COL4A3 / Collagen alpha-3(IV) chain · IHC design guide

Design Immunohistochemistry for COL4A3

Plan paraffin section IHC for COL4A3 using its extracellular basement membrane location (UniProt) and observed cytoplasmic and extracellular tissue staining (HPA tissue IHC). Compare tissue controls and interpret staining with the protein’s secreted location in mind (UniProt).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for COL4A3 (IHC for COL4A3): expected localisation Extracellular basement membrane (UniProt); cytoplasmic tissue staining (HPA tissue IHC), antibody A01755-3, validated IHC image, and IHC protocol steps
Printable COL4A3 IHC protocol sheet — expected localisation Extracellular basement membrane (UniProt); cytoplasmic tissue staining (HPA tissue IHC), antibody A01755-3, controls and protocol steps. Open the full COL4A3 IHC guide →

COL4A3 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 Extracellular basement membrane (UniProt); cytoplasmic tissue staining (HPA tissue IHC)
Staining pattern Cytoplasmic and extracellular positivity in several tissues (HPA tissue IHC)
Antigen retrieval EDTA pH 8.0 HIER, heat-mediated (datasheet A01755-3)
Positive control ⓘ Appendix+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 sections (standard IHC practice; not target-specific). Selected-image fixative and duration unreported (datasheet A01755-3); verify before use.
Caveat Secreted COL4A3 may stain beyond its producing cells (UniProt)
Regulation Staining intensity varies by tissue (HPA tissue IHC)
Isoform / epitope 5 isoforms; no cytoplasmic segment; check chain/tumstatin epitope (UniProt)
Section 1

Recommended COL4A3 IHC & IF Protocols

The catalog antibody has a datasheet IHC-P protocol (datasheet: A01755-3). The published options below cover human lung multiplex IHC and mouse inner ear chromogenic IHC (PMC13452252; PMC7619435).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human gastric cancer tissue; fixative not specified (datasheet A01755-3)
FixationImage fixative and duration unreported (datasheet A01755-3); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat retrieval: EDTA pH 8.0 (datasheet A01755-3); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet A01755-3)
Primary antibodyRabbit anti-COL4A3, 2-5 μg/ml (datasheet A01755-3)
Primary incubationOvernight at 4 °C (datasheet A01755-3)
DetectionStreptavidin-biotin complex (SABC), DAB chromogen (datasheet A01755-3)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultCOL4A3-positive staining in glandular cells of appendix (HPA tissue IHC: Medium). HPA tissue profile: Cytoplasmic expression and extracellular positivity in several tissues. No signal in the no-primary control.
💡Decision noteStart with heat-mediated EDTA retrieval at pH 8.0 for the catalog antibody (datasheet: A01755-3). The mouse inner ear study used a different retrieval protocol (PMC7619435).
Section 2

What Is the Expected COL4A3 Staining Pattern?

COL4A3 is a secreted protein found in extracellular matrix and basement membranes, with no transmembrane segment (UniProt Q01955 localization/topology). On paraffin sections, expect staining associated with extracellular structures as well as cytoplasmic staining in some cells: HPA describes both patterns and rates its tissue IHC reliability Approved (HPA tissue IHC). Appendix glandular cells are one documented medium-positive cell population (HPA tissue IHC).

