This website uses cookies to ensure you get the best experience on our website.
- Table of Contents
NXF3 / Nuclear RNA export factor 3 · IHC design guide
Design Immunohistochemistry for NXF3
Plan chromogenic NXF3 IHC in paraffin sections using seminiferous duct cells as a positive reference (HPA tissue IHC). Assess nuclear and cytoplasmic staining cautiously because presumed off-target binding was observed (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
NXF3 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 and cytoplasmic staining in tissue (HPA tissue IHC) | |
| Staining pattern | Seminiferous duct cells show nuclear and cytoplasmic staining (HPA tissue IHC) | |
| Antigen retrieval | Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen) | |
| Positive control | Gallbladder+1 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 sections (standard IHC practice; not target-specific); Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A11497) | |
| Caveat | Presumed off-target staining and low RNA–IHC concordance (HPA tissue IHC) | |
| Regulation | High in testis; low in few other tissues (UniProt) | |
| Isoform / epitope | 2 isoforms; no transmembrane segment; check epitope coverage (UniProt) |
Section 1
Recommended NXF3 IHC & IF Protocols
Compare the catalog antibody’s IHC-P protocol (datasheet) with the published NXF3 IHC protocol (PMC3919940).
| Sample | Paraffin-embedded human kidney carcinoma tissue; fixative not specified (datasheet A11497) |
| Fixation | Image fixative and duration unreported (datasheet A11497); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat-induced epitope retrieval in Tris-EDTA buffer, pH 9.0, 20 min at 95–98 °C (standard rule: nuclear antigen) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% normal serum of the secondary host, 30 min, room temperature (standard) |
| Primary antibody | Rabbit anti-NXF3, 1:50-1:200 (datasheet A11497) |
| Primary incubation | Overnight at 4 °C (standard) |
| Detection | HRP-polymer secondary, DAB chromogen 5–10 min (standard) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | NXF3-positive staining in glandular cells of gallbladder (HPA tissue IHC: Medium). HPA tissue profile: Nuclear and cytoplasmic expression in several tissues most abundant in cells in seminiferous ducts. No signal in the no-primary control. |
💡Decision noteStart with Tris-EDTA pH 9.0 retrieval at 95–98 °C for 20 min (page retrieval); the article specifies microwave retrieval without conditions (PMC3919940).
Section 2
What Is the Expected NXF3 Staining Pattern?
NXF3 shuttles between nucleus and cytoplasm and has no transmembrane segment (UniProt Q9H4D5). In paraffin section IHC, expect nuclear and cytoplasmic staining most prominently in cells of seminiferous ducts, with medium staining also reported in gallbladder glandular cells (HPA: tissue IHC). Interpret with caution: HPA rates tissue IHC Approved but reports low consistency with RNA expression and presumed off target binding that was disregarded (HPA: tissue IHC reliability).
| Nuclear and cytoplasmic staining in cells of seminiferous ducts. | This matches the reported IHC distribution; the listed testis signal is medium, so strong staining is not required for a positive call (HPA: tissue IHC). Confirm that signal follows identifiable cells rather than section edges or deposits (general IHC practice). |
| Predominantly membranous or extracellular staining, with little signal in nuclei or cytoplasm. | That distribution conflicts with NXF3 nuclear and cytoplasmic localization and its lack of a transmembrane segment (UniProt Q9H4D5; HPA: tissue IHC). Review morphology and controls before attributing it to NXF3; this pattern alone cannot identify the artifact's cause. |
| Prominent staining in an HPA listed negative cell population, such as adipocytes in adipose tissue. | HPA reports these cells as not detected (HPA: tissue IHC). Consider antibody cross reactivity or endogenous detection activity; compare a no primary control and cell morphology (general IHC practice). HPA also notes presumed off target binding in its tissue assessment (HPA: reliability). |
| Diffuse color across tissue, empty spaces, or the section background. | A distribution that does not track cells is unsuitable for compartment scoring (general IHC practice). Check the no primary control, blocking, reagent exposure, and wash steps (general IHC practice); the supplied HPA and UniProt records do not identify an NXF3 specific background mechanism. |
| No signal in cells of seminiferous ducts on a testis section. | This misses an HPA reported medium positive population (HPA: tissue IHC). First assess tissue preservation, staining run controls, antibody dilution, detection, and retrieval using the validated IHC procedure (general IHC practice); absence alone cannot distinguish a technical failure from sample variation. |
💡Expected NXF3 appearanceCall a convincing positive when cells in seminiferous ducts show cellular nuclear and cytoplasmic staining around the reported medium level (HPA: tissue IHC); isolated membrane, extracellular, or cell free color is a suspect positive because NXF3 is nuclear and cytoplasmic (UniProt Q9H4D5; general IHC practice).
