organism	gene	go_id	go_label	evidence_type	reference	action	summary
ARATH	AT5G02500	GO:0005829	cytosol	RCA	PMID:21166475	REMOVE	Negated cytosol localization based on RCA conflicts with positive cytosol evidence for HSC70-1.
ARATH	BCAT3	GO:0005829	cytosol	RCA	PMID:21166475	ACCEPT	NOT annotation (negated): BCAT3 was not found in the experimentally defined cytosolic proteome. This negative assertion agrees with the chloroplast targeting of BCAT3 shown by GFP fusion and with plastid proteomics.
ARATH	CLV3	GO:0002221	pattern recognition receptor signaling pathway	IEP	PMID:22923673	ACCEPT	This is a NOT (negated) annotation recording that CLV3 does not act through a pattern recognition receptor (FLS2) signaling pathway. It directly counters the earlier claim (PMID:21499263) that CLV3p triggers FLS2-mediated immunity. Segonzac et al. could not reproduce CLV3p recognition by FLS2 and showed SAM immunity is independent of CLV3 perception. The negation should be retained.
ARATH	CRY2	GO:0016301	kinase activity	IDA	PMID:17073458	ACCEPT	Correct negated annotation: Arabidopsis CRY2 is not an autokinase.
ARATH	CRY2	GO:0046777	protein autophosphorylation	IDA	PMID:17073458	ACCEPT	Correct negated annotation: AtCRY2 does not carry out protein autophosphorylation.
ARATH	DRB1	GO:0015030	Cajal body	IDA	PMID:17369351	ACCEPT	The NOT Cajal-body annotation separates HYL1/DCL1 dicing bodies from Cajal bodies.
ARATH	GAI	GO:0009909	regulation of flower development	IMP	PMID:11606552	ACCEPT	NOT annotation. In the rga gai double null, flower development defects of ga1-3 were NOT restored, indicating GAI is not required for (does not regulate) flower development in this context (RGL1/RGL2 dominate).
ARATH	GAI	GO:0010029	regulation of seed germination	IMP	PMID:11606552	ACCEPT	NOT annotation. rga gai double null did not restore seed germination defects of ga1-3, indicating GAI is not the DELLA responsible for germination repression (RGL2 dominates).
ARATH	GAI	GO:0010029	regulation of seed germination	IGI	PMID:11606552	ACCEPT	NOT annotation (genetic interaction). Same conclusion - GAI loss does not rescue germination defects.
ARATH	GAI	GO:0080154	regulation of fertilization	IMP	PMID:11606552	ACCEPT	NOT annotation. This study (PMID:11606552) concerns vegetative growth, germination and flower development; the negation of fertilization regulation is consistent with GAI not being required for reproductive/fertility defect rescue in this context.
ARATH	GAI	GO:0080154	regulation of fertilization	IGI	PMID:11606552	ACCEPT	NOT annotation (genetic interaction), same negation as above.
ARATH	GAI	GO:1905613	regulation of developmental vegetative growth	IMP	PMID:11606552	ACCEPT	NOT annotation. gai-t6 single mutant alone has little effect on vegetative growth, so by itself GAI does not measurably regulate developmental vegetative growth (the effect requires combination with rga).
ARATH	GAI	GO:2000024	regulation of leaf development	IMP	PMID:11606552	ACCEPT	NOT annotation. Consistent with gai-t6 single mutant having little effect; GAI alone does not measurably regulate leaf development.
ARATH	GID1A	GO:0009739	response to gibberellin	IGI	PMID:24961590	KEEP_AS_NON_CORE	NOT|involved_in (IGI, with UniProtKB:Q9LYC1) from the fruit-set redundancy study. The negation reflects a specific genetic combination in which GID1A did not show a measurable contribution to a particular GA response readout, consistent with masking by redundant paralogs.
ARATH	OST1	GO:0005829	cytosol	RCA	PMID:21166475	REMOVE	A reviewed-computational-analysis (RCA) NOT-cytosol assignment derived from a cytosolic-proteome dataset (OST1 not recovered in the cytosolic fraction). This is contradicted by direct experimental IDA cytosol/cytoplasm localization.
ARATH	PIF3	GO:0007623	circadian rhythm	IMP	PMID:16055924	ACCEPT	A NOT annotation correctly recording that PIF3 does not have a significant role in the circadian clock; over/under-expression does not affect period length or light resetting.
ARATH	RDR6	GO:0035196	miRNA processing	IMP	PMID:16682356	ACCEPT	RDR6 is not part of canonical miRNA precursor processing.
ARATH	RGA	GO:0009909	regulation of flower development	IMP	PMID:11606552	ACCEPT	A NOT annotation. Dill and Sun (2001) showed that removing RGA and GAI did NOT restore flower development defects of ga1-3, indicating RGA/GAI are not the DELLAs responsible for the flower development arm in this genetic context. The negated annotation is correctly supported.
ARATH	RGA	GO:0009909	regulation of flower development	IGI	PMID:11606552	ACCEPT	Genetic-interaction NOT annotation paralleling the IMP version; rga gai double mutant does not restore ga1-3 flower development defects.
ARATH	RGA	GO:0010029	regulation of seed germination	IMP	PMID:11606552	ACCEPT	A NOT annotation. Removing RGA and GAI did not restore the seed germination defect of ga1-3, indicating RGA/GAI are not the major DELLAs for germination (RGL2 is). Correctly negated and supported.
ARATH	RGA	GO:0010029	regulation of seed germination	IGI	PMID:11606552	ACCEPT	Genetic-interaction NOT annotation paralleling the IMP version. rga gai does not restore germination defects of ga1-3.
ARATH	RGA	GO:0080154	regulation of fertilization	IMP	PMID:11606552	ACCEPT	A NOT annotation derived from the observation that rga gai does not rescue the reproductive (flower development/fertility) defects of ga1-3. The negation is consistent with the paper, though 'regulation of fertilization' is a somewhat loose mapping of the reported flower/fertility defect.
ARATH	RGA	GO:0080154	regulation of fertilization	IGI	PMID:11606552	ACCEPT	Genetic-interaction NOT annotation paralleling the IMP version.
ARATH	RGA	GO:1905613	regulation of developmental vegetative growth	IMP	PMID:11606552	REMOVE	A NOT annotation. This is mechanistically questionable: RGA and GAI are in fact the major repressors of GA-promoted vegetative growth (rga gai rescues stem elongation, leaf expansion, rosette radius of ga1-3). The negation of an unsigned 'regulation of developmental vegetative growth' likely reflects a curation interpretation; the correctly-signed annotation (negative regulation, below) is the appropriate one.
ARATH	SCR	GO:0042803	protein homodimerization activity	IPI	PMID:17446396	ACCEPT	NOT annotation - SCR does not homodimerize; it forms a heterodimer with SHR (the partner recorded is SHR, AGI AT3G54220 being SCR itself in the WITH field reflects the assay context).
ARATH	TOC1	GO:0000976	transcription cis-regulatory region binding	IDA	PMID:19286557	ACCEPT	Negated annotation reflecting the 2009 finding that TOC1 did not bind the CCA1 promoter (TCP-binding-site region) directly by EMSA/Y1H and was instead recruited via CHE. Later work (2012) showed TOC1 does bind other elements (T1ME/G-box) directly via the CCT domain, so this negation is specific to that promoter region/assay context.
ARATH	WUS	GO:0019827	stem cell population maintenance	IDA	PMID:15705957	ACCEPT	This is a NOT annotation indicating that WUS is not necessary or sufficient for stem cell specification in the experimental context of PMID:15705957. The study reports that WUS is neither necessary nor sufficient for stem cell specification, supporting the negated qualifier.
BOVIN	CRYAA	GO:0042026	protein refolding	IDA	PMID:7487869	ACCEPT	"NOT annotation for protein refolding from PMID:7487869. This is a critical annotation that explicitly states bovine alpha-crystallin does NOT perform protein refolding. PMID:7487869 demonstrated that ""alpha-crystallin has substrate specificity different from other chaperones and recognizes specific non-native intermediates formed on the denaturation pathway only, with no affinity for intermediates formed on the refolding pathway."" This establishes that alpha-crystallin is a holdase, not a foldase: it binds proteins during denaturation to prevent aggregation but does not assist in refolding."
DANRE	coq8a	GO:0004672	protein kinase activity	ISS	GO_REF:0000024	KEEP_AS_NON_CORE	NOT protein kinase activity (GO:0004672) is retained as non-core negative evidence in the conflicting COQ8A kinase record.
DANRE	coq8a	GO:0006468	protein phosphorylation	ISS	GO_REF:0000024	KEEP_AS_NON_CORE	NOT protein phosphorylation (GO:0006468) is retained because COQ8A is not established as acting through protein phosphorylation.
DANRE	fgf8a	GO:0055011	atrial cardiac muscle cell differentiation	IMP	PMID:19395641	ACCEPT	NOT: fgf8 is not required for atrial (venous pole) cardiomyocyte addition.
DANRE	tbx5a	GO:0048794	swim bladder development	IGI	PMID:30352852	ACCEPT	NOT swim bladder development (negated).
DANRE	tbx5a	GO:0048794	swim bladder development	IMP	PMID:30352852	ACCEPT	NOT swim bladder development (negated).
DANRE	tbx5a	GO:0048794	swim bladder development	IMP	PMID:30352852	ACCEPT	NOT swim bladder development (negated).
DANRE	tbx5b	GO:0048794	swim bladder development	IGI	PMID:30352852	ACCEPT	NOT swim bladder development (negated).
DANRE	tbx5b	GO:0048794	swim bladder development	IMP	PMID:30352852	ACCEPT	NOT swim bladder development (negated).
DERPT	Derp23	GO:0008061	chitin binding	IDA	PMID:26602749	ACCEPT	This is a NOT (negated) annotation: GOA records that Der p 23 does NOT bind chitin. Despite its peritrophin-A (ChtBD2) chitin-binding-domain fold, direct assays (PMID:26602749) found no chitin binding in vitro, as also stated in UniProt. The negation is correct and informative.
DICDI	gcA	GO:0019722	calcium-mediated signaling	IGI	PMID:40295210	ACCEPT	NOT annotation. In gca/sgc double-null cells, the intracellular calcium response to external calcium is only slightly delayed rather than abolished, indicating that GCA (and cGMP synthesis) is not required for calcium-mediated signaling. The negation is supported.
DICDI	pdsA	GO:0005886	plasma membrane	IDA	PMID:19477920	ACCEPT	The NOT plasma-membrane annotation is supported by direct imaging of functional tagged PdsA during chemotaxis.
