id: A0A9L0JKH1
gene_symbol: FOXJ3
taxon:
  id: NCBITaxon:9793
  label: Equus asinus
status: COMPLETE
description: >-
  Assessment of the 2 ProtNLM2 GO predictions for donkey FOXJ3 (A0A9L0JKH1, DONKEY40 cohort), using
  the reviewed human ortholog Q9UPW0, experimental evidence on mouse Foxj3 (PMID:19914232), and a donkey-human alignment (98.1% identity; fork-head domain
  aligned without gaps). Both predictions (sequence-specific DNA binding; DNA-binding transcription
  factor activity) are biologically correct. Each exact term is already in donkey GOA through InterPro2GO,
  and donkey GOA also holds the more specific RNA polymerase II-specific forms from TreeGrafter, so both
  are scored LSP. The ProtNLM2 evidence records tie these predictions to those TreeGrafter terms. ProtNLM2
  emitted no function text or subcellular-location statement for this accession in the snapshot.
source_documents:
- projects/PROTNLM_EVALUATION/donkey40/donkey40-predictions.tsv
- projects/PROTNLM_EVALUATION/donkey40/donkey40-evidence.tsv
- genes/EQUAS/FOXJ3/FOXJ3-goa.tsv
- genes/EQUAS/FOXJ3/FOXJ3-bioinformatics/RESULTS.md
- genes/EQUAS/FOXJ3/FOXJ3-bioinformatics/human-Q9UPW0-uniprot.txt
predictions:
- source_method: ProtNLM2
  source_version: UniProt API snapshot 2026-10-14
  predicted_term:
    id: GO:0043565
    label: sequence-specific DNA binding
  predicted_term_type: GO_MF
  review:
    assessment: LSP
    confidence_score: 2
    summary: The donkey protein carries a complete fork-head winged-helix DNA-binding domain that aligns
      without gaps to human FOXJ3 (98.1% identity), and mouse Foxj3 binds a conserved forkhead binding
      site in the Mef2c skeletal muscle enhancer. The prediction is therefore correct. The exact term is already present in donkey GOA (InterPro2GO),
      and donkey GOA also has the more specific RNA polymerase II cis-regulatory region sequence-specific
      DNA binding (TreeGrafter), which the ProtNLM2 evidence record cites. The prediction is less precise
      than existing annotation. Training-set membership is unknown. This accession is an exon-skipping isoform lacking full-length (A0A8C4PFN5) residues 211-253, a segment outside the fork-head domain with no mapped functional feature; the fork-head domain (78-173) is identical to the full-length model, so the product retains what this activity needs.
    supported_by:
    - reference_id: PMID:19914232
      supporting_text: Foxj3 transcriptionally activates the Mef2c gene in a dose dependent fashion
        and binds to the conserved FBS
    - reference_id: file:EQUAS/FOXJ3/FOXJ3-bioinformatics/RESULTS.md
      supporting_text: The fork-head DNA-binding domain (donkey 78-173) aligns without gaps
- source_method: ProtNLM2
  source_version: UniProt API snapshot 2026-10-14
  predicted_term:
    id: GO:0003700
    label: DNA-binding transcription factor activity
  predicted_term_type: GO_MF
  review:
    assessment: LSP
    confidence_score: 2
    summary: FOXJ3 is a forkhead transcription factor; the mouse ortholog activates Mef2c transcription
      through a conserved forkhead binding site in its enhancer (PMID:19914232). The donkey
      protein is 98.1% identical to human FOXJ3 with an intact fork-head domain, so the prediction is
      correct. The exact term is in donkey GOA (InterPro2GO) and the more specific DNA-binding transcription
      factor activity, RNA polymerase II-specific is in donkey GOA from TreeGrafter; the prediction is less
      precise than that. Training-set membership is unknown. This accession is an exon-skipping isoform lacking full-length (A0A8C4PFN5) residues 211-253, a segment outside the fork-head domain with no mapped functional feature; the fork-head domain (78-173) is identical to the full-length model, so the product retains what this activity needs.
    supported_by:
    - reference_id: file:EQUAS/FOXJ3/FOXJ3-bioinformatics/human-Q9UPW0-uniprot.txt
      supporting_text: Transcriptional activator of MEF2C involved in the regulation
    - reference_id: PMID:19914232
      supporting_text: Foxj3 transcriptionally activates the Mef2c gene in a dose dependent fashion
    - reference_id: file:EQUAS/FOXJ3/FOXJ3-bioinformatics/RESULTS.md
      supporting_text: The donkey sequence A0A9L0JKH1 (580 residues) aligns to human Q9UPW0 (622 residues)
        with 98.1% identity among 579 paired residues.
references:
- id: PMID:19914232
  title: Foxj3 transcriptionally activates Mef2c and regulates adult skeletal muscle fiber type identity.
  findings: []
- id: file:EQUAS/FOXJ3/FOXJ3-bioinformatics/RESULTS.md
  title: 'FOXJ3: donkey-human sequence comparison'
  findings: []
- id: file:EQUAS/FOXJ3/FOXJ3-bioinformatics/human-Q9UPW0-uniprot.txt
  title: UniProtKB/Swiss-Prot record Q9UPW0 (human FOXJ3), downloaded 2026-10-14
  findings: []