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SF3A2 / Splicing factor 3A subunit 2 · IHC design guide
Design Immunohistochemistry for SF3A2
Plan SF3A2 staining in paraffin sections using the catalog antibody at 2–5 μg/ml (datasheet A11289-2). Assess nuclear staining across tissues, with high staining reported in colon glandular cells and cerebellar Purkinje cells (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
SF3A2 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 | Nuclear staining across tissues (HPA tissue IHC) | |
| Staining pattern | Widespread nuclear staining across cell types (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A11289-2) | |
| Positive control | Cerebellum+4 more · see all | |
| Negative control | None in HPA (detected in all 45 tissues); use no-primary + isotype controls |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A11289-2) | |
| Caveat | Ubiquitous staining limits negative-tissue controls (HPA tissue IHC) | |
| Regulation | Expression regulation is not annotated (UniProt) | |
| Isoform / epitope | 0 isoforms annotated; no signal or propeptide cleavage (UniProt) |
Section 1
Recommended SF3A2 IHC & IF Protocols
The catalog antibody’s IHC-P protocol is accompanied by published SF3A2 staining protocols for mouse xenografts (PMC12809199) and human colorectal tissue (PMC12702133).
| Sample | Paraffin-embedded human liver cancer tissue; fixative not specified (datasheet A11289-2) |
| Fixation | Image fixative and duration unreported (datasheet A11289-2); 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 A11289-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A11289-2) |
| Primary antibody | Rabbit anti-SF3A2, 2-5 μg/ml (datasheet A11289-2) |
| Primary incubation | Overnight at 4 °C (datasheet A11289-2) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A11289-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SF3A2-positive staining in purkinje cells of cerebellum (HPA tissue IHC: High). HPA tissue profile: Ubiquitous nuclear expression. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval (datasheet A11289-2); consider citrate pH 6.0 if optimizing against the xenograft protocol (PMC12809199).
Section 2
What Is the Expected SF3A2 Staining Pattern?
SF3A2 is a nuclear spliceosome protein with no transmembrane segment (UniProt Q15428: location, function, topology). In paraffin sections, expect nuclear staining across many cell types, with high staining reported in Purkinje cells and several glandular cell populations (HPA: ubiquitous nuclear expression; listed high-staining cells). HPA rates the tissue IHC profile Enhanced, reflecting high consistency between antibody staining and RNA expression data (HPA: reliability description).
| Many cell types show nuclear signal; Purkinje cells or listed glandular cells stain strongly. | This fits the reported ubiquitous nuclear profile and High staining in those populations (HPA: tissue IHC). Compare nuclei within the same section and tissue context; High describes the reported cell populations, not a requirement that every nucleus have identical intensity. |
| Signal is predominantly cytoplasmic or outlines cell membranes while nuclei remain faint. | That distribution conflicts with nuclear SF3A2 and supported nucleoplasmic localization (UniProt Q15428: subcellular location; HPA: ICC-IF). Check whether chromogen deposits, nonspecific binding, or tissue pigment could explain the apparent compartment before assigning it to SF3A2 (standard IHC practice). |
| Only an unexpected cell population stains, especially with little nuclear signal in nearby listed high-staining cells. | Consider cross-reactivity or endogenous detection activity (standard IHC practice). HPA reports broad nuclear expression, so staining in a cell type absent from its High list is not, by itself, evidence of an error (HPA: ubiquitous nuclear expression; listed High cells). |
| Color spreads through stroma, extracellular spaces, or most of the section without clear nuclear boundaries. | Treat this as background until controls establish a specific nuclear component (standard IHC practice). The reported SF3A2 pattern is nuclear, and its annotated protein has no transmembrane segment (HPA: tissue IHC profile; UniProt Q15428: topology). |
| There is no nuclear signal in a section containing a listed High-staining population. | The result conflicts with the HPA tissue observation for that population, but one negative section does not establish absent SF3A2 (HPA: listed High cells). Review tissue identity and assay controls, then investigate retrieval, antibody incubation, and detection as general IHC variables (standard IHC practice). |
💡Expected SF3A2 appearanceCall a result positive when nuclei across the section are clearly labeled, with strong signal in a listed High-staining population where present; predominant membrane, extracellular, or nucleus-sparing color is suspect (HPA: ubiquitous nuclear expression and listed High cells; UniProt Q15428: nuclear location).
