[
  {
    "rank": 1,
    "gene": "CTDSP2",
    "horse_accession": "F7A4N8",
    "human_comparison_accession": "O14595",
    "hypothesis": "The horse protein F7A4N8 enables kinase activity.",
    "source_prediction": {
      "accession": "F7A4N8",
      "taxon_id": "9796",
      "type": "GO",
      "id": "GO:0016301",
      "text": "F:kinase activity"
    },
    "current_assessment": "UNC",
    "selection_reason": "Highest priority: the short model is not simply an intact phosphatase mislabeled as a kinase. Structural/family assignment could turn an unresolved claim into a defensible conclusion.",
    "desired_resolution": "A supported kinase mechanism, a well-supported incompatible fold, or an explicit failure to identify the protein.",
    "prompt_file": "projects/PROTNLM_EVALUATION/mammal-benchmark/openscientist-selection/01-CTDSP2-kinase-activity-prompt.md",
    "sequence_sha256": "94788163d6db3dbca3e1432762d7b2a1e8b57e1be2048c233c505a07a0b5042c",
    "launch_argv": [
      "just",
      "gene-hypothesis-research",
      "openscientist",
      "HORSE",
      "CTDSP2",
      "--focus-type",
      "function-assignment",
      "--hypothesis",
      "The horse protein F7A4N8 enables kinase activity.",
      "--slug",
      "horse40-kinase-activity",
      "--context",
      "# Focused function hypothesis\n\nHypothesis: The horse protein F7A4N8 enables kinase activity.\n\nTarget: Equus caballus (NCBITaxon:9796), UniProt F7A4N8. Gene label: CTDSP2; verify identity independently rather than treating the label as proof.\n\nTarget GO claim: GO:0016301 \u2014 kinase activity. Verify its definition and scope.\n\n## Decisive question\n\nDetermine whether this exact sequence supports a kinase fold and phosphotransfer mechanism. Establish its family independently; if a kinase mechanism is unsupported, identify the strongest alternative explanation without assuming the gene label is correct.\n\n## Identity and sequence inputs\n\n- Target record: https://www.uniprot.org/uniprotkb/F7A4N8/entry\n- Human comparison lead: https://www.uniprot.org/uniprotkb/O14595/entry (CTDSP2). Establish the relevant orthology/isoform relationship rather than assuming it.\n- Frozen current UniProt sequence: 174 residues; SHA-256 `94788163d6db3dbca3e1432762d7b2a1e8b57e1be2048c233c505a07a0b5042c`.\n- These are current sequences downloaded for the cohort on 2026-09-08. Identity with the original prediction-time input has not been established. Evaluate the supplied sequence explicitly; document any different sequence used.\n\n```fasta\n>F7A4N8 Equus caballus CTDSP2\nMEHGSIITQARREDALVLTKQGLVSKSSPKKPRGRNIFKALFCCFRAQHVGQSSPSTELS\nTYKEEANTIAKSDLLQCLQYQFYQGIRFWGTARVHPTAALASISMSRALHRPQGRRGRGA\nSTVSSFSTSWPSSGASLGCSLSSRLLDKPRSSQSSAGGLLGLSWWQISAACLWF\n```\n\n## Evidence and deliverable\n\nUse primary literature and public sequence, structural and genomic resources. Select analyses that answer the decisive question; this is not a general gene review. Assess support and contrary evidence, and allow an unresolved outcome. Distinguish directly observed horse evidence, justified mammalian transfer, and results for a different protein model.\n\nDo not consult the ai-gene-review repository's existing judgments, research syntheses or local bioinformatics analyses. Those are held out for comparison. Do not use agreement with ARBA or another prediction as biological validation. Preserve reproducible methods, accessions/versions, actual computation outputs and primary-source URLs/DOIs/PMIDs. Report the decisive findings and limitations, not just a verdict.\n",
      "--term-id",
      "GO:0016301",
      "--term-label",
      "kinase activity"
    ],
    "expected_report": "genes/HORSE/CTDSP2/CTDSP2-hypotheses/horse40-kinase-activity/openscientist.md",
    "status": "SUBMITTED",
    "dry_run": "PASSED",
    "job_id": "afc0ec57-89dc-46a6-96c5-4cf6b718a414",
    "submitted_at": "2026-09-08T22:57:05.797296Z"
  },
  {
    "rank": 2,
    "gene": "SIRT5",
    "horse_accession": "F6S899",
    "human_comparison_accession": "Q9NXA8",
    "hypothesis": "The horse protein F6S899 catalyzes NAD-dependent lysine desuccinylation.",
    "source_prediction": {
      "accession": "F6S899",
      "taxon_id": "9796",
      "type": "function",
      "id": "",
      "text": "NAD-dependent lysine demalonylase, desuccinylase and deglutarylase that specifically removes malonyl, succinyl and glutaryl groups on target proteins. Has weak NAD-dependent protein deacetylase activity; however this activity may not be physiologically relevant in vivo"
    },
