
        
TTTTT
1 -- int12NA CSA 4
rs558327311,2
C--51408474(+) TTTTT-/T/TT  
        
GGCAG
1 -- int11NA 2
rs42961521,2
C,A--51415534(+) ctactA/Gctgct 2 -- nc-transcript-variant0--------
rs735187741,2
C,F--51582233(+) CTATTC/TTCAAA 1 -- us2k11Minor allele frequency- T:0.50WA 2
rs735187761,2
C,F--51582243(+) AAGTAA/TGAAAC 1 -- us2k12Minor allele frequency- T:0.19WA 120
rs1828609681,2
--51582291(+) TGTTCC/TGTTAT 1 -- us2k10--------
rs170863701,2
C,F,H--51582362(+) ATTACA/GTAAAA 1 -- us2k118Minor allele frequency- G:0.23NA EA NS WA 1418
rs782156591,2
F--51582459(+) TATTTC/TTAGGA 1 -- us2k11Minor allele frequency- T:0.11WA 118
rs1869526371,2
C--51582613(+) AATTGC/TTTAAT 1 -- us2k10--------
rs1917422011,2
--51582663(+) TCAACA/TAAAGG 1 -- us2k10--------

HapMap Linkage Disequilibrium report for ATXN8OS (70681345 - 70713885 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for ATXN8OS:    About this table    
Variant IDTypeSubtypePubMed ID
nsv455967CNV Loss19166990

Human Gene Mutation Database (HGMD): ATXN8OS
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing ATXN8OS
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 603680OMIM information: 600825 612344    
OMIM disorders: 608768  
5 diseases for ATXN8OS:    
About MalaCards
spinocerebellar ataxia type 8    infantile onset spinocerebellar ataxia    friedreich ataxia    spinocerebellar ataxia
ataxia


Find genes that share disorders with ATXN8OS           About GenesLikeMe

4 Novoseek inferred disease relationships for ATXN8OS gene    About this table

Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
sca12 95.6 9 12140678 (3), 14960773 (2), 19235102 (1)
spinocerebellar ataxias 89.6 2 18708037 (1), 16184604 (1)
friedreich ataxia 79.8 2 18708037 (1), 12140678 (1)
neurodegenerative diseases 61.8 1 16184604 (1)

GeneTests: ATXN8OS
GeneReviews: ATXN8OS
Genetic Association Database (GAD): ATXN8OS
Human Genome Epidemiology (HuGE) Navigator: ATXN8OS (12 documents)

Export disorders for ATXN8OS 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 ATXN8OS gene, integrated from 10 sources (see all 37):
(articles sorted by number of sources associating them with ATXN8OS)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Polymorphism of trinucleotide repeats in non-translated regions of SCA8 and SCA12 genes: allele distribution in a Polish control group. (PubMed id 14960773)1, 4, 9 SuA8ek A....Zaremba J. (J. Appl. Genet. 2004)
  2. Analysis of SCA8 and SCA12 loci in 134 Italian ataxic patients negative for SCA1-3, 6 and 7 CAG expansions. (PubMed id 12140678)1, 4, 9 Brusco A....Orsi L. (J. Neurol. 2002)
  3. Screening for premutation in the FMR1 gene in male patients suspected of spinocerebellar ataxia. (PubMed id 19235102)1, 4, 9 Rajkiewicz M....Zaremba J. (Neurol. Neurochir. Pol. 2008)
  4. [Studies on the CTA/CTG trinucleotide repeats of ATXN8OS gene in Chinese Hans]. (PubMed id 18841561)1, 4 Wang J....Tang B. (Zhonghua Yi Xue Yi Chuan Xue Za Zhi 2008)
  5. Bidirectional expression of CUG and CAG expansion transcripts and intranuclear polyglutamine inclusions in spinocerebellar ataxia type 8. (PubMed id 16804541)1, 3 Moseley M.L.... Ranum L.P.W. (Nat. Genet. 2006)
  6. Expanded trinucleotide repeats in the TBP/SCA17 gene mapped to chromosome 6q27 are associated with schizophrenia. (PubMed id 16054804)1, 4 Chen C.M....Lee-Chen G.J. (Schizophr. Res. 2005)
  7. Spinocerebellar ataxia type 8 in Scotland: genetic and clinical features in seven unrelated cases and a review of published reports. (PubMed id 14966165)1, 4 Zeman A....Warner J. (J. Neurol. Neurosurg. Psychiatr. 2004)
  8. Molecular genetics of hereditary spinocerebellar ataxia: mutation analysis of spinocerebellar ataxia genes and CAG/CTG repeat expansion detection in 225 Italian families. (PubMed id 15148151)1, 4 Brusco A....Taroni F. (Arch. Neurol. 2004)
  9. SCA8 repeat expansion: large CTA/CTG repeat alleles are more common in ataxic patients, including those with SCA6. (PubMed id 12545428)1, 4 Izumi Y....Kawakami H. (Am. J. Hum. Genet. 2003)
  10. SCA8 in the Spanish population including one homozygous patient. (PubMed id 12431257)1, 4 TazA^n B....MilA M. (Clin. Genet. 2002)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Disorders
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: 6315 HGNC: 10561 Ensembl:ENSG00000230223 euGenes: HUgn6315 ECgene: ATXN8OS
H-InvDB: ATXN8OS

(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 ATXN8OS 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 ATXN8OS gene:
Search GeneIP for patents involving ATXN8OS

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(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, LSBio, eBioscience, 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
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The GeneCards human gene database gene index: 1 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

Hot genes      Disease genes      ATXN8OS gene at Home site.
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