ftz-f1 review notes

Scope and exact product

Review target: M9NFK2, 803 aa, taxon 7227, FlyBase FBgn0001078. All 12 seeded GOA rows are electronic and have been reviewed without changing their source terms, qualifiers, or evidence fields. The free-text ProtNLM prediction is adjudicated separately in ftz-f1-protnlm-function-review.md.

The current M9NFK2 sequence is exactly identical to P33244-2, reviewed isoform A: 803/803 aa, SHA256 8e47b8779f9e0ee27c6b92a56b1170a84a3c05cd7eade1dd500c5d6d3c6082b7. The entire common tail, target residues 175–803, matches P33244-1 residues 399–1027. Source files and a generic equality checker are in ftz-f1-isoform-records. M9NFK2 has the PROSITE-defined DNA-binding domain at 281–356 and regulatory LBD at 568–800. These domains lie wholly within the shared tail; the 2018 NMR construct (long-product residues 785–1027) therefore corresponds to the target's identical residues 561–803.

UniProt's isoform A sequence change cites Lavorgna et al. PMID:8096644(https://pubmed.ncbi.nlm.nih.gov/8096644/), DOI 10.1073/pnas.90.7.3004, who cloned the midprepupal developmental isoform. Together with its N-terminal sequence this supports betaFTZ-F1 identity, despite the potentially confusing A/B database labels. Historical papers report older protein lengths; the older labels and lengths should not substitute for current sequence matching. Ensembl also maps M9NFK2 to ftz-f1-RA/RC products. Current sequence equality does not prove the sequence originally supplied to ProtNLM.

Primary evidence

The publication caches for these sources are present. PMID:29547262 has full text; the other listed records are abstract-only in the local cache. Decisive quoted claims occur in those abstracts. No missing full text is described as available, and no experimental curator assertion is removed on the basis of an abstract's silence.

Annotation decisions

All source rows have a decision: five ACCEPT, six MODIFY, one KEEP_AS_NON_CORE. The core function is sequence-specific RNA polymerase II transcriptional regulation in the nucleus. Generic DNA binding and transcription annotations are made more informative using already-seeded specific terms. Zinc binding is retained as a structural, non-core property.

QuickGO definitions checked on 2026-09-08:

The ProtNLM thyroid specificity is PLI, with the raw record explicitly attributing the paragraph's phmmer hit to Japanese flounder THRB Q91279. Exact identity to a reviewed FTZ-F1 product, NR5A-specific structural/functional evidence, and the NR1 thyroid-receptor match provide a concrete subfamily-confusion explanation. This does not rest on ARBA, an AI review's prose, an assumed taxon exclusion, or an invented negative hormone-binding experiment.

Remaining biological question

Can an endogenous phospholipid alter full-length betaFTZ-F1 cofactor recruitment and transcription in vivo? This question is distinct from the unsupported T3/T4 receptor specificity. A future assay should measure both binding and transcriptional regulation with appropriate NR5A and thyroid-receptor controls, while preserving the target's isoform identity.

Provider research and validation

Falcon/Edison research completed successfully on 2026-09-08 (481 seconds), with its provider artifact preserved. It supports the overall nuclear transcription-factor and developmental-competence synthesis and offers additional steroidogenesis source leads. Its locus-wide discussion does not resolve the exact M9NFK2 isoform, and the ligand assessment needs the independently retrieved 2018 NMR/phospholipid-binding paper. The curated decisions therefore cite primary experiments and sequence records directly. The validator advisory suggesting a deep-research citation is intentionally left as an advisory; quoting the provider's summary would not add evidence to those primary-source-supported decisions.

just validate DROME ftz-f1 passes with no errors and that single advisory. The scaffolded gene history record validates. The HTML review has been rendered. The generic FASTA equality checker gives the expected identical result for M9NFK2/P33244-2 and nonidentical results for the longer P33244-1 control and synthetic control sequences.

2026-10-20 — Full re-review, independent of the ProtNLM2 predictions

Scope: re-examined all 12 GOA rows, the description and core functions. ProtNLM2 output was not consulted.

Identity of the benchmark accession

Evolutionary grounding

Changes in this re-review