    "current_assessment": "UNC (atomic narrative claim)",
    "selection_reason": "Highest priority: unusual cofactor-site and C-terminal sequence features make an independent structure-aware assessment valuable. Focus on one reaction rather than all sirtuin chemistry.",
    "desired_resolution": "Whether the submitted sequence plausibly retains a functional desuccinylase apparatus, or whether only a different transcript/model supports it.",
    "prompt_file": "projects/PROTNLM_EVALUATION/mammal-benchmark/openscientist-selection/02-SIRT5-nad-dependent-desuccinylation-prompt.md",
    "sequence_sha256": "61bce25d76191fa8ce4d18a700c25beab8f0bcb857f8af2f8eb343b76bfc0fd0",
    "launch_argv": [
      "just",
      "gene-hypothesis-research",
      "openscientist",
      "HORSE",
      "SIRT5",
      "--focus-type",
      "function-assignment",
      "--hypothesis",
      "The horse protein F6S899 catalyzes NAD-dependent lysine desuccinylation.",
      "--slug",
      "horse40-nad-dependent-desuccinylation",
      "--context",
      "# Focused function hypothesis\n\nHypothesis: The horse protein F6S899 catalyzes NAD-dependent lysine desuccinylation.\n\nTarget: Equus caballus (NCBITaxon:9796), UniProt F6S899. Gene label: SIRT5; verify identity independently rather than treating the label as proof.\n\n## Decisive question\n\nEvaluate the structural and cofactor requirements for this single catalytic activity in the exact sequence. Compare characterized mammalian proteins and relevant public structures. Distinguish a functional target protein from a family label or a different transcript product.\n\n## Identity and sequence inputs\n\n- Target record: https://www.uniprot.org/uniprotkb/F6S899/entry\n- Human comparison lead: https://www.uniprot.org/uniprotkb/Q9NXA8/entry (SIRT5). Establish the relevant orthology/isoform relationship rather than assuming it.\n- Frozen current UniProt sequence: 282 residues; SHA-256 `61bce25d76191fa8ce4d18a700c25beab8f0bcb857f8af2f8eb343b76bfc0fd0`.\n- These are current sequences downloaded for the cohort on 2026-09-08. Identity with the original prediction-time input has not been established. Evaluate the supplied sequence explicitly; document any different sequence used.\n\n```fasta\n>F6S899 Equus caballus SIRT5\nMRPLQIVHSRLISRLCCGLKSAASTQTKICLTMARPSSNMADFRKFFAKAKHIVVISGAG\nISAESGVPTFRGAGGYWRKWKAQDLATPQAFARNPSQVWEFYHYRREVVQTKEPNPGHLA\nIAQCEARLHKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPI\nCPALSGKGSPDPETQSARIPAENLPRWEHPLWSILPPCLPPRCLPGEFQWPNSTWKPPQP\nQADSGFISRGPVVRLFLKPLLTKPKLFLNCPGEGRNYSASVY\n```\n\n## Evidence and deliverable\n\nUse primary literature and public sequence, structural and genomic resources. Select analyses that answer the decisive question; this is not a general gene review. Assess support and contrary evidence, and allow an unresolved outcome. Distinguish directly observed horse evidence, justified mammalian transfer, and results for a different protein model.\n\nDo not consult the ai-gene-review repository's existing judgments, research syntheses or local bioinformatics analyses. Those are held out for comparison. Do not use agreement with ARBA or another prediction as biological validation. Preserve reproducible methods, accessions/versions, actual computation outputs and primary-source URLs/DOIs/PMIDs. Report the decisive findings and limitations, not just a verdict.\n"
    ],
    "expected_report": "genes/HORSE/SIRT5/SIRT5-hypotheses/horse40-nad-dependent-desuccinylation/openscientist.md",
    "status": "SUBMITTED",
    "dry_run": "PASSED",
    "job_id": "fa33ef4a-c7eb-4095-8ef4-b52b64beb163",
    "submitted_at": "2026-09-08T22:57:06.277939Z"
  },
  {
    "rank": 3,
    "gene": "OLFML2A",
    "horse_accession": "A0A9L0SKW1",
    "human_comparison_accession": "Q68BL7",
    "hypothesis": "The horse protein A0A9L0SKW1 localizes to the extracellular matrix.",
    "source_prediction": {
      "accession": "A0A9L0SKW1",
      "taxon_id": "9796",
      "type": "GO",
      "id": "GO:0031012",
      "text": "C:extracellular matrix"
    },
    "current_assessment": "UNC",
    "selection_reason": "Highest priority: extracellular family biology is strong, but the selected sequence raises a targeting question. This can test whether our caution about the exact model is warranted.",
    "desired_resolution": "Independent targeting and transcript evidence supporting or limiting ECM localization of this accession; not a general claim about the gene family.",
    "prompt_file": "projects/PROTNLM_EVALUATION/mammal-benchmark/openscientist-selection/03-OLFML2A-extracellular-matrix-localization-prompt.md",
