Atxn1 ataxin 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Atxn1provided by RGD
Official Full Name: ataxin 1provided by RGD
Primary source: RGD:3624
See related: EnsemblRapid:ENSRNOG00000016998 AllianceGenome:RGD:3624
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: Predicted to enable several functions, including POZ domain binding activity; identical protein binding activity; and single-stranded RNA binding activity. Predicted to be involved in several processes, including learning or memory; negative regulation of transcription by RNA polymerase II; and social behavior. Predicted to act upstream of or within several processes, including negative regulation of insulin-like growth factor receptor signaling pathway; positive regulation of glial cell proliferation; and visual learning. Predicted to be located in cytosol; nuclear inclusion body; and nuclear lumen. Predicted to be part of protein-containing complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in spinocerebellar ataxia type 1. Orthologous to human ATXN1 (ataxin 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Brain (RPKM 74.0), Muscle (RPKM 72.7) and 9 other tissues See more
Orthologs: human mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 17p14

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	17	NC_086035.1 (18943397..19354751)
RS_2023_06	previous assembly	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_086035.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The possibility that CrCDC and Sca-1(+) cells rather than c-Kit(+) cells may be used therapeutically to preserve cardiac function and energy metabolism after myocardial infarction.
Title: Transplantation of cardiac Sca-1-positive cells rather than c-Kit-positive cells preserves mitochondrial oxygen consumption of the viable myocardium following myocardial infarction in rats.
CD24 and Sca-1 in the mammary glands were expressed at lower level in 6-week-old female rats than in 9-week-old female rats.
Title: [Expressions of Sca-1, CD24 and Muc1 in quiescent mammary glands of female rats].
expression of SCA1 gene is prominent in LH-producing cells and is not under direct control of gonadal factor(s) in both genders
Title: Prominent expression of spinocerebellar ataxia type-1 (SCA1) gene encoding ataxin-1 in LH-producing cells, LbetaT2.

Submit: New GeneRIF Correction

General gene information

Go to the top of the page Help

Markers

BE106629 (e-PCR)
- UniSTS:246342

RH132155 (e-PCR)
- UniSTS:215438

RH133713 (e-PCR)
- UniSTS:216996

BF386213 (e-PCR)
- UniSTS:243627

AI502631 (e-PCR)
- UniSTS:226239

RH138268 (e-PCR)
- UniSTS:220355

D17Wox16 (e-PCR)
- UniSTS:517844

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables POZ domain binding	ISO Inferred from Sequence Orthology more info
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology 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

Process	Evidence Code	Pubs
acts_upstream_of_or_within adult locomotory behavior	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
involved_in brain development	IBA Inferred from Biological aspect of Ancestor 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
acts_upstream_of insulin-like growth factor receptor signaling pathway	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
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	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
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
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 phosphorylation	ISO Inferred from Sequence Orthology 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 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 transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within visual learning	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
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
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

Go to the top of the page Help

Preferred Names: ataxin-1

Names: spinocerebellar ataxia 1; spinocerebellar ataxia type 1 protein homolog

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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)

NM_012726.3 → NP_036858.1 ataxin-1

See identical proteins and their annotated locations for NP_036858.1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000017

UniProtKB/Swiss-Prot

Q63540

UniProtKB/TrEMBL

A6J718

Related

ENSRNOP00000023140.2, ENSRNOT00000023140.6

Conserved Domains (2) summary

smart00536
Location:547 → 662

AXH; domain in Ataxins and HMG containing proteins

PHA03247
Location:79 → 241

PHA03247; large tegument protein UL36; Provisional

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086035.1 Reference GRCr8

Range

18943397..19354751

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039095353.2 → XP_038951281.1 ataxin-1 isoform X1

UniProtKB/Swiss-Prot

Q63540

UniProtKB/TrEMBL

A6J718

Conserved Domains (2) summary

smart00536
Location:547 → 662

AXH; domain in Ataxins and HMG containing proteins

PHA03247
Location:79 → 241

PHA03247; large tegument protein UL36; Provisional
XM_039095354.2 → XP_038951282.1 ataxin-1 isoform X1

UniProtKB/Swiss-Prot

Q63540

UniProtKB/TrEMBL

A6J718

Conserved Domains (2) summary

smart00536
Location:547 → 662

AXH; domain in Ataxins and HMG containing proteins

PHA03247
Location:79 → 241

PHA03247; large tegument protein UL36; Provisional
XM_039095351.2 → XP_038951279.1 ataxin-1 isoform X1

UniProtKB/Swiss-Prot

Q63540

UniProtKB/TrEMBL

A6J718

Conserved Domains (2) summary

smart00536
Location:547 → 662

AXH; domain in Ataxins and HMG containing proteins

PHA03247
Location:79 → 241

PHA03247; large tegument protein UL36; Provisional
XM_063276067.1 → XP_063132137.1 ataxin-1 isoform X1

