ALYREF / THO complex subunit 4 · IHC design guide

Design Immunohistochemistry for ALYREF

Plan chromogenic IHC for ALYREF in paraffin sections using its widespread nuclear tissue pattern as the staining reference (HPA tissue IHC). The guide covers consistent fixation, antibody incubation, detection and interpretation, with catalog antibody conditions for human tissue (datasheet M03580).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for ALYREF (IHC for ALYREF): expected localisation Nuclear staining across tissues (HPA tissue IHC), antibody M03580, validated IHC image, and IHC protocol steps
Printable ALYREF IHC protocol sheet — expected localisation Nuclear staining across tissues (HPA tissue IHC), antibody M03580, controls and protocol steps. Open the full ALYREF IHC guide →

ALYREF 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 staining across tissues (HPA tissue IHC)
Staining pattern Widespread nuclear staining, including marrow cells (HPA tissue IHC)
Antigen retrieval EDTA pH 8.0 HIER, heat-mediated (datasheet M03580)
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 Ubiquitous staining limits negative tissue controls (HPA tissue IHC)
Regulation Staining-related regulation unspecified (UniProt)
Isoform / epitope No annotated isoforms; chain 2–257; epitope unknown (UniProt)
Section 1

Recommended ALYREF IHC & IF Protocols

Compare the catalog antibody’s IHC-P protocol (datasheet: M03580) with published ALYREF staining in hepatocellular carcinoma (PMC9079359) and retinoblastoma (PMC12439426).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human lung cancer tissue; fixative not specified (datasheet M03580)
FixationImage fixative and duration unreported (datasheet M03580); 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 M03580); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet M03580)
Primary antibodyRabbit monoclonal (clone 22A24) anti-ALYREF, 1:50 (datasheet M03580)
Primary incubationOvernight at 4 °C (datasheet M03580)
DetectionHRP-conjugated secondary, DAB chromogen (datasheet M03580)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultALYREF-positive staining in adipocytes of adipose tissue (HPA tissue IHC: High). HPA tissue profile: Ubiquitous nuclear expression. No signal in the no-primary control.
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval for the catalog antibody (datasheet: M03580); citrate pH 6.0 is a published alternative (PMC12439426).
Section 2

What Is the Expected ALYREF Staining Pattern?

ALYREF should appear predominantly in nuclei across many cell types in paraffin sections (HPA tissue IHC: supported, ubiquitous nuclear expression). High staining is reported in bone marrow hematopoietic cells, adipocytes, glandular cells, respiratory epithelial cells and selected brain cells (HPA tissue IHC). Nuclear speckles and some cytoplasmic transit are biologically plausible (UniProt Q86V81: subcellular location). ALYREF has no transmembrane segment, so a membrane outline is unexpected (UniProt Q86V81: topology).

