Reading the record for Stag1 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 Stag1 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 9 E3.3- E4NCBI: 9:100,479,762-100,840,597 on the plus strand, GRCm39 (GCF_000001635.27), sequence NC_000075.7, annotation GCF_000001635.27-RS_2024_02 of 2024-02-01Ensembl: 9:100,479,740-100,841,428 on the plus strand, GRCm39 (GCA_000001635.9), release 116Coordinates are one-based with both ends included, as each source reports them.
Also known as
SA-1, Scc3
Gene identity, from NCBI Datasets · NCBI Datasets 18.38.0 · read · MGI:1098658Data from NCBI, provided as is; NCBI's policies and disclaimers apply.
Silence this gene
The order page opens with Stag1 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
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.
03 / Expression by tissue
Where Stag1 is expressed
Ready in a moment
14 / Silencing this gene
From Stag1 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.
The median is the middle sample of a tissue, so a gene expressed in a few cells of a mixed tissue reads low here and may still be the one your cell type needs. Nothing on this panel is adjusted or averaged across tissues; each figure is the source's own, and a tissue GTEx did not sample is absent from the chart.
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 Stag1 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 Stag1
Ready in a moment
06 / Pathways
Where Stag1 acts, as Reactome curates it
Ready in a moment
07 / Disease associations
Diseases linked to Stag1
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 Stag1
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 Stag1 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
Ready in a moment
11 /MicroRNAs
MicroRNAs hosted within Stag1
Ready in a moment
12 / Long non-coding RNAs
Long non-coding RNAs at the Stag1 locus
Ready in a moment
13 / Literature
Papers that mention Stag1
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 chromatin binding activity.
NCBI Gene summary
11 RefSeq and 34 Ensembl transcripts on GRCm39; RefSeq Select NM_009282.5; Ensembl canonical ENSMUST00000129269.8. 8 RefSeq transcripts of Stag1 carry no exon placement.
NCBI Datasets · Ensembl
Expression by tissue: not available for mouse. GTEx holds human tissues only, and the Human Protein Atlas is keyed on human genes.
The 25 highest-scoring STRING partners at or above a combined score of 0.4, of up to 25 asked for; Smc1a, Smc3, Rad21 lead.
STRING v12.0
0 curated, 5 inferred Reactome pathways for Q9D3E6 in mouse, v97.
Reactome
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.
Human STAG1 by 3 of 3 votes; rat Stag1 by 3 of 3 votes. RGD is not answering, so the ortholog list could not be shown. Try again later. Reference abf35e5f-5b4.
Alliance · NCBI · Ensembl Compara
No annotated microRNA lies within Stag1 in Ensembl release 116, on GRCm39.
Ensembl · miRBase
No annotated long non-coding RNA overlaps Stag1 in Ensembl release 116, on GRCm39.
Ensembl
1,424 PubMed-indexed papers mention Stag1 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
Gene summary
Enables chromatin binding activity. Predicted to be involved in mitotic spindle assembly and sister chromatid cohesion. Located in chromatin. Is expressed in several structures, including alimentary system; brain; genitourinary system; integumental system; and respiratory system. Human ortholog(s) of this gene implicated in autosomal dominant intellectual developmental disorder 47. Orthologous to human STAG1 (STAG1 cohesin complex component).
Provided by Alliance of Genome Resources, Jul 2025, through NCBI Gene. NCBI disclaimer
Component of cohesin complex, a complex required for the cohesion of sister chromatids after DNA replication. The cohesin complex apparently forms a large proteinaceous ring within which sister chromatids can be trapped. At anaphase, the complex is cleaved and dissociates from chromatin, allowing sister chromatids to segregate. The cohesin complex may also play a role in spindle pole assembly during mitosis (By similarity)
NCBI Gene summary · NCBI Gene annotation RS_2024_02 · read · NCBI Gene 20842Data from NCBI, provided as is; NCBI's policies and disclaimers apply.
UniProtKB function · 2026_03 · read · UniProt Q9D3E6UniProt 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.
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 19 transcripts
coding sequence, tall
untranslated region, thin
non-coding exon
intron, fixed width
Genomic strand: plus. Drawn 5' to 3', so exon 1 sits at the left here and at the lowest coordinate on the chromosome.
NM_009282.5NM_009282.5RefSeq 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 20842Data from NCBI, provided as is; NCBI's policies and disclaimers apply.
Ensembl 34 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_030244173.2XM_030244173.2
XM_011242692.3XM_011242692.3
XM_030244172.2XM_030244172.2
NM_001357265.2NM_001357265.2
XM_006510925.2XM_006510925.2
NM_001420288.1NM_001420288.1
NM_001357264.2NM_001357264.2
XM_036154768.1XM_036154768.1
XM_006510924.4XM_006510924.4
NM_001420289.1NM_001420289.1
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 34 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. Not drawn, because the source gave no placement: NM_001433809.1, NM_001433812.1, NM_001433810.1, NM_001433813.1, NM_001433811.1, NM_001433814.1, NM_001433815.1, NM_001433816.1.
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 22 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.
1,258 residues, reviewed Q9D3E6; 12 entries from the member databases this page shows along the chain; mean pLDDT 78.5; no experimental structure at PDBe.
