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PEX1 / Peroxisomal ATPase PEX1 · IHC design guide
Design Immunohistochemistry for PEX1
Plan chromogenic PEX1 IHC in paraffin sections with the catalog antibody at 2–5 μg/ml (datasheet A03025-1). Assess cytoplasmic staining against the HPA tissue IHC profile, which reports low consistency with RNA expression (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
PEX1 Immunohistochemistry Experimental Design Guide
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
Must know before staining
| Expected localisation | Cytoplasmic tissue staining (HPA tissue IHC); peroxisome membrane association (UniProt) | |
| Staining pattern | Cytoplasmic staining in several tissues (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A03025-1) | |
| Positive control | Appendix+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation consistent across paraffin sections (standard IHC practice; not target-specific) | |
| Caveat | Staining has low consistency with RNA expression (HPA tissue IHC) | |
| Regulation | Low tissue specificity (HPA tissue RNA) | |
| Isoform / epitope | Two isoforms; epitope coverage is unspecified (UniProt) |
Section 1
Recommended PEX1 IHC & IF Protocols
The catalog antibody protocol uses EDTA pH 8.0 retrieval (datasheet A03025-1). One published PEX1 IHC protocol for mouse eye sections is listed below (PMC5026821).
| Sample | Paraffin-embedded human colon cancer tissue; fixative not specified (datasheet A03025-1) |
| Fixation | Image fixative and duration unreported (datasheet A03025-1); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: EDTA pH 8.0 (datasheet A03025-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A03025-1) |
| Primary antibody | Rabbit anti-PEX1, 2-5 μg/ml (datasheet A03025-1) |
| Primary incubation | Overnight at 4 °C (datasheet A03025-1) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A03025-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | PEX1-positive staining in glandular cells of appendix (HPA tissue IHC: Medium). HPA tissue profile: Cytoplasmic expression in several tissues. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA pH 8.0 for the catalog antibody (datasheet A03025-1); compare microwave citrate pH 6.0 if optimizing retrieval (PMC5026821).
Section 2
What Is the Expected PEX1 Staining Pattern?
PEX1 is cytosolic and associates with peroxisomal membranes through PEX26; it has no transmembrane segment (UniProt O43933: subcellular location, topology). In paraffin-section IHC, expect cytoplasmic staining in several tissues, including medium staining in specified glandular and respiratory epithelial cells (HPA: tissue IHC). The HPA tissue profile is Approved but has low consistency between antibody staining and RNA expression, so interpret tissue comparisons cautiously (HPA: tissue IHC reliability).
| Cytoplasmic staining in appendix, breast, colon or duodenal glandular cells, or bronchial respiratory epithelial cells. | This matches HPA's medium staining in those specified cell types and its broader cytoplasmic tissue profile (HPA: tissue IHC). PEX1's cytosolic and peroxisome-associated locations support a cytoplasmic interpretation (UniProt O43933: subcellular location). Discrete peroxisomes need not be resolved in chromogenic sections (standard IHC practice). |
| Predominantly nuclear staining, with little cytoplasmic staining in the expected cells. | A nuclear-only pattern conflicts with the reported cytosolic and peroxisome-associated locations (UniProt O43933: subcellular location; HPA: peroxisomes, supported). Treat it as suspect staining; review controls and detection conditions before assigning it to PEX1 (standard IHC practice). |
| Clear staining in a cell type reported as not detected, such as adipocytes or bone-marrow hematopoietic cells. | That finding conflicts with the cell-specific HPA IHC observations, although a not-detected score is not proof of absolute absence (HPA: adipocytes and hematopoietic cells, not detected; tissue IHC reliability). Check for cross-reactivity or endogenous detection activity using appropriate controls (standard IHC practice). Do not extend a cell-type score to every cell in its tissue. |
| Broad, diffuse color covers cells and surrounding tissue, obscuring cytoplasmic boundaries. | This cannot establish the reported cell-specific cytoplasmic pattern (HPA: tissue IHC profile). Excess detection background or insufficient blocking or washing can obscure localization (standard IHC practice). Compare a no-primary control and inspect whether color remains associated with the expected cells (standard IHC practice). |
| No visible signal in an otherwise evaluable positive tissue, such as appendix glandular cells. | HPA reports medium staining in appendix glandular cells, so an absent result warrants a technical check (HPA: appendix glandular cells, medium). A negative slide alone does not establish absent PEX1: examine tissue preservation, antibody and detection controls, then compare another listed positive cell type (standard IHC practice; HPA: tissue IHC). |
💡Expected PEX1 appearanceCall a result consistent with PEX1 when medium cytoplasmic staining is present in HPA-listed glandular or respiratory epithelial cells; nuclear-only staining or prominent color in HPA not-detected cell types is suspect (HPA: tissue IHC; UniProt O43933: subcellular location).
