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SF3A1 / Splicing factor 3A subunit 1 · IHC design guide
Design Immunohistochemistry for SF3A1
Plan chromogenic SF3A1 IHC in paraffin sections around the expected nuclear staining pattern (HPA tissue IHC). Use the catalog antibody at 2–5 μg/ml (datasheet A05483-1) and score nuclear signal across the cells of interest.
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
SF3A1 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 tissue staining (HPA tissue IHC) | |
| Staining pattern | Nuclear staining in glandular, glial and hematopoietic cells (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A05483-1) | |
| Positive control | Adrenal gland+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 | Keep fixation consistent across compared paraffin sections. (selected-SKU IHC image A05483-1) | |
| Caveat | Ubiquitous staining limits tissue-negative controls (HPA tissue IHC) | |
| Regulation | Ubiquitously expressed (UniProt) | |
| Isoform / epitope | 2 isoforms; epitope coverage is unspecified (UniProt) |
Section 1
Recommended SF3A1 IHC & IF Protocols
The catalog antibody’s IHC-P protocol (datasheet A05483-1) is accompanied by one published SF3A1 IHC protocol (PMC13267591).
| Sample | Paraffin-embedded human spleen tissue; fixative not specified (datasheet A05483-1) |
| Fixation | Image fixative and duration unreported (datasheet A05483-1); 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 A05483-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A05483-1) |
| Primary antibody | Rabbit anti-SF3A1, 2-5 μg/ml (datasheet A05483-1) |
| Primary incubation | Overnight at 4 °C (datasheet A05483-1) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A05483-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | SF3A1-positive staining in glandular cells of adrenal gland (HPA tissue IHC: High). HPA tissue profile: Ubiquitous nuclear expression. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA retrieval at pH 8.0 (datasheet A05483-1); the published protocol does not specify retrieval conditions (PMC13267591).
Section 2
What Is the Expected SF3A1 Staining Pattern?
SF3A1 should stain nuclei across many cell types, with high staining reported in several glandular, respiratory epithelial, hematopoietic, and neural cell populations (HPA: ubiquitous nuclear expression; HPA: listed high-staining cells). Nuclear speckles are also consistent with its location (UniProt Q15459: nucleus and nuclear speckles). HPA rates the tissue IHC pattern Enhanced, citing agreement between staining and RNA expression (HPA: Enhanced reliability). SF3A1 has no transmembrane segment (UniProt Q15459: topology).
| Nuclear staining appears across several cell populations in an intact section. | This fits the reported ubiquitous nuclear pattern; compare intensity within identified cell types and keep the nuclear counterstain visible when judging localization (HPA: ubiquitous nuclear expression; general IHC practice). |
| Staining appears concentrated in distinct spots within nuclei. | Nuclear speckles are compatible with SF3A1 localization, although chromogenic IHC may not resolve them clearly. Do not require visible speckles for a positive IHC call (UniProt Q15459: nuclear speckles; HPA: nucleoplasm and nuclear speckles by ICC-IF; general IHC practice). |
| Strong staining is predominantly cytoplasmic or outlines cell membranes. | That distribution conflicts with the reported nuclear location and has no support from SF3A1 topology. Assess background, detection artifacts, and antibody specificity before calling it SF3A1 (HPA: ubiquitous nuclear expression; UniProt Q15459: no transmembrane segment; general IHC practice). |
| A conspicuous signal appears only in an unexpected cell population or a structure without nuclei. | Check cell identity against the counterstain. Restricted off-pattern staining can reflect cross-reactivity or endogenous detection activity, but SF3A1's broad expression means an unfamiliar positive cell type alone is not proof of either (HPA: ubiquitous nuclear expression; general IHC practice). |
| A listed high-staining population has no convincing nuclear signal. | This warrants a technical check before interpreting the specimen as SF3A1-negative. HPA reports high staining in several populations, including bone-marrow hematopoietic cells and bronchial respiratory epithelial cells, but provides no target-specific fixation sensitivity here (HPA: High in listed cells; general IHC practice). |
💡Expected SF3A1 appearanceCall a positive IHC result when clearly nuclear staining is visible in appropriate cells, including listed high-staining populations; prominent cytoplasmic, membranous, or nucleus-independent deposit is an off-pattern signal to investigate (HPA: ubiquitous nuclear expression and listed High levels; UniProt Q15459: nuclear location; general IHC practice).
