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DCLK3 / Serine/threonine-protein kinase DCLK3 · IHC design guide
Design Immunohistochemistry for DCLK3
Plan chromogenic DCLK3 IHC on paraffin sections around the reported caudate axonal pattern (HPA tissue IHC). Interpret staining alongside the annotated cytoplasmic and nuclear localisation (UniProt), and keep fixation consistent across sections (standard IHC practice).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
DCLK3 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 | Caudate axons (HPA tissue IHC); cytoplasm and nucleus (UniProt) | |
| Staining pattern | Mainly caudate axons; Bergmann glia cytoplasm/membrane (HPA tissue IHC) | |
| Antigen retrieval | Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen) | |
| Positive control | Breast+4 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 paraffin sections. (standard IHC practice; not target-specific) | |
| Caveat | Caudate glia stain, but hippocampal glia were undetected (HPA tissue IHC) | |
| Regulation | Brain/testis tissue-enhanced RNA (HPA RNA specificity) | |
| Isoform / epitope | No annotated isoforms, signal peptide or propeptide (UniProt) |
Section 1
Recommended DCLK3 IHC & IF Protocols
The catalog antibody’s IHC-P protocol is paired with published DCLK3 staining protocols for macaque brain (PMC5917821) and colorectal cancer tumor sections (PMC13602744).
| Sample | Paraffin-embedded human brain tissue; fixative not specified (datasheet A15882) |
| Fixation | Image fixative and duration unreported (datasheet A15882); 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-DCLK3, 1:100-1:300 (datasheet A15882) |
| 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 | DCLK3-positive staining in myoepithelial cells of breast (HPA tissue IHC: Medium). HPA tissue profile: Expressed in several tissues, mainly expressed in axons in caudate. No signal in the no-primary control. |
💡Decision noteTry Tris-EDTA pH 9.0 retrieval at 95–98 °C for 20 min first (page retrieval rule: nuclear antigen; UniProt Q9C098: nucleus).
Section 2
What Is the Expected DCLK3 Staining Pattern?
In paraffin-section IHC, expect DCLK3 staining in several tissues, with axonal staining prominent in caudate and medium staining reported in caudate glial cells, cerebral cortex neuropil, and selected non-neural cells (HPA tissue IHC: Approved; pending external verification). DCLK3 is annotated in the cytoplasm and nucleus and has no transmembrane segment (UniProt Q9C098: subcellular location; topology). Assess compartment and cell identity together.
| Caudate shows axonal staining, with medium staining in glial cells; cerebral cortex neuropil also stains (HPA tissue IHC). | This fits the reported brain pattern (HPA tissue IHC). Score the structures and cells actually stained rather than treating every cell in the section as positive. An Approved IHC profile remains pending external verification (HPA tissue IHC: reliability); agreement with the reference pattern supports interpretation but does not establish specificity on its own. |
| Signal appears solely along cell surfaces or in extracellular spaces, without a plausible intracellular pattern. | Review this as a possible artifact: DCLK3 is annotated in the cytoplasm and nucleus and lacks a transmembrane segment (UniProt Q9C098: location; topology). A nuclear component alone cannot be rejected solely on compartment grounds because UniProt also lists the nucleus (UniProt Q9C098: location). Compare morphology and controls before assigning a compartment. |
| Strong staining is widespread in a cell population reported as undetected, such as adipocytes or cardiomyocytes (HPA tissue IHC). | Check for cross-reactivity or endogenous detection activity (general IHC practice). HPA reports DCLK3 as undetected in those specific cell populations, not necessarily throughout their tissues (HPA tissue IHC). A discrepant result warrants comparison with a no-primary control and an expected-positive section; it does not, by itself, identify the source of signal. |
| Brown chromogen broadly covers tissue and obscures cell boundaries or the expected axonal pattern. | Diffuse background makes localization unreliable (general chromogenic IHC practice). Evaluate the no-primary control, tissue pigment, and whether staining remains associated with recognizable cells or processes. The HPA caudate profile emphasizes axons and also reports medium glial staining (HPA tissue IHC); uniform haze cannot be scored as that pattern. |
| An expected-positive section has no interpretable signal, including in caudate axons or reported medium-positive cells (HPA tissue IHC). | First check assay performance with appropriate controls, reagent handling, and detection steps (general IHC practice). HPA reports expression across several tissues, but its IHC reliability is Approved and pending external verification (HPA tissue IHC). A blank section alone cannot distinguish assay failure from variation in the sampled tissue. |
💡Expected DCLK3 appearanceCall a section positive when staining resolves in the reported cells or processes—especially caudate axons, with medium staining reported in caudate glia or cerebral cortex neuropil (HPA tissue IHC)—and treat uniform haze or exclusively extracellular signal as suspect (general IHC interpretation; UniProt Q9C098: intracellular location).
