NtR (CG6698) is a Drosophila membrane protein of the Cys-loop ligand-gated ion-channel superfamily. It has an N-terminal signal peptide, a farnesoic acid O-methyltransferase-like (Methyltransf_FA) domain of unknown role, an extracellular neurotransmitter-gated channel ligand-binding domain with a conserved Cys-loop disulfide, and four C-terminal transmembrane segments, consistent with a plasma-membrane channel subunit. It is related to nicotinic acetylcholine receptor subunits but forms a divergent branch: it lacks the loop-C vicinal cysteines that bind acetylcholine in alpha subunits and the M2 GEK ring that sets cation selectivity. Its activating ligand, ion selectivity, partner subunits, tissue of action and physiological role have not been determined.
Existing Annotations Review
GO Term
Evidence
Action
Reason
GO:0005230 extracellular ligand-gated monoatomic ion channel activity
IEA GO_REF:0000002
ACCEPT
Summary: Broad Cys-loop ligand-gated channel activity is the best-supported molecular function, inferred from superfamily membership.
Reason: NtR has a signal peptide, a Neur_chan_LBD ligand-binding domain with an intact Cys-loop disulfide (C337-C351) and four C-terminal hydrophobic segments, and it falls inside the Cys-loop LGIC superfamily both in PANTHER (PTHR18945) and in an independent ML tree. Every characterised member of this superfamily is a ligand-gated channel subunit, so this broad term is an appropriate superfamily-level inference. Ligand and ion selectivity are unknown, and the hallmark selectivity motif is not conserved, so nothing more specific is supported.
The data support membership in the Cys-loop ligand-gated channel superfamily (Cys-loop, ligand-binding domain, four hydrophobic segments)
file:DROME/NtR/NtR-family-evidence.md
The published Cys-loop ligand-gated ion-channel tree in Matthews et al. (2018), Extended Data Figure 10d, includes Dmel NTR as a distinct branch outside both shaded nicotinic acetylcholine-receptor groups.
Summary: Plasma membrane is the expected location for a Cys-loop channel subunit with signal peptide and four TM segments.
Reason: The PAINT node PTN001054635 sits at the base of the PTHR18945 Cys-loop superfamily, whose members are plasma membrane channels; NtR retains the signal peptide plus ECD plus four-TM topology. This is a superfamily-level, not nAChR-specific, inference and is not affected by NtR's divergence at the ACh-binding and selectivity sites.
The data support membership in the Cys-loop ligand-gated channel superfamily (Cys-loop, ligand-binding domain, four hydrophobic segments)
file:DROME/NtR/NtR-family-evidence.md
The published Cys-loop ligand-gated ion-channel tree in Matthews et al. (2018), Extended Data Figure 10d, includes Dmel NTR as a distinct branch outside both shaded nicotinic acetylcholine-receptor groups.
Summary: nAChR complex membership is propagated from a bilaterian nAChR node; NtR has lost key nAChR hallmarks.
Reason: PANTHER 19.0 places NtR in PTHR18945:SF430 beside nAChRalpha2, so this IBA follows mechanically from an nAChR PAINT node. Two lines of target-specific evidence argue that NtR has diverged from the ancestral nAChR state the node encodes: (1) an independent maximum-likelihood Cys-loop tree (Matthews et al. 2018, Extended Data Fig. 10d) places Dmel NTR on a long branch outside both the core and divergent nAChR groups, with no Aedes ortholog; (2) NtR lacks the loop-C vicinal cysteine pair that forms the acetylcholine-binding site of alpha subunits and lacks the M2 GEK intermediate ring that confers cation selectivity in all nAChRs, and the Cys-loop FPFD motif is replaced. No ligand, selectivity, expression-site or electrophysiological data exist for NtR. Assembly with nAChR subunits cannot be excluded, so the term is not refuted, but the transfer is most likely an over-propagation from the subfamily.
Propagation Review
Root cause:PROPAGATION BAD
Failure modes:FUNCTIONAL DIVERGENCEPSEUDO OR SUBACTIVITY LOSS
Sources checked:
PANTHER:PTN000435923SUPPORTS SOURCE BUT NOT TARGET
Bilaterian nAChR node; NtR is placed beneath it by PANTHER but lies outside the nAChR clade in an independent tree and lacks loop-C vicinal Cys and the M2 GEK ring. Donor count and target self-inclusion are not objections.
