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JMY / Junction-mediating and -regulatory protein · IHC design guide
Design Immunohistochemistry for JMY
Plan JMY staining in paraffin sections using the cytoplasmic tissue pattern reported by HPA (HPA tissue IHC). Interpret nuclear staining in light of JMY’s condition-dependent localisation, and treat tissue staining as uncertain because antibody staining and RNA expression show low consistency (UniProt; HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
JMY 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 staining in most tissues (HPA tissue IHC) | |
| Staining pattern | Cytoplasmic staining across multiple tissue cell types (HPA tissue IHC) | |
| Antigen retrieval | Tris-EDTA pH 9.0 HIER, heat-mediated (datasheet A05423) | |
| Positive control | Appendix+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 tissue sections. (standard IHC practice; not target-specific) | |
| Caveat | Staining has low concordance with RNA expression (HPA tissue IHC) | |
| Regulation | DNA damage: nuclear accumulation (UniProt) | |
| Isoform / epitope | 2 isoforms; epitope differences unreported (UniProt) |
Section 1
Recommended JMY IHC & IF Protocols
Compare the catalog antibody's IHC-P protocol (datasheet A05423) with the published JMY stain of NSCLC tissue and adjacent controls (PMC12357428).
| Sample | Paraffin-embedded human liver cancer tissue; fixative not specified (datasheet A05423) |
| Fixation | Image fixative and duration unreported (datasheet A05423); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: Tris-EDTA pH 9.0 (datasheet A05423); 20 min, 95–100 °C (standard) |
| 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-JMY, 1:50 recommended; image 1:200 (datasheet A05423) |
| 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 | JMY-positive staining in glandular cells of appendix (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression in most tissues. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated Tris-EDTA retrieval at pH 9.0 (datasheet A05423); the published IHC method reports retrieval without specifying conditions (PMC12357428 methods).
Section 2
What Is the Expected JMY Staining Pattern?
JMY is mainly nuclear in most cell types, but can also occupy the cytoplasm, cytoskeleton and cytoplasmic vesicles (UniProt Q8N9B5). In tissue IHC, expect predominantly cytoplasmic staining in the cell types reported as positive by HPA, such as appendix glandular cells and bronchial respiratory epithelial cells (HPA: High; HPA: cytoplasmic expression in most tissues). Interpret this pattern cautiously: HPA rates its tissue IHC evidence Uncertain, and JMY has no transmembrane segment (HPA: Uncertain; UniProt Q8N9B5 topology).
| Cytoplasmic chromogen in appendix glandular cells or bronchial respiratory epithelial cells, with clear cell boundaries. | This fits the reported tissue pattern (HPA: High in both cell types; HPA: cytoplasmic expression in most tissues). Compare intensity with the rest of the section and a same-run control; HPA rates the IHC evidence Uncertain (HPA: Uncertain). |
| Nuclear signal accompanies cytoplasmic staining, or the balance between compartments varies by cell. | Nuclear JMY is biologically plausible: UniProt places it in the nucleus in most cell types and describes redistribution with cell state (UniProt Q8N9B5). Nuclear staining alone cannot establish a biological shift in a paraffin section; HPA's nucleoplasmic ICC-IF assignment is Uncertain (HPA: subcellular, Uncertain). |
| Signal appears only on extracellular surfaces or as a continuous plasma-membrane rim. | That pattern does not match the listed nuclear, cytoplasmic and vesicular locations or the absence of a transmembrane segment (UniProt Q8N9B5). Check morphology, chromogen deposits and controls before calling it JMY (general IHC practice). |
| Strong signal appears in adipocytes or ovarian follicle cells, or staining spreads evenly across unrelated cell types. | HPA reports JMY as Not detected in those two cell types, so cross-reactivity or endogenous detection activity is possible (HPA: Not detected; general IHC practice). Because tissue IHC reliability is Uncertain, a mismatch prompts verification rather than an automatic rejection (HPA: Uncertain). |
| A diffuse haze obscures cell borders, or an expected positive compartment has no discernible signal. | Diffuse haze limits localization calls; absent staining in a reported positive tissue may reflect an assay failure or variable tissue staining (general IHC practice; HPA: Uncertain). Review controls and section quality before interpreting either result as JMY biology. |
💡Expected JMY appearanceA credible positive is discernible cytoplasmic staining in reported High cell types, such as appendix glandular cells, with possible nuclear signal; diffuse haze or a membrane-only rim is suspect (HPA: High; HPA: cytoplasmic expression in most tissues; UniProt Q8N9B5).