DROME	Akt1	GO:0008284	positive regulation of cell population proliferation	IMP	PMID:10587646	KEEP_AS_NON_CORE	Akt1 promotes cell population proliferation through growth signaling.
DROME	BicD	GO:0003729	mRNA binding	NAS	PMID:12446149	ACCEPT	NOT mRNA binding (NAS, from a review of motor-driven mRNA transport). BicD is recruited to localizing transcripts through the RNA-binding protein Egalitarian rather than by binding RNA itself.
DROME	CG34171	GO:0004252	serine-type endopeptidase activity	IKR	PMID:30367934	ACCEPT	Retain the explicit NOT annotation: the selected short product lacks the catalytic-serine region.
DROME	CG43124	GO:0004252	serine-type endopeptidase activity	IKR	PMID:30367934	ACCEPT	Accept the negated peptidase annotation: CG43124 is a noncatalytic serine-protease homolog.
DROME	CG43124	GO:0008233	peptidase activity	IKR	GO_REF:0000047	ACCEPT	Accept the negated peptidase annotation: CG43124 is a noncatalytic serine-protease homolog.
DROME	CG4793	GO:0004252	serine-type endopeptidase activity	IBA	GO_REF:0000033	ACCEPT	The negated peptidase annotation is consistent with the disrupted catalytic machinery of CG4793.
DROME	CG4793	GO:0004252	serine-type endopeptidase activity	IKR	PMID:12568721	ACCEPT	The negated peptidase annotation is consistent with the disrupted catalytic machinery of CG4793.
DROME	CG4793	GO:0004252	serine-type endopeptidase activity	IKR	PMID:30367934	ACCEPT	The negated peptidase annotation is consistent with the disrupted catalytic machinery of CG4793.
DROME	CG4793	GO:0008233	peptidase activity	IKR	GO_REF:0000047	ACCEPT	The negated peptidase annotation is consistent with the disrupted catalytic machinery of CG4793.
DROME	CRY	GO:0003913	DNA photolyase activity	IMP	PMID:10063806	ACCEPT	CRY lacks DNA photolyase activity (negated).
DROME	Dic4	GO:0005310	dicarboxylic acid transmembrane transporter activity	IDA	PMID:21130726	ACCEPT	Retain the experimentally supported NOT annotation. Recombinant Dic4 lacked detectable transport in the reported assay, including the dicarboxylate-carrier comparison. This does not exclude an untested physiological substrate.
DROME	Dic4	GO:0006835	dicarboxylic acid transport	IDA	PMID:21130726	ACCEPT	Retain the experimentally supported NOT annotation. Recombinant Dic4 lacked detectable transport in the reported assay, including the dicarboxylate-carrier comparison. This does not exclude an untested physiological substrate.
DROME	N	GO:0007615	anesthesia-resistant memory	IMP	PMID:15220476	KEEP_AS_NON_CORE	N IMP annotation to 'anesthesia-resistant memory'. Loss or gain of Notch function alters this process, one of the many developmental or physiological contexts in which Notch receptor signaling is deployed.
DROME	Nepl19	GO:0008233	peptidase activity	IKR	GO_REF:0000047	ACCEPT	Retain the NOT peptidase assertion. The exact protein replaces the first zinc ligand and catalytic glutamate in the neprilysin HExxH motif, while retaining downstream M13 structure. Two alignment strategies and an active mouse control support this loss, consistent with the published Nepl classification.
DROME	Nepl19	GO:0008233	peptidase activity	IKR	PMID:34189422	ACCEPT	Retain the NOT peptidase assertion. The exact protein replaces the first zinc ligand and catalytic glutamate in the neprilysin HExxH motif, while retaining downstream M13 structure. Two alignment strategies and an active mouse control support this loss, consistent with the published Nepl classification.
DROME	P28159	GO:0007451	dorsal/ventral lineage restriction, imaginal disc	NAS	PMID:11253649	KEEP_AS_NON_CORE	Su(H) NAS annotation to 'dorsal/ventral lineage restriction, imaginal disc'. Su(H) is the CSL transcription factor of the Notch pathway, and its loss or misregulation alters this developmental process.
DROME	klg	GO:0007615	anesthesia-resistant memory	IMP	PMID:19104051	ACCEPT	NOT annotation (negated): Matsuno et al. (2009) show that Klingon is acutely required for protein-synthesis-dependent long-term memory but specifically NOT for anesthesia-resistant memory (ARM). This negative finding correctly records that klg does not function in the ARM branch of consolidated memory.
DROME	scaf	GO:0004252	serine-type endopeptidase activity	IKR	PMID:12568721	ACCEPT	Accepted as a negated catalytic annotation: Scaf is an S1-family serine-protease homolog rather than an active serine endopeptidase.
DROME	scaf	GO:0004252	serine-type endopeptidase activity	IKR	PMID:30367934	ACCEPT	Accepted as a negated catalytic annotation supported by the 2018 S1-family reclassification of Drosophila SPs and SPHs.
DROME	scaf	GO:0008233	peptidase activity	IKR	GO_REF:0000047	ACCEPT	Accepted: the key-residue rule correctly negates generic peptidase activity for catalytically inactive Scaf.
EMENI	fluG	GO:0004356	glutamine synthetase activity	IMP	PMID:7926755	ACCEPT	NOT annotation. FluG does NOT have glutamine synthetase activity: despite belonging to the GS family and carrying a GS-like domain required for signal production, the mutant analysis EXCLUDED a physiological glutamine synthetase activity rather than leaving it undemonstrated.
EMENI	fluG	GO:1901704	L-glutamine biosynthetic process	IMP	PMID:7926755	ACCEPT	NOT annotation. FluG is NOT involved in L-glutamine biosynthesis - the process counterpart of the excluded glutamine synthetase activity above.
NEUCR	cao-1	GO:0016116	carotenoid metabolic process	IDA	PMID:23893079	ACCEPT	NOT annotation asserting that CAO-1 is not involved in carotenoid metabolism. This is strongly supported: heterologously expressed CAO-1 failed to convert beta-carotene or any carotenoid/apocarotenoid substrate, and cao-1 expression is light-independent, unlike carotenoid-pathway genes.
SCHPO	Epe1	GO:0031507	heterochromatin formation	IDA	PMID:25831549	UNDECIDED	This negative annotation (NOT|involved_in) captures the curator's intent that Epe1 opposes rather than promotes heterochromatin assembly, but it contradicts the seven accepted GO:0033696 heterochromatin boundary formation rows under the true-path rule, so it is left undecided.
SCHPO	Shu1	GO:0098711	iron ion import across plasma membrane	IMP	PMID:25733668	ACCEPT	This annotation has a NOT qualifier in the original GOA data, indicating Shu1 is NOT involved in direct iron ion import. This is correct - Shu1 imports heme (which contains iron) rather than free iron ions. The NOT annotation properly distinguishes heme transport from direct iron transport.
SCHPO	atf1	GO:0141194	siRNA-mediated heterochromatin formation	IDA	PMID:15218150	ACCEPT	Correctly negated: Atf1/Pcr1 act in a mechanism PARALLEL to and INDEPENDENT of the RNAi (siRNA) pathway for heterochromatin nucleation. Deletion of atf1 alone has little effect, but combined with RNAi mutants abolishes nucleation, showing Atf1 is not part of the siRNA-mediated route.
SCHPO	cdc15	GO:0097753	membrane bending	IMP	PMID:26702831	ACCEPT	This is a NOT annotation. Although F-BAR proteins are canonically associated with membrane curvature, the study demonstrates that oligomerization, NOT membrane bending, underlies Cdc15 function in cytokinesis. The negation is therefore correct: Cdc15 does not require membrane-bending activity for its essential cytokinetic role.
SCHPO	cdc2	GO:0051292	nuclear pore complex assembly	EXP	PMID:35354597	ACCEPT	Cdc2 is NOT involved in nuclear pore complex assembly; quantitative NPC analysis found no role.
SCHPO	chk1	GO:0006281	DNA repair	EXP	PMID:8497322	ACCEPT	Correctly negated. Chk1 is a checkpoint signaling kinase that arrests the cell cycle in response to damage but does not itself carry out DNA repair.
SCHPO	pmp20	GO:0042744	hydrogen peroxide catabolic process	EXP	PMID:20356456	ACCEPT	Retain the experimentally supported NOT annotation.
SCHPO	pmp20	GO:0004601	peroxidase activity	IDA	PMID:20356456	ACCEPT	Retain the experimentally supported NOT annotation.
SCHPO	pol5	GO:0042790	nucleolar large rRNA transcription by RNA polymerase I	ISO	PMID:31745560	ACCEPT	This NOT ISO annotation distinguishes Pol5's conserved pre-rRNA assembly role from direct participation in nucleolar Pol I transcription.
SCHPO	wee1	GO:0031568	mitotic G1 cell size control checkpoint signaling	IMP	PMID:872890	ACCEPT	Correct negation. In fission yeast cell size is controlled predominantly at the G2/M transition through Wee1; the analogous G1 size requirement is normally cryptic and Wee1 is not implicated in a G1 size-control checkpoint. The NOT qualifier appropriately records that Wee1 does not act in G1 size control.