| Tissue and cell context (HPA: tissue IHC) | HPA reports High staining in cerebellar Purkinje cells; glandular cells of cervix, colon, duodenum, epididymis, gallbladder, and parathyroid gland; and pancreatic exocrine glandular cells. It also reports low tissue RNA specificity and ubiquitous nuclear protein expression. Use these as pattern references, not as an exclusive list of positive cells (HPA: tissue IHC). |
| Antibody evidence (HPA: antibody validation) | Both HPA042843 and HPA049439 have Enhanced IHC status; HPA049439 also has Supported ICC status (HPA: antibody records). These ratings support the reported patterns for those antibodies. They do not validate an unrelated antibody or prove that every visible deposit is specific. |
| Protein location and processing (UniProt Q15428) | UniProt places SF3A2 in the nucleus and annotates no transmembrane segment, signal peptide, or propeptide; the annotated chain spans residues 1–464 (UniProt Q15428: location, topology, processing). These annotations support a nuclear interpretation. They supply no evidence that a particular fixation or retrieval condition changes staining. |
| IF/ICC Q: Where should signal appear? (HPA: ICC-IF) | A: In the nucleoplasm (HPA: supported main location). This cross-check describes localization only; IF/ICC has its own guide, and the IHC observations here do not establish an IF/ICC protocol. |
| Situation | Likely cause | Next action |
|---|---|---|
| No nuclear staining in a listed High-staining population. | Possible assay failure or tissue mismatch; the observation alone does not identify which step failed (HPA: listed High cells; standard IHC practice). | Confirm tissue and cell identity; check a known-positive section, primary-antibody step, retrieval, and detection controls (standard IHC practice). Do not infer SF3A2-specific fixation sensitivity from this result. |
| Cytoplasmic or membrane staining dominates. | The compartment disagrees with nuclear and nucleoplasmic references; nonspecific signal or a reading error is possible (UniProt Q15428: location; HPA: ICC-IF; standard IHC practice). | Compare with the nuclear counterstain and a primary-omission control; reassess deposits and morphology before scoring positive nuclei (standard IHC practice). |
| Staining appears restricted to an unexpected cell type. | Cross-reactivity or endogenous detection activity is possible, although HPA's High list is not an exclusion list (HPA: ubiquitous nuclear expression; standard IHC practice). | Check whether the signal is nuclear, compare nearby expected cells, and review negative and detection controls (standard IHC practice). |
| Diffuse color obscures nuclear boundaries. | Excess nonspecific binding, detection background, or inadequate washing may obscure localization (standard IHC practice). | Review blocking, antibody dilution, washing, and chromogen development against controls; score only interpretable nuclei (standard IHC practice). |
| Color persists when primary antibody is omitted. | The detection system or tissue may contribute signal independently of primary-antibody binding (standard IHC practice). | Inspect endogenous enzyme or biotin activity where relevant, and adjust the matching block or detection method (standard IHC practice). |
| Staining varies sharply between regions of one section. | Uneven reagent coverage or tissue handling may produce a technical gradient (standard IHC practice). | Inspect section integrity and reagent coverage, then repeat with consistent processing before interpreting regional differences (standard IHC practice). |
Experiment evidence
IHC & IF images showing SF3A2 staining
A11289-2 · IHCIHC analysis of SF3A2 using anti-SF3A2 antibody (A11289-2). SF3A2 was detected in a paraffin-embedded section of human liver cancer tissue.
A11289-2 · IHCIHC analysis of SF3A2 using anti-SF3A2 antibody (A11289-2). SF3A2 was detected in a paraffin-embedded section of human lung adenocarcinoma t
A11289-2 · IFIF analysis of SF3A2 using anti-SF3A2 antibody (A11289-2) and anti-Beta Tubulin antibody (M01857-3). SF3A2 was detected in immunocytochemica
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000104897-SF3A2/tissue/cerebral+cortex#imid_13630407
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000104897-SF3A2/tissue/colon#imid_13630325
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000104897-SF3A2/tissue/liver#imid_13630334
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000104897-SF3A2/tissue/kidney#imid_13630335
HPA · ICC-IF HEK293Human Protein Atlas immunofluorescence, HEK293, antibody HPA049439; green = SF3A2, blue = nucleus, red = microtubules.
