FANCI

Summary: The verified ancestral nucleoplasm assertion agrees with target immunofluorescence.

Reason: Actual PANTHER v19 tree/MSA and the GO:0005654 IBD at PTN000497925 place the 1328-residue human target within the inherited clade. Human Q9NVI1 in the WITH list is legitimate experimental grounding, not circularity. Current HPA HPA040379 images and classifications in A-431 and U-251MG support nucleoplasm. The inherited chromatin quotation is related nuclear context, not a claim that chromatin and nucleoplasm are identical GO compartments.

Summary: The valid ancestral DNA-damage-response assertion has an experimentally grounded donor and target support.

Reason: The actual PTHR21818 v19 target path carries the GO:0006974 IBD at PTN000497925. Its Dictyostelium donor DDB_G0293476 resolves to Q54BR4 and experimental PMID:19763158. Actual Methods, Results and Figure 2 show fncI disruption, Southern-confirmed deletion and reduced colony survival after one-hour cisplatin exposure in Ax2-derived amoebae; the measured contribution is moderate, not absent. Human PMID:17412408 independently reports repair, G2/M and intra-S checkpoint effects after FANCI depletion. Retain this broader response scope rather than equating every response with physical ICL removal. No donor-count or self-WITH criticism is warranted.

Summary: Specify positive regulation of protein monoubiquitination.

Reason: The actual IBD at PTN000497925 names human Q9NVI1 and chicken A0A8V0YNA7; target self-WITH is valid. PMID:18931676 Figure 6 and human U2OS Methods show that FANCI phosphosite mutants reduce FANCD2 monoubiquitination. Its phosphomimetic experiments quoted here concern chicken DT40 cells. Purified chicken FANCI stimulation of FANCD2 monoubiquitination in PMID:22287633 is independent biochemical corroboration, with human E1/UBE2T but chicken FANCI/FANCD2/FANCL. These are performed regulatory effects on FANCD2, distinct from FANCI merely receiving ubiquitin in PMID:19589784. Current GO:1902527 is the specific is_a descendant for this measured modification. The current chicken accession has no surviving experimental GOA row in the retrieved record, so its precise historical export lineage remains unresolved without undermining the original experiments.

Proposed replacements: positive regulation of protein monoubiquitination

Summary: FANCI is experimentally part of the FANCI–FANCD2 DNA repair complex.

Reason: The actual GO:1990391 IBD at PTN000497925 is inherited by the displayed human target and legitimately uses human Q9NVI1 experimental evidence. PMID:32269332 Methods describe full-length human FANCI/FANCD2 reconstitution and cryo-EM DNA-bound complexes. This supports DNA-repair-complex membership without calling FANCI a member of the distinct FA core ligase or an obligate heterodimer in every state. A bounded current QuickGO FANCI-name search and direct children of GO:1990391 yielded no matching named ID2 child; no identifier was invented. The assays do not establish equivalent assembly by all four natural products.

Summary: FANCI occupies supported nuclear pools beyond soluble nucleoplasm.

Reason: The actual UniProt SL-0191 mapping is valid. PMID:17412408 reports human FANCI nuclear damage foci, chromatin association and occasional nuclear-rim staining; HPA independently assigns nucleoplasm. The complete PMID:19465922 abstract and curated UniProt location note also place FANCI at mitotic chromosome fragile sites. Since GO:0005654 excludes chromosomes, replacing all nuclear evidence by nucleoplasm would lose supported breadth. These sources do not establish the localization of all four natural products.

Summary: Refine the supported nonnuclear pool to cytosol.

Reason: The UniProt SL-0086-to-cytoplasm mapping is genuine; its source citation to PMID:18445686 remains immutable and that paper is assessed separately. Independent current HPA data explicitly classify cytosol in A-431 and U-251MG, with corresponding images inspected and enhanced antibody validation. GO:0005829 specifies the cytoplasmic compartment outside organelles. This supports a more precise positive location rather than the inherited claim that all cytoplasmic FANCI is minor and non-functional. No activity of that pool or isoform-specific localization is established by these images.