What am I looking at on my slide?
Distinct nuclear staining in bone marrow hematopoietic cells, with evaluable unstained background (HPA tissue IHC: High).This fits the reported ubiquitous nuclear profile and provides a useful known-positive tissue for judging a run (HPA tissue IHC: supported). A brown nuclear signal in IHC does not establish whether individual nuclear speckles are resolved; speckles are an approved ICC-IF location (HPA subcellular).
A continuous membrane rim, or cytoplasmic staining that dominates while nuclei remain blank (UniProt Q86V81: topology and location).Question the result: ALYREF lacks a transmembrane segment and is chiefly nuclear, although cytoplasmic travel with mRNA is reported (UniProt Q86V81: topology and location). Review the counterstain and compare a known-positive section before assigning a biological redistribution (HPA tissue IHC: ubiquitous nuclear expression).
Signal appears only in cells outside the reported high-staining groups, while expected nuclei are blank (HPA tissue IHC: High-cell listings).Consider nonspecific antibody binding or endogenous chromogen activity (general IHC practice). An unlisted cell type is not automatically negative: HPA describes ubiquitous nuclear expression and supplies no negative tissue list (HPA tissue IHC). Assess compartment and controls together.
Brown haze covers nuclei and surrounding tissue, obscuring cell boundaries (general IHC practice).A widespread deposit cannot be scored reliably as ALYREF nuclear staining (HPA tissue IHC: ubiquitous nuclear profile; general IHC practice). Check background in a no-primary control and examine blocking, washes and chromogen development as general IHC variables, without assuming a target-specific cause.
No nuclear signal in bone marrow hematopoietic cells or another listed high-staining population (HPA tissue IHC: High).Treat the run as unresolved before calling the specimen ALYREF-negative (HPA tissue IHC: supported, High). Check that the assay detects its positive control; review antibody suitability, retrieval and detection as general IHC practice. The supplied sources report no ALYREF-specific retrieval or fixation sensitivity.
💡Expected ALYREF appearanceCall a section positive when identifiable cells show predominantly nuclear staining, including clear signal in a reported High population such as bone marrow hematopoietic cells (HPA tissue IHC); diffuse brown haze or an isolated membrane rim is suspect (general IHC practice; UniProt Q86V81: topology).
How each factor affects the staining
Cell population and intensityHPA reports High staining in adipocytes, adrenal and appendix glandular cells, bone marrow hematopoietic cells, bronchial respiratory epithelial cells, caudate glial cells and cerebellar granular-layer cells (HPA tissue IHC). These are examples, not a ranked intensity scale or a list of exclusive positives (HPA tissue IHC: ubiquitous nuclear expression).
Subcellular distributionNuclear and nuclear-speckle localization is reported by UniProt; nucleoplasm and nuclear speckles are approved ICC-IF locations (UniProt Q86V81: location; HPA subcellular). Cytoplasmic travel is reported with mRNA-bound EJC (UniProt Q86V81: location). A chiefly cytoplasmic IHC pattern therefore needs control-based review.
IHC antibody evidenceHPA019799 and CAB016281 have Supported IHC status; HPA061282 has no listed IHC status (HPA antibodies). These statuses describe the listed antibodies, so do not transfer them to a different catalog antibody or infer its dilution, epitope or performance (HPA antibodies).
IF/ICC Q: What pattern should I expect?A: Nucleoplasmic signal with nuclear speckles is the approved HPA ICC-IF pattern (HPA subcellular). HPA019799 is ICC Enhanced and HPA061282 ICC Approved (HPA antibodies). This localization guides interpretation only; the supplied record gives no IF/ICC protocol for this section.
Retrieval and specimen preparationThe supplied UniProt and HPA records give no ALYREF-specific retrieval condition or fixation effect. If an IHC run fails, review retrieval against the assay's own validated instructions as general IHC practice; do not infer epitope masking from HPA staining levels or UniProt modifications.
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
Known-positive bone marrow nuclei are blank (HPA tissue IHC: High in hematopoietic cells).An assay or detection failure is possible (general IHC practice); absence alone does not establish biological loss.Verify the positive control, catalog antibody's IHC-P suitability, retrieval and detection steps (general IHC practice). No ALYREF-specific retrieval setting is supplied.
Predominantly cytoplasmic signal replaces the expected nuclear pattern (HPA tissue IHC: ubiquitous nuclear expression).Some cytoplasmic ALYREF is plausible, but an exclusively cytoplasmic result conflicts with the reported dominant location (UniProt Q86V81: location).Check nuclear counterstain and compare a listed High population on the same run (general IHC practice; HPA tissue IHC). Avoid scoring cytoplasm alone as confirmation.
Membrane outlines stain more clearly than nuclei (UniProt Q86V81: topology and location).A membrane-dominant pattern is inconsistent with the absence of a transmembrane segment (UniProt Q86V81: topology).Compare the no-primary control and review nonspecific binding or chromogen deposit (general IHC practice); seek nuclear staining in a known-positive tissue (HPA tissue IHC).
Diffuse brown background prevents nuclear scoring (general IHC practice).Nonspecific binding, endogenous detection activity or excess chromogen development may contribute (general IHC practice); the source record identifies no ALYREF-specific cause.Inspect a no-primary control, then review blocking, washes and development against the validated IHC workflow (general IHC practice). Score only distinguishable cellular nuclei.
Unexpected cells stain while a listed High population remains blank (HPA tissue IHC).Cross-reactivity or endogenous detection activity is possible (general IHC practice), but HPA's ubiquitous nuclear profile prevents treating unlisted cells as inherently negative (HPA tissue IHC).Compare cellular localization, morphology and controls; repeat with an independently validated antibody if available (general IHC practice; HPA antibodies: two Supported IHC entries).
Nuclei stain, but individual speckles cannot be distinguished in chromogenic IHC (HPA tissue IHC; HPA subcellular).HPA's speckle assignment comes from ICC-IF, while its tissue IHC summary reports ubiquitous nuclear expression (HPA subcellular; HPA tissue IHC).Interpret a clear nuclear IHC result at the compartment level (HPA tissue IHC). Use the separate IF/ICC guide when speckle-level localization is the experimental question (HPA subcellular).