| Localization and topology | PEX1 is cytosolic and anchored to peroxisomal membranes through PEX26, without a transmembrane segment (UniProt O43933: subcellular location, topology). Assess cytoplasmic localization in IHC; do not require a continuous membrane outline or individually visible puncta in a chromogenic section (standard IHC practice). |
| Tissue and cell-type selection | Use a specified medium-staining cell type as a positive reference, such as colon glandular cells or bronchial respiratory epithelial cells (HPA: tissue IHC). HPA also lists low staining in several other cell types; a weak result there is less decisive than a result in a listed medium-staining reference (HPA: tissue IHC). |
| Evidence strength | The tissue pattern is Approved despite low consistency with RNA expression, while antibody HPA020235 is IHC Approved (HPA: tissue IHC reliability; HPA: antibody validation). These labels support comparison with the observed pattern but do not establish that every section or cell will stain identically (HPA: tissue IHC reliability). |
| IF/ICC Q: What pattern is expected? | A: Peroxisomal localization is supported in ICC-IF, with images listed for A-431 and U2OS (HPA: subcellular; HPA: antibody validation). This is a compartment reference for the separate IF/ICC guide; the tissue IHC profile reports cytoplasmic expression rather than a requirement to resolve individual peroxisomes (HPA: tissue IHC). |
| Situation | Likely cause | Next action |
|---|---|---|
| The expected glandular or respiratory epithelial cells are unstained. | The result conflicts with HPA's medium-staining examples, but the slide alone cannot distinguish a technical miss from sample variation (HPA: tissue IHC; standard IHC practice). | Verify tissue identity and cell preservation, then review the IHC-validated antibody and detection controls; repeat against another HPA-listed medium-staining cell type if needed (HPA: tissue IHC; standard IHC practice). |
| Color is strongest in nuclei. | Nuclear-dominant color does not match the reported cytosolic and peroxisome-associated location (UniProt O43933: subcellular location; HPA: subcellular). | Compare the no-primary control, counterstain and cytoplasmic signal; reassess staining specificity before scoring nuclear color as PEX1 (standard IHC practice). |
| Adipocytes or bone-marrow hematopoietic cells appear strongly positive. | HPA scores those specific cell types as not detected; cross-reactivity or endogenous detection activity is possible (HPA: tissue IHC; standard IHC practice). | Run a no-primary control and appropriate detection controls, then compare localization with a listed medium-staining cell type; report the discordance if it persists (standard IHC practice; HPA: tissue IHC). |
| Diffuse color makes cell-level scoring difficult. | Background can mask the reported cytoplasmic distribution and cell-type differences (HPA: tissue IHC profile; standard IHC practice). | Inspect a no-primary control and review blocking, washing and detection development; score PEX1 only where cell boundaries and cytoplasmic color can be distinguished (standard IHC practice). |
| A low-staining tissue gives a weak or absent result. | HPA lists low staining in thyroid and salivary glandular cells, esophageal squamous epithelial cells, pancreatic exocrine cells, ovarian follicle cells and endometrial glandular cells (HPA: tissue IHC). | Use one of HPA's specified medium-staining cell types to assess assay performance before treating a weak low-level example as a failed run (HPA: tissue IHC; standard IHC practice). |
| IHC looks cytoplasmic, but individual peroxisomal puncta are unclear. | HPA describes tissue IHC as cytoplasmic and separately supports peroxisomal localization by ICC-IF; chromogenic section detail may not resolve each organelle (HPA: tissue IHC; HPA: subcellular; standard IHC practice). | Judge the IHC result against the reported cell-type and cytoplasmic pattern; use the separate IF/ICC guide when organelle-level localization is the experimental question (HPA: tissue IHC; HPA: subcellular). |
Experiment evidence
IHC & IF images showing PEX1 staining
A03025-1 · IHCIHC analysis of PEX1 using anti-PEX1 antibody (A03025-1). PEX1 was detected in a paraffin-embedded section of human colon cancer tissue. Hea