Proposed replacements: cytosol

Summary: FANCI contributes to more than one demonstrated DNA-repair response.

Reason: Official IPR026171 is the FANCI family and maps to DNA repair; actual target membership was verified. Human PMID:17412408 reports MMC-sensitive chromosome breakage and complementation, and separately an I-SceI-induced DR-U2OS homologous-recombination reporter impaired by four FANCI siRNAs. The broad term therefore preserves repair breadth beyond ICL repair alone. FANCI contributes DNA binding and ID2 assembly rather than providing FANCL ubiquitin-transfer chemistry or the nucleases that cut DNA. The reporter does not establish a standalone FANCI recombinase.

Summary: FANCI–FANCD2 association is supported, while generic protein binding remains a non-core interaction description.

Reason: FANCD2 (Q9BXW9) is the imported partner. The original abstract and authentic supplemental Methods support the cellular interaction context; the main interaction panels remain unread. Purified human ID2 preparations and structures independently establish association (PMID:32269332). Retain the supported interaction as non-core under the project binding exception. These assays do not establish all-natural-product equivalence or an autonomous FANCI enzyme activity.

Summary: The FANCD2 partner context is supported as part of the ID2-associated protein interaction evidence.

Reason: The imported partner is FANCD2 (Q9BXW9), distinct from FAN1 in the separate context. PMID:20603015 recovers FANCI/FANCD2 in crosslinked GFP-FAN1 purifications and endogenous FAN1 co-immunoprecipitates; purified human ID2 independently establishes FANCI–FANCD2 assembly. Retain this supported association as non-core under the project exception, without interpreting cellular coassociation as an isolated binary interface or FANCI nuclease activity.

Summary: FANCI association with the protein phosphatase CTDP1 supports a specific binding refinement.

Reason: CTDP1 (Q9Y5B0), the imported partner, supplies the BRCT domain and protein phosphatase activity. The original affinity experiment and endogenous/tagged cellular co-immunoprecipitations (Figure 1H/I) support protein phosphatase binding, GO:0019903. They do not establish purified binary contact or an isolated FANCI dephosphorylation reaction. The historical construct has not been mapped to the four current products.

Proposed replacements: protein phosphatase binding

Summary: FANCI participates in the chromatin-associated ID2 repair complex.

Reason: PMID:19965384 directly measures replication-dependent chromatin loading of FANCI and FANCD2 in Xenopus egg extracts, using recombinant Xenopus ID2 and a site-specific cisplatin interstrand cross-link substrate. The inspected main Results distinguish this chromatin pool from soluble protein and connect loading to replication and FANCD2 monoubiquitination. This is conserved pathway evidence for the imported human NAS annotation, not a human FANCI fractionation experiment. Independent human FANCI evidence includes chromatin-associated material in PMID:31240132 and purified human ID2 bound to DNA in PMID:32269332. Together these support chromatin localization without equating all nuclear FANCI with chromatin, assigning a nuclease activity, or extending the historical constructs to all four natural products.

Summary: FANCI makes a structural and regulatory contribution to interstrand cross-link repair.

Reason: Xenopus egg-extract depletion and WT-ID2 rescue in PMID:19965384 establish replication-coupled ICL repair; the FANCD2 ubiquitination-site mutant fails to restore repair. Independent human FANCI/ID2 binding and clamp experiments establish FANCI’s structural contribution. The incision and lesion-bypass readouts do not assign FANCI nuclease or polymerase chemistry, or establish equivalence of all natural products.

Summary: Purified human FANCI is a structural subunit of the ID2 DNA repair complex.

Reason: Purified full-length human FANCI/FANCD2 structures show FANCI contacting DNA and FANCD2 within the ID2 repair complex. Singly FANCD2-monoubiquitinated ID2 can form the clamp. This establishes complex membership without an obligate heterodimer in every state, invariant DNA preference or equivalence of all natural products. No more specific named ID2 GO complex was verified.

