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- Table of Contents
SNX9 / Sorting nexin-9 · Western blot design guide
Design a Western Blot for SNX9
Source-linked SNX9 Western blot protocol options, expected-band and isoform facts, troubleshooting for weak or shifted signal, and recommended anti-SNX9 WB antibodies. Everything you need to plan the experiment before you commit precious samples.
Evidence assembled September 2026 · For research use; verify linked source records and product datasheet before use
SNX9 Western Blot Experimental Design Guide
Expected bands, source-linked protocol options, controls and antibodies — the at-a-glance facts below, then the full design guide.
Must know before running
| Expected band | ~66.6 kDa | |
| Observed band | ~78 kDa | |
| Gel | 5–20% (catalog A03796-2) | |
| Positive control | Appendix (IHC candidate; verify WB) +4 more | |
| Negative control | Suggested KO / knockdown lysate |
Important caveats
Reasons your observed band may differ from the expected size.
| PTM | Phosphorylated + Acetylated | |
| Caveat | Modification-state controls | |
| Gene-set association | MSigDB Hallmark membership | |
| Isoform | 1 isoform(s) |
Section 1
Source-Linked SNX9 Western Blot Protocol Options
The A03796-2 protocol combines labelled catalog values with standard starting conditions. Published comparisons retain their own sample, reagent and detection scope.
| Sample / lysate | human K562, human 293T, human placenta (catalog A03796-2) |
| Gel % | 5–20% (catalog A03796-2) |
| Load | 30 ug; reducing conditions (catalog A03796-2) |
| Transfer | a nitrocellulose membrane at 150 mA for 50-90 minutes (catalog A03796-2) |
| Membrane | nitrocellulose membrane (catalog A03796-2) |
| Blocking | 5% non-fat milk/TBS for 1.5 hour at RT (catalog A03796-2) |
| Primary antibody | A03796-2 · 0.25 μg/mL (catalog A03796-2) |
| Primary incubation | overnight at 4°C (catalog A03796-2) |
| Secondary antibody | goat anti-rabbit IgG-HRP, 1:5000 (catalog A03796-2) |
| Secondary incubation | 1.5 hour at RT (catalog A03796-2) |
| Wash | TBS-0.1%Tween 3 times with 5 minutes each (catalog A03796-2) |
| Detection | ECL (catalog A03796-2) |
Section 2
What Is the Expected SNX9 Western Blot Band Size?
SNX9 is predicted at 66.6 kDa and observed near 78 kDa in reducing Western blots; the cause of the difference is not established.
| Band near 78 kDa | Empirical SNX9 band in reducing whole-cell and tissue lysates; identity still requires controls |
| Band near 66.6 kDa | Near the UniProt predicted mass; identity requires controls |
| Higher band near twice the monomer size | Could reflect an SNX9 homodimer if the complex survives electrophoresis; this migration is unverified |
| Doublet near the monomer region | Could reflect distinct SNX9 phosphorylation states; a visible separation is unverified |
💡Expected SNX9 appearanceUniProt predicts 66.6 kDa, while antibody QC shows an SNX9 band near 78 kDa under reducing conditions; the cause of the difference is unestablished, so confirm identity with appropriate controls.
| UniProt predicted mass | 66.6 kDa calculated; the empirical reducing-condition band is near 78 kDa, with no established cause for the difference |
| SNX9 homodimer and homooligomer | Could appear at a higher mass if an intact complex survives electrophoresis; no such band is established |
| Phosphorylation at Ser116, Ser121, Ser197, Ser200, Thr216 and Tyr239 | May affect mobility, but a visible shift is not established |
| Acetylation at Lys288 | Adds a modification, but a visible size shift is not established |
| Situation | Likely cause | Next action |
|---|---|---|
| No band in lysate | SNX9 signal may be below detection in the sampled lysate | Check lysate loading and antibody performance with a positive-control lysate |
| Band higher than expected | The empirical SNX9 band is near 78 kDa rather than the predicted 66.6 kDa; its cause is unestablished | Compare with the 78 kDa QC band and verify identity with an independent antibody or SNX9 depletion |
| Band lower than expected | A lower band has no assigned SNX9 form in the supplied features | Check molecular-weight calibration and verify identity with SNX9 depletion |
| Multiple bands | SNX9 has phosphorylation sites and forms oligomers, but neither feature establishes the identity of extra bands | Compare reducing and non-reducing lanes and test band identity with SNX9 depletion |
| Weak or no signal | SNX9 associates with cytoplasmic vesicle and cell membranes, so sample recovery may affect signal | Check extraction and loading, then compare with a positive-control lysate |
Experiment evidence
Western blot images showing SNX9 band
A03796-2 · SNX9
← swipe / scroll for more images →
Real WB data behind the band-size expectations in this section.
Sample controls for SNX9 Western blot
🧪HPA-IHC candidate guidance (verify in WB): For positive controls for SNX9 in Western blot, you can use appendix lysate.
Positive control: Appendix (IHC candidate; verify WB)
Negative control: Suggested KO / knockdown lysate
Loading controls: Run GAPDH, β-actin, and a total-protein stain alongside the samples.
