NTN3 (Netrin-3) is a secreted extracellular matrix protein belonging to the netrin/laminin family. Netrins are chemotropic factors that guide axon migration during neural development. NTN3 contains a laminin N-terminal domain, three laminin EGF-like domains, and a netrin (NTR) domain. The protein is secreted and localized to the extracellular matrix where it functions as an axon guidance cue, binding to netrin receptors such as DCC and UNC5 family members on growth cones. NTN3 has restricted expression, predominantly in spinal cord. It is NOT a transcription factor despite erroneous IBA annotations suggesting transcription factor activity.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0000981
DNA-binding transcription factor activity, RNA polymerase II-specific
|
IBA
GO_REF:0000033 |
REMOVE |
Summary: Erroneous IBA propagation from PANTHER:PTN000180816. NTN3 is a secreted axon guidance protein with no DNA-binding domains. See file:interpro/panther/PTHR10574/PTHR10574-review.md for detailed family analysis.
Reason: NTN3 belongs to PTHR10574 (Netrin/Laminin family), not PTHR11636 (POU domain TFs). Erroneous phylogenetic grouping with POU-domain transcription factors.
Supporting Evidence:
file:interpro/panther/PTHR10574/PTHR10574-review.md
CRITICAL ANNOTATION ERROR section documents erroneous IBA from PTN000180816
|
|
GO:0006357
regulation of transcription by RNA polymerase II
|
IBA
GO_REF:0000033 |
REMOVE |
Summary: Erroneous IBA propagation - same root cause as GO:0000981. See family review.
Reason: NTN3 is a secreted extracellular protein, not a transcription regulator.
Supporting Evidence:
file:interpro/panther/PTHR10574/PTHR10574-review.md
See CRITICAL ANNOTATION ERROR section
|
|
GO:0000978
RNA polymerase II cis-regulatory region sequence-specific DNA binding
|
IBA
GO_REF:0000033 |
REMOVE |
Summary: Erroneous IBA propagation - same root cause as GO:0000981. See family review.
Reason: NTN3 has no DNA-binding domains (laminin/EGF/NTR domains only).
Supporting Evidence:
file:interpro/panther/PTHR10574/PTHR10574-review.md
See CRITICAL ANNOTATION ERROR section
|
|
GO:0005737
cytoplasm
|
IEA
GO_REF:0000117 |
KEEP AS NON CORE |
Summary: This annotation is likely over-general or misleading. While NTN3 may transit through the cytoplasm during biosynthesis before secretion via the ER-Golgi pathway, its functional localization is extracellular. The ARBA machine learning annotation is technically not wrong but does not reflect the protein's primary functional location.
Reason: NTN3 is synthesized in the cytoplasm and transits through the secretory pathway, so transient cytoplasmic presence during biosynthesis is expected. However, the mature functional protein is secreted to the extracellular matrix. This annotation is not incorrect but is not informative about the core function or localization of NTN3.
Supporting Evidence:
UniProt:O00634
-!- SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix
|
|
GO:0007409
axonogenesis
|
IEA
GO_REF:0000117 |
ACCEPT |
Summary: This annotation is appropriate but could be more specific. NTN3 is a netrin family member that functions in axon guidance, which is a subprocess of axonogenesis. The ARBA annotation captures a relevant biological process for this protein.
Reason: Netrins are well-established axon guidance cues that regulate axonogenesis by guiding the growth and direction of axons during neural development. While GO:0007411 (axon guidance) is more specific, axonogenesis is an appropriate broader term. The annotation aligns with established netrin family function.
Supporting Evidence:
UniProt:O00634
-!- FUNCTION: Netrins control guidance of CNS commissural axons and peripheral motor axons.
PMID:9143507
The netrins define a family of chemotropic factors that have been shown to play a central role in axon guidance.
|
|
GO:0005515
protein binding
|
IPI
PMID:26190107 A Floor-Plate Extracellular Protein-Protein Interaction Scre... |
MARK AS OVER ANNOTATED |
Summary: This annotation is supported by experimental evidence from PMID:26190107 showing NTN3 interacts with DRAXIN. However, "protein binding" is uninformative and the interaction is with a secreted netrin antagonist rather than a netrin receptor.
Reason: While the experimental evidence (IPI from PMID:26190107) demonstrates protein-protein interaction between NTN3 and DRAXIN, the term "protein binding" is too general and uninformative. DRAXIN is a secreted antagonist that competes with DCC/UNC5 family receptors for netrin binding, not itself a netrin receptor, so GO:1990890 netrin receptor binding is not an appropriate replacement term for this interaction.
Supporting Evidence:
PMID:26190107
The assembled floor-plate network contains 47 interactions including the hitherto-not-reported interaction between Netrin-1 and Draxin.
UniProt:O00634
O00634; Q8NBI3: DRAXIN; NbExp=2; IntAct=EBI-10831998, EBI-10827752
|
|
GO:0005102
signaling receptor binding
|
IEA
GO_REF:0000107 |
ACCEPT |
Summary: This annotation is appropriate. NTN3 is a secreted ligand that binds to netrin receptors (DCC, UNC5 family members) on target cells to mediate axon guidance. The annotation correctly captures the molecular function of NTN3 as a receptor ligand, though netrin receptor binding (GO:1990890) would be more specific.
Reason: NTN3 functions as a secreted signaling molecule that binds to cell surface receptors (netrin receptors) to mediate chemotropic guidance of axons. This is a core molecular function of netrin family proteins. The annotation appropriately captures the receptor binding activity, transferred from mouse ortholog (UniProtKB:Q9R1A3).
Supporting Evidence:
UniProt:O00634
-!- FUNCTION: Netrins control guidance of CNS commissural axons and peripheral motor axons.
file:human/NTN3/NTN3-deep-research-falcon.md
NTN3/Netrin-3 is summarized as a secreted extracellular ligand that binds UNC5-family receptors, neogenin, and DCC-family receptors.
|
|
GO:1990890
netrin receptor binding
|
NAS | NEW |
Summary: Add the more specific molecular-function term for NTN3's receptor-ligand activity. The Falcon report summarizes direct binding evidence for NTN3/Netrin-3 with canonical netrin receptors, including UNC5-family receptors, neogenin, and DCC-family receptors, with comparatively strong binding to UNC5B and UNC5C in available datasets.
Reason: Existing GO:0005102 signaling receptor binding is directionally correct but too broad for a netrin ligand. GO:1990890 captures the core receptor-binding molecular function without misusing the term for the separate DRAXIN antagonist interaction.
Supporting Evidence:
file:human/NTN3/NTN3-deep-research-falcon.md
Binding data summarized in the report support NTN3 as a netrin receptor ligand, with comparatively strong binding to UNC5B and UNC5C in available datasets.
|
|
GO:0005576
extracellular region
|
IEA
GO_REF:0000107 |
ACCEPT |
Summary: This annotation is correct and represents a core localization for NTN3. The protein contains a signal peptide and is secreted to the extracellular space where it functions as an axon guidance cue.