HPA · ICC-IF HEK293Human Protein Atlas immunofluorescence, HEK293, antibody HPA049439; green = SF3A2, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for SF3A2 IHC & IF
🧪Start with colon: glandular cells should show SF3A2 staining (HPA: High in colon glandular cells), with predominantly nuclear signal (UniProt Q15428: nucleus). HPA detects SF3A2 in all 45 scored tissues, so it provides no negative tissue; use no-primary and isotype controls, and regard cells on the positive slide as internally negative only if their nuclei show no signal above control background, without assuming any cell type is SF3A2-negative (HPA: no negative tissue rows).
Positive control tissue: Cerebellum (Purkinje cells, HPA High)
Negative control tissue: None in HPA: SF3A2 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show SF3A2 in HEK293, U-251MG, U2OS, NIH 3T3, with annotated localisation: Nucleoplasm (supported) (HPA subcellular).
Technical controls: Run a secondary-only section with primary antibody omitted and a matched rabbit IgG isotype control, because the selected IHC caption uses a rabbit primary and goat anti-rabbit secondary (A11289-2 caption). Include SF3A2 knockout material as a biological negative if available, or a cognate-peptide block if the peptide is available (standard IHC specificity controls). Quench endogenous peroxidase and check for residual DAB background in the colon section (A11289-2 caption: HRP/DAB detection; standard chromogenic IHC practice).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported, and the selected paraffin-section caption does not state a fixative (A11289-2 caption: fixative unreported). Heat-mediated EDTA retrieval at pH 8.0 was used in the selected IHC example, but its necessity has not been established by the supplied evidence (A11289-2 caption). Is frozen-section staining or IF/ICC easier? No matched comparison is supplied; HPA supports nucleoplasmic IF/ICC localization, while the demonstrated chromogenic workflow uses paraffin sections, and colon sections should be checked for endogenous peroxidase background (HPA: nucleoplasm, supported; A11289-2 caption: paraffin section and HRP/DAB detection).
HPA tissue IHC evidence for SF3A2
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — High 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 |
|---|---|---|---|---|
| Cerebellum | Purkinje cells | High | Protein (IHC) | HPA → |
| Cervix | Glandular cells | High | Protein (IHC) | HPA → |
| Colon | Glandular cells | High | Protein (IHC) | HPA → |
| Duodenum | Glandular cells | High | Protein (IHC) | HPA → |
| Epididymis | Glandular cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: SF3A2 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Section 3
Advanced SF3A2 IHC Tips
SF3A2 is a nuclear spliceosome protein (UniProt Q15428). Use nuclear staining and matched controls to assess signal in paraffin section IHC.
Which retrieval conditions should I start with for SF3A2 in paraffin sections?
Start with heat mediated antigen retrieval in EDTA, pH 8.0, for paraffin sections (datasheet A11289-2). The selected tissue IHC image used that retrieval before overnight incubation with 2 μg/ml primary antibody at 4°C (datasheet A11289-2). If nuclear staining is weak, compare a second retrieval condition on adjacent sections while keeping antibody concentration, detection and development time constant (standard IHC practice). Include a known positive section, such as colon glandular cells, and a no primary control in the same run (HPA: High in colon glandular cells; standard IHC practice). Judge retrieval by nuclear signal and tissue preservation together, since damaged sections can make staining hard to interpret (UniProt Q15428 localisation; standard IHC practice).
How should I handle fixation when SF3A2 nuclear staining is inconsistent?