| Tissue and cell selection | Use the reported High cell populations as candidate positive controls and adipocytes or ovarian follicle cells as comparison populations (HPA: High; HPA: Not detected). HPA labels the tissue IHC profile Uncertain, so these are observed patterns rather than independently verified controls (HPA: Uncertain). |
| Compartment and cell state | UniProt lists nuclear, cytoskeletal and vesicular locations, including autophagosome membrane during starvation-induced autophagy (UniProt Q8N9B5). Thus cytoplasmic staining need not be uniform; infer a state-dependent change only with suitable experimental controls (general IHC practice). |
| Antibody evidence and isoforms | The listed tissue IHC antibody HPA043308 has Uncertain validation, and the other listed antibody has no IHC validation entry (HPA: antibodies). UniProt records two JMY isoforms; without an epitope map here, isoform recognition cannot be predicted (UniProt Q8N9B5). |
| Topology and processing | JMY has no transmembrane segment, signal peptide or propeptide; UniProt lists a single chain spanning residues 1–988 (UniProt Q8N9B5). Treat a surface-only or secreted-looking pattern as a reason to inspect assay specificity, not as expected topology. |
| Retrieval and detection | No JMY-specific antigen-retrieval or fixation-sensitivity result is supplied (UniProt Q8N9B5; HPA: tissue IHC). If signal is weak, adjust retrieval and antibody dilution using section controls; check endogenous detection activity with the appropriate control (general IHC practice). |
| IF/ICC Q&A: Should it reproduce tissue IHC? | No direct match is established: HPA reports mainly nucleoplasmic ICC-IF localization, marked Uncertain, while tissue IHC is mainly cytoplasmic and also Uncertain (HPA: subcellular; HPA: tissue IHC). Assess each application's controls separately (general IHC practice). |
| Situation | Likely cause | Next action |
|---|---|---|
| No signal in appendix glandular cells or bronchial respiratory epithelium. | These are reported High populations, but HPA's tissue IHC reliability is Uncertain; a failed staining run is also possible (HPA: High; HPA: Uncertain; general IHC practice). | Check the same-run positive control, section integrity and detection reagents, then optimize retrieval and dilution within the IHC-validated antibody's instructions (general IHC practice). |
| Only a plasma-membrane rim or extracellular deposit stains. | The location conflicts with UniProt's nuclear and cytoplasmic assignments and lack of a transmembrane segment (UniProt Q8N9B5 topology). | Inspect chromogen distribution and tissue edges; compare a no-primary control and an independent specificity control before assigning the signal to JMY (general IHC practice). |
| Adipocytes or ovarian follicle cells stain strongly. | HPA reports JMY as Not detected in these populations; nonspecific antibody binding or endogenous detection activity may account for signal (HPA: Not detected; general IHC practice). | Compare no-primary and detection controls, then verify cell identity and staining in a reported High population on the same run (general IHC practice; HPA: High). |
| Brown haze obscures cytoplasm and nuclei. | Background can arise from incomplete blocking, excess antibody or endogenous detection activity (general IHC practice). | Review blocking and wash steps, titrate the primary antibody and inspect the no-primary control before scoring localization (general IHC practice). |
| Nuclear staining predominates over cytoplasmic staining. | Nuclear JMY is plausible, whereas HPA describes tissue IHC as mainly cytoplasmic and ICC-IF nucleoplasmic localization as Uncertain (UniProt Q8N9B5; HPA: tissue IHC; HPA: subcellular). | Score nuclei and cytoplasm separately, verify cell morphology and compare controlled sections; do not infer DNA damage from localization alone (general IHC practice). |
| Staining varies sharply between sections or cell populations. | UniProt describes context-dependent localization, and HPA reports low consistency between antibody staining and RNA data (UniProt Q8N9B5; HPA: Uncertain). | Run sections together, compare the same cell type and compartment, and record intensity and distribution separately before drawing a biological conclusion (general IHC practice). |
Experiment evidence
IHC & IF images showing JMY staining
A05423 · IHCImmunohistochemical analysis of paraffin-embedded human liver cancer. 1, Antibody was diluted at 1:200 (4° overnight). 2, Tris-EDTA, pH9.0 w
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000152409-JMY/tissue/cerebral+cortex#imid_11585711
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000152409-JMY/tissue/colon#imid_11585629
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000152409-JMY/tissue/liver#imid_11585638
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000152409-JMY/tissue/kidney#imid_11585623
HPA · ICC-IF HEK293Human Protein Atlas immunofluorescence, HEK293, antibody HPA037508; green = JMY, blue = nucleus, red = microtubules.
