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- Table of Contents
PEX3 / Peroxisomal biogenesis factor 3 · Western blot design guide
Design a Western Blot for PEX3
Source-linked PEX3 Western blot protocol options, expected-band and isoform facts, troubleshooting for weak or shifted signal, and recommended anti-PEX3 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
PEX3 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 | ~42.1 kDa | |
| Gel | 12–15% (standard starting point) | |
| Positive control | Adrenal gland (IHC candidate; verify WB) +4 more | |
| Negative control | Adipose tissue (IHC candidate; verify WB) |
Important caveats
Reasons your observed band may differ from the expected size.
| PTM | — | |
| Caveat | — | |
| Gene-set association | MSigDB C7 membership | |
| Isoform | 1 isoform(s) |
Section 1
Source-Linked PEX3 Western Blot Protocol Options
The A04166-1 protocol combines labelled catalog values with standard starting conditions. Published comparisons retain their own sample, reagent and detection scope.
| Sample / lysate | extracts of various cell lines, (catalog A04166-1) |
| Gel % | 12–15% (standard starting point) |
| Load | 20–30 µg total protein per lane; optimize for abundance (standard starting point) |
| Transfer | Standard semi-dry transfer; verify efficiency (standard starting point) |
| Membrane | 0.45 µm PVDF (standard starting point) |
| Blocking | 5% milk or 5% BSA in TBST (standard starting point) |
| Primary antibody | A04166-1 · 1:1000 (catalog A04166-1) |
| Primary incubation | Overnight at 4 °C (standard starting point) |
| Secondary antibody | Species-matched HRP conjugate at validated dilution (standard starting point) |
| Secondary incubation | 1 h at room temperature (standard starting point) |
| Wash | 3 × 5 min in TBST (standard starting point) |
| Detection | ECL (catalog A04166-1) |
Section 2
What Is the Expected PEX3 Western Blot Band Size?
PEX3 is predicted at 42.1 kDa; membrane localization may affect recovery, but the supplied evidence does not establish its apparent migration.
| Single band near 42.1 kDa | Consistent with the predicted PEX3 mass, pending band-identity controls |
| Band in a membrane fraction | Consistent with PEX3 localization to the peroxisome membrane |
| Weak band in whole-cell lysate | Membrane-associated PEX3 may be poorly recovered |
| Little or no band in a soluble fraction | Consistent with PEX3 being a multi-pass membrane protein |
💡Expected PEX3 appearancePEX3 is predicted to be 42.1 kDa, but no empirical band size is supplied; confirm any candidate band with band-identity controls.
| UniProt predicted mass | Places full-length PEX3 near 42.1 kDa |
| UniProt molecular weight | The reported 42,140 Da corresponds to the 42.1 kDa prediction |
| Full-length sequence of 373 residues | Defines the protein represented by the predicted mass; no smaller processed product is listed |
| Multi-pass membrane topology | Its effect on apparent migration is not established by the supplied features |
| Situation | Likely cause | Next action |
|---|---|---|
| No band in lysate | Membrane-associated PEX3 may be poorly extracted | Check membrane protein recovery and examine a membrane-enriched fraction |
| Weak or no signal | Low recovery of peroxisome membrane protein | Verify solubilization and include a positive-control lysate |
| Band higher than expected | The supplied features do not establish an upward size shift | Check band identity with PEX3 knockdown or an independent antibody |
| Band lower than expected | No cleaved PEX3 product is listed | Check band identity and sample integrity |
| Multiple bands | Additional bands are unassigned; only one isoform is listed | Compare with PEX3 knockdown and an independent antibody |
Experiment evidence
Western blot images showing PEX3 band
A04166-1 · PEX3
A04166 · PEX3
A04166 · PEX3
← swipe / scroll for more images →
Real WB data behind the band-size expectations in this section.
Sample controls for PEX3 Western blot
🧪HPA-IHC candidate guidance (verify in WB): For positive controls for PEX3 in Western blot, you can use adrenal gland tissue, which HPA scores High.
