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Atxn1 ataxin 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 25049, updated on 6-May-2021

Summary

Official Symbol
Atxn1provided by RGD
Official Full Name
ataxin 1provided by RGD
Primary source
RGD:3624
See related
Ensembl:ENSRNOG00000016998
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Sca1
Summary
human homolog contains an expanded CAG nucleotide repeat region that causes the neurodegenerative disorder spinocerebellar ataxia type 1 (SCA1) [RGD, Feb 2007]
Expression
Biased expression in Brain (RPKM 74.0), Muscle (RPKM 72.7) and 9 other tissues See more
Orthologs
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Genomic context

See Atxn1 in Genome Data Viewer
Location:
17p14
Exon count:
22
Annotation release Status Assembly Chr Location
108 current mRatBN7.2 (GCF_015227675.2) 17 NC_051352.1 (18737491..19142360)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 17 NC_005116.4 (19160986..19533814)

Chromosome 17 - NC_051352.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108348532 Neighboring gene uncharacterized LOC102554492 Neighboring gene uncharacterized LOC120097815 Neighboring gene uncharacterized LOC120097816 Neighboring gene U6 spliceosomal RNA Neighboring gene guanosine monophosphate reductase

Genomic regions, transcripts, and products

Expression

  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables RNA binding ISO
Inferred from Sequence Orthology
more info
 
enables chromatin binding ISO
Inferred from Sequence Orthology
more info
 
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
 
enables molecular_function ND
No biological Data available
more info
 
enables poly(G) binding ISO
Inferred from Sequence Orthology
more info
 
enables poly(G) binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables poly(U) RNA binding ISO
Inferred from Sequence Orthology
more info
 
enables poly(U) RNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables protein C-terminus binding ISO
Inferred from Sequence Orthology
more info
 
enables protein C-terminus binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables protein self-association ISO
Inferred from Sequence Orthology
more info
 
enables protein self-association ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within adult locomotory behavior ISO
Inferred from Sequence Orthology
more info
 
involved_in anatomical structure development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in biological_process ND
No biological Data available
more info
 
involved_in brain development ISO
Inferred from Sequence Orthology
more info
 
involved_in brain development ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within excitatory postsynaptic potential ISO
Inferred from Sequence Orthology
more info
 
involved_in learning ISO
Inferred from Sequence Orthology
more info
 
involved_in learning ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within lung alveolus development ISO
Inferred from Sequence Orthology
more info
 
involved_in memory ISO
Inferred from Sequence Orthology
more info
 
involved_in memory ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within negative regulation of insulin-like growth factor receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of phosphorylation ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in nuclear export ISO
Inferred from Sequence Orthology
more info
 
involved_in nuclear export ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within positive regulation of glial cell proliferation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in social behavior ISO
Inferred from Sequence Orthology
more info
 
involved_in social behavior ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within visual learning ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
is_active_in cellular_component ND
No biological Data available
more info
 
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in cytosol IEA
Inferred from Electronic Annotation
more info
 
located_in cytosol ISO
Inferred from Sequence Orthology
more info
 
located_in nuclear inclusion body ISO
Inferred from Sequence Orthology
more info
 
located_in nuclear inclusion body ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in nuclear matrix ISO
Inferred from Sequence Orthology
more info
 
located_in nuclear matrix ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in nucleolus IEA
Inferred from Electronic Annotation
more info
 
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in postsynapse IEA
Inferred from Electronic Annotation
more info
 
part_of protein-containing complex ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
ataxin-1
Names
spinocerebellar ataxia 1
spinocerebellar ataxia type 1 protein homolog

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.

mRNA and Protein(s)

  1. NM_012726.3NP_036858.1  ataxin-1

    See identical proteins and their annotated locations for NP_036858.1

    Status: PROVISIONAL

    Source sequence(s)
    JACYVU010000288
    UniProtKB/Swiss-Prot
    Q63540
    Related
    ENSRNOP00000023140.2, ENSRNOT00000023140.4
    Conserved Domains (2) summary
    smart00536
    Location:547662
    AXH; domain in Ataxins and HMG containing proteins
    PHA03247
    Location:79241
    PHA03247; large tegument protein UL36; Provisional

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 108 details...Open this link in a new tab

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

Reference mRatBN7.2 Primary Assembly

Genomic

  1. NC_051352.1 Reference mRatBN7.2 Primary Assembly

    Range
    18737491..19142360
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039095353.1XP_038951281.1  ataxin-1 isoform X1

    Conserved Domains (2) summary
    smart00536
    Location:547662
    AXH; domain in Ataxins and HMG containing proteins
    PHA03247
    Location:79241
    PHA03247; large tegument protein UL36; Provisional
  2. XM_039095364.1XP_038951292.1  ataxin-1 isoform X1