Target specific sensitivity to fixation is unknown from the supplied evidence, and the selected paraffin section caption does not state a fixative (datasheet A11289-2). Record the fixative, fixation duration, processing batch and section age for each specimen before comparing staining intensity (standard IHC practice). Test suspect samples alongside a reliably staining control section using the same EDTA, pH 8.0 retrieval and detection run (datasheet A11289-2; standard IHC practice). If differences persist, evaluate nuclear staining and tissue morphology together rather than assigning the cause to fixation alone (UniProt Q15428 localisation; standard IHC practice). Keep processing conditions consistent across groups intended for quantitative comparison (standard IHC practice).
What staining pattern is credible for SF3A2, and how should I investigate cytoplasmic signal?
Expect predominantly nuclear staining in paraffin sections because SF3A2 is nuclear and HPA describes ubiquitous nuclear expression (UniProt Q15428 localisation; HPA: tissue IHC profile). Its supported subcellular location is the nucleoplasm, so assess DAB against a nuclear counterstain before scoring cells (HPA: subcellular localisation; standard IHC practice). Diffuse cytoplasmic DAB without convincing nuclear signal warrants review of the no primary control, peroxidase block and antibody concentration (standard IHC practice). The selected image used 2 μg/ml primary antibody overnight at 4°C, providing a documented starting concentration and incubation (datasheet A11289-2). Compare suspect staining with an HPA high staining cell population on a control section processed in the same run (HPA: positive tissue IHC; standard IHC practice).
Could an SF3A2 isoform or modification explain variable IHC staining?
The supplied UniProt record lists 0 isoforms and a single chain spanning residues 1–464, so it supplies no isoform specific staining expectation (UniProt Q15428 isoforms and processing). It lists acetylation at residues 1 and 10 and phosphorylation at residue 153, but no antibody epitope is supplied (UniProt Q15428 modified residues; datasheet A11289-2). Do not attribute staining differences to those modifications without epitope mapping or direct validation (standard IHC practice). Compare adjacent sections under the documented EDTA, pH 8.0 retrieval before changing detection conditions (datasheet A11289-2; standard IHC practice). If the pattern remains unexpected, assess nuclear localisation and independent antibody validation before drawing a biological conclusion (UniProt Q15428 localisation; standard IHC practice).
How can I check SF3A2 localisation by multiplex IF?
For a separate IF experiment, pair SF3A2 with a validated marker for the cell population being examined and a nuclear counterstain to identify nuclei within each cell type (standard IF practice). HPA reports high IHC staining in colon glandular cells, which can guide cell identification but does not establish IF performance in that tissue (HPA: High in colon glandular cells). Choose spectrally separated fluorophores and inspect unstained tissue for autofluorescence before assigning a weak channel to SF3A2 (standard IF practice). SF3A2 is nucleoplasmic and has no transmembrane segment, so use permeabilisation suitable for access to a nuclear epitope (HPA: subcellular localisation; UniProt Q15428 topology; standard IF practice). Validate fixation, permeabilisation and antibody concentration for IF independently of the paraffin section IHC caption (datasheet A11289-2; standard IF practice).
What should I check when SF3A2 DAB staining obscures nuclei?
Run a no primary control and inspect whether brown signal follows tissue edges, damaged areas or structures lacking intact nuclei (standard IHC practice). Check the peroxidase blocking step and shorten DAB development if the control also darkens, because endogenous enzyme activity and excessive development can raise chromogenic background (standard IHC practice). The selected image used a 10% goat serum block, 2 μg/ml primary antibody and a peroxidase linked secondary reagent (datasheet A11289-2). If the no primary control is clean, titrate the primary around the documented concentration while holding retrieval and development constant (datasheet A11289-2; standard IHC practice). Score SF3A2 only where staining can be assigned to intact nuclei (UniProt Q15428 localisation; standard IHC practice).
How should I quantify SF3A2 across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and region of interest before scoring, then measure the percentage of nuclei positive for SF3A2 (UniProt Q15428 localisation; standard IHC practice). An H score can combine nuclear intensity categories with the percentage of cells in each category; record the thresholds and keep them fixed across slides (standard IHC practice). Normalise counts to the number of intact, eligible nuclei in each region, or report positive nuclear density per mm² when tissue area is the comparison unit (standard IHC practice). Exclude necrosis, folds and section edges consistently, and review the nuclear counterstain when segmentation is uncertain (standard IHC practice). Process comparison groups with matched retrieval, staining and DAB development conditions (standard IHC practice).
