rbm-39
C. elegans
RRM domain-containing protein
What the model saw
Gene: rbm-39 Organism: Caenorhabditis elegans Known functions: RRM domain-containing protein. RNA binding. chromatin DNA binding. nucleic acid binding.
View unredacted entry
RRM domain-containing protein. RNA binding. chromatin DNA binding. nucleic acid binding.
Solver output
RBM-39 is an RRM (RNA Recognition Motif) domain-containing protein with RNA binding and chromatin DNA binding activities, suggesting roles in both pre-mRNA splicing/processing and transcriptional regulation. In mammals, RBM39 is a splicing factor and transcriptional co-activator involved in alternative splicing regulation. While splicing fidelity is important for proteostasis and genome integrity, the dual chromatin and RNA binding functions make it difficult to assign a clear pro- or anti-longevity role without direct experimental evidence in C. elegans. The gene could influence longevity through epigenetic/transcriptional regulation or RNA processing, but these functions are broad and do not map cleanly to a single aging hallmark with a defined directionality.
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 "unclear" while the ground truth is "pro_longevity." The model's reasoning is plausible but overly cautious — it correctly identifies RBM-39's RNA binding and chromatin functions but fails to commit to a direction. The model's confidence of 0.35 reflects genuine uncertainty, making this an "appropriately uncertain" failure rather than a confident wrong answer. The mechanistic reasoning about splicing and transcriptional regulation is reasonable but not specifically tied to the pro-longevity finding in C. elegans. The model did not identify any specific experimental evidence linking rbm-39 to longevity in C. elegans, which would have been necessary to arrive at the correct answer.
Raw API responses
solver
{
"reasoning": "RBM-39 is an RRM (RNA Recognition Motif) domain-containing protein with RNA binding and chromatin DNA binding activities, suggesting roles in both pre-mRNA splicing/processing and transcriptional regulation. In mammals, RBM39 is a splicing factor and transcriptional co-activator involved in alternative splicing regulation. While splicing fidelity is important for proteostasis and genome integrity, the dual chromatin and RNA binding functions make it difficult to assign a clear pro- or anti-longevity role without direct experimental evidence in C. elegans. The gene could influence longevity through epigenetic/transcriptional regulation or RNA processing, but these functions are broad and do not map cleanly to a single aging hallmark with a defined directionality.",
"confidence": 0.35,
"key_pathways": [
"pre-mRNA splicing and alternative splicing",
"chromatin-associated transcriptional regulation",
"RNA processing and nucleic acid binding"
],
"mechanism_class": "epigenetic_alterations",
"longevity_influence": "unclear"
}advisor
{
"notes": "The model predicted \"unclear\" while the ground truth is \"pro_longevity.\" The model's reasoning is plausible but overly cautious — it correctly identifies RBM-39's RNA binding and chromatin functions but fails to commit to a direction. The model's confidence of 0.35 reflects genuine uncertainty, making this an \"appropriately uncertain\" failure rather than a confident wrong answer. The mechanistic reasoning about splicing and transcriptional regulation is reasonable but not specifically tied to the pro-longevity finding in C. elegans. The model did not identify any specific experimental evidence linking rbm-39 to longevity in C. elegans, which would have been necessary to arrive at the correct answer.",
"failure_mode": "appropriately_uncertain",
"answer_correct": false,
"mechanism_correct": false,
"reasoning_quality": 2,
"ground_truth_questionable": false
}