    "sequence_sha256": "069f390f83475c7f4749a7dff36c9d553c6334ea6dc0d2004ab814d07ef297ab",
    "launch_argv": [
      "just",
      "gene-hypothesis-research",
      "openscientist",
      "HORSE",
      "OLFML2A",
      "--focus-type",
      "function-assignment",
      "--hypothesis",
      "The horse protein A0A9L0SKW1 localizes to the extracellular matrix.",
      "--slug",
      "horse40-extracellular-matrix-localization",
      "--context",
      "# Focused function hypothesis\n\nHypothesis: The horse protein A0A9L0SKW1 localizes to the extracellular matrix.\n\nTarget: Equus caballus (NCBITaxon:9796), UniProt A0A9L0SKW1. Gene label: OLFML2A; verify identity independently rather than treating the label as proof.\n\nTarget GO claim: GO:0031012 \u2014 extracellular matrix. Verify its definition and scope.\n\n## Decisive question\n\nDetermine whether the exact sequence and credible transcript model support entry into the secretory pathway and extracellular-matrix residence. Distinguish secretion from matrix association, and distinguish the supplied protein from alternative products of the locus.\n\n## Identity and sequence inputs\n\n- Target record: https://www.uniprot.org/uniprotkb/A0A9L0SKW1/entry\n- Human comparison lead: https://www.uniprot.org/uniprotkb/Q68BL7/entry (OLFML2A). Establish the relevant orthology/isoform relationship rather than assuming it.\n- Frozen current UniProt sequence: 599 residues; SHA-256 `069f390f83475c7f4749a7dff36c9d553c6334ea6dc0d2004ab814d07ef297ab`.\n- These are current sequences downloaded for the cohort on 2026-09-08. Identity with the original prediction-time input has not been established. Evaluate the supplied sequence explicitly; document any different sequence used.\n\n```fasta\n>A0A9L0SKW1 Equus caballus OLFML2A\nMDSQVFGDMDQVRMTSEGSDCRCKCIMRPLSKDACSRVRSGRARVEDFYTVETVSSGTDC\nRCSCTAPPSSLNPCENEWKMEKLKKQAPELLKLQSMVASQMNTLEESIKANLSRENEVVR\nESMRHFSEQLKHYENHSAIMMSIKKELSSLGLQLLQKDAATAPAAGPATGPGSKAQDTAG\nGKGKDTNKYGSMQKSFVDRGLPKAPKEKLLKVEKLRKEGSKSRFPQPTGKPRALAQQQAV\nVRGITYYKAGRKEATEAVADNALKGTSWLEQLPPRVEGRPSEPNSAEHDEARPRTSEGVD\nLAPGTPASDPTPTPTPTTTTSPMSTEPPSRPEVPSQGREASCEGTLRAVDPPVRHHSYGR\nHEGAWMKDPAARDDRIYVTNYYYGNSLVEFRNLENFKQGRWSNMYKLPYNWIGTGHVVYQ\nGAFYYNRAFTKNIIKYDLRQRFVASWALLPDVVYEDTTPWKWRGHSDIDFAVDESGLWVI\nYPAVDDRDEAQPEVIVLSRLDPGDLSVHRETTWKTRLRRNSYGNCFLVCGILYAVDTYNQ\nREGQVAYAFDTHTGTDARPQLPFLNEHAYTTQIDYNPKERVLYAWDNGHQLTYTLHFVV\n```\n\n## Evidence and deliverable\n\nUse primary literature and public sequence, structural and genomic resources. Select analyses that answer the decisive question; this is not a general gene review. Assess support and contrary evidence, and allow an unresolved outcome. Distinguish directly observed horse evidence, justified mammalian transfer, and results for a different protein model.\n\nDo not consult the ai-gene-review repository's existing judgments, research syntheses or local bioinformatics analyses. Those are held out for comparison. Do not use agreement with ARBA or another prediction as biological validation. Preserve reproducible methods, accessions/versions, actual computation outputs and primary-source URLs/DOIs/PMIDs. Report the decisive findings and limitations, not just a verdict.\n",
      "--term-id",
      "GO:0031012",
      "--term-label",
      "extracellular matrix"
    ],
    "expected_report": "genes/HORSE/OLFML2A/OLFML2A-hypotheses/horse40-extracellular-matrix-localization/openscientist.md",
    "status": "SUBMITTED",
    "dry_run": "PASSED",
    "job_id": "b1705385-7aa1-4aae-8a1d-05d642bf8045",
    "submitted_at": "2026-09-08T22:57:05.345390Z"
  },
  {
    "rank": 4,
    "gene": "SHLD2",
    "horse_accession": "A0A9L0RGD6",
    "human_comparison_accession": "Q86V20",
    "hypothesis": "The horse protein A0A9L0RGD6 positively regulates double-strand break repair via nonhomologous end joining.",
    "source_prediction": {
      "accession": "A0A9L0RGD6",
      "taxon_id": "9796",
      "type": "GO",
      "id": "GO:2001034",
      "text": "P:positive regulation of double-strand break repair via nonhomologous end joining"
    },
    "current_assessment": "UNC",
    "selection_reason": "Highest priority: human isoforms separate recruitment from end protection. An independent assessment of the horse protein could resolve several related repair claims without treating localization as proof.",
    "desired_resolution": "Whether repair competence follows from the exact architecture, and which conclusions concern a different isoform or require an experiment.",
