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COPS5 / COP9 signalosome complex subunit 5 · IHC design guide
Design Immunohistochemistry for COPS5
Plan chromogenic COPS5 IHC in paraffin sections around nuclear and cytoplasmic staining (HPA tissue IHC). Score the compartments separately because IFIT3 can diminish nuclear localisation (UniProt).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
COPS5 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 across tissues (HPA tissue IHC) | |
| Staining pattern | Cells across tissues show nuclear and cytoplasmic signal (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet M01849-2) | |
| Positive control | Adipose tissue+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 sections (standard IHC practice; not target-specific) | |
| Caveat | IFIT3 can diminish nuclear localisation (UniProt) | |
| Regulation | Expression regulation not specified (UniProt) | |
| Isoform / epitope | 0 annotated isoforms; no extracellular domain to map (UniProt) |
Section 1
Recommended COPS5 IHC & IF Protocols
Compare the catalog antibody's IHC-P protocol (datasheet M01849-2) with four published COPS5 IHC methods for paraffin-embedded tissues (PMC4932188; PMC5945527; PMC5722579; PMC5777718).
| Sample | Paraffin-embedded human esophageal squamous carcinoma tissue; fixative not specified (datasheet M01849-2) |
| Fixation | Image fixative and duration unreported (datasheet M01849-2); 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 M01849-2); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet M01849-2) |
| Primary antibody | Mouse monoclonal (clone 4G9) anti-COPS5, 2μg/ml (datasheet M01849-2) |
| Primary incubation | Overnight at 4 °C (datasheet M01849-2) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet M01849-2) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | COPS5-positive staining in adipocytes of adipose tissue (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic and nuclear expression in all tissues. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval for the catalog antibody (datasheet M01849-2). Published protocols using other antibodies specify citrate pH 6.0 or BOND ER1 (PMC5722579; PMC5777718; PMC5945527).
Section 2
What Is the Expected COPS5 Staining Pattern?
COPS5 is expected in the nucleus and cytoplasm, including the perinuclear region (UniProt Q92905). HPA reports cytoplasmic and nuclear IHC staining across tissues, with high staining in several listed cell populations; its tissue IHC assessment is Supported, with medium consistency between staining and RNA expression (HPA tissue IHC). COPS5 has no transmembrane segment (UniProt Q92905 topology).
| Nuclear and cytoplasmic staining appears in the expected cells of a reference section. | This fits the reported tissue IHC pattern (HPA tissue IHC) and COPS5 localisation (UniProt Q92905). Compare cells and compartments with the reference; a single positive area alone does not establish antibody specificity. |
| Staining is confined to cell membranes or extracellular material, with little nuclear or cytoplasmic signal. | Treat a predominantly membranous or extracellular pattern as suspect: COPS5 has no transmembrane segment, and its reported locations are intracellular (UniProt Q92905 topology and subcellular location). Inspect morphology and detection controls before interpreting it as COPS5. |
| Strong staining appears chiefly in an unexpected cell population within a reference tissue. | Check cell identity against the HPA cell-level pattern; examples of high staining include adipocytes in adipose tissue and hematopoietic cells in bone marrow (HPA tissue IHC). Unexpected staining can reflect cross-reactivity or endogenous detection activity (general IHC practice). |
| Diffuse color covers tissue spaces, obscures cell boundaries, or is similar in many structures. | This prevents a reliable compartment call. Consider nonspecific antibody binding, endogenous detection activity, or excessive chromogen development (general IHC practice). The expected signal should be attributable to nuclei and/or cytoplasm (HPA tissue IHC; UniProt Q92905). |
| A reference section shows no convincing signal in cells reported as strongly positive. | A negative result in, for example, adrenal glandular cells or bronchial respiratory epithelial cells conflicts with their high HPA staining (HPA tissue IHC). Check section integrity, detection controls, and the validated IHC workflow before concluding that COPS5 is absent. |
💡Expected COPS5 appearanceCall a section positive when identifiable cells show nuclear and cytoplasmic chromogen, with high staining in the selected HPA reference population; isolated membrane or extracellular color is suspect (HPA tissue IHC; UniProt Q92905 topology).