Reason: NTN3 is a secreted protein (signal peptide residues 1-27) that localizes to the extracellular region, specifically the extracellular matrix. This is the primary functional localization for netrin family proteins where they establish chemotropic gradients for axon guidance.
Supporting Evidence:
UniProt:O00634
-!- SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix
|
|
GO:0005794
Golgi apparatus
|
IEA
GO_REF:0000107 |
KEEP AS NON CORE |
Summary: This annotation is acceptable as NTN3 is a secreted protein that transits through the Golgi apparatus during biosynthesis. The annotation likely reflects Golgi localization during the secretory pathway.
Reason: As a secreted protein, NTN3 passes through the Golgi apparatus during biosynthesis and maturation. While this is not the final functional localization, it is a valid component of the secretory pathway that NTN3 uses. The annotation is not incorrect but represents transient localization rather than core function.
Supporting Evidence:
UniProt:O00634
-!- SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix
|
|
GO:0007411
axon guidance
|
NAS
PMID:9143507 The NTN2L gene encoding a novel human netrin maps to the aut... |
ACCEPT |
Summary: This is a core annotation for NTN3 supported by the primary characterization paper. PMID:9143507 describes NTN3 (then called NTN2L) as a member of the netrin family of chemotropic factors that play a central role in axon guidance. The annotation appropriately captures the primary biological function of this protein.
Reason: Axon guidance is the core biological function of netrin family proteins including NTN3. The cited paper (PMID:9143507) explicitly states that netrins play a central role in axon guidance. This is well-supported by the literature on netrin family function.
Supporting Evidence:
PMID:9143507
The netrins define a family of chemotropic factors that have been shown to play a central role in axon guidance.
UniProt:O00634
-!- FUNCTION: Netrins control guidance of CNS commissural axons and peripheral motor axons.
|
Q: Has NTN3-specific receptor binding been characterized, or is receptor binding inferred from netrin-1 studies? Most functional studies focus on NTN1 (Netrin-1). Direct evidence for NTN3-receptor interactions would strengthen annotations.
Q: What is the functional relationship between NTN3 and DRAXIN in axon guidance? PMID:26190107 shows netrin-DRAXIN interaction. Understanding if this applies specifically to NTN3 would inform annotation.
Experiment: Receptor binding assays to confirm NTN3 binds DCC and UNC5 receptors directly. This would provide direct evidence for GO:1990890 annotation specific to NTN3.
Experiment: Axon guidance assays in NTN3 knockout or knockdown models to confirm NTN3 specifically functions in axon guidance rather than relying on family membership inference.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Human NTN3 encodes Netrin-3, a secreted laminin-like guidance cue historically referred to as NTN2L (netrin-2-like), consistent with UniProt O00634’s naming and “precursor” (secreted) status. A foundational cloning/characterization study identified mouse netrin-3 (Ntn3) as the ortholog of human NTN2L/NTN3, with high sequence identity and the canonical netrin domain structure (domains VI, V subdomains, and C). This cross-species mapping and conserved receptor binding support that the literature summarized here corresponds to the correct human target (NTN3/O00634). (wang1999netrin3amouse pages 1-2, wang1999netrin3amouse pages 4-5)
Netrins are secreted or membrane-associated proteins that regulate axon guidance and broader tissue morphogenesis by engaging specific cell-surface receptors. Netrin-3 (NTN3) is one of the secreted netrins in mammals, and is commonly considered part of a receptor–ligand system that can influence cell migration, survival, and differentiation depending on receptor context. (gao2024researchprogressof pages 2-5)
A recent cancer-focused review emphasizes that several netrin receptors (including DCC, UNC5 family, and NEO1) function as dependence receptors, meaning signaling outcomes differ depending on whether ligand is present; ligand binding supports survival/migration/differentiation, while ligand absence can allow pro-apoptotic signaling. This conceptual framework is often used to interpret netrin pathway roles in tumor biology. (gao2024researchprogressof pages 2-5)
Netrin-3 has the canonical netrin architecture (domains VI, V, C) defined by homology to other netrins. This was explicitly documented in the original cloning and protein characterization of murine netrin-3 orthologous to human NTN3/NTN2L. (wang1999netrin3amouse pages 1-2, wang1999netrin3amouse pages 4-5)
Netrin-3 is a secreted extracellular protein. Developmental expression studies in mouse indicated netrin-3 is produced in specific tissues and acts extracellularly to bind netrin receptors on responding cells. (wang1999netrin3amouse pages 1-2, wang1999netrin3amouse pages 7-8)
Mouse netrin-3 was shown to bind receptors from the DCC family (DCC and neogenin/NEO1) and the UNC5 family, but with comparatively weaker binding to DCC than to several other receptors tested. (wang1999netrin3amouse pages 1-2, wang1999netrin3amouse pages 7-8)
Two independent quantitative datasets illustrate netrin-3’s receptor preference pattern:
(A) Equilibrium binding (mouse netrin-3; 1999):
- UNC5H1: Kd 6.2 nM
- UNC5H2: Kd 3.3 nM
- UNC5H3: Kd 4.5 nM
- Neogenin: Kd 3.0 nM
- DCC: Kd 11.5 nM
These results support the conclusion that netrin-3 binds multiple canonical netrin receptors, with lower affinity for DCC than for UNC5 receptors/neogenin in that assay system. (wang1999netrin3amouse pages 7-8)
(B) Bio-layer interferometry (BLI; netrin-3 ortholog surrogate used for biophysics; 2021 figure):
- DCC: Kd 31.0 ± 0.1 nM
- UNC5A: Kd 106.0 ± 4.3 nM
- UNC5B: Kd 8.8 ± 0.2 nM
- UNC5C: Kd 4.3 ± 0.2 nM
- Neogenin (Neo1): Kd 51.7 ± 0.1 nM
This dataset again highlights relatively strong binding to UNC5B/UNC5C compared with DCC and UNC5A. (jiang2021targetingnetrin‐3in media f2f71bc0, jiang2021targetingnetrin‐3in media 4186dfe0)
Mouse netrin-3 is strongly expressed in sensory ganglia during peripheral nerve development, as well as in mesenchymal cells and muscles at relevant developmental stages, and is described as largely excluded from the CNS at early stages. Functionally, netrin-3 can mimic netrin-1’s outgrowth-promoting activity on commissural axons and chemorepulsive activity in a motor axon assay, but it has lower specific outgrowth activity than netrin-1. (wang1999netrin3amouse pages 1-2, wang1999netrin3amouse pages 7-8)
A quantitative comparison in explant outgrowth assays reported that optimal commissural outgrowth required about 120 µg/mL netrin-3, approximately fourfold higher than netrin-1 under the conditions described, consistent with lower specific activity. (wang1999netrin3amouse pages 7-8)
In embryonic lung development, netrin gene expression analysis showed that netrin-3 (Ntn3) is transcribed diffusely at low levels throughout lung endoderm and mesoderm (E11.5 in the study). In the same work, the authors emphasized that DCC and Unc5b are expressed in lung epithelial cells and could transduce netrin signals during branching morphogenesis; mechanistic in vitro morphogenesis experiments mainly focused on netrin-1/netrin-4 effects, so NTN3’s direct functional role in branching morphogenesis remains less directly established in the provided evidence. (liu2004novelrolefor pages 1-2)