    "prompt_file": "projects/PROTNLM_EVALUATION/mammal-benchmark/openscientist-selection/04-SHLD2-nhej-promotion-prompt.md",
    "sequence_sha256": "23a8bbd5f9a69c949ff70deeaae91430af52e92bb435042251f70404110d2f95",
    "launch_argv": [
      "just",
      "gene-hypothesis-research",
      "openscientist",
      "HORSE",
      "SHLD2",
      "--focus-type",
      "function-assignment",
      "--hypothesis",
      "The horse protein A0A9L0RGD6 positively regulates double-strand break repair via nonhomologous end joining.",
      "--slug",
      "horse40-nhej-promotion",
      "--context",
      "# Focused function hypothesis\n\nHypothesis: The horse protein A0A9L0RGD6 positively regulates double-strand break repair via nonhomologous end joining.\n\nTarget: Equus caballus (NCBITaxon:9796), UniProt A0A9L0RGD6. Gene label: SHLD2; verify identity independently rather than treating the label as proof.\n\nTarget GO claim: GO:2001034 \u2014 positive regulation of double-strand break repair via nonhomologous end joining. Verify its definition and scope.\n\n## Decisive question\n\nEvaluate whether the exact protein has the molecular apparatus needed for this repair role. Compare experimentally characterized mammalian isoforms and structures. Distinguish complex recruitment from execution of the repair-supporting mechanism.\n\n## Identity and sequence inputs\n\n- Target record: https://www.uniprot.org/uniprotkb/A0A9L0RGD6/entry\n- Human comparison lead: https://www.uniprot.org/uniprotkb/Q86V20/entry (SHLD2). Establish the relevant orthology/isoform relationship rather than assuming it.\n- Frozen current UniProt sequence: 883 residues; SHA-256 `23a8bbd5f9a69c949ff70deeaae91430af52e92bb435042251f70404110d2f95`.\n- These are current sequences downloaded for the cohort on 2026-09-08. Identity with the original prediction-time input has not been established. Evaluate the supplied sequence explicitly; document any different sequence used.\n\n```fasta\n>A0A9L0RGD6 Equus caballus SHLD2\nMSGGSQVHIFWGAPIGPLKMTVSQEPTSLVSTTDPWKKIQLLYNQHSLHLKDDKCKHKNL\nEDCQVLDAAGPSDLLNGHFLANSVNRSAHVKDDFVHCISETETTKSHKIPPLEMSGIPNS\nDVQICGFKGRVQHLTEEEKCQQLFSENKKIADEQHKDQSNICGQNFPKNSLHLDPKCAAI\nLDLVCGTEQINIGPGAAETKRVPTGHRERQTQRLEFFPSSTVDEPRSERAARKDSALNIS\nTDTEFLSVMTSSQVAFLAQRKYKGQNSVNKGIVNMEIEPKASHGEMRKREDNLIKPNDGF\nAEGSESGQTEAYSLELFSPVCPETESSNIRINSDKGLEENTGSQELFTFENKLLPDEICI\nESCSSGILCSQGNTFLKSSGKRNRTSEDKLGHSKALSKVLQESKKMKLVSNARDPPVEMG\nQRNVSKFHGVKKTSLIKNCGSKSQKYNCLVMVLSPCHVKEINIKSGPNSGSKVPLATITV\nIDQSEVKKKVFLWRTAAFWAFTVFLGDIVLLTDVTIHDDHWVGERVLQSTFTSQLLNLGS\nYSSVQPEEYSSMVSDVVLQDLLAYVSSKHSYLKDLPQRRPQKMNSIEFVELACLRPDILV\nHAVVRVVDITVLTEAVYSYRGQKQRKVMLTVEQTQGQHYVLVLWGPGAAWYPQLQRKKDY\nIWEFKYLFVQRNCVLENLELHTTPWSSCESLFDDDIRAVTFKAKFQKSTSSFVKMSDLAV\nHLEDKCSGVILIKAQILELVFPTTAAQKIALNARSSLKSIFSSLPNIVYTGCAKCGLELE\nTDENRIYRQCFSCLPFTMKKIYYSAPRRGHLWHGRRRLAPRLAGGRRGPLCGEGAEPLPA\nGRKQLPPATGFLAPRLLPRQCEPASQAFPETRGKNCRRFEDNP\n```\n\n## Evidence and deliverable\n\nUse primary literature and public sequence, structural and genomic resources. Select analyses that answer the decisive question; this is not a general gene review. Assess support and contrary evidence, and allow an unresolved outcome. Distinguish directly observed horse evidence, justified mammalian transfer, and results for a different protein model.\n\nDo not consult the ai-gene-review repository's existing judgments, research syntheses or local bioinformatics analyses. Those are held out for comparison. Do not use agreement with ARBA or another prediction as biological validation. Preserve reproducible methods, accessions/versions, actual computation outputs and primary-source URLs/DOIs/PMIDs. Report the decisive findings and limitations, not just a verdict.\n",
      "--term-id",
      "GO:2001034",
      "--term-label",
      "positive regulation of double-strand break repair via nonhomologous end joining"
    ],
    "expected_report": "genes/HORSE/SHLD2/SHLD2-hypotheses/horse40-nhej-promotion/openscientist.md",
    "status": "SUBMITTED",
    "dry_run": "PASSED",
    "job_id": "1af435bf-ce24-49b9-933b-8fd164d53de3",
    "submitted_at": "2026-09-08T22:57:07.256146Z"
  },
  {
    "rank": 5,
    "gene": "PTPRN2",
    "horse_accession": "A0A9L0T4W6",
    "human_comparison_accession": "Q92932",
    "hypothesis": "The horse protein A0A9L0T4W6 participates in protein dephosphorylation.",
    "source_prediction": {
      "accession": "A0A9L0T4W6",
      "taxon_id": "9796",
      "type": "GO",
      "id": "GO:0006470",
      "text": "P:protein dephosphorylation"
    },
    "current_assessment": "UNC",