PANTHER 19.0 classification files place Q9W288 in PTHR18945:SF430
file:DROME/NtR/NtR-family-evidence.md
The published Cys-loop ligand-gated ion-channel tree in Matthews et al. (2018), Extended Data Figure 10d, includes Dmel NTR as a distinct branch outside both shaded nicotinic acetylcholine-receptor groups.
Summary: Correct but general; the more specific monoatomic ion transmembrane transport (GO:0034220) is already carried by NtR.
Reason: Ion transport is entailed by Cys-loop channel membership, but channel conduction is transmembrane transport. Per repository guidance a correct but general term is refined to the specific supported descendant already on the gene.
Summary: Calcium permeability is a property of specific nAChR subunits; NtR lacks the conserved selectivity-filter motif.
Reason: PANTHER 19.0 places NtR in PTHR18945:SF430 beside nAChRalpha2, so this IBA follows mechanically from an nAChR PAINT node. Two lines of target-specific evidence argue that NtR has diverged from the ancestral nAChR state the node encodes: (1) an independent maximum-likelihood Cys-loop tree (Matthews et al. 2018, Extended Data Fig. 10d) places Dmel NTR on a long branch outside both the core and divergent nAChR groups, with no Aedes ortholog; (2) NtR lacks the loop-C vicinal cysteine pair that forms the acetylcholine-binding site of alpha subunits and lacks the M2 GEK intermediate ring that confers cation selectivity in all nAChRs, and the Cys-loop FPFD motif is replaced. No ligand, selectivity, expression-site or electrophysiological data exist for NtR. Assembly with nAChR subunits cannot be excluded, so the term is not refuted, but the transfer is most likely an over-propagation from the subfamily. Calcium permeability in particular depends on pore-lining residues that NtR does not conserve.
Propagation Review
Root cause:PROPAGATION BAD
Failure modes:FUNCTIONAL DIVERGENCEPSEUDO OR SUBACTIVITY LOSS
Sources checked:
PANTHER:PTN000434994SUPPORTS SOURCE BUT NOT TARGET
Calcium transport was seeded at this node mainly by nAChR alpha7/alpha9-type and nematode subunits; NtR lacks the M2 GEK ring that underpins cation selectivity.
PANTHER 19.0 classification files place Q9W288 in PTHR18945:SF430
file:DROME/NtR/NtR-family-evidence.md
The published Cys-loop ligand-gated ion-channel tree in Matthews et al. (2018), Extended Data Figure 10d, includes Dmel NTR as a distinct branch outside both shaded nicotinic acetylcholine-receptor groups.
Summary: Cholinergic synaptic transmission requires acetylcholine gating, which is not supported for NtR.
Reason: PANTHER 19.0 places NtR in PTHR18945:SF430 beside nAChRalpha2, so this IBA follows mechanically from an nAChR PAINT node. Two lines of target-specific evidence argue that NtR has diverged from the ancestral nAChR state the node encodes: (1) an independent maximum-likelihood Cys-loop tree (Matthews et al. 2018, Extended Data Fig. 10d) places Dmel NTR on a long branch outside both the core and divergent nAChR groups, with no Aedes ortholog; (2) NtR lacks the loop-C vicinal cysteine pair that forms the acetylcholine-binding site of alpha subunits and lacks the M2 GEK intermediate ring that confers cation selectivity in all nAChRs, and the Cys-loop FPFD motif is replaced. No ligand, selectivity, expression-site or electrophysiological data exist for NtR. Assembly with nAChR subunits cannot be excluded, so the term is not refuted, but the transfer is most likely an over-propagation from the subfamily.
Propagation Review
Root cause:PROPAGATION BAD
Failure modes:FUNCTIONAL DIVERGENCEPSEUDO OR SUBACTIVITY LOSS
Sources checked:
PANTHER:PTN001054960SUPPORTS SOURCE BUT NOT TARGET
Insect/arthropod cholinergic node; NtR's placement under it conflicts with an independent tree and with loss of ACh-binding and selectivity hallmarks.
