SEC13 / Protein SEC13 homolog · IHC design guide

Design Immunohistochemistry for SEC13

Plan SEC13 chromogenic IHC in paraffin sections using the catalog antibody's documented staining conditions. Compare cytoplasmic staining with tissue controls while accounting for the reported inconsistency between antibody staining and RNA expression (HPA tissue IHC).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use

Immunohistochemistry protocol sheet for SEC13 (IHC for SEC13): expected localisation Cytoplasmic tissue staining (HPA tissue IHC), antibody A04346-1, validated IHC image, and IHC protocol steps — Printable **SEC13** IHC protocol sheet — expected localisation Cytoplasmic tissue staining (HPA tissue IHC), antibody A04346-1, controls and protocol steps. Open the full SEC13 IHC guide →

Navigate to: Protocols Staining pattern Controls Antibodies

SEC13 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)
	Staining pattern	Cytoplasmic staining in most tissues (HPA tissue IHC)
	Antigen retrieval	EDTA pH 8.0 HIER, heat-mediated (datasheet A04346-1)
	Positive control ⓘ	Breast+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 conditions consistent across sections. (standard IHC practice; not target-specific)
	Caveat	Antibody staining has low consistency with RNA expression (HPA tissue IHC)
	Regulation	Staining intensity regulation is unreported (UniProt)
	Isoform / epitope	4 isoforms; their antibody epitope coverage is unknown (UniProt; datasheet A04346-1)

Section 1

Recommended SEC13 IHC & IF Protocols

The catalog antibody’s IHC-P protocol is accompanied by two published SEC13 IHC methods using tissue sections (datasheet A04346-1; PMC13358067; PMC9861657).

Recommended immunohistochemistry (IHC-P) protocol parameters
Sample	Paraffin-embedded human brain tissue; fixative not specified (datasheet A04346-1)
Fixation	Image fixative and duration unreported (datasheet A04346-1); 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 A04346-1); 20 min, 95–100 °C (standard)
Peroxidase block	3% H2O2, 10 min, room temperature (standard)
Blocking	10% goat serum (datasheet A04346-1)
Primary antibody	Rabbit anti-SEC13, 2-5 μg/ml (datasheet A04346-1)
Primary incubation	Overnight at 4 °C (datasheet A04346-1)
Detection	HRP-conjugated secondary, DAB chromogen (datasheet A04346-1)
Counterstain	Hematoxylin, blue, dehydrate and mount (standard)
Expected result	SEC13-positive staining in glandular cells of breast (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression in most tissues. No signal in the no-primary control.

💡Decision noteStart with heat-mediated EDTA at pH 8.0 for the catalog antibody (datasheet A04346-1); the breast tissue study used citrate at pH 6.0 (PMC13358067).

Section 2

What Is the Expected SEC13 Staining Pattern?

SEC13 is associated with COPII vesicles, the endoplasmic reticulum, lysosome membranes and nuclear pores; it has no transmembrane segment (UniProt P55735). In tissue IHC, expect chiefly cytoplasmic staining in many cell types, including strong staining in breast and prostate glandular cells and cervical squamous cells (HPA tissue IHC). HPA rates the tissue staining Approved but reports low agreement with RNA data and pending external verification (HPA tissue IHC).

What am I looking at on my slide?
Cytoplasmic stain is high in breast or prostate glandular cells, or cervical squamous cells (HPA tissue IHC).	This matches the reported positive cell types and the predominantly cytoplasmic tissue pattern (HPA tissue IHC). Judge the stain in those cells, rather than assigning one score to the whole section. Nuclear pore association is biologically plausible (UniProt P55735), but HPA tissue IHC does not establish a distinct nuclear rim pattern.
Stain is confined to extracellular material or cell borders, with no convincing cytoplasmic signal in positive cells.	That distribution does not match HPA's predominantly cytoplasmic tissue pattern (HPA tissue IHC). Recheck morphology and controls before calling it SEC13. Nuclear staining alone needs a separate assessment: SEC13 associates with nuclear pores (UniProt P55735), and ICC-IF reports nucleoplasmic localization (HPA subcellular).
Adipocytes stain strongly while adjacent expected positive cells do not (HPA tissue IHC).	HPA reports SEC13 as not detected in adipocytes, so the reversal raises concern for nonspecific staining or detection artefact (HPA tissue IHC). It does not make all adipose tissue a negative control: interpret the named cell type and compare it with a positive section.
Brown color spreads across stroma, lumina and cells without clear cellular boundaries.	This is difficult to score as SEC13 because the reported tissue signal is cellular and mainly cytoplasmic (HPA tissue IHC). In chromogenic IHC, widespread color may reflect background or endogenous detection activity; use a no-primary control and inspect whether staining follows cell morphology.
Breast glandular cells remain unstained in a section chosen as a positive control (HPA: High).	A technical failure or an unsuitable section is possible; absence alone does not establish biological loss. Confirm the expected cells are present, review the run controls and repeat the stain if needed. HPA's Approved tissue profile has low agreement with RNA data and awaits external verification (HPA tissue IHC).