⚠️Feasibility: HPA lists no tissue as undetected, so use siRNA knockdown or a KO line for a negative control.
HPA tissue expression evidence for SNX9
Comprehensive Human Protein Atlas IHC scoring per tissue. Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Higher expression tissues · candidate positive controls from IHC
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Appendix | glandular cells | High | Protein (IHC) | HPA → |
| Colon | endothelial cells | High | Protein (IHC) | HPA → |
| Endometrium | glandular cells | High | Protein (IHC) | HPA → |
| Epididymis | glandular cells | High | Protein (IHC) | HPA → |
| Fallopian tube | ciliated cells (ciliary rootlets) | High | Protein (IHC) | HPA → |
Lower expression tissues · IHC evidence, not confirmed WB-negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Caudate | glial cells | Low | Protein (IHC) | HPA → |
| Heart muscle | cardiomyocytes | Low | Protein (IHC) | HPA → |
| Hippocampus | glial cells | Low | Protein (IHC) | HPA → |
| Parathyroid gland | glandular cells | Low | Protein (IHC) | HPA → |
| Skeletal muscle | myocytes | Low | Protein (IHC) | HPA → |
Section 3
Advanced SNX9 Western Blot Tips
Deeper troubleshooting and optimisation questions for SNX9, answered from its protein features.
How should SNX9 band migration be interpreted?
Band shift · Use the separately labelled calculated mass and catalog-observed evidence above. A sequence annotation does not establish an observed migration shift. Verify target identity with orthogonal controls.
Are multiple SNX9 isoform bands expected?
Isoforms · Only one isoform is supplied, with no alternative sequence. Do not assign additional bands to SNX9 isoforms based on these features alone.
Which SNX9 modifications are mapped?
PTM · UniProt lists phosphoserine at 116, 121, 197 and 200; phosphothreonine at 216; phosphotyrosine at 239; and N6-acetyllysine at 288. These are UniProt coordinates, which may differ from paper or antibody numbering. Their presence does not establish a visible band shift.
Does this guide establish induction of SNX9?
Induction · No general induction response is established by this guide. A pathway or gene-set association is not evidence of induction in a particular specimen. Verify the relevant treatment and control in a target-specific experiment.
What transfer method to use for SNX9 Western blot?
Transfer · SNX9 is predicted at 66.6 kDa and observed near 78 kDa. Check transfer efficiency in that size range with a total-protein stain. Its peripheral membrane localization does not, by itself, specify a special transfer method.
How should blocking be optimized?
Blocking · Standard workflow guidance: follow the A03796-2 datasheet where specified. Otherwise compare 5% milk or 5% BSA in TBST; for a phospho-specific assay start with BSA. Optimize background and specific signal with matched controls.
How should SNX9 be quantified across cellular fractions?
Quantitation · SNX9 is listed in the cytoplasm and on the cytoplasmic side of cell and vesicle membranes, as well as at the trans-Golgi network and ruffles. Quantify matched fractions consistently; a change in one fraction alone may reflect redistribution rather than a change in total SNX9.
Why might SNX9 appear near 78 kDa instead of 66.6 kDa?
Interpretation · The observed band is about 78 kDa, while the predicted mass is 66.6 kDa. The listed modifications do not establish the cause of this difference. Confirm band identity before attributing the apparent mass to a specific modification.
SNX9 is listed as a homodimer and homooligomer and as a heterodimer with SNX18. Those interactions make oligomers worth considering, but a higher band alone does not identify its composition. Compare sample preparation conditions and verify band identity.
The supplied features list no signal peptide, propeptide or alternative sequence that would predict a shorter mature form. Treat a lower band as unidentified until its SNX9 identity is verified; these features do not establish its cause.
SNX9 is listed as a homodimer and homooligomer and as a heterodimer with SNX18. Those interactions make oligomers worth considering, but a higher band alone does not identify its composition. Compare sample preparation conditions and verify band identity.
The supplied features list no signal peptide, propeptide or alternative sequence that would predict a shorter mature form. Treat a lower band as unidentified until its SNX9 identity is verified; these features do not establish its cause.
Boster reagents
SNX9 Western Blot Antibodies
Catalog antibodies with Western blot application and product-specific WB images. Evaluate suitability with the reported sample, controls and experimental conditions.
Real WB data
Anti-SH3PX1/SNX9 Antibody Picoband®
Cat # A03796-2
The catalog reports one anti-SNX9 antibody for Western blot, A03796-2, with stated human reactivity. Its image shows a band near 78 kDa in human K562, 293T, and placenta lysates; the expected size is 67 kDa. No further validation evidence is supplied.
Which to pick: A03796-2 is the only listed option. Its WB image uses human K562, 293T, and placenta lysates at 0.25 μg/mL, making those the documented starting contexts. The observed 78 kDa band differs from the expected 67 kDa size.
Source: BosterBio SNX9 gene-info card — filtered to Western-blot-capable antibodies; each card shows that product's actual WB validation figure.
References
- UniProt Consortium. UniProt entry Q9Y5X1.
- Human Protein Atlas. SNX9 tissue expression.
- PMC12686149 — target-verified WB comparison
- PMC6617759 — target-verified WB comparison
- PMC5356600 — target-verified WB comparison