STAAU	ant	GO:0009012	aminoglycoside 3''-adenylyltransferase activity	IDA	PMID:29871922	ACCEPT	The negated annotation is retained; this ANT(9) enzyme should not be asserted as aminoglycoside 3''-adenylyltransferase activity.
human	A1CF	GO:0003725	double-stranded RNA binding	IDA	PMID:11871661	ACCEPT	Direct assays show that A1CF does not bind double-stranded APOB mRNA with high affinity; they do not exclude every possible dsRNA interaction.
human	A3GALT2	GO:0001962	alpha-1,3-galactosyltransferase activity	IDA	PMID:18630988	UNDECIDED	The original NOT remains represented, with conflicting construct-specific negative and weak positive assays unresolved.
human	ABCB4	GO:0099038	ceramide floppase activity	IDA	PMID:8898203	UNDECIDED	The source NOT assertion is broader than the negative lipid panel verified here.
human	ABCB4	GO:0099040	ceramide translocation	IDA	PMID:8898203	UNDECIDED	The source NOT assertion is broader than the negative lipid panel verified here.
human	ABCD4	GO:0005777	peroxisome	IDA	PMID:19010322	ACCEPT	NOT annotation - ABCD4 does NOT localize to peroxisomes. This study showed P70R/ABCD4 localizes to the ER, not peroxisomes.
human	ABCD4	GO:0005777	peroxisome	IDA	PMID:27456980	ACCEPT	NOT annotation - ABCD4 does NOT localize to peroxisomes; it is an ER/lysosomal protein.
human	ABHD5	GO:0004806	triacylglycerol lipase activity	ISS	GO_REF:0000024	ACCEPT	The NOT annotation correctly separates ABHD5 from the triglyceride hydrolase it activates.
human	ABI3	GO:0018108	peptidyl-tyrosine phosphorylation	IDA	PMID:17101133	ACCEPT	"CORRECT negative annotation. PMID:17101133 explicitly tested and showed that ""NESH (Abi-3) had no such effect"" on promoting c-Abl-mediated phosphorylation, unlike Abi-1 and Abi-2 which do promote this activity. This negative annotation correctly captures that ABI3/NESH does NOT participate in peptidyl-tyrosine phosphorylation processes."
human	ABL1	GO:0097100	supercoiled DNA binding	IDA	PMID:9558345	ACCEPT	ABL1 does NOT bind supercoiled DNA (negative annotation with NOT qualifier).
human	AGO1	GO:0090625	siRNA-mediated gene silencing by mRNA destabilization	IDA	PMID:15260970	UNDECIDED	The negated process annotation remains unresolved because target cleavage and nonendonucleolytic mRNA destabilization have different scope.
human	AGO1	GO:0035279	miRNA-mediated gene silencing by mRNA destabilization	IDA	PMID:15260970	UNDECIDED	The negated process annotation remains unresolved because target cleavage and nonendonucleolytic mRNA destabilization have different scope.
human	AGO1	GO:0004521	RNA endonuclease activity	IDA	PMID:23809764	ACCEPT	Wild-type human AGO1 lacks the tested target-RNA endonuclease activity.
human	AGO3	GO:0090625	siRNA-mediated gene silencing by mRNA destabilization	IDA	PMID:15260970	ACCEPT	This NOT annotation is appropriate for the PMID:15260970 assay context; AGO3 did not behave as the AGO2-like siRNA-guided target-cleavage Argonaute in that study.
human	AGO3	GO:0035279	miRNA-mediated gene silencing by mRNA destabilization	IDA	PMID:15260970	REMOVE	This older NOT annotation should be removed because later AGO3-specific evidence supports guide-dependent miRNA-paired target cleavage.
human	AGO4	GO:0090625	siRNA-mediated gene silencing by mRNA destabilization	IDA	PMID:15260970	UNDECIDED	The source NOT assertion remains unresolved: cleavage-specific ontology wording and slicing-independent decay must be distinguished.
human	AGO4	GO:0035279	miRNA-mediated gene silencing by mRNA destabilization	IDA	PMID:15260970	UNDECIDED	The source NOT assertion remains unresolved: cleavage-specific ontology wording and slicing-independent decay must be distinguished.
human	AGR2	GO:0034976	response to endoplasmic reticulum stress	IMP	PMID:25666625	REMOVE	The NOT annotation conflicts with later evidence that AGR2 contributes to ER stress/proteostasis regulation and that AGR2 H117Y is impaired in alleviating tunicamycin-induced ER stress.
human	AKTIP	GO:0019787	ubiquitin-like protein transferase activity	NAS	PMID:18799622	ACCEPT	This is a NOT annotation explicitly stating AKTIP does NOT have ubiquitin-like protein transferase activity, consistent with it lacking the catalytic cysteine.
human	ANO10	GO:0005229	intracellularly calcium-gated chloride channel activity	IDA	PMID:21984732	UNDECIDED	The original negative channel assertion cannot yet be reconciled across the experimental contexts.
human	ANO5	GO:0005229	intracellularly calcium-gated chloride channel activity	IDA	PMID:22075693	UNDECIDED	The NOT calcium-gated chloride-channel assertion remains unresolved across assay contexts.
human	APC	GO:0045296	cadherin binding	IDA	PMID:7890674	ACCEPT	Preserve the tested negative cadherin-binding assertion.
human	APP	GO:0030425	dendrite	IDA	PMID:17251419	ACCEPT	NOT annotation - Lacor et al. (2007) showed Abeta oligomers (ADDLs) bind to dendritic spines, not dendrite shafts. The annotation indicates where full-length APP or its products are NOT found. This study focused on Abeta oligomer binding specificity to excitatory pyramidal neurons.
human	APP	GO:0032590	dendrite membrane	TAS	PMID:20032460	ACCEPT	NOT annotation - Zhao et al. (2010) showed that Abeta oligomers (ADDLs) bind specifically to dendritic spines expressing surface AMPA receptors (particularly GluR2), not the general dendrite membrane. The specificity is for postsynaptic compartments.
human	APP	GO:0097060	synaptic membrane	IDA	PMID:17308309	ACCEPT	NOT annotation - De Felice et al. (2007) showed Abeta oligomers (ADDLs) bind specifically at or near NMDA receptors, not the general synaptic membrane. The study showed ADDLs co-immunoprecipitate with NMDA-R subunits and require NMDA-R activation for their effects.
human	ARFGEF1	GO:0005096	GTPase activator activity	IDA	PMID:15644318	ACCEPT	A NOT annotation, asserting that BIG1 does not stimulate GTP hydrolysis. It is the correct reading of an experiment in which BIG1 did the opposite - it inhibited the Rho-GAP activity of myosin IXb, with an IC50 of 0.06 microM, by competing with RhoA for the myosin IXb zinc finger/GAP domain.
human	ARHGAP11B	GO:0005096	GTPase activator activity	IDA	PMID:25721503	ACCEPT	A NOT annotation asserting that ARHGAP11B does not have Rho GTPase-activating activity. One of the best-founded rows in the record, and the key to the gene: the truncation that removed the activity is what made the protein able to amplify basal progenitors.
human	ARHGAP11B	GO:0005096	GTPase activator activity	IDA	PMID:27957544	ACCEPT	The same NOT annotation from the paper that dissected the cause. Modern ARHGAP11B has no RhoGAP activity in cells, while the reconstructed ancestral protein, which has a complete GAP domain, does.
human	ARHGAP11B	GO:0043547	positive regulation of GTPase activity	IDA	PMID:27957544	ACCEPT	The process-side counterpart of the negated molecular function: ARHGAP11B does not positively regulate GTPase activity.
human	ARIH1	GO:0031462	Cul2-RING ubiquitin ligase complex	IDA	PMID:27565346	KEEP_AS_NON_CORE	This NOT-qualified Cul2-RING complex annotation is retained as a non-core, experiment-specific negative result from PMID:27565346, but it conflicts with positive CUL2 interaction evidence from PMID:24076655 and with UniProt text citing both PMID:24076655 and PMID:27565346 for neddylated CUL2 interaction. The most defensible interpretation is context-dependent assay behavior rather than a global absence of CUL2 association.
human	ARL3	GO:0005929	cilium	IDA	PMID:17646400	REMOVE	NOT located in cilium, from a GFP-tagged localization screen of Rab and Arl GTPases in serum-starved hTERT-RPE1 cells (Yoshimura et al. 2007), in which overexpressed EGFP-Arl family members other than ARL13B were not detected on primary cilia (Fig. S2 A).
human	ARL6	GO:0005929	cilium	IDA	PMID:17646400	ACCEPT	NOT located_in cilium from a Rab/Arf GTPase overexpression screen (Yoshimura et al.) in which only Rab8a was enriched at cilia; ARL6 was not enriched in that specific assay. This negative result is assay-context-specific and is contradicted by multiple direct endogenous localization studies showing ARL6 in cilia.
human	ASAH1	GO:0005769	early endosome	IDA	PMID:12764132	ACCEPT	Retain the condition-specific NOT localization assertion.
human	ASAH1	GO:0005783	endoplasmic reticulum	IDA	PMID:12764132	ACCEPT	Retain the condition-specific NOT localization assertion.
human	ATG9A	GO:0000421	autophagosome membrane	IDA	PMID:22456507	ACCEPT	Autophagosome membrane; ATG9A-containing membrane is incorporated into the forming autophagosome.
human	ATL3	GO:0006888	endoplasmic reticulum to Golgi vesicle-mediated transport	IMP	PMID:18270207	ACCEPT	The NOT annotation is supported: ATL perturbation did not generally block anterograde ER-to-Golgi trafficking in the VSVG-GFP assay.
human	AZIN2	GO:0004586	ornithine decarboxylase activity	IBA	GO_REF:0000033	ACCEPT	NOT: AZIN2 does not have ornithine decarboxylase activity. It is a catalytically dead paralog of ODC in the Orn/Lys/Arg decarboxylase family.
human	BAG2	GO:0032436	positive regulation of proteasomal ubiquitin-dependent protein catabolic process	ISS	PMID:19228967	ACCEPT	The NOT annotation is well justified - BAG2 routes tau to a ubiquitin-INDEPENDENT proteasomal pathway while inhibiting CHIP, so it does not promote ubiquitin-dependent proteasomal catabolism.
human	BMP4	GO:0003150	muscular septum morphogenesis	ISS	GO_REF:0000024	KEEP_AS_NON_CORE	The muscular-septum NOT assertion is supported within the conditional anterior-heart-field mouse model.
human	BMP4	GO:0003198	epithelial to mesenchymal transition involved in endocardial cushion formation	ISS	GO_REF:0000024	KEEP_AS_NON_CORE	The cushion-EMT NOT assertion is supported for initial EMT in the conditional mouse explant assay.
human	BMP4	GO:0003215	cardiac right ventricle morphogenesis	ISS	GO_REF:0000024	KEEP_AS_NON_CORE	The right-ventricle NOT assertion is supported for myocardial morphology in the conditional mouse model.
human	BMP4	GO:0003277	apoptotic process involved in endocardial cushion morphogenesis	ISS	GO_REF:0000024	KEEP_AS_NON_CORE	The cushion-apoptosis NOT assertion is supported in proximal outflow cushions at the measured embryonic stages.
human	BMP4	GO:1902893	regulation of miRNA transcription	IMP	PMID:18548003	KEEP_AS_NON_CORE	The transcriptional NOT result is specific to the tested miR-21 response.
human	BMP4	GO:1905072	cardiac jelly development	ISS	GO_REF:0000024	KEEP_AS_NON_CORE	The cardiac-jelly NOT assertion is supported for initial jelly formation in the conditional anterior-heart-field model.
human	BMPR1A	GO:0010665	regulation of cardiac muscle cell apoptotic process	ISS	GO_REF:0000024	KEEP_AS_NON_CORE	The NOT assertion is retained as a bounded mouse developmental observation, not universal absence of an apoptosis role.
