HAVCR1 / Hepatitis A virus cellular receptor 1 · IHC design guide

Design Immunohistochemistry for HAVCR1

Plan chromogenic HAVCR1 IHC in paraffin sections using kidney tubules as a tissue reference (HPA tissue IHC). Interpret cytoplasmic and membranous epithelial staining in light of HPA’s uncertain staining reliability (HPA tissue IHC).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use

Immunohistochemistry protocol sheet for HAVCR1 (IHC for HAVCR1): expected localisation Cytoplasmic and membranous in glandular epithelia (HPA tissue IHC), antibody PA1624, validated IHC image, and IHC protocol steps — Printable **HAVCR1** IHC protocol sheet — expected localisation Cytoplasmic and membranous in glandular epithelia (HPA tissue IHC), antibody PA1624, controls and protocol steps. Open the full HAVCR1 IHC guide →

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HAVCR1 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 and membranous in glandular epithelia (HPA tissue IHC)
	Staining pattern	Most glandular epithelia show cytoplasmic and membrane staining (HPA tissue IHC)
	Antigen retrieval	Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen)
	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 paraffin-section fixation consistent across samples. (standard IHC practice; not target-specific)
	Caveat	Low agreement between antibody staining and RNA limits confidence (HPA tissue IHC)
	Regulation	Injured kidney tubules express HAVCR1 (UniProt)
	Isoform / epitope	No listed isoforms; extracellular vs cytoplasmic epitope matters (UniProt)

Section 1

Recommended HAVCR1 IHC & IF Protocols

The catalog antibody’s IHC-P protocol (datasheet) is accompanied by published HAVCR1 IHC methods from three studies (PMC12094995; PMC11702950; PMC11585238).

Recommended immunohistochemistry (IHC-P) protocol parameters
Sample	Tissue sections; selected-image fixative not specified (standard IHC workflow)
Fixation	Image fixative and duration unreported (datasheet PA1624); 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 citrate buffer, pH 6.0, 20 min at 95–98 °C (standard rule: cytoplasmic / membrane 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-HAVCR1, 0.5-1μg/ml (datasheet PA1624)
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	HAVCR1-positive staining in glandular cells of appendix (HPA tissue IHC: Medium). HPA tissue profile: Cytoplasmic and membranous expression in most glandular epithelia. No signal in the no-primary control.

💡Decision noteStart with citrate pH 6.0 HIER at 95–98 °C for 20 min (page antigen retrieval); the published methods use high-pressure heat, microwave citrate, or pressure-cooker EDTA retrieval (PMC12094995; PMC11702950; PMC11585238).

Section 2

What Is the Expected HAVCR1 Staining Pattern?

HAVCR1 is a membrane protein with an extracellular region at residues 21–295, a transmembrane segment at 296–316, and a cytoplasmic tail at 317–364 (UniProt Q96D42 topology). In paraffin-section IHC, expect cytoplasmic and membranous staining in glandular epithelia, including kidney tubular cells (HPA tissue IHC). Interpret this pattern cautiously: HPA rates its tissue staining reliability Uncertain because antibody staining and RNA expression have low consistency (HPA tissue IHC).

What am I looking at on my slide?
Membranous and cytoplasmic staining in kidney tubular cells, with moderate intensity.	This matches HPA's Medium kidney tubular-cell staining and its broader cytoplasmic and membranous epithelial profile (HPA tissue IHC). A membrane-associated pattern is consistent with HAVCR1 topology, while UniProt also places the protein in phagocytic cups and phagosomes (UniProt Q96D42 subcellular location). HPA's Uncertain tissue reliability limits how strongly staining alone identifies HAVCR1 (HPA tissue IHC).
Moderate cytoplasmic and membranous staining in intestinal or other listed glandular cells.	HPA reports Medium staining in appendix, colon, rectum, small-intestine and gallbladder glandular cells, and in liver cholangiocytes (HPA tissue IHC). Compare the stained cells with section morphology and controls; HPA's low staining-versus-RNA consistency means this pattern is supportive, not conclusive (HPA tissue IHC; standard IHC practice).
Predominantly nuclear staining, without a discernible epithelial membrane or cytoplasmic pattern.	A nuclear-only pattern does not match UniProt's membrane, phagocytic-cup and phagosome locations or HPA's tissue profile (UniProt Q96D42 subcellular location; HPA tissue IHC). Treat it as possible nonspecific staining and review control sections, antibody concentration and detection conditions before scoring it as HAVCR1 (standard IHC practice).
Strong staining in a cell population HPA lists as not detected, or widespread color across the section.	For example, HPA reports HAVCR1 as Not detected in adipocytes and lung alveolar cells (HPA tissue IHC). Unexpected staining may reflect antibody cross-reactivity or endogenous detection activity; color that also covers stroma or blank areas suggests background (standard IHC practice). HPA's uncertain reliability prevents using one negative tissue as absolute proof (HPA tissue IHC).
No staining in a kidney section expected to contain tubules, while counterstain and tissue morphology remain visible.	HPA observed Medium staining in kidney tubular cells, so absent signal merits a technical check (HPA tissue IHC; standard IHC practice). It does not by itself establish that HAVCR1 is absent: HPA rates its tissue staining reliability Uncertain (HPA tissue IHC). Check a concurrently stained positive reference and the assay controls (standard IHC practice).