A kidney development preprint discussing netrin signaling reports that vascular smooth muscle cells in vitro express receptors including NEO1 and UNC5B, and that signaling through these receptors supports endothelial vascular smooth muscle coverage. While this section focuses on netrin-1, it reinforces that UNC5B/NEO1 are plausible transducers for netrin ligands in vascular contexts, consistent with netrin-3’s demonstrated ability to bind these receptor families. (honeycutt2023netrin1directs pages 14-17, wang1999netrin3amouse pages 7-8)
A 2023 study titled “Netrin-3 suppresses diabetic neuropathic pain…” was retrieved only as supplementary materials in the current tool context. From these supplement pages:
- Adult mouse Ntn-3 is expressed in multiple neural tissues (qPCR; n=5–6). (pan2023netrin3suppressesdiabetic pages 1-9)
- Ntn-3 knockout mice showed no significant baseline developmental/behavioral defects, including no significant differences in baseline sensory assays (mechanical allodynia, cold allodynia, thermal hyperalgesia; n=6–17 depending on assay). (pan2023netrin3suppressesdiabetic pages 1-9)
- AAV-driven Ntn-3 overexpression in DRG was predominantly in CGRP+ neurons (n=3). (pan2023netrin3suppressesdiabetic pages 1-9)
Because the main article text and primary experimental figures were not available in the retrieved text chunk, mechanistic conclusions about pain suppression and receptor pathways cannot be reliably summarized here beyond these supporting data. (pan2023netrin3suppressesdiabetic pages 1-9)
A key translational paper reported that NTN3 is selectively expressed in neuroblastoma (NB) and small cell lung cancer (SCLC) (neuroectodermal/neuroendocrine lineages), with netrin-3 and netrin-1 expression described as mutually exclusive in these contexts. Mechanistically, NTN3 expression was linked to:
- MYCN regulation in neuroblastoma (ChIP-seq enhancer/promoter occupancy; MYCN pathway enrichment in high-NTN3 patients P=0.039, FDR q=0.025). (jiang2021targetingnetrin‐3in pages 5-7, jiang2021targetingnetrin‐3in pages 5-5)
- ASCL1 or NeuroD1 regulation in SCLC. (jiang2021targetingnetrin‐3in pages 1-2, jiang2021targetingnetrin‐3in pages 5-7)
NTN3 expression was reported to correlate with neuroblastoma stage/aggressiveness and overall survival. Specifically, one analysis reported 150-month overall survival of 72.5% (low NTN3) vs 46.6% (high NTN3), P=0.029; a subgroup with ≥2× NTN3 expression had 28.5% overall survival (P=0.002). (jiang2021targetingnetrin‐3in pages 1-2)
A figure-based dataset from the same work shows Kaplan–Meier curves where high NTN3 is associated with worse overall survival in a cohort of 181 patients (P=0.0294) and a larger cohort of 498 patients (P ≤ 0.0001), with a stage-4 trend P=0.0514. (jiang2021targetingnetrin‐3in media f2f71bc0, jiang2021targetingnetrin‐3in media 4186dfe0)
Functional experiments support a causal role for NTN3 in tumor growth/engraftment:
- In SCLC xenograft/engraftment assays, CRISPR targeting of NTN3 delayed or inhibited engraftment; reported guide-level p-values include H82 (sG1 P=0.0022; sG2,sG3 ≤0.001) and H69 (sG1 P=0.017; sG2 P=0.028; sG3 P=0.001). (jiang2021targetingnetrin‐3in pages 8-9)
- In chick CAM tumor assays for NB lines, NTN3 silencing reduced tumor size (reported p=0.0011 and p=0.0025 in two lines/experiments as excerpted). (jiang2021targetingnetrin‐3in pages 5-5)
A 2024 eLife paper identifies netrin pathway components as essential for survival of dormant high-grade serous ovarian cancer (HGSOC) spheroids. The authors state that Netrin-1 and Netrin-3 and their receptors are required for low-level ERK activation supporting survival in dormancy conditions. They further report that sorting TCGA cases by high expression of Netrin-1 and -3 reveals significantly shorter overall survival, and that this trend is evident even in cases that only overexpress Netrin-3. (perampalam2024netrinsignalingmediates pages 10-13)
The anti-netrin-1 humanized monoclonal antibody NP137 (developed against netrin-1) was discussed as relevant to NTN3 because the NP137 epitope in netrin-1 shares ~90% homology with the corresponding region in netrin-3, supporting cross-reactivity and enabling functional interference with netrin-3 in relevant tumor models. (jiang2021targetingnetrin‐3in pages 1-2, jiang2021targetingnetrin‐3in pages 5-7)
Because NTN3 is secreted, the NB/SCLC study suggests it “could thus emerge as a diagnostic marker” potentially measurable in blood, though it also reports difficulties validating commercial antibodies for immunohistochemistry, indicating practical assay-development limitations. (jiang2021targetingnetrin‐3in pages 8-9)
Open Targets lists small evidence sets connecting NTN3 to neurological pain-related conditions (trigeminal nerve disease/neuralgia) and cancer-related phenotypes (including cancer, nonpapillary renal cell carcinoma, prostate cancer), but with only 2 evidence items per association in the retrieved output, so these associations should be treated as hypothesis-supporting rather than definitive. (OpenTargets Search: -NTN3)
A 2023 ccRCC-focused paper that mined GTEx and Human Protein Atlas datasets reports:
- NTN3 mRNA tends to be low across tissues, with relatively higher expression in testes, liver, and endometrium. (ke2023netrinfamilygenes pages 6-9)
- HPA immunohistochemistry summary described NTN3 protein detection more broadly in cavity-containing tissues, including esophagus, bronchus, nasal cavity, and kidney. (ke2023netrinfamilygenes pages 6-9)
In ccRCC TCGA analyses, NTN3 was described as downregulated in tumors but not significantly different in paired tumor/adjacent samples (n=72 pairs) and was the exception to netrin-family genes showing strong ROC performance (AUC>0.8). (ke2023netrinfamilygenes pages 6-9)
Across foundational developmental neurobiology and modern cancer biology, the most evidence-supported “primary function” for NTN3/Netrin-3 is as a secreted extracellular ligand that binds UNC5 family receptors, neogenin, and DCC-family receptors to modulate cellular navigation and survival programs, with a consistent pattern of stronger binding to UNC5B/UNC5C than to DCC in multiple binding datasets. (wang1999netrin3amouse pages 7-8, jiang2021targetingnetrin‐3in media f2f71bc0, jiang2021targetingnetrin‐3in media 4186dfe0)
The strongest human disease evidence to date (in the retrieved corpus) places NTN3 as a lineage-associated dependency factor in neuroblastoma and small cell lung cancer, and as part of a broader netrin signaling module supporting survival of dormant ovarian cancer spheroids, making ligand–receptor interference a plausible therapeutic strategy in specific contexts (with NP137 cross-reactivity as a concrete implementation path). (jiang2021targetingnetrin‐3in pages 1-2, jiang2021targetingnetrin‐3in pages 8-9, jiang2021targetingnetrin‐3in pages 5-5, perampalam2024netrinsignalingmediates pages 10-13)
The following table consolidates the main functional-annotation claims and quantitative data for NTN3.