Sample controls for ALYREF IHC & IF

🧪Run bone marrow first and expect hematopoietic cells to stain (HPA: High in bone marrow hematopoietic cells). HPA detects ALYREF in all 45 scored tissues (HPA: no negative tissue); use no-primary and isotype controls for the negative comparison, while mature erythrocytes on the positive slide should lack nuclear staining because they are anucleate (standard histology).
Positive control tissue: Adipose tissue (Adipocytes, HPA High)
Negative control tissue: None in HPA: ALYREF 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 ALYREF in A-431, U-251MG, U2OS, HEK293, U2OS, siRNA 2 (10x), U2OS, siRNA 2 (40x), U2OS, scrambled (10x), U2OS, scrambled (40x), with annotated localisation: Nucleoplasm (approved), Nuclear speckles (approved) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only section, a matched rabbit IgG isotype control (selected-SKU caption: rabbit primary antibody), and ALYREF-knockout material as a biological negative. Block endogenous peroxidase and inspect erythrocyte-associated background before interpreting bone marrow DAB staining (standard chromogenic IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported in the supplied evidence, and the selected-SKU paraffin-section caption does not state a fixative (selected-SKU caption: fixative unreported). Heat retrieval with EDTA at pH 8.0 was used for the pictured paraffin section, but retrieval dependence is unreported (selected-SKU caption: EDTA pH 8.0); frozen-section suitability is also unreported. IF/ICC offers a localisation readout in nucleoplasm and nuclear speckles (HPA: approved ICC-IF locations), while bone marrow DAB interpretation requires attention to endogenous peroxidase background (standard chromogenic IHC practice).

HPA tissue IHC evidence for ALYREF

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — High 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

TissueCell typeLevelEvidenceSource
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 Adipocytes High Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
None in HPA: ALYREF is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
Section 3

Advanced ALYREF IHC Tips

Use nuclear staining as the main readout for ALYREF in paraffin section IHC, while checking retrieval, background and compartment specific controls (HPA: ubiquitous nuclear expression).

