Human Gene ATN1 (uc001qry.1) Description and Page Index
  Description: Homo sapiens atrophin 1 (ATN1), transcript variant 2, mRNA.
RefSeq Summary (NM_001940): Dentatorubral pallidoluysian atrophy (DRPLA) is a rare neurodegenerative disorder characterized by cerebellar ataxia, myoclonic epilepsy, choreoathetosis, and dementia. The disorder is related to the expansion from 7-35 copies to 49-93 copies of a trinucleotide repeat (CAG/CAA) within this gene. The encoded protein includes a serine repeat and a region of alternating acidic and basic amino acids, as well as the variable glutamine repeat. Alternative splicing results in two transcripts variants that encode the same protein. [provided by RefSeq, Jul 2016].
Transcript (Including UTRs)
   Position: hg19 chr12:7,043,003-7,045,891 Size: 2,889 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr12:7,043,165-7,045,891 Size: 2,727 Coding Exon Count: 4 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureOther SpeciesmRNA DescriptionsOther Names
GeneReviewsModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:7,043,003-7,045,891)mRNA (may differ from genome)Protein (486 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIOMIM
PubMedStanford SOURCEWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ATN1
CDC HuGE Published Literature: ATN1
Positive Disease Associations: myotonic dystrophy type 1 , schizophrenia
Related Studies:
  1. myotonic dystrophy type 1
    Savic, D. et al. 2001, Is the 31 CAG repeat allele of the spinocerebellar ataxia 1 (SCA1) gene locus non-specifically associated with trinucleotide expansion diseases?, Psychiatric genetics. 2001 Dec;11(4):201-5. [PubMed 11807410]
    Allele frequency distributions for all tested loci were similar in these three groups with the exception of the SCA1 locus. In DM1 patients, the SCA1 allele with 31 CAG repeats account for 40.4% of all chromosomes tested, which is significantly higher than in two other groups (11.3% in healthy controls and 6.6% in the group of non-triplet diseased patients; P < 0.001, Fisher's exact test). This is consistent with our previous findings in HD patients. The absence of this association in non-triplet diseases as well as in healthy controls could indicate a possible role of this SCA1 allele with 31 repeats in triplet diseases. Here we discuss a possible role of the SCA1 region in pathological trinucleotide repeat expansions.
  2. schizophrenia
    Morris-Rosendahl DJ et al. 1997, Analysis of the CAG repeats in the SCA1 and B37 genes in schizophrenic and bipolar I disorder patients: tentative association between B37 and schizophrenia., American journal of medical genetics. 1997 May;74(3):324-30. [PubMed 9184318]

-  MalaCards Disease Associations
  MalaCards Gene Search: ATN1
Diseases sorted by gene-association score: dentatorubro-pallidoluysian atrophy* (1389), spinocerebellar ataxia 1 (17), spinocerebellar ataxia 17 (15), cerebellar ataxia (11), early myoclonic encephalopathy (11), autosomal dominant cerebellar ataxia (11), machado-joseph disease (7), spinocerebellar ataxia 12 (6), hereditary ataxia (6), progressive relapsing multiple sclerosis (5), huntington disease (4), leukoencephalopathy with vanishing white matter (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 203.84 RPKM in Ovary
Total median expression: 4502.25 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -60.00162-0.370 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  BC051795 - Homo sapiens atrophin 1, mRNA (cDNA clone MGC:57647 IMAGE:4181592), complete cds.
D31840 - Homo sapiens DRPLA mRNA, complete cds.
D38529 - Homo sapiens mRNA for DRPLA protein, complete cds.
JD560143 - Sequence 541167 from Patent EP1572962.
U23851 - Human atrophin-1 mRNA, complete cds.
JD357640 - Sequence 338664 from Patent EP1572962.
JD287941 - Sequence 268965 from Patent EP1572962.
JD200210 - Sequence 181234 from Patent EP1572962.
EU446506 - Synthetic construct Homo sapiens clone IMAGE:100070339; IMAGE:100011715; FLH258371.01L atrophin 1 (ATN1) gene, encodes complete protein.
AB209345 - Homo sapiens mRNA for atrophin-1 variant protein.
Z22814 - H.sapiens ORF, complete CDS.
L10377 - Human (clone CTG-B37) mRNA sequence.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001940, NP_001931, U23851
UCSC ID: uc001qry.1
RefSeq Accession: NM_001940

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene ATN1:
ataxias (Hereditary Ataxia Overview)
drpla (DRPLA)
dystonia-ov (Hereditary Dystonia Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: U23851.1
exon count: 4CDS single in 3' UTR: no RNA size: 4168
ORF size: 1458CDS single in intron: no Alignment % ID: 99.95
txCdsPredict score: 2451.00frame shift in genome: no % Coverage: 36.73
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: no retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.