    "selection_reason": "Priority 2: an informative pseudoenzyme/process distinction. A mechanistic synthesis could resolve a claim that neither domain classification nor generic catalytic inactivity settles.",
    "desired_resolution": "Evidence for a specific protein-dephosphorylation mechanism, or a clear account of why only lipid chemistry/other processes are supported.",
    "prompt_file": "projects/PROTNLM_EVALUATION/mammal-benchmark/openscientist-selection/05-PTPRN2-protein-dephosphorylation-prompt.md",
    "sequence_sha256": "6e469207454cac638b007421577b3c8140a28f2f24ed1e0ee900486ad5d7c821",
    "launch_argv": [
      "just",
      "gene-hypothesis-research",
      "openscientist",
      "HORSE",
      "PTPRN2",
      "--focus-type",
      "function-assignment",
      "--hypothesis",
      "The horse protein A0A9L0T4W6 participates in protein dephosphorylation.",
      "--slug",
      "horse40-protein-dephosphorylation",
      "--context",
      "# Focused function hypothesis\n\nHypothesis: The horse protein A0A9L0T4W6 participates in protein dephosphorylation.\n\nTarget: Equus caballus (NCBITaxon:9796), UniProt A0A9L0T4W6. Gene label: PTPRN2; verify identity independently rather than treating the label as proof.\n\nTarget GO claim: GO:0006470 \u2014 protein dephosphorylation. Verify its definition and scope.\n\n## Decisive question\n\nIdentify a direct or regulatory mechanism for participation in protein dephosphorylation. Separate phosphoprotein substrates from phosphoinositide substrates, and establish whether characterized mammalian mechanisms transfer to this protein. Lack of intrinsic catalysis alone does not exclude participation.\n\n## Identity and sequence inputs\n\n- Target record: https://www.uniprot.org/uniprotkb/A0A9L0T4W6/entry\n- Human comparison lead: https://www.uniprot.org/uniprotkb/Q92932/entry (PTPRN2). Establish the relevant orthology/isoform relationship rather than assuming it.\n- Frozen current UniProt sequence: 976 residues; SHA-256 `6e469207454cac638b007421577b3c8140a28f2f24ed1e0ee900486ad5d7c821`.\n- These are current sequences downloaded for the cohort on 2026-09-08. Identity with the original prediction-time input has not been established. Evaluate the supplied sequence explicitly; document any different sequence used.\n\n```fasta\n>A0A9L0T4W6 Equus caballus PTPRN2\nMGPPLALLLLLLLLPRGPPAAPATRARPLPGLLGCLFEDGLCRPSETCVDGFTWQDDYTQ\nHVMAQELSNLPKTYPQHPESSNPARTSMQSVDNEKRYSQEGDIALAKALQRYLPYLEALS\nQATTSNLLPRMKHGRPPSEGEDALAESVLTYVAQTSALTYAPMPREDYPAGHPLRTLSRL\nQPDELSPKVVGSVDRQNLVAALGAYAAQKHPPPPREGDPGLHNLLHAPWREPRVLSAPAT\nPQKWPLSPGDPKHPLGRGDEALIQSLLKDLRRHQVDMASLSPLDPEEMARVIANAMQGVG\nTEGEREEAGMGVGGEPGEQVDSPEAGLHEARKVGDVRDNRVQDDDDRVYEEVNRLSLTLG\nDLLQDPGSQFLPGAPPLVESFKTEIKKSEDPGASLSSEEESAGVENVRSQTYVKELLERP\nQVDGFGEFQRQIPGAWKEDRRLEAGAQERSGEGLELEVQPSEESGYIVTETDPLSLEKGK\nELLAGVARLLEVPMSVFVDIDVVGPAVTFKVSANVLNVTTAEAVEAAVENKDNLEKTSGL\nKILQTGVGSKSKLKLRPHQAEQEDSTKFIVLTLISVAAILGVLLASGVIYCLRHSSHYRL\nKEKLSGPGGHAGLDATAYQELCRQRMAVRTSDRPEAPHTSRISSVSSQFSDGPMPSPSAR\nSSTSSWSEEPAQPNMDISTGHMVLAYMEDHLKNKNRLEKEWEALCAYQAEPSSSLVAQRE\nENVPKNRCPAVLTYDHSRILLKSENSHSNSDYINASPIMDHDPRNPAYIATQGPLPATVA\nDFWQMVWESGCVVIVMLTPLSENGVRQCYHYWPDEGSNLYHIYEVNLVSEHIWCEDFLVR\nSFYLKNLQTNETRTVTQFHFLSWYDQGVPSSTRSLLDFRRKVNKCYRGRSCPIIVHCSDG\nAGRSGTYVLIDMVLNKMAKGSTVITSHRGARTCTWGGTQLGFFESMLPVRGRHCRRSHTG\nWKTIRVLCTSRSLLGS\n```\n\n## Evidence and deliverable\n\nUse primary literature and public sequence, structural and genomic resources. Select analyses that answer the decisive question; this is not a general gene review. Assess support and contrary evidence, and allow an unresolved outcome. Distinguish directly observed horse evidence, justified mammalian transfer, and results for a different protein model.\n\nDo not consult the ai-gene-review repository's existing judgments, research syntheses or local bioinformatics analyses. Those are held out for comparison. Do not use agreement with ARBA or another prediction as biological validation. Preserve reproducible methods, accessions/versions, actual computation outputs and primary-source URLs/DOIs/PMIDs. Report the decisive findings and limitations, not just a verdict.\n",
      "--term-id",
      "GO:0006470",
      "--term-label",
      "protein dephosphorylation"
    ],
    "expected_report": "genes/HORSE/PTPRN2/PTPRN2-hypotheses/horse40-protein-dephosphorylation/openscientist.md",
    "status": "SUBMITTED",
    "dry_run": "PASSED",
    "job_id": "01e2100b-655d-4f8a-8893-9aa9ca0f0c68",
    "submitted_at": "2026-09-08T22:57:08.231716Z"
  },
  {
    "rank": 6,
    "gene": "MTMR9",
    "horse_accession": "A0A9L0T3C1",