💡Expected SEC13 appearanceA convincing positive is predominantly cytoplasmic stain reaching high intensity in breast or prostate glandular cells or cervical squamous cells (HPA tissue IHC); isolated extracellular or tissue-wide brown deposit without cell-associated staining warrants artefact checks.

How each factor affects the staining
Tissue and cell-type selection	Breast and prostate glandular cells and cervical squamous cells are reported high; bone marrow hematopoietic cells are medium (HPA tissue IHC). Adipocytes and kidney glomerular cells are reported not detected (HPA tissue IHC). These labels apply to the specified cells, not every cell in those tissues.
Tissue IHC evidence	The tissue profile is Approved, with low consistency between antibody staining and RNA expression and external verification pending (HPA tissue IHC). HPA035292 is Approved for IHC; the supplied antibody summary does not mark it Enhanced (HPA antibodies). Treat unexpected patterns as provisional until controls and morphology support them.
Antibody and isoform coverage	SEC13 has 4 annotated isoforms, and the listed protein chain spans residues 2–322 (UniProt P55735). The payload gives no antibody epitope or isoform coverage. A difference between reagents therefore cannot be assigned to a particular isoform from these records alone.
Antigen retrieval	For paraffin-section IHC, assess retrieval and antibody dilution against a positive control as general workflow practice. No SEC13-specific retrieval condition, dilution or fixation sensitivity is supplied here; HPA staining levels do not establish how fixation affects SEC13 detection.
IF/ICC Q: What localization should be expected?	A: HPA reports supported nucleoplasmic and vesicular localization in ICC-IF, with images from A-549 and HeLa (HPA subcellular). This complements UniProt's nuclear pore and vesicle annotations (UniProt P55735); it does not prescribe an IF protocol or override the predominantly cytoplasmic tissue IHC profile (HPA tissue IHC).

Why is my staining missing, weak or wrong?
Situation	Likely cause	Next action
Expected positive cells show no chromogenic signal.	The section, retrieval, antibody incubation or detection run may have failed; breast glandular cells are reported high (HPA tissue IHC).	Verify the named cells are present, inspect a run positive control and repeat with checked retrieval and detection conditions. No SEC13-specific retrieval setting or dilution is supplied.
Most cells and stroma show similar brown haze.	Nonspecific background or endogenous detection activity can obscure the cell-associated cytoplasmic pattern reported by HPA (HPA tissue IHC).	Compare a no-primary control, check blocking and washes, and assess whether color follows intact cells. Adjust detection conditions using controls before scoring.
Only cell borders or extracellular deposits appear positive.	That localization is discordant with the predominantly cytoplasmic tissue profile (HPA tissue IHC).	Inspect section morphology and no-primary control; compare with a section containing HPA-listed positive cells. Do not assign a SEC13 score to deposit-only staining.
A presumed negative tissue contains stained cells.	HPA's not detected calls identify specific cells, such as adipocytes or glomerular cells, rather than whole tissues (HPA tissue IHC).	Identify the stained cell type before judging specificity. Score adipocytes or glomerular cells separately from their neighbors (HPA tissue IHC).
Nuclear staining differs from the expected tissue pattern.	SEC13 is associated with nuclear pores (UniProt P55735), and ICC-IF reports nucleoplasmic signal (HPA subcellular); tissue IHC is described chiefly as cytoplasmic (HPA tissue IHC).	Record cytoplasmic and nuclear compartments separately. Check controls and morphology before treating nuclear signal as either confirmed SEC13 or artefact.
A repeat stain gives a different intensity ranking across tissues.	HPA reports low agreement between tissue staining and RNA expression and says external verification is pending (HPA tissue IHC). Technical variation may also affect chromogenic scores.	Run the same positive-control tissue alongside samples, compare the same cell types and record the control result. Avoid interpreting intensity changes from unmatched sections alone.