| Which tissue and cells provide a reference? | HPA lists high staining in adipocytes, adrenal and breast glandular cells, bronchial respiratory epithelial cells, bone marrow hematopoietic cells, caudate glia, and cerebellar granular-layer cells (HPA tissue IHC). Use the corresponding cell population when judging a section. |
| How broadly should staining be expected? | HPA describes cytoplasmic and nuclear expression across tissues and low RNA tissue specificity (HPA tissue IHC). Its supplied record lists no negative tissue reference; lack of staining in an unlisted population is therefore not a validated negative control. |
| How much weight should the IHC pattern carry? | The tissue IHC assessment is Supported and reports medium agreement with RNA expression (HPA tissue IHC). HPA004845 and CAB004242 have Supported IHC status, while no IHC status is supplied for HPA051531 (HPA antibodies). Interpret borderline staining with controls and morphology. |
| Does processing or topology predict surface staining? | UniProt reports no signal peptide, propeptide, transmembrane segment, or glycosylation sites for COPS5 (UniProt Q92905). These annotations support an intracellular interpretation; they do not establish tissue-specific staining strength or a fixation effect. |
| What should IF/ICC show? | HPA reports enhanced nucleoplasmic localisation in ICC-IF images from A-431, K-562, and U2OS (HPA subcellular ICC-IF). UniProt also lists cytosolic and perinuclear locations (UniProt Q92905). Compare IF localisation with its own controls; this ICC-IF observation is not an IHC staining intensity standard. |
| Situation | Likely cause | Next action |
|---|---|---|
| A listed high-staining reference population is blank. | The assay may have failed; absence conflicts with the reported high reference staining (HPA tissue IHC). | Confirm the intended cells are present, then check the IHC-validated antibody, antigen retrieval, detection reagents, and a working positive control (general IHC practice). |
| Signal appears only along cell borders. | A border-only pattern does not match reported nuclear and cytoplasmic COPS5 localisation (HPA tissue IHC; UniProt Q92905). | Inspect an adjacent section and detection controls for nonspecific edge or membrane staining; score intracellular signal only when cell boundaries and compartments are clear (general IHC practice). |
| Chromogen is widespread in cell-free areas. | Diffuse deposition may arise from nonspecific binding or detection background (general IHC practice). | Review the no-primary control, blocking, washes, antibody concentration, and chromogen development (general IHC practice); reassess localisation after background is reduced. |
| A cell population looks positive despite a discordant reference pattern. | Cross-reactivity or endogenous detection activity is possible (general IHC practice); HPA's tissue assessment has medium RNA agreement (HPA tissue IHC). | Verify morphology and compare an appropriate no-primary or detection control; avoid assigning COPS5 from color alone (general IHC practice). |
| Nuclear staining is present but cytoplasmic staining is faint. | Nuclear enrichment can be compatible with the HPA ICC-IF nucleoplasm result; tissue IHC reports both compartments (HPA subcellular ICC-IF; HPA tissue IHC). | Assess the sampled cell type and control section before calling a compartment absent; record nuclear and cytoplasmic staining separately (general IHC practice). |
| Nuclei and cytoplasm are too dark to distinguish. | Overdeveloped chromogen or concentrated antibody can obscure localisation (general IHC practice). | Use the IHC-validated antibody's documented conditions as a starting point, then adjust concentration or development within the assay workflow and retain a positive control (general IHC practice). |
Experiment evidence
IHC & IF images showing COPS5 staining
M01849-2 · IHCIHC analysis of JAB1 using anti-JAB1 antibody (M01849-2). JAB1 was detected in paraffin-embedded section of human esophageal squamous carcin
M01849-2 · IHCIHC analysis of JAB1 using anti-JAB1 antibody (M01849-2). JAB1 was detected in paraffin-embedded section of human liver cancer tissue. Heat
M01849-2 · IFIF analysis of JAB1 using anti-JAB1 antibody (M01849-2). JAB1 was detected in immunocytochemical section of T-47D cells. Enzyme antigen retr
PB9490 · IHCIHC analysis of JAB1 using anti-JAB1 antibody (PB9490). JAB1 was detected in a paraffin-embedded section of human mammary cancer tissue. Hea
PB9490 · IHCIHC analysis of JAB1 using anti-JAB1 antibody (PB9490). JAB1 was detected in a paraffin-embedded section of mouse testis tissue. Heat mediat
PB9490 · IFICC analysis of JAB1 using anti-JAB1 antibody (PB9490). JAB1 was detected in immunocytochemical section of A431 cell. Enzyme antigen retriev
