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PTPRZ1 / Receptor-type tyrosine-protein phosphatase zeta · Western blot design guide
Design a Western Blot for PTPRZ1
Source-linked PTPRZ1 Western blot protocol options, expected-band and isoform facts, troubleshooting for weak or shifted signal, and recommended anti-PTPRZ1 WB antibodies. Everything you need to plan the experiment before you commit precious samples.
Evidence assembled September 2026 · For research use; verify linked source records and product datasheet before use
PTPRZ1 Western Blot Experimental Design Guide
Expected bands, source-linked protocol options, controls and antibodies — the at-a-glance facts below, then the full design guide.
Must know before running
| Expected band | ~254.6 kDa | |
| Gel | 4–12% gradient (standard starting point) | |
| Positive control | Cerebral cortex (IHC candidate; verify WB) +3 more | |
| Negative control | Adipose tissue (IHC candidate; verify WB) |
Important caveats
Reasons your observed band may differ from the expected size.
| PTM | Glycosylated + Phosphorylated | |
| Caveat | Modification-state controls | |
| Gene-set association | MSigDB C7 membership | |
| Isoform | 3 isoform(s) |
Section 1
Source-Linked PTPRZ1 Western Blot Protocol Options
The A03510 protocol combines labelled catalog values with standard starting conditions. Published comparisons retain their own sample, reagent and detection scope.
| Sample / lysate | various cells (catalog A03510) |
| Gel % | 4–12% gradient (standard starting point) |
| Load | 20–30 µg total protein per lane; optimize for abundance (standard starting point) |
| Transfer | Wet/tank transfer; optimize duration (standard starting point) |
| Membrane | 0.45 µm PVDF (standard starting point) |
| Blocking | 5% milk or 5% BSA in TBST (standard starting point) |
| Primary antibody | A03510 · 1:500 (catalog A03510) |
| Primary incubation | Overnight at 4 °C (standard starting point) |
| Secondary antibody | Species-matched HRP conjugate at validated dilution (standard starting point) |
| Secondary incubation | 1 h at room temperature (standard starting point) |
| Wash | 3 × 5 min in TBST (standard starting point) |
| Detection | ECL; bracket exposures to avoid saturation (standard starting point) |
Section 2
What Is the Expected PTPRZ1 Western Blot Band Size?
PTPRZ1 has a predicted full-length mass of 254.6 kDa; glycosylation, signal-peptide removal, and isoforms could affect migration, but no observed band is supplied.
| Band near 254.6 kDa | May represent the predicted full-length precursor; identity requires controls. |
| Band above 254.6 kDa | N-linked glycosylation is possible, but its effect on migration is unconfirmed. |
| Band slightly below the precursor | May reflect removal of the 1–24 signal peptide. |
| Several bands at different positions | Isoforms 1, 2, and 3 may contribute; distinct migration is unconfirmed. |
| Little or no band in lysate | A shed extracellular form may be present in conditioned medium. |
💡Expected PTPRZ1 appearanceThe predicted full-length precursor is 254.6 kDa; no empirical band size is supplied, so use peptide blocking and appropriate sample controls to establish band identity.
| Predicted full-length mass | 254.6 kDa is the sequence-based reference, not a validated blot position. |
| N-linked glycosylation at Asn105 and other listed sites | May increase apparent size or broaden migration if occupied; the shift is unquantified. |
| Signal peptide at residues 1–24 | Its removal makes the mature chain smaller than the precursor; migration is unquantified. |
| Splice isoforms 1, 2, and 3 | May differ in apparent size; their masses and band separation are unknown. |
| Situation | Likely cause | Next action |
|---|---|---|
| No band in lysate | Extracellular-domain shedding may reduce the cellular signal. | Check conditioned medium alongside membrane-enriched lysate. |
| Band higher than expected | Occupancy of the listed N-linked glycosylation sites may affect migration. | Compare matched samples before and after N-glycan removal; confirm identity by peptide blocking. |
| Band lower than expected | Signal-peptide removal or extracellular-domain shedding may yield a smaller species. | Compare lysate with conditioned medium and verify the band with a second epitope antibody. |
| Broad smear instead of sharp band | Variable N-linked glycosylation may broaden migration. | Compare matched samples before and after N-glycan removal. |
| Multiple bands | Isoforms 1, 2, and 3 or differing N-glycan occupancy may contribute. | Use peptide blocking and compare matched samples before and after N-glycan removal. |
| Weak or no signal | The target may be concentrated in the membrane fraction or shed into medium. | Check membrane-enriched lysate and conditioned medium with a positive control. |
Experiment evidence
Western blot images showing PTPRZ1 band
A03510 · PTPRZ1
A03510 · PTPRZ1
A03510 · PTPRZ1
← swipe / scroll for more images →
Real WB data behind the band-size expectations in this section.
Sample controls for PTPRZ1 Western blot
🧪HPA-IHC candidate guidance (verify in WB): For positive controls for PTPRZ1 in Western blot, you can use cerebral cortex tissue, where HPA reports high expression.
Positive control: Cerebral cortex (IHC candidate; verify WB)
Negative control: Adipose tissue (IHC candidate; verify WB)
Loading controls: Run GAPDH, β-actin, and a total-protein stain such as Ponceau alongside the samples.
⚠️Feasibility: PTPRZ1 is membrane-bound, but its shed extracellular domain may require an extracellular sample to detect.