A03025-1 · IHCIHC analysis of PEX1 using anti-PEX1 antibody (A03025-1). PEX1 was detected in a paraffin-embedded section of human colon tissue. Heat media
A03025-1 · IFIF analysis of PEX1 using anti-PEX1 antibody (A03025-1). PEX1 was detected in a paraffin-embedded section of human colon cancer tissue. Heat
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000127980-PEX1/tissue/cerebral+cortex#imid_5347464
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000127980-PEX1/tissue/colon#imid_5347406
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000127980-PEX1/tissue/liver#imid_5347399
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000127980-PEX1/tissue/kidney#imid_5347392
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA020235; green = PEX1, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA020235; green = PEX1, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for PEX1 IHC & IF
🧪Run colon first and assess its glandular cells for PEX1 staining (HPA: Medium in colon glandular cells). Use adipose tissue as a negative comparator (HPA: Not detected in adipocytes); on the colon slide, treat other cells as internal background comparators only after confirming they lack specific staining, because the supplied HPA rows identify no internal-negative cell type.
Positive control tissue: Appendix (Glandular cells, HPA Medium)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show PEX1 in A-431, U2OS, with annotated localisation: Peroxisomes (supported) (HPA subcellular).
Technical controls: Include no-primary (secondary-only), a rabbit immunoglobulin isotype control matched to the primary antibody’s clonality, and PEX1-knockout material as a biological negative (hero caption: rabbit anti-PEX1). For colon sections, quench endogenous peroxidase and check background before interpreting DAB signal (hero caption: HRP/DAB detection; standard IHC practice).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported, and the fixative is unreported in the selected A03025-1 tissue-IHC caption. That caption uses heat-mediated retrieval in EDTA at pH 8.0, but does not establish that retrieval is required for every specimen or that frozen sections are easier. IF/ICC Q: Is a punctate signal plausible? A: Yes—peroxisomal localization is supported in HPA ICC-IF images from A-431 and U2OS (HPA: Peroxisomes, supported); assess autofluorescence separately in any tissue IF experiment (standard IF practice).
HPA tissue IHC evidence for PEX1
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Low consistency between antibody staining and RNA expression data.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Appendix | Glandular cells | Medium | Protein (IHC) | HPA → |
| Breast | Glandular cells | Medium | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | Medium | Protein (IHC) | HPA → |
| Colon | Glandular cells | Medium | Protein (IHC) | HPA → |
| Duodenum | Glandular cells | Medium | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Caudate | Glial cells | Not detected | Protein (IHC) | HPA → |
| Cerebellum | Cells in granular layer | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced PEX1 IHC Tips
Troubleshoot PEX1 staining in paraffin sections by checking retrieval, cytoplasmic localisation, controls and cell-level scoring before interpreting intensity differences.
Which retrieval conditions should I start with for PEX1 chromogenic IHC?
Start with heat-mediated antigen retrieval in EDTA buffer at pH 8.0 for paraffin sections (datasheet A03025-1). The selected PEX1 image used this retrieval before overnight incubation at 4°C with 2 μg/ml antibody, so keep those conditions paired for the first comparison (datasheet A03025-1). If staining is weak, adjust heating duration in small steps while holding section thickness, detection chemistry and tissue controls constant (standard IHC practice). Compare cytoplasmic signal in colon glandular cells with background in the same run, and avoid treating stronger overall DAB colour as proof of improved specificity (HPA: Medium in colon glandular cells; standard IHC practice).
How should I troubleshoot weak PEX1 staining when fixation records are incomplete?
