id: C6T1A2 gene_symbol: C6T1A2 product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:3847 label: Glycine max description: >- C6T1A2 is the 210-residue product of soybean GLYMA_17G165600 (Glyma17g18110; NCBI Gene 732609, also recorded as ZFP1). It is a plant Q-type C2H2 zinc-finger protein. It has a single C2H2 zinc finger (residues 79-106) carrying the plant-specific QALGGH motif (residues 92-97), disordered N-terminal and central regions with an acidic N-terminus, and a C-terminal LDLRL sequence that matches the LxLxL EAR-like transcriptional repression motif. This domain organisation is typical of single-finger plant C2H2 transcription factors, so the protein most likely acts as a nuclear, sequence-specific DNA-binding transcription factor, possibly a repressor. In PANTHER it belongs to subfamily SF9 of PTHR47593. SF9 is a lineage that arose by a duplication in the core eudicots (Pentapetalae) and contains no experimentally characterised member. The Arabidopsis ZFP proteins that regulate ABA responses during germination (ZFP3, ZFP4, ZFP7) are only about 35% identical to it and are placed in a different PANTHER tree. No gene-specific experimental study of C6T1A2 has been published. Its transcript was cloned in a soybean drought-associated transcription factor ORFeome. existing_annotations: - term: id: GO:0003700 label: DNA-binding transcription factor activity evidence_type: ISS original_reference_id: UniProtKB:C6T1A2 review: summary: >- Proposed annotation. GOA has no annotation for C6T1A2. The protein has one C2H2 zinc finger with the plant Q-type QALGGH motif, the signature of single-finger plant C2H2 transcription factors, and its transcript was cloned in a soybean transcription factor ORFeome. No experimental assay of C6T1A2 or of any PTHR47593:SF9 member exists, so this is a domain-level inference. action: NEW reason: >- The Q-type C2H2 zinc finger is a DNA-binding domain, and the QALGGH helix is conserved across the plant single-finger transcription factors (the Arabidopsis ZFP proteins and soybean SF8/SF9 paralogs; see RESULTS-rereview.md). This makes DNA-binding transcription factor activity the best-supported molecular function. The inference does not come from a PAINT node: the PAINT GO:0000976 node (PTN009184003) is in the PANTHER PTHR45730 tree, which does not contain C6T1A2. A more specific term (e.g. repressor activity, implied by the EAR-like motif) is not asserted, because no repression assay exists. supported_by: - reference_id: UniProtKB:C6T1A2 supporting_text: 'FT DOMAIN 79..106' - reference_id: UniProtKB:C6T1A2 supporting_text: 'PROSITE; PS50157; ZINC_FINGER_C2H2_2; 1.' - reference_id: file:SOYBN/C6T1A2/C6T1A2-bioinformatics/RESULTS-rereview.md supporting_text: The QALGGH motif of plant Q-type C2H2 zinc fingers is present at residues 92-97. - reference_id: PMID:26268547 supporting_text: Cys2(C2)His2(H2)-type zinc fingers (ZFs), constituting - term: id: GO:0005634 label: nucleus evidence_type: ISS original_reference_id: UniProtKB:C6T1A2 review: summary: >- Proposed annotation. A protein whose only folded domain is a DNA-binding C2H2 zinc finger and that is predicted to act as a transcription factor is expected in the nucleus. The location has not been tested for C6T1A2 or any SF9 member. Related Arabidopsis single-finger ZFPs in a different PANTHER family are nuclear (e.g. ZFP3). action: NEW reason: >- The nuclear location follows from the inferred transcription factor activity. Arabidopsis ZFP3 is a nuclear C2H2 zinc-finger protein, but it sits in another PANTHER family, so it is cited only as class-level context, not as an ortholog transfer. Earlier support taken from a ProtNLM2 prediction review has been removed. supported_by: - reference_id: file:SOYBN/C6T1A2/C6T1A2-deep-research-falcon.md supporting_text: this protein is predicted to function as a DNA-binding transcription factor localized to the nucleus - reference_id: PMID:24808098 supporting_text: ZFP3, a nuclear C2H2 zinc finger protein references: - id: PMID:26268547 title: "Soybean transcription factor ORFeome associated with drought resistance: a valuable resource to accelerate research on abiotic stress resistance" findings: - statement: C6T1A2 (Glyma17g18110.1) was cloned as part of a soybean transcription factor ORFeome associated with drought resistance (GenBank KT031152). The C2H2 zinc fingers are one of the seven largest transcription factor families in the collection. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Source of the KT031152 sequence. It classifies the gene as a C2H2-ZF transcription factor but contains no gene-specific functional data. - id: PMID:24808098 title: The Arabidopsis ZINC FINGER PROTEIN3 Interferes with Abscisic Acid and Light Signaling in Seed Germination and Plant Development. findings: - statement: Arabidopsis ZFP3 is a nuclear C2H2 zinc-finger protein. Overexpression of ZFP3 and the related Arabidopsis ZFP1, ZFP4, ZFP6 and ZFP7 confers ABA insensitivity at germination. reference_review: relevance: LOW correctness: VERIFIED review_notes: >- Abstract only. It concerns Arabidopsis ZFPs, which PANTHER 19 places in the PTHR45730 tree, not in the PTHR47593:SF9 lineage of C6T1A2. The Arabidopsis ZFP1 named here is not soybean ZFP1 (C6T1A2). The paper is used only as class-level context for nuclear localisation; its ABA findings are not transferred. - id: UniProtKB:C6T1A2 title: UniProtKB entry C6T1A2 (C6T1A2_SOYBN), C2H2-Zn transcription factor, Glycine max. findings: - statement: 210-aa unreviewed (TrEMBL) protein with a single C2H2-type zinc finger domain (residues 79-106), two disordered regions, and an N-terminal acidic compositional bias. - statement: InterPro classifies the protein in IPR053266 (Zinc_finger_protein_7), IPR036236 (Znf_C2H2_sf) and IPR013087 (Znf_C2H2_type). PANTHER places it in PTHR47593:SF9 (C2H2-TYPE DOMAIN-CONTAINING PROTEIN) within PTHR47593 (ZINC FINGER PROTEIN 4-LIKE). - statement: The only GO annotation in the UniProt DR lines is GO:0008270 (zinc ion binding, IEA:UniProtKB-KW). The GOA export has no rows. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Direct UniProt entry, PE 2 (transcript level), with computational annotation only. The IPR053266 name "Zinc_finger_protein_7" is a family label and does not establish orthology to Arabidopsis ZFP7. - id: file:SOYBN/C6T1A2/C6T1A2-bioinformatics/RESULTS-rereview.md title: C6T1A2 re-review bioinformatics - motif positions, pairwise identities and PANTHER 19 tree placement. findings: - statement: The QALGGH motif is at residues 92-97 and a C-terminal LDLRL EAR-like match is at 206-210. C6T1A2 is identical to A0A2K7G974 (ZFP1). - statement: C6T1A2 is in PTHR47593:SF9, a lineage produced by a Pentapetalae duplication (PTN002935045). The PTHR47593 tree has no Arabidopsis leaves and no PAINT nodes. The ZFP7/ZFP4 PAINT nodes are in the PTHR45730 tree. - statement: Arabidopsis ZFP7, ZFP4, ZFP3 and ZFP2 are 34-37% identical overall to C6T1A2. reference_review: relevance: HIGH correctness: VERIFIED review_notes: Reproducible scripts in the same folder. Results are not hard-coded. - id: file:SOYBN/C6T1A2/C6T1A2-deep-research-falcon.md title: Deep-research report (falcon / Edison Scientific Literature) - functional annotation of soybean C6T1A2 / Glyma17g18110.1 (C6T1A2). findings: - statement: No gene-specific experimental literature was identified for C6T1A2 / Glyma17g18110.1 from soybean. - statement: Based on InterPro domain annotation, the protein is predicted to function as a DNA-binding transcription factor localized to the nucleus. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Correctly reports that no gene-specific literature exists. Its functional statements are domain-based inference only. - id: file:SOYBN/C6T1A2/C6T1A2-hypotheses/core-function-1-go-0003700/openscientist.md title: OpenScientist hypothesis investigation - DNA-binding transcription factor activity findings: - statement: >- Reports the QALGGH motif at residues 92-97 and a C-terminal EAR-like motif, both reproduced independently in RESULTS-rereview.md. It also calls Arabidopsis ZFP7 the "direct ortholog" with 60.9% zinc-finger identity. reference_review: relevance: LOW correctness: DISPUTED review_notes: >- No longer used as support. The motif positions are reproduced by the re-review scripts. Its claims that ZFP7 is the direct ortholog of C6T1A2, and that GmZAT10-1 (a two-finger ZAT protein) gives same-species evidence, are not supported by PANTHER 19 tree placement: ZFP7 is in PTHR45730 and is 36% identical overall. Its AlphaFold pLDDT values were not re-verified. - id: file:SOYBN/C6T1A2/C6T1A2-protnlm-predictions-review.yaml title: ProtNLM2 prediction review for C6T1A2 - nucleus and ABA signaling predictions. findings: - statement: Prediction-review file for ProtNLM2 outputs (not consulted in the 2026-10-20 re-review). reference_review: relevance: NONE correctness: UNVERIFIED review_notes: >- Kept for provenance only. The 2026-10-20 full re-review was done independently of ProtNLM2 predictions, and this file is no longer cited as support for any annotation or core function. core_functions: - description: >- Predicted sequence-specific DNA-binding transcription factor, acting in the nucleus through a single plant Q-type (QALGGH) C2H2 zinc finger. A C-terminal EAR-like LxLxL motif suggests it may act as a repressor. This is inferred from domain architecture only. No member of its PANTHER subfamily (PTHR47593:SF9) has been characterised experimentally. molecular_function: id: GO:0003700 label: DNA-binding transcription factor activity locations: - id: GO:0005634 label: nucleus supported_by: - reference_id: UniProtKB:C6T1A2 supporting_text: 'FT DOMAIN 79..106' - reference_id: file:SOYBN/C6T1A2/C6T1A2-bioinformatics/RESULTS-rereview.md supporting_text: The QALGGH motif of plant Q-type C2H2 zinc fingers is present at residues 92-97. - reference_id: file:SOYBN/C6T1A2/C6T1A2-bioinformatics/RESULTS-rereview.md supporting_text: C-terminal LDLRL at residues 206-210 matches the LxLxL EAR-like repression motif proposed_new_terms: [] suggested_questions: - question: Does C6T1A2 bind DNA through its QALGGH zinc finger (and if so, which sequence, for example the AGT core bound by other Q-type ZFPs)? Does its EAR-like C-terminus make it a transcriptional repressor? experts: [] - question: The PAINT nodes listed in interpro/panther/PTHR47593/PTHR47593-paint.tsv (PTN008158895, PTN009184003) belong to the PANTHER 19 PTHR45730 tree. Should PTHR47593 (which contains C6T1A2) receive its own PAINT review? Did the Pentapetalae SF8/SF9 duplication separate functionally distinct lineages? experts: [] - question: Does any PTHR47593:SF9 member act in ABA or drought responses, given that the ABA role is established only for Arabidopsis ZFPs in a different PANTHER tree? experts: - Henry T. Nguyen suggested_experiments: - description: Test C6T1A2 in a yeast GAL4-BD or plant protoplast LUC reporter assay, with and without the C-terminal LDLRL motif, for activation or repression activity. Define its DNA-binding specificity by EMSA or DAP-seq. hypothesis: C6T1A2 binds specific DNA sequences via its Q-type C2H2 zinc finger and represses transcription through its EAR-like motif. experiment_type: transcription factor activity assay - description: Localise a C6T1A2-GFP fusion in soybean protoplasts or Nicotiana benthamiana leaf epidermis. hypothesis: C6T1A2 localizes to the nucleus. experiment_type: subcellular localization by fluorescent protein fusion - description: Phenotype CRISPR/Cas9 mutants of the SF9 paralogs (GLYMA_17G165600 together with the GLYMA_05G100900 homeolog) under ABA and drought treatments, measuring germination and stress-responsive gene expression. hypothesis: SF9 ZFPs modulate ABA or drought responses in soybean, as the paralogous Arabidopsis ZFPs do. experiment_type: loss-of-function genetics with stress phenotyping