💡Expected HAVCR1 appearanceCall a positive result when epithelial cells show interpretable Medium membranous and cytoplasmic staining, especially kidney tubules or HPA-listed glandular cells (HPA tissue IHC); isolated nuclear color or uniform staining across unrelated cells is suspect (UniProt Q96D42 subcellular location; standard IHC practice).

How each factor affects the staining
Compartment and topology	HAVCR1 spans the membrane once, with extracellular residues 21–295 and cytoplasmic residues 317–364 (UniProt Q96D42 topology). UniProt also locates it at phagocytic cups and in phagosomes, so cytoplasmic signal can fit its biology (UniProt Q96D42 subcellular location). The payload does not map either IHC antibody's epitope; topology alone cannot prescribe antigen retrieval (HPA antibodies; UniProt Q96D42 topology).
Tissue and cell selection	HPA reports Medium staining in kidney tubular cells, several glandular epithelia, cholangiocytes and urothelial cells (HPA tissue IHC). It reports no detection in the specified adipocytes, cardiomyocytes, lung alveolar cells and other listed populations (HPA tissue IHC). Use matched cell populations when comparing sections; HPA's Uncertain reliability makes these reference patterns provisional (HPA tissue IHC; standard IHC practice).
Antibody evidence	The supplied HPA antibody record assigns CAB075697 an IHC status of Uncertain; HPA007173 has no IHC status in that record (HPA antibodies). The tissue page likewise reports Uncertain reliability owing to low staining-versus-RNA consistency (HPA tissue IHC). Reconcile any unexpected pattern with controls and morphology before drawing a target-specific conclusion (standard IHC practice).
ICC-IF context	For IF/ICC, HPA summarizes vesicle localization as Uncertain and lists images from A-549, CACO-2, U2OS, RPTEC/TERT1 and serum-starved hTERT-RPE1 cells (HPA subcellular). This is a separate cell-imaging observation; interpret paraffin-section chromogenic staining using the tissue IHC profile and controls (HPA tissue IHC; standard IHC practice).

Why is my staining missing, weak or wrong?
Situation	Likely cause	Next action
Kidney tubular cells lack visible chromogen.	A missed assay step or weak detection is possible; HPA reports Medium tubular staining but rates its tissue evidence Uncertain (HPA tissue IHC; standard IHC practice).	Check a concurrently processed positive section, primary-antibody application, detection reagents and counterstain; change antigen retrieval only through controlled optimization, since no HAVCR1-specific retrieval effect is supplied (standard IHC practice).
Signal is diffuse over tissue and blank areas.	Excess background can arise from antibody concentration, insufficient washing or endogenous detection activity in chromogenic IHC (standard IHC practice).	Inspect a no-primary control, review blocking and wash steps, and optimize antibody and detection conditions against the positive section (standard IHC practice).
Signal is mainly nuclear.	That compartment conflicts with the reported membrane, phagocytic-cup and phagosome locations and with HPA's membranous and cytoplasmic tissue profile (UniProt Q96D42 subcellular location; HPA tissue IHC).	Review the no-primary control, cell morphology and staining concentration; avoid scoring nuclear-only color as HAVCR1 without independent support (standard IHC practice).
Adipocytes or lung alveolar cells stain strongly.	HPA lists those cell populations as Not detected; cross-reactivity or endogenous detection activity is possible, although HPA's tissue reliability is Uncertain (HPA tissue IHC; standard IHC practice).	Compare cell-specific staining with a positive reference and no-primary control, then repeat under adjusted antibody or detection conditions if the unexpected pattern persists (standard IHC practice).
Expected epithelial staining disappears while background remains.	High background may obscure a cell-specific pattern; HPA's expected glandular profile is cytoplasmic and membranous (HPA tissue IHC; standard IHC practice).	First reduce nonspecific color with control-guided blocking, washing and detection optimization; then reassess epithelial membranes and cytoplasm against morphology (standard IHC practice).
IF/ICC shows vesicles but the paraffin IHC section lacks a matching punctate pattern.	HPA's ICC-IF vesicle assignment is Uncertain, while its tissue IHC profile is cytoplasmic and membranous (HPA subcellular; HPA tissue IHC).	Score the paraffin section against its epithelial tissue pattern and IHC controls; use the separate IF/ICC guide for cell-imaging interpretation (HPA tissue IHC; standard IHC practice).

