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MEX3D / RNA-binding protein MEX3D · IHC design guide
Design Immunohistochemistry for MEX3D
Plan MEX3D chromogenic IHC in paraffin sections using the catalog antibody at 2.5 μg/mL (datasheet). Compare cytoplasmic staining across tissues and assess nuclear staining by cell type (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
MEX3D 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 across tissues; nuclear in some cell types (HPA tissue IHC) | |
| Staining pattern | Cytoplasmic staining in all tissues; nuclear in some cells (HPA tissue IHC) | |
| Antigen retrieval | Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen) | |
| Positive control | Placenta+4 more · see all | |
| Negative control | Adipose tissue+1 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 A13697) | |
| Caveat | High trophoblast staining despite testis-enriched RNA (HPA tissue IHC) | |
| Regulation | RNA is testis-enriched (HPA tissue RNA) | |
| Isoform / epitope | 3 isoforms; epitope coverage is unspecified (UniProt) |
Section 1
Recommended MEX3D IHC & IF Protocols
The catalog antibody IHC-P protocol is paired with one published MEX3D IHC protocol for cervical tissue (PMC9072549).
| Sample | Tissue sections; selected-image fixative not specified (standard IHC workflow) |
| Fixation | Image fixative and duration unreported (datasheet A13697); 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-MEX3D, 2.5 μg/mL (datasheet A13697) |
| 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 | MEX3D-positive staining in trophoblastic cells of placenta (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression in all tissues combined with nuclear expression in several different cell types. No signal in the no-primary control. |
💡Decision noteStart with Tris-EDTA pH 9.0 retrieval at 95–98 °C for 20 min (page antigen retrieval); MEX3D also localizes to the nucleus (UniProt Q86XN8).
Section 2
What Is the Expected MEX3D Staining Pattern?
MEX3D is predominantly cytoplasmic and can shuttle into the nucleus; it has no transmembrane segment (UniProt Q86XN8 localisation and topology). In paraffin tissue sections, expect cytoplasmic staining across tissues, with nuclear staining in some cell types (HPA: tissue IHC profile). Trophoblastic cells in placenta and spermatogonia in testis show high staining (HPA: High). HPA rates the tissue IHC pattern Approved, with medium agreement with RNA data and external verification pending (HPA: reliability).
| Clear cytoplasmic signal in placental trophoblastic cells or testicular spermatogonia; some nuclei also stain. | This fits the strongest listed tissue IHC examples (HPA: High in both cell types). Nuclear signal can fit MEX3D shuttling (UniProt Q86XN8 localisation), but its presence need not be uniform: HPA reports nuclear expression in several cell types, without assigning it to every positive cell (HPA: tissue IHC profile). |
| Signal is confined to cell borders, extracellular material, or another compartment without convincing cellular cytoplasm. | That distribution conflicts with the predominantly cytoplasmic localisation and lack of a transmembrane segment (UniProt Q86XN8 localisation and topology). Treat it as a possible staining artefact; review morphology and detection controls before assigning it to MEX3D (general IHC practice). Nuclear signal alone also needs context because shuttling is documented (UniProt Q86XN8 localisation). |
| Strong staining appears in adipocytes or caudate glial cells while expected positive cells stain weakly. | Those specific cell types are reported as not detected by tissue IHC (HPA: adipocytes and caudate glial cells). Consider cross-reactivity or endogenous detection activity, then inspect a detection-only control (general IHC practice). Do not call an entire adipose or caudate section negative solely from those cell-specific entries (HPA: tissue IHC profile). |
| Colour spreads across stroma, blank areas, or most cells without discernible cellular boundaries. | Diffuse deposition is hard to reconcile with the reported cellular cytoplasmic pattern (HPA: tissue IHC profile). It can obscure both positive and low-level cells; assess a no-primary control, blocking, washing, and detection development as general IHC troubleshooting, without treating any one cause as established for MEX3D. |
| No interpretable signal appears in placental trophoblastic cells or testicular spermatogonia. | Both are high-staining reference cells in HPA tissue IHC (HPA: High). First verify that the relevant cells are present and the section and detection run are interpretable (general IHC practice). A blank section alone does not show that MEX3D is absent; HPA's Approved assessment has medium RNA agreement and awaits external verification (HPA: reliability). |
💡Expected MEX3D appearanceCall the result positive when cellular cytoplasmic staining is clear in trophoblastic cells or spermatogonia, where HPA reports high staining; nuclear staining may coexist (HPA: High and tissue IHC profile; UniProt Q86XN8 localisation). Border-only, extracellular, or diffuse colour without a convincing cellular pattern is suspect (UniProt Q86XN8 topology; general IHC practice).
