Reading the record for Atxn3 from NCBI Gene and Ensembl.Still reading. A first read of a gene can take a while; this page waits up to 115 seconds for it, and its scripts then bring in the page, or a line saying what did not arrive.
The full name, the identifiers, the location and the notes from the sources arrive with the record. Nothing is filled in ahead of it.
Order door
The door to order for Atxn3 opens with the record, which decides which product it carries. The order page itself is open now.
HGNC and MANE Select: not available for mouse. HGNC names human genes; MGI is the authority here, and MANE Select is defined for human transcripts only.
Location
Cytogenetic band 12 ENCBI: 12:101,885,160-101,928,139 on the minus strand, GRCm39 (GCF_000001635.27), sequence NC_000078.7, annotation GCF_000001635.27-RS_2024_02 of 2024-02-01Ensembl: 12:101,885,157-101,924,512 on the minus strand, GRCm39 (GCA_000001635.9), release 116Coordinates are one-based with both ends included, as each source reports them.
Also known as
Mjd, ATX3, MJD1, Sca3, ataxin-3, 2210008M02Rik
Gene identity, from NCBI Datasets · NCBI Datasets 18.38.0 · read · MGI:1099442Data from NCBI, provided as is; NCBI's policies and disclaimers apply.
Silence this gene
The order page opens with Atxn3 and mouse filled in. The sequences are designed against the transcripts below; the price is on that page.
Reading NCBI Gene and UniProt.Still reading. A first read of a gene can take a while; this page waits up to 30 seconds for it, and its scripts then bring in the panel, or a line saying what did not arrive.
02 / Transcripts and isoforms
The RNA a design targets
Reading NCBI Datasets and Ensembl.Still reading. A first read of a gene can take a while; this page waits up to 80 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.
Ready in a moment
Reading NCBI Datasets and Ensembl.Still reading. A first read of a gene can take a while; this page waits up to 80 seconds for it, and its scripts then bring in the panel, or a line saying what did not arrive.
14 / Silencing this gene
From Atxn3 to a sequence that silences it
The AUMsilence™ platform designs the sequences against the mouse transcripts on this page. Six decisions are yours before it does. What is written under each is AUM's guidance; the timings and the concentrations are in the usage guide below.
01
Choose the region
A knockdown oligonucleotide can sit in the 5' untranslated region, the coding sequence or the 3' untranslated region, and all three are used. The coding sequence and the 3' untranslated region are the usual first choices for an RNase H design; the 5' end near the start codon suits a steric block. The map above shows where each region sits on the isoforms it draws.
02
Cover the isoforms you mean
An exon every isoform carries silences the whole gene; an exon only some isoforms carry silences those and spares the rest. Decide which you want before a sequence is chosen, and check the reference transcript (MANE Select in human; RefSeq Select and Ensembl canonical in mouse and rat) is the one your cells express.
03
Think across species early
The orthologs panel says whether mouse and rat carry the same gene. Whether one oligonucleotide can serve two species is a sequence question, settled at design by matching the candidate against each transcript, not by the protein identity shown there.
04
Check expression in your model
A transcript that is not expressed in your cells cannot show knockdown. Confirm the gene is expressed in the cell type and condition you will use, from your own data or a reference atlas, before the order. The expression panel above gives GTEx's median per tissue for a human gene; for mouse and rat it says that no atlas is on this page yet.
03 / Expression by tissue
Where Atxn3 is expressed
Ready in a moment
Reading GTEx and the Human Protein Atlas.Still reading. A first read of a gene can take a while; this page waits up to 80 seconds for it, and its scripts then bring in the panel, or a line saying what did not arrive.
04 / Protein
The protein Atxn3 encodes
Reading UniProt, InterPro, AlphaFold DB and PDBe.Still reading. A first read of a gene can take a while; this page waits up to 80 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.
Ready in a moment
05 / Interactions
Proteins STRING associates with Atxn3
Reading STRING.Still reading. A first read of a gene can take a while; this page waits up to 50 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.
Ready in a moment
06 / Pathways
Where Atxn3 acts, as Reactome curates it
Reading UniProt and Reactome.Still reading. A first read of a gene can take a while; this page waits up to 60 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.
Ready in a moment
07 / Disease associations
Diseases linked to Atxn3
Ready in a moment
Reading Open Targets and ClinGen.Still reading. A first read of a gene can take a while; this page waits up to 105 seconds for it, and its scripts then bring in the panel, or a line saying what did not arrive.
08 / Variants
Classified variants of Atxn3
Ready in a moment
Reading ClinVar.Still reading. A first read of a gene can take a while; this page waits up to 60 seconds for it, and its scripts then bring in the panel, or a line saying what did not arrive.
