id: A0A9L0I7X9
gene_symbol: IRF9
taxon:
  id: NCBITaxon:9793
  label: Equus asinus
status: COMPLETE
description: Assessment of 3 ProtNLM2 GO predictions for donkey IRF9 (A0A9L0I7X9), the DNA-binding subunit
  of the ISGF3 transcription factor. The donkey protein sits in PANTHER subfamily PTHR11949:SF26 (IRF9) with
  human Q00978 and conserves the IRF DNA-binding domain (98 of 108 residues identical, all five pentad tryptophans
  conserved). All three predictions are biologically correct and already present as exact terms in the donkey
  GOA record. Positive regulation of transcription by RNA polymerase II matches the accepted core process (CNN).
  Transcription cis-regulatory region binding and DNA-binding transcription factor activity are true but less
  specific than the RNA polymerase II cis-regulatory sequence-specific DNA binding and RNA polymerase II-specific
  transcription factor terms accepted for this protein in the gene review (LSP). ProtNLM2 emitted no non-GO
  function-text or subcellular-location output for this accession in the frozen snapshot.
source_documents:
- genes/EQUAS/IRF9/IRF9-uniprot.txt
- genes/EQUAS/IRF9/IRF9-goa.tsv
- genes/EQUAS/IRF9/IRF9-ai-review.yaml
- genes/EQUAS/IRF9/IRF9-bioinformatics/human_Q00978-uniprot.txt
- genes/EQUAS/IRF9/IRF9-bioinformatics/RESULTS.md
- genes/EQUAS/IRF9/IRF9-bioinformatics/dbd_check.md
- projects/PROTNLM_EVALUATION/donkey40/donkey40-predictions.tsv
predictions:
- source_method: ProtNLM2
  source_version: UniProt API snapshot 2026-10-14
  predicted_term:
    id: GO:0045944
    label: positive regulation of transcription by RNA polymerase II
  predicted_term_type: GO_BP
  review:
    assessment: CNN
    confidence_score: 2
    summary: ISGF3, of which IRF9 is the DNA-binding subunit, activates RNA polymerase II transcription of
      interferon-stimulated genes, and human IRF9 is required for ISRE-driven reporter transcription. The
      donkey protein is in the same PANTHER subfamily (PTHR11949:SF26) with a conserved DNA-binding domain,
      which justifies the transfer. The exact term is already in the donkey GOA record and is accepted as
      the core process in the gene review, so the prediction is correct but not novel.
    supported_by:
    - reference_id: PMID:1630447
      supporting_text: Alpha interferon stimulates transcription by converting the positive transcriptional regulator
        ISGF3 from a latent to an active form.
    - reference_id: PMID:30143481
      supporting_text: U2A cells transfected with IRF9-Δex7 exhibited abolished luciferase transcription when
        luciferase production was driven from an IFN-stimulated response element (ISRE) promoter
    - reference_id: file:EQUAS/IRF9/IRF9-bioinformatics/dbd_check.md
      supporting_text: '98 of 108 residues identical in donkey A0A9L0I7X9.'
- source_method: ProtNLM2
  source_version: UniProt API snapshot 2026-10-14
  predicted_term:
    id: GO:0000976
    label: transcription cis-regulatory region binding
  predicted_term_type: GO_MF
  review:
    assessment: LSP
    confidence_score: 2
    summary: IRF9 binds the interferon-stimulated response element through its tryptophan-pentad DNA-binding
      domain, which is conserved in the donkey protein; human ISGF3-gamma binds DNA sequence-specifically.
      The term is correct and already in the donkey GOA record, but the gene review accepts the more specific
      descendant GO:0000978 (RNA polymerase II cis-regulatory region sequence-specific DNA binding; is_a
      ancestry checked in OLS4) on the basis of the PTHR11949:SF26 subfamily transfer and human data, and
      marks this term TOO_GENERAL. The prediction is therefore less precise than an existing supported annotation.
    supported_by:
    - reference_id: PMID:1630447
      supporting_text: ISGF3 gamma translated in vitro from recombinant clones bound DNA with a specificity indistinguishable
        from that of ISGF3 gamma purified from HeLa cells
    - reference_id: file:EQUAS/IRF9/IRF9-bioinformatics/dbd_check.md
      supporting_text: human W80 -> donkey W80
- 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: IRF9 supplies the sequence-specific DNA recognition of ISGF3 and acts as an RNA polymerase II
      transcription factor. The term is correct and already in the donkey GOA record, but the gene review
      accepts the more specific descendant GO:0000981 (DNA-binding transcription factor activity, RNA polymerase
      II-specific; is_a ancestry checked in OLS4) as the core function and marks this term TOO_GENERAL. The
      prediction is therefore less precise than an existing supported annotation.
    supported_by:
    - reference_id: file:EQUAS/IRF9/IRF9-bioinformatics/human_Q00978-uniprot.txt
      supporting_text: 'FUNCTION: Transcription factor that plays an essential role in anti-'
    - reference_id: PMID:1630447
      supporting_text: ISGF3 gamma serves as the DNA recognition subunit
references:
- id: PMID:1630447
  title: Subunit of an alpha-interferon-responsive transcription factor is related to interferon regulatory factor and Myb families of DNA-binding proteins.
  findings: []
- id: PMID:30143481
  title: Life-threatening influenza pneumonitis in a child with inherited IRF9 deficiency.
  findings: []
- id: file:EQUAS/IRF9/IRF9-bioinformatics/human_Q00978-uniprot.txt
  title: UniProt Swiss-Prot record for human IRF9 (Q00978)
  findings: []
- id: file:EQUAS/IRF9/IRF9-bioinformatics/dbd_check.md
  title: IRF9 DNA-binding domain check
  findings: []