M01849 · IHCFigure 5. IHC analysis of JAB1/COPS5 using anti-JAB1/COPS5 antibody (M01849). JAB1/COPS5 was detected in a paraffin-embedded section of huma
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000121022-COPS5/tissue/cerebral+cortex#imid_1950900
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000121022-COPS5/tissue/colon#imid_1950842
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000121022-COPS5/tissue/liver#imid_1950843
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000121022-COPS5/tissue/kidney#imid_1950836
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA004845; green = COPS5, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA004845; green = COPS5, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for COPS5 IHC & IF
🧪Start with breast tissue: glandular cells should stain strongly (HPA: High in breast glandular cells). HPA detects COPS5 in all 45 scored tissues, so there is no listed negative tissue; use no-primary and isotype controls, and treat cells without visible staining on the positive slide as background references rather than confirmed COPS5-negative cells (HPA: no negative rows; detected in all 45 scored tissues).
Positive control tissue: Adipose tissue (Adipocytes, HPA High)
Negative control tissue: None in HPA: COPS5 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 COPS5 in A-431, K-562, U2OS, with annotated localisation: Nucleoplasm (enhanced) (HPA subcellular).
Technical controls: Run a secondary-only slide and a concentration-matched mouse IgG isotype control, plus a COPS5 knockout specimen if available (selected-SKU tissue-IHC caption: mouse primary antibody; standard IHC practice). For chromogenic detection, block endogenous peroxidase and check endogenous biotin background before using the caption’s biotinylated secondary and SABC–DAB system (selected-SKU tissue-IHC caption; standard IHC practice).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported, and the selected M01849-2 paraffin-section caption does not state the fixative (selected-SKU tissue-IHC caption). That caption uses heat retrieval in EDTA at pH 8.0, so use it as the initial IHC-P retrieval condition and assess background from the biotin-based detection system (selected-SKU tissue-IHC caption; standard IHC practice). IF/ICC offers a nucleoplasmic localization readout in A-431, K-562 and U2OS cells, but the supplied evidence does not establish that IF or frozen sections are easier than IHC-P (HPA: enhanced nucleoplasmic localization and ICC-IF image cell lines).
HPA tissue IHC evidence for COPS5
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.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | High | Protein (IHC) | HPA → |
| 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 → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: COPS5 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Section 3
Advanced COPS5 IHC Tips
Troubleshoot COPS5 staining in paraffin sections by checking retrieval, compartment patterns, controls and scoring before interpreting differences between specimens.
What retrieval should I try when COPS5 staining is weak in paraffin sections?
Start with heat-mediated retrieval in EDTA pH 8.0 for this catalog antibody (datasheet M01849-2). The selected paraffin-section example used that retrieval, followed by 10% goat serum blocking and 2 μg/ml primary antibody overnight at 4°C (datasheet M01849-2). If staining remains weak, compare a slightly shorter and longer heating interval on adjacent sections while keeping buffer, antibody concentration and detection constant (standard IHC practice). Judge recovery by cellular nuclear and cytoplasmic signal together with preservation of tissue morphology; excessive heat can damage sections and make an apparent gain in staining misleading (HPA: cytoplasmic and nuclear tissue expression; standard IHC practice).
Could fixation explain weak or uneven COPS5 staining?
The selected paraffin-section caption does not report its fixative, so target-specific fixation sensitivity cannot be determined from this example (datasheet M01849-2). Record each specimen’s fixative, fixation duration and processing history, then compare sections prepared under matched conditions before attributing staining differences to COPS5 abundance (standard IHC practice). For the catalog antibody, hold EDTA pH 8.0 retrieval and the 2 μg/ml overnight primary incubation constant while examining fixation effects (datasheet M01849-2; standard IHC practice). Check nuclear detail and section integrity alongside signal intensity, because poor preservation can make compartment scoring unreliable even when chromogen is visible (standard IHC practice).
