{"gene":"UMAD1","run_date":"2026-04-28T21:43:01","timeline":{"discoveries":[],"current_model":"No mechanistic findings about UMAD1 in the available literature (corpus appears contaminated with off-target papers)."},"narrative":{"teleology":[],"mechanism_profile":null,"mechanistic_narrative":"No mechanistic findings about UMAD1 in the available literature (corpus appears contaminated with off-target papers)."},"prefetch_data":{"uniprot":{"accession":"C9J7I0","full_name":"UBAP1-MVB12-associated (UMA)-domain containing protein 1","aliases":["RPA3 antisense RNA 1","RPA3 opposite strand"],"length_aa":137,"mass_kda":15.2,"function":"","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/C9J7I0/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/UMAD1","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":77,"dependency_fraction":0.012987012987012988},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"TSG101","stoichiometry":10.0},{"gene":"VPS37B","stoichiometry":4.0}],"url":"https://opencell.sf.czbiohub.org/search/UMAD1","total_profiled":1310},"omim":[],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/UMAD1"},"hgnc":{"alias_symbol":[],"prev_symbol":["RPA3-AS1","RPA3OS"]},"alphafold":{"accession":"C9J7I0","domains":[{"cath_id":"-","chopping":"19-130","consensus_level":"medium","plddt":62.86,"start":19,"end":130}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/C9J7I0","model_url":"https://alphafold.ebi.ac.uk/files/AF-C9J7I0-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-C9J7I0-F1-predicted_aligned_error_v6.png","plddt_mean":61.44},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=UMAD1","jax_strain_url":"https://www.jax.org/strain/search?query=UMAD1"},"sequence":{"accession":"C9J7I0","fasta_url":"https://rest.uniprot.org/uniprotkb/C9J7I0.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/C9J7I0/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/C9J7I0"}},"corpus_meta":[{"pmid":"30146317","id":"PMC_30146317","title":"The Evf2 Ultraconserved Enhancer lncRNA Functionally and Spatially Organizes Megabase Distant Genes in the Developing Forebrain.","date":"2018","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/30146317","citation_count":67,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"32737115","id":"PMC_32737115","title":"Association of the RPA3-UMAD1 locus with interstitial lung diseases complicated with rheumatoid arthritis in Japanese.","date":"2020","source":"Annals of the rheumatic diseases","url":"https://pubmed.ncbi.nlm.nih.gov/32737115","citation_count":28,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"36585686","id":"PMC_36585686","title":"Genome-wide placental DNA methylations in fetal overgrowth and associations with leptin, adiponectin and fetal growth factors.","date":"2022","source":"Clinical epigenetics","url":"https://pubmed.ncbi.nlm.nih.gov/36585686","citation_count":16,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"33042427","id":"PMC_33042427","title":"The combination of circRNA-UMAD1 and Galectin-3 in peripheral circulation is a co-biomarker for predicting lymph node metastasis of thyroid carcinoma.","date":"2020","source":"American journal of translational research","url":"https://pubmed.ncbi.nlm.nih.gov/33042427","citation_count":13,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"29773854","id":"PMC_29773854","title":"Genome-wide haplotype association analysis of primary biliary cholangitis risk in Japanese.","date":"2018","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/29773854","citation_count":6,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"26496610","id":"PMC_26496610","title":"A human interactome in three quantitative dimensions organized by stoichiometries and abundances.","date":"2015","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/26496610","citation_count":1015,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"32296183","id":"PMC_32296183","title":"A reference map of the human binary protein interactome.","date":"2020","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/32296183","citation_count":849,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"35271311","id":"PMC_35271311","title":"OpenCell: Endogenous tagging for the cartography of human cellular organization.","date":"2022","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/35271311","citation_count":432,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"16344560","id":"PMC_16344560","title":"Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes.","date":"2005","source":"Genome research","url":"https://pubmed.ncbi.nlm.nih.gov/16344560","citation_count":409,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"23251661","id":"PMC_23251661","title":"Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.","date":"2012","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23251661","citation_count":312,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"12690205","id":"PMC_12690205","title":"Human chromosome 7: DNA sequence and biology.","date":"2003","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/12690205","citation_count":154,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"30561431","id":"PMC_30561431","title":"A protein-protein interaction map of the TNF-induced NF-κB signal transduction pathway.","date":"2018","source":"Scientific data","url":"https://pubmed.ncbi.nlm.nih.gov/30561431","citation_count":74,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"21216879","id":"PMC_21216879","title":"A