| Compartment and topology (UniProt Q86XN8 localisation and topology) | Predominant cytoplasmic localisation sets the primary compartment to assess. Nucleus is also annotated because MEX3D shuttles through the CRM1 export pathway (UniProt Q86XN8 localisation). No transmembrane segment is annotated, so a membrane-only outline lacks support as the expected pattern (UniProt Q86XN8 topology). |
| Cell-specific tissue contrast (HPA: tissue IHC) | Placental trophoblastic cells and testicular spermatogonia are high; the listed adrenal, appendix, breast, bronchus, cerebellum, and cervix cell types are medium (HPA: tissue IHC levels). Adipocytes and caudate glial cells are not detected (HPA: tissue IHC). Compare the identified cells, since these labels do not describe every cell in each organ. |
| Evidence strength (HPA: reliability and antibody HPA065385) | The tissue pattern is Approved, but its agreement with RNA expression is medium and external verification is pending (HPA: reliability). Antibody HPA065385 is IHC Approved, with no ICC status supplied (HPA: antibodies). These entries support a tissue IHC expectation; they do not establish an ICC or IF staining pattern. |
| Isoforms and modifications (UniProt Q86XN8 sequence annotations) | Three isoforms and phosphorylated residues at positions 510 and 514 are annotated (UniProt Q86XN8). No epitope or isoform coverage is supplied, so these annotations cannot predict which isoforms the IHC antibody detects or whether phosphorylation changes its staining. Interpret the observed tissue pattern without making either inference. |
| Protein staining versus RNA specificity (HPA: tissue IHC and RNA specificity) | HPA calls RNA tissue enriched in testis while reporting cytoplasmic protein staining across tissues (HPA: RNA specificity and tissue IHC profile). Use the IHC cell-level observations to judge a stained section. The RNA label alone does not make staining outside testis unexpected, and HPA reports only medium consistency between antibody staining and RNA data (HPA: reliability). |
| Situation | Likely cause | Next action |
|---|---|---|
| Placental trophoblastic cells and testicular spermatogonia are blank. | The expected high-staining cells may be absent from the examined area (HPA: High), or the IHC run may have failed (general IHC practice). | Confirm cell identity on the counterstained section, then review the run's positive control and detection steps (general IHC practice). Do not infer MEX3D absence from an uninterpretable run. |
| Signal is only nuclear. | Nuclear localisation is possible, but HPA describes cytoplasmic expression across tissues (UniProt Q86XN8 localisation; HPA: tissue IHC profile). | Recheck cell boundaries, counterstain, and positive-reference cells; record the nuclear-only result separately from the expected cytoplasmic pattern (general IHC practice; HPA: tissue IHC profile). |
| Adipocytes or caudate glial cells stain strongly. | These cells are listed as not detected; cross-reactivity or endogenous detection activity is possible (HPA: tissue IHC; general IHC practice). | Inspect a no-primary or detection-only control and compare staining in identified cells, rather than judging the whole tissue as one compartment (general IHC practice). |
| Colour is diffuse or fills cell-free spaces. | Nonspecific background or detection deposition may be obscuring the reported cellular pattern (HPA: tissue IHC profile; general IHC practice). | Check the no-primary control and review blocking, washes, and chromogen development; score MEX3D only where cell-level localisation remains interpretable (general IHC practice). |
| Medium or low reference cells look weaker than high reference cells. | HPA reports different staining levels by cell type, including medium and low entries (HPA: tissue IHC levels). | Compare like cell types and run conditions before calling a weak field failed; use trophoblastic cells or spermatogonia as the listed high-staining references (HPA: High; general IHC practice). |
| IF/ICC shows a pattern that seems inconsistent with the tissue IHC expectation. | HPA supplies no main ICC-IF location or cell-line images, and HPA065385 has no ICC status in this payload (HPA: subcellular and antibodies). | Treat the IF/ICC observation as unverified here and consult the separate IF/ICC guide; retain the tissue IHC comparison for paraffin sections (HPA: tissue IHC profile). |
Experiment evidence
IHC & IF images showing MEX3D staining
A13697 · IHCImmunohistochemistry of Rkhd1 in human small intestine tissue with Rkhd1 antibody at 2.5 μg/mL.