human	BMPR1A	GO:1905292	regulation of neural crest cell differentiation	ISS	GO_REF:0000024	UNDECIDED	The neural-crest NOT assertion requires an exact donor-source and timing reconciliation.
human	BMPR2	GO:0003148	outflow tract septum morphogenesis	ISS	GO_REF:0000024	UNDECIDED	Preserve the negated outflow-tract-septum assertion pending resolution of allele and anatomical context.
human	BMPR2	GO:0003181	atrioventricular valve morphogenesis	ISS	GO_REF:0000024	UNDECIDED	The negated atrioventricular-valve assertion is context-dependent and unresolved.
human	BMPR2	GO:0048738	cardiac muscle tissue development	ISS	GO_REF:0000024	UNDECIDED	Preserve the NOT cardiac-muscle-development transfer with conditional-knockout limits.
human	BMPR2	GO:0061626	pharyngeal arch artery morphogenesis	ISS	GO_REF:0000024	UNDECIDED	Preserve the NOT pharyngeal-arch-artery assertion pending donor-context clarification.
human	BRAF	GO:0031267	small GTPase binding	IPI	PMID:12194967	ACCEPT	"NOT (negated) IPI annotation for GO:0031267 small GTPase binding from Kontani et al. 2002 J Biol Chem (PMID:12194967 — Di-Ras, a distinct subgroup of Ras family GTPases with unique biochemical properties). Owing to effector-domain substitutions (Ile at the position corresponding to Ha-Ras Asp-33), the paper shows Di-Ras1/Di-Ras2 ""fails to interact with the Ras-binding domain of Raf, resulting in no stimulation of mitogen-activated protein kinase."" This is a deliberate, experimentally-grounded negative finding: the BRAF RAS-binding domain does not engage the Di-Ras subgroup of small GTPases."
human	BRCA2	GO:0004402	histone acetyltransferase activity	IDA	PMID:9824164	ACCEPT	BRCA2 associates with acetyltransferase activity when bound to P/CAF. This study shows HAT activity comes from P/CAF, not BRCA2 itself.
human	C1GALT1C1	GO:0016263	N-acetylgalactosaminide beta-1,3-galactosyltransferase activity	IMP	PMID:37216524	ACCEPT	This is a NOT annotation: GOA explicitly asserts that C1GALT1C1 does not enable N-acetylgalactosaminide beta-1,3-galactosyltransferase activity. The curators drew exactly the right distinction from this paper. Patient cells carrying hypomorphic C1GALT1C1 variants show substantially reduced T-synthase activity, but the paper's conclusion is that this is a chaperonopathy: Cosmc is required for the activity to be present, while the activity itself belongs to C1GALT1.
human	CALR3	GO:0005509	calcium ion binding	IDA	PMID:21590275	ACCEPT	Unlike calreticulin-1, CALR3 does not bind calcium; the experimental data support this negated annotation.
human	CANX	GO:0070062	extracellular exosome	IDA	PMID:21235781	ACCEPT	This NOT annotation states calnexin is absent from these exosomes, consistent with its use as a non-exosomal ER marker.
human	CASP12	GO:0004197	cysteine-type endopeptidase activity	IKR	PMID:12054529	ACCEPT	NOT: CASP12 does not have cysteine-type endopeptidase activity (IKR, inferred from key catalytic residues). Human caspase-12 is an inactive 'pseudo-caspase'.
human	CDK5	GO:0008017	microtubule binding	TAS	PMID:17491008	MARK_AS_OVER_ANNOTATED	Microtubule binding is over-attributed to CDK5 itself.
human	CDK5RAP3	GO:2000060	positive regulation of ubiquitin-dependent protein catabolic process	IDA	PMID:16173922	ACCEPT	Negated (NOT) IDA annotation: CDK5RAP3/LZAP does NOT positively regulate ubiquitin-dependent protein catabolic process. Consistent with LZAP reversing ARF inhibition of HDM2 and maintaining p53 stability rather than promoting its degradation.
human	CDK5RAP3	GO:0005730	nucleolus	IDA	PMID:16173922	ACCEPT	Negated (NOT) IDA annotation: CDK5RAP3/LZAP is NOT localized to the nucleolus (in this study).
human	CEP290	GO:0051011	microtubule minus-end binding	IDA	PMID:16682973	ACCEPT	NOT microtubule minus-end binding (IDA, Sayer et al. 2006).
human	CHMP3	GO:0006997	nucleus organization	IMP	PMID:20616062	ACCEPT	NOT annotation per GOA (UniProt) indicating CHMP3 is not directly involved in nucleus organization.
human	CHMP3	GO:0007080	mitotic metaphase chromosome alignment	IMP	PMID:20616062	ACCEPT	NOT annotation per GOA (UniProt) indicating CHMP3 is not directly involved in mitotic metaphase chromosome alignment.
human	CHMP3	GO:1901673	regulation of mitotic spindle assembly	IMP	PMID:20616062	ACCEPT	NOT annotation per GOA (UniProt) indicating CHMP3 is not directly involved in regulation of mitotic spindle assembly.
human	CHMP3	GO:1903541	regulation of exosomal secretion	IMP	PMID:22660413	ACCEPT	NOT annotation per GOA indicating CHMP3 is not directly involved in regulation of exosomal secretion.
human	CHMP6	GO:1903541	regulation of exosomal secretion	IMP	PMID:22660413	ACCEPT	Retain the existing NOT annotation for exosome secretion.
human	CLU	GO:0016887	ATP hydrolysis activity	IDA	PMID:11123922	ACCEPT	PMID:11123922 explicitly demonstrated that CLU lacks detectable ATPase activity. This is a NOT annotation confirming CLU is an ATP-independent chaperone.
human	COQ8A	GO:0004672	protein kinase activity	IDA	PMID:27499294	ACCEPT	"NOT protein kinase activity. Stefely et al. 2016 directly demonstrated that COQ8, despite its protein-kinase-like fold, lacks canonical protein kinase activity in trans. This negated annotation is correct and important — it explicitly counters the naive ""protein kinase"" assignment implied by the family name (ADCK, aarF domain-containing kinase). Accept as-is."
human	COQ8A	GO:0006468	protein phosphorylation	IDA	PMID:27499294	ACCEPT	NOT involved_in protein phosphorylation. Consistent with the finding that COQ8 does not perform canonical protein-kinase phosphotransfer in trans; the protein instead functions via ATPase / small-molecule (possibly lipid) activity and complex-Q stabilization. Correct negated annotation; accept as-is.
human	COQ8B	GO:0004672	protein kinase activity	IDA	PMID:27499294	ACCEPT	NOT annotation: family-level biochemical assays (COQ8A/yeast Coq8p, applied to COQ8B by the naming/orthology framework of this paper) showed no canonical protein kinase activity in trans toward general substrates. This negation is correctly recorded and refers to general in-trans kinase behaviour; it does not contradict the later, specific ATP-dependent COQ3 phosphorylation by COQ8B (PMID:38425362). Retained as a NOT annotation.
human	COQ8B	GO:0006468	protein phosphorylation	IDA	PMID:27499294	ACCEPT	NOT annotation paralleling the NOT protein kinase activity: no general in-trans protein phosphorylation was detected for the COQ8 family in this study. Correctly recorded; the specific COQ3 phosphorylation by COQ8B (PMID:38425362) is a distinct, later finding on a defined substrate. Retained as a NOT annotation.
human	CPT1C	GO:0004095	carnitine O-palmitoyltransferase activity	ISS	GO_REF:0000024	ACCEPT	Negated (NOT) annotation correctly stating that CPT1C does NOT have carnitine O-palmitoyltransferase activity. This is explicitly supported by experimental and review literature showing CPT1C has markedly reduced canonical CPT1 enzymatic activity (CPT1C-deep-research-falcon.md).
human	CPT1C	GO:0005739	mitochondrion	ISS	GO_REF:0000024	ACCEPT	Negated (NOT) annotation correctly stating CPT1C is NOT localized to mitochondria. Unlike CPT1A and CPT1B which are outer mitochondrial membrane proteins, CPT1C localizes to the ER (PMID:25751282, PMID:30135643).
human	CPT1C	GO:0006631	fatty acid metabolic process	ISS	GO_REF:0000024	ACCEPT	Negated (NOT) annotation correctly stating CPT1C is NOT involved in fatty acid metabolic process. This distinguishes CPT1C from CPT1A/B which function in fatty acid transport into mitochondria for beta-oxidation. Recent reviews confirm CPT1C functions as a malonyl-CoA sensor rather than in fatty acid metabolism (CPT1C-deep-research-falcon.md).
human	CPT1C	GO:0009437	carnitine metabolic process	ISS	GO_REF:0000024	ACCEPT	Negated (NOT) annotation correctly stating CPT1C is NOT involved in carnitine metabolic process. CPT1C binds malonyl-CoA and palmitoyl-CoA but does not catalyze carnitine-dependent acyl transfer.
human	CRMP1	GO:0006208	pyrimidine nucleobase catabolic process	IBA	GO_REF:0000033	ACCEPT	The curated NOT assertion for CRMP1 concerns pyrimidine nucleobase catabolism specifically.
human	CRMP1	GO:0004157	dihydropyrimidinase activity	IBA	GO_REF:0000033	ACCEPT	NOT: CRMP1 does not have dihydropyrimidinase activity. It belongs to the metallo-dependent hydrolase superfamily but lacks the conserved metal-cofactor-binding residues required for catalysis (UniProt CAUTION).
human	CRY1	GO:0003904	deoxyribodipyrimidine photo-lyase activity	IDA	PMID:8909283	ACCEPT	CRY1 lacks cyclobutane pyrimidine dimer photolyase activity (negated).
human	CRY1	GO:0003914	DNA (6-4) photolyase activity	IDA	PMID:8909283	ACCEPT	CRY1 lacks (6-4) photolyase activity (negated).
human	CRY2	GO:0000719	photoreactive repair	IDA	PMID:12627958	ACCEPT	Ozgur and Sancar 2003 confirmed that hCRY2 lacks photorepair activity (PMID:12627958). This is a correctly negated annotation documenting the absence of photolyase function.
human	CRY2	GO:0003904	deoxyribodipyrimidine photo-lyase activity	IDA	PMID:8909283	ACCEPT	Hsu et al. 1996 demonstrated that purified hCRY2 lacks photolyase activity on cyclobutane pyrimidine dimers (PMID:8909283). Correctly negated annotation.