Should COPS5 appear in nuclei, cytoplasm, or both?
Expect both nuclear and cytoplasmic staining in tissue: the tissue profile reports expression in both compartments across tissues (HPA: tissue IHC profile). Cytosolic, perinuclear and nuclear locations are annotated, while enhanced nucleoplasmic localisation appears in cell imaging (UniProt Q92905 subcellular location; HPA: subcellular localisation). Score nuclei and cytoplasm separately in intact cells, using the same counterstain threshold and compartment definitions across specimens (standard IHC practice). A change in nuclear signal may be biologically relevant because nuclear localisation diminishes in the presence of IFIT3, but a staining shift alone cannot establish that mechanism (UniProt Q92905 subcellular location; standard IHC interpretation).
How should I investigate an unexpected COPS5 staining pattern without epitope details?
The supplied record lists 0 isoforms, an MPN domain at residues 55–192, no transmembrane segment and no annotated glycosylation sites (UniProt Q92905 record). Those features do not locate this antibody’s epitope or establish how processing exposes it in paraffin sections (UniProt Q92905 record; standard IHC interpretation). Check the catalog antibody’s documented immunogen or epitope before making domain-specific claims, and compare staining across retrieval conditions using identical detection settings (standard IHC practice). If staining disagrees with the expected nuclear and cytoplasmic distribution, investigate specificity with an independent antibody or a suitable loss-of-target control before invoking an undocumented isoform (HPA: tissue IHC profile; standard IHC practice).
How can I adapt the COPS5 localisation question to multiplex IF?
Use a cell-type marker appropriate to the tissue being studied so COPS5 signal can be assigned to the intended cells rather than nearby populations (standard IF practice). Select fluorophores after checking tissue autofluorescence, and place the weaker signal in a channel with good separation from that background (standard IF practice). Because COPS5 has no transmembrane segment and is annotated in cytosol and nucleus, permeabilisation should allow antibody access to intracellular epitopes; optimise its strength against cell morphology and nuclear retention (UniProt Q92905 topology and subcellular location; standard IF practice). Assess nuclear and cytoplasmic signal separately, with single-channel controls for bleed-through, before comparing IF localisation with chromogenic IHC (HPA: tissue IHC profile; standard IF practice).
What should I check when COPS5 DAB staining looks diffuse or nonspecific?
First compare the stained section with a no-primary control to identify signal arising from the detection system rather than primary-antibody binding (standard IHC practice). The selected example used 10% goat serum blocking, a biotinylated secondary antibody, streptavidin–biotin detection and DAB, so background should be assessed within that detection workflow (datasheet M01849-2). Check peroxidase blocking, endogenous biotin where relevant, washing and chromogen development on matched sections; these are general IHC controls, not demonstrated COPS5-specific effects (standard IHC practice). Diffuse extracellular colour or signal concentrated at tissue edges should be questioned against the expected cellular nuclear and cytoplasmic pattern before changing the primary concentration (HPA: tissue IHC profile; standard IHC practice).
How should I score COPS5 staining across paraffin-section samples? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and tissue region before scoring, then measure nuclear and cytoplasmic staining separately because both compartments are expected (HPA: tissue IHC profile; standard IHC practice). For a chromogenic series, report the percentage of positive cells and an H-score based on the same intensity categories and positivity threshold for every section (standard IHC practice). Normalise counts to eligible intact cells, or express positive-cell counts per mm² of viable tissue when comparing areas of different sizes (standard IHC practice). Keep retrieval, primary incubation and DAB development consistent, and review slides without relying on colour intensity alone to infer changes in COPS5 activity (datasheet M01849-2; UniProt Q92905 function; standard IHC practice).
How can I distinguish genuine COPS5 staining from tissue or detection artefacts?