HPA · ICC-IF HEK293Human Protein Atlas immunofluorescence, HEK293, antibody HPA037508; green = JMY, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for JMY IHC & IF
🧪Run appendix first; its glandular cells should stain (HPA: High in appendix glandular cells). Use ovary follicle cells as the negative tissue (HPA: Not detected in ovary follicle cells); non-glandular cells on the appendix slide should be assessed for background, but their JMY-negative status is not established by the supplied HPA row.
Positive control tissue: Appendix (Glandular cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show JMY in HEK293, Rh30, U2OS, with annotated localisation: Nucleoplasm (uncertain) (HPA subcellular).
Technical controls: Include no-primary (secondary-only), a control immunoglobulin matched to the primary antibody’s host species, class, and clonality, and JMY-knockout tissue or a peptide-block control if the immunizing peptide is available (standard IHC practice). Quench endogenous peroxidase and check appendix inflammatory cells for residual chromogenic signal; assess endogenous biotin if using avidin–biotin detection (standard IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected paraffin-section caption does not state a fixative (A05423 caption). The caption uses Tris-EDTA at pH 9.0 for retrieval, but whether retrieval is essential is unreported (A05423 caption); the available ICC-IF images do not establish that IF or frozen sections are easier (HPA: HEK293, Rh30, U2OS ICC-IF images). Endogenous peroxidase in appendix inflammatory cells can mimic chromogenic staining (standard IHC practice).
HPA tissue IHC evidence for JMY
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Uncertain — Low consistency between antibody staining and RNA expression data. Pending external verification.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Appendix | Glandular cells | High | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | High | Protein (IHC) | HPA → |
| Cervix | Squamous epithelial cells | High | Protein (IHC) | HPA → |
| Colon | Endothelial cells | High | Protein (IHC) | HPA → |
| Duodenum | Glandular cells | High | Protein (IHC) | HPA → |
Section 3
Advanced JMY IHC Tips
Troubleshooting for JMY chromogenic IHC in paraffin sections, with one entry for the separate IF/ICC workflow (datasheet A05423).
How should I adjust retrieval when JMY staining is weak in paraffin sections?
Start with heat-mediated Tris-EDTA at pH 9.0 for antigen retrieval (datasheet A05423). The documented starting condition for the catalog antibody is 1:200 at 4 °C overnight in paraffin-embedded human liver cancer (datasheet A05423). Keep section preparation, heating, and cooling consistent; the caption does not specify a retrieval duration, so establish one empirically (datasheet A05423; standard IHC practice). If staining remains weak, compare a milder retrieval condition on adjacent sections while holding detection constant (standard IHC practice). Assess both nuclear and cytoplasmic signal because JMY can occupy either compartment (UniProt Q8N9B5 subcellular location).
Could fixation explain variable JMY staining between paraffin blocks?