PEX1-specific sensitivity to fixation is unknown: the selected paraffin-section caption does not state a fixative, and its retrieval conditions cannot establish fixation tolerance (datasheet A03025-1). Record each specimen’s fixative and fixation duration when available, then compare sections processed together using the same EDTA pH 8.0 retrieval and detection conditions (datasheet A03025-1; standard IHC practice). Examine morphology alongside staining, since poorly preserved tissue can make a weak or uneven chromogenic result difficult to interpret (standard IHC practice). If fixation history differs between specimens, qualify any intensity comparison until a consistently processed control shows that the assay performs reproducibly (standard IHC practice).
Should PEX1 look diffuse or punctate in paraffin sections?
Expect cytoplasmic staining in tissue IHC, while recognising that PEX1 is cytosolic and associates with peroxisomal membranes through PEX26 via PEX6 (HPA: cytoplasmic expression in several tissues; UniProt O43933 subcellular and subunit). PEX1 has no transmembrane segment, so membrane association does not make a crisp cell-surface rim the expected pattern (UniProt O43933 topology and subcellular). HPA reports supported peroxisomal localisation by ICC/IF, but chromogenic paraffin sections may not resolve individual organelles (HPA subcellular; standard IHC practice). Assess cellular compartment at high magnification with a counterstain, and compare the pattern with a no-primary control before calling isolated brown granules specific (standard IHC practice).
Could isoforms or epitope accessibility explain inconsistent PEX1 staining?
PEX1 has 2 annotated isoforms, but the supplied evidence does not map this antibody’s epitope to either one (UniProt O43933 isoforms; datasheet A03025-1). Its annotated chain spans residues 1–1283, with phosphoserines reported at 354, 1181, 1209 and 1211; those annotations alone do not establish an IHC staining effect (UniProt O43933 processing and modified residues). Check the antibody’s documented immunogen or epitope before interpreting a discrepant sample as isoform-specific, and avoid assigning a phosphorylation-dependent effect without direct evidence (standard IHC practice). Hold retrieval and detection settings constant across sections so technical variation does not masquerade as epitope biology (standard IHC practice).
How can IF help check a questionable PEX1 IHC pattern?
Use IF as an orthogonal localisation check when chromogenic IHC appears compartmentally ambiguous; HPA reports supported PEX1 localisation to peroxisomes in ICC/IF (HPA subcellular). In tissue multiplexing, pair PEX1 with a glandular epithelial marker when examining colon glandular cells, which HPA scores at Medium intensity (HPA: Medium in colon glandular cells; standard IF practice). Choose spectrally separated fluorophores and inspect unstained tissue for autofluorescence before assigning puncta to PEX1 (standard IF practice). Because PEX1 is cytosolic and associates with peroxisomal membranes without a transmembrane segment, optimise permeabilisation for access to its cytosolic epitope, whose exact position on this antibody is unreported (UniProt O43933 topology and subcellular; datasheet A03025-1; standard IF practice).
What should I check when PEX1 DAB staining is widespread?
The selected paraffin-section image used 10% goat serum blocking, 2 μg/ml primary antibody overnight at 4°C, a peroxidase-conjugated secondary and DAB development (datasheet A03025-1). Check a no-primary section for secondary-reagent staining and include a peroxidase block to assess endogenous enzyme contribution to DAB colour (standard IHC practice). If background persists, compare shorter DAB development and lower primary concentration while keeping retrieval at EDTA pH 8.0 for the initial optimisation series (datasheet A03025-1; standard IHC practice). Judge improvement by clearer cytoplasmic cell staining and reduced signal in control areas, rather than by a uniformly paler slide (HPA: cytoplasmic expression in several tissues; standard IHC practice).
How should I score PEX1 across paraffin tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the compartment and cell population before scoring: HPA reports Medium PEX1 staining in colon glandular cells and an overall cytoplasmic tissue pattern (HPA tissue IHC). Score the percentage of positive cells and staining intensity, or calculate an H-score from prespecified intensity categories, using identical thresholds and DAB development across slides (standard IHC practice). Normalise positive counts or signal area to the number of evaluable target cells or target tissue area in mm², and exclude necrotic or damaged regions by a documented rule (standard IHC practice). Report tissue processing and batch alongside scores because HPA rates its tissue staining Approved with low consistency against RNA expression (HPA reliability; standard IHC practice).