What should I change when ALYREF nuclear staining is weak after retrieval?
Start with heat mediated retrieval in EDTA at pH 8.0 for paraffin sections (datasheet M03580). The selected ALYREF tissue image used that retrieval, followed by 10% goat serum blocking, antibody at 1:50 overnight at 4°C, and DAB detection (datasheet M03580). If nuclei remain weak, compare retrieval duration across adjacent sections while holding antibody dilution and detection constant; inspect tissue integrity because excessive heating can impair interpretation (standard IHC practice). Score nuclear signal against a matched no primary control, since ALYREF is expected in nuclei and nuclear speckles (HPA: subcellular; standard IHC practice).
Could fixation explain inconsistent ALYREF staining between paraffin blocks?
Target specific fixation sensitivity is unknown: the selected paraffin section caption does not state a fixative (datasheet M03580). Record each block's fixation history, section age and retrieval conditions before comparing nuclear staining, because these preanalytical differences can affect IHC signal (standard IHC practice). Keep EDTA at pH 8.0 and the antibody dilution at 1:50 constant during the comparison, matching the documented tissue image conditions (datasheet M03580). Include sections processed together and compare nuclear signal within the same cell population; a difference alone cannot establish an ALYREF specific fixation effect (HPA: ubiquitous nuclear expression; standard IHC practice).
How should I interpret ALYREF staining outside the nucleus?
Treat nuclear staining as the primary IHC readout: tissue IHC shows ubiquitous nuclear expression, while subcellular imaging places ALYREF in nucleoplasm and nuclear speckles (HPA: tissue IHC; HPA: subcellular). Some cytoplasmic signal is biologically plausible because ALYREF travels with an mRNA bound exon junction complex, but cytoplasmic DAB alone is insufficient to establish that process (UniProt Q86V81: subcellular; standard IHC practice). Compare nuclear and cytoplasmic staining within intact cells and examine a no primary control for diffuse deposit (standard IHC practice). If cytoplasm dominates while nuclei are blank, review retrieval, background and tissue preservation before assigning ALYREF localisation (HPA: subcellular; standard IHC practice).
Could an epitope difference explain uneven nuclear ALYREF staining?
The supplied record lists 0 isoforms and places the RNA recognition motif at residues 106–182; neither fact identifies this antibody's epitope (UniProt Q86V81: isoforms, domains; datasheet M03580: epitope not stated). ALYREF also has reported modified residues, including phosphoserine at 8 and alternative arginine modifications at 38, so modification dependent masking is a hypothesis, not a demonstrated IHC effect (UniProt Q86V81: modified residues). Compare adjacent sections under the documented EDTA pH 8.0 retrieval while changing one staining variable at a time (datasheet M03580; standard IHC practice). Do not interpret variable intensity as an isoform map without epitope information and orthogonal evidence (standard IHC practice).
How can IF help assess questionable ALYREF localisation in tissue?
For the separate IF/ICC assessment, choose a marker for the cell population under examination and multiplex it with ALYREF to assign signal to the right cells (standard IF practice). Expect nucleoplasmic and speckled nuclear signal, while allowing for reported cytoplasmic transit; the supplied subcellular profile includes ICC/IF images but does not validate the catalog antibody for IF (HPA: subcellular; UniProt Q86V81: subcellular). Choose fluorophores after checking tissue autofluorescence and include single stain controls to assess bleed through (standard IF practice). ALYREF has no transmembrane segment, so permeabilisation should provide access to intracellular nuclear epitopes; optimise it without assuming the antibody's epitope is known (UniProt Q86V81: topology; standard IF practice).
What causes diffuse brown signal around ALYREF positive nuclei?
Check a no primary section first: diffuse brown deposit there points to detection chemistry or tissue background rather than antibody dependent ALYREF staining (standard IHC practice). The documented tissue image used a peroxidase linked secondary, DAB, 10% goat serum blocking and antibody at 1:50 (datasheet M03580). Apply a peroxidase block when using HRP and compare blocking, wash stringency and DAB development across adjacent sections, changing one factor at a time (standard IHC practice). Preserve the expected nuclear pattern as the decision criterion; excessive brown signal outside nuclei can obscure a genuine ALYREF result (HPA: tissue IHC; standard IHC practice).
How should I score ALYREF IHC when most cells have nuclear staining? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and count intact nuclei in comparable regions, excluding necrosis, folds and section edges before scoring (standard IHC practice). Because the tissue profile describes ubiquitous nuclear expression, report nuclear intensity with an H score or the percentage of positive nuclei rather than treating any brown pixel as positive (HPA: tissue IHC; standard IHC practice). If cell abundance differs, normalise positive nuclei to all evaluable nuclei in that population; for spatial comparisons, report positive cell density per mm² of evaluable tissue (standard IHC practice). Keep retrieval, DAB development, imaging and positivity thresholds consistent across samples, and report cytoplasmic staining separately (datasheet M03580: retrieval and DAB; standard IHC practice).
How can I distinguish genuine ALYREF staining from IHC artefact?
A convincing result places signal mainly in intact nuclei, consistent with ubiquitous nuclear tissue staining and nucleoplasmic or speckled localisation (HPA: tissue IHC; HPA: subcellular). High nuclear staining has been reported in adipocytes, hematopoietic cells and respiratory epithelial cells, so check cell identity before calling a pattern unexpected (HPA: adipose tissue, bone marrow, bronchus). Question staining confined to section edges or necrotic areas, and compare a no primary section for endogenous enzyme activity or nonspecific DAB deposit (standard IHC practice). Predominantly extracellular or membrane outlined signal conflicts with ALYREF's intracellular localisation and lack of a transmembrane segment, and warrants technical review (UniProt Q86V81: subcellular, topology; standard IHC practice).
Boster reagents