What am I looking at on my slide?
Extracellular staining follows a basement-membrane outline, with staining in the relevant cells.This fits COL4A3 matrix localization (UniProt Q01955 localization). HPA also reports cytoplasmic and extracellular positivity across several tissues (HPA tissue IHC). Judge the pattern against the particular tissue and cell population; extracellular staining need not appear equally strong beside every cell.
Nuclei are the dominant stained compartment, without a convincing extracellular pattern.A predominantly nuclear result conflicts with the reported extracellular and cytoplasmic locations (UniProt Q01955 localization; HPA tissue IHC). Treat it as a possible staining artifact and review control sections before assigning it to COL4A3.
Strong staining appears in a cell population documented as undetected.For example, HPA reports no staining in bone-marrow hematopoietic cells (HPA tissue IHC). Staining there warrants checks for cross-reactivity or endogenous chromogen-generating activity; a negative cell-level report does not establish that every extracellular structure in that tissue must be negative.
Brown signal spreads across tissue and background with little anatomical definition.The pattern cannot be confidently assigned to the reported cytoplasmic or extracellular distribution (HPA tissue IHC). Compare a section processed without primary antibody and review blocking and washing as general chromogenic IHC practice.
A documented medium-positive cell population has no visible signal.Absent appendix glandular-cell staining, for example, disagrees with HPA's medium IHC observation (HPA tissue IHC). First verify the positive control and tissue preservation; one failed section does not establish that COL4A3 is absent from the specimen.
💡Expected COL4A3 appearanceCall an IHC result positive when anatomically defined extracellular staining and appropriate cellular staining are visible, such as medium appendix glandular-cell signal (UniProt Q01955 localization; HPA tissue IHC); dominant nuclear staining or widespread featureless chromogen is suspect.
How each factor affects the staining
Extracellular deposition and cellular signalCOL4A3 is secreted and belongs to basement-membrane matrix (UniProt Q01955 localization). HPA nevertheless describes cytoplasmic expression alongside extracellular positivity (HPA tissue IHC); cytoplasmic staining alone should be interpreted in its tissue context, not automatically rejected.
Anatomical contextUniProt places COL4A3 with COL4A4 and COL4A5 in glomerular and tubular basement membranes (UniProt Q01955 localization). HPA's supplied IHC summary does not score kidney, so that anatomical expectation is not an HPA-confirmed positive-control result.
Tissue-source disagreementHPA reports medium staining in placenta trophoblastic cells and skin keratinocytes (HPA tissue IHC), while UniProt cites reports of absent expression in placenta and skin (UniProt Q01955 tissue specificity). Record the sampled cells and pattern instead of treating either source as a universal tissue-wide rule.
Antibody validationHPA042064 is rated Approved for IHC and Supported for ICC (HPA antibodies). Approved is the supplied IHC status; the record does not provide an Enhanced IHC rating or establish that every staining feature was reproduced by independent antibodies.
Processing and isoformsUniProt lists 5 isoforms, a signal peptide at residues 1–28, and a tumstatin region at 1426–1670 (UniProt Q01955 processing/isoforms). The supplied record gives no epitope for the IHC-validated antibody, so it cannot establish which forms or processed regions this stain detects.
ICC/IF Q&A: should intracellular fluorescence match tissue IHC?HPA reports mainly vesicular ICC/IF localization, with additional endoplasmic-reticulum signal, and lists HeLa and U2OS images (HPA subcellular). That cell-based observation provides context for intracellular signal; tissue IHC also has an extracellular pattern (HPA tissue IHC).
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
No stain in appendix glandular cellsThis conflicts with their documented medium IHC level (HPA tissue IHC); the section or detection run may have failed.Check a documented positive-control section, tissue integrity, primary-antibody step, and detection reagents (general IHC-P practice).
No glomerular basement-membrane outlineUniProt places COL4A3 in the GBM (UniProt Q01955 localization), but the supplied HPA IHC summary gives no kidney score (HPA tissue IHC).Check whether basement membranes are intact and compare the run with a documented HPA-positive tissue; avoid calling the kidney result definitive from this summary alone.
Predominantly nuclear stainingThe compartment conflicts with UniProt extracellular localization and HPA's cytoplasmic/extracellular profile (UniProt Q01955 localization; HPA tissue IHC).Compare a section processed without primary antibody, then review blocking, detection, and antibody concentration (general IHC-P practice).
Strong staining in lung macrophagesHPA lists lung macrophages as Low, so strong signal needs confirmation; chromogenic background or cross-reactivity is possible (HPA tissue IHC).Compare the no-primary control and review endogenous enzyme blocking if enzyme-based detection is used (general chromogenic IHC practice).
Diffuse brown background obscures structureThe result cannot be matched confidently to HPA's cytoplasmic and extracellular profile (HPA tissue IHC).Inspect control sections, washing, blocking, and detection exposure before scoring the specimen (general IHC-P practice).
Placenta or skin staining seems to contradict a tissue-specificity noteHPA reports medium staining in selected cells there (HPA tissue IHC); UniProt also records reports of absent expression in those tissues (UniProt Q01955 tissue specificity).Document the stained cell type and compartment, compare controls, and report the source disagreement rather than reclassifying the result solely by tissue name.