human	CRY2	GO:0003914	DNA (6-4) photolyase activity	IDA	PMID:8909283	ACCEPT	Hsu et al. 1996 demonstrated that purified hCRY2 lacks (6-4) photolyase activity (PMID:8909283). Correctly negated annotation.
human	CRYAA	GO:0042026	protein refolding	ISS	GO_REF:0000024	KEEP_AS_NON_CORE	"NOT annotation for protein refolding (ISS from bovine ortholog via GO_REF:0000024). This is a critical annotation that explicitly states CRYAA does NOT perform protein refolding. CRYAA is a holdase chaperone that prevents aggregation of denatured proteins but does not actively refold them. This is consistent with all experimental evidence: PMID:8943244 describes the chaperone-like activity as ""the ability to suppress nonspecific aggregation"" with no mention of refolding capability. The negated GOA assertion is therefore consistent with CRYAA being a holdase without foldase activity. This NOT annotation should be retained because it records the biologically important distinction between CRYAA holdase activity and active protein refolding."
human	CWC27	GO:0003755	peptidyl-prolyl cis-trans isomerase activity	IDA	PMID:20676357	ACCEPT	Negated (NOT) IDA annotation recording that CWC27 (SDCCAG-10) does NOT have peptidyl-prolyl cis-trans isomerase activity, based on direct biochemical assay showing no tetrapeptide isomerase activity and no cyclosporin binding.
human	CYB5R4	GO:0016174	NAD(P)H oxidase H2O2-forming activity	IDA	PMID:15131110	ACCEPT	Correctly negated annotation. The 2004 enzymology concluded that NCB5OR is not an NAD(P)H oxidase for superoxide/H2O2 production, refuting the earlier oxidase interpretation.
human	CYP11B2	GO:0034651	cortisol biosynthetic process	IMP	PMID:9703385	ACCEPT	NOT|involved_in cortisol biosynthetic process. In CMO-deficiency patients, cortisol and its precursors are in the normal range despite defective aldosterone synthesis, indicating CYP11B2 is not required for cortisol production (that is the role of CYP11B1).
human	DAB2IP	GO:0035662	Toll-like receptor 4 binding	IDA	PMID:19948740	ACCEPT	This is a NOT annotation indicating DAB2IP does not directly bind TLR4. The cited study shows DAB2IP disrupts the TLR4-TIRAP-MyD88 complex rather than acting as a direct TLR4-binding factor.
human	DCTN1	GO:0098930	axonal transport	IMP	PMID:18364389	REMOVE	NOT axonal transport, based on the absence of detectable transport inhibition in G59S p150Glued transgenic mice.
human	DPYSL2	GO:0006208	pyrimidine nucleobase catabolic process	IBA	GO_REF:0000033	ACCEPT	The curated NOT assertion for DPYSL2 concerns pyrimidine nucleobase catabolism specifically.
human	DPYSL2	GO:0004157	dihydropyrimidinase activity	IBA	GO_REF:0000033	ACCEPT	NOT: DPYSL2 does not have dihydropyrimidinase activity. It belongs to the metallo-dependent hydrolase superfamily but lacks the conserved metal-cofactor-binding residues required for catalysis (UniProt CAUTION).
human	DPYSL3	GO:0006208	pyrimidine nucleobase catabolic process	IBA	GO_REF:0000033	ACCEPT	The curated NOT assertion for DPYSL3 concerns pyrimidine nucleobase catabolism specifically.
human	DPYSL3	GO:0004157	dihydropyrimidinase activity	IBA	GO_REF:0000033	ACCEPT	NOT: DPYSL3 does not have dihydropyrimidinase activity. It belongs to the metallo-dependent hydrolase superfamily but lacks the conserved metal-cofactor-binding residues required for catalysis (UniProt CAUTION).
human	DPYSL4	GO:0006208	pyrimidine nucleobase catabolic process	IBA	GO_REF:0000033	ACCEPT	The curated NOT assertion for DPYSL4 concerns pyrimidine nucleobase catabolism specifically.
human	DPYSL4	GO:0004157	dihydropyrimidinase activity	IBA	GO_REF:0000033	ACCEPT	NOT: DPYSL4 does not have dihydropyrimidinase activity. It belongs to the metallo-dependent hydrolase superfamily but lacks the conserved metal-cofactor-binding residues required for catalysis (UniProt CAUTION).
human	DPYSL5	GO:0004157	dihydropyrimidinase activity	IBA	GO_REF:0000033	ACCEPT	This is a NOT (negated) annotation: DPYSL5 does NOT enable dihydropyrimidinase activity. Although DPYSL5 belongs to the metallo-dependent hydrolase (dihydropyrimidinase/amidohydrolase) superfamily and is ~57% identical to dihydropyrimidinase, it lacks the conserved metal-cofactor-binding residues required for catalysis (UniProt CAUTION).
human	DPYSL5	GO:0006208	pyrimidine nucleobase catabolic process	IBA	GO_REF:0000033	ACCEPT	NOT (negated) annotation: DPYSL5 is NOT involved in pyrimidine nucleobase catabolism. This is the process counterpart of the absent dihydropyrimidinase activity.
human	DUOX1	GO:0004601	peroxidase activity	IDA	PMID:19460756	ACCEPT	peroxidase activity: This is a NOT annotation: the isolated human N-terminal DUOX1 peroxidase-like domain did not bind heme or exhibit intrinsic peroxidase activity. It does not negate heme binding in the separate transmembrane oxidase domain.
human	EDEM1	GO:0004571	mannosyl-oligosaccharide 1,2-alpha-mannosidase activity	IDA	PMID:12610306	KEEP_AS_NON_CORE	A negated (NOT) experimental annotation reflecting the original proposal that EDEM1 lacks alpha-1,2-mannosidase activity, based on overexpression biochemistry. Later endogenous-knockout analysis (PMID:25092655) demonstrated that EDEM1 does possess weak mannosidase activity, so this negation is superseded but retained as the curated record of the early finding.
human	EDEM2	GO:0004571	mannosyl-oligosaccharide 1,2-alpha-mannosidase activity	IDA	PMID:15537790	KEEP_AS_NON_CORE	A negated (NOT) experimental annotation reflecting the original characterization, in which recombinant EDEM2 showed no alpha-1,2-mannosidase activity, leading to a proposed lectin role. Endogenous-knockout analysis (PMID:25092655) and the E117Q mutant later established that EDEM2 does possess mannosidase activity, so this negation is superseded but retained as the curated record of the early finding.
human	EIF3G	GO:0005634	nucleus	IDA	PMID:12426392	KEEP_AS_NON_CORE	The study reported nuclear exclusion of eIF3 in its baseline-cell context, supporting the negated localization under those conditions.
human	ENDOU	GO:0008236	serine-type peptidase activity	IDA	PMID:18936097	ACCEPT	PMID:18936097 shows ENDOU lacks serine-type peptidase activity (negative result in chromogenic protease assays) and is instead an RNA endonuclease.
human	ERCC4	GO:0010521	telomerase inhibitor activity	IDA	PMID:18812185	ACCEPT	XPF controls telomere length via TRF2 regulation and a nuclease-independent mechanism, NOT by inhibiting telomerase; the negated annotation is informative.
human	ERP27	GO:0003756	protein disulfide isomerase activity	IBA	GO_REF:0000033	ACCEPT	This is a NOT (negated) annotation stating that ERP27 does NOT have protein disulfide isomerase activity. This is correct - ERP27 lacks the CXXC active-site motif and is a redox-inactive PDI-family member.
human	ERP29	GO:0003756	protein disulfide isomerase activity	IKR	PMID:9738895	ACCEPT	This is a NOT (negated) annotation - ERP29 does NOT have protein disulfide isomerase activity, because it lacks the CXXC thioredoxin-box motif. The negation is correct.
human	FBXO25	GO:0005730	nucleolus	IDA	PMID:16278047	ACCEPT	Direct-assay negative annotation indicating FBXO25 is NOT located in the nucleolus, refining its nuclear localization to non-nucleolar (subnuclear dot-like) domains.
human	GALK1	GO:0016020	membrane	IDA	PMID:8908517	ACCEPT	Curated NOT|located_in membrane (IDA), based on in vitro translation showing the GALK1 protein is cytosolic and not associated with the ER membrane. An informative negation.
human	GALM	GO:0042803	protein homodimerization activity	IDA	PMID:12753898	ACCEPT	Negated (NOT) annotation: GALM does not have protein homodimerization activity. Biochemical and structural characterization established that GALM is a monomer.
human	GBA	GO:0007005	mitochondrion organization	IMP	PMID:25456120	ACCEPT	NOT annotation: in GBA-N370S iPSC-derived dopamine neurons, mitochondria showed normal morphology and distribution, so GBA is annotated as NOT involved in mitochondrion organization.
human	GBA	GO:0031175	neuron projection development	IMP	PMID:25456120	ACCEPT	NOT annotation: neurite outgrowth rates were similar between GBA-N370S and control neurons, so GBA is annotated as NOT involved in neuron projection development.
human	GBA1	GO:0007005	mitochondrion organization	IMP	PMID:25456120	MARK_AS_OVER_ANNOTATED	Mitochondrion organization is not supported as a direct GBA1 process by the cited iPSC twin study.
human	GBA1	GO:0031175	neuron projection development	IMP	PMID:25456120	MARK_AS_OVER_ANNOTATED	Neuron projection development is too broad and indirect for the GBA1 iPSC disease-model evidence.
human	GCH1	GO:0032496	response to lipopolysaccharide	IEP	PMID:15604419	KEEP_AS_NON_CORE	This annotation is marked as NOT (negative). The study shows GCH1 is NOT induced by LPS alone in endothelial cells, but requires combined cytokine signaling.
human	GLUD2	GO:0005829	cytosol	IDA	PMID:18688271	ACCEPT	Correct NOT annotation. Unlike its paralog GLUD1 (which is both mitochondrial and cytoplasmic), GLUD2 is specifically targeted to mitochondria because of a positively selected E7K substitution in its mitochondrial targeting sequence, and is not appreciably cytosolic. Accept this well-supported negative annotation.
human	GTPBP2	GO:0003746	translation elongation factor activity	IDA	PMID:30108131	ACCEPT	Directly demonstrated NEGATIVE result - GTPBP2 lacks eEF1A-like elongation activity, distinguishing it from its paralog GTPBP1. The negation is informative and consistent with GTPBP2 acting as a ribosome-rescue / quality-control GTPase rather than a productive elongation factor.
