Gene Ontology annotation through association of InterPro records with GO terms
Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity
Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Automatic Gene Ontology annotation based on Rhea mapping
Electronic Gene Ontology annotations created by ARBA machine learning models
Combined Automated Annotation using Multiple IEA Methods
UniProtKB entry Q6PBW5 for Danio rerio rpe65a
Falcon deep research report for Danio rerio rpe65a (Q6PBW5)
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Falcon confirms gene identity: zebrafish has two RPE65 paralogs and rpe65a is the ocular,
RPE-expressed visual-cycle isomerohydrolase (Q6PBW5), whereas rpe65b is extra-ocular.
"only one paralog, RPE65a, is expressed in the zebrafish eye (in the RPE)"
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Falcon establishes the core molecular function: Rpe65a is the retinoid isomerohydrolase of the
canonical RPE visual cycle, converting all-trans-retinyl esters to 11-cis-retinol plus a fatty acid,
enabling regeneration of 11-cis-retinal chromophore for opsins.
"Rpe65a is the **retinoid isomerohydrolase** of the canonical RPE visual cycle that converts **all-trans-retinyl esters → 11-cis-retinol + fatty acid**, enabling regeneration of **11-cis-retinal** chromophore for opsins."
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Falcon supports that the direct substrate is membrane-associated all-trans-retinyl ester (not free
retinol) and that the iron cofactor functions as a Lewis acid for O-alkyl cleavage and isomerization,
so RPE65 differs from oxygenase carotenoid cleavage dioxygenases (relevant to the dioxygenase/oxidoreductase
over-annotations).
"Mechanistically, RPE65 differs from oxygenase CCDs: in oxygenase reactions (e.g., NinaB), iron activates dioxygen, whereas in RPE65 the iron is understood as functioning as a **Lewis acid** supporting O-alkyl cleavage and isomerization."
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Falcon localizes Rpe65a to the retinal pigment epithelium; in zebrafish, rods depend strongly on this
canonical RPE visual cycle while larval cones can use parallel intra-retinal pathways, explaining the
incomplete loss of vision on rpe65a knockdown.
"rpe65a** is the ocular paralog and localizes to the **retinal pigment epithelium (RPE)**."
Evidence for RPE65-independent vision in the cone-dominated zebrafish retina.
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rpe65a, not rpe65b, is expressed in light-sensitive structures and its retinal expression is confined to the RPE.
"In crosssections it became clear that retinal RPE65a expression was confined to RPE cells"
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Morpholino knockdown reduces 11-cis-retinal and alters rod outer segments.
"Targeted gene knockdown of RPE65 resulted in morphologically altered rod outer segments and overall reduced 11- cis -retinal levels."
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Cone vision persists in RPE65a-deficient larvae.
"Cone vision of RPE65-deficient larvae remained functional as demonstrated by behavioural tests and by metabolite profiling for retinoids."
Identification of the key residues determining the product specificity of isomerohydrolase.
An alternative isomerohydrolase in the retinal Müller cells of a cone-dominant species.
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RPE65c, RPE65a and 13cIMH are distinct zebrafish genes.
"zebrafish RPE65c, RPE65a and 13cIMH are three homologous proteins encoded by distinct genes"
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rpe65a knockdown does not fully abolish 11-cis-retinal regeneration.
"morpholino-mediated knockdown of zebrafish RPE65a (an orthologue of human RPE65) did not completely attenuate 11cRAL regeneration in the zebrafish eye"
Non-photopic and photopic visual cycles differentially regulate immediate, early, and late phases of cone photoreceptor-mediated vision.
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Rpe65a is expressed exclusively in the RPE.
"In zebrafish, Rpe65a is exclusively expressed in the RPE, whereas a contentious Rpe65c isoform was localized to retinal Müller glia"
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rpe65a knockdown reduces but does not abolish 11-cis-retinal synthesis.
"Zebrafish rpe65a knockdown significantly reduced but did not completely attenuate 11cRAL synthesis, supporting the presence of an alternative pathway for chromophore synthesis in zebrafish retinae"
Carotenoid cleavage enzymes evolved convergently to generate the visual chromophore.
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RPE65 primary chemistry is retinyl ester hydrolysis, distinct from carotenoid oxygenation.
"two homologous enzymes catalyzing distinct primary chemistry on disparate substrates—retinyl ester hydrolysis in the case of RPE65 and carotenoid oxygenation in the case of NinaB—both possess the ability to catalyze trans–cis isomerization at a C11–C12 retinoid/carotenoid double bond"