| Tissue and cell selection | Testis cells in seminiferous ducts and gallbladder glandular cells are listed at medium IHC staining (HPA: tissue IHC). Several other cells are listed low or not detected (HPA: tissue IHC). Compare matched cell types when judging a result; a negative cell population cannot substitute for an assay positive control (general IHC practice). |
| IHC evidence strength | HPA rates tissue IHC Approved, while reporting low agreement between antibody staining and RNA expression and disregarded presumed off target binding (HPA: tissue IHC reliability). Treat unexpected positive cells as provisional and weigh location, morphology, and controls together (general IHC practice). |
| Isoforms and epitope coverage | UniProt lists 2 NXF3 isoforms, with an RRM at residues 113–192 and an NTF2 domain at 344–494 (UniProt Q9H4D5). The payload gives no antibody epitope or isoform coverage; do not assign an unexpected staining pattern to one isoform without separate evidence. |
| IF/ICC Q: where should signal appear? | HPA reports supported nucleoplasmic localization in ICC IF images and lists THP-1, U-251MG, and U2OS as imaged cell lines (HPA: subcellular ICC IF). UniProt also describes nuclear–cytoplasmic shuttling (UniProt Q9H4D5). That IF observation informs localization; it does not establish an IHC staining intensity for those cell lines. |
| Situation | Likely cause | Next action |
|---|---|---|
| Testis positive control is blank. | Cells in seminiferous ducts are reported medium positive (HPA: tissue IHC); a blank run may reflect a failed staining step (general IHC practice). | Verify tissue identity and run controls, then review the IHC validated antibody dilution, retrieval, detection reagents, and counterstain (general IHC practice). |
| Only membrane outlines stain. | Membrane only signal conflicts with nuclear and cytoplasmic NXF3 and its lack of a transmembrane segment (UniProt Q9H4D5). | Inspect cell morphology and a no primary control; withhold an NXF3 positive call until the expected compartments are demonstrable (general IHC practice). |
| Adipocytes stain strongly. | Adipocytes in adipose tissue are listed not detected (HPA: tissue IHC); off target or detection activity is plausible, though the source does not assign a cause to this sample. | Compare no primary staining and adjacent cell types, and repeat with an appropriate antibody control if available (general IHC practice). |
| Brown color covers cells and blank spaces. | Noncellular color can arise from nonspecific detection or residual substrate (general IHC practice); neither source specifies an NXF3 related cause. | Check no primary background, blocking, washes, and detection timing before scoring compartments (general IHC practice). |
| Nuclei stain, but cytoplasm is faint. | HPA supports nucleoplasmic ICC IF localization, while tissue IHC reports nuclear and cytoplasmic expression (HPA: subcellular ICC IF; HPA: tissue IHC). | Score each compartment separately and compare the same cell population with the run control; avoid treating the IF result as an IHC intensity standard (general IHC practice). |
| Gallbladder glandular cells stain, but testis does not. | Both populations are reported medium in HPA tissue IHC, so discordance calls for slide level review rather than an assumed tissue rule (HPA: tissue IHC). | Confirm the sampled testis contains seminiferous ducts, then compare preservation and run performance using the same IHC workflow (general IHC practice). |
Experiment evidence
IHC & IF images showing NXF3 staining
A11497 · IHCImmunohistochemistry (IHC) analyzes of NXF3 (N104) pAb in paraffin-embedded human kidney carcinoma tissue at 1:50.showing cytoplasmic and nu
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000147206-NXF3/tissue/cerebral+cortex#imid_18259047
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000147206-NXF3/tissue/colon#imid_18258957
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000147206-NXF3/tissue/liver#imid_18258974
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000147206-NXF3/tissue/kidney#imid_18258959
HPA · ICC-IF THP-1Human Protein Atlas immunofluorescence, THP-1, antibody HPA046757; green = NXF3, blue = nucleus, red = microtubules.