UniProtKB/Swiss-Prot

Q63540

UniProtKB/TrEMBL

A6J718
XM_039095363.2 → XP_038951291.1 ataxin-1 isoform X1

UniProtKB/Swiss-Prot

Q63540

UniProtKB/TrEMBL

A6J718

Conserved Domains (2) summary

smart00536
Location:547 → 662

AXH; domain in Ataxins and HMG containing proteins

PHA03247
Location:79 → 241

PHA03247; large tegument protein UL36; Provisional
XM_039095352.2 → XP_038951280.1 ataxin-1 isoform X1

UniProtKB/Swiss-Prot

Q63540

UniProtKB/TrEMBL

A6J718

Conserved Domains (2) summary

smart00536
Location:547 → 662

AXH; domain in Ataxins and HMG containing proteins

PHA03247
Location:79 → 241

PHA03247; large tegument protein UL36; Provisional
XM_039095364.2 → XP_038951292.1 ataxin-1 isoform X1

UniProtKB/Swiss-Prot

Q63540

UniProtKB/TrEMBL

A6J718

Conserved Domains (2) summary

smart00536
Location:547 → 662

AXH; domain in Ataxins and HMG containing proteins

PHA03247
Location:79 → 241

PHA03247; large tegument protein UL36; Provisional
XM_063276064.1 → XP_063132134.1 ataxin-1 isoform X1

UniProtKB/Swiss-Prot

Q63540

UniProtKB/TrEMBL

A6J718
XM_063276066.1 → XP_063132136.1 ataxin-1 isoform X1

UniProtKB/Swiss-Prot

Q63540

UniProtKB/TrEMBL

A6J718
XM_039095356.2 → XP_038951284.1 ataxin-1 isoform X1

UniProtKB/Swiss-Prot

Q63540

UniProtKB/TrEMBL

A6J718

Conserved Domains (2) summary

smart00536
Location:547 → 662

AXH; domain in Ataxins and HMG containing proteins

PHA03247
Location:79 → 241

PHA03247; large tegument protein UL36; Provisional
XM_063276065.1 → XP_063132135.1 ataxin-1 isoform X1

UniProtKB/Swiss-Prot

Q63540

UniProtKB/TrEMBL

A6J718
XM_039095361.2 → XP_038951289.1 ataxin-1 isoform X1

UniProtKB/Swiss-Prot

Q63540

UniProtKB/TrEMBL

A6J718

Conserved Domains (2) summary

smart00536
Location:547 → 662

AXH; domain in Ataxins and HMG containing proteins

PHA03247
Location:79 → 241

PHA03247; large tegument protein UL36; Provisional
XM_039095357.2 → XP_038951285.1 ataxin-1 isoform X1

UniProtKB/Swiss-Prot

Q63540

UniProtKB/TrEMBL

A6J718

Conserved Domains (2) summary

smart00536
Location:547 → 662

AXH; domain in Ataxins and HMG containing proteins

PHA03247
Location:79 → 241

PHA03247; large tegument protein UL36; Provisional
XM_039095366.2 → XP_038951294.1 ataxin-1 isoform X1

UniProtKB/Swiss-Prot

Q63540

UniProtKB/TrEMBL

A6J718

Conserved Domains (2) summary

smart00536
Location:547 → 662

AXH; domain in Ataxins and HMG containing proteins

PHA03247
Location:79 → 241

PHA03247; large tegument protein UL36; Provisional
XM_063276068.1 → XP_063132138.1 ataxin-1 isoform X1

UniProtKB/Swiss-Prot

Q63540

UniProtKB/TrEMBL

A6J718
XM_039095365.2 → XP_038951293.1 ataxin-1 isoform X1

UniProtKB/Swiss-Prot

Q63540

UniProtKB/TrEMBL

A6J718

Conserved Domains (2) summary

smart00536
Location:547 → 662

AXH; domain in Ataxins and HMG containing proteins

PHA03247
Location:79 → 241

PHA03247; large tegument protein UL36; Provisional
XM_039095368.2 → XP_038951296.1 ataxin-1 isoform X1

UniProtKB/Swiss-Prot

Q63540

UniProtKB/TrEMBL

A6J718

Conserved Domains (2) summary

smart00536
Location:547 → 662

AXH; domain in Ataxins and HMG containing proteins

PHA03247
Location:79 → 241

PHA03247; large tegument protein UL36; Provisional
XM_039095367.2 → XP_038951295.1 ataxin-1 isoform X1

UniProtKB/Swiss-Prot

Q63540

UniProtKB/TrEMBL

A6J718

Conserved Domains (2) summary

smart00536
Location:547 → 662

AXH; domain in Ataxins and HMG containing proteins

PHA03247
Location:79 → 241

PHA03247; large tegument protein UL36; Provisional