A13697 · IFImmunofluorescence of rkhd1 in human small intestine tissue with rkhd1 antibody at 20 μg/mL.
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000181588-MEX3D/tissue/cerebral+cortex#imid_17824299
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000181588-MEX3D/tissue/colon#imid_17824209
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000181588-MEX3D/tissue/liver#imid_17824210
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000181588-MEX3D/tissue/kidney#imid_17824211
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for MEX3D IHC & IF
🧪Run placenta first and require staining in trophoblastic cells (HPA: High in trophoblastic cells); run adipose tissue as the negative comparator, expecting no detectable staining in adipocytes (HPA: Not detected in adipocytes). On the placenta slide, treat cells outside the trophoblastic compartment that lack specific staining as internal background comparators; the supplied HPA rows do not identify a particular placental cell type as negative (HPA: placenta trophoblastic cells High).
Positive control tissue: Placenta (Trophoblastic cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA carries no ICC-IF cell line for MEX3D; derive a cell-line control from the positive tissue's cell type (Trophoblastic cells) and confirm it by RNA or western blot first.
Technical controls: Include a no-primary, secondary-only control; an isotype control matched to the primary antibody’s host species and clonality; and a biological specificity control such as MEX3D knockout material or immunizing-peptide competition when available (standard IHC practice). For chromogenic IHC in placenta, quench endogenous peroxidase and check for endogenous biotin if using biotin-based detection (standard IHC practice).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported, and the selected A13697 tissue-IHC caption leaves the fixative unreported (selected tissue-IHC caption: fixative not stated). Retrieval dependence is unreported; compare heat-induced retrieval with no retrieval on matched paraffin sections (standard IHC practice). The supplied evidence does not establish whether frozen sections or IF would be easier for MEX3D (HPA: no ICC-IF images); in placenta, check blood-rich areas for endogenous peroxidase background when interpreting chromogenic staining (standard IHC practice).
HPA tissue IHC evidence for MEX3D
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Medium 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 |
|---|---|---|---|---|
| Placenta | Trophoblastic cells | High | Protein (IHC) | HPA → |
| Testis | Spermatogonia cells | High | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Medium | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Medium | Protein (IHC) | HPA → |
| Breast | Glandular cells | Medium | Protein (IHC) | HPA → |
Section 3
Advanced MEX3D IHC Tips
Troubleshoot MEX3D staining by checking retrieval, compartment pattern, controls, and cell-specific signal before comparing sections.
How should I retrieve MEX3D in paraffin sections when staining is weak?
Start with Tris-EDTA at pH 9.0, heated to 95–98 °C for 20 min (page retrieval rule: nuclear antigen). Keep section thickness, cooling, and detection conditions consistent while comparing retrieval runs, so a change in signal can be assigned to retrieval (standard IHC practice). MEX3D occurs in both cytoplasm and nucleus, so assess both compartments rather than judging retrieval solely by nuclear intensity (UniProt Q86XN8: subcellular location). If signal remains weak, test a milder retrieval condition on serial sections alongside the stated method, with the same positive tissue and no-primary control; excessive retrieval can damage morphology or increase background (standard IHC practice).