| Tissue and cell selection | HPA describes ubiquitous nuclear expression and low tissue RNA specificity, so a listed High population can serve as a practical positive reference; there is no supplied HPA negative tissue to treat as a target-negative control (HPA: tissue IHC and RNA specificity). |
| Antibody evidence | Two rabbit polyclonal antibodies, HPA000690 and HPA030083, have Enhanced IHC status. This supports the reported pattern across independent reagents or orthogonal data; it does not establish that every unexpected deposit is specific (HPA: antibody validation). |
| Antigen retrieval and detection | Use the documented conditions for the IHC-validated antibody and assess controls when adjusting retrieval or chromogen exposure. No SF3A1-specific retrieval requirement, dilution, or fixation effect is supplied (general IHC practice; HPA: tissue IHC source scope). |
| Isoforms and processing | UniProt lists two isoforms and a chain spanning residues 2–793, with no signal peptide or propeptide. Without an antibody epitope map, these facts cannot predict isoform coverage or a second staining compartment (UniProt Q15459: isoforms and processing). |
| Modified residues | UniProt records several modified residues, including phosphoserines, but the supplied evidence does not connect them to IHC intensity or epitope recognition. Do not infer a tissue-specific staining shift from those annotations (UniProt Q15459: modified residues). |
| IF/ICC Q&A | What localization is expected by IF/ICC? Nucleoplasm and nuclear speckles; HPA reports enhanced evidence for both and lists images from A-431, U-251MG, and U2OS. This localization check does not specify an IF/ICC protocol (HPA: subcellular ICC-IF). |
| Situation | Likely cause | Next action |
|---|---|---|
| A listed High population has little or no nuclear staining. | The section, retrieval, primary-antibody step, or detection may have failed; the supplied sources do not identify an SF3A1-specific fixation effect (HPA: listed High staining; general IHC practice). | Check tissue integrity and a run control, then verify the documented IHC-P steps and detection reagents before assigning a biological negative result (general IHC practice). |
| Signal is mainly cytoplasmic or membranous. | The distribution conflicts with reported nuclear localization; nonspecific binding or detection background is possible (UniProt Q15459: nuclear location and no transmembrane segment; general IHC practice). | Compare with a matched negative reagent control, inspect nuclear counterstaining, and confirm the pattern with a separately validated antibody where available (general IHC practice; HPA: two Enhanced IHC antibodies). |
| Brown deposit covers much of the section and obscures nuclei. | Diffuse background can arise from nonspecific binding, endogenous detection activity, or excessive detection development (general IHC practice). | Review blocking and detection controls, wash steps, and chromogen development; judge SF3A1 only where the nuclear pattern can be resolved (general IHC practice; HPA: ubiquitous nuclear expression). |
| Only scattered unexpected cells or nucleus-free structures stain. | Cross-reactivity or endogenous detection activity may explain a restricted off-pattern signal; broad SF3A1 expression alone does not identify a negative cell type (HPA: ubiquitous nuclear expression; general IHC practice). | Identify the stained structures with the counterstain, compare reagent controls, and seek agreement with an independently validated antibody before interpreting them as specific (general IHC practice; HPA: antibody validation). |
| Nuclei stain, but discrete speckles cannot be seen. | Chromogenic section IHC may lack the spatial resolution needed to distinguish speckles from nucleoplasmic staining (general IHC practice; HPA: nucleoplasm and nuclear speckles by ICC-IF). | Score convincing nuclear staining as compatible with the IHC pattern; consult the separate IF/ICC guide if subnuclear localization is the experimental endpoint (HPA: ubiquitous nuclear IHC and subcellular ICC-IF). |
| Staining intensity varies between cell populations. | HPA reports High staining in specific populations while describing broad nuclear expression overall; intensity variation alone does not establish specificity or a fixation effect (HPA: tissue IHC). | Compare like cell populations under the same staining conditions and report compartment and intensity separately; investigate any loss of nuclear localization (general IHC practice; HPA: ubiquitous nuclear expression). |
