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ATXN1 ataxin 1 [ Homo sapiens (human) ]

Gene ID: 6310, updated on 27-Nov-2024

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
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (16299112..16761460, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (16171667..16634155, complement)
RS_2024_09 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 ATAC-STARR-seq lymphoblastoid active region 24097 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24098 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16215087-16215263 Neighboring gene CRISPRi-validated cis-regulatory element chr6.847 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16217722-16217944 Neighboring gene CRISPRi-validated cis-regulatory element chr6.848 Neighboring gene RNA, U6 small nuclear 1114, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16956 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16957 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 ATAC-STARR-seq lymphoblastoid active region 24099 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:16303323-16303902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24100 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16310151-16310359 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:16320601-16321434 Neighboring gene guanosine monophosphate reductase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24102 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:16327606-16328166 Neighboring gene ataxin 1 repeat instability region Neighboring gene uncharacterized LOC127903862 Neighboring gene Sharpr-MPRA regulatory region 3581 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16387334-16387547 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24103 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24107 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24111 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16603501-16603686 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24112 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24113 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16958 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 ATAC-STARR-seq lymphoblastoid silent region 16959 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16960 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16961 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16962 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:16761792-16762007 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 MPRA-validated peak5695 silencer 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 not available

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 RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
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 
Process Evidence Code Pubs
involved_in RNA processing NAS
Non-traceable Author Statement
more info
PubMed 
involved_in brain development IBA
Inferred from Biological aspect of Ancestor
more info
 
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
 
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
 
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
    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
    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_2024_08

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)