How do I distinguish genuine SF3A2 staining from artefact?
A credible positive is staining assigned to intact nuclei, consistent with SF3A2 nuclear localisation and HPA's ubiquitous nuclear IHC profile (UniProt Q15428 localisation; HPA: tissue IHC profile). HPA reports high staining in Purkinje cells and several glandular cell populations, offering documented populations for comparison when those tissues are available (HPA: positive tissue IHC). Treat predominant cytoplasmic signal, edge restricted DAB and staining over necrosis as patterns requiring control review (UniProt Q15428 localisation; standard IHC practice). Check a no primary section for background, including endogenous peroxidase signal, before calling faint staining positive (standard IHC practice). Interpret intensity changes only after checking intact nuclei, comparable processing and the same scoring thresholds across sections (standard IHC practice).
Boster reagents
Best SF3A2 / Splicing factor 3A subunit 2 IHC Antibodies
A11289-2 has IHC images from paraffin-embedded human tissues and an IF image from U2OS cells (catalog image captions). Its listed reactivity is Human, Mouse and Rat (catalog: reactivity).
Real IHC data
Anti-SF3A2 Antibody ®
Cat # A11289-2
A11289-2 has IHC images from paraffin-embedded human liver cancer, lung adenocarcinoma, placenta and rectum adenocarcinoma sections (catalog: IHC image captions). A11289-2 also has an IF image from U2OS cells and lists IF and ICC among its applications (catalog: IF image caption; applications).
Which to pick: For tissue IHC, choose A11289-2: its human paraffin-section captions use EDTA retrieval at pH 8.0 and 2 μg/ml primary antibody; the fixative is unreported (catalog: IHC image captions). For IF/ICC, choose the same SKU: its U2OS IF caption uses 5 μg/ml primary antibody (catalog: IF image caption). For cross-species work, A11289-2 lists Human, Mouse and Rat reactivity, while its supplied IHC images document human sections (catalog: reactivity; IHC image captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q15428 (SF3A2_HUMAN, Splicing factor 3A subunit 2).
- Human Protein Atlas. SF3A2 tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. SF3A2 subcellular location (ICC-IF): Localized to the nucleoplasm..
- Human Protein Atlas. SF3A2 antibody validation summary (2 antibodies).
- Preliminary exploration of the putative function of SF3A2 in clear cell renal cell carcinoma. Molecular medicine reports 2026 — PMC12809199.
- SF3A2: a promising therapeutic target and predictive biomarker for immunotherapy in colorectal cancer. International journal of medical sciences 2026 — PMC12702133.
- NEDD4 ameliorates myocardial reperfusion injury by preventing macrophages pyroptosis. Cell communication and signaling : CCS 2023 — PMC9896697.
- PubMed PMID:8211113 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:15057824 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for SF3A2 (Splicing factor 3A subunit 2). Expected localisation Nuclear staining across tissues (HPA tissue IHC). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A11289-2). Validated IHC antibody: A11289-2 at 2-5 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Cerebellum (Purkinje cells); negative None in HPA (detected in all 45 tissues); use no-primary + isotype controls. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human liver cancer tissue; fixative not specified (datasheet A11289-2); 2. Fixation: Image fixative and duration unreported (datasheet A11289-2); 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 A11289-2); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A11289-2); 8. Primary antibody: Rabbit anti-SF3A2, 2-5 μg/ml (datasheet A11289-2); 9. Primary incubation: Overnight at 4 °C (datasheet A11289-2). Watch for: Fixation: Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A11289-2); Caveat: Ubiquitous staining limits negative-tissue controls (HPA tissue IHC); Isoform / epitope: 0 isoforms annotated; no signal or propeptide cleavage (UniProt); Regulation: Expression regulation is not annotated (UniProt). Evidence: UniProt Q15428, HPA tissue IHC · Enhanced, HPA ICC-IF · nucleoplasm., Datasheet A11289-2, PMC12809199, PMC12702133. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/SF3A2/immunohistochemistry-ihc-guide.