PANTHER 19.0 classification files place Q9W288 in PTHR18945:SF430
file:DROME/NtR/NtR-family-evidence.md
The published Cys-loop ligand-gated ion-channel tree in Matthews et al. (2018), Extended Data Figure 10d, includes Dmel NTR as a distinct branch outside both shaded nicotinic acetylcholine-receptor groups.
Summary: contributes_to acetylcholine-gated cation channel activity from a node seeded by Dalpha1/2/5; NtR lacks the ACh-binding and cation-selectivity hallmarks.
Reason: PANTHER 19.0 places NtR in PTHR18945:SF430 beside nAChRalpha2, so this IBA follows mechanically from an nAChR PAINT node. Two lines of target-specific evidence argue that NtR has diverged from the ancestral nAChR state the node encodes: (1) an independent maximum-likelihood Cys-loop tree (Matthews et al. 2018, Extended Data Fig. 10d) places Dmel NTR on a long branch outside both the core and divergent nAChR groups, with no Aedes ortholog; (2) NtR lacks the loop-C vicinal cysteine pair that forms the acetylcholine-binding site of alpha subunits and lacks the M2 GEK intermediate ring that confers cation selectivity in all nAChRs, and the Cys-loop FPFD motif is replaced. No ligand, selectivity, expression-site or electrophysiological data exist for NtR. Assembly with nAChR subunits cannot be excluded, so the term is not refuted, but the transfer is most likely an over-propagation from the subfamily. The contributes_to qualifier (subunit of a heteromer) is respected, but even as a complementary subunit NtR would lack the cation-selectivity ring.
Propagation Review
Root cause:PROPAGATION BAD
Failure modes:FUNCTIONAL DIVERGENCEPSEUDO OR SUBACTIVITY LOSS
Sources checked:
PANTHER:PTN001825467SUPPORTS SOURCE BUT NOT TARGET
Seeded by Dmel nAChRalpha1, alpha2 and alpha5. NtR shares PANTHER SF430 with alpha2 but lacks loop-C vicinal Cys and the M2 GEK ring; treat transfer as over-propagation pending ligand/selectivity data.
PANTHER 19.0 classification files place Q9W288 in PTHR18945:SF430
file:DROME/NtR/NtR-family-evidence.md
The published Cys-loop ligand-gated ion-channel tree in Matthews et al. (2018), Extended Data Figure 10d, includes Dmel NTR as a distinct branch outside both shaded nicotinic acetylcholine-receptor groups.
Summary: Ion conduction across the membrane is the process directly executed by a Cys-loop channel subunit.
Reason: Propagated from PTN000434994. This broad transport term does not depend on acetylcholine gating or calcium selectivity and follows from Cys-loop superfamily membership. Which ions are conducted is unknown.
The data support membership in the Cys-loop ligand-gated channel superfamily (Cys-loop, ligand-binding domain, four hydrophobic segments)
file:DROME/NtR/NtR-family-evidence.md
The published Cys-loop ligand-gated ion-channel tree in Matthews et al. (2018), Extended Data Figure 10d, includes Dmel NTR as a distinct branch outside both shaded nicotinic acetylcholine-receptor groups.
Summary: Plausible consequence of channel activity, but sign and ion basis are unknown.
Reason: If NtR conducts ions it will affect membrane potential, so this broad PTN000434994 propagation is not refuted. It is a downstream consequence of the core channel function rather than a separately informative role, and the ion selectivity that would determine its effect is unknown.
The data support membership in the Cys-loop ligand-gated channel superfamily (Cys-loop, ligand-binding domain, four hydrophobic segments)
file:DROME/NtR/NtR-family-evidence.md
The published Cys-loop ligand-gated ion-channel tree in Matthews et al. (2018), Extended Data Figure 10d, includes Dmel NTR as a distinct branch outside both shaded nicotinic acetylcholine-receptor groups.
Summary: Derived by inter-ontology inference from over-propagated cholinergic channel IBAs; no synaptic evidence for NtR.
Reason: Inferred by GO_REF:0000108 from the IBA cholinergic/acetylcholine-gated channel annotations, which are themselves judged over-propagated for NtR (no loop-C vicinal cysteines, no M2 GEK cation-selectivity ring, placement outside the nAChR clade in an independent tree). No synaptic localization or neuronal function has been shown for NtR, so this downstream term inherits the same over-annotation.
