CG13096 is a 681-residue protein containing ribosomal-uL1-like domains associated with ribosome biogenesis proteins. Its architecture suggests an RNA-associated role, but the exact molecular activity, RNA substrate, and localization of this fly product remain unresolved.
Exact input: H0RNN8, 681 residues. The accession was fetched explicitly with the gene-directory alias; no canonical-sequence substitution is made.
Raw emitted predictions: CG13096-predictions-source.json. Source features: CG13096-uniprot.txt, with an exact extraction in CG13096-sequence-evidence.json.
These are sequence/domain observations or explicitly named feature predictions, not measurements of biological function. ARBA assertions and ProtNLM-derived UniProt names are not counted as validation.
DR InterPro; IPR053110; Ribosomal_L1-TF.
DR InterPro; IPR023674; Ribosomal_uL1-like.
DR InterPro; IPR028364; Ribosomal_uL1/biogenesis.
The snapshot emits names and location/keyword statements, with no GO or EC prediction for this target. Each actual statement is assessed below; no GO term has been substituted for it. Categories follow the function-prediction rubric, with nonspecific “uncharacterized” names marked UNC because they contain no testable function. CNN records an independently supported existing annotation; it does not assert a particular training-set composition.
| Kind | Verbatim emitted statement | Assessment | Evidence and limitation |
|---|---|---|---|
| Name | Uncharacterized protein | UNC | Uncharacterized protein supplies no testable function. Ribosomal-uL1-like architecture narrows the likely biology but does not establish an intrinsic ribosomal-subunit role. |
| Location | Nucleolus (SL-0188) | UNC | Ribosomal-uL1-like domains occur in ribosome-biogenesis factors and make nucleolar localization plausible. The exact target has no localization experiment or curated GO localization in the retrieved evidence, so nucleolar residence is not established. |
| Location | Nucleus (SL-0191) | UNC | A nuclear location is compatible with ribosome biogenesis but is not established solely by the uL1-like fold. The exact target needs localization or a well-resolved characterized ortholog inference. |
No target-specific primary finding is used to establish a molecular activity here. The current assessment is bounded by exact-record architecture and the explicitly identified curated inferences.
The accession-specific GOA fetch contains no existing annotation rows. The molecular activity remains unresolved; no broad GO root or invented function is added to create apparent coverage.
Genuine external literature research is requested through the repository Falcon wrapper, with perplexity-lite configured as fallback. Provider output is retained separately as CG13096-deep-research-<provider>.md; its source leads are checked against the underlying publications and exact sequence record.
ProtNLM2 output and the prediction files were not used in this section.
From the UniProt record: N-terminal disordered region 1-248 (lysine/alanine-rich, basic), Pfam PF00687 / CDD cd00403 ribosomal-L1 domain in the middle, disordered acidic tail 579-681 (611-681 almost entirely D/E). That combination, a basic N-terminal region, an L1 fold and a long acidic tail, is typical of nucleolar ribosome-biogenesis factors and not of ribosomal proteins.
New script CG13096-bioinformatics/l1_family_placement.py, results in CG13096-bioinformatics/RESULTS.md.
- phmmer with CG13096 as query: top hits human RSL1D1 (E=3.8e-25), mouse Rsl1d1 (4.1e-25) and worm F53F4.11 (2.7e-21). Human RPL10A is much weaker (3.3e-06). There are no significant hits to the PANTHER co-members (Candida NRI1, Dictyostelium DDB_G0279335, VZV ORF11) or to mitochondrial uL1m.
- In the NJ tree CG13096 pairs with worm F53F4.11, apart from the NRI1/DDB_G0279335/VZV cluster. Deep internal branches are very short, so the branching order between lineages is unresolved.
- UniProt cross-references: CG13096, RSL1D1, yeast UTP30 and yeast CIC1 share eggNOG KOG1685 and OrthoDB 10251727at2759. Candida NRI1 (the PANTHER co-member) is in a different eggNOG/OrthoDB group (ENOG502QQIF; 4084568at2759).
- Alliance orthology: CG13096 maps to RSL1D1 (human, mouse, frog, zebrafish) by OrthoFinder, OrthoInspector, PhylomeDB and SonicParanoid, and to worm F53F4.11 by five methods including Ensembl Compara. PANTHER does not support either call.
- PANTHER disagreement. PANTHER 19.0 puts CG13096 in PTHR48162:SF1 (family "YALI0A06930P"), while RSL1D1, UTP30 and CIC1 are in PTHR23105 (SF31/SF203). No fly protein is assigned to PTHR23105:SF31 or SF203. The family review interpro/panther/PTHR48162/PTHR48162-review.yaml (functional_coherence UNKNOWN) lists only CG13096 and VZV ORF11 as SF1 members. It omits the Candida NRI1 and Dictyostelium DDB_G0279335 SF1 members that are in the PANTHER 19.0 classification files, and it does not mention that orthology resources other than PANTHER group CG13096 with RSL1D1. I read PTHR48162 as a split of a highly divergent sequence, not a functionally distinct subfamily. No PAINT node with experimental annotations covers CG13096, so no IBA-style transfer applies.
- CG13096 is not mitochondrial uL1m (mRpL1 = CG7494, PTHR36427) and not a cytoplasmic uL1 (RpL10Aa/RpL10Ab).
The benchmark is the full-length product, and its canonical entry Q9VLK2 is the same gene in this folder, so the same_gene_canonical rule does not apply. The closest experimentally characterized relative is human RSL1D1 (O76021): nucleolar, with experimental UniProt function annotation. It is supported by orthology methods, eggNOG/OrthoDB and the phmmer/tree analysis, but not by PANTHER. The repo has no RSL1D1 review.
None found in modules/ that include CG13096 (no ribosome-biogenesis/pre-ribosome module exists; dmel_cytoplasmic_ribosome.yaml and dmel_mitochondrial_ribosome.yaml do not and should not include it).