    "human_comparison_accession": "Q96QG7",
    "hypothesis": "The horse protein A0A9L0T3C1 negatively regulates autophagy.",
    "source_prediction": {
      "accession": "A0A9L0T3C1",
      "taxon_id": "9796",
      "type": "GO",
      "id": "GO:0010507",
      "text": "P:negative regulation of autophagy"
    },
    "current_assessment": "UNC",
    "selection_reason": "Priority 2: the broad regulator role is supported, but transfer of the particular downstream phenotype remains uncertain. This checks whether a domain-junction difference really warrants withholding the process.",
    "desired_resolution": "Whether a conserved productive partner interaction supports the negative autophagy effect, rather than merely demonstrating binding or altered autophagy markers.",
    "prompt_file": "projects/PROTNLM_EVALUATION/mammal-benchmark/openscientist-selection/06-MTMR9-negative-autophagy-regulation-prompt.md",
    "sequence_sha256": "0a21ea798953b735f23b338b4365a2eaa154a29b4f4db7db9c773e81a7022f3d",
    "launch_argv": [
      "just",
      "gene-hypothesis-research",
      "openscientist",
      "HORSE",
      "MTMR9",
      "--focus-type",
      "function-assignment",
      "--hypothesis",
      "The horse protein A0A9L0T3C1 negatively regulates autophagy.",
      "--slug",
      "horse40-negative-autophagy-regulation",
      "--context",
      "# Focused function hypothesis\n\nHypothesis: The horse protein A0A9L0T3C1 negatively regulates autophagy.\n\nTarget: Equus caballus (NCBITaxon:9796), UniProt A0A9L0T3C1. Gene label: MTMR9; verify identity independently rather than treating the label as proof.\n\nTarget GO claim: GO:0010507 \u2014 negative regulation of autophagy. Verify its definition and scope.\n\n## Decisive question\n\nEvaluate the partner-dependent mechanism for this process and whether the exact protein supports it. Identify experimentally grounded partners and substrate pathways. Distinguish complex formation, enzyme regulation and the direction of an autophagy phenotype.\n\n## Identity and sequence inputs\n\n- Target record: https://www.uniprot.org/uniprotkb/A0A9L0T3C1/entry\n- Human comparison lead: https://www.uniprot.org/uniprotkb/Q96QG7/entry (MTMR9). Establish the relevant orthology/isoform relationship rather than assuming it.\n- Frozen current UniProt sequence: 507 residues; SHA-256 `0a21ea798953b735f23b338b4365a2eaa154a29b4f4db7db9c773e81a7022f3d`.\n- These are current sequences downloaded for the cohort on 2026-09-08. Identity with the original prediction-time input has not been established. Evaluate the supplied sequence explicitly; document any different sequence used.\n\n```fasta\n>A0A9L0T3C1 Equus caballus MTMR9\nMEFAELIRTPRVDNVVLHRPFYPAVEGTLCLTGHHLILSSRQDNTEELWLLHSNIDAIDK\nRFVGPLGTIIIKCKDFRIIQLDIPGMEECLNIASSIETSEWRLSYVNKEFAVCPSYPPIV\nIVPKSIDDEALRKVATFRHGGRFPVLSYYHKKNGMVIMRSGQPLTGTNGRRCKEDEKLIN\nATLRAGKRGYIIDTRSLTVAQQARAKGGGFEQEAHYPQWRRIHKSIERYHILQESLIKLV\nEACNDQTHNMDRWLSKLEASNWLTHIKEILTTACLAAQCIDREGASILIHGTEGTDSTLQ\nVTSLAQIILEPRSRTIRGFEALIEREWLQAGHPFQQRCAQSAYCNSKQKWESPVFLLFLD\nCVWQILRQFPCSFEFNENFLIMLFEHAYASQFGTFLGNNESERCKLKLQQKTMSLWSWVN\nRPSELRKFTSPLFEANNLVIWPSVAPQSLHLWEGIFLRWNRSSKYLDEAYEEMVNIIEYN\nKELQAKVNILRRQLAELETEDGMQESP\n```\n\n## Evidence and deliverable\n\nUse primary literature and public sequence, structural and genomic resources. Select analyses that answer the decisive question; this is not a general gene review. Assess support and contrary evidence, and allow an unresolved outcome. Distinguish directly observed horse evidence, justified mammalian transfer, and results for a different protein model.\n\nDo not consult the ai-gene-review repository's existing judgments, research syntheses or local bioinformatics analyses. Those are held out for comparison. Do not use agreement with ARBA or another prediction as biological validation. Preserve reproducible methods, accessions/versions, actual computation outputs and primary-source URLs/DOIs/PMIDs. Report the decisive findings and limitations, not just a verdict.\n",
      "--term-id",
      "GO:0010507",
      "--term-label",
      "negative regulation of autophagy"
    ],
    "expected_report": "genes/HORSE/MTMR9/MTMR9-hypotheses/horse40-negative-autophagy-regulation/openscientist.md",
    "status": "SUBMITTED",
    "dry_run": "PASSED",
    "job_id": "d5e0df06-43d8-4578-91fd-2c6c739db7a4",
    "submitted_at": "2026-09-08T22:57:06.743883Z"
  },
  {
    "rank": 7,
    "gene": "WDPCP",
    "horse_accession": "A0A3Q2KRK8",
    "human_comparison_accession": "O95876",