Source: UniProt Q96D42 Human Protein Atlas tissue Human Protein Atlas subcellular

Experiment evidence

IHC & IF images showing HAVCR1 staining

PA1624 · IHCAnti-TIM 1 antibody, PA1624, IHC(P) IHC(P): Human Tonsil Tissue

PA1624 · IFAnti-TIM 1 antibody, PA1624, ICC ICC: K562 Cell

Immunofluorescence Validation of TIM-1 in Human Testis Immunofluorescent analysis of 4% paraformaldehyde-fixed human testis tissue labeling TIM-1 with A01306-1 at 10 μg/mL, followed by goat anti-rabbit IgG secondary antibody at 1/500 dilution (red) and DAPI staining (blue).

A01306-1 · IFImmunofluorescence Validation of TIM-1 in Human Testis Immunofluorescent analysis of 4% paraformaldehyde-fixed human testis tissue labeling

HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000113249-HAVCR1/tissue/cerebral+cortex#imid_19707619

HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000113249-HAVCR1/tissue/colon#imid_19707537

HPA · RectumHuman Protein Atlas IHC, Rectum. Source: https://www.proteinatlas.org/ENSG00000113249-HAVCR1/tissue/rectum#imid_19707513

HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000113249-HAVCR1/tissue/liver#imid_19707554

HPA · ICC-IF A-549Human Protein Atlas immunofluorescence, A-549, antibody HPA007173; green = HAVCR1, blue = nucleus, red = microtubules.

← swipe / scroll for more images →

Real IHC / IF data behind the staining-pattern expectations in this section.

Sample controls for HAVCR1 IHC & IF

🧪Run kidney first and look for staining in tubular cells (HPA: Medium in kidney cells in tubules). Use adipose tissue adipocytes as the negative tissue (HPA: Not detected in adipocytes); on the kidney slide, compare tubular staining with non-tubular cells that show only counterstain, without assuming those cells are biologically negative.

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 HAVCR1 in A-549, CACO-2, U2OS, RPTEC/TERT1, hTERT-RPE1 (serum starved), with annotated localisation: Vesicles (uncertain) (HPA subcellular).

Technical controls: Include a no-primary, secondary-only control; an irrelevant immunoglobulin control matched to the primary antibody’s host species and isotype; and HAVCR1-knockout tissue as a biological negative (standard IHC practice). In kidney sections, quench endogenous peroxidase for chromogenic detection and assess endogenous biotin if using avidin–biotin detection (standard IHC practice).

⚠️Feasibility: A target-specific fixation window and antigen-retrieval dependency are unreported in the supplied evidence; the selected PA1624 tissue-IHC caption also leaves the fixative unreported (selected-SKU caption: fixative not stated). The evidence does not establish whether frozen sections or IF are easier than paraffin IHC for HAVCR1. Kidney background from endogenous peroxidase or biotin can complicate chromogenic interpretation, so evaluate it with the detection controls (standard IHC practice).

HPA tissue IHC evidence for HAVCR1

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Uncertain — Low 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
Appendix	Glandular cells	Medium	Protein (IHC)	HPA →
Colon	Glandular cells	Medium	Protein (IHC)	HPA →
Gallbladder	Glandular cells	Medium	Protein (IHC)	HPA →
Kidney	Cells in tubules	Medium	Protein (IHC)	HPA →
Liver	Cholangiocytes	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 →
Caudate	Glial cells	Not detected	Protein (IHC)	HPA →
Cerebellum	Cells in granular layer	Not detected	Protein (IHC)	HPA →
Esophagus	Squamous epithelial cells	Not detected	Protein (IHC)	HPA →

Section 3

Advanced HAVCR1 IHC Tips

These questions address HAVCR1 staining in paraffin sections with chromogenic detection; the immunofluorescence entry covers the related imaging workflow.

How should I optimize retrieval when HAVCR1 staining is weak in paraffin sections?