human	HACD2	GO:0004725	protein tyrosine phosphatase activity	IMP	PMID:15024066	ACCEPT	"Correct NOT (negated) annotation. Despite the ""protein tyrosine phosphatase-like"" (PTPLB) family name, HACD2 has no phosphatase activity; a Pro-101 mutation did not restore any phosphatase activity. This informative negation should be retained."
human	HDAC6	GO:0047611	acetylspermidine deacetylase activity	IDA	PMID:28516954	ACCEPT	This is a NOT annotation. PMID:28516954 demonstrated that HDAC6 does NOT have acetylspermidine deacetylase activity - this activity is specific to HDAC10.
human	HDAC6	GO:0106047	polyamine deacetylation	IDA	PMID:28516954	ACCEPT	This is a NOT annotation. PMID:28516954 demonstrated that HDAC6 is NOT involved in polyamine deacetylation - this activity is specific to HDAC10.
human	HDAC6	GO:0106048	spermidine deacetylation	IDA	PMID:28516954	ACCEPT	This is a NOT annotation. PMID:28516954 demonstrated that HDAC6 is NOT involved in spermidine deacetylation - this activity is specific to HDAC10.
human	HSPA6	GO:0070370	cellular heat acclimation	IMP	PMID:21231916	ACCEPT	NOT annotation for GO:0070370 (cellular heat acclimation) from Hageman et al. (2011) (PMID:21231916). The authors showed that siRNA-mediated blocking of HSPA6 did not impair the development of heat-induced thermotolerance, and that overexpression of HSPA6 did not protect cells from heat-induced cell death (unlike HSPA1A). This negative result is informative and demonstrates that despite being heat-inducible, HSPA6 does not contribute to acquired thermotolerance, distinguishing it functionally from HSPA1A.
human	HSPB8	GO:0004672	protein kinase activity	IDA	PMID:14985082	ACCEPT	Although HSPB8 was originally named protein kinase H11, recombinant HSPB8 has negligible autophosphorylation and cannot phosphorylate model substrates; the kinase activity is refuted. The NOT (negated) annotation is correct.
human	HSPD1	GO:0044406	adhesion of symbiont to host	IDA	PMID:20633027	KEEP_AS_NON_CORE	Retain the source-specific interaction or host-associated effect as non-core.
human	IDO1	GO:0046006	regulation of activated T cell proliferation	IMP	PMID:25310899	ACCEPT	NOT annotation. In renal tubular epithelial cells, the IDO inhibitor 1-methyl-L-tryptophan only partially restored or failed to restore suppressed CD4+/CD8+ T-cell proliferation, indicating that IDO does not account for the regulation of activated T-cell proliferation in this system (other factors, e.g. ICAM-1, were implicated). The negation correctly captures this.
human	IL10	GO:1903659	regulation of complement-dependent cytotoxicity	IMP	PMID:16034134	ACCEPT	NOT annotation: IL-10 does NOT regulate complement-dependent cytotoxicity based on PMID:16034134.
human	IL10	GO:2000352	negative regulation of endothelial cell apoptotic process	IMP	PMID:16034134	ACCEPT	NOT annotation: IL-10 does NOT negatively regulate endothelial cell apoptotic process based on PMID:16034134.
human	ILK	GO:0004674	protein serine/threonine kinase activity	IDA	PMID:20005845	ACCEPT	NOT: ILK does not have protein serine/threonine kinase activity. Structural and biochemical work established it as a pseudokinase scaffold (UniProt now names it 'Scaffold protein ILK').
human	ILK	GO:0004674	protein serine/threonine kinase activity	IDA	PMID:21524996	ACCEPT	NOT: ILK does not have protein serine/threonine kinase activity. Structural and biochemical work established it as a pseudokinase scaffold (UniProt now names it 'Scaffold protein ILK').
human	LGALS3	GO:2001200	positive regulation of dendritic cell differentiation	IDA	PMID:16116184	ACCEPT	This is a NOT annotation. PMID:16116184 shows galectin-9 (not galectin-3) induces dendritic-cell maturation; galectin-3 lacks this activity. The negated annotation correctly records the absence of this function for galectin-3.
human	LMAN1	GO:0034498	early endosome to Golgi transport	IMP	PMID:18287528	ACCEPT	ERGIC-53 functions in the ER-ERGIC-Golgi early secretory pathway and COPI-dependent retrograde recycling; the study shows its role is in maintaining ERGIC/Golgi architecture via COPI, with no role in early endosome to Golgi transport. The NOT qualifier correctly records that ERGIC-53 does NOT act in this endosomal pathway.
human	LONP1	GO:0001018	mitochondrial promoter sequence-specific DNA binding	IDA	PMID:9485316	ACCEPT	The NOT annotation correctly distinguishes single-stranded promoter-element binding from double-stranded promoter binding.
human	LRP5	GO:0019534	toxin transmembrane transporter activity	IMP	PMID:18350154	ACCEPT	IMP annotation from PMID:18350154 associates LRP5 with toxin transmembrane transporter activity; evidence specificity and core relevance were reviewed.
human	LRP6	GO:0019534	toxin transmembrane transporter activity	IMP	PMID:18350154	ACCEPT	IMP annotation from PMID:18350154 associates LRP6 with toxin transmembrane transporter activity; evidence specificity, source support, and core relevance were reviewed.
human	LRPPRC	GO:0051015	actin filament binding	IDA	PMID:12762840	ACCEPT	The study explicitly showed LRPPRC does NOT colocalize with actin filaments. This is a negated annotation (NOT actin filament binding).
human	MAP1S	GO:0051015	actin filament binding	IDA	PMID:12762840	ACCEPT	Curated NOT (negated) annotation - this study found MAP1S does NOT bind actin filaments under the tested conditions. Note a separate study (PMID:15528209) reported positive actin filament binding (light chain), so this activity is context/construct-dependent.
human	MAP1S	GO:0004536	DNA nuclease activity	IDA	PMID:15907802	ACCEPT	Curated NOT (negated) annotation - the study showed MAP1S binds DNA but does NOT have DNA nuclease activity. The negation is appropriate and informative.
human	MVB12B	GO:0043130	ubiquitin binding	IDA	PMID:20654576	ACCEPT	MVB12B does NOT bind ubiquitin; this is an experimentally-supported negated (NOT) annotation.
human	MVD	GO:0005777	peroxisome	IDA	PMID:14972328	ACCEPT	MVD is explicitly NOT located in the peroxisome; earlier peroxisomal claims were refuted by direct localization studies.
human	MVK	GO:0005777	peroxisome	IDA	PMID:14730012	ACCEPT	NOT|located_in peroxisome — direct experimental evidence that human MK is not peroxisomal.
human	MYO5A	GO:1903358	regulation of Golgi organization	IMP	PMID:24006491	ACCEPT	NOT regulation of Golgi organization (IMP).
human	NAMPT	GO:0008286	insulin receptor signaling pathway	IDA	PMID:17983582	ACCEPT	"Correctly negated (NOT) annotation. This study showed that extracellular NAMPT does NOT exert insulin-mimetic effects in vitro or in vivo, but instead acts via systemic NAD+/NMN biosynthesis. The negation refutes the earlier ""visfatin as insulin-mimetic"" hypothesis. Retain as negated."
human	NAMPT	GO:0060612	adipose tissue development	IDA	PMID:17983582	ACCEPT	Correctly negated (NOT) annotation, consistent with the same study showing eNAMPT lacks insulin-mimetic activity and acts through NAD+ biosynthesis rather than as a direct adipogenic/insulin-mimetic hormone. Retain as negated.
human	NME2	GO:0004518	nuclease activity	IDA	PMID:19435876	KEEP_AS_NON_CORE	Correct negated annotation. NME2 was tested for nuclease activity in this c-MYC/NHE context and found not to cleave the substrate.
human	NME2	GO:0005925	focal adhesion	IDA	PMID:11919189	KEEP_AS_NON_CORE	Kept as non-core. Peripheral membrane/actin-edge localizations fit NME2 roles in local GTP supply and membrane remodeling but are not its primary localization.
human	NRXN1	GO:0050885	neuromuscular process controlling balance	IMP	PMID:19896112	ACCEPT	NOT annotation: patients with biallelic NRXN1 defects had normal or only mildly delayed motor milestones, which the curator read as absence of a role in balance.
human	NUFIP1	GO:0003677	DNA binding	IDA	PMID:15107825	ACCEPT	NOT annotation — NUFIP1 does not directly bind DNA; it stimulates RNA polymerase II transcription via protein-protein interactions (BRCA1, P-TEFb/Cyclin T1) rather than direct DNA binding.
human	PANK4	GO:0004594	pantothenate kinase activity	IBA	GO_REF:0000033	ACCEPT	NOT (negated): PANK4 does NOT have pantothenate kinase activity. Although it belongs to the type II pantothenate kinase family, its kinase domain is degenerate; PANK4 is a 'pseudo-pantothenate kinase'.
human	PANK4	GO:0004594	pantothenate kinase activity	IMP	PMID:30927326	ACCEPT	NOT (negated): PANK4 does NOT have pantothenate kinase activity. Although it belongs to the type II pantothenate kinase family, its kinase domain is degenerate; PANK4 is a 'pseudo-pantothenate kinase'.
human	PARK7	GO:0032679	regulation of TRAIL production	IMP	PMID:21785459	ACCEPT	NOT annotation - DJ-1 does NOT regulate TRAIL production (PMID:21785459). DJ-1 inhibits TRAIL-induced apoptosis by blocking DISC assembly, not by affecting TRAIL levels.
human	PARK7	GO:0036524	protein deglycase activity	IDA	PMID:31653696	ACCEPT	NOT annotation - Andreeva et al. demonstrated DJ-1 does NOT possess protein deglycase activity. Apparent deglycase activity results from conversion of free methylglyoxal in fast equilibrium with hemithioacetals, not direct deglycation (PMID:31653696).
human	PARK7	GO:0009438	methylglyoxal metabolic process	IDA	PMID:27903648	ACCEPT	NOT annotation - Pfaff et al. found no evidence for DJ-1 involvement in methylglyoxal detoxification in Drosophila and attributed in vitro cysteine deglycase activity to a TRIS buffer artifact (PMID:27903648). Note this contradicts other studies showing DJ-1 glyoxalase activity.
human	PARK7	GO:0001046	core promoter sequence-specific DNA binding	IC	PMID:15790595	ACCEPT	NOT annotation - DJ-1 does NOT bind DNA directly at core promoter sequences (PMID:15790595). DJ-1 functions as a transcriptional coactivator through protein-protein interactions rather than direct DNA binding.