| Category | Key findings | Primary supporting citation context IDs |
|---|---|---|
| identity/domains | Human NTN3 corresponds to Netrin-3 (historically NTN2L; netrin-2-like), a secreted netrin family protein. Foundational cloning work on the orthologous mouse protein showed the canonical netrin architecture with VI, V, and C domains and high identity to human NTN2L/NTN3, supporting the UniProt O00634 assignment. A recent review lists human NTN3 at 16p13.3, 580 aa, ~61 kDa. | (wang1999netrin3amouse pages 1-2, wang1999netrin3amouse pages 4-5, gao2024researchprogressof pages 2-5) |
| localization | NTN3/Netrin-3 is a secreted extracellular guidance cue. During embryogenesis in mouse, netrin-3 is highly expressed in sensory ganglia, mesenchymal cells, and muscle, with relative exclusion from early CNS ventral spinal cord; in lung development, netrin-3 transcripts are diffuse at low levels throughout endoderm and mesoderm rather than restricted to basal lamina-enriched proximal buds like netrin-4. | (wang1999netrin3amouse pages 1-2, wang1999netrin3amouse pages 7-8, liu2004novelrolefor pages 1-2) |
| receptors/binding | Mouse netrin-3 binds canonical netrin receptors with reported equilibrium Kd values: UNC5H1 6.2 nM, UNC5H2 3.3 nM, UNC5H3 4.5 nM, neogenin 3.0 nM, DCC 11.5 nM, indicating weaker DCC binding than other receptors. Jiang et al. used a netrin-3 ortholog surrogate and reported Kd values by BLI: DCC 31.0 ± 0.1 nM, UNC5A 106.0 ± 4.3 nM, UNC5B 8.8 ± 0.2 nM, UNC5C 4.3 ± 0.2 nM, Neogenin 51.7 ± 0.1 nM; strongest binding was to UNC5B/UNC5C. | (wang1999netrin3amouse pages 7-8, jiang2021targetingnetrin‐3in pages 5-7, jiang2021targetingnetrin‐3in media f2f71bc0, jiang2021targetingnetrin‐3in media 4186dfe0) |
| developmental roles | Foundational evidence supports a developmental axon-guidance role, especially in the peripheral nervous system: murine netrin-3 promotes commissural axon outgrowth and repels trochlear motor axons, but with lower specific activity than netrin-1; optimal commissural outgrowth required about 120 µg/mL netrin-3, ~4-fold higher than netrin-1. In embryonic lung, NTN3 is present transcriptionally but the morphogenetic inhibition data were strongest for netrin-1/netrin-4, so NTN3’s lung role remains less directly established. | (wang1999netrin3amouse pages 1-2, wang1999netrin3amouse pages 7-8, liu2004novelrolefor pages 1-2, liu2004novelrolefor pages 2-5) |
| pain/neuronal | In adult mouse, Ntn-3 is expressed in multiple neural tissues. In the diabetic neuropathic pain study’s supplementary data, Ntn-3 knockout mice showed normal development and baseline sensory behavior (mechanical, cold, thermal assays; no significant differences), and AAV-Ntn-3 overexpression in DRG was predominantly in CGRP+ neurons. Supplementary analyses also showed no significant effect of Ntn-3 deficiency on diabetes-associated peripheral axon loss or spinal cord gliosis. | (pan2023netrin3suppressesdiabetic pages 1-9) |
| cancer roles | Neuroblastoma (NB) and small cell lung cancer (SCLC) are the clearest human cancer contexts for NTN3. NTN3 is selectively/highly expressed in NB and SCLC, apparently mutually exclusive with NTN1; expression is driven by MYCN in NB and ASCL1/NeuroD1 in SCLC. In NB, high NTN3 correlated with poorer overall survival: 72.5% vs 46.6% OS at 150 months for low vs high NTN3 (P = 0.029); a subgroup with ≥2× NTN3 had 28.5% OS (P = 0.002). In another cohort, Kaplan–Meier associations were significant in 181 patients (P = 0.0294) and 498 patients (P ≤ 0.0001), with stage-4 trend P = 0.0514. MYCN-pathway enrichment in high-NTN3 NB was P = 0.039, FDR q = 0.025. CRISPR/knockdown reduced tumor growth/engraftment: CAM assays p = 0.0011 and p = 0.0025 after NTN3 silencing in NB lines; SCLC engraftment delays/inhibition with CRISPR had H82 guide p-values 0.0022, ≤0.001, ≤0.001 and H69 guide p-values 0.017, 0.028, 0.001. In ovarian cancer dormancy, Netrin signaling involving Netrin-1/-3 supports survival of dormant spheroids, and high Netrin-1/-3 expression associated with shorter overall survival. | (jiang2021targetingnetrin‐3in pages 1-2, jiang2021targetingnetrin‐3in pages 8-9, jiang2021targetingnetrin‐3in pages 5-7, jiang2021targetingnetrin‐3in pages 5-5, perampalam2024netrinsignalingmediates pages 10-13, jiang2021targetingnetrin‐3in media f2f71bc0, jiang2021targetingnetrin‐3in media 4186dfe0) |
| therapeutics/biomarkers | The anti-netrin-1 antibody NP137 recognizes a V2-domain epitope with about 90% sequence homology in netrin-3, supporting cross-reactivity and providing proof-of-concept for NTN3 targeting. Jiang et al. showed genetic silencing or antibody interference delayed tumor engraftment and reduced tumor growth in NB/SCLC models. The authors also noted secreted NTN3 could emerge as a diagnostic marker, potentially blood-detectable, although they could not validate available anti-NTN3 antibodies for IHC. | (jiang2021targetingnetrin‐3in pages 1-2, jiang2021targetingnetrin‐3in pages 8-9, jiang2021targetingnetrin‐3in pages 5-7) |
| expression in human tissues | In GTEx/HPA-based analyses, NTN3 mRNA is generally low across human tissues, with relatively higher expression in testis, liver, and endometrium. Human Protein Atlas immunohistochemistry data summarized in ccRCC work indicated broader protein detection in cavity-containing tissues including esophagus, bronchus, nasal cavity, and kidney. | (ke2023netrinfamilygenes pages 6-9) |
| databases | Open Targets currently shows limited disease-target evidence for NTN3, including associations to trigeminal nerve disease, trigeminal neuralgia, cancer, nonpapillary renal cell carcinoma, and prostate cancer, but evidence size is small (2 evidence items for listed associations). In ccRCC TCGA analyses, NTN3 was downregulated but not significantly different in 72 paired tumor-adjacent samples and did not show strong diagnostic performance (exception to AUC > 0.8 genes). In single-gene Cox analysis, NTN3 behaved as a DFS risk factor (HR > 1) but was not highlighted as an independent prognostic factor. | (OpenTargets Search: -NTN3, ke2023netrinfamilygenes pages 6-9) |
Table: This table summarizes the main experimentally supported functional annotation points for human NTN3/Netrin-3, including identity, receptor binding, developmental roles, cancer relevance, and tissue expression. It also highlights the strongest quantitative findings and the context IDs that support each row.