Summary: Actual HPA data support FANCI nucleoplasm localization.

Reason: HPA ENSG00000140525 reports mainly nucleoplasm, with enhanced HPA040379 validation and nucleoplasm plus cytosol calls in A-431 and U-251MG. Selected images from both lines were viewed. The antibody antigen exactly matches residues 1179 onward of the displayed product and corresponding sequences in the 1268- and 1267-residue products; it does not exactly match the natural 252-residue product. This supports target localization but neither resolves which long isoform supplies the signal nor proves absolute antibody specificity. HeLa images were not assessed.

Summary: FANCI positively regulates FANCD2 monoubiquitination, supporting the specific process term.

Reason: PMID:18931676 separately tests chicken DT40 cells and human U2OS cells. The actual human Figure 6 and Methods show that FANCI phosphosite substitutions reduce FANCD2 monoubiquitination and foci; the chicken phosphomimetic and knockout/rescue experiments have their own organism and mutant scope. The specific supported outcome is monoubiquitination, matching current GO:1902527, an is_a child of GO:0031398. Independent purified assays in PMID:22287633 use chicken FANCI/FANCD2/FANCL with human E1/UBE2T: the FANCI Ex6 DNA-binding-defective mutant retains complex formation but loses efficient stimulation of FANCD2 monoubiquitination, whereas FANCI K525R can still stimulate it. Thus FANCI contributes DNA-dependent organization/regulation and is not merely the ubiquitination substrate. FANCL and UBE2T execute ubiquitin transfer; neither their catalytic activity nor uniform behavior of the four natural human products is assigned to FANCI.

Proposed replacements: positive regulation of protein monoubiquitination

Summary: Independent human imaging supports a cytosolic FANCI pool; the original IDA paper remains an access-limited source.

Reason: PMID:18445686 was verified by identifier and abstract, but its operative FANCI localization material was not recovered through the finite publisher/author routes. An EML3-focused title and a predominantly nuclear repair role do not disprove the curator’s experimental cytoplasmic annotation. Independently inspected current Human Protein Atlas XML and the selected HPA040379 A-431 and U-251MG images support nucleoplasm plus cytosol. This positive target evidence supports refinement to GO:0005829 for the cytosolic pool without retrospectively claiming to have read the 2008 FANCI experiment. Enhanced antibody validation does not establish absolute specificity: the HeLa BAC-GFP validation is mainly nuclear and the XML explicitly notes additional antibody locations. The refinement is neither exclusive localization nor a denial of other cytoplasmic pools, and it does not resolve natural-product identities. The inherited assertion that a cytoplasmic pool is necessarily nonfunctional is unsupported and is withdrawn.

Proposed replacements: cytosol

Summary: Reactome explicitly places the FANCI protein in nucleoplasm during ID2 monoubiquitination.

Reason: Reactome:R-HSA-6785361 was traced through actual event/participant links to human Q9NVI1 proteoforms with coordinates 1–1328 and their own GO:0005654 compartment. Phosphorylated FANCI 6788480 occurs in the input and composite-catalyst assembly; monoubiquitinated FANCI 6785321 occurs in the output. FANCI is itself a substrate here; FANCL and UBE2T perform ubiquitin transfer. Its independently demonstrated promotion of FANCD2 monoubiquitination is a separate claim.

Summary: Reactome explicitly places the FANCI protein in nucleoplasm during nuclease recruitment.

Reason: Reactome:R-HSA-6785732 was traced through actual event/participant links to human Q9NVI1 proteoforms with coordinates 1–1328 and their own GO:0005654 compartment. Monoubiquitinated FANCI 6785321 persists in the ID2-containing input and nuclease-loaded output. FAN1/SLX4 recruitment contacts emphasized by the summation involve monoubiquitinated FANCD2; they are not automatically binary FANCI contacts.