HPA · ICC-IF THP-1Human Protein Atlas immunofluorescence, THP-1, antibody HPA046757; green = NXF3, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for NXF3 IHC & IF
🧪Run testis first and look for staining in cells in the seminiferous ducts (HPA: Medium); use adipose tissue as the negative tissue and assess its adipocytes for background staining (HPA: Not detected). On the testis slide, compare duct cells with adjacent cells outside the ducts as an internal background check; their NXF3 status is not established by the supplied HPA rows (HPA: Medium in cells in seminiferous ducts).
Positive control tissue: Gallbladder (Glandular cells, HPA Medium)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show NXF3 in THP-1, U-251MG, U2OS, with annotated localisation: Nucleoplasm (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control; host- and class-matched rabbit IgG for the polyclonal primary; and an NXF3 knockout sample as a biological negative (selected A11497 caption: N104 pAb and anti-rabbit secondary). For chromogenic detection, quench endogenous peroxidase and check for endogenous biotin background if using the caption’s biotin–avidin detection system (selected A11497 caption: biotinylated secondary and avidin–peroxidase).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the fixative is unreported in the selected A11497 paraffin-section caption (selected A11497 caption: fixative not stated). Retrieval dependence is also unreported; compare retrieval conditions during IHC optimization, and do not assume frozen sections or IF are easier from the available evidence (selected A11497 caption: paraffin-section IHC; HPA: supported nucleoplasmic ICC-IF localisation). In testis, densely packed seminiferous nuclei can make nuclear chromogen scoring difficult; score the HPA-listed duct cells against local background (HPA: Medium in cells in seminiferous ducts).
HPA tissue IHC evidence for NXF3
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Low consistency between antibody staining and RNA expression data. Presumed off target binding observed and disregarded.). 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 |
|---|---|---|---|---|
| Gallbladder | Glandular cells | Medium | Protein (IHC) | HPA → |
| Testis | Cells in seminiferous ducts | 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 → |
| Appendix | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced NXF3 IHC Tips
Troubleshoot NXF3 staining in paraffin sections by checking retrieval, compartment, cell type and controls before assigning biological meaning.
How should I retrieve NXF3 in paraffin sections when nuclear staining is weak?
Start with Tris-EDTA pH 9.0 heat-induced epitope retrieval at 95–98 °C for 20 min (page retrieval rule: nuclear antigen). Let slides cool in retrieval buffer, then compare staining in seminiferous duct cells with a matched no-primary control; these cells show medium tissue staining (HPA tissue IHC). The catalog image shows nuclear and cytoplasmic staining at 1:50, but its caption does not report retrieval conditions (catalog antibody A11497 caption). If staining remains weak, test a citrate pH 6.0 retrieval condition on adjacent sections, keeping detection and scoring identical; this is a general IHC optimization, not a documented NXF3 requirement (standard IHC practice).
Could fixation explain weak or uneven NXF3 staining?