09 / Constraint
How much variation Atxn3 tolerates
Ready in a moment
Reading gnomAD and Open Targets.Still reading. A first read of a gene can take a while; this page waits up to 45 seconds for it, and its scripts then bring in the panel, or a line saying what did not arrive.
10 / Orthologs
The same gene in mouse, rat and human
Reading the Alliance, NCBI, Ensembl Compara and RGD.Still reading. A first read of a gene can take a while; this page waits up to 145 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.
Ready in a moment
11 /MicroRNAs
MicroRNAs hosted within Atxn3
Reading Ensembl and miRBase.Still reading. A first read of a gene can take a while; this page waits up to 110 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.
Ready in a moment
12 / Long non-coding RNAs
Long non-coding RNAs at the Atxn3 locus
Reading Ensembl.Still reading. A first read of a gene can take a while; this page waits up to 110 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.
Ready in a moment
13 / Literature
Papers that mention Atxn3
Reading Europe PMC.Still reading. A first read of a gene can take a while; this page waits up to 55 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.
Ready in a moment
05
Run the controls
A scramble control of the same chemistry, a positive control against a gene known to knock down in your cells, untreated cells, and a mock condition where a transfection reagent is used. Read knockdown at the RNA level first, then at the protein; the usage guide gives the timing and the concentrations to start from.
06
Pick the product
AUMsilence sdASO needs no transfection reagent and works in the cells that resist one. AUMsilence toASO is the transfection-optimised version of the same design, and AUMsiRNA™ is the siRNA route. The selection guide compares them.
For research use only. Not for use in diagnostic or therapeutic procedures.
Enables cysteine-type deubiquitinase activity and ubiquitin protein ligase…
NCBI Gene summary
Expression by tissue: not available for mouse. GTEx holds human tissues only, and the Human Protein Atlas is keyed on human genes.
Disease associations: not available for mouse. Open Targets and ClinGen curate human genes only. The human ortholog's page carries the associations.
Clinical variants: not available for mouse. ClinVar holds human variants only.
Constraint: not available for mouse. gnomAD and Open Targets carry constraint for human genes only.
Gene summary
Enables cysteine-type deubiquitinase activity and ubiquitin protein ligase binding activity. Involved in cellular response to misfolded protein; monoubiquitinated protein deubiquitination; and protein catabolic process. Acts upstream of or within several processes, including cellular response to heat; exploration behavior; and ubiquitin-dependent protein catabolic process. Located in mitochondrial matrix; mitochondrial membrane; and nuclear inclusion body. Is expressed in several structures, including alimentary system; brain; hemolymphoid system gland; musculature; and testis. Used to study Machado-Joseph disease. Human ortholog(s) of this gene implicated in Machado-Joseph disease and late onset Parkinson's disease. Orthologous to human ATXN3 (ataxin 3).
Provided by Alliance of Genome Resources, Jun 2026, through NCBI Gene. NCBI disclaimer
Deubiquitinating enzyme involved in protein homeostasis maintenance, transcription, cytoskeleton regulation, myogenesis and degradation of misfolded chaperone substrates (By similarity). Binds long polyubiquitin chains and trims them, while it has weak or no activity against chains of 4 or less ubiquitins (By similarity). Involved in degradation of misfolded chaperone substrates via its interaction with STUB1/CHIP: recruited to monoubiquitinated STUB1/CHIP, and restricts the length of ubiquitin chain attached to STUB1/CHIP substrates and preventing further chain extension (PubMed:21855799). Interacts with key regulators of transcription and represses transcription: acts as a histone-binding protein that regulates transcription (By similarity). Acts as a negative regulator of mTORC1 signaling in response to amino acid deprivation by mediating deubiquitination of RHEB, thereby promoting RHEB inactivation by the TSC-TBC complex (By similarity). Regulates autophagy via the deubiquitination of 'Lys-402' of BECN1 leading to the stabilization of BECN1 (PubMed:28445460)
NCBI Gene summary · NCBI Gene annotation RS_2024_02 · read · NCBI Gene 110616Data from NCBI, provided as is; NCBI's policies and disclaimers apply.
UniProtKB function · 2026_03 · read · UniProt Q9CVD2UniProt data are available under the Creative Commons Attribution 4.0 licence.
Expression by tissue: not available for mouse. GTEx holds human tissues only, and the Human Protein Atlas is keyed on human genes.
Mouse tissue expression, from Bgee and Expression Atlas, joins this page in a later phase. Nothing from the human ortholog is shown in its place; its own page is a step away through the species switch above.