Source: UniProt P55735 Human Protein Atlas tissue Human Protein Atlas subcellular

Experiment evidence

IHC & IF images showing SEC13 staining

IHC analysis of SEC13 using anti-SEC13 antibody (A04346-1). SEC13 was detected in a paraffin-embedded section of human brain tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH 8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 2 μg/ml rabbit anti-SEC13 Antibody (A04346-1) overnight at 4°C. Peroxidase Conjugated Goat Anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using HRP Conjugated Rabbit IgG Super Vision Assay Kit (Catalog # SV0002) with DAB as the chromogen.

A04346-1 · IHCIHC analysis of SEC13 using anti-SEC13 antibody (A04346-1). SEC13 was detected in a paraffin-embedded section of human brain tissue. Heat me

IF analysis of SEC13L1/SEC13 using anti-SEC13L1/SEC13 antibody (A04346-1). SEC13L1/SEC13 was detected in an immunocytochemical section of A549 cells. Enzyme antigen retrieval was performed using IHC enzyme antigen retrieval reagent (AR0022) for 15 mins. The cells were blocked with 10% goat serum. And then incubated with 5 μg/mL rabbit anti-SEC13L1/SEC13 Antibody (A04346-1) overnight at 4°C. DyLight®488 Conjugated Goat Anti-Rabbit IgG (BA1127) was used as secondary antibody at 1:100 dilution and incubated for 30 minutes at 37°C. The section was counterstained with DAPI. Visualize using a fluorescence microscope and filter sets appropriate for the label used.

A04346-1 · IFIF analysis of SEC13L1/SEC13 using anti-SEC13L1/SEC13 antibody (A04346-1). SEC13L1/SEC13 was detected in an immunocytochemical section of A5

HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000157020-SEC13/tissue/cerebral+cortex#imid_10851911

HPA · EsophagusHuman Protein Atlas IHC, Esophagus. Source: https://www.proteinatlas.org/ENSG00000157020-SEC13/tissue/esophagus#imid_10851867

HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000157020-SEC13/tissue/colon#imid_10851837

HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000157020-SEC13/tissue/liver#imid_10851830

HPA · ICC-IF A-549Human Protein Atlas immunofluorescence, A-549, antibody HPA057943; green = SEC13, blue = nucleus, red = microtubules.

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Real IHC / IF data behind the staining-pattern expectations in this section.

Sample controls for SEC13 IHC & IF

🧪Run breast first: glandular cells should stain (HPA: High in breast glandular cells). Use adipose tissue as the negative comparator (HPA: Not detected in adipocytes); cells without specific staining on the breast slide should show only background chromogen, but HPA does not identify a particular internal cell type as negative (HPA: breast glandular cells High).

Positive control tissue: Breast (Glandular cells, HPA High)

Negative control tissue: Adipose tissue (HPA Not detected)

ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show SEC13 in A-549, HeLa, with annotated localisation: Nucleoplasm (supported), Vesicles (supported) (HPA subcellular).

Technical controls: Include a no-primary, secondary-only control and a concentration-matched nonimmune rabbit IgG isotype control (caption: rabbit anti-SEC13 primary; standard IHC practice). Use SEC13 knockout material as a biological negative if available, and quench endogenous peroxidase before HRP/DAB detection in the breast section (standard IHC practice; caption: HRP/DAB detection).

⚠️Feasibility: No target-specific fixation window or fixation effect is reported in the supplied evidence; the selected A04346-1 paraffin-section caption does not state a fixative (caption: fixative unreported). The demonstrated paraffin-section procedure used heat retrieval in EDTA at pH 8.0, but retrieval dependence has not been established (caption: EDTA heat retrieval). HPA shows supported nucleoplasm and vesicle localization in ICC/IF images from A-549 and HeLa, but the evidence does not establish that frozen sections or IF are easier than paraffin IHC (HPA: supported nucleoplasm and vesicles; caption: paraffin-section IHC).