References
(wang1999netrin3amouse pages 1-2): Hao Wang, Neal G. Copeland, Debra J. Gilbert, Nancy A. Jenkins, and Marc Tessier-Lavigne. Netrin-3, a mouse homolog of human ntn2l, is highly expressed in sensory ganglia and shows differential binding to netrin receptors. The Journal of Neuroscience, 19:4938-4947, Jun 1999. URL: https://doi.org/10.1523/jneurosci.19-12-04938.1999, doi:10.1523/jneurosci.19-12-04938.1999. This article has 202 citations.
(wang1999netrin3amouse pages 4-5): Hao Wang, Neal G. Copeland, Debra J. Gilbert, Nancy A. Jenkins, and Marc Tessier-Lavigne. Netrin-3, a mouse homolog of human ntn2l, is highly expressed in sensory ganglia and shows differential binding to netrin receptors. The Journal of Neuroscience, 19:4938-4947, Jun 1999. URL: https://doi.org/10.1523/jneurosci.19-12-04938.1999, doi:10.1523/jneurosci.19-12-04938.1999. This article has 202 citations.
(gao2024researchprogressof pages 2-5): Xing Gao, Jiazhou Ye, Xi Huang, Shilin Huang, Wenfeng Luo, Dandan Zeng, Shizhou Li, Minchao Tang, Rongyun Mai, Yongqiang Li, Yan Lin, and Rong Liang. Research progress of the netrins and their receptors in cancer. Journal of Cellular and Molecular Medicine, Mar 2024. URL: https://doi.org/10.1111/jcmm.18241, doi:10.1111/jcmm.18241. This article has 6 citations and is from a peer-reviewed journal.
(wang1999netrin3amouse pages 7-8): Hao Wang, Neal G. Copeland, Debra J. Gilbert, Nancy A. Jenkins, and Marc Tessier-Lavigne. Netrin-3, a mouse homolog of human ntn2l, is highly expressed in sensory ganglia and shows differential binding to netrin receptors. The Journal of Neuroscience, 19:4938-4947, Jun 1999. URL: https://doi.org/10.1523/jneurosci.19-12-04938.1999, doi:10.1523/jneurosci.19-12-04938.1999. This article has 202 citations.
(jiang2021targetingnetrin‐3in media f2f71bc0): Shan Jiang, Mathieu Richaud, Pauline Vieugué, Nicolas Rama, Jean‐Guy Delcros, Maha Siouda, Mitsuaki Sanada, Anna‐Rita Redavid, Benjamin Ducarouge, Maëva Hervieu, Silvia Breusa, Ambroise Manceau, Charles‐Henry Gattolliat, Nicolas Gadot, Valérie Combaret, David Neves, Sandra Ortiz‐Cuaran, Pierre Saintigny, Olivier Meurette, Thomas Walter, Isabelle Janoueix‐Lerosey, Paul Hofman, Peter Mulligan, David Goldshneider, Patrick Mehlen, and Benjamin Gibert. Targeting netrin‐3 in small cell lung cancer and neuroblastoma. EMBO Molecular Medicine, Mar 2021. URL: https://doi.org/10.15252/emmm.202012878, doi:10.15252/emmm.202012878. This article has 25 citations and is from a highest quality peer-reviewed journal.
(jiang2021targetingnetrin‐3in media 4186dfe0): Shan Jiang, Mathieu Richaud, Pauline Vieugué, Nicolas Rama, Jean‐Guy Delcros, Maha Siouda, Mitsuaki Sanada, Anna‐Rita Redavid, Benjamin Ducarouge, Maëva Hervieu, Silvia Breusa, Ambroise Manceau, Charles‐Henry Gattolliat, Nicolas Gadot, Valérie Combaret, David Neves, Sandra Ortiz‐Cuaran, Pierre Saintigny, Olivier Meurette, Thomas Walter, Isabelle Janoueix‐Lerosey, Paul Hofman, Peter Mulligan, David Goldshneider, Patrick Mehlen, and Benjamin Gibert. Targeting netrin‐3 in small cell lung cancer and neuroblastoma. EMBO Molecular Medicine, Mar 2021. URL: https://doi.org/10.15252/emmm.202012878, doi:10.15252/emmm.202012878. This article has 25 citations and is from a highest quality peer-reviewed journal.
(liu2004novelrolefor pages 1-2): Yuru Liu, Elke Stein, Timothy Oliver, Yong Li, William J Brunken, Manuel Koch, Marc Tessier-Lavigne, and Brigid L.M Hogan. Novel role for netrins in regulating epithelial behavior during lung branching morphogenesis. Current Biology, 14:897-905, May 2004. URL: https://doi.org/10.1016/j.cub.2004.05.020, doi:10.1016/j.cub.2004.05.020. This article has 229 citations and is from a highest quality peer-reviewed journal.
(honeycutt2023netrin1directs pages 14-17): Samuel E. Honeycutt, Pierre-Emmanuel Y. N'Guetta, Deanna M. Hardesty, Yubin Xiong, Shamus L. Cooper, Matthew J. Stevenson, and Lori L. O'Brien. Netrin 1 directs vascular patterning and maturity in the developing kidney. Development, Nov 2023. URL: https://doi.org/10.1242/dev.201886, doi:10.1242/dev.201886. This article has 29 citations and is from a domain leading peer-reviewed journal.
(pan2023netrin3suppressesdiabetic pages 1-9): Weiping Pan, Xueyin N. Huang, Zikai Yu, Qiong-Qiong Ding, Li-Ping Xia, Jianfeng Hua, Bokai Gu, Qisong Xiong, Hualin Yu, Junbo Wang, Zhenzhong Xu, Linghui Zeng, Ge Bai, and Huaqing Liu. Netrin-3 suppresses diabetic neuropathic pain by gating the intra-epidermal sprouting of sensory axons. Neuroscience Bulletin, 39:745-758, Jan 2023. URL: https://doi.org/10.1007/s12264-022-01011-8, doi:10.1007/s12264-022-01011-8. This article has 4 citations and is from a peer-reviewed journal.