| Tissue and cell selection | Brain and testis are tissue-enhanced at the RNA level (HPA tissue RNA). For protein IHC, HPA specifically reports caudate axons and medium staining in caudate glia, cerebral cortex neuropil, breast myoepithelial cells, kidney tubule cells, and other listed populations (HPA tissue IHC). RNA enrichment alone does not specify which cells will stain on a slide. |
| Compartment evidence | UniProt annotates cytoplasm and nucleus (UniProt Q9C098: location). HPA ICC-IF instead reports mainly cytosol plus vesicles (HPA subcellular: approved). Those ICC-IF observations can inform a compartment check, but they do not establish how vesicles or nuclei must appear in chromogenic paraffin-section IHC. |
| Protein topology and processing | DCLK3 has no transmembrane segment, signal peptide, or annotated propeptide; UniProt lists one chain spanning residues 1–648 (UniProt Q9C098: topology; processing). This supports caution with a purely surface or secreted-looking pattern. The record does not provide an antibody epitope or target-specific retrieval behavior. |
| Antibody validation scope | HPA040685 is listed as IHC Approved, while HPA053234 is listed as ICC Approved without an IHC status in this payload (HPA antibodies). The tissue IHC profile is Approved but pending external verification (HPA tissue IHC: reliability). Do not transfer the ICC antibody's status to paraffin-section IHC. |
| Reported absence and low staining | HPA lists adipocytes, cardiomyocytes, and several other specified populations as not detected, while lung macrophages and several glandular or epithelial populations are low (HPA tissue IHC). Use the named cell population when comparing sections. A low or undetected reference result is less useful for diagnosing a failed assay than a reported medium-positive population. |
| Situation | Likely cause | Next action |
|---|---|---|
| Caudate lacks the reported axonal staining (HPA tissue IHC). | Possible assay failure, sampling difference, or weak signal; the image pattern alone cannot separate these causes (general IHC practice). | Check a reported medium-positive population in the same run and review primary-antibody, detection, and counterstain records (general IHC practice). If changing retrieval conditions, treat that as routine assay optimization; no DCLK3-specific fixation or retrieval effect is supplied. |
| Only sharp nuclear staining is visible. | Nuclear location is annotated, but the supplied HPA tissue pattern does not establish nuclear-only IHC as the expected result (UniProt Q9C098: location; HPA tissue IHC). | Compare with caudate axons and other reported positive cells, then check control sections (HPA tissue IHC; general IHC practice). Avoid calling nuclei inherently wrong: UniProt lists the nucleus (UniProt Q9C098: location). |
| Adipocytes or cardiomyocytes stain strongly and widely (HPA tissue IHC: not detected). | Cross-reactivity or endogenous detection activity is possible (general IHC practice); disagreement with HPA does not identify which occurred. | Compare an adjacent no-primary control and the expected-positive section; score the named cell population separately from surrounding tissue (general IHC practice; HPA tissue IHC). |
| Diffuse chromogen makes cell types and processes hard to distinguish. | Background deposition, tissue pigment, or endogenous activity can obscure specific staining (general chromogenic IHC practice). | Inspect the no-primary control and unstained tissue appearance, then review blocking and detection conditions (general IHC practice). Score DCLK3 only where the pattern remains anatomically interpretable against the HPA tissue reference. |
| Punctate intracellular staining is treated as proof of a positive paraffin section. | HPA reports vesicles in ICC-IF, while its tissue IHC summary emphasizes caudate axons (HPA subcellular; HPA tissue IHC). | Evaluate puncta alongside cell identity, tissue morphology, and IHC controls (general IHC practice). ICC-IF localization is supporting context, not a required chromogenic IHC pattern. |
| Can the ICC-IF images define the expected IHC result? | HPA reports cytosol and vesicles in ICC-IF, and lists ICC approval for HPA053234; its listed IHC approval belongs to HPA040685 (HPA subcellular; HPA antibodies). | Use the HPA tissue IHC profile to judge paraffin-section staining. Consult the separate IF/ICC guide for fluorescence interpretation; do not infer an IHC protocol or interchangeable antibody validation from the ICC-IF images. |
Experiment evidence
IHC & IF images showing DCLK3 staining
A15882 · IHCImmunohistochemistry analysis of paraffin-embedded human brain, using DCLK3 Antibody. The picture on the right is blocked with the synthesiz
A15882-1 · IHCImmunohistochemistry of DCLK3 in mouse brain tissue with DCLK3 Antibody at 5 μg/mL.
