{"gene":"ZMAT5","run_date":"2026-04-28T23:00:24","timeline":{"discoveries":[{"year":2025,"finding":"ZMAT5 is a component of the 13-subunit human U11 snRNP complex of the minor spliceosome. Cryo-EM structures in apo and substrate-bound forms show that ZMAT5 is positioned near the 5' end of U11 snRNA, where it stabilizes binding of the incoming U12-type 5' splice site (5'SS) during recognition by the minor spliceosome.","method":"Cryo-EM reconstruction of human U11 snRNP in apo and substrate-bound forms","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 — cryo-EM structure with both apo and substrate-bound forms, revealing direct mechanistic role of ZMAT5 in 5'SS recognition","pmids":["39809272"],"is_preprint":false}],"current_model":"ZMAT5 is a subunit of the human U11 snRNP within the minor spliceosome, positioned near the 5' end of U11 snRNA where it stabilizes binding of incoming U12-type 5' splice sites during pre-mRNA splicing, as established by cryo-EM structures of the complex in apo and substrate-bound states."},"narrative":{"teleology":[{"year":2025,"claim":"The structural basis by which the minor spliceosome recognizes U12-type 5′ splice sites was unknown; cryo-EM of the human U11 snRNP revealed that ZMAT5 sits near the 5′ end of U11 snRNA and directly stabilizes 5′SS binding, establishing its mechanistic role in minor intron recognition.","evidence":"Cryo-EM reconstruction of human U11 snRNP in apo and substrate-bound conformations","pmids":["39809272"],"confidence":"High","gaps":["No loss-of-function or mutagenesis data defining which ZMAT5 residues are essential for 5′SS stabilization","Contribution of ZMAT5 to minor spliceosome activity in vivo (e.g., splicing efficiency of U12-type introns) has not been tested","Whether ZMAT5 participates in later spliceosomal complexes beyond U11 snRNP is unresolved"]},{"year":null,"claim