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    ATXN1 ataxin 1 [ Homo sapiens (human) ]

    Gene ID: 6310, updated on 7-Sep-2023

    Summary

    Official Symbol
    ATXN1provided by HGNC
    Official Full Name
    ataxin 1provided by HGNC
    Primary source
    HGNC:HGNC:10548
    See related
    Ensembl:ENSG00000124788 MIM:601556; AllianceGenome:HGNC:10548
    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
    ATX1; SCA1; D6S504E
    Summary
    The autosomal dominant cerebellar ataxias (ADCA) are a heterogeneous group of neurodegenerative disorders characterized by progressive degeneration of the cerebellum, brain stem and spinal cord. Clinically, ADCA has been divided into three groups: ADCA types I-III. ADCAI is genetically heterogeneous, with five genetic loci, designated spinocerebellar ataxia (SCA) 1, 2, 3, 4 and 6, being assigned to five different chromosomes. ADCAII, which always presents with retinal degeneration (SCA7), and ADCAIII often referred to as the `pure' cerebellar syndrome (SCA5), are most likely homogeneous disorders. Several SCA genes have been cloned and shown to contain CAG repeats in their coding regions. ADCA is caused by the expansion of the CAG repeats, producing an elongated polyglutamine tract in the corresponding protein. The expanded repeats are variable in size and unstable, usually increasing in size when transmitted to successive generations. The function of the ataxins is not known. This locus has been mapped to chromosome 6, and it has been determined that the diseased allele contains 40-83 CAG repeats, compared to 6-39 in the normal allele, and is associated with spinocerebellar ataxia type 1 (SCA1). Alternative splicing results in multiple transcript variants, with one variant encoding multiple distinct proteins, ATXN1 and Alt-ATXN1, due to the use of overlapping alternate reading frames. [provided by RefSeq, Nov 2017]
    Expression
    Ubiquitous expression in endometrium (RPKM 6.8), brain (RPKM 6.7) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
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    Genomic context

    See ATXN1 in Genome Data Viewer
    Location:
    6p22.3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (16299112..16761460, complement)
    RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (16171667..16634155, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (16299343..16761691, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene CRISPRi-validated cis-regulatory element chr6.847 Neighboring gene CRISPRi-validated cis-regulatory element chr6.848 Neighboring gene RNA, U6 small nuclear 1114, pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr6:16259269-16259823 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:16262581-16263080 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:16264120-16264690 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:16264691-16265260 Neighboring gene Sharpr-MPRA regulatory region 9524 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:16303323-16303902 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:16320601-16321434 Neighboring gene guanosine monophosphate reductase Neighboring gene ataxin 1 repeat instability region Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:16327606-16328166 Neighboring gene uncharacterized LOC127903862 Neighboring gene Sharpr-MPRA regulatory region 3581 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:16672541-16673042 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:16723974-16724586 Neighboring gene HNF1 motif-containing MPRA enhancer 207 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:16762145-16763344 Neighboring gene uncharacterized LOC124901268 Neighboring gene Sharpr-MPRA regulatory region 6173 Neighboring gene ATXN1 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory regions 2171 and 6041 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:16891317-16891884 Neighboring gene uncharacterized LOC107986573

    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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Spinocerebellar ataxia type 1 Compare labs

    EBI GWAS Catalog

    Description
    Common genetic variation and antidepressant efficacy in major depressive disorder: a meta-analysis of three genome-wide pharmacogenetic studies.
    EBI GWAS Catalog
    Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
    EBI GWAS Catalog
    Genome-wide association study of a quantitative disordered gambling trait.
    EBI GWAS Catalog
    Reduced expression of the Kinesin-Associated Protein 3 (KIFAP3) gene increases survival in sporadic amyotrophic lateral sclerosis.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Vif vif HIV-1 Vif upregulates the expression of ataxin 1 (ATXN1) in Vif-expression T cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables poly(G) binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables poly(U) RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein self-association IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in RNA processing NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in brain development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in learning ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in memory ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in nervous system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in nuclear export IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in social behavior ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in nuclear inclusion body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nuclear matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    ataxin-1
    Names
    alternative ataxin1
    spinocerebellar ataxia type 1 protein

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_011571.1 RefSeqGene

      Range
      5001..467379
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_863

    mRNA and Protein(s)

    1. NM_000332.4NP_000323.2  ataxin-1 isoform ATXN1

      See identical proteins and their annotated locations for NP_000323.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes multiple distinct proteins due to the use of alternative translation initiation codons. The longer 815 aa protein (ATXN1, PMID:23705062) represents the canonical protein, while a shorter protein (Alt-ATXN1, PMID:23705062) that uses a different reading frame has also been described. This RefSeq represents the longer protein, ATXN1. Variant 2 also encodes ATXN1.
      Source sequence(s)
      AL009031, AL031120, AL034375, AL137003
      Consensus CDS
      CCDS34342.1
      UniProtKB/Swiss-Prot
      P54253, Q17S02, Q9UJG2, Q9Y4J1
      UniProtKB/TrEMBL
      Q96FF1
      Related
      ENSP00000244769.3, ENST00000244769.8
      Conserved Domains (2) summary
      smart00536
      Location:573688
      AXH; domain in Ataxins and HMG containing proteins
      pfam12547
      Location:415445
      ATXN-1_C; Capicua transcriptional repressor modulator
    2. NM_001128164.2NP_001121636.1  ataxin-1 isoform ATXN1

      See identical proteins and their annotated locations for NP_001121636.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. This variant encodes the same protein represented by the longer protein encoded by variant 1, ATXN1.
      Source sequence(s)
      AL009031, BC011026, BP365416, X79204
      Consensus CDS
      CCDS34342.1
      UniProtKB/Swiss-Prot
      P54253, Q17S02, Q9UJG2, Q9Y4J1
      UniProtKB/TrEMBL
      Q96FF1
      Related
      ENSP00000416360.1, ENST00000436367.6
      Conserved Domains (2) summary
      smart00536
      Location:573688
      AXH; domain in Ataxins and HMG containing proteins
      pfam12547
      Location:415445
      ATXN-1_C; Capicua transcriptional repressor modulator
    3. NM_001357857.2NP_001344786.1  ataxin-1 isoform Alt-ATXN1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes multiple distinct proteins due to the use of alternative translation initiation codons. The longer, 815 aa protein represents the canonical protein, while a shorter 185 aa protein(Alt-ATXN1, PMID:23760502) that uses a different reading frame has also been described. Alt-ATXN1 does not share structural similarity to the ATXN1, but has been shown to interact with the ATXN1. This RefSeq represents the shorter protein, Alt-ATXN1.
      Source sequence(s)
      AL009031, BC011026, X79204
      Consensus CDS
      CCDS87367.1
      UniProtKB/TrEMBL
      A0A2R8YCF3, L0EPB8
      Related
      ENSP00000493530.1, ENST00000642969.1

    RNA

    1. NR_152111.3 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL137003, BC047894, BQ016046
    2. NR_152112.3 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL137003, BC011026, BC047894, BQ016046
    3. NR_152113.3 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL137003, BC047894, BQ016046, DB291268
      Related
      ENST00000676138.1
    4. NR_152114.3 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL137003, BC047894, BQ016046, DB291268, X79204

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      16299112..16761460 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      16171667..16634155 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)