A15882-1 · IFImmunofluorescence of DLCK3 in human brain tissue with DLCK3 antibody at 20 μg/mL.
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000163673-DCLK3/tissue/cerebral+cortex#imid_20396189
HPA · CaudateHuman Protein Atlas IHC, Caudate. Source: https://www.proteinatlas.org/ENSG00000163673-DCLK3/tissue/basal+ganglia#imid_1102
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000163673-DCLK3/tissue/colon#imid_20396099
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000163673-DCLK3/tissue/liver#imid_20396116
HPA · ICC-IF JURKATHuman Protein Atlas immunofluorescence, JURKAT, antibody HPA053234; green = DCLK3, blue = nucleus, red = microtubules.
HPA · ICC-IF JURKATHuman Protein Atlas immunofluorescence, JURKAT, antibody HPA053234; green = DCLK3, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for DCLK3 IHC & IF
🧪Run breast first and score staining in myoepithelial cells (HPA: Medium in breast myoepithelial cells). Use adipose tissue as the negative comparator, scoring adipocytes (HPA: Not detected in adipocytes); on the breast slide, other cells should show background-level staining when used as internal negatives, but their DCLK3 status is unconfirmed (HPA: breast result specifies myoepithelial cells).
Positive control tissue: Breast (Myoepithelial cells, HPA Medium)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show DCLK3 in JURKAT, SH-SY5Y, U2OS, with annotated localisation: Cytosol (approved) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control and an isotype control matched to the primary antibody’s host species and clonality (standard IHC practice); use peptide blocking as a biological specificity check because the catalog antibody’s brain paraffin-section image includes a peptide-blocked comparison (A15882 caption). Check endogenous peroxidase background before chromogenic detection in breast tissue (standard IHC practice).
⚠️Feasibility: A DCLK3-specific fixation window and the effect of fixation are unreported, and the selected paraffin-section caption does not state a fixative (A15882 caption). Antigen retrieval requirements and whether frozen sections or IF are easier are unreported in the supplied evidence; assess retrieval conditions empirically for IHC-P (A15882 caption: paraffin section). When scoring breast ducts, distinguish staining in the thin myoepithelial layer from adjacent cell staining or chromogen background (HPA: Medium in breast myoepithelial cells; standard IHC practice).
HPA tissue IHC evidence for DCLK3
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — 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 |
|---|---|---|---|---|
| Breast | Myoepithelial cells | Medium | Protein (IHC) | HPA → |
| Caudate | Glial cells | Medium | Protein (IHC) | HPA → |
| Cerebellum | Bergmann glia - cytoplasm/membrane | Medium | Protein (IHC) | HPA → |
| Cerebral cortex | Neuropil | Medium | Protein (IHC) | HPA → |
| Kidney | Cells in tubules | Medium | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Colon | Endothelial cells | Not detected | Protein (IHC) | HPA → |
| Endometrium | Cells in endometrial stroma | Not detected | Protein (IHC) | HPA → |
| Esophagus | Squamous epithelial cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced DCLK3 IHC Tips
Troubleshoot DCLK3 staining in paraffin sections by checking retrieval, controls, cellular location, and scoring before interpreting chromogenic signal.
What should I change if DCLK3 staining is weak after retrieval?
Start with Tris-EDTA at pH 9.0 for heat-induced retrieval at 95–98 °C for 20 min (page retrieval setting). If staining remains weak, compare a milder retrieval condition on adjacent sections while holding antibody concentration and detection constant; excessive heating can damage morphology and obscure cell boundaries (standard IHC practice). Record heating and cooling conditions, then assess signal in the catalog antibody’s paraffin-embedded human brain preparation alongside its peptide-blocked control (caption: A15882). Because DCLK3 is annotated in both cytoplasm and nucleus, inspect each compartment rather than treating weak nuclear staining alone as retrieval failure (UniProt Q9C098: subcellular locations).