Experiment evidence
IHC & IF images showing SF3A1 staining
A05483-1 · IHCIHC analysis of SF3A1 using anti-SF3A1 antibody (A05483-1). SF3A1 was detected in a paraffin-embedded section of human spleen tissue. Heat m
A05483-1 · IHCIHC analysis of SF3A1 using anti-SF3A1 antibody (A05483-1). SF3A1 was detected in a paraffin-embedded section of human larynx squamous cell
A05483-1 · IFIF analysis of SF3A1 and Tubulin alpha using anti-SF3A1 antibody (A05483-1) and anti-Tubulin alpha antibody (M03989-3). SF3A1 and Tubulin al
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000099995-SF3A1/tissue/cerebral+cortex#imid_195834
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000099995-SF3A1/tissue/colon#imid_195760
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000099995-SF3A1/tissue/liver#imid_195777
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000099995-SF3A1/tissue/kidney#imid_195762
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA030083; green = SF3A1, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA030083; green = SF3A1, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for SF3A1 IHC & IF
🧪Run breast first and expect nuclear staining in its glandular cells (HPA: High in breast glandular cells; UniProt Q15459: nucleus and nuclear speckles). HPA detects SF3A1 in all 45 scored tissues, so it provides no negative tissue or validated negative cell population within the positive slide; use the no-primary and isotype slides to assess background rather than treating unstained cells as confirmed negatives (HPA: no negative rows; detected in all 45 tissues).
Positive control tissue: Adrenal gland (Glandular cells, HPA High)
Negative control tissue: None in HPA: SF3A1 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 SF3A1 in A-431, U-251MG, U2OS, with annotated localisation: Nucleoplasm (enhanced), Nuclear speckles (enhanced) (HPA subcellular).
Technical controls: Include a secondary-only slide, a slide with concentration-matched rabbit isotype IgG matched to the primary antibody’s clonality when known, and, if available, SF3A1-knockout material processed alongside the positive tissue (selected-SKU caption: rabbit primary and anti-rabbit secondary; standard IHC controls). Quench endogenous peroxidase and check background before interpreting DAB staining (selected-SKU caption: peroxidase detection with DAB; standard chromogenic IHC practice).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported, and the selected-SKU paraffin-section caption does not state the fixative (selected-SKU caption: fixative unreported). Heat retrieval in EDTA at pH 8.0 was used for the illustrated spleen section, but that example does not establish that retrieval is required for every specimen (selected-SKU caption: EDTA heat retrieval). IF/ICC images support nucleoplasmic and nuclear-speckle localization in A-431, U-251MG and U2OS cells; they do not establish that frozen sections or IF are easier than paraffin IHC (HPA: subcellular ICC-IF images; selected-SKU caption: paraffin-section IHC).
HPA tissue IHC evidence for SF3A1
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 |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Appendix | Glandular cells | High | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Breast | Glandular cells | High | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: SF3A1 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Section 3
Advanced SF3A1 IHC Tips
Troubleshoot SF3A1 chromogenic IHC by checking nuclear localisation, tissue controls and the documented conditions for the catalog antibody.
Which retrieval conditions should I try first for weak SF3A1 staining?
Start with heat mediated retrieval in EDTA at pH 8.0 for paraffin sections (datasheet A05483-1). The documented human spleen staining used 2 μg/ml primary antibody overnight at 4°C, so reproduce that concentration before changing retrieval conditions (datasheet A05483-1). Compare a weak section with a concurrently processed positive control, such as spleen, and assess nuclear signal against background (datasheet A05483-1; UniProt Q15459 localisation; standard IHC practice). If staining remains weak, optimise heating and cooling on matched sections while keeping detection conditions constant (standard IHC practice). Record tissue preservation and section handling so a retrieval change is not mistaken for a sample difference (standard IHC practice).
How can fixation affect SF3A1 staining in paraffin sections?