Best ALYREF / THO complex subunit 4 IHC Antibodies

Two anti-ALYREF antibodies have IHC images from human paraffin sections (catalog image captions); one also has IF/ICC data from A431 cells (A03580-3 IF image caption). Both list human, mouse and rat reactivity (catalog).

Real IHC data IHC analysis of ALY using anti-ALY antibody (M03580). ALY was detected in a paraffin-embedded section of human lung 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 1:50 rabbit anti-ALY Antibody (M03580) overnight at 4°C. Peroxidase Conjugated Goat Anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using HRP Conjugated Rabbit IgG Super Vision Assay Kit (Catalog # SV0002) with DAB as the chromogen.
Anti-Aly Rabbit Monoclonal Antibody
Cat # M03580
Real IHC data IHC analysis of ALYREF using anti-ALYREF antibody (A03580-3). ALYREF was detected in a paraffin-embedded section of human liver 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-ALYREF Antibody (A03580-3) overnight at 4°C. Peroxidase Conjugated Goat Anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using HRP Conjugated Rabbit IgG Super Vision Assay Kit (Catalog # SV0002) with DAB as the chromogen.
Anti-ALYREF Antibody ®
Cat # A03580-3

M03580 will render with human lung cancer paraffin-section IHC data; its other IHC captions show human lymphoma, glioma and testis cancer sections (M03580 IHC image captions). A03580-3 will render with human liver cancer paraffin-section IHC data and also has A431 cell IF/ICC data (A03580-3 IHC and IF image captions).

Which to pick: For tissue IHC, choose M03580 if a rabbit monoclonal with several illustrated human paraffin-section samples is useful (M03580 catalog; M03580 IHC image captions); its illustrated protocol used EDTA retrieval at pH 8.0 and a 1:50 primary dilution (M03580 IHC image captions). For IF/ICC, choose A03580-3 because its A431 image documents fluorescence detection at 5 μg/ml (A03580-3 IF image caption). Both list human, mouse and rat reactivity, while their illustrated tissue IHC is human paraffin sections only; neither IHC caption reports the fixative (catalog reactivity; M03580 and A03580-3 IHC image captions).

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

References

  1. UniProt Consortium. UniProt entry Q86V81 (THOC4_HUMAN, THO complex subunit 4).
  2. Human Protein Atlas. ALYREF tissue IHC expression (reliability: Supported).
  3. Human Protein Atlas. ALYREF subcellular location (ICC-IF): Localized to the nucleoplasm and nuclear speckles..
  4. Human Protein Atlas. ALYREF antibody validation summary (3 antibodies).
  5. ALYREF associated with immune infiltration is a prognostic biomarker in hepatocellular carcinoma. Translational oncology 2022 — PMC9079359.
  6. Comprehensive analysis of ALYREF gene expression and its correlation with immunotherapy efficacy and circulating tumor cells in bladder cancer. Scientific reports 2025 — PMC12618602.
  7. ALYREF/THOC4 expression and cell growth modulation in retinoblastoma. Pathology, research and practice 2024 — PMC12439426.
  8. Drosophila Ref1/ALYREF regulates transcription and toxicity associated with ALS/FTD disease etiologies. Acta neuropathologica communications 2019 — PMC6487524.
  9. PubMed PMID:16625196 — UniProt-cited evidence.
  10. PubMed PMID:15489334 — UniProt-cited evidence.
  11. PubMed PMID:9952027 — UniProt-cited evidence.