genome-wide association study identifies novel loci associated with circulating IGF-I and IGFBP-3.","date":"2011","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/21216879","citation_count":59,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"36138187","id":"PMC_36138187","title":"NUDT21 limits CD19 levels through alternative mRNA polyadenylation in B cell acute lymphoblastic leukemia.","date":"2022","source":"Nature immunology","url":"https://pubmed.ncbi.nlm.nih.gov/36138187","citation_count":46,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"24556642","id":"PMC_24556642","title":"Genome-wide association study of primary dentition pit-and-fissure and smooth surface caries.","date":"2014","source":"Caries research","url":"https://pubmed.ncbi.nlm.nih.gov/24556642","citation_count":31,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"27609421","id":"PMC_27609421","title":"TNIP2 is a Hub Protein in the NF-κB Network with Both Protein and RNA Mediated Interactions.","date":"2016","source":"Molecular & cellular proteomics : MCP","url":"https://pubmed.ncbi.nlm.nih.gov/27609421","citation_count":28,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"32393512","id":"PMC_32393512","title":"SUMOylation of DDX39A Alters Binding and Export of Antiviral Transcripts to Control Innate Immunity.","date":"2020","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/32393512","citation_count":27,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"21221126","id":"PMC_21221126","title":"Genome-wide association study of serious blistering skin rash caused by drugs.","date":"2011","source":"The pharmacogenomics journal","url":"https://pubmed.ncbi.nlm.nih.gov/21221126","citation_count":23,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"20448139","id":"PMC_20448139","title":"UMA and MABP domains throw light on receptor endocytosis and selection of endosomal cargoes.","date":"2010","source":"Bioinformatics (Oxford, England)","url":"https://pubmed.ncbi.nlm.nih.gov/20448139","citation_count":21,"is_preprint":false,"source_track":"gene2pubmed"}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4233,"output_tokens":34,"usd":0.006605},"stage2":{"model":"","input_tokens":0,"output_tokens":0,"usd":0.0},"total_usd":0.029456,"stage1_batch_id":"msgbatch_01RPbVc9PDH9zQmYK5Hs6srm","stage2_batch_id":"msgbatch_01JVbVLzeKN2yVrsGp3zC8aM","note":"batch pricing = 50% of standard","round2_stage1":{"model":"claude-sonnet-4-6","input_tokens":10744,"output_tokens":898,"usd":0.022851},"round2_rules_fired":"R1"},"stage1_raw":"```json\n{\n  \"discoveries\": [],\n  \"current_model\": \"No mechanistic findings in the available literature.\"\n}\n```\n\n--- ROUND 2 (R2/R3, augmented corpus) ---\n\nI'll classify each paper first, then extract discoveries only from KEPT papers.\n\n**Classification:**\n\n1. PMID:30146317 — Evf2 lncRNA paper; UMAD1 is mentioned only as a distant target gene activated by Evf2 lncRNA. No mechanistic study of the UMAD1 protein itself. EXCLUDE (expression/regulatory association, not protein mechanism).\n\n2. PMID:32737115 — GWAS of RA-ILD; UMAD1 mentioned as a locus. EXCLUDE (GWAS association, no protein mechanism).\n\n3. PMID:36585686 — Epigenome-wide study; UMAD1 mentioned as a methylated gene. EXCLUDE (epigenetic association, no protein mechanism).\n\n4. PMID:33042427 — circRNA-UMAD1 paper. This describes a circular RNA from the UMAD1 locus, NOT the canonical UMAD1 protein. EXCLUDE (case B: alt-locus product).\n\n5. PMID:29773854 — PBC GWAS; UMAD1 mentioned as a haplotype locus. EXCLUDE (GWAS association, no protein mechanism).\n\n**Gene2pubmed papers:**\n\n6. PMID:26496610 — Large HeLa interactome study; UMAD1 may appear in dataset but no specific mechanistic finding about UMAD1 protein is described in the abstract. EXCLUDE.\n\n7. PMID:32296183 — HuRI binary interactome; no specific UMAD1 mechanistic finding in abstract. EXCLUDE.\n\n8. PMID:35271311 — OpenCell; systematic localization/interaction resource. UMAD1 may be included but no specific mechanistic finding described in abstract. EXCLUDE.\n\n9. PMID:16344560 — Alternative promoters genome-wide; no specific UMAD1 mechanistic finding. EXCLUDE.\n\n10. PMID:23251661 — Childhood obesity GWAS; no UMAD1 specific mechanism. EXCLUDE.\n\n11. PMID:12690205 — Chr7 sequence annotation; no UMAD1 protein mechanism. EXCLUDE.\n\n12. PMID:30561431 — TNF/NF-κB PPI map; no specific UMAD1 mechanism. EXCLUDE.\n\n13. PMID:21216879 — IGF GWAS; no UMAD1 mechanism. EXCLUDE.\n\n14. PMID:36138187 — NUDT21/CD19; no UMAD1 mechanism. EXCLUDE.\n\n15. PMID:24556642 — Dental caries GWAS; no UMAD1 mechanism. EXCLUDE.\n\n16. PMID:27609421 — TNIP2/NF-κB; no UMAD1 mechanism. EXCLUDE.\n\n17. PMID:32393512 — DDX39A SUMOylation; no UMAD1 mechanism. EXCLUDE.\n\n18. PMID:21221126 — SJS/TEN GWAS; no UMAD1 mechanism. EXCLUDE.\n\n19. PMID:20448139 — UMA/MABP domain paper; describes UMA domain found in MVB12 and UBAP1 (ESCRT-I components), not the UMAD1 protein specifically. EXCLUDE (domain nomenclature collision, not about the UMAD1 gene product).\n\nAll papers are EXCLUDE. No mechanistic findings about the canonical UMAD1 protein are present in this corpus.\n\n```json\n{\n  \"discoveries\": [],\n  \"current_model\": \"No mechanistic findings about UMAD1 in the available literature (corpus appears contaminated with off-target papers).\"\n}\n```","stage2_raw":"\n\n--- ROUND 2 (refusal — no on-target evidence) ---\n"}