Use citrate pH 6.0 heat-induced epitope retrieval at 95–98 °C for 20 min (page retrieval setting). If staining is weak, first confirm that sections reached the stated temperature and received the full heating time, then compare adjacent sections with and without retrieval while holding detection constant (standard IHC practice). Score epithelial membrane and cytoplasmic signal separately because both patterns are reported in tissue, while a vesicular pattern is also biologically plausible (HPA tissue IHC; UniProt Q96D42 subcellular location). If optimization still fails, test an alternative retrieval condition as a fallback and judge it against tissue controls and background, since no alternative HAVCR1-specific condition is supplied (standard IHC practice).

Could fixation explain weak HAVCR1 staining despite adequate retrieval?

The selected PA1624 tissue caption identifies paraffin IHC in human tonsil but does not state the fixative, so target-specific fixation sensitivity is unknown (PA1624 tissue-IHC caption). Record the fixative, fixation duration, processing history, and section age before comparing staining across specimens (standard IHC practice). Run adjacent sections through the same citrate pH 6.0, 95–98 °C, 20 min retrieval and identical detection to assess whether a processing batch tracks the weak signal (page retrieval setting; standard IHC practice). Include a tissue control in each run, but do not attribute a negative section to fixation alone when antigen abundance and antibody performance have not been checked (standard IHC practice).

Should HAVCR1 stain membranes, cytoplasm, or intracellular puncta?

HAVCR1 has an extracellular segment at residues 21–295, a transmembrane segment at 296–316, and a cytoplasmic tail at 317–364 (UniProt Q96D42 topology). In paraffin IHC, assess membrane-associated staining alongside cytoplasmic staining because both are reported in glandular epithelia, and note puncta separately because vesicular localisation is reported with uncertain confidence (HPA tissue IHC; HPA subcellular). In injured kidney epithelium, phagocytic uptake provides a biological reason to examine intracellular signal without assuming every punctum is specific (UniProt Q96D42 function). Compare the pattern with cellular morphology and negative controls, and score diffuse nuclear-only staining as suspect because the supplied locations do not include the nucleus (UniProt Q96D42 subcellular location; standard IHC practice).

How does an unknown antibody epitope affect interpretation of HAVCR1 staining?

The supplied record lists 0 isoforms, but it does not specify the PA1624 antibody epitope, so section staining cannot be assigned to a particular extracellular or intracellular sequence (UniProt Q96D42 isoforms; PA1624 tissue-IHC caption). HAVCR1 spans an extracellular region at 21–295, a membrane segment at 296–316, and a cytoplasmic tail at 317–364 (UniProt Q96D42 topology). Four glycosylation sites are annotated at residues 65, 263, 277, and 291; their effect on this antibody's paraffin staining is unreported (UniProt Q96D42 glycosylation; PA1624 tissue-IHC caption). Request epitope documentation before interpreting a selective loss of membrane staining, and compare morphology, controls, and retrieval consistently across specimens (standard IHC practice).

How can IF help check an ambiguous HAVCR1 IHC pattern?

For a separate IF experiment, pair HAVCR1 with a validated marker of the cell population under examination, such as tubular epithelial cells in kidney, and compare overlap at single-cell resolution (HPA tissue IHC: kidney tubules; standard IF practice). Select fluorophores after measuring tissue autofluorescence and include single-label controls so spectral bleed-through is distinguishable from genuine overlap (standard IF practice). If the antibody recognises the extracellular region, compare nonpermeabilised and permeabilised preparations; access to a cytoplasmic-tail epitope generally requires permeabilisation, but the PA1624 epitope is unspecified (UniProt Q96D42 topology; PA1624 tissue-IHC caption; standard IF practice). Interpret puncta cautiously because vesicular localisation has uncertain support and this IHC caption supplies no IF fixation or validation details (HPA subcellular; PA1624 tissue-IHC caption).

How do I separate HAVCR1 signal from chromogenic background?

Compare a no-primary control and an isotype control, where appropriate, with the stained section to identify detection-system or nonspecific antibody signal (standard IHC practice). For peroxidase-based chromogenic IHC, use an endogenous peroxidase block before DAB development and inspect pigment or precipitate that persists independently of the primary antibody (standard IHC practice). Titrate the catalog antibody and detection intensity while preserving the same citrate pH 6.0, 95–98 °C, 20 min retrieval across the comparison (page retrieval setting; standard IHC practice). Treat staining that ignores epithelial boundaries or appears equally in negative controls as background, while assessing plausible membrane and cytoplasmic patterns in the relevant cells (HPA tissue IHC; standard IHC practice).