HPA tissue IHC evidence for SEC13

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Low consistency between antibody staining and RNA expression data. Pending external verification.). 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
Breast	Glandular cells	High	Protein (IHC)	HPA →
Cervix	Squamous epithelial cells	High	Protein (IHC)	HPA →
Esophagus	Squamous epithelial cells	High	Protein (IHC)	HPA →
Prostate	Glandular cells	High	Protein (IHC)	HPA →
Tonsil	Squamous epithelial cells	High	Protein (IHC)	HPA →

Undetected expression · recommended negative controls

Tissue	Cell type	Level	Evidence	Source
Adipose tissue	Adipocytes	Not detected	Protein (IHC)	HPA →
Cerebellum	Cells in granular layer	Not detected	Protein (IHC)	HPA →
Hippocampus	Glial cells	Not detected	Protein (IHC)	HPA →
Kidney	Cells in glomeruli	Not detected	Protein (IHC)	HPA →
Liver	Cholangiocytes	Not detected	Protein (IHC)	HPA →

Section 3

Advanced SEC13 IHC Tips

Troubleshoot SEC13 staining in paraffin sections by checking retrieval, compartment pattern, controls and cell type before interpreting chromogenic signal.

Which retrieval conditions should I try first for SEC13 in paraffin sections?

Start with heat mediated antigen retrieval in EDTA at pH 8.0 (datasheet A04346-1). The selected paraffin section example used that retrieval before incubation with 2 μg/ml catalog antibody overnight at 4°C (datasheet A04346-1). If staining is weak, check that sections were fully deparaffinised and heated evenly, then vary retrieval time in small steps while keeping a known positive section alongside each run (standard IHC practice). Compare signal and tissue integrity together; stronger diffuse staining after more heating does not, by itself, establish better SEC13 detection (standard IHC practice).

How should I troubleshoot weak SEC13 staining when fixation history is uncertain?

SEC13 specific sensitivity to fixation is unknown from the supplied evidence; the selected paraffin section caption does not state a fixative (datasheet A04346-1). Record the available fixation and processing history, and compare affected sections with a known positive section processed in the same run (standard IHC practice). Use the documented EDTA retrieval at pH 8.0 as the starting condition before changing incubation or detection steps (datasheet A04346-1). If only one specimen fails, inspect morphology and staining in other antigens on that specimen before assigning the failure to SEC13 epitope loss (standard IHC practice).

What SEC13 staining pattern should I expect in chromogenic IHC?

Assess cytoplasmic staining in the context of cell morphology: tissue IHC reports cytoplasmic expression in most tissues, with high staining in breast glandular cells and cervix squamous epithelial cells (HPA: tissue IHC). SEC13 also functions at COPII coated vesicles and nuclear pores, including both sides of the pore in interphase (UniProt P55735: function and subcellular location). A perinuclear or finely punctate component can therefore be biologically plausible, but bright uniform nuclear DAB alone needs corroboration (UniProt P55735: subcellular location; standard IHC interpretation). Score epithelial and stromal compartments separately so staining in neighboring cells does not obscure the cell type being assessed (standard IHC practice).

Can SEC13 isoforms or modified residues explain discordant staining?

SEC13 has 4 reported isoforms and modified residues including phosphoserine at positions 184 and 309 (UniProt P55735: isoforms and modified residues). The supplied IHC caption does not identify the catalog antibody epitope, so these features cannot establish which isoforms or modified forms its staining detects (datasheet A04346-1; UniProt P55735: isoforms). Check the antibody immunogen or epitope documentation before attributing differences between specimens to alternative splicing or phosphorylation (standard antibody validation practice). When comparing reagents, stain adjacent sections under matched retrieval and detection conditions and interpret discordance as an antibody validation question first (standard IHC practice).

How can I use IF to check an ambiguous SEC13 IHC pattern?

Use IF as a separate localisation check: supported nucleoplasmic and vesicular staining has been reported in cell images, whereas tissue IHC broadly reports cytoplasmic staining (HPA: subcellular; HPA: tissue IHC). Multiplex SEC13 with a marker for the cell type under study, and choose fluorophores whose signal is distinguishable from autofluorescence in that specimen (standard IF practice). Adjust permeabilisation to give antibody access to the nucleoplasmic epitope or the relevant side of a vesicle membrane; SEC13 has no annotated transmembrane segment (UniProt P55735: topology; standard IF practice). Include single stain and no primary controls before using IF localisation to interpret DAB staining (standard IF practice).