human	PARK7	GO:0003690	double-stranded DNA binding	IDA	PMID:22683601	ACCEPT	NOT annotation - DJ-1 does NOT bind double-stranded DNA directly (PMID:22683601). Consistent with its role as a transcriptional coactivator via protein-protein interactions rather than direct DNA binding.
human	PARK7	GO:0003697	single-stranded DNA binding	IDA	PMID:22683601	ACCEPT	NOT annotation - DJ-1 does NOT bind single-stranded DNA (PMID:22683601). Consistent with other negated DNA binding annotations.
human	PDCD6IP	GO:0006997	nucleus organization	IMP	PMID:20616062	ACCEPT	Retain existing negated PDCD6IP annotation: NOT nucleus organization.
human	PDCD6IP	GO:0007080	mitotic metaphase chromosome alignment	IMP	PMID:20616062	ACCEPT	Retain existing negated PDCD6IP annotation: NOT mitotic metaphase chromosome alignment.
human	PDCD6IP	GO:1901673	regulation of mitotic spindle assembly	IMP	PMID:20616062	ACCEPT	Retain existing negated PDCD6IP annotation: NOT regulation of mitotic spindle assembly.
human	PDGFA	GO:0072124	regulation of glomerular mesangial cell proliferation	IDA	PMID:11788434	ACCEPT	Negated annotation: the cited metanephric mesenchymal-cell study found that PDGF-A/PDGF-AA did not drive the mesangial-cell proliferative response measured through DNA synthesis.
human	PDGFA	GO:2000278	regulation of DNA biosynthetic process	IDA	PMID:11788434	ACCEPT	Negated annotation: this row should not be read as a positive DNA-synthesis function; PDGF-A/PDGF-AA lacked the cited metanephric mesenchyme response, with the clearest DNA-synthesis support coming from the paired PMID:11788434 evidence.
human	PDGFA	GO:2000278	regulation of DNA biosynthetic process	IDA	PMID:19019919	ACCEPT	Negated annotation: the cited metanephric mesenchyme evidence indicates that PDGF-A/PDGF-AA did not stimulate the DNA-synthesis response in the tested context.
human	PDGFB	GO:0030097	hemopoiesis	IMP	PMID:11264163	ACCEPT	hemopoiesis is supported for PDGFB in the context of its mature extracellular PDGF ligand function.
human	PEX12	GO:0061630	ubiquitin protein ligase activity	IDA	PMID:24662292	ACCEPT	PMID:24662292 demonstrated that PEX12 does NOT possess intrinsic E3 ubiquitin-protein ligase activity. The RING domain of PEX12 is degenerate and coordinates only one zinc ion. Instead, PEX12 activates the E3 activity of PEX10. This is an important negated annotation distinguishing PEX12 from PEX10.
human	PICALM	GO:1902003	regulation of amyloid-beta formation	ISS	PMID:26005850	ACCEPT	This is a NOT annotation for regulation of amyloid-beta formation; it should be retained because the cited disease-model evidence supports amyloid-beta clearance/transcytosis rather than amyloid-beta production by PICALM.
human	PLD4	GO:0004630	D-type glycerophospholipase activity	ISS	GO_REF:0000024	ACCEPT	This is a NOT annotation correctly stating that PLD4 does NOT have phospholipase D activity. This is accurate and important to retain.
human	PMVK	GO:0005777	peroxisome	IDA	PMID:14729858	ACCEPT	Correct NOT annotation. Multiple techniques (subcellular fractionation, digitonin permeabilization, immunofluorescence, immunoelectron microscopy) found no peroxisomal PMVK, overturning the earlier peroxisomal claim.
human	PPIB	GO:0006457	protein folding	IMP	PMID:20089953	ACCEPT	This is a NOT (negated) annotation - in PPIB-null osteogenesis imperfecta, collagen folding is NORMAL, unlike P3H1/CRTAP deficiency which delays collagen folding. Thus PPIB is not required for the overall rate of collagen folding in this assay.
human	PPIB	GO:1901873	regulation of post-translational protein modification	IMP	PMID:20089953	ACCEPT	A NOT (negated) annotation - PPIB deficiency does not reduce collagen post-translational modification (e.g. prolyl 3-hydroxylation remains normal in the PPIB-null OI), distinguishing it from P3H1/CRTAP loss.
human	RAB1B	GO:0090557	establishment of endothelial intestinal barrier	IMP	PMID:23885123	UNDECIDED	NOT establishment of endothelial intestinal barrier. Two separate problems: the supporting evidence cannot be located in the cached full text, and the term names the wrong cell layer for the study it cites.
human	RAB1B	GO:0019068	virion assembly	IMP	PMID:21680502	ACCEPT	Virion assembly, annotated twice from one paper with opposite polarity - an IMP NOT and an IGI positive. Read together they are a correct paralog-redundancy record, not a contradiction.
human	RHBDF1	GO:0004252	serine-type endopeptidase activity	IBA	GO_REF:0000033	ACCEPT	NOT (negated): RHBDF1 (iRhom1) does NOT have serine-type endopeptidase activity. Although it belongs to the rhomboid peptidase S54 family, it is an inactive rhomboid (pseudoprotease) lacking the catalytic Ser (position 720).
human	RHBDF1	GO:0004252	serine-type endopeptidase activity	IDA	PMID:21439629	ACCEPT	NOT (negated): RHBDF1 (iRhom1) does NOT have serine-type endopeptidase activity. Although it belongs to the rhomboid peptidase S54 family, it is an inactive rhomboid (pseudoprotease) lacking the catalytic Ser (position 720).
human	ROR1	GO:0004714	transmembrane receptor protein tyrosine kinase activity	IBA	GO_REF:0000033	ACCEPT	NOT: ROR1 does not have transmembrane receptor tyrosine kinase activity. Its kinase domain is degenerate (very low activity in vitro; does not bind ATP) - an inactive/pseudokinase RTK.
human	ROR1	GO:0007169	cell surface receptor protein tyrosine kinase signaling pathway	IBA	GO_REF:0000033	ACCEPT	NOT: ROR1 is not involved in cell-surface receptor protein tyrosine kinase signaling (as a catalytic RTK).
human	ROR1	GO:0005524	ATP binding	IDA	PMID:24107129	ACCEPT	NOT: ROR1 does not bind ATP (IDA) - its degenerate kinase domain lacks nucleotide binding.
human	RP2	GO:0007023	post-chaperonin tubulin folding pathway	IDA	PMID:11847227	ACCEPT	NOT: RP2 does not function in the post-chaperonin tubulin folding pathway.
human	RPS3	GO:0019104	DNA N-glycosylase activity	IDA	PMID:18610840	ACCEPT	Recombinant human RPS3 cleaved AP sites by beta-elimination but did NOT cleave substrates containing oxidized/deaminated bases (8-oxoguanine, uracil, hypoxanthine, etc.), so it lacks DNA glycosylase activity.
human	RPS3	GO:0019104	DNA N-glycosylase activity	TAS	PMID:15707971	ACCEPT	Despite a sequence prediction of glycosylase activity, RPS3 does not have glycosylase activity; it acts as an endonuclease on damaged DNA.
human	RUBCN	GO:0005794	Golgi apparatus	IDA	PMID:19270696	ACCEPT	The negated Golgi colocalization annotation is supported by curated localization evidence.
human	SEPHS1	GO:0016260	L-selenocysteine biosynthetic process	IMP	PMID:15534230	ACCEPT	NOT annotation: SEPHS1 does not function in de novo L-selenocysteine biosynthesis. Human Sps1 only weakly complemented an E. coli selD mutant and only when L-selenocysteine was supplied, indicating dependence on a selenium salvage/recycling system rather than selenite assimilation (which SPS2 supports). This correctly negates the biosynthetic role and is consistent with the in vitro absence of selenophosphate synthase activity.
human	SIRT1	GO:1990404	NAD+-protein mono-ADP-ribosyltransferase activity	TAS	PMID:17456799	UNDECIDED	Review notes that some sirtuins have ADP-ribosyltransferase activity but does not specify SIRT1.
human	SIRT1	GO:0005730	nucleolus	IDA	PMID:16079181	KEEP_AS_NON_CORE	SIRT1 is not reported as nucleolar in this study.
human	SIRT1	GO:0003950	NAD+ poly-ADP-ribosyltransferase activity	TAS	PMID:17456799	UNDECIDED	Review notes that some sirtuins have ADP-ribosyltransferase activity but does not specify SIRT1.
human	SIRT1	GO:0005737	cytoplasm	IDA	PMID:15469825	ACCEPT	This study does not report cytoplasmic localization; the NOT annotation is acceptable.
human	SIRT2	GO:1990404	NAD+-protein mono-ADP-ribosyltransferase activity	TAS	PMID:17456799	ACCEPT	This is a NOT annotation indicating SIRT2 does not have NAD+-protein mono-ADP-ribosyltransferase activity per the cited review.
human	SIRT2	GO:0003950	NAD+ poly-ADP-ribosyltransferase activity	TAS	PMID:17456799	ACCEPT	This is a NOT annotation indicating SIRT2 does not have NAD+ poly-ADP- ribosyltransferase activity.
human	SIRT5	GO:0003950	NAD+ poly-ADP-ribosyltransferase activity	TAS	PMID:17456799	UNDECIDED	The family-level sirtuin review does not isolate the experimental basis for the target-specific absence of poly-ADP-ribosyltransferase activity.
human	SIRT5	GO:0006476	protein deacetylation	IDA	PMID:22076378	UNDECIDED	The annotation is NOT protein deacetylation. The cited study measures weak in-vitro deacetylation while supporting acidic deacylation as the major activity; that distinction does not by itself establish complete absence of the biological process.
human	SIRT5	GO:1990404	NAD+-protein mono-ADP-ribosyltransferase activity	TAS	PMID:17456799	UNDECIDED	The family-level reference alone does not isolate the experimental basis for the target-specific NOT mono-ADP-ribosyltransferase annotation.
human	SLC25A19	GO:0030233	deoxynucleotide transmembrane transporter activity	IDA	PMID:15539640	ACCEPT	NOT annotation: experimental evidence shows SLC25A19 (DNC) does not function physiologically as a deoxynucleotide transporter. Reconstituted DNC transported dNTPs only at millimolar Km (~1000x above physiological), and DNC over-expression/knockdown did not affect mitochondrial dNTP uptake or mtDNA depletion. Correctly recorded as a negated annotation.
human	SLC25A19	GO:0030233	deoxynucleotide transmembrane transporter activity	IDA	PMID:17035501	ACCEPT	NOT annotation supported by the Slc25a19 knockout mouse: mitochondrial ribo- and deoxyribonucleoside triphosphate levels were normal and no mtDNA depletion occurred, showing deoxynucleotide transport is not the primary function. Correctly recorded as negated.