(jiang2021targetingnetrin‐3in pages 5-7): Shan Jiang, Mathieu Richaud, Pauline Vieugué, Nicolas Rama, Jean‐Guy Delcros, Maha Siouda, Mitsuaki Sanada, Anna‐Rita Redavid, Benjamin Ducarouge, Maëva Hervieu, Silvia Breusa, Ambroise Manceau, Charles‐Henry Gattolliat, Nicolas Gadot, Valérie Combaret, David Neves, Sandra Ortiz‐Cuaran, Pierre Saintigny, Olivier Meurette, Thomas Walter, Isabelle Janoueix‐Lerosey, Paul Hofman, Peter Mulligan, David Goldshneider, Patrick Mehlen, and Benjamin Gibert. Targeting netrin‐3 in small cell lung cancer and neuroblastoma. EMBO Molecular Medicine, Mar 2021. URL: https://doi.org/10.15252/emmm.202012878, doi:10.15252/emmm.202012878. This article has 25 citations and is from a highest quality peer-reviewed journal.
(jiang2021targetingnetrin‐3in pages 5-5): Shan Jiang, Mathieu Richaud, Pauline Vieugué, Nicolas Rama, Jean‐Guy Delcros, Maha Siouda, Mitsuaki Sanada, Anna‐Rita Redavid, Benjamin Ducarouge, Maëva Hervieu, Silvia Breusa, Ambroise Manceau, Charles‐Henry Gattolliat, Nicolas Gadot, Valérie Combaret, David Neves, Sandra Ortiz‐Cuaran, Pierre Saintigny, Olivier Meurette, Thomas Walter, Isabelle Janoueix‐Lerosey, Paul Hofman, Peter Mulligan, David Goldshneider, Patrick Mehlen, and Benjamin Gibert. Targeting netrin‐3 in small cell lung cancer and neuroblastoma. EMBO Molecular Medicine, Mar 2021. URL: https://doi.org/10.15252/emmm.202012878, doi:10.15252/emmm.202012878. This article has 25 citations and is from a highest quality peer-reviewed journal.
(jiang2021targetingnetrin‐3in pages 1-2): Shan Jiang, Mathieu Richaud, Pauline Vieugué, Nicolas Rama, Jean‐Guy Delcros, Maha Siouda, Mitsuaki Sanada, Anna‐Rita Redavid, Benjamin Ducarouge, Maëva Hervieu, Silvia Breusa, Ambroise Manceau, Charles‐Henry Gattolliat, Nicolas Gadot, Valérie Combaret, David Neves, Sandra Ortiz‐Cuaran, Pierre Saintigny, Olivier Meurette, Thomas Walter, Isabelle Janoueix‐Lerosey, Paul Hofman, Peter Mulligan, David Goldshneider, Patrick Mehlen, and Benjamin Gibert. Targeting netrin‐3 in small cell lung cancer and neuroblastoma. EMBO Molecular Medicine, Mar 2021. URL: https://doi.org/10.15252/emmm.202012878, doi:10.15252/emmm.202012878. This article has 25 citations and is from a highest quality peer-reviewed journal.
(jiang2021targetingnetrin‐3in pages 8-9): Shan Jiang, Mathieu Richaud, Pauline Vieugué, Nicolas Rama, Jean‐Guy Delcros, Maha Siouda, Mitsuaki Sanada, Anna‐Rita Redavid, Benjamin Ducarouge, Maëva Hervieu, Silvia Breusa, Ambroise Manceau, Charles‐Henry Gattolliat, Nicolas Gadot, Valérie Combaret, David Neves, Sandra Ortiz‐Cuaran, Pierre Saintigny, Olivier Meurette, Thomas Walter, Isabelle Janoueix‐Lerosey, Paul Hofman, Peter Mulligan, David Goldshneider, Patrick Mehlen, and Benjamin Gibert. Targeting netrin‐3 in small cell lung cancer and neuroblastoma. EMBO Molecular Medicine, Mar 2021. URL: https://doi.org/10.15252/emmm.202012878, doi:10.15252/emmm.202012878. This article has 25 citations and is from a highest quality peer-reviewed journal.
(perampalam2024netrinsignalingmediates pages 10-13): Pirunthan Perampalam, James I MacDonald, Komila Zakirova, Daniel T Passos, Sumaiyah Wasif, Yudith Ramos-Valdes, Maeva Hervieu, Patrick Mehlen, Rob Rottapel, Benjamin Gibert, Rohann JM Correa, Trevor G Shepherd, and Frederick A Dick. Netrin signaling mediates survival of dormant epithelial ovarian cancer cells. eLife, Jul 2024. URL: https://doi.org/10.7554/elife.91766.3, doi:10.7554/elife.91766.3. This article has 11 citations and is from a domain leading peer-reviewed journal.
(OpenTargets Search: -NTN3): Open Targets Query (-NTN3, 5 results). Buniello, A. et al. (2025). Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery. Nucleic Acids Research.
(ke2023netrinfamilygenes pages 6-9): Shuai Ke, Jiayu Guo, Qinghua Wang, Haoren Shao, Mu He, Tao Li, T. Qiu, and Jiayu Guo. Netrin family genes as prognostic markers and therapeutic targets for clear cell renal cell carcinoma: netrin-4 acts through the wnt/β-catenin signaling pathway. Cancers, 15:2816, May 2023. URL: https://doi.org/10.3390/cancers15102816, doi:10.3390/cancers15102816. This article has 11 citations.
(liu2004novelrolefor pages 2-5): Yuru Liu, Elke Stein, Timothy Oliver, Yong Li, William J Brunken, Manuel Koch, Marc Tessier-Lavigne, and Brigid L.M Hogan. Novel role for netrins in regulating epithelial behavior during lung branching morphogenesis. Current Biology, 14:897-905, May 2004. URL: https://doi.org/10.1016/j.cub.2004.05.020, doi:10.1016/j.cub.2004.05.020. This article has 229 citations and is from a highest quality peer-reviewed journal.
id: O00634
gene_symbol: NTN3
product_type: PROTEIN
status: DRAFT
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: >-
NTN3 (Netrin-3) is a secreted extracellular matrix protein belonging to the netrin/laminin family.