Target specific fixation sensitivity is unknown: the catalog image describes a paraffin embedded human spleen section but does not state its fixative (datasheet A05483-1). Record each specimen’s fixative and fixation history, then compare similarly processed sections before attributing signal differences to SF3A1 abundance (standard IHC practice). Excessive or inconsistent fixation can alter epitope accessibility in IHC generally, so evaluate a control section alongside every processing batch (standard IHC practice). Use the documented EDTA retrieval at pH 8.0 as the starting condition for this antibody (datasheet A05483-1). Judge any fixation adjustment by preserved morphology and reproducible nuclear staining, without inferring a SF3A1 specific effect from tissue patterns (UniProt Q15459 localisation; standard IHC practice).
What staining pattern supports specific SF3A1 detection?
Expect predominantly nuclear staining because SF3A1 is reported in the nucleus and nuclear speckles (UniProt Q15459 localisation). Tissue IHC shows ubiquitous nuclear expression, while cell imaging places SF3A1 in the nucleoplasm and nuclear speckles (HPA tissue IHC; HPA subcellular). In chromogenic sections, score nuclear signal within morphologically intact cells rather than requiring individual speckles to resolve by light microscopy (standard IHC practice). Compare stained and unstained nuclei within the same tissue compartment and include a control processed with the same retrieval and detection steps (standard IHC practice). Strong diffuse cytoplasmic colour without corresponding nuclear signal warrants checking background and antibody specificity before biological interpretation (UniProt Q15459 localisation; standard IHC practice).
Can this IHC result distinguish SF3A1 isoforms or modified epitopes?
The record lists 2 SF3A1 isoforms, but the supplied antibody caption does not identify its epitope or establish isoform selectivity (UniProt Q15459 isoforms; datasheet A05483-1). SF3A1 contains a ubiquitin like region at residues 707–793 and reported modified residues, including phosphoserines at 320 and 329 (UniProt Q15459 domains; UniProt Q15459 modified residues). Those features alone cannot establish whether this antibody detects every isoform or whether modification changes staining (standard interpretation practice). For a specific isoform or modification claim, obtain epitope mapping and validation in matched specimens before assigning a chromogenic pattern (standard IHC practice). Until then, report the readout as SF3A1 immunoreactivity, with the antibody identity and retrieval conditions stated (datasheet A05483-1; standard reporting practice).
How should I plan complementary SF3A1 immunofluorescence?
Treat IF as a separately optimised assay: the documented antibody example is chromogenic IHC in a paraffin embedded spleen section (datasheet A05483-1). Pair nuclear SF3A1 staining with a validated cell type marker when examining a compartment such as bone marrow hematopoietic cells (UniProt Q15459 localisation; HPA tissue IHC: High in hematopoietic cells; standard IF practice). Choose spectrally separated fluorophores and assess tissue autofluorescence before assigning a weak nuclear signal, favouring a far red channel if background there is lower (standard IF practice). Permeabilise sufficiently for antibody access to the nucleoplasm and speckles, then check that nuclear morphology remains intact (HPA subcellular; standard IF practice). Optimise fixation and permeabilisation with IF controls; the IHC caption supplies no IF fixation condition (datasheet A05483-1; standard IF practice).
What should I check when brown staining obscures nuclei?
First compare the nuclear pattern with a section lacking primary antibody to identify detection system background (UniProt Q15459 localisation; standard IHC practice). Block endogenous peroxidase before HRP detection, particularly when evaluating cell rich tissue, and inspect the control for residual chromogen deposition (standard IHC practice). The documented spleen example used 10% goat serum blocking, a peroxidase conjugated secondary incubated for 30 minutes at 37°C, and DAB development (datasheet A05483-1). If diffuse colour persists, optimise blocking, washing and primary concentration on paired sections while retaining a known positive control (standard IHC practice). Exclude pigment, tissue folds and damaged edges before calling widespread staining biological (standard IHC practice).
How should I quantify SF3A1 across tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell compartment and score nuclear signal only, consistent with the expected localisation (UniProt Q15459 localisation; HPA tissue IHC). An H score can combine nuclear intensity and the percentage of positive cells; report the intensity categories and scoring threshold explicitly (standard IHC practice). Alternatively, report percentage positive nuclei or positive nuclei per mm² when cell density varies between fields (standard IHC practice). Normalise comparisons to the number of evaluable nuclei within the same annotated cell population, and use matched staining batches and exposure conditions (standard IHC practice). Record excluded necrotic, folded or edge regions so differences in tissue quality do not appear as SF3A1 changes (standard IHC practice).