Sample controls for COL4A3 IHC & IF

🧪Run appendix first: its glandular cells are scored Medium for COL4A3, and assess staining in the glandular compartment with attention to basement membranes (HPA: Appendix glandular cells, Medium; UniProt Q01955: basement membrane localization). Use caudate as the negative tissue because glial cells are scored Not detected; on the appendix slide, nuclei and gland lumens should lack specific basement-membrane signal and provide internal background comparisons (HPA: Caudate glial cells, Not detected; UniProt Q01955: extracellular matrix localization).
Positive control tissue: Appendix (Glandular cells, HPA Medium)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show COL4A3 in HeLa, U2OS, with annotated localisation: Vesicles (approved) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control and a concentration-matched rabbit IgG control appropriate to the catalog antibody’s format; confirm specificity with knockout material or peptide competition if the immunizing peptide is available (selected A01755-3 caption: rabbit primary antibody; standard IHC practice). Block endogenous peroxidase and check for endogenous biotin background when using the reported biotinylated secondary and streptavidin–biotin DAB detection (selected A01755-3 caption: SABC/DAB detection; standard IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected A01755-3 paraffin-section caption does not state a fixative; fixation therefore cannot be established from that caption (selected A01755-3 caption: fixative not stated). For paraffin IHC, the caption provides a starting condition of heat-mediated EDTA retrieval at pH 8.0 and 2 μg/ml primary antibody overnight at 4°C, but it does not establish whether retrieval is required (selected A01755-3 caption). The supplied evidence does not establish whether frozen sections or IF are easier; in appendix, distinguish any gland-lumen DAB deposit from staining along basement membranes (HPA: Appendix glandular cells, Medium; UniProt Q01955: basement membrane localization; standard IHC interpretation). The selected A01755-3 tissue-IHC caption documents paraffin sections, but does not specify the fixative (selected-SKU IHC image A01755-3).

HPA tissue IHC evidence for COL4A3

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — At least one protein variant secreted, tissue location of RNA and protein might differ and correlation is complex.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.

Positive expression · recommended positive controls

TissueCell typeLevelEvidenceSource
Appendix Glandular cells Medium Protein (IHC) HPA →
Cervix Glandular cells Medium Protein (IHC) HPA →
Gallbladder Glandular cells Medium Protein (IHC) HPA →
Placenta Trophoblastic cells Medium Protein (IHC) HPA →
Skin Keratinocytes Medium Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
Adipose tissue Adipocytes Not detected Protein (IHC) HPA →
Adrenal gland Glandular cells Not detected Protein (IHC) HPA →
Bone marrow Hematopoietic cells Not detected Protein (IHC) HPA →
Breast Adipocytes Not detected Protein (IHC) HPA →
Caudate Glial cells Not detected Protein (IHC) HPA →
Section 3

Advanced COL4A3 IHC Tips

Troubleshoot COL4A3 chromogenic IHC by assessing basement-membrane staining, secretory compartments and the processing details documented for the catalog antibody.