The selected paraffin-section caption does not report its fixative, and target-specific fixation sensitivity for JMY is unknown (datasheet A05423). Record fixative, fixation duration, processing history, and block age before comparing cases; these variables can affect antigen accessibility in IHC (standard IHC practice). Compare sections processed together using the documented pH 9.0 Tris-EDTA retrieval and 1:200 primary dilution (datasheet A05423). If staining differs, vary retrieval on matched sections while keeping antibody incubation and detection constant (standard IHC practice). Do not assign a fixation effect from JMY localisation or phosphorylation sites alone (UniProt Q8N9B5 subcellular location and modified residues).
Should JMY staining be nuclear, cytoplasmic, or vesicular?
Score nuclear and cytoplasmic compartments separately: JMY is reported in the nucleus, cytoskeleton-associated cytoplasm, and cytoplasmic vesicles (UniProt Q8N9B5 subcellular location). Nuclear accumulation can accompany DNA damage, whereas cytoplasmic recruitment to autophagy-associated membranes is reported during nutrient stress (UniProt Q8N9B5 subcellular location). HPA describes cytoplasmic staining in most tissues but rates its tissue IHC reliability uncertain (HPA tissue IHC). HPA also reports mainly nucleoplasmic localisation in cell imaging, with an uncertain location assignment (HPA subcellular). For chromogenic sections, compare compartment patterns within intact cells and across matched conditions before treating a shift as biological (standard IHC practice; UniProt Q8N9B5 subcellular location).
Can this antibody distinguish JMY isoforms or phosphorylation states in IHC?
JMY has 2 annotated isoforms, but the supplied caption does not map the catalog antibody’s epitope (UniProt Q8N9B5 isoforms; datasheet A05423). An IHC signal therefore cannot identify an isoform without epitope mapping and appropriate validation material (standard IHC practice). The record lists a WH2 domain at residues 921–938 and several phosphoserines, including positions 115, 121, and 974 (UniProt Q8N9B5 domains and modified residues). These features matter only if the antibody’s binding region overlaps or responds to them, which is unreported here (datasheet A05423). Compare independently validated antibodies or defined controls before assigning an isoform or modification-specific interpretation (standard IHC practice).
How can I investigate JMY localisation by multiplex IF/ICC?
Use IF/ICC as a separate localisation experiment; the supplied catalog evidence documents chromogenic IHC in paraffin sections (datasheet A05423). Multiplex JMY with a marker for the expected cell population, such as an epithelial marker when examining bronchial respiratory epithelial cells, and include a nuclear counterstain (HPA tissue IHC: bronchus; standard IF practice). Choose well-separated fluorophores and consider a far-red channel if tissue autofluorescence compromises shorter wavelengths (standard IF practice). JMY lacks a transmembrane segment and has nuclear and cytoplasmic locations, so optimise permeabilisation for access to its intracellular epitope (UniProt Q8N9B5 topology and subcellular location; standard IF practice). Interpret puncta alongside compartment controls rather than treating every bright spot as an autophagosome (UniProt Q8N9B5 subcellular location; standard IF practice).
What controls help separate JMY staining from chromogenic background?
Run a no-primary control and inspect the same compartments as the test section; this helps reveal detection-system and tissue-derived signal (standard IHC practice). Include a peroxidase block before peroxidase-based chromogenic detection, and monitor DAB development consistently across sections (standard IHC practice). Begin with the documented 1:200 primary and 1:200 secondary dilutions, then titrate if diffuse staining obscures cellular boundaries (datasheet A05423; standard IHC practice). Compare intact cells with nearby damaged or necrotic regions, where nonspecific chromogen deposition can complicate reading (standard IHC practice). Because HPA rates tissue staining reliability uncertain, background reduction alone does not establish JMY specificity (HPA tissue IHC).
How should I score JMY across cases with different cellular composition? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and viable tissue area before scoring, then record nuclear and cytoplasmic JMY separately (standard IHC practice; UniProt Q8N9B5 subcellular location). An H-score combines the percentage of cells at intensities 0–3 into a 0–300 score; report the compartment and scoring rules (standard IHC practice). Alternatively, report the percentage of positive eligible cells or positive-cell density per mm², depending on the biological question (standard IHC practice). Normalise cell counts to the eligible population and density to viable tissue area, excluding folds and necrosis (standard IHC practice). Keep retrieval, detection, thresholds, and sampling consistent because HPA tissue staining has uncertain reliability (datasheet A05423; HPA tissue IHC; standard IHC practice).