What should I score when HAVCR1 staining varies across a section? ⚠ ANSWER MARKED FOR VERIFICATION

Define the cell compartment and region of interest before scoring: kidney tubular cells or the specified glandular epithelium are supported tissue contexts (HPA tissue IHC). Report the percentage of positive target cells and an intensity-weighted H-score, recording membrane and cytoplasmic staining separately when both occur (HPA tissue IHC; standard IHC practice). For spatial analyses, count positive cells per mm² of viable target tissue and normalise to the total number of eligible cells or the measured viable target area, rather than the whole section (standard IHC practice). Apply one threshold and the same controls across batches, and disclose that HPA rates tissue staining reliability as uncertain because antibody staining and RNA expression have low consistency (HPA tissue IHC).

Which HAVCR1 staining patterns warrant a specificity check?

A credible tissue pattern follows cell morphology and can include membrane and cytoplasmic staining in glandular epithelia or kidney tubular cells (HPA tissue IHC). Vesicular signal can fit the reported cellular locations, but the HPA vesicle assignment is uncertain, so puncta alone do not establish specificity (UniProt Q96D42 subcellular location; HPA subcellular). Investigate nuclear-only staining, signal concentrated at section edges or necrotic areas, and DAB deposits reproduced in no-primary controls as possible artefacts (UniProt Q96D42 subcellular location; standard IHC practice). Compare the suspect area with viable neighbouring tissue, matched controls, and the recorded cell type before calling it HAVCR1-positive, particularly because HPA rates its tissue IHC reliability as uncertain (HPA tissue IHC; standard IHC practice).

Boster reagents

Best HAVCR1 / Hepatitis A virus cellular receptor 1 IHC Antibodies

PA1624 has human tonsil paraffin-section IHC and K562 ICC images (PA1624 captions); A01306-1 has human testis and mouse kidney IF images (A01306-1 captions).

Real IHC data Anti-TIM 1 antibody, PA1624, IHC(P) IHC(P): Human Tonsil Tissue

Anti-TIM 1/HAVCR1 Antibody ®

Cat # PA1624

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Real IF data Immunofluorescence Validation of TIM-1 in Human Testis Immunofluorescent analysis of 4% paraformaldehyde-fixed human testis tissue labeling TIM-1 with A01306-1 at 10 μg/mL, followed by goat anti-rabbit IgG secondary antibody at 1/500 dilution (red) and DAPI staining (blue).

Anti-TIM-1 HAVCR1 Antibody

Cat # A01306-1

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PA1624 is listed for human IHC, IF and ICC, with human tonsil paraffin-section IHC and K562 ICC images (PA1624 applications, reactivity and captions). A01306-1 is listed for human and mouse IF, with images of 4% paraformaldehyde-fixed human testis and mouse kidney (A01306-1 applications, reactivity and IF captions).

Which to pick: Choose PA1624 for human paraffin-section tissue IHC at the listed 0.5–1 μg/mL dilution; its IHC caption does not report the fixative (PA1624 datasheet and IHC caption). For ICC, PA1624 has a K562 image; for tissue IF, A01306-1 has human testis and mouse kidney images (PA1624 ICC caption; A01306-1 IF captions). Choose polyclonal A01306-1 for human/mouse IF because both species are listed and pictured; PA1624 lists human reactivity only (A01306-1 datasheet and IF captions; PA1624 reactivity).

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

References

UniProt Consortium. UniProt entry Q96D42 (HAVR1_HUMAN, Hepatitis A virus cellular receptor 1).
Human Protein Atlas. HAVCR1 tissue IHC expression (reliability: Uncertain).
Human Protein Atlas. HAVCR1 subcellular location (ICC-IF): Localized to vesicles..
Human Protein Atlas. HAVCR1 antibody validation summary (2 antibodies).
Combining biomarkers to construct a novel predictive model for predicting preoperative lymph node metastasis in early gastric cancer. Frontiers in oncology 2025 — PMC12094995.
Sinapic acid alleviates renal ischemia-reperfusion injury by regulating oxidative stress, apoptosis, and inflammation. Turkish journal of medical sciences 2025 — PMC12419044.
Macrophage autophagy protects against acute kidney injury by inhibiting renal inflammation through the degradation of TARM1. Autophagy 2025 — PMC11702950.
Integration of the bulk transcriptome and single-cell transcriptome reveals efferocytosis features in lung adenocarcinoma prognosis and immunotherapy by combining deep learning. Cancer cell international 2024 — PMC11585238.
PubMed PMID:9658108 — UniProt-cited evidence.
PubMed PMID:15372022 — UniProt-cited evidence.
PubMed PMID:15489334 — UniProt-cited evidence.