How do I separate genuine SF3A1 staining from artefact?
A credible result places signal in intact nuclei, consistent with SF3A1 localisation and the reported ubiquitous nuclear tissue profile (UniProt Q15459 localisation; HPA tissue IHC). Check cell identity before treating a stronger field as a target change: high staining is reported in glandular, hematopoietic, glial and respiratory epithelial cells (HPA tissue IHC). Cytoplasmic only colour, tissue edge accentuation and necrotic deposits call for review of morphology and controls (UniProt Q15459 localisation; standard IHC practice). A section without primary antibody helps reveal endogenous enzyme activity or detection background under the same chromogenic conditions (standard IHC practice). Interpret intensity differences only after accounting for cell composition, fixation history and batch effects (standard IHC practice).
Boster reagents
Best SF3A1 / Splicing factor 3A subunit 1 IHC Antibodies
A05483-1 has real SF3A1 IHC images from human paraffin sections and IF images from human and rat paraffin sections and PC-3 cells (A05483-1 image captions).
Real IHC data
Anti-SF3A1 Antibody ®
Cat # A05483-1
A05483-1 has pictured IHC staining in human spleen, larynx squamous cell carcinoma, liver cancer, and lung adenocarcinoma paraffin sections (A05483-1 IHC image captions). The same SKU has pictured IF staining in PC-3 cells, human intestinal cancer paraffin sections, and rat colon paraffin sections (A05483-1 IF image captions).
Which to pick: For tissue IHC, choose A05483-1: its own spleen image used EDTA pH 8 retrieval and 2 μg/ml primary antibody on a paraffin section; the fixative is unreported (A05483-1 IHC image caption). For IF/ICC, choose A05483-1, which lists both applications and has corresponding cell and tissue images (catalog applications; A05483-1 IF image captions). For cross-species work, A05483-1 lists Human, Mouse, and Rat reactivity, while its stated IHC assay species are Human and Rat; clonality is unreported (catalog reactivity; datasheet IHC assay species; catalog clone field).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q15459 (SF3A1_HUMAN, Splicing factor 3A subunit 1).
- Human Protein Atlas. SF3A1 tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. SF3A1 subcellular location (ICC-IF): Localized to the nucleoplasm and nuclear speckles..
- Human Protein Atlas. SF3A1 antibody validation summary (2 antibodies).
- Pharmacological targeting of SF3a1-MDM4 splicing vulnerability in ovarian cancer with rifaximin and antisense oligonucleotide. Journal of translational medicine 2026 — PMC13267591.
- PubMed PMID:7489498 — UniProt-cited evidence.
- PubMed PMID:15461802 — UniProt-cited evidence.
- PubMed PMID:10591208 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for SF3A1 (Splicing factor 3A subunit 1). Expected localisation Nuclear tissue staining (HPA tissue IHC). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A05483-1). Validated IHC antibody: A05483-1 at 2-5 μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Adrenal gland (Glandular 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 spleen tissue; fixative not specified (datasheet A05483-1); 2. Fixation: Image fixative and duration unreported (datasheet A05483-1); 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 A05483-1); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A05483-1); 8. Primary antibody: Rabbit anti-SF3A1, 2-5 μg/ml (datasheet A05483-1); 9. Primary incubation: Overnight at 4 °C (datasheet A05483-1). Watch for: Fixation: Keep fixation consistent across compared paraffin sections. (selected-SKU IHC image A05483-1); Caveat: Ubiquitous staining limits tissue-negative controls (HPA tissue IHC); Isoform / epitope: 2 isoforms; epitope coverage is unspecified (UniProt); Regulation: Ubiquitously expressed (UniProt). Evidence: UniProt Q15459, HPA tissue IHC · Enhanced, HPA ICC-IF · nucleoplasm and nuclear speckles., Datasheet A05483-1, PMC13267591. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/SF3A1/immunohistochemistry-ihc-guide.