ALX3

Summary: ALX3 associates with regulatory chromatin.

Reason: TFClass places ALX3 among sequence-specific homeodomain transcription factors. Mouse Alx3 directly occupies insulin promoters in chromatin immunoprecipitation experiments (PMID:16825292); human homeodomain DNA-binding assays independently support the molecular basis of chromatin association (PMID:38600112). Retain the broad chromatin location without specifying a human target promoter from mouse data.

Summary: Retain sequence-specific recognition of transcriptional regulatory DNA.

Reason: The PAINT assertion at PTN004692309 is consistent with human ALX3 homeodomain binding and mouse promoter occupancy/transactivation. These experiments support the inherited regulatory DNA-binding function. The exact ancestral IBD placement was not recovered, so no independent reconstruction of that node is claimed.

Summary: ALX3 functions as a DNA-binding transcription factor.

Reason: The PAINT assignment agrees with its homeodomain architecture and experimentally measured DNA recognition. Mouse Alx3 acts on a defined insulin-promoter enhancer with E47, providing direct transcriptional regulation rather than inference from a developmental phenotype alone. Tissue-specific mouse targets are not asserted as measured human targets.

Summary: The homeobox mapping captures ALX3 transcription-factor activity.

Reason: The InterPro homeobox signature is corroborated by human ALX3 homeodomain DNA-binding measurements and ortholog promoter occupancy/transactivation. This supports the transcription-factor function of the intact gene product rather than assigning an enzymatic activity to its conserved domain.

Summary: The TFClass transcription-factor assignment is supported.

Reason: ALX3 has a paired-class homeodomain with experimentally measured human DNA-binding activity. Mouse Alx3 directly binds a promoter element and modulates reporter transcription with an interacting transcription factor. Together these support the curated TFClass function.

Summary: Retain the broad DNA-binding domain mapping.

Reason: Human ALX3 homeodomain variants and their wild-type reference construct were tested by protein-binding microarrays. The DNA-binding fold and direct measurements support this valid broader InterPro annotation; the existing sequence-specific rows already retain its greater specificity.

Summary: ALX3 transcriptional activity occurs in the nucleus.

Reason: The PAINT nuclear assignment is compatible with ALX3 regulatory DNA binding, chromatin occupancy and transcriptional control. The positive ortholog promoter experiments support the cellular context of this conserved activity. Exact PTN004692309 placement was not recovered; this does not establish a phylogenetic error.

Summary: Retain the curated nuclear-location mapping.

Reason: The Swiss-Prot nuclear location agrees with the homeodomain transcription-factor role and experimentally demonstrated chromatin occupancy by mouse Alx3. No additional cytoplasmic or membrane activity is inferred.

Summary: ALX3 directly regulates transcription through DNA binding.

Reason: The domain mapping is supported by Alx3 promoter occupancy, a defined DNA regulatory element and cofactor-dependent transactivation in the mouse study. The broad process accurately describes what the gene product does without assigning every downstream developmental outcome.

Summary: Retain regulation of RNA polymerase II transcription.

Reason: The ancestral PAINT assignment agrees with the direct promoter-binding and transcriptional activation mechanism measured for Alx3, and human ALX3 has experimentally confirmed DNA-binding capacity. Exact ancestral placement remains unexamined; no transfer failure is inferred.

Summary: The specific neuron-development role remains unresolved.

Reason: GO:0048666 concerns progression from initial neuronal commitment to a mature functional neuron. Mouse head-mesenchyme and neural-tube-closure defects (PMID:20534379) do not themselves demonstrate a neuronal maturation step. Adult hypothalamic expression and altered energy regulation (PMID:39129011) likewise establish neuronal context without directly testing development. The PTN001216073 IBD and supporting clade experiments were not recovered, so the inherited assertion is preserved as UNDECIDED rather than rejected from incomplete phylogenetic evidence.

Summary: Retain the experimental sequence-specific DNA-binding assertion.

Reason: The original study assayed 542 human transcription factors by methylation-sensitive SELEX. The cached text does not expose the ALX3-specific supplemental record; its absence from that excerpt is not evidence of a wrong-gene annotation. Independent human ALX3 homeodomain microarray results (PMID:38600112) confirm DNA recognition, supporting acceptance of the curator assertion. No ALX3-specific preference for methylated CpG is inferred from family-level observations.

Summary: Retain sequence-specific double-stranded DNA binding.

Reason: The electronic ARBA assertion is supported independently by the existing curated experimental annotation and human ALX3 homeodomain microarray assays. This retains the measured binding activity without inferring a particular methylation preference or native target promoter.