When is a JMY-positive pattern convincing rather than artefactual?
A convincing result resolves signal within intact cells in a plausible nuclear, cytoplasmic, or vesicular compartment (UniProt Q8N9B5 subcellular location; standard IHC practice). Check whether stained cells match the intended population; HPA reports high staining in bronchial respiratory epithelial cells but no detected staining in adipocytes, with uncertain overall tissue IHC reliability (HPA tissue IHC). Treat isolated section-edge staining, necrotic deposits, and no-primary-control signal as possible artefacts (standard IHC practice). Residual endogenous enzyme activity can also produce chromogen unrelated to antibody binding, so examine the peroxidase-block control workflow (standard IHC practice). Confirm consequential localisation claims with an independent specificity control or orthogonal evidence, especially when assigning a stress-related compartment shift (UniProt Q8N9B5 subcellular location; standard IHC practice).
Boster reagents
Best JMY / Junction-mediating and -regulatory protein IHC Antibodies
A05423 has an IHC image of paraffin-embedded human liver cancer (A05423 image caption). Human and Mouse reactivity is listed; no IF figure is provided (catalog reactivity; catalog IF images).
Real IHC data
Anti-JMY Antibody
Cat # A05423
A05423 is listed for IHC and has an image of paraffin-embedded human liver cancer (catalog applications; A05423 image caption). It lists Human and Mouse reactivity, but the image documents human tissue only (catalog reactivity; A05423 image caption).
Which to pick: For tissue IHC, choose A05423 for paraffin sections; its image caption does not report the fixative (A05423 image caption). For IF/ICC, no listed SKU has an IF application or figure (catalog applications; catalog IF images). For cross-species work, A05423 lists Human and Mouse reactivity, though its IHC image shows human tissue only; its host is Rabbit and clonality is unreported (catalog reactivity/host/clone; A05423 image caption).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q8N9B5 (JMY_HUMAN, Junction-mediating and -regulatory protein).
- Human Protein Atlas. JMY tissue IHC expression (reliability: Uncertain).
- Human Protein Atlas. JMY subcellular location (ICC-IF): Mainly localized to the nucleoplasm..
- Human Protein Atlas. JMY antibody validation summary (2 antibodies).
- m6A-modified circZNF548 regulates exosomal miR-7108-3p to activate CD3(+)CD8(+) T cells and suppress NSCLC growth by JMY. BMC biology 2025 — PMC12357428.
- Junction-mediating and regulatory protein (JMY) is a promoting protein for radial migration of cortical neurons. Cell death discovery 2026 — PMC13031400.
- PubMed PMID:15372022 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for JMY (Junction-mediating and -regulatory protein). Expected localisation Cytoplasmic staining in most tissues (HPA tissue IHC). Antigen retrieval: Tris-EDTA pH 9.0 HIER, heat-mediated (datasheet A05423). Validated IHC antibody: A05423 at 1:50 recommended; image 1:200 (the product's own IHC validation image is shown). Controls (HPA): positive Appendix (Glandular cells); negative Adipose tissue. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Paraffin-embedded human liver cancer tissue; fixative not specified (datasheet A05423); 2. Fixation: Image fixative and duration unreported (datasheet A05423); 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: Tris-EDTA pH 9.0 (datasheet A05423); 20 min, 95–100 °C (standard); 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-JMY, 1:50 recommended; image 1:200 (datasheet A05423); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across tissue sections. (standard IHC practice; not target-specific); Caveat: Staining has low concordance with RNA expression (HPA tissue IHC); Isoform / epitope: 2 isoforms; epitope differences unreported (UniProt); Regulation: DNA damage: nuclear accumulation (UniProt). Evidence: UniProt Q8N9B5, HPA tissue IHC · Uncertain, HPA ICC-IF · Mainly localized to the nucleoplasm., Datasheet A05423, PMC12357428. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/JMY/immunohistochemistry-ihc-guide.