Supporting Evidence:
file:DROME/NtR/NtR-family-evidence.md
The published Cys-loop ligand-gated ion-channel tree in Matthews et al. (2018), Extended Data Figure 10d, includes Dmel NTR as a distinct branch outside both shaded nicotinic acetylcholine-receptor groups.
they argue against transferring acetylcholine gating, cation/calcium selectivity or cholinergic synaptic roles from the subfamily
file:DROME/NtR/NtR-deep-research-falcon.md
No ligand-binding or electrophysiological experiment establishes association with a neuronal channel.
GO:0060078 regulation of postsynaptic membrane potential
IEA GO_REF:0000108
MARK AS OVER ANNOTATED
Summary: Derived by inter-ontology inference from over-propagated cholinergic channel IBAs; no synaptic evidence for NtR.
Reason: Inferred by GO_REF:0000108 from the IBA cholinergic/acetylcholine-gated channel annotations, which are themselves judged over-propagated for NtR (no loop-C vicinal cysteines, no M2 GEK cation-selectivity ring, placement outside the nAChR clade in an independent tree). No synaptic localization or neuronal function has been shown for NtR, so this downstream term inherits the same over-annotation.
Supporting Evidence:
file:DROME/NtR/NtR-family-evidence.md
The published Cys-loop ligand-gated ion-channel tree in Matthews et al. (2018), Extended Data Figure 10d, includes Dmel NTR as a distinct branch outside both shaded nicotinic acetylcholine-receptor groups.
Summary: Derived by inter-ontology inference from over-propagated cholinergic channel IBAs; no synaptic evidence for NtR.
Reason: Inferred by GO_REF:0000108 from the IBA cholinergic/acetylcholine-gated channel annotations, which are themselves judged over-propagated for NtR (no loop-C vicinal cysteines, no M2 GEK cation-selectivity ring, placement outside the nAChR clade in an independent tree). No synaptic localization or neuronal function has been shown for NtR, so this downstream term inherits the same over-annotation.
Supporting Evidence:
file:DROME/NtR/NtR-family-evidence.md
The published Cys-loop ligand-gated ion-channel tree in Matthews et al. (2018), Extended Data Figure 10d, includes Dmel NTR as a distinct branch outside both shaded nicotinic acetylcholine-receptor groups.
Summary: Derived by inter-ontology inference from over-propagated cholinergic channel IBAs; no synaptic evidence for NtR.
Reason: Inferred by GO_REF:0000108 from the IBA cholinergic/acetylcholine-gated channel annotations, which are themselves judged over-propagated for NtR (no loop-C vicinal cysteines, no M2 GEK cation-selectivity ring, placement outside the nAChR clade in an independent tree). No synaptic localization or neuronal function has been shown for NtR, so this downstream term inherits the same over-annotation.
Supporting Evidence:
file:DROME/NtR/NtR-family-evidence.md
The published Cys-loop ligand-gated ion-channel tree in Matthews et al. (2018), Extended Data Figure 10d, includes Dmel NTR as a distinct branch outside both shaded nicotinic acetylcholine-receptor groups.
they argue against transferring acetylcholine gating, cation/calcium selectivity or cholinergic synaptic roles from the subfamily
file:DROME/NtR/NtR-deep-research-falcon.md
No ligand-binding or electrophysiological experiment establishes association with a neuronal channel.
GO:0099565 chemical synaptic transmission, postsynaptic
IEA GO_REF:0000108
MARK AS OVER ANNOTATED
Summary: Derived by inter-ontology inference from over-propagated cholinergic channel IBAs; no synaptic evidence for NtR.
Reason: Inferred by GO_REF:0000108 from the IBA cholinergic/acetylcholine-gated channel annotations, which are themselves judged over-propagated for NtR (no loop-C vicinal cysteines, no M2 GEK cation-selectivity ring, placement outside the nAChR clade in an independent tree). No synaptic localization or neuronal function has been shown for NtR, so this downstream term inherits the same over-annotation.