Positive control: Adrenal gland (IHC candidate; verify WB)
Negative control: Adipose tissue (IHC candidate; verify WB)
Loading controls: Run GAPDH, β-actin, and a total-protein stain such as Ponceau alongside the samples.
⚠️Feasibility: PEX3 is a multi-pass peroxisome membrane protein, so membrane enrichment may improve detection.
HPA tissue expression evidence for PEX3
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 |
|---|---|---|---|---|
| Adrenal gland | glandular cells | High | Protein (IHC) | HPA → |
| Bronchus | respiratory epithelial cells | High | Protein (IHC) | HPA → |
| Colon | glandular cells | High | Protein (IHC) | HPA → |
| Kidney | cells in tubules | High | Protein (IHC) | HPA → |
| Nasopharynx | respiratory epithelial cells | High | Protein (IHC) | HPA → |
Lower expression tissues · IHC evidence, not confirmed WB-negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | adipocytes | Not detected | Protein (IHC) | HPA → |
| Bone marrow | hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Cervix | glandular cells | Not detected | Protein (IHC) | HPA → |
| Caudate | neuronal cells | Low | Protein (IHC) | HPA → |
| Esophagus | squamous epithelial cells | Low | Protein (IHC) | HPA → |
Section 3
Advanced PEX3 Western Blot Tips
Deeper troubleshooting and optimisation questions for PEX3, answered from its protein features.
How should PEX3 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.
Could a second PEX3 band represent an annotated isoform?
Isoforms · Only one isoform is listed, with no alternative sequence. An additional band cannot be assigned to an annotated PEX3 isoform from these features.
Do annotated modifications explain unexpected PEX3 bands?
PTM · No modified residues or glycosylation sites are listed. The features therefore do not support assigning an unexpected band to a specific modification; verify its identity before interpreting it.
Does this guide establish induction of PEX3?
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 PEX3 Western blot?
Transfer · PEX3 is a 42.1-kDa multi-pass membrane protein. These features do not specify a transfer method. Check recovery on the membrane and protein remaining in the gel when optimizing transfer conditions.
Does PEX3 require a particular blocking reagent?
Blocking · No blocking reagent is specified by these features. Compare blockers under otherwise identical conditions and choose the one that gives a clear PEX3 signal with low background.
How should PEX3 band intensity be quantified?
Quantitation · Measure the same identified PEX3 band across samples and normalize for sample loading. PEX3 resides in the peroxisome membrane, so interpret a change in its signal in the context of the peroxisomal material present.
Should PEX3 run exactly at its predicted 42.1 kDa?
Interpretation · 42.1 kDa is the predicted mass; no observed band position is supplied. PEX3 is a multi-pass peroxisome membrane protein, but that feature alone does not establish an apparent mass shift. Confirm band identity before attributing any difference to PEX3.
No signal peptide or propeptide is annotated for PEX3. These features provide no basis for assigning a smaller band to cleavage of either region.
No signal peptide or propeptide is annotated for PEX3. These features provide no basis for assigning a smaller band to cleavage of either region.
Boster reagents
PEX3 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-Peroxin 3 PEX3 Antibody
Cat # A04166-1
Real WB data
Anti-Peroxin 3 PEX3 Antibody
Cat # A04166
The catalog reports two anti-PEX3 antibodies, A04166-1 and A04166. Both report human, mouse, and rat reactivity and have Western blot images. Their captions mention various cell lines or cells without naming specimens, so the images do not establish species-specific WB performance.
Which to pick: Both have WB images and list the same reactivity. Pick A04166-1 if you want documented starting conditions: 1:1000 antibody dilution, 25 µg protein per lane, and ECL detection. The supplied caption for A04166 gives no comparable setup details.
Source: BosterBio PEX3 gene-info card — filtered to Western-blot-capable antibodies; each card shows that product's actual WB validation figure.
References
- UniProt Consortium. UniProt entry P56589.
- Human Protein Atlas. PEX3 tissue expression.
- PMC5560687 — target-verified WB comparison
- PMC11217276 — target-verified WB comparison
- PMC8658024 — target-verified WB comparison