Could fixation explain weak or uneven MEX3D staining?
Target-specific fixation sensitivity is unknown because no MEX3D fixation comparison is supplied, and the selected tissue image does not state its fixative (A13697 tissue-IHC caption). Record fixation duration and processing history for each specimen, then compare sections processed together before changing the antibody concentration (standard IHC practice). Uneven fixation can alter morphology and apparent antigen availability, so inspect preserved tissue and compare staining away from section edges (standard IHC practice). Do not infer a MEX3D-specific fixation effect from its cytoplasmic and nuclear locations or phosphorylation sites (UniProt Q86XN8: subcellular location and modified residues); use a controlled fixation comparison to investigate that possibility.
Should MEX3D staining be cytoplasmic, nuclear, or both?
Expect a predominantly cytoplasmic pattern, while allowing nuclear signal because MEX3D shuttles through the CRM1 export pathway (UniProt Q86XN8: subcellular location). Tissue IHC reports cytoplasmic expression across tissues and nuclear expression in several cell types, so compartment proportions can differ between cells (HPA tissue IHC: staining profile). Score cytoplasmic and nuclear staining separately in morphologically identified cells, using the same counterstain and scoring criteria across sections (standard IHC practice). If staining is confined to an unexpected structure, check retrieval, antibody background, and no-primary controls before interpreting it as a new MEX3D location (UniProt Q86XN8: subcellular location; standard IHC practice).
Can this stain distinguish MEX3D isoforms or phosphorylation states?
MEX3D has 3 annotated isoforms, but the supplied tissue image does not define which isoforms its antibody detects (UniProt Q86XN8: isoforms; A13697 tissue-IHC caption). Its 2 KH domains span residues 179–240 and 273–334, and annotated phosphorylation includes residues 510 and 514 (UniProt Q86XN8: domains and modified residues). Without an epitope map and isoform-specific validation, report the result as MEX3D immunoreactivity rather than an individual isoform or phosphorylation state (standard IHC interpretation). If that distinction matters, obtain epitope documentation and compare validated isoform- or modification-specific reagents on matched sections with appropriate controls (standard IHC practice).
How can I examine the MEX3D pattern by multiplex immunofluorescence?
Use IF as a separate assay and confirm that the chosen antibody works under its own fixation and staining conditions before comparing it with chromogenic IHC (standard IF practice). Pair MEX3D with a validated marker for the expected cell type in the tissue examined; trophoblastic cells in placenta and spermatogonia in testis are high-staining examples in tissue IHC (HPA tissue IHC: positive cells). Choose spectrally separated fluorophores after checking tissue autofluorescence and include single-stain controls to assess channel bleed-through (standard IF practice). MEX3D has no transmembrane segment and occupies cytoplasm and nucleus, so permeabilise fixed cells or sections to access intracellular epitopes, then assess nuclear overlap with a counterstain (UniProt Q86XN8: topology and subcellular location; standard IF practice).
What should I check when MEX3D staining is diffuse or widespread?
First compare the stained section with a no-primary control and inspect whether colour follows cells, section edges, or damaged tissue (standard chromogenic IHC practice). Quench endogenous peroxidase before peroxidase-based detection, optimise blocking, and shorten chromogen development if background persists (standard chromogenic IHC practice). Broad cytoplasmic staining alone is not unexpected for MEX3D, since tissue IHC describes cytoplasmic expression across tissues (HPA tissue IHC: staining profile). If nearly every compartment stains equally, titrate the primary antibody against a positive section and a control section; the 2.5 µg/mL in the selected image caption documents that image, not a universal working concentration (A13697 tissue-IHC caption; standard IHC practice).