Summary: Reactome explicitly places the FANCI protein in nucleoplasm during ICL unhooking.

Reason: Reactome:R-HSA-6785986 was traced through actual event/participant links to human Q9NVI1 proteoforms with coordinates 1–1328 and their own GO:0005654 compartment. Monoubiquitinated FANCI 6785321 remains in input, output and the composite-catalyst assembly. The named nucleases perform incision; inclusion in that assembly does not give FANCI nuclease activity.

Summary: Reactome explicitly places the FANCI protein in nucleoplasm during POLN recruitment.

Reason: Reactome:R-HSA-6786155 was traced through actual event/participant links to human Q9NVI1 proteoforms with coordinates 1–1328 and their own GO:0005654 compartment. Monoubiquitinated FANCI 6785321 persists in input and POLN-containing output. The modeled recruitment role emphasizes FANCD2 and PCNA; this location assertion does not establish autonomous FANCI polymerase recruitment or chemistry.

Summary: Reactome explicitly places the FANCI protein in nucleoplasm during POLN translesion synthesis.

Reason: Reactome:R-HSA-6786166 was traced through actual event/participant links to human Q9NVI1 proteoforms with coordinates 1–1328 and their own GO:0005654 compartment. Monoubiquitinated FANCI 6785321 occurs in input, output and the composite-catalyst assembly. POLN performs DNA synthesis; the shared location does not transfer polymerase chemistry to FANCI.

Summary: Reactome explicitly places the FANCI protein in nucleoplasm during ID2 deubiquitination.

Reason: Reactome:R-HSA-6786171 was traced through actual event/participant links to human Q9NVI1 proteoforms with coordinates 1–1328 and their own GO:0005654 compartment. Monoubiquitinated FANCI 6785321 occurs in the substrate assembly and phosphorylated FANCI 6788480 in the output. USP1:WDR48 performs deubiquitination; FANCI is not assigned that enzyme activity.

Summary: Reactome explicitly places the FANCI protein in nucleoplasm during ATR-mediated phosphorylation.

Reason: Reactome:R-HSA-6788392 was traced through actual event/participant links to human Q9NVI1 proteoforms with coordinates 1–1328 and their own GO:0005654 compartment. Unmodified FANCI 419529 occurs in input and composite-catalyst routes, while phosphorylated FANCI 6788480 occurs in output. ATR is the kinase and FANCI is one of its substrates.

Summary: The membrane-fraction annotation remains unresolved because the target-level original result was not recovered.

Reason: The original NK-cell membrane-fraction target table and fraction controls were not recovered. Its positive proteomics abstract alone cannot verify the FANCI result. Absence of a transmembrane segment or nuclear enrichment does not contradict peripheral membrane association; contamination has not been demonstrated. Retain UNDECIDED until the operative evidence can be assessed.

Summary: The specific POLN association is supported as a non-core repair partnership.

Reason: Endogenous POLN immunoprecipitation from human S-phase HeLa cells and tagged-POLN experiments support the Q7Z5Q5 partnership. Benzonase was used, but the authors leave open association within a larger repair structure. Retain DNA polymerase binding as a non-core interaction without inferring direct binary contact, FANCI polymerase chemistry or processivity-cofactor activity.

Summary: Reactome explicitly places the FANCI protein in nucleoplasm during ID2 and UBE2T recruitment.

Reason: Reactome:R-HSA-6785342 was traced through actual event/participant links to human Q9NVI1 proteoforms with coordinates 1–1328 and their own GO:0005654 compartment. Unmodified FANCI 419529 occurs in the ID2 input and DNA-bound output. The model distinguishes ID2 binding from UBE2T recruitment by FANCL.

Summary: Reactome explicitly places the FANCI protein in nucleoplasm during FANCD2–FANCI assembly.

