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- Table of Contents
Plan paraffin-section U2AF2 IHC around its ubiquitous nuclear pattern (HPA tissue IHC). Use high-staining glandular cells or kidney tubules to assess nuclear signal, while accounting for lower staining in glial cells and myocytes (HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Ubiquitous nuclear staining (HPA tissue IHC) | |
| Staining pattern | Nuclear staining across many tissue cell types (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet M03639-1) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | None in HPA (detected in all 45 tissues); use no-primary + isotype controls |
| Fixation | Keep fixation consistent across sections. (standard IHC practice; not target-specific) | |
| Caveat | Glial cells and myocytes may stain weakly (HPA tissue IHC) | |
| Regulation | Low tissue specificity (HPA tissue RNA) | |
| Isoform / epitope | Two isoforms; epitope coverage is unspecified (UniProt; datasheets) |
Compare the catalog antibody’s IHC-P protocol (datasheet M03639-1) with three published U2AF2 IHC methods (PMC12924209; PMC7487667; PMC5033661).
| Sample | Paraffin-embedded human gallbladder adenocarcinoma tissue; fixative not specified (datasheet M03639-1) |
| Fixation | Image fixative and duration unreported (datasheet M03639-1); 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 M03639-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet M03639-1) |
| Primary antibody | Mouse monoclonal (clone 3G9) anti-U2AF2, 2μg/ml (datasheet M03639-1) |
| Primary incubation | Overnight at 4 °C (datasheet M03639-1) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet M03639-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | U2AF2-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. |
U2AF2 is a nuclear protein without a transmembrane segment (UniProt P26368: subcellular location and topology). In paraffin-section IHC, expect nuclear staining across many cell types, with high staining reported in colon glandular cells, kidney tubule cells and lymph-node germinal center cells (HPA: ubiquitous nuclear expression; High in those cells). HPA rates its tissue IHC profile Supported, with medium consistency between antibody staining and RNA expression (HPA: tissue IHC reliability).
| Clear nuclear chromogen in colon glandular cells or kidney tubule cells, with discernible nuclear boundaries. | This fits the reported compartment and high-staining cell populations (HPA: ubiquitous nuclear expression; High in colon glandular cells and kidney tubule cells). Compare intensity within the same run; a strong nucleus in one section is not an absolute intensity standard across preparations (general IHC practice). |
| Predominantly cytoplasmic or membranous signal, with little nuclear staining. | This conflicts with the expected nuclear distribution (UniProt P26368: Nucleus; HPA: ubiquitous nuclear expression). Review antibody specificity and staining controls before interpreting it as U2AF2; the supplied sources do not establish a cytoplasmic IHC pattern (HPA: tissue IHC profile). |
| Strong signal in skeletal myocytes, smooth muscle cells or breast adipocytes, especially when expected high-staining cells are weak. | HPA lists these populations as Low, not negative (HPA: Low in skeletal myocytes, smooth muscle cells and breast adipocytes). Unexpected dominance could reflect cross-reactivity or endogenous detection activity; inspect controls before assigning a cause (general IHC practice). |
| Chromogen appears broadly over tissue, including spaces between cells, so nuclei cannot be distinguished. | Diffuse background cannot establish the reported nuclear pattern (HPA: ubiquitous nuclear expression). Check the no-primary control, blocking and detection conditions; these checks assess general IHC background and do not identify a U2AF2-specific mechanism (general IHC practice). |
| Little or no nuclear signal in colon glandular cells while other staining controls perform as expected. | This is discordant with a reported high-staining population (HPA: High in colon glandular cells). Recheck the antibody's IHC-P instructions and run controls. A single negative section cannot establish absence of U2AF2, and HPA supplies no negative tissue reference (HPA: tissue IHC profile). |
| Compartment and tissue context (UniProt P26368: Nucleus; HPA: tissue IHC profile). | U2AF2 has no transmembrane segment (UniProt P26368: topology). Score nuclear signal in identifiable cells; HPA's ubiquitous nuclear profile makes a completely unstained tissue a poor assumed negative control (HPA: ubiquitous nuclear expression; no negative tissue listed). |
| Relative staining levels (HPA: tissue IHC profile). | HPA reports High staining in adrenal, colon, duodenal, epididymal, fallopian-tube and gallbladder glandular cells, kidney tubule cells, and lymph-node germinal center cells (HPA: High). Glial cells in hippocampus and caudate and several other listed populations are Low, not proven absent (HPA: Low). |
| Antibody evidence (HPA: antibody validation). | HPA043562 and CAB010910 are each listed as IHC Supported; HPA041943 has no IHC status in the supplied list (HPA: antibody validation). The tissue profile is Supported with medium RNA–staining consistency, so resolve conflicting slides with controls rather than treating the profile as absolute (HPA: tissue IHC reliability). |