NXF3-specific sensitivity to fixation is unknown: the catalog paraffin-section caption does not state a fixative, and the supplied records provide no controlled fixation comparison (catalog antibody A11497 caption). Record the fixative and fixation duration for each specimen, and compare similarly processed sections before attributing intensity differences to NXF3 expression (standard IHC practice). In a troubleshooting series, hold section thickness, retrieval and antibody conditions constant while changing one processing variable at a time (standard IHC practice). Use an internal tissue control and a no-primary slide to distinguish lost antigen signal from processing background; neither establishes a target-specific fixation effect (standard IHC practice).
Should NXF3 staining appear in nuclei, cytoplasm, or both?
Score nuclear and cytoplasmic chromogen separately because NXF3 shuttles between those compartments (UniProt Q9H4D5 subcellular record). The selected paraffin-section image reports both nuclear and cytoplasmic staining in human kidney carcinoma tissue at 1:50 (catalog antibody A11497 caption). Nucleoplasm is the supported location in cell imaging, while tissue IHC describes nuclear and cytoplasmic expression in several tissues (HPA subcellular; HPA tissue IHC). Confirm that nuclear color lies within counterstained nuclei and that cytoplasmic color follows cell boundaries; diffuse deposits over empty spaces or section edges warrant a background check before compartment scoring (standard IHC practice).
Can an unknown antibody epitope complicate NXF3 isoform interpretation?
NXF3 has 2 listed isoforms, but the supplied antibody caption does not locate its epitope or demonstrate isoform selectivity (UniProt Q9H4D5 isoforms; catalog antibody A11497 caption). Its RRM spans residues 113–192 and its NTF2 domain spans 344–494; neither domain assignment identifies what this antibody recognizes (UniProt Q9H4D5 domains). Treat positive chromogen as antibody reactivity consistent with NXF3, rather than evidence for a particular isoform, until epitope mapping or an isoform-specific control is available (standard IHC interpretation). Compare matched sections across retrieval conditions, because a change in staining after retrieval alone cannot establish isoform specificity (standard IHC practice).
How should I adapt NXF3 assessment to a multiplex IF experiment?
For a separate IF assay, pair NXF3 with a validated marker identifying the expected cell population; seminiferous duct cells are a supported tissue-IHC reference, while nucleoplasm is supported by cell imaging (HPA tissue IHC; HPA subcellular). Choose spectrally separated fluorophores after checking tissue autofluorescence in an unstained section, and reserve a cleaner channel for weaker signal (standard IF practice). Because NXF3 lacks a transmembrane segment and is reported in nuclei and cytoplasm, permeabilise fixed cells sufficiently to admit antibody to intracellular epitopes, then titrate conditions to preserve cell structure (UniProt Q9H4D5 topology and subcellular record; standard IF practice). Include single-color and no-primary controls before interpreting colocalisation; the catalog paraffin-section caption does not validate an IF protocol (standard IF practice; catalog antibody A11497 caption).
What should I check when NXF3 chromogen appears across the whole section?
Run a no-primary control through the complete secondary and chromogen sequence; the catalog tissue image used PBS instead of primary antibody as its negative control (catalog antibody A11497 caption). Quench endogenous peroxidase before peroxidase-based detection, block nonspecific binding, and inspect reagent-only deposits on a matched section (standard IHC practice). If widespread staining persists, titrate the primary below the pictured 1:50 condition and check whether the secondary or avidin-based detection contributes signal; the image used a biotinylated secondary followed by avidin-peroxidase (catalog antibody A11497 caption; standard IHC practice). Treat uniform edge staining, necrotic deposits and signal in the no-primary slide as artefact until resolved (standard IHC practice).
How can I quantify NXF3 staining across specimens? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring: seminiferous duct cells show medium staining, and NXF3 may appear in both nucleus and cytoplasm (HPA tissue IHC; UniProt Q9H4D5 subcellular record). For each compartment, record the percentage of positive cells and an intensity-based H-score using the same threshold and scoring scale across slides (standard IHC practice). Alternatively, report positive-cell density per mm² within a consistently defined tissue area, excluding folds, necrosis and edge artefact (standard IHC practice). Normalise cell counts to eligible cells or sampled area, and compare sections processed and imaged together with the same controls (standard IHC practice).