Reason: Reactome:R-HSA-6785594 was traced through actual event/participant links to human Q9NVI1 proteoforms with coordinates 1–1328 and their own GO:0005654 compartment. FANCI 419529 is a direct input and a component of the ID2 output. Actual human reconstitution in PMID:32269332 independently supports the complex.

Summary: Reactome explicitly places the FANCI protein in nucleoplasm during ATR–ATRIP recruitment.

Reason: Reactome:R-HSA-6788385 was traced through actual event/participant links to human Q9NVI1 proteoforms with coordinates 1–1328 and their own GO:0005654 compartment. Unmodified FANCI 419529 persists in the ID2-containing input and ATR–ATRIP-containing output. Named RPA/core-protein contacts do not establish an isolated FANCI–ATRIP interaction.

Summary: Reactome explicitly places the FANCI protein in nucleoplasm during CDK12-dependent expression.

Reason: Reactome:R-HSA-6797712 was traced through actual event/participant links to human Q9NVI1 proteoforms with coordinates 1–1328 and their own GO:0005654 compartment. FANCI 419529 is reached through output set 6797713, not as the transcriptional catalyst. The event concerns CDK12/POLR2A-mediated gene expression; the FANCI protein has its own nucleoplasm compartment independently of the nuclear location of its gene.

Summary: Retain the inherited DNA secondary structure binding proposal with direct human evidence and state-specific limits.

Reason: Retain this inherited authored proposal rather than create another annotation. Current GO:0000217 covers binding to DNA secondary structures, including branched/junction substrates. Purified human 1328-residue FANCI and C-terminal fragments in PMID:19589784 bind DNA directly and preferentially bind Holliday-junction/Y substrates in the inspected competition assays and Figure 2. That paper calls the 1328-residue reagent isoform 1; this historical label must not be equated with today’s 1268-residue Q9NVI1-1. PMID:32269332 supplies independent human ID2 structures and binding assays: unmodified ID2 has modest branched-substrate preference, while monoubiquitination remodels it into a clamp on ordinary duplex DNA and reduces that preference. The term therefore describes an experimentally demonstrated activity, not an invariant preference of every modification state. PMID:27694619 additionally tests purified chicken FANCI DNA-binding mutants in RAD51-filament protection; those assays are conserved support rather than human mutant experiments. The same-role comparator check finds current four-way-junction-binding annotations on RAD51C and XRCC2; its child GO:0000400 would represent only part of FANCI’s tested substrate range. The current FANCD2 query did not verify the inherited claim that it carries GO:0003697, so that claim is not retained. The fixed current GO-CAM index has no FANCI/Q9NVI1 entry; this is not evidence of curator omission. No imported annotation or other proposed replacement in this file is an ancestor/descendant DNA-binding assertion. The independent target assays, not pathway completeness, justify retaining the single existing proposal. All four historical supporting quotations retain their exact paths and reference associations.

Summary: FANCI associates with FAN1-containing repair material, with the indirect-complex and crosslinker limits retained.

Reason: FAN1 (Q9Y2M0) is the imported partner. Crosslinked GFP-FAN1 purifications and endogenous co-immunoprecipitation recover FANCI; FAN1 UBZ mutation disrupts this association. Retain the supported interaction as non-core under the project exception. These results do not establish purified FANCI–FAN1 contact, FANCI ubiquitin recognition or FANCI nuclease activity.

Summary: Human FANCI has a directly demonstrated nucleolar pool.

Reason: Human HeLa subcellular fractionation with compartment controls and FANCI immunofluorescence with fibrillarin and RPA194 support nucleolar localization (PMID:30692263, Figure 1A–D/F–O, Figure 2D–M and the corresponding Results and Methods). This adds a specific compartment beyond the imported nucleus term, which does not entail nucleolus. It does not establish exclusive localization, equivalence of all natural products or a particular catalytic role in ribosome biogenesis. Original main text and figure captions were read; figure pixels, movies and detailed supplemental procedures were not independently inspected.