Netrins are chemotropic factors that guide axon migration during neural development. NTN3 contains
a laminin N-terminal domain, three laminin EGF-like domains, and a netrin (NTR) domain. The protein
is secreted and localized to the extracellular matrix where it functions as an axon guidance cue,
binding to netrin receptors such as DCC and UNC5 family members on growth cones. NTN3 has restricted
expression, predominantly in spinal cord. It is NOT a transcription factor despite erroneous IBA
annotations suggesting transcription factor activity.
existing_annotations:
- term:
id: GO:0000981
label: DNA-binding transcription factor activity, RNA polymerase II-specific
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
Erroneous IBA propagation from PANTHER:PTN000180816. NTN3 is a secreted axon guidance
protein with no DNA-binding domains. See file:interpro/panther/PTHR10574/PTHR10574-review.md
for detailed family analysis.
action: REMOVE
reason: >-
NTN3 belongs to PTHR10574 (Netrin/Laminin family), not PTHR11636 (POU domain TFs).
Erroneous phylogenetic grouping with POU-domain transcription factors.
supported_by:
- reference_id: file:interpro/panther/PTHR10574/PTHR10574-review.md
supporting_text: "CRITICAL ANNOTATION ERROR section documents erroneous IBA from PTN000180816"
- term:
id: GO:0006357
label: regulation of transcription by RNA polymerase II
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
Erroneous IBA propagation - same root cause as GO:0000981. See family review.
action: REMOVE
reason: >-
NTN3 is a secreted extracellular protein, not a transcription regulator.
supported_by:
- reference_id: file:interpro/panther/PTHR10574/PTHR10574-review.md
supporting_text: "See CRITICAL ANNOTATION ERROR section"
- term:
id: GO:0000978
label: RNA polymerase II cis-regulatory region sequence-specific DNA binding
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
Erroneous IBA propagation - same root cause as GO:0000981. See family review.
action: REMOVE
reason: >-
NTN3 has no DNA-binding domains (laminin/EGF/NTR domains only).
supported_by:
- reference_id: file:interpro/panther/PTHR10574/PTHR10574-review.md
supporting_text: "See CRITICAL ANNOTATION ERROR section"
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000117
review:
summary: >-
This annotation is likely over-general or misleading. While NTN3 may transit through the
cytoplasm during biosynthesis before secretion via the ER-Golgi pathway, its functional
localization is extracellular. The ARBA machine learning annotation is technically not wrong
but does not reflect the protein's primary functional location.
action: KEEP_AS_NON_CORE
reason: >-
NTN3 is synthesized in the cytoplasm and transits through the secretory pathway, so transient
cytoplasmic presence during biosynthesis is expected. However, the mature functional protein
is secreted to the extracellular matrix. This annotation is not incorrect but is not
informative about the core function or localization of NTN3.
supported_by:
- reference_id: UniProt:O00634
supporting_text: "-!- SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix"
- term:
id: GO:0007409
label: axonogenesis
evidence_type: IEA
original_reference_id: GO_REF:0000117
review:
summary: >-
This annotation is appropriate but could be more specific. NTN3 is a netrin family member
that functions in axon guidance, which is a subprocess of axonogenesis. The ARBA annotation
captures a relevant biological process for this protein.
action: ACCEPT
reason: >-
Netrins are well-established axon guidance cues that regulate axonogenesis by guiding the
growth and direction of axons during neural development. While GO:0007411 (axon guidance)
is more specific, axonogenesis is an appropriate broader term. The annotation aligns with
established netrin family function.
supported_by:
- reference_id: UniProt:O00634
supporting_text: "-!- FUNCTION: Netrins control guidance of CNS commissural axons and peripheral motor axons."
- reference_id: PMID:9143507
supporting_text: "The netrins define a family of chemotropic factors that have been shown to play a central role in axon guidance."
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:26190107
review:
summary: >-
This annotation is supported by experimental evidence from PMID:26190107 showing NTN3
interacts with DRAXIN. However, "protein binding" is uninformative and the interaction
is with a secreted netrin antagonist rather than a netrin receptor.
action: MARK_AS_OVER_ANNOTATED
reason: >-
While the experimental evidence (IPI from PMID:26190107) demonstrates protein-protein
interaction between NTN3 and DRAXIN, the term "protein binding" is too general and
uninformative. DRAXIN is a secreted antagonist that competes with DCC/UNC5 family
receptors for netrin binding, not itself a netrin receptor, so GO:1990890 netrin
receptor binding is not an appropriate replacement term for this interaction.
supported_by:
- reference_id: PMID:26190107
supporting_text: "The assembled floor-plate network contains 47 interactions including the hitherto-not-reported interaction between Netrin-1 and Draxin."
- reference_id: UniProt:O00634
supporting_text: "O00634; Q8NBI3: DRAXIN; NbExp=2; IntAct=EBI-10831998, EBI-10827752"
- term:
id: GO:0005102
label: signaling receptor binding
evidence_type: IEA
original_reference_id: GO_REF:0000107
review:
summary: >-
This annotation is appropriate. NTN3 is a secreted ligand that binds to netrin receptors
(DCC, UNC5 family members) on target cells to mediate axon guidance. The annotation
correctly captures the molecular function of NTN3 as a receptor ligand, though netrin
receptor binding (GO:1990890) would be more specific.
action: ACCEPT
reason: >-
NTN3 functions as a secreted signaling molecule that binds to cell surface receptors
(netrin receptors) to mediate chemotropic guidance of axons. This is a core molecular
function of netrin family proteins. The annotation appropriately captures the receptor
binding activity, transferred from mouse ortholog (UniProtKB:Q9R1A3).
additional_reference_ids:
- UniProt:O00634
supported_by:
- reference_id: UniProt:O00634
supporting_text: "-!- FUNCTION: Netrins control guidance of CNS commissural axons and peripheral motor axons."
- reference_id: file:human/NTN3/NTN3-deep-research-falcon.md
supporting_text: "NTN3/Netrin-3 is summarized as a secreted extracellular ligand that binds UNC5-family receptors, neogenin, and DCC-family receptors."
- term:
id: GO:1990890
label: netrin receptor binding
evidence_type: NAS
review:
summary: >-
Add the more specific molecular-function term for NTN3's receptor-ligand
activity. The Falcon report summarizes direct binding evidence for NTN3/Netrin-3
with canonical netrin receptors, including UNC5-family receptors, neogenin,
and DCC-family receptors, with comparatively strong binding to UNC5B and
UNC5C in available datasets.
action: NEW
reason: >-
Existing GO:0005102 signaling receptor binding is directionally correct
but too broad for a netrin ligand. GO:1990890 captures the core receptor-binding
molecular function without misusing the term for the separate DRAXIN antagonist
interaction.
supported_by:
- reference_id: file:human/NTN3/NTN3-deep-research-falcon.md
supporting_text: "Binding data summarized in the report support NTN3 as a netrin receptor ligand, with comparatively strong binding to UNC5B and UNC5C in available datasets."
