SHLD2

UniProt ID: A0A9L0RGD6
Organism: Equus caballus
Review Status: IN PROGRESS
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Gene Description

SHLD2 is a shieldin-family protein with conserved recruitment and OB-fold regions. The selected horse model is expected to associate with nuclear DNA-break repair machinery, but its divergent C-terminus leaves the integrity of the DNA-end-protection module uncertain. In characterized mammalian proteins, shieldin scaffolding and DNA binding restrain resection and favor non-homologous end joining.

References

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External Prediction Reviews

These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.

ProtNLM2 External predictions

View prediction review YAML Ā· SHLD2-protnlm-predictions-review.yaml Ā· Review status: COMPLETE

Nuclear and DNA-break localization are supported by conserved SHLD2 recruitment biology. The core OB1/OB2 end-protection module supports the NHEJ and anti-HR predictions despite a likely C-terminal gene-model artifact; actin localization and isotype switching remain unresolved.

Source documents: projects/PROTNLM_EVALUATION/mammal-benchmark/horse40-predictions.csv Ā· projects/PROTNLM_EVALUATION/mammal-benchmark/predictions.jsonl.gz Ā· projects/PROTNLM_EVALUATION/mammal-benchmark/paired-sequences/SHLD2.json Ā· genes/HORSE/SHLD2/SHLD2-hypotheses/horse40-nhej-promotion/openscientist.md

Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.

GO:2001034 positive regulation of double-strand break repair via nonhomologous end joining GO_BP
COR — Correct novel prediction Review score: 2/2
Prediction method: ProtNLM2 Ā· Version: UniProt API snapshot 2026-09-08
Review rationale: Mammalian SHLD2 experiments support this repair-process role, and the OpenScientist audit resolved the selected horse sequence as a justified orthology transfer. A likely C-terminal frameshift corrupts OB3, but it leaves the conserved SHLD3/REV7 recruitment segment and the OB1/OB2 ssDNA-binding execution module intact, so the horse model retains the apparatus that restricts DNA end resection and promotes NHEJ. This is a homology-based ISS/IBA transfer, not direct horse evidence.
Supporting Evidence:
GO:0015629 actin cytoskeleton GO_CC
UNC — Uncertain Review score: 1/2
Prediction method: ProtNLM2 Ā· Version: UniProt API snapshot 2026-09-08
Review rationale: HPA reports an additional actin-filament pool of human SHLD2 with supported antibody-based reliability, so this prediction is not contradicted merely by SHLD2 being a nuclear repair protein. However, the secondary localization is cell-line dependent and its targeting mechanism is uncharacterized; family membership and global sequence identity do not establish conservation of this particular pool in the selected horse isoform. The main nuclear localization has substantially stronger mechanistic support. A conserved targeting determinant or independent localization evidence is needed to resolve this exact transfer.
Supporting Evidence:
GO:0035861 site of double-strand break GO_CC
COR — Correct novel prediction Review score: 2/2
Prediction method: ProtNLM2 Ā· Version: UniProt API snapshot 2026-09-08
Review rationale: The selected horse protein belongs to the SHLD2 family and retains its OB-fold architecture; its alignment with human SHLD2 covers 94.9% of the human sequence with 70.2% identity among paired residues. Human SHLD2 recruitment to double-strand breaks and conserved shieldin domains support this location in horse. This is a supported transfer new relative to the frozen horse GOA, not a claim that the model training set lacked mammalian SHLD2 annotations.
Supporting Evidence:
GO:0005654 nucleoplasm GO_CC
COR — Correct novel prediction Review score: 2/2
Prediction method: ProtNLM2 Ā· Version: UniProt API snapshot 2026-09-08
Review rationale: The selected horse protein belongs to the SHLD2 family and retains its OB-fold architecture; its alignment with human SHLD2 covers 94.9% of the human sequence with 70.2% identity among paired residues. The human HPA nucleoplasmic signal agrees with nuclear damage-focus studies, supporting conservation of the principal nuclear compartment. This is a supported transfer new relative to the frozen horse GOA, not a claim that the model training set lacked mammalian SHLD2 annotations.
Supporting Evidence:
GO:2000042 negative regulation of double-strand break repair via homologous recombination GO_BP
COR — Correct novel prediction Review score: 2/2
Prediction method: ProtNLM2 Ā· Version: UniProt API snapshot 2026-09-08
Review rationale: Mammalian SHLD2 experiments support this repair-process role, and the OpenScientist audit resolved the selected horse sequence as a justified orthology transfer. The likely OB3 frameshift should be verified against a corrected transcript, but the OB1/OB2 ssDNA-binding execution module and N-terminal recruitment segment are conserved, supporting the anti-resection mechanism that negatively regulates double-strand break repair by homologous recombination.
Supporting Evidence:
GO:0045830 positive regulation of isotype switching GO_BP
UNC — Uncertain Review score: 1/2
Prediction method: ProtNLM2 Ā· Version: UniProt API snapshot 2026-09-08
Review rationale: Mammalian SHLD2 and shieldin experiments connect this repair pathway to immunoglobulin class-switch recombination, but GO:0045830 is a tissue-restricted downstream immunological process. The OpenScientist audit supports transfer of the conserved OB1/OB2-dependent NHEJ and anti-HR repair module to horse SHLD2, but it did not evaluate GO:0045830 or provide horse B-cell or CSR evidence. This more specific process therefore remains unresolved until the conserved repair activity is tied to the relevant horse immune context.
Supporting Evidence:
  • PMID:29656893: "Recruitment ofĀ shieldin to DSBs, via the ATM-RNF8-RNF168-53BP1-RIF1 axis, promotes NHEJ-dependent repair of intrachromosomal breaks, immunoglobulin class-switch recombination (CSR), and fusion of unprotected telomeres."
  • file:HORSE/SHLD2/SHLD2-uniprot.txt: "DR InterPro; IPR029715; FAM35A."
  • file:HORSE/SHLD2/SHLD2-bioinformatics/RESULTS.md: "share 70.2% identity among 792 paired residues."
  • PMID:30022168: "Importantly, both mutants localized to DSB sites (ED Fig 10cd) and interacted with the other members of the Shieldin complex (ED Fig 10e). Therefore, the SHLD2-m1 and SHLD2S mutants are defective in suppressing HR."
  • file:HORSE/SHLD2/SHLD2-bioinformatics/RESULTS.md: "Beyond that point the horse C-terminus is substantially divergent and gapped. This is not a complete match to either human isoform."

Deep Research

OpenScientist

(SHLD2-hypotheses/horse40-nhej-promotion/openscientist.md)

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šŸ“š Additional Documentation

Notes

(SHLD2-notes.md)

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Bioinformatics Results

(RESULTS.md)

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Protnlm Function Review

(SHLD2-protnlm-function-review.md)

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šŸ“„ View Raw YAML

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