How should I quantify MEX3D across tissues with different cell populations? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, because MEX3D staining can be cytoplasmic with nuclear staining in some cells (HPA tissue IHC: staining profile). For a specified cell population, record the percentage positive and an intensity-based H-score separately for cytoplasm and nucleus, applying the same thresholds across batches (standard IHC practice). For spatial comparisons, count positive cells per mm² of viable, annotated tissue and normalise counts to the number of eligible cells or measured viable area (standard IHC practice). Include matched controls and report cell-type composition; high staining in placental trophoblastic cells or testicular spermatogonia should not be interpreted as equivalent whole-tissue intensity (HPA tissue IHC: positive cells).
How can I distinguish credible MEX3D staining from artefact?
A credible pattern follows intact cell boundaries and may include cytoplasm plus cell-dependent nuclear signal, consistent with the reported tissue pattern and shuttling location (HPA tissue IHC: staining profile; UniProt Q86XN8: subcellular location). Check the identity of stained cells: placental trophoblastic cells and testicular spermatogonia are reported as high, whereas adipocytes are reported as not detected (HPA tissue IHC: positive and negative cells). Treat edge-restricted colour, necrotic regions, and signal reproduced in a no-primary or peroxidase-control section as possible artefact (standard chromogenic IHC practice). HPA labels its tissue IHC reliability Approved while noting medium agreement with RNA data and pending external verification, so support unexpected patterns with controls and independent evidence (HPA tissue IHC: reliability description).
Boster reagents
Best MEX3D / RNA-binding protein MEX3D IHC Antibodies
The catalog antibody has IHC and IF images from human small intestine tissue (A13697 image captions) and lists human reactivity (A13697 catalog reactivity).
Real IHC data
Anti-Rkhd1 MEX3D Antibody
Cat # A13697
A13697 lists IHC-P and shows staining in human small intestine tissue at 2.5 μg/mL (A13697 applications; A13697 IHC image caption). It also lists IF and shows staining in human small intestine tissue at 20 μg/mL (A13697 applications; A13697 IF image caption).
Which to pick: For tissue IHC, choose A13697: it lists IHC-P, and its own image shows human small intestine tissue; the fixative is unreported (A13697 applications; A13697 IHC image caption). For IF, choose A13697; ICC is not separately listed, and clonality is unreported (A13697 applications; A13697 catalog clone field). No cross-species choice is documented because A13697 lists human reactivity only (A13697 catalog reactivity).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q86XN8 (MEX3D_HUMAN, RNA-binding protein MEX3D).
- Human Protein Atlas. MEX3D tissue IHC expression (reliability: Approved).
- Human Protein Atlas. MEX3D subcellular location (ICC-IF): Highest expression in REH: 41.7 nTPM.
- Human Protein Atlas. MEX3D antibody validation summary (1 antibodies).
- RNA-binding protein MEX3D promotes cervical carcinoma tumorigenesis by destabilizing TSC22D1 mRNA. Cell death discovery 2022 — PMC9072549.
- PubMed PMID:17267406 — UniProt-cited evidence.
- PubMed PMID:15057824 — UniProt-cited evidence.
- PubMed PMID:14769789 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for MEX3D (RNA-binding protein MEX3D). Expected localisation Cytoplasmic across tissues; nuclear in some cell types (HPA tissue IHC). Antigen retrieval: Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen). Validated IHC antibody: A13697 at 2.5 μg/mL (the product's own IHC validation image is shown). Controls (HPA): positive Placenta (Trophoblastic cells); negative Adipose tissue. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Tissue sections; selected-image fixative not specified (standard IHC workflow); 2. Fixation: Image fixative and duration unreported (datasheet A13697); 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-MEX3D, 2.5 μg/mL (datasheet A13697); 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 A13697); Caveat: High trophoblast staining despite testis-enriched RNA (HPA tissue IHC); Isoform / epitope: 3 isoforms; epitope coverage is unspecified (UniProt); Regulation: RNA is testis-enriched (HPA tissue RNA). Evidence: UniProt Q86XN8, HPA tissue IHC · Approved, HPA cell-line RNA · Highest expression in REH: 41.7 nTPM, Datasheet A13697, PMC9072549. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/MEX3D/immunohistochemistry-ihc-guide.