id: A0A9L0IK51
gene_symbol: RBM41
taxon:
  id: NCBITaxon:9793
  label: Equus asinus
status: COMPLETE
description: >-
  Assessment of the single ProtNLM2 GO prediction for donkey RBM41 (A0A9L0IK51), an RRM protein of the
  RBM41/RNPC3 family (PANTHER PTHR16105:SF2, the same subfamily as human RBM41). RNA binding is correct,
  supported by direct RRM-snRNA binding experiments on the human ortholog, but less precise than the U12
  snRNA binding already in donkey GOA and accepted in the gene review (LSP). ProtNLM2 also emitted a
  subcellular location of Nucleus (not scored); this is consistent with the human ortholog's association
  with minor spliceosomal snRNPs and Cajal bodies. No function text was emitted.
source_documents:
- projects/PROTNLM_EVALUATION/donkey40/donkey40-predictions.tsv
- genes/EQUAS/RBM41/RBM41-goa.tsv
- genes/EQUAS/RBM41/RBM41-bioinformatics/human-Q96IZ5-uniprot.txt
- genes/EQUAS/RBM41/RBM41-bioinformatics/interpro-IPR045164.md
- genes/EQUAS/RBM41/RBM41-bioinformatics/RESULTS.md
- genes/EQUAS/RBM41/RBM41-ai-review.yaml
predictions:
- source_method: ProtNLM2
  source_version: UniProt API snapshot 2026-10-14
  predicted_term:
    id: GO:0003723
    label: RNA binding
  predicted_term_type: GO_MF
  review:
    assessment: LSP
    confidence_score: 2
    summary: >-
      RNA binding is directly supported for the human ortholog, which sits in the same PANTHER subfamily
      (PTHR16105:SF2): the isolated human RBM41 RRM binds the U12 and U6atac snRNA 3' hairpins with
      low-micromolar affinity, and RNP1 point mutations or RRM deletion abolish its snRNA associations in
      cells. The donkey RRM is 78 of 79 residues identical to the human RRM, so the transfer is well
      justified. The exact term is already in donkey GOA, and donkey GOA also carries the more specific
      U12 snRNA binding (TreeGrafter), which the gene review accepts as the core function while marking
      RNA binding as too general. Because a supported, more specific annotation exists, the prediction is
      correct but less precise (LSP).
    supported_by:
    - reference_id: PMID:38499487
      supporting_text: the RBM41 RRM has a low micromolar affinity to both U12 (Kd= 2.14 μM) and U6atac
        hairpins (Kd= 3.78 μM; Figure 2D)
    - reference_id: PMID:38499487
      supporting_text: The Q352A and F354A mutations and deletion of the RRM led to dramatic loss of the
        U12, U4atac and U6atac interactions
    - reference_id: file:EQUAS/RBM41/RBM41-bioinformatics/RESULTS.md
      supporting_text: 'DOMAIN RRM: human [309, 387] KN -> donkey [333, 411] KN; 78 of 79 human residues in
        this span are identical'
    - reference_id: file:EQUAS/RBM41/RBM41-bioinformatics/interpro-IPR045164.md
      supporting_text: It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind
        hairpin III of the U12 small nuclear RNA (snRNA).
references:
- id: PMID:38499487
  title: Distinct functions for the paralogous RBM41 and U11/U12-65K proteins in the minor spliceosome.
  findings: []
- id: file:EQUAS/RBM41/RBM41-bioinformatics/human-Q96IZ5-uniprot.txt
  title: UniProt record for human RBM41 (Q96IZ5)
  findings: []
- id: file:EQUAS/RBM41/RBM41-bioinformatics/interpro-IPR045164.md
  title: InterPro IPR045164 RBM41/RNPC3 family description
  findings: []
- id: file:EQUAS/RBM41/RBM41-bioinformatics/RESULTS.md
  title: 'RBM41: donkey-human sequence comparison'
  findings: []