What retrieval should I use when COL4A3 staining is weak in paraffin sections?
Start with heat-mediated retrieval in EDTA at pH 8.0 for the catalog antibody (datasheet A01755-3). Its paraffin-section example used this retrieval before incubation with 2 μg/ml primary antibody overnight at 4°C (caption A01755-3). If staining is weak, verify that sections reached retrieval temperature consistently, then compare retrieval duration on matched sections while holding antibody concentration and detection constant (standard IHC practice). Assess whether signal follows basement membranes, since COL4A3 is an extracellular-matrix protein and colocalizes with COL4A4 and COL4A5 in glomerular and tubular basement membranes (UniProt Q01955 localisation). Excessively harsh retrieval can damage tissue architecture, making a stronger-looking signal harder to interpret (standard IHC practice).
How should I troubleshoot possible fixation effects on COL4A3 IHC?
Target-specific sensitivity to fixation is unknown from the supplied evidence; the catalog example identifies a paraffin-embedded section but does not state its fixative (caption A01755-3). Record the fixative, fixation time and processing history for each specimen before comparing staining intensity (standard IHC practice). Use sections processed together and apply the documented EDTA pH 8.0 heat retrieval consistently, so processing differences do not obscure an antibody comparison (datasheet A01755-3; standard IHC practice). If signal varies, compare matched sections while changing one processing variable at a time and inspect basement-membrane preservation (standard IHC practice; UniProt Q01955 localisation). Do not attribute that variation to a COL4A3-specific fixation effect without direct evidence.
Which staining compartments are plausible for COL4A3 in tissue IHC?
Prioritize a basement-membrane or other extracellular pattern: COL4A3 is secreted, has no transmembrane segment and colocalizes with COL4A4 and COL4A5 in glomerular and tubular basement membranes (UniProt Q01955 localisation and topology). HPA also reports cytoplasmic expression and extracellular positivity across tissues, so cytoplasmic staining alone needs careful validation (HPA tissue IHC profile). Vesicular and endoplasmic-reticulum localisation in cultured cells offers a possible secretory-pathway explanation, but does not establish the identity of a tissue-IHC signal (HPA subcellular). Compare the stain with basement-membrane anatomy and an adjacent section, and assess whether intracellular staining appears in the expected cellular context (standard IHC practice). Avoid treating diffuse nuclear staining as the expected pattern for this extracellular protein (UniProt Q01955 localisation).
Could epitope choice explain different COL4A3 patterns between antibodies?
COL4A3 has 5 listed isoforms, so first check which sequence region each antibody recognizes before comparing IHC results (UniProt Q01955 isoforms; standard IHC practice). The chain includes an NC1 domain at residues 1445–1669, while the annotated tumstatin region spans 1426–1670 (UniProt Q01955 processing and domains). An antibody's epitope and isoform coverage are not specified here, so neither NC1 recognition nor pan-isoform detection can be assumed. COL4A3 also has an annotated glycosylation site at residue 253; whether that modification affects this antibody's staining is unknown (UniProt Q01955 glycosylation). Review the antibody's epitope documentation and compare anatomical patterns under matched retrieval and detection conditions (standard IHC practice).
How can IF help assess an ambiguous COL4A3 IHC pattern?
Use IF as a separate validation experiment while keeping the chromogenic IHC pattern anchored to basement-membrane anatomy (UniProt Q01955 localisation; standard IHC practice). Multiplex COL4A3 with a glandular epithelial marker when examining stomach glands, whose cells show medium HPA IHC positivity, and consider COL4A4 or COL4A5 to assess matrix colocalisation (HPA tissue IHC; UniProt Q01955 localisation). Choose spectrally separated fluorophores and inspect unstained tissue for autofluorescence before assigning a weak signal (standard IF practice). Because COL4A3 has no transmembrane segment, use permeabilisation only when probing an intracellular secretory-pathway epitope; minimize it for an accessible extracellular epitope (UniProt Q01955 topology; HPA subcellular; standard IF practice). IF conditions require their own validation and should not be inferred from the paraffin IHC caption (caption A01755-3).
What should I check when COL4A3 DAB staining appears widespread?
The catalog example used 10% goat serum block, biotinylated goat anti-rabbit secondary, an avidin–biotin detection complex and DAB (caption A01755-3). Include a no-primary control to identify detection-system background, and apply a peroxidase block as a general chromogenic IHC step (standard IHC practice). If broad brown signal persists, inspect endogenous biotin contribution to the avidin–biotin workflow and compare with an appropriate alternative detection system (caption A01755-3; standard IHC practice). Titrate primary antibody around the documented 2 μg/ml condition while keeping exposure and development comparable (caption A01755-3; standard IHC practice). Judge improvement by preservation of anatomically plausible extracellular or basement-membrane staining, not by overall darkness (UniProt Q01955 localisation).
How should I quantify COL4A3 staining without conflating matrix and cellular signal? ⚠ ANSWER MARKED FOR VERIFICATION
Define basement-membrane regions before scoring, because COL4A3 is an extracellular-matrix component that localizes to basement membranes (UniProt Q01955 localisation). For chromogenic IHC, measure DAB-positive basement-membrane length or area and normalize it to total evaluable basement-membrane length or tissue area, respectively (standard IHC image analysis). If the study asks about HPA-reported cellular staining, score the percentage of positive cells or an H-score separately within a defined cell population (HPA tissue IHC profile; standard IHC scoring). Hold section thickness, illumination, colour deconvolution and threshold rules constant across samples (standard IHC image analysis). Exclude folds, tissue loss and necrosis from the denominator, and report the compartment scored (standard IHC scoring).
How do I distinguish true COL4A3 staining from IHC artefact?
A credible result should fit the sampled anatomy: COL4A3 is an extracellular basement-membrane protein, although HPA also reports cytoplasmic and extracellular tissue staining (UniProt Q01955 localisation; HPA tissue IHC profile). In the catalog example, COL4A3 was detected in a paraffin-embedded human gastric cancer section, but that image alone does not define every positive cell or compartment (caption A01755-3). Check unexpected nuclear or uniformly diffuse staining against a no-primary control and adjacent tissue architecture (UniProt Q01955 localisation; standard IHC practice). Discount staining confined to section edges, folds or necrotic areas, and investigate brown deposits caused by endogenous enzyme activity (standard IHC practice). Corroborate uncertain basement-membrane patterns with COL4A4 or COL4A5 localisation on matched material (UniProt Q01955 localisation; standard IHC practice).
Boster reagents