human	SLC25A19	GO:0030302	deoxynucleotide transport	IDA	PMID:15539640	ACCEPT	NOT annotation: SLC25A19 is not physiologically involved in deoxynucleotide transport (no effect on mitochondrial dNTP uptake or mtDNA maintenance). Correctly recorded as negated.
human	SPARC	GO:0005737	cytoplasm	IDA	PMID:1737102	ACCEPT	PMID:1737102 localized platelet osteonectin to alpha-granule membranes rather than cytoplasm.
human	SPARC	GO:0005739	mitochondrion	IDA	PMID:1737102	ACCEPT	PMID:1737102 did not detect mitochondrial localization of platelet osteonectin.
human	SPARC	GO:0005886	plasma membrane	IDA	PMID:1737102	ACCEPT	PMID:1737102 localized osteonectin to alpha-granule membranes and did not report plasma membrane localization in resting platelets.
human	STAT1	GO:0043542	endothelial cell migration	IMP	PMID:16585190	ACCEPT	PMID:16585190 reports STAT1 activation inhibits angiogenesis and tube formation; GOA captures this PMID as NOT involved in endothelial cell migration.
human	TBCK	GO:0006468	protein phosphorylation	NAS	PMID:12471243	ACCEPT	A NOT annotation: GOA asserts that TBCK is not involved in protein phosphorylation. Read the qualifier - this is the negative of the term, and it is the assertion that the 2026 biochemistry supports.
human	TFRC	GO:0001558	regulation of cell growth	IMP	PMID:7556058	ACCEPT	This NOT annotation derives from a study primarily on the GPI-anchored transferrin homolog p97/melanotransferrin, using TfR-deficient CHO cells transfected with human TfR. The negated regulation-of-cell-growth annotation indicates TfR1 was not shown to regulate cell growth in this system.
human	TFRC	GO:0042127	regulation of cell population proliferation	IMP	PMID:7556058	ACCEPT	This NOT annotation derives from the p97/melanotransferrin iron-uptake study using TfR-transfected CHO cells, indicating TfR1 was not shown to regulate cell proliferation in this experimental system.
human	TMEM120A	GO:0005216	monoatomic ion channel activity	IMP	PMID:34374645	ACCEPT	Negative assertion - TMEM120A does NOT enable ion channel activity, from failure to reproduce mechanosensitive currents in cells and in reconstituted liposomes.
human	TMEM120A	GO:0005216	monoatomic ion channel activity	IDA	PMID:34409941	ACCEPT	Negative assertion - TMEM120A is not sufficient to mediate poking- or stretch-induced currents, assayed with Piezo1 and TMEM63A positive controls in Piezo1-knockout HEK cells.
human	TMEM120A	GO:0005216	monoatomic ion channel activity	IDA	PMID:34465718	ACCEPT	Negative assertion - cryo-EM structures reveal no ion-conduction pathway and the authors decline to call TMEM120A a channel.
human	TMEM63A	GO:0017128	phospholipid scramblase activity	IDA	PMID:39716028	ACCEPT	NOT annotation: in a scramblase-null cellular background, human TMEM63A - unlike TMEM63B - did not confer phospholipid scrambling.
human	TMEM65	GO:0005432	calcium:sodium antiporter activity	IDA	PMID:40200126	UNDECIDED	A NOT annotation: Garbincius et al. conclude that TMEM65 is an NCLX binding partner required for sodium-dependent mitochondrial calcium efflux, but is not itself the exchanger, because the TMEM65 effect is abolished by deletion or pharmacological inhibition of NCLX.
human	TOMM40	GO:0005739	mitochondrion	IMP	PMID:11745481	REMOVE	PMID:11745481 (Das et al. 2001) identified TOMM40 as p38.5/Haymaker and reported differential expression in malignant cells. The NOT annotation for mitochondrion localization is incorrect — TOMM40 is definitively a mitochondrial protein. This may reflect early confusion about the gene identity.
human	TOP2A	GO:0005730	nucleolus	IDA	PMID:9049244	ACCEPT	PMID:9049244 reports TOP2A is not localized inside nucleoli in A431 cells.
human	TOP2B	GO:0005730	nucleolus	IDA	PMID:9049244	ACCEPT	NOT annotation from PMID:9049244 indicating TOP2B is EXCLUDED from nucleoli during normal interphase. This is important negative evidence that corrects earlier erroneous reports.
human	TSG101	GO:0061631	ubiquitin conjugating enzyme activity	IKR	PMID:9241264	ACCEPT	The negated ubiquitin-conjugating-enzyme annotation is correct for TSG101.
human	UPB1	GO:0008270	zinc ion binding	IDA	PMID:29976570	ACCEPT	NOT annotation correctly asserting that human UPB1 does not bind zinc, refuting an earlier sequence-based prediction.
human	UPF3A	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IDA	PMID:16601204	ACCEPT	NOT annotation. In the assay of PMID:16601204, UPF3A did not function in (canonical) NMD, consistent with UPF3A being only marginally active in promoting decay compared with UPF3B. This negation is an important, deliberate curation.
human	VAPA	GO:0007029	endoplasmic reticulum organization	IMP	PMID:18713837	ACCEPT	VAPA partner recruitment contributes to ER organization and membrane traffic.
human	VAPA	GO:0034975	protein folding in endoplasmic reticulum	IMP	PMID:18713837	UNDECIDED	A direct protein-folding role is not established by the inspected trafficking evidence.
human	VAPA	GO:0070971	endoplasmic reticulum exit site	IDA	PMID:18713837	ACCEPT	VAPA partner recruitment contributes to ER organization and membrane traffic.
human	WIPI2	GO:0005776	autophagosome	IDA	PMID:20505359	ACCEPT	NOT autophagosome. A deliberate negative annotation: WIPI2 marks the phagophore and is not retained on the completed autophagosome.
human	WIPI2	GO:0097352	autophagosome maturation	IMP	PMID:20505359	ACCEPT	NOT autophagosome maturation. WIPI2 depletion does not block maturation; it blocks an earlier step.
human	WT1	GO:0045893	positive regulation of DNA-templated transcription	IDA	PMID:9815658	ACCEPT	The +KTS isoform (P19544-1) does NOT activate transcription. PMID:9815658 shows the SRY promoter was strongly activated by WT1(-KTS) isoforms but was NOT activated by WT1(+KTS) isoforms. The +KTS tripeptide insertion alters DNA binding capability. This is a classic example of isoform-specific function where the two splice variants have opposite activities.
human	YTHDF3	GO:0045948	positive regulation of translational initiation	IDA	PMID:32492408	UNDECIDED	Explicit negative assertion - with all three DF paralogs analysed together, no translation-promoting effect was detectable in HeLa cells.
mouse	Pld4	GO:0004630	D-type glycerophospholipase activity	IDA	PMID:21085684	ACCEPT	This annotation has a NOT qualifier in the GOA file (line 24), indicating PLD4 does NOT have phospholipase D activity. This negative annotation correctly reflects that PLD4 lacks this activity despite its misleading name.
rat	Ghr	GO:0031623	receptor internalization	ISO	GO_REF:0000121	KEEP_AS_NON_CORE	NOT annotation indicating the short isoform (GHBP, isoform 2, lacking transmembrane and cytoplasmic domains) does NOT undergo receptor internalization. Consistent with the lack of transmembrane domain in this isoform.
rat	Ghr	GO:0046898	response to cycloheximide	ISO	GO_REF:0000121	KEEP_AS_NON_CORE	NOT annotation for the short isoform (GHBP). The soluble isoform does not show response to cycloheximide (translation inhibitor), as it is already secreted.
rat	Ptk7	GO:0004714	transmembrane receptor protein tyrosine kinase activity	ISO	GO_REF:0000121	ACCEPT	The annotation explicitly asserts NOT receptor tyrosine kinase activity, and that negation is correct. PTK7 is a receptor pseudokinase. Human structural evidence identifies an occluded ATP site and noncanonical catalytic motifs; the corresponding rat residues are conserved. PTK7-dependent phosphorylation is mediated by associated active kinases such as Src, not intrinsic receptor tyrosine kinase activity.
rat	Ptk7	GO:0005524	ATP binding	ISO	GO_REF:0000121	ACCEPT	Retain the explicit NOT ATP binding annotation. PTK7 fails to bind ATP in the characterized receptor pseudokinase mechanism. The rat protein retains the human pocket-occluding residues and ALG motif, providing a sequence-supported reason not to transfer ATP binding from active kinase relatives.
rat	Ptk7	GO:0016301	kinase activity	ISO	GO_REF:0000121	ACCEPT	The NOT kinase activity annotation correctly captures catalytic inactivity. A kinase-like fold does not confer kinase catalysis. The conserved PTK7 pocket blocks ATP binding; Src is the active kinase in the experimentally resolved junctional module.
rat	Rnase1	GO:0051607	defense response to virus	ISO	GO_REF:0000121	ACCEPT	This is a negated GO annotation: the source asserts Rnase1 is NOT involved in defense response to virus. Accepting it preserves the explicit negation rather than treating the process as a non-core positive function.
rat	Slc5a1	GO:1902476	chloride transmembrane transport	ISO	GO_REF:0000121	UNDECIDED	ISO annotation for chloride transport. This is unexpected - SGLT1 is not known as a chloride transporter. May be an erroneous annotation.
worm	hsp-12.3	GO:0051082	unfolded protein binding	IDA	PMID:9744800	ACCEPT	NOT annotation (negated IDA) for unfolded protein binding based on Kokke et al. 1998 (PMID:9744800). The study directly tested recombinant HSP-12.3 for chaperone-like activity and found it devoid of the ability to prevent aggregation of denaturing substrate proteins. This negative result is consistent with the structural analysis showing that HSP-12.3 forms tetramers rather than the large oligomeric complexes required for chaperone function. GO:0051082 is now formally obsolete, but the negation is still informative as it indicates this protein does not have holdase activity.
worm	hsp-12.6	GO:0051082	unfolded protein binding	IDA	PMID:9139746	ACCEPT	NOT annotation (negated IDA) for unfolded protein binding based on Leroux et al. 1997 (PMID:9139746). The study directly tested recombinant HSP-12.6 for chaperone activity and found it unable to prevent thermally induced aggregation of test substrates. This negative result is consistent with the structural analysis showing HSP-12.6 is monomeric. GO:0051082 is now formally obsolete, but the negation is still informative as it documents the absence of holdase activity.