- term:
id: GO:0005576
label: extracellular region
evidence_type: IEA
original_reference_id: GO_REF:0000107
review:
summary: >-
This annotation is correct and represents a core localization for NTN3. The protein
contains a signal peptide and is secreted to the extracellular space where it functions
as an axon guidance cue.
action: ACCEPT
reason: >-
NTN3 is a secreted protein (signal peptide residues 1-27) that localizes to the extracellular
region, specifically the extracellular matrix. This is the primary functional localization
for netrin family proteins where they establish chemotropic gradients for axon guidance.
supported_by:
- reference_id: UniProt:O00634
supporting_text: "-!- SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix"
- term:
id: GO:0005794
label: Golgi apparatus
evidence_type: IEA
original_reference_id: GO_REF:0000107
review:
summary: >-
This annotation is acceptable as NTN3 is a secreted protein that transits through the
Golgi apparatus during biosynthesis. The annotation likely reflects Golgi localization
during the secretory pathway.
action: KEEP_AS_NON_CORE
reason: >-
As a secreted protein, NTN3 passes through the Golgi apparatus during biosynthesis and
maturation. While this is not the final functional localization, it is a valid component
of the secretory pathway that NTN3 uses. The annotation is not incorrect but represents
transient localization rather than core function.
supported_by:
- reference_id: UniProt:O00634
supporting_text: "-!- SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix"
- term:
id: GO:0007411
label: axon guidance
evidence_type: NAS
original_reference_id: PMID:9143507
review:
summary: >-
This is a core annotation for NTN3 supported by the primary characterization paper.
PMID:9143507 describes NTN3 (then called NTN2L) as a member of the netrin family of
chemotropic factors that play a central role in axon guidance. The annotation appropriately
captures the primary biological function of this protein.
action: ACCEPT
reason: >-
Axon guidance is the core biological function of netrin family proteins including NTN3.
The cited paper (PMID:9143507) explicitly states that netrins play a central role in
axon guidance. This is well-supported by the literature on netrin family function.
supported_by:
- reference_id: PMID:9143507
supporting_text: "The netrins define a family of chemotropic factors that have been shown to play a central role in axon guidance."
- reference_id: UniProt:O00634
supporting_text: "-!- FUNCTION: Netrins control guidance of CNS commissural axons and peripheral motor axons."
references:
- id: file:interpro/panther/PTHR10574/PTHR10574-review.md
title: PANTHER Family Review - Laminin/Netrin Extracellular Matrix (PTHR10574)
findings:
- statement: NTN1/NTN3 have erroneous IBA annotations from PANTHER node PTN000180816 which incorrectly grouped netrins with POU-domain TFs
- statement: PTHR10574 proteins are secreted ECM/guidance proteins with no DNA-binding domains
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings:
- statement: The IBA annotations for transcription factor activity propagated to NTN3 are erroneous due to phylogenetic tree construction error
- id: GO_REF:0000107
title: Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara
findings:
- statement: Ortholog-based transfer from mouse Ntn3 for cellular component and molecular function terms is appropriate
- id: GO_REF:0000117
title: Electronic Gene Ontology annotations created by ARBA machine learning models
findings:
- statement: ARBA annotation for axonogenesis is appropriate; cytoplasm annotation is technically correct but not informative
- id: PMID:26190107
title: A Floor-Plate Extracellular Protein-Protein Interaction Screen Identifies Draxin as a Secreted Netrin-1 Antagonist.
findings:
- statement: Demonstrates protein-protein interaction between netrins and DRAXIN
supporting_text: "The assembled floor-plate network contains 47 interactions including the hitherto-not-reported interaction between Netrin-1 and Draxin."
- statement: DRAXIN competes with netrin receptors for binding to Netrin-1
supporting_text: "demonstrated that Draxin competes with Netrin receptors for binding to Netrin-1"
- statement: NTN3 interaction with DRAXIN confirmed by IntAct (2 experiments)
supporting_text: "The assembled floor-plate network contains 47 interactions including the hitherto-not-reported interaction between Netrin-1 and Draxin."
- id: PMID:9143507
title: The NTN2L gene encoding a novel human netrin maps to the autosomal dominant polycystic kidney disease region on chromosome 16p13.3.
findings:
- statement: First description of human NTN3 (originally called NTN2L)
supporting_text: "We describe the characterization of a novel human netrin-2-like gene, designated NTN2L, and its transcript."
- statement: Netrins are chemotropic factors central to axon guidance
supporting_text: "The netrins define a family of chemotropic factors that have been shown to play a central role in axon guidance."
- statement: NTN3 has restricted expression pattern, detected in spinal cord by RT-PCR
supporting_text: "The NTN2L gene has a restricted pattern of expression; its transcript is undetectable by Northern analysis in all tissues examined, but can be recovered from spinal cord RNA by RT-PCR."
- statement: Predicted 580-amino-acid protein with homology to chicken, Drosophila netrins and C. elegans UNC-6
supporting_text: "The NTN2L gene is predicted to encode a 580-amino-acid protein having homology to the chicken and Drosophila netrins and to Caenorhabditis elegans UNC-6."
- id: file:human/NTN3/NTN3-deep-research-falcon.md
title: Falcon deep research report for human NTN3
findings:
- statement: NTN3 encodes secreted Netrin-3, a laminin-like extracellular guidance cue that binds canonical netrin receptors including DCC, NEO1, and UNC5-family receptors.
- statement: Binding data summarized in the report support NTN3 as a netrin receptor ligand, with comparatively strong binding to UNC5B and UNC5C in available datasets.
core_functions:
- description: >-
NTN3 functions as a secreted axon guidance cue that binds netrin receptors (DCC, UNC5 family)
to mediate chemotropic guidance of CNS commissural axons and peripheral motor axons.
molecular_function:
id: GO:1990890
label: netrin receptor binding
directly_involved_in:
- id: GO:0007411
label: axon guidance
locations:
- id: GO:0005576
label: extracellular region
supported_by:
- reference_id: PMID:9143507
supporting_text: "The netrins define a family of chemotropic factors that have been shown to play a central role in axon guidance."
- reference_id: file:human/NTN3/NTN3-deep-research-falcon.md
supporting_text: "NTN3/Netrin-3 is summarized as a secreted extracellular ligand that binds UNC5-family receptors, neogenin, and DCC-family receptors to modulate cellular navigation and survival programs."
suggested_questions:
- question: >-
Has NTN3-specific receptor binding been characterized, or is receptor binding
inferred from netrin-1 studies? Most functional studies focus on NTN1 (Netrin-1).
Direct evidence for NTN3-receptor interactions would strengthen annotations.
- question: >-
What is the functional relationship between NTN3 and DRAXIN in axon guidance?
PMID:26190107 shows netrin-DRAXIN interaction. Understanding if this applies
specifically to NTN3 would inform annotation.
suggested_experiments:
- description: >-
Receptor binding assays to confirm NTN3 binds DCC and UNC5 receptors directly.
This would provide direct evidence for GO:1990890 annotation specific to NTN3.
- description: >-
Axon guidance assays in NTN3 knockout or knockdown models to confirm NTN3
specifically functions in axon guidance rather than relying on family membership inference.