What should I check when SEC13 DAB staining is diffuse or widespread?

First compare the signal with a no primary control and inspect tissue edges, folds and poorly preserved regions for nonspecific deposition (standard IHC practice). The selected paraffin section used 10% goat serum block, a peroxidase conjugated secondary for 30 minutes at 37°C, and DAB development (datasheet A04346-1). Include an endogenous peroxidase block and control DAB development time as general chromogenic IHC measures (standard IHC practice). Because SEC13 is reported as cytoplasmic in most tissues, widespread cytoplasmic color alone cannot establish specificity; compare cell type and compartment with controls (HPA: tissue IHC; standard IHC interpretation).

How should I quantify SEC13 staining across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION

Define the cell population and compartment before scoring, because tissue IHC reports cytoplasmic expression in most tissues and different staining levels across cell types (HPA: tissue IHC). For cell level analysis, report percent positive cells and an H-score from 0–300, based on intensity grades 0–3 (standard IHC scoring practice). For spatial analysis, report positive cell density per mm² of viable, annotated tissue and exclude folds and necrosis (standard IHC scoring practice). Normalise comparisons to the same cell population, sampled viable area, staining run and scoring threshold, with blinded review where feasible (standard IHC scoring practice).

How can I distinguish true SEC13 positivity from artefact?

A credible result should recur in intact cells of a defined type and show a plausible cytoplasmic, vesicular or nuclear pore related pattern (HPA: tissue IHC; UniProt P55735: subcellular location). Treat signal concentrated at cut edges, folds or necrotic areas as suspect, and use a no primary control to assess nonspecific DAB deposition or endogenous enzyme activity (standard IHC practice). HPA lists high staining in breast glandular cells but no detection in adipocytes, providing cell type examples for interpretation rather than universal positive or negative controls (HPA: tissue IHC). Resolve unexpected patterns with another validated reagent or an orthogonal assay; HPA labels its tissue staining approved while noting low agreement with RNA expression (HPA: reliability description).

Boster reagents

Best SEC13 / Protein SEC13 homolog IHC Antibodies

A04346-1 has IHC data from a human paraffin-embedded brain section and IF/ICC data from A549 cells (catalog image captions). Its listed reactivity covers human, mouse and rat (catalog applications/reactivity).

Real IHC data

Anti-SEC13L1/SEC13 Antibody ®

Cat # A04346-1

View product →

A04346-1 was demonstrated by chromogenic IHC on a human paraffin-embedded brain section, with EDTA pH 8.0 retrieval and 2 μg/ml primary antibody (IHC image caption). A04346-1 was also demonstrated by IF/ICC on A549 cells at 5 μg/ml (IF image caption).

Which to pick: Choose A04346-1 for paraffin-section IHC because its own IHC image shows that preparation; the fixative is unreported (IHC image caption). Choose the same SKU for IF/ICC because its own IF image shows staining in A549 cells (IF image caption). For mouse or rat samples, A04346-1 lists reactivity with both species, but the supplied IHC and IF images show human tissue and A549 cells, respectively (catalog reactivity; IHC and IF image captions).

Each figure is that product's own IHC / IF validation image from its datasheet.

References

UniProt Consortium. UniProt entry P55735 (SEC13_HUMAN, Protein SEC13 homolog).
Human Protein Atlas. SEC13 tissue IHC expression (reliability: Approved).
Human Protein Atlas. SEC13 subcellular location (ICC-IF): Localized to the nucleoplasm and vesicles..
Human Protein Atlas. SEC13 antibody validation summary (2 antibodies).
Integrated pan cancer analysis with breast cancer validation identifies SEC13 homolog as prognostic biomarker and immunotherapy target. Scientific reports 2026 — PMC13358067.
Obesity Modifies the Proteomic Profile of the Periodontal Ligament. International journal of molecular sciences 2023 — PMC9861657.
PubMed PMID:7987303 — UniProt-cited evidence.
PubMed PMID:9110174 — UniProt-cited evidence.
PubMed PMID:14702039 — UniProt-cited evidence.