Best COL4A3 / Collagen alpha-3(IV) chain IHC Antibodies

Two anti-COL4A3 antibodies have paraffin-section IHC images from human tissue (catalog image captions); one also has an IF image from COS7 cells (A01755-1 image caption).

Real IHC data IHC analysis of COL4A3 using anti-COL4A3 antibody (A01755-3). COL4A3 was detected in a paraffin-embedded section of human gastric cancer tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH 8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 2 μg/ml rabbit anti-COL4A3 Antibody (A01755-3) overnight at 4°C. Biotinylated goat anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using Strepavidin-Biotin-Complex (SABC) (Catalog # SA1022) with DAB as the chromogen.
Anti-COL4A3 Antibody
Cat # A01755-3
Real IHC data Immunohistochemistry analysis of paraffin-embedded human brain tissue, using Collagen IV alpha3 Antibody. The picture on the right is blocked with the synthesized peptide.
Anti-Collagen alpha-3(IV) chain COL4A3 Antibody
Cat # A01755-1

A01755-3 will render with IHC data from paraffin-embedded human gastric cancer tissue (A01755-3 image caption). A01755-1 will render with IHC data from paraffin-embedded human brain tissue; its separate IF image shows COS7 cells (A01755-1 image captions).

Which to pick: For human tissue IHC, choose A01755-3 when its documented paraffin-section procedure is useful: 2 μg/ml primary antibody after EDTA retrieval at pH 8.0 (A01755-3 image caption). For IF or mouse samples, choose A01755-1 because IF and IHC are listed applications and Human and Mouse are listed reactivities; its IHC image shows paraffin-embedded human brain tissue (A01755-1 catalog and image caption). The fixative is unreported in both IHC captions (A01755-1 and A01755-3 image captions).

Each figure is that product's own IHC / IF validation image from its datasheet.

References

  1. UniProt Consortium. UniProt entry Q01955 (CO4A3_HUMAN, Collagen alpha-3(IV) chain).
  2. Human Protein Atlas. COL4A3 tissue IHC expression (reliability: Approved).
  3. Human Protein Atlas. COL4A3 subcellular location (ICC-IF): Mainly localized to vesicles. In addition localized to the endoplasmic reticulum..
  4. Human Protein Atlas. COL4A3 antibody validation summary (1 antibodies).
  5. Characterization of Ocular Morphology in Col4a3-/- Mice as a Murine Model for Alport Syndrome. Translational vision science & technology 2024 — PMC11268448.
  6. A single-nucleus transcriptomic characterization of EGFR G719X/S768I double-mutant lung adenocarcinoma identifies an immunosuppressive niche defined by COL4A3-CD44 interaction. Translational oncology 2026 — PMC13452252.
  7. An Overlapping Case of Alport Syndrome and Thin Basement Membrane Disease. Journal of clinical medicine research 2016 — PMC5012249.
  8. Low level of expression of known deafness genes Kcne1, Kcnj10 or Col4a3 is sufficient to maintain hearing in mice. Hearing research 2025 — PMC7619435.
  9. PubMed PMID:8083201 — UniProt-cited evidence.
  10. PubMed PMID:11134255 — UniProt-cited evidence.
  11. PubMed PMID:15815621 — UniProt-cited evidence.