Supporting Evidence:
file:DROME/NtR/NtR-family-evidence.md
The published Cys-loop ligand-gated ion-channel tree in Matthews et al. (2018), Extended Data Figure 10d, includes Dmel NTR as a distinct branch outside both shaded nicotinic acetylcholine-receptor groups.
they argue against transferring acetylcholine gating, cation/calcium selectivity or cholinergic synaptic roles from the subfamily
file:DROME/NtR/NtR-deep-research-falcon.md
No ligand-binding or electrophysiological experiment establishes association with a neuronal channel.
Core Functions
Predicted subunit of a Cys-loop ligand-gated ion channel at the plasma membrane; the activating ligand, ion selectivity and partner subunits are unknown, and acetylcholine gating is not supported by its sequence.
The data support membership in the Cys-loop ligand-gated channel superfamily (Cys-loop, ligand-binding domain, four hydrophobic segments)
file:DROME/NtR/NtR-family-evidence.md
The published Cys-loop ligand-gated ion-channel tree in Matthews et al. (2018), Extended Data Figure 10d, includes Dmel NTR as a distinct branch outside both shaded nicotinic acetylcholine-receptor groups.
Q: Does NtR form a functional channel on its own or with nAChR subunits, and if so what ligand gates it and which ions does it conduct, given that it lacks loop-C vicinal cysteines and the M2 GEK ring?
Q: Is PTHR18945:SF430 (PANTHER 19.0, grouping NtR with nAChRalpha2) or PTHR36695 (UniProt cross-reference) the correct PANTHER placement for Q9W288, and should PAINT add a loss (IRD) node for the NtR branch for acetylcholine-specific terms?
Q: What, if anything, is the function of the N-terminal Methyltransf_FA-like domain, which is unusual for a Cys-loop channel subunit?
Suggested Experiments
Experiment: Express NtR alone and with Dalpha/Dbeta nAChR subunits (with chaperones such as RIC-3 or TMX3) in Xenopus oocytes and screen a ligand panel (acetylcholine, GABA, glutamate, histamine, biogenic amines, pH) by two-electrode voltage clamp, measuring reversal potentials for ion selectivity.
Experiment: Endogenously tag NtR by CRISPR knock-in to determine tissue and subcellular localization (neuronal versus hemocyte or other tissues) before testing synaptic roles.
External Prediction Reviews
These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
The generic ligand-gated channel prediction is supported by Cys-loop channel architecture, while ligand identity, calcium permeability and cholinergic signaling remain unresolved.
Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.
GO:0005230 extracellular ligand-gated monoatomic ion channel activityGO_MF
CNN — Correct but not novel Review score: 2/2
Prediction method: ProtNLM2 · Version: UniProt API snapshot 2026-09-08
Review rationale: The generic ligand-gated channel claim is supported by the target's Cys-loop architecture (signal peptide, Neur_chan_LBD ligand-binding domain with an intact Cys-loop disulfide, four C-terminal hydrophobic segments) and by the published Cys-loop channel-family tree, which includes Dmel NTR. The exact term is already in the exact-accession GOA record (IEA, InterPro2GO), which the gene review accepts as the best-supported molecular function, so the prediction is correct but not novel. No PubMed literature on NtR (CG6698) function was found. NtR lies outside the identified nicotinic receptor groups, so this broad result does not validate the narrower acetylcholine-gating or calcium-permeability annotations. The OpenScientist audit reached the same split, retaining broad channel terms and downscoping the acetylcholine, calcium and cholinergic assignments as untested computational propagation.
file:DROME/NtR/NtR-family-evidence.md: "The published Cys-loop ligand-gated ion-channel tree in Matthews et al. (2018), Extended Data Figure 10d, includes Dmel NTR as a distinct branch outside both shaded nicotinic acetylcholine-receptor groups."
PMID:30429615: "Many insecticides act on ion channels, and we curated members of the Cys-loop ligand-gated ion channel (Cys-loop LGIC) superfamily in AaegL5."
file:DROME/NtR/NtR-hypotheses/ntr-cholinergic-calcium-and-synaptic-functions/openscientist.md: "NtR is a *bona fide* member of the Cys-loop ligand-gated ion channel (LGIC) superfamily: it has a *bona fide* extracellular neurotransmitter-gated ion-channel ligand-binding domain (Pfam PF02931), one canonical Cys-loop signature (C337–x13–C351), and a four-transmembrane-helix C-terminal region (M1–M4) in the expected Cys-loop topology"