    Conserved Domains (2) summary
    smart00536
    Location:547662
    AXH; domain in Ataxins and HMG containing proteins
    PHA03247
    Location:79241
    PHA03247; large tegument protein UL36; Provisional
  3. XM_039095354.1XP_038951282.1  ataxin-1 isoform X1

    Conserved Domains (2) summary
    smart00536
    Location:547662
    AXH; domain in Ataxins and HMG containing proteins
    PHA03247
    Location:79241
    PHA03247; large tegument protein UL36; Provisional
  4. XM_039095363.1XP_038951291.1  ataxin-1 isoform X1

    Conserved Domains (2) summary
    smart00536
    Location:547662
    AXH; domain in Ataxins and HMG containing proteins
    PHA03247
    Location:79241
    PHA03247; large tegument protein UL36; Provisional
  5. XM_039095355.1XP_038951283.1  ataxin-1 isoform X1

    Conserved Domains (2) summary
    smart00536
    Location:547662
    AXH; domain in Ataxins and HMG containing proteins
    PHA03247
    Location:79241
    PHA03247; large tegument protein UL36; Provisional
  6. XM_039095352.1XP_038951280.1  ataxin-1 isoform X1

    Conserved Domains (2) summary
    smart00536
    Location:547662
    AXH; domain in Ataxins and HMG containing proteins
    PHA03247
    Location:79241
    PHA03247; large tegument protein UL36; Provisional
  7. XM_039095351.1XP_038951279.1  ataxin-1 isoform X1

    Conserved Domains (2) summary
    smart00536
    Location:547662
    AXH; domain in Ataxins and HMG containing proteins
    PHA03247
    Location:79241
    PHA03247; large tegument protein UL36; Provisional
  8. XM_039095362.1XP_038951290.1  ataxin-1 isoform X1

    Conserved Domains (2) summary
    smart00536
    Location:547662
    AXH; domain in Ataxins and HMG containing proteins
    PHA03247
    Location:79241
    PHA03247; large tegument protein UL36; Provisional
  9. XM_039095360.1XP_038951288.1  ataxin-1 isoform X1

    Conserved Domains (2) summary
    smart00536
    Location:547662
    AXH; domain in Ataxins and HMG containing proteins
    PHA03247
    Location:79241
    PHA03247; large tegument protein UL36; Provisional
  10. XM_039095356.1XP_038951284.1  ataxin-1 isoform X1

    Conserved Domains (2) summary
    smart00536
    Location:547662
    AXH; domain in Ataxins and HMG containing proteins
    PHA03247
    Location:79241
    PHA03247; large tegument protein UL36; Provisional
  11. XM_039095359.1XP_038951287.1  ataxin-1 isoform X1

    Conserved Domains (2) summary
    smart00536
    Location:547662
    AXH; domain in Ataxins and HMG containing proteins
    PHA03247
    Location:79241
    PHA03247; large tegument protein UL36; Provisional
  12. XM_039095357.1XP_038951285.1  ataxin-1 isoform X1

    Conserved Domains (2) summary
    smart00536
    Location:547662
    AXH; domain in Ataxins and HMG containing proteins
    PHA03247
    Location:79241
    PHA03247; large tegument protein UL36; Provisional
  13. XM_039095361.1XP_038951289.1  ataxin-1 isoform X1

    Conserved Domains (2) summary
    smart00536
    Location:547662
    AXH; domain in Ataxins and HMG containing proteins
    PHA03247
    Location:79241
    PHA03247; large tegument protein UL36; Provisional
  14. XM_039095366.1XP_038951294.1  ataxin-1 isoform X1

    Conserved Domains (2) summary
    smart00536
    Location:547662
    AXH; domain in Ataxins and HMG containing proteins
    PHA03247
    Location:79241
    PHA03247; large tegument protein UL36; Provisional
  15. XM_039095365.1XP_038951293.1  ataxin-1 isoform X1

    Conserved Domains (2) summary
    smart00536
    Location:547662
    AXH; domain in Ataxins and HMG containing proteins
    PHA03247
    Location:79241
    PHA03247; large tegument protein UL36; Provisional
  16. XM_039095368.1XP_038951296.1  ataxin-1 isoform X1

    Conserved Domains (2) summary
    smart00536
    Location:547662
    AXH; domain in Ataxins and HMG containing proteins
    PHA03247
    Location:79241
    PHA03247; large tegument protein UL36; Provisional
  17. XM_039095367.1XP_038951295.1  ataxin-1 isoform X1

    Conserved Domains (2) summary
    smart00536
    Location:547662
    AXH; domain in Ataxins and HMG containing proteins
    PHA03247
    Location:79241
    PHA03247; large tegument protein UL36; Provisional
  18. XM_039095369.1XP_038951297.1  ataxin-1 isoform X1

    Conserved Domains (2) summary
    smart00536
    Location:547662
    AXH; domain in Ataxins and HMG containing proteins
    PHA03247
    Location:79241
    PHA03247; large tegument protein UL36; Provisional
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