| Isoforms and antibody recognition (UniProt P26368: isoforms and domains). | UniProt lists two isoforms and three RNA recognition motifs, at residues 149–231, 259–337 and 385–466 (UniProt P26368: isoforms; RRM domains). The payload does not map any listed antibody's epitope, so isoform coverage and epitope-specific interpretation remain undetermined (HPA: supplied antibody list). |
| Processing and modifications (UniProt P26368: processing and modified residues). | The supplied record lists no signal peptide or propeptide, a chain spanning residues 2–475, and several modified residues (UniProt P26368: processing; modified residues). It supplies no evidence that these features change paraffin-section staining or antigen retrieval; use the catalog antibody's IHC-P instructions for its workflow (general IHC practice). |
| IF/ICC question: what should fluorescence look like? (HPA: subcellular ICC-IF). | HPA supports nucleoplasmic and nuclear-speckle localization in ICC-IF and additionally lists a cytokinetic bridge (HPA: subcellular ICC-IF). That cellular detail informs interpretation, but does not establish a speckled pattern in chromogenic paraffin-section IHC (HPA: subcellular ICC-IF; tissue IHC profile). |
| Situation | Likely cause | Next action |
|---|---|---|
| The expected high-staining population lacks nuclear color (HPA: High in colon glandular cells). | Assay failure or weak detection is possible; HPA does not establish target-specific fixation sensitivity (HPA: tissue IHC profile; general IHC practice). | Check a reported high-staining control, the run's detection controls and the catalog antibody's IHC-P instructions before interpreting the section (HPA: High in colon glandular cells; general IHC practice). |
| Nuclei look weak, but the whole section has a light haze (HPA: expected nuclear profile). | Background may obscure true nuclear contrast; its source is not determined by the U2AF2 profile (HPA: tissue IHC profile; general IHC practice). | Inspect no-primary and detection controls; review blocking, washes and chromogen development under the established IHC workflow (general IHC practice). |
| Signal is mainly cytoplasmic or outlines cell borders (UniProt P26368: Nucleus). | The distribution disagrees with both UniProt nuclear localization and HPA nuclear tissue staining (UniProt P26368: Nucleus; HPA: ubiquitous nuclear expression). | Compare a reported high-staining tissue and a no-primary control; reassess specificity before scoring this signal as U2AF2 (HPA: High in colon glandular cells; general IHC practice). |
| Low-listed cells stain more strongly than nearby high-listed cells (HPA: tissue IHC levels). | Cross-reactivity or endogenous detection activity is possible, but this contrast alone does not prove either cause (HPA: Low and High populations; general IHC practice). | Check no-primary and detection controls, then compare nuclear localization and cell identity across the same section (HPA: ubiquitous nuclear expression; general IHC practice). |
| Different IHC runs give conflicting nuclear intensity (HPA: tissue IHC reliability). | Run variation is possible; HPA reports medium consistency between antibody staining and RNA expression, not an invariant intensity scale (HPA: tissue IHC reliability; general IHC practice). | Compare matched controls and scoring criteria across runs; follow the catalog antibody's IHC-P instructions for dilution and retrieval rather than inferring settings from HPA (general IHC practice). |
| A nucleus lacks visible speckles in paraffin-section IHC (HPA: ICC-IF nuclear speckles). | Speckles are supported in HPA ICC-IF; the supplied tissue IHC profile specifies ubiquitous nuclear expression without a speckle requirement (HPA: subcellular ICC-IF; tissue IHC profile). | Judge chromogenic IHC against nuclear localization in reported high-staining cells; consult the separate IF/ICC guide when assessing fluorescence detail (HPA: tissue IHC profile; subcellular ICC-IF). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — Medium 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.
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | High | Protein (IHC) | HPA → |
| Colon | Glandular cells | High | Protein (IHC) | HPA → |
| Duodenum | Glandular cells | High | Protein (IHC) | HPA → |
| Epididymis | Glandular cells | High | Protein (IHC) | HPA → |
| Fallopian tube | Glandular cells | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: U2AF2 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Troubleshoot U2AF2 staining in paraffin sections by checking retrieval, nuclear localisation, detection background, and compartment specific scoring.
Three anti-U2AF2 antibodies have paraffin-section IHC images (catalog IHC captions); each also lists IF/ICC and human, mouse, and rat reactivity (catalog applications/reactivity).
M03639-1 and M03639 each show IHC in human gallbladder adenocarcinoma paraffin sections (respective catalog IHC captions); both list IF/ICC (catalog applications). A03639-2 shows IHC in human mammary cancer and mouse and rat spleen paraffin sections (catalog IHC captions), plus IF in HeLa cells (catalog IF caption).
Which to pick: For tissue IHC, choose A03639-2 when cross-species image evidence matters: its own IHC captions show human mammary cancer and mouse and rat spleen paraffin sections (catalog IHC captions). For IF/ICC, A03639-2 has a HeLa cell IF image (catalog IF caption); M03639-1 and M03639 each have an A549 cell IF image and are mouse monoclonals (catalog IF captions; catalog clone/host). The IHC captions specify paraffin sections but do not report the fixative (catalog IHC captions).