HPA tissue expression evidence for PTPRZ1
Comprehensive Human Protein Atlas IHC scoring per tissue. Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Higher expression tissues · candidate positive controls from IHC
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Cerebral cortex | neuropil | High | Protein (IHC) | HPA → |
| Caudate | glial cells | Medium | Protein (IHC) | HPA → |
| Cerebellum | molecular layer cells - cytoplasm/membrane | Medium | Protein (IHC) | HPA → |
| Hippocampus | neuronal cells | Medium | Protein (IHC) | HPA → |
Lower expression tissues · IHC evidence, not confirmed WB-negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | adipocytes | Not detected | Protein (IHC) | HPA → |
| Adrenal gland | glandular cells | Not detected | Protein (IHC) | HPA → |
| Appendix | glandular cells | Not detected | Protein (IHC) | HPA → |
| Bone marrow | hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Breast | adipocytes | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced PTPRZ1 Western Blot Tips
Deeper troubleshooting and optimisation questions for PTPRZ1, answered from its protein features.
How should PTPRZ1 band migration be interpreted?
Band shift · Use the separately labelled calculated mass and catalog-observed evidence above. A sequence annotation does not establish an observed migration shift. Verify target identity with orthogonal controls.
How could PTPRZ1 isoforms affect band interpretation?
Isoforms · Three isoforms are listed. Relative to the canonical sequence, isoform 3 lacks residues 755–1614, while isoforms 2 and 3 lack residues 1723–1729. Check whether the antibody epitope is retained before assigning bands to isoforms. These sequence differences alone do not establish their apparent band sizes.
Which PTPRZ1 glycosylation sites matter when assessing heterogeneous bands?
PTM · UniProt lists 19 N-linked sites and chondroitin sulfate attachment at Ser587, Ser637, Ser997, Ser1549 and Ser1551. Ser637 is annotated as alternate to phosphorylation. Glycosylation could contribute to heterogeneous migration, but the annotations do not prove that any particular band reflects a glycoform.
The supplied UniProt coordinates are phosphoserines 637, 639 and 2055, and phosphothreonines 1684 and 1687. Ser637 phosphorylation is annotated as alternate to chondroitin sulfate attachment. Check that any phospho-specific antibody uses the same sequence numbering; these sites do not establish a visible band shift.
The supplied UniProt coordinates are phosphoserines 637, 639 and 2055, and phosphothreonines 1684 and 1687. Ser637 phosphorylation is annotated as alternate to chondroitin sulfate attachment. Check that any phospho-specific antibody uses the same sequence numbering; these sites do not establish a visible band shift.
Does this guide establish induction of PTPRZ1?
Induction · No general induction response is established by this guide. A pathway or gene-set association is not evidence of induction in a particular specimen. Verify the relevant treatment and control in a target-specific experiment.
What transfer method to use for PTPRZ1 Western blot?
Transfer · Start by assessing high-mass transfer with a total-protein stain on the membrane and a post-transfer gel: canonical PTPRZ1 is predicted at 254.6 kDa and is a membrane proteoglycan. Optimize transfer conditions if protein remains in the gel. The supplied features do not identify a uniquely validated transfer method.
How should blocking be optimized?
Blocking · Standard workflow guidance: follow the A03510 datasheet where specified. Otherwise compare 5% milk or 5% BSA in TBST; for a phospho-specific assay start with BSA. Optimize background and specific signal with matched controls.
How should PTPRZ1 bands be quantified across samples?
Quantitation · Use the same antibody and sample fraction across comparisons, and check whether its epitope occurs in all isoforms being measured. Isoform 1 is membrane-associated, and UniProt notes an apparently shed extracellular form. Quantify distinct bands separately unless their identities are established; total signal may combine different forms.
Why might PTPRZ1 migrate differently from 254.6 kDa?
Interpretation · 254.6 kDa is the predicted mass. PTPRZ1 has a signal peptide at residues 1–24 and 24 annotated glycosylation sites. These features may affect apparent migration, but they do not establish a visible shift or explain a particular band; no observed band size was supplied.
Consider the three isoforms, annotated glycosylation, and the apparently shed extracellular form of isoform 1. Compare membrane and secreted fractions and confirm that the antibody epitope is present in the proposed form. The supplied features cannot identify an unexpected band by size alone.
Consider the three isoforms, annotated glycosylation, and the apparently shed extracellular form of isoform 1. Compare membrane and secreted fractions and confirm that the antibody epitope is present in the proposed form. The supplied features cannot identify an unexpected band by size alone.
Boster reagents
PTPRZ1 Western Blot Antibodies
Catalog antibodies with Western blot application and product-specific WB images. Evaluate suitability with the reported sample, controls and experimental conditions.
Real WB data
Anti-PTP zeta PTPRZ1 Antibody
Cat # A03510
The catalog reports A03510 for PTPRZ1 Western blotting, with reported human, mouse, and rat reactivity. Its WB image caption describes various cells tested at 1:500 but does not identify the cells or establish species-specific WB validation.
Which to pick: A03510 is the only listed option and has a WB image. Check that its reported reactivity covers your sample; the supplied caption does not identify which cells were blotted.
Source: BosterBio PTPRZ1 gene-info card — filtered to Western-blot-capable antibodies; each card shows that product's actual WB validation figure.
References
- UniProt Consortium. UniProt entry P23471.
- Human Protein Atlas. PTPRZ1 tissue expression.
- PMC8890887 — target-verified WB comparison
- PMC10524925 — target-verified WB comparison
- PMC6267809 — target-verified WB comparison