    "hypothesis": "The horse protein A0A3Q2KRK8 participates in cell projection organization.",
    "source_prediction": {
      "accession": "A0A3Q2KRK8",
      "taxon_id": "9796",
      "type": "GO",
      "id": "GO:0030030",
      "text": "P:cell projection organization"
    },
    "current_assessment": "COR",
    "selection_reason": "Supported comparison case: the current review accepts the broad role despite sequence differences. Including it tests both excessive caution and overly permissive transfer; it is not presumed gold truth.",
    "desired_resolution": "Independent support, narrowing or refutation of the broad process, with the consequences of sequence variation evaluated proportionately.",
    "prompt_file": "projects/PROTNLM_EVALUATION/mammal-benchmark/openscientist-selection/07-WDPCP-cell-projection-organization-prompt.md",
    "sequence_sha256": "a132072d392ff9ec8d0962a571a5ae3534476ecfc0679bdeb9051777f3aa5a0a",
    "launch_argv": [
      "just",
      "gene-hypothesis-research",
      "openscientist",
      "HORSE",
      "WDPCP",
      "--focus-type",
      "function-assignment",
      "--hypothesis",
      "The horse protein A0A3Q2KRK8 participates in cell projection organization.",
      "--slug",
      "horse40-cell-projection-organization",
      "--context",
      "# Focused function hypothesis\n\nHypothesis: The horse protein A0A3Q2KRK8 participates in cell projection organization.\n\nTarget: Equus caballus (NCBITaxon:9796), UniProt A0A3Q2KRK8. Gene label: WDPCP; verify identity independently rather than treating the label as proof.\n\nTarget GO claim: GO:0030030 \u2014 cell projection organization. Verify its definition and scope.\n\n## Decisive question\n\nEvaluate the molecular scaffold and experimental basis for the broad cell-projection-organization process. Compare relevant mammalian structures and isoforms, and distinguish alterations affecting a specific biochemical property from those that undermine the whole process.\n\n## Identity and sequence inputs\n\n- Target record: https://www.uniprot.org/uniprotkb/A0A3Q2KRK8/entry\n- Human comparison lead: https://www.uniprot.org/uniprotkb/O95876/entry (WDPCP). Establish the relevant orthology/isoform relationship rather than assuming it.\n- Frozen current UniProt sequence: 705 residues; SHA-256 `a132072d392ff9ec8d0962a571a5ae3534476ecfc0679bdeb9051777f3aa5a0a`.\n- These are current sequences downloaded for the cohort on 2026-09-08. Identity with the original prediction-time input has not been established. Evaluate the supplied sequence explicitly; document any different sequence used.\n\n```fasta\n>A0A3Q2KRK8 Equus caballus WDPCP\nMSFCLTELHLWSLKNTLHIGDRDIGVYQYYDKKDPPVTDHGNLEEKQKLAESRDYPWTLK\nNRRPEKLRDSLKELEELMQNSQCVLSKWNNKYVCQLLFGSGVLVSLSLSGPQLEKVVIDR\nSLVGKLISDTISDALLTDSFIILSFFAQNKLCFIQFTKKMGSPDVNKRLEKLSALDYKIS\nYYEIPGPVNRTTERRLAINCVQDIVVCWWPLVSDDAWPWAPISSEKNRANLLLLGYAQGR\nLEVLSSVRTEWDPLDVRFGTKQPYQVLTVERSISVDKEPMADSCIYEYVRNKIHCVSVTR\nIPLRSKAISCCRNVTEDKLILGCEDSSLILYETHRRVTLLAQAELLPSLICCHPTGSILL\nVGSNQGELQIFDMALSPINIQLLAEDRSPRETLQFNKFFDVSSGLVQMQWIAPQVVSQKP\nDSGDIYDLLFLRFDRGPLGVLLFKLGIFTRGQLGLVDIIFQYIHCDEICEAINILSSMNW\nDTLGHQCFISMSAIVNHLLRQKLTPEREAQLEASLGTFYAPTRPLLDSTVLEYRDQISKY\nARRFFHHLLRYQRFEKAFLLAVDIGARDLFMDIHYLALDKGELALAEVARKKASDIDAES\nITSGVELLGPLHRGDTLNEAFVGLSLAPQREDTFPDNLPHFCSVHRHIIQQRTLNVSSNG\nQVFNRRNKLEKDTCAGSLMPKTCNEEDQSFDVASYWKHQQWTMYA\n```\n\n## Evidence and deliverable\n\nUse primary literature and public sequence, structural and genomic resources. Select analyses that answer the decisive question; this is not a general gene review. Assess support and contrary evidence, and allow an unresolved outcome. Distinguish directly observed horse evidence, justified mammalian transfer, and results for a different protein model.\n\nDo not consult the ai-gene-review repository's existing judgments, research syntheses or local bioinformatics analyses. Those are held out for comparison. Do not use agreement with ARBA or another prediction as biological validation. Preserve reproducible methods, accessions/versions, actual computation outputs and primary-source URLs/DOIs/PMIDs. Report the decisive findings and limitations, not just a verdict.\n",
      "--term-id",
      "GO:0030030",
      "--term-label",
      "cell projection organization"
    ],
    "expected_report": "genes/HORSE/WDPCP/WDPCP-hypotheses/horse40-cell-projection-organization/openscientist.md",
    "status": "SUBMITTED",
    "dry_run": "PASSED",
    "job_id": "ac0cfe8c-36e5-4c9e-b265-29144d66ec45",
    "submitted_at": "2026-09-08T22:57:07.751014Z"
  },
  {
    "rank": 8,