When is an apparent NXF3-positive cell likely to be artefactual?
A plausible result is cellular nuclear or cytoplasmic staining, particularly in seminiferous duct cells; these patterns have supporting records (UniProt Q9H4D5 subcellular record; HPA tissue IHC). Interpret an isolated signal in an unexpected compartment or cell population cautiously, since HPA reports low agreement between antibody staining and RNA data and disregarded presumed off-target staining (HPA tissue IHC reliability). Check for color concentrated at cut edges, over necrotic material or in the no-primary control before counting positive cells (standard IHC practice). Also inspect endogenous peroxidase contribution in a peroxidase-based assay; a positive catalog image alone does not resolve specificity in a new specimen (standard IHC practice; catalog antibody A11497 caption).
Boster reagents
Best NXF3 / Nuclear RNA export factor 3 IHC Antibodies
One human-reactive anti-NXF3 antibody has IHC data from paraffin-embedded kidney carcinoma tissue (A11497 image caption). No IF data are supplied (A11497 catalog).
Real IHC data
Anti-NXF3 (N104) Antibody
Cat # A11497
A11497 is listed for human IHC (A11497 catalog: applications and reactivity). Its IHC image shows nuclear and cytoplasmic staining in paraffin-embedded human kidney carcinoma at 1:50, alongside a control without primary antibody (A11497 image caption).
Which to pick: Choose A11497 for paraffin-section IHC: it is a rabbit polyclonal antibody listed for human IHC, with a recommended dilution of 1:50–1:200 (A11497 catalog), and its image documents staining in a paraffin-embedded human kidney carcinoma section (A11497 image caption). The fixative is unreported (A11497 image caption). No listed SKU supports an IF/ICC or cross-species recommendation: A11497 lists IHC and WB applications and human reactivity only (A11497 catalog).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q9H4D5 (NXF3_HUMAN, Nuclear RNA export factor 3).
- Human Protein Atlas. NXF3 tissue IHC expression (reliability: Approved).
- Human Protein Atlas. NXF3 subcellular location (ICC-IF): Localized to the nucleoplasm..
- Human Protein Atlas. NXF3 antibody validation summary (2 antibodies).
- Prognostic significance of nuclear RNA export factor 3 in hepatocellular carcinoma. Oncology letters 2014 — PMC3919940.
- PubMed PMID:11073998 — UniProt-cited evidence.
- PubMed PMID:11545741 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for NXF3 (Nuclear RNA export factor 3). Expected localisation Nuclear and cytoplasmic staining in tissue (HPA tissue IHC). Antigen retrieval: Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen). Validated IHC antibody: A11497 at 1:50-1:200 (the product's own IHC validation image is shown). Controls (HPA): positive Gallbladder (Glandular cells); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human kidney carcinoma tissue; fixative not specified (datasheet A11497); 2. Fixation: Image fixative and duration unreported (datasheet A11497); 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-induced epitope retrieval in Tris-EDTA buffer, pH 9.0 , 20 min at 95–98 °C…; 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% normal serum of the secondary host, 30 min , room temperature (standard); 8. Primary antibody: Rabbit anti-NXF3, 1:50-1:200 (datasheet A11497); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across sections (standard IHC practice; not target-specific); Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A11497); Caveat: Presumed off-target staining and low RNA–IHC concordance (HPA tissue IHC); Isoform / epitope: 2 isoforms; no transmembrane segment; check epitope coverage (UniProt); Regulation: High in testis; low in few other tissues (UniProt). Evidence: UniProt Q9H4D5, HPA tissue IHC · Approved, HPA ICC-IF · nucleoplasm., Datasheet A11497, PMC3919940. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/NXF3/immunohistochemistry-ihc-guide.