Acot1

Summary: This very long-chain fatty acid (VLCFA, longer than C22) annotation is an IBA phylogenetic inference made across the whole ACOT family panel (which includes paralogs with broader substrate ranges). Rat Acot1 is characterized as a long-chain (C12-C20) acyl-CoA thioesterase with no documented activity on substrates above C20 - UniProt records it as "More active towards saturated and unsaturated long chain fatty acyl-CoAs (C12-C20)" and the falcon deep research describes it exclusively as a long-chain thioesterase (C12-C20). VLCFA per GO:0000038 requires aliphatic tails of more than 22 carbons, which falls outside the experimentally supported substrate range; the closest accurate process term is GO:0001676 (long-chain fatty acid metabolic process), which is separately annotated. This VLCFA term is therefore an over-annotation propagated from family members with different substrate ranges.

Reason: IBA family-level inference that conflicts with the experimentally documented C12-C20 (long-chain) substrate range for rat Acot1; very long-chain (longer than C22) activity is not supported by UniProt or the deep research, so the long-chain term GO:0001676 is the accurate process term. The longest curated substrate for rat Acot1 and for its human ortholog is eicosanoyl-CoA (C20), which GO classes as long-chain (13-22 carbons); no target-specific activity on chains longer than C22 has been reported.

Summary: IBA from the amniote ACOT1/ACOT2 node PTN000793330, whose seed evidence includes rat Acot1 itself (RGD:70894) and the human and mouse orthologs. Hydrolysis of C12-C20 acyl-CoAs to free fatty acids is a direct step in cellular long-chain fatty acid metabolism, and the rat enzyme (ACH2/CTE-I) was purified with activity on C12-C16 acyl-CoAs.

Reason: The node placement is sound and the rat protein carries its own experimental support for long-chain acyl-CoA hydrolysis (PMID:7906114); GO:0001676 (13-22 carbons) matches the documented substrate range.

Summary: This peroxisome annotation is an IBA phylogenetic inference made across the whole ACOT family panel, which includes peroxisomal paralogs. Rat Acot1 is specifically a cytosolic enzyme - UniProt records its subcellular location as "Cytoplasm, cytosol" (PMID:9490035) with no peroxisomal localization, and the falcon deep research consistently places Acot1 in the cytosol while explicitly assigning the peroxisomal localization to the distinct paralogs Acot3-6. The peroxisome term is therefore an over-annotation propagated from family members with different localization.

Reason: IBA family-level localization that conflicts with experimental and review evidence placing rat Acot1 in the cytosol, not the peroxisome; the peroxisomal localization belongs to the distinct Acot3-6 paralogs. Current PAINT places an IRD (NOT) for this term at PTN000793338 (2026-07-10), the rodent Acot1/Acot2 clade, so this IBA is no longer propagated by PAINT and remains only in the cached GOA file. The IRD agrees with this verdict.

Summary: IBA from PTN001286267 (ACOT family node). Acot1 hydrolyzes long-chain acyl-CoAs to free fatty acid plus CoA, directly consuming acyl-CoA and so participating in acyl-CoA metabolism and setting cytosolic acyl-CoA/CoA pools.

Reason: Acyl-CoA hydrolysis is the gene product's own catalytic step in acyl-CoA metabolism; the function is conserved across the family node and documented for the rat enzyme.

Summary: IBA from PTN001286267, with rat Acot1 (RGD:70894) among the seed members. Fatty acyl-CoA hydrolase activity is the defining activity of Acot1, experimentally shown for the purified rat enzyme.

Reason: Correct, conserved core activity; the more specific child GO:0052816 (long-chain) is separately annotated and is the preferred core term.

Summary: Cytosol is the experimentally established and defining subcellular location of Acot1 - UniProt records "Cytoplasm, cytosol" with experimental evidence (ECO:0000269|PubMed:9490035), and the falcon deep research consistently places Acot1 in the cytosol. This is the same localization evidence used to argue that the peroxisome IBA is an over-annotation, so cytosol is accepted as a core localization that distinguishes Acot1 from its mitochondrial (Acot2) and peroxisomal (Acot3-6) paralogs.

Reason: Cytosolic localization is experimentally supported (PMID:9490035) and is the defining compartment for rat Acot1, distinguishing it from its differently-localized paralogs.

Summary: InterPro (IPR016662, long-chain acyl-CoA thioesterase) mapping to acyl-CoA metabolic process. Consistent with the enzyme's hydrolysis of long-chain acyl-CoAs.

Reason: Acot1 directly hydrolyzes acyl-CoAs, a step in acyl-CoA metabolism; the domain-based inference agrees with the experimental biochemistry.

Summary: The thiolester hydrolase activity annotation is related to Acot1 function, but it is too generic compared with the supported specific term: long-chain fatty acyl-CoA hydrolase activity (GO:0052816), which matches the documented C12-C20 substrate preference and is the most specific accurate molecular function.

Reason: The annotation is directionally related to Acot1 but is too broad; the specific long-chain catalytic activity is more informative and is the most specific accurate term already supported in this review.

Proposed replacements: long-chain fatty acyl-CoA hydrolase activity

Summary: RHEA-derived annotation from dodecanoyl-CoA (RHEA:30135) and decanoyl-CoA (RHEA:40059) hydrolysis. GO:0052815 covers acyl chains of 6 to 12 carbons, so dodecanoyl-CoA (C12) hydrolysis, which UniProt records for rat Acot1 with experimental evidence from PMID:7906114, falls within it. The purified rat enzyme is active on C12-C16 acyl-CoAs, but its preference is long-chain (C12-C20).

Reason: Previously MODIFY to the long-chain term. On re-review the medium-chain term is not wrong, because the C12 substrate is experimentally hydrolyzed by the rat enzyme and is medium-chain by the GO definition, and the absence of activity on C8 or shorter does not exclude C10-C12. It is retained as a real but secondary activity; long-chain fatty acyl-CoA hydrolase activity (GO:0052816) is the core term.

Summary: Acot1 is characterized as a long-chain acyl-CoA thioesterase active toward C12-C20 substrates; long-chain fatty acyl-CoA hydrolase activity is the most specific accurate term.

Reason: The long-chain term is more specific than fatty acyl-CoA hydrolase activity and matches Acot1 substrate preference.

Summary: The fatty acid metabolic process annotation is plausible for Acot1 but should be kept as non-core context rather than used to define the gene product function.

Reason: Correct but general (UniPathway UPA00199 mapping); the specific child GO:0001676 long-chain fatty acid metabolic process is the informative process term for Acot1.

Summary: IDA from Yamada et al. 1994, who purified two long-chain acyl-CoA hydrolases (ACH1, ACH2) from liver cytosol of peroxisome-proliferator-treated rats; ACH2 corresponds to Acot1 and was active on C12-C16 acyl-CoAs.

Reason: Direct biochemical evidence for the rat enzyme hydrolyzing long-chain acyl-CoAs, a step in long-chain fatty acid metabolism.

Summary: IDA from the purification of rat liver cytosolic long-chain acyl-CoA hydrolases (PMID:7906114), including palmitoyl-CoA kinetics for ACH2 (Acot1).

Reason: Direct enzymatic evidence on the rat protein for the defining activity of Acot1.

Summary: The negative regulation of cardiac muscle cell apoptotic process annotation is plausible for Acot1 but should be kept as non-core context rather than used to define the gene product function.

Reason: Rat H9c2 cardiomyoblast overexpression and siRNA knockdown of Acot1 changed apoptosis (PMID:23226270), so the IMP is a real experimental result for the rat gene. The anti-apoptotic effect is attributed by the authors to reduced long-chain acyl-CoA overload, i.e. a downstream consequence of the thioesterase activity, so it is kept as non-core.

Summary: This very long-chain fatty acid (VLCFA, longer than C22) annotation is an ISO inference projected from human ACOT1 (UniProtKB:Q86TX2). As for the parallel IBA annotation, rat Acot1's experimentally documented substrate range is long-chain C12-C20 (UniProt; falcon deep research), with no activity reported above C20. GO:0000038 requires aliphatic tails of more than 22 carbons, outside the supported range, so this is an over-annotation; the accurate process term is the separately-annotated GO:0001676 (long-chain fatty acid metabolic process).

Reason: ISO inference that conflicts with the experimentally documented C12-C20 (long-chain) substrate range for rat Acot1; very long-chain (longer than C22) activity is not supported, so the long-chain term GO:0001676 is the accurate process term. The longest substrate UniProt records for either the rat protein or the human donor is eicosanoyl-CoA (C20), which is long-chain under the GO definitions (13-22 carbons long-chain, more than 22 very long-chain); the donor's own IDA (PMID:16940157, abstract-only in cache) could not be checked for data on chains longer than C22.

Summary: ISO from mouse Acot1 (MGI:1349396), the direct ortholog. Long-chain acyl-CoA hydrolysis is conserved between the mouse and rat CTE-I enzymes (cloned together in PMID:9490035) and is experimentally shown for the rat enzyme.

Reason: Orthology-based transfer of a core process from the mouse ortholog, consistent with rat-specific biochemistry (PMID:7906114).

Summary: Cytosol is the experimentally established and defining subcellular location of Acot1 (UniProt "Cytoplasm, cytosol", ECO:0000269|PubMed:9490035; falcon deep research). This ISO annotation is consistent with the experimental evidence and with the rationale for marking the peroxisome IBA as an over-annotation, so cytosol is accepted as a core localization.

Reason: Cytosolic localization is experimentally supported (PMID:9490035) and is the defining compartment for rat Acot1, distinguishing it from its differently-localized paralogs.

Summary: ISO from human ACOT1 (UniProtKB:Q86TX2). Acyl-CoA hydrolysis by Acot1 directly consumes long-chain acyl-CoAs, consistent with the donor annotation.

Reason: Conserved core process between orthologs; supported by rat biochemistry.

Summary: ISO from mouse Acot1 (MGI:1349396). Recombinant mouse CTE-I hydrolyzes long-chain acyl-CoAs, and the rat enzyme has the same activity.

Reason: Conserved core activity, independently established for the rat protein (PMID:7906114).

Summary: IDA from Lindquist et al. 1998, who cloned rat and mouse CTE-I (Acot1) cDNAs and expressed the recombinant enzyme, which was mainly active with long-chain acyl-CoAs. The recombinant expression in the abstract is of the mouse cDNA; the full text (not cached) may include rat data, and the activity is in any case the established function of the rat enzyme.

Reason: Fatty acyl-CoA hydrolase activity is the defining activity of Acot1 and is independently shown for the rat enzyme (PMID:7906114), so the curator's call is accepted.

Summary: ISO from human ACOT1 (UniProtKB:Q86TX2), a donor-split sibling of the mouse-donor ISO row for the same term. Human ACOT1 carries an IDA for long-chain fatty acid metabolic process (PMID:16940157); the rat ortholog hydrolyzes C12-C20 acyl-CoAs.

Reason: Conserved core process; the human-donor transfer agrees with rat-specific biochemistry (PMID:7906114).

Summary: ISO from human ACOT1 (UniProtKB:Q86TX2), a donor-split sibling of the mouse-donor ISO row. Human ACOT1 has an IDA for fatty acyl-CoA hydrolase activity (PMID:16940157), and several catalytic activities in the rat UniProt entry are themselves inferred from this donor.

Reason: Core activity conserved between orthologs and directly shown for the rat enzyme (PMID:7906114).