    "gene": "WEE1",
    "horse_accession": "F6TY09",
    "human_comparison_accession": "P30291",
    "hypothesis": "The horse protein F6TY09 participates in female pronucleus assembly.",
    "source_prediction": {
      "accession": "F6TY09",
      "taxon_id": "9796",
      "type": "GO",
      "id": "GO:0035038",
      "text": "P:female pronucleus assembly"
    },
    "current_assessment": "UNC",
    "selection_reason": "Lower priority: an important paralog-versus-redundancy question, but literature synthesis may still leave horse participation unresolved. Include one such biological-process case to test the limits of sequence-based adjudication.",
    "desired_resolution": "A species- and paralog-specific mechanistic conclusion; persistence of uncertainty is acceptable if the missing evidence is experimental.",
    "prompt_file": "projects/PROTNLM_EVALUATION/mammal-benchmark/openscientist-selection/08-WEE1-female-pronucleus-assembly-prompt.md",
    "sequence_sha256": "f46f1c6be9cdfa7025987fbd2b3d5f5a49a4e7cbb69d75d9101e8b34234429d4",
    "launch_argv": [
      "just",
      "gene-hypothesis-research",
      "openscientist",
      "HORSE",
      "WEE1",
      "--focus-type",
      "function-assignment",
      "--hypothesis",
      "The horse protein F6TY09 participates in female pronucleus assembly.",
      "--slug",
      "horse40-female-pronucleus-assembly",
      "--context",
      "# Focused function hypothesis\n\nHypothesis: The horse protein F6TY09 participates in female pronucleus assembly.\n\nTarget: Equus caballus (NCBITaxon:9796), UniProt F6TY09. Gene label: WEE1; verify identity independently rather than treating the label as proof.\n\nTarget GO claim: GO:0035038 \u2014 female pronucleus assembly. Verify its definition and scope.\n\n## Decisive question\n\nResolve the relevant mammalian paralogs and original oocyte perturbation experiments, then assess transfer to horse. Distinguish participation from necessity or sufficiency and evaluate plausible compensation. Identify any direct horse expression or functional evidence.\n\n## Identity and sequence inputs\n\n- Target record: https://www.uniprot.org/uniprotkb/F6TY09/entry\n- Human comparison lead: https://www.uniprot.org/uniprotkb/P30291/entry (WEE1). Establish the relevant orthology/isoform relationship rather than assuming it.\n- Frozen current UniProt sequence: 646 residues; SHA-256 `f46f1c6be9cdfa7025987fbd2b3d5f5a49a4e7cbb69d75d9101e8b34234429d4`.\n- These are current sequences downloaded for the cohort on 2026-09-08. Identity with the original prediction-time input has not been established. Evaluate the supplied sequence explicitly; document any different sequence used.\n\n```fasta\n>F6TY09 Equus caballus WEE1\nMSFLSRQQPPPPRRAAASCSLRQKLIFSPCSDCEEEEEEEEEEGSGHSTGEDSAFQEPDS\nPLPPARSPTEPGPERRRSPGPAPGSPGELEEDMLLRGACTGADAAGGGAEGDSWEEEGFG\nSSSPVKSPAAAYFLASCFSPVRCGGPGDASPRGYGARGAAEGPCSPLPDQPGTPPHKTFR\nKLRLFDTPHTPKSLLSKARGIDSSSVKLRSGSLFMDTEKSGKRELDMRQTPQVNINPFTP\nDSVLFHSSGQCRRRKRTYWNDSCGEDMEASDYEFEDETRPAKRITITESNMKSRYTTEFH\nELEKIGSGEFGSVFKCVKRLDGCIYAIKRSKKPLAGSVDEQNALREVYAHAVLGQHSHVV\nRYFSAWAEDDHMLIQNEYCNGGSLADAISENYRRMSYFTEVDLKDLLLQVGRGLRYIHSM\nSLVHMDIKPSNIFISRTSIPNAASEEGDEDDWASNKVMFKIGDLGHVTRISSPQVEEGDS\nRFLANEVLQENYTHLPKADIFALALTVVCAAGAEPLPRNGDEWHEIRQGRLPRIPQVLSQ\nEFTELLKVMIHPDPERRPSAMALVKHSVLLSASRKSAEQLRIELNAEKFKNSLLQKELKK\nAQMAKAAAEERALFTDRMATRSTTQSNRTARLIGKKMNRSVSLTIY\n```\n\n## Evidence and deliverable\n\nUse primary literature and public sequence, structural and genomic resources. Select analyses that answer the decisive question; this is not a general gene review. Assess support and contrary evidence, and allow an unresolved outcome. Distinguish directly observed horse evidence, justified mammalian transfer, and results for a different protein model.\n\nDo not consult the ai-gene-review repository's existing judgments, research syntheses or local bioinformatics analyses. Those are held out for comparison. Do not use agreement with ARBA or another prediction as biological validation. Preserve reproducible methods, accessions/versions, actual computation outputs and primary-source URLs/DOIs/PMIDs. Report the decisive findings and limitations, not just a verdict.\n",
      "--term-id",
      "GO:0035038",
      "--term-label",
      "female pronucleus assembly"
    ],
    "expected_report": "genes/HORSE/WEE1/WEE1-hypotheses/horse40-female-pronucleus-assembly/openscientist.md",
    "status": "SUBMITTED",
    "dry_run": "PASSED",
    "job_id": "980d6e10-73fe-4604-b8e5-63ddd111f8eb",
    "submitted_at": "2026-09-08T22:57:04.504090Z"
  }
]