Not available
Disease associations: not available for mouse. Open Targets and ClinGen curate human genes only. The human ortholog's page carries the associations.
Not available
Clinical variants: not available for mouse. ClinVar holds human variants only.
Not available
Constraint: not available for mouse. gnomAD and Open Targets carry constraint for human genes only.
2,584 PubMed-indexed papers mention Atxn3 at Europe PMC, newest first. Europe PMC ignores letter case, so the count also covers the human symbol where it differs from this one only in case.
Europe PMC
0 curated, 2 inferred Reactome pathways for Q9CVD2 in mouse, v97.
Reactome
355 residues, reviewed Q9CVD2; 10 entries from the member databases this page shows along the chain; mean pLDDT 74.12; no experimental structure at PDBe.
UniProt · InterPro · AlphaFold DB · PDBe
The 25 highest-scoring STRING partners at or above a combined score of 0.4, of up to 25 asked for; Vcp, Itpr1, Prkn lead.
STRING v12.0
Human ATXN3 by 3 of 3 votes; rat Atxn3 by 3 of 3 votes. RGD is not answering, so the ortholog list could not be shown. Try again later. Reference 95b2c765-4fc.
Alliance · NCBI · Ensembl Compara
No annotated microRNA lies within Atxn3 in Ensembl release 116, on GRCm39.
Ensembl · miRBase
No annotated long non-coding RNA overlaps Atxn3 in Ensembl release 116, on GRCm39.
Ensembl
9 RefSeq and 39 Ensembl transcripts on GRCm39; RefSeq Select NM_029705.3; Ensembl canonical ENSMUST00000021606.12.
NCBI Datasets · Ensembl
Placed on GRCm39 (GCF_000001635.27). MANE Select: not available for mouse. The reference here is the RefSeq Select transcript and the Ensembl canonical transcript, which need not be the same model.
RefSeq 9 transcripts
coding sequence, tall
untranslated region, thin
non-coding exon
intron, fixed width
Genomic strand: minus. Drawn 5' to 3', so exon 1 sits at the left here and at the highest coordinate on the chromosome.
NM_029705.3NM_029705.3RefSeq Select
A window on one transcript
One pixel of the map above stands for several bases, and a block too short to see is drawn wider than its own scale, so the map chooses a region and the sequence here chooses the window. Click an exon on a row of the map, or drag across a row; then set the exact start and end below.
These controls are ready in a moment.
No transcript is chosen.
Once a window is chosen this panel shows its length, its G and C count as a percentage of that length, the letters it is made of, the exons it falls in, whether it crosses a junction, and its antisense strand.
NCBI Datasets, RefSeq transcripts · NCBI Datasets 18.38.0; GCF_000001635.27-RS_2024_02 · read · NCBI Gene 110616Data from NCBI, provided as is; NCBI's policies and disclaimers apply.
Ensembl 39 transcripts
A window on one transcript
One pixel of the map above stands for several bases, and a block too short to see is drawn wider than its own scale, so the map chooses a region and the sequence here chooses the window. Click an exon on a row of the map, or drag across a row; then set the exact start and end below.
These controls are ready in a moment.
No transcript is chosen.
Once a window is chosen this panel shows its length, its G and C count as a percentage of that length, the letters it is made of, the exons it falls in, whether it crosses a junction, and its antisense strand.
Lengths are spliced lengths, as each source states them. Exon ranks follow the strand: on a minus-strand gene exon 1 has the highest genomic coordinate. Reference assembly for mouse: GRCm39.
XM_030246522.2XM_030246522.2
XM_036157162.1XM_036157162.1
XM_030246526.2XM_030246526.2
XM_030246523.1XM_030246523.1
XM_036157164.1XM_036157164.1
XM_036157163.1XM_036157163.1
NM_001167914.1NM_001167914.1
XR_004937404.1XR_004937404.1
scale
Drawn 5' to 3' from each transcript's exons as placed on the reference assembly; exon 1 is the 5' exon on the transcript's own strand. Exon blocks are to scale with each other, except 2 blocks too short to see, widened to a fixed few pixels; introns are drawn at one fixed width whatever their length, so the map is not to scale along the chromosome. Numbers are exon ranks along the strand; a rank is omitted where the exon is too narrow to carry it.
Drawn 5' to 3' from each transcript's exons as placed on the reference assembly; exon 1 is the 5' exon on the transcript's own strand. Exon blocks are to scale with each other; introns are drawn at one fixed width whatever their length, so the map is not to scale along the chromosome. Numbers are exon ranks along the strand; a rank is omitted where the exon is too narrow to carry it.
