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.
- PMID:29789392: "Expression of FAM35A isoform 1 in 293T cells (FigĀ 4D) restored NHEJ to normal levels (FigĀ 4E)."
- 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."
- file:HORSE/SHLD2/SHLD2-hypotheses/horse40-nhej-promotion/openscientist.md: "the frameshift leaves OB1 and OB2 ā the domains that execute ssDNA binding and resection blockade ā intact"
- file:human/SHLD2/SHLD2-hpa.xml: "Mainly localized to the nucleoplasm. In addition localized to the actin filaments."
- file:HORSE/SHLD2/SHLD2-bioinformatics/RESULTS.md: "share 70.2% identity among 792 paired residues."
- 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: "/note="Shieldin complex subunit 2 first OB fold""
- file:HORSE/SHLD2/SHLD2-bioinformatics/RESULTS.md: "share 70.2% identity among 792 paired residues."
- file:human/SHLD2/SHLD2-hpa.xml: "Mainly localized to the nucleoplasm. In addition localized to the actin filaments."
- PMID:29789392: "FAM35A re-localized in damaged cell nuclei"
- file:HORSE/SHLD2/SHLD2-bioinformatics/RESULTS.md: "share 70.2% identity among 792 paired residues."
- PMID:29789392: "However, the BRCA1āmutant cells formed damageādependent nuclear RAD51 foci following FAM35A depletion, suggesting that 5ā² end resection was more active in the absence of FAM35A (FigĀ 5B)."
- 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."
- file:HORSE/SHLD2/SHLD2-hypotheses/horse40-nhej-promotion/openscientist.md: "Human ortholog carries this (IDA); mechanistically the more *direct* description of resection blockade"
- 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."