When is a PEX1-positive IHC result convincing?
A convincing result shows reproducible cytoplasmic staining in morphologically intact cells, with colon glandular cells offering a documented Medium-staining reference (HPA tissue IHC; standard IHC practice). A dominant nuclear or cell-surface pattern conflicts with the reported cytosolic and peroxisome-associated distribution and warrants checking staining controls (UniProt O43933 subcellular and topology; HPA subcellular). Treat section-edge colour, necrotic deposits and DAB signal persisting without primary antibody as potential artefacts, and check peroxidase blocking when endogenous enzyme is suspected (standard IHC practice). Interpret intensity differences cautiously because HPA labels tissue staining Approved while reporting low consistency between antibody staining and RNA expression (HPA reliability).
Boster reagents
Best PEX1 / Peroxisomal ATPase PEX1 IHC Antibodies
A03025-1 has IHC and IF images from human paraffin-embedded colon cancer tissue; its IHC images also include human colon tissue (catalog image captions).
Real IHC data
Anti-PEX1 Antibody ®
Cat # A03025-1
A03025-1 is listed for human IHC and IF (catalog applications and reactivity). Its IHC images show human paraffin-embedded colon cancer and colon tissue, while its IF image shows human paraffin-embedded colon cancer tissue (catalog image captions).
Which to pick: Choose A03025-1 for human paraffin-section IHC; its IHC captions do not report the fixative (catalog IHC image captions). For IF, A03025-1 has an image from human paraffin-embedded colon cancer tissue, but ICC validation is unreported (catalog IF image caption and applications). No cross-species option is supported: A03025-1 lists human reactivity only, and its clonality is unreported (catalog reactivity and clone field).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry O43933 (PEX1_HUMAN, Peroxisomal ATPase PEX1).
- Human Protein Atlas. PEX1 tissue IHC expression (reliability: Approved).
- Human Protein Atlas. PEX1 subcellular location (ICC-IF): Localized to the peroxisomes..
- Human Protein Atlas. PEX1 antibody validation summary (1 antibodies).
- Heimler Syndrome With Tooth Agenesis, Abnormal Enamel and Dentin Mineralization, Root Maldevelopment, and PEX1 Mutation. International dental journal 2025 — PMC12172258.
- Spectrum of PEX1 and PEX6 variants in Heimler syndrome. European journal of human genetics : EJHG 2016 — PMC5026821.
- PubMed PMID:9398848 — UniProt-cited evidence.
- PubMed PMID:9398847 — UniProt-cited evidence.
- PubMed PMID:9539740 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for PEX1 (Peroxisomal ATPase PEX1). Expected localisation Cytoplasmic tissue staining (HPA tissue IHC); peroxisome membrane association (UniProt). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A03025-1). Validated IHC antibody: A03025-1 at 2-5 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Appendix (Glandular cells); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human colon cancer tissue; fixative not specified (datasheet A03025-1); 2. Fixation: Image fixative and duration unreported (datasheet A03025-1); verify before use.; 3. Sectioning: 4–5 µm sections on charged slides (standard); 4. Deparaffinisation: Xylene, graded ethanol series to water (standard); 5. Antigen retrieval: Heat retrieval: EDTA pH 8.0 (datasheet A03025-1); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A03025-1); 8. Primary antibody: Rabbit anti-PEX1, 2-5 μg/ml (datasheet A03025-1); 9. Primary incubation: Overnight at 4 °C (datasheet A03025-1). Watch for: Fixation: Keep fixation consistent across paraffin sections (standard IHC practice; not target-specific); Caveat: Staining has low consistency with RNA expression (HPA tissue IHC); Isoform / epitope: Two isoforms; epitope coverage is unspecified (UniProt); Regulation: Low tissue specificity (HPA tissue RNA). Evidence: UniProt O43933, HPA tissue IHC · Approved, HPA ICC-IF · peroxisomes., Datasheet A03025-1, PMC5026821. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/PEX1/immunohistochemistry-ihc-guide.