A credible pattern places signal within intact nuclei, cytoplasm or both, consistent with the reported tissue distribution and cellular locations of COPS5 (HPA: tissue IHC profile; UniProt Q92905 subcellular location). Confirm which cells are stained using the counterstain and tissue morphology, since the tissue profile describes broad expression rather than a unique diagnostic cell type (HPA: tissue IHC profile; standard IHC practice). Discount edge-concentrated staining, necrotic areas and no-primary-control signal, and check endogenous enzyme activity when interpreting DAB deposits (standard IHC practice). Finally, treat a nuclear-to-cytoplasmic difference as a localisation observation; staining alone does not prove IFIT3 involvement or COP9 signalosome catalytic activity (UniProt Q92905 subcellular location and function; standard IHC interpretation).
Boster reagents
Best COPS5 / COP9 signalosome complex subunit 5 IHC Antibodies
The catalog shows COPS5 staining in human paraffin sections and human cells, with additional mouse and rat tissue IHC images (catalog image captions).
Real IHC data
Anti-JAB1 Antibody ® (monoclonal, 4G9)
Cat # M01849-2
Real IHC data
Anti-JAB1/COPS5 Antibody ®
Cat # PB9490
Real IHC data
Anti-JAB1 Monoclonal Antibody
Cat # M01849
M01849-2 has a human esophageal squamous carcinoma paraffin IHC image and a T-47D IF image (catalog image captions); M01849 has a human breast cancer paraffin IHC image (catalog image caption). PB9490 has paraffin IHC images from human mammary cancer, mouse testis and rat testis, plus a chromogenic A431 ICC image (catalog image captions).
Which to pick: For tissue IHC, M01849-2 is a mouse monoclonal used at 2 μg/ml in its paraffin image, while M01849 is a rabbit monoclonal used at 1:50 in its paraffin image (catalog metadata and image captions). For IF/ICC, M01849-2 has a T-47D fluorescence image; M01849 lists IF/ICC applications, while PB9490 lists IF/ICC but its A431 image uses chromogenic detection (catalog applications and image captions). For cross-species tissue work, PB9490 has human, mouse and rat paraffin IHC images (catalog image captions); the fixative is unreported in these captions (catalog image captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q92905 (CSN5_HUMAN, COP9 signalosome complex subunit 5).
- Human Protein Atlas. COPS5 tissue IHC expression (reliability: Supported).
- Human Protein Atlas. COPS5 subcellular location (ICC-IF): Localized to the nucleoplasm..
- Human Protein Atlas. COPS5 antibody validation summary (3 antibodies).
- COPS5 amplification and overexpression confers tamoxifen-resistance in ERα-positive breast cancer by degradation of NCoR. Nature communications 2016 — PMC4932188.
- COP9 signalosome subunit 5 regulates cancer metastasis by deubiquitinating SNAIL. Oncotarget 2018 — PMC5945527.
- Increased Jab1/COPS5 is associated with therapeutic response and adverse outcome in lung cancer and breast cancer patients. Oncotarget 2017 — PMC5722579.
- Analysis of differential gene expression profile identifies novel biomarkers for breast cancer. Oncotarget 2017 — PMC5777718.
- PubMed PMID:8837781 — UniProt-cited evidence.
- PubMed PMID:9341143 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for COPS5 (COP9 signalosome complex subunit 5). Expected localisation Nuclear and cytoplasmic staining across tissues (HPA tissue IHC). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet M01849-2). Validated IHC antibody: M01849-2 at 2μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Adipose tissue (Adipocytes); 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 esophageal squamous carcinoma tissue; fixative not specified (datasheet M01849-2); 2. Fixation: Image fixative and duration unreported (datasheet M01849-2); 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 M01849-2); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet M01849-2); 8. Primary antibody: Mouse monoclonal (clone 4G9) anti-COPS5, 2μg/ml (datasheet M01849-2); 9. Primary incubation: Overnight at 4 °C (datasheet M01849-2). Watch for: Fixation: Keep fixation consistent across sections (standard IHC practice; not target-specific); Caveat: IFIT3 can diminish nuclear localisation (UniProt); Isoform / epitope: 0 annotated isoforms; no extracellular domain to map (UniProt); Regulation: Expression regulation not specified (UniProt). Evidence: UniProt Q92905, HPA tissue IHC · Supported, HPA ICC-IF · nucleoplasm., Datasheet M01849-2, PMC4932188, PMC5945527. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/COPS5/immunohistochemistry-ihc-guide.