How can I troubleshoot variable DCLK3 staining between paraffin blocks?
The selected A15882 image documents paraffin-embedded human brain but does not state its fixative, so DCLK3-specific fixation sensitivity is unknown (caption: A15882). Compare blocks with documented fixation and processing histories, and run them together with the same retrieval, antibody incubation, and chromogenic development conditions (standard IHC practice). Use adjacent sections to judge tissue preservation, especially whether cell boundaries and nuclei remain interpretable after retrieval (standard IHC practice). If a block is faint, check a positive control processed with that block before assigning the difference to DCLK3 expression; the image caption cannot establish how this antigen responds to any particular fixative (caption: A15882).
Does DCLK3 staining in both nuclei and cytoplasm make sense?
Yes: DCLK3 is annotated in cytoplasm and nucleus, so assess both compartments in each morphologically identified cell population (UniProt Q9C098: subcellular locations). HPA reports mainly cytosolic localisation with an additional vesicular signal in its subcellular dataset, while its tissue profile describes prominent axonal expression in caudate (HPA: subcellular; HPA: tissue profile). In chromogenic sections, compare nuclear, somatic, and process staining against the peptide-blocked A15882 image and a reagent control developed in parallel (caption: A15882; standard IHC practice). Diffuse colour across every compartment or concentrated at damaged section edges warrants a background check before calling it a DCLK3 localisation pattern (standard IHC practice).
How should epitope uncertainty affect interpretation of DCLK3 staining?
The supplied record lists a 648-amino-acid DCLK3 chain, a kinase domain at residues 356–613, and no annotated isoforms (UniProt Q9C098: processing, domains, isoforms). It gives no antibody epitope position, so do not claim that a nuclear or cytoplasmic signal represents a particular domain or splice form (record: epitope unspecified; UniProt Q9C098: subcellular locations). The A15882 caption reports that a synthesized peptide blocks staining in paraffin-embedded human brain, providing an antibody-binding control for that image (caption: A15882). Review the antibody’s documented immunogen before comparing staining across preparations, and pair peptide blocking with tissue morphology and reagent controls when judging specificity (standard IHC practice).
How can I follow up a chromogenic DCLK3 result with multiplex IF?
Treat multiplex IF as a separate assay: choose a marker for the cell population being assessed, such as a glial marker when following up the reported caudate glial signal (HPA: caudate glial cells; standard IF practice). Select a DCLK3 fluorophore in a channel with low measured tissue autofluorescence, and include unstained and single-label controls to evaluate bleed-through (standard IF practice). DCLK3 has no annotated transmembrane segment and is assigned to cytoplasm and nucleus, so optimise permeabilisation for intracellular access while preserving morphology (UniProt Q9C098: topology and subcellular locations; standard IF practice). HPA’s approved cytosolic and additional vesicular observations offer a localisation comparison, but they do not validate this catalog antibody for IF (HPA: subcellular; caption: A15882).
What explains widespread brown signal outside plausible DCLK3-positive structures?
First inspect the no-primary control, endogenous peroxidase block, and DAB development time; these are general chromogenic IHC checks rather than DCLK3-specific evidence (standard IHC practice). Compare signal in intact structures with colour at folds, cut edges, and necrotic areas, where staining can be misleading (standard IHC practice). DCLK3 is annotated in cytoplasm and nucleus, and HPA describes axonal enrichment in caudate, so a uniform extracellular coating deserves particular scrutiny (UniProt Q9C098: subcellular locations; HPA: tissue profile). If background persists, adjust blocking, washes, and antibody concentration one variable at a time, retaining the A15882 peptide-blocked preparation as a relevant binding control (standard IHC practice; caption: A15882).
What should I score when comparing DCLK3 across paraffin sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the compartment and cell population before scoring: HPA reports medium staining in caudate glial cells and cerebellar Bergmann glia, with prominent axonal expression in caudate (HPA: tissue IHC and profile). For identifiable cells, record percentage positive and staining intensity with a consistent H-score rule; for process-rich regions, measure positive area or labelled profiles per mm² (standard IHC quantification practice). Normalise cell scores to eligible cells and process measurements to analysed tissue area, excluding folds, tears, and necrosis by a prespecified rule (standard IHC quantification practice). Keep retrieval, imaging, threshold, and DAB development consistent across compared sections, and report nuclear and cytoplasmic scores separately when both are present (standard IHC quantification practice; UniProt Q9C098: subcellular locations).
When is a DCLK3-positive IHC pattern convincing rather than artefactual?
A convincing call combines preserved morphology, plausible cytoplasmic or nuclear staining, and a reproducible pattern in the cell population under study (UniProt Q9C098: subcellular locations; standard IHC practice). Compare the finding with HPA’s caudate axonal profile and reported medium signals in caudate glia or cerebellar Bergmann glia, without treating those patterns as universal requirements (HPA: tissue profile and IHC). Check whether staining disappears in the A15882 peptide-blocked human brain image and whether no-primary and peroxidase controls remain clean in your run (caption: A15882; standard IHC practice). Treat staining confined to section edges, necrosis, or an implausible compartment as provisional until repeat sections and controls resolve it (standard IHC practice).
Boster reagents
Best DCLK3 / Serine/threonine-protein kinase DCLK3 IHC Antibodies
Two anti-DCLK3 antibodies have IHC images from human or mouse brain; one also has IF images from both species (catalog: image captions).
Real IHC data
Anti-DCAMKL3 DCLK3 Antibody
Cat # A15882
Real IHC data
Anti-DCLK3 Antibody
Cat # A15882-1
A15882 has IHC data from paraffin-embedded human brain and lists human and mouse reactivity (catalog: IHC image caption and reactivity). A15882-1 has IHC data from mouse brain and IF data from human and mouse brain (catalog: IHC and IF image captions).
Which to pick: For paraffin-section IHC, choose A15882 when a human-brain example is most relevant; its caption does not report the fixative (catalog: A15882 IHC image caption). For tissue IF, choose A15882-1 because it has images from both species; ICC is listed under neither product's applications (catalog: A15882-1 IF image captions; both application lists). Both list human and mouse reactivity, so use the specimen-matched images to guide a cross-species choice; both are rabbit antibodies, and clone status is unreported (catalog: reactivity, host, clone fields).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q9C098 (DCLK3_HUMAN, Serine/threonine-protein kinase DCLK3).
- Human Protein Atlas. DCLK3 tissue IHC expression (reliability: Approved).
- Human Protein Atlas. DCLK3 subcellular location (ICC-IF): Mainly localized to the cytosol. In addition localized to vesicles..
- Human Protein Atlas. DCLK3 antibody validation summary (2 antibodies).
- The striatal kinase DCLK3 produces neuroprotection against mutant huntingtin. Brain : a journal of neurology 2018 — PMC5917821.
- Uncovering the mechanism of DCLK3 in colorectal cancer progression through WGCNA and machine learning. BMC cancer 2026 — PMC13602744.
- Deciphering the unique autoregulatory mechanisms and substrate specificity of the understudied DCLK3 kinase linked to neurodegenerative diseases. The Journal of biological chemistry 2025 — PMC12509982.
- PubMed PMID:11214970 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:17344846 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for DCLK3 (Serine/threonine-protein kinase DCLK3). Expected localisation Caudate axons (HPA tissue IHC); cytoplasm and nucleus (UniProt). Antigen retrieval: Tris-EDTA pH 9.0 HIER, 95–98 °C, 20 min (rule: nuclear antigen). Validated IHC antibody: A15882 at 1:100-1:300 (the product's own IHC validation image is shown). Controls (HPA): positive Breast (Myoepithelial cells); negative Adipose tissue. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Paraffin-embedded human brain tissue; fixative not specified (datasheet A15882); 2. Fixation: Image fixative and duration unreported (datasheet A15882); 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-DCLK3, 1:100-1:300 (datasheet A15882); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across paraffin sections. (standard IHC practice; not target-specific); Caveat: Caudate glia stain, but hippocampal glia were undetected (HPA tissue IHC); Isoform / epitope: No annotated isoforms, signal peptide or propeptide (UniProt); Regulation: Brain/testis tissue-enhanced RNA (HPA RNA specificity). Evidence: UniProt Q9C098, HPA tissue IHC · Approved, HPA ICC-IF · Mainly localized to the cytosol. In addition localized to vesicles., Datasheet A15882, PMC5917821, PMC13602744. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/DCLK3/immunohistochemistry-ihc-guide.