exos-3
C. elegans
Exosome complex component RRP40
What the model saw
Gene: exos-3 Organism: Caenorhabditis elegans Known functions: Exosome complex component RRP40. RNA binding.
View unredacted entry
Exosome complex component RRP40. RNA binding.
Solver output
exos-3 encodes the RRP40 subunit of the RNA exosome complex, a conserved 3'-to-5' RNA degradation machinery responsible for processing and surveillance of a broad range of RNA substrates including rRNA, snoRNA, mRNA, and non-coding RNAs. Proper RNA quality control via the exosome prevents accumulation of aberrant transcripts that could disrupt proteostasis and gene expression fidelity. In C. elegans, RNA surveillance pathways intersect with epigenetic regulation and small RNA pathways that are known to influence lifespan. Loss of exosome function leads to dysregulated RNA metabolism, accumulation of cryptic unstable transcripts, and potential disruption of chromatin-associated RNA processing, all of which are associated with accelerated aging phenotypes. Thus, the normal function of exos-3 in maintaining transcriptome integrity is expected to support longevity.
GenAge curators classify each gene's normal function as promoting (Pro-Longevity) or opposing (Anti-Longevity) longevity, based on synthesis across studies. Loss-of-function effects can vary from this depending on the manipulation.
Advisor judgment
The model predicted pro_longevity but the ground truth is anti_longevity. The model's reasoning assumed that exos-3 (RRP40 subunit of the RNA exosome) supports longevity by maintaining RNA quality control and transcriptome integrity. However, the ground truth indicates exos-3 is anti_longevity, meaning its normal function actually limits lifespan (i.e., loss of exos-3 extends lifespan, or overexpression shortens it). The model's mechanistic reasoning was plausible in general terms but led to the wrong conclusion. The model also incorrectly classified the mechanism as "epigenetic_alterations" when RNA surveillance/degradation would be more accurately classified as RNA metabolism or proteostasis. The confidence of 0.55 was relatively low, showing some appropriate uncertainty, but the prediction was still wrong.
Raw API responses
solver
{
"reasoning": "exos-3 encodes the RRP40 subunit of the RNA exosome complex, a conserved 3'-to-5' RNA degradation machinery responsible for processing and surveillance of a broad range of RNA substrates including rRNA, snoRNA, mRNA, and non-coding RNAs. Proper RNA quality control via the exosome prevents accumulation of aberrant transcripts that could disrupt proteostasis and gene expression fidelity. In C. elegans, RNA surveillance pathways intersect with epigenetic regulation and small RNA pathways that are known to influence lifespan. Loss of exosome function leads to dysregulated RNA metabolism, accumulation of cryptic unstable transcripts, and potential disruption of chromatin-associated RNA processing, all of which are associated with accelerated aging phenotypes. Thus, the normal function of exos-3 in maintaining transcriptome integrity is expected to support longevity.",
"confidence": 0.55,
"key_pathways": [
"RNA exosome-mediated RNA surveillance",
"3'-to-5' RNA degradation and quality control",
"non-coding RNA processing"
],
"mechanism_class": "epigenetic_alterations",
"longevity_influence": "pro_longevity"
}advisor
{
"notes": "The model predicted pro_longevity but the ground truth is anti_longevity. The model's reasoning assumed that exos-3 (RRP40 subunit of the RNA exosome) supports longevity by maintaining RNA quality control and transcriptome integrity. However, the ground truth indicates exos-3 is anti_longevity, meaning its normal function actually limits lifespan (i.e., loss of exos-3 extends lifespan, or overexpression shortens it). The model's mechanistic reasoning was plausible in general terms but led to the wrong conclusion. The model also incorrectly classified the mechanism as \"epigenetic_alterations\" when RNA surveillance/degradation would be more accurately classified as RNA metabolism or proteostasis. The confidence of 0.55 was relatively low, showing some appropriate uncertainty, but the prediction was still wrong.",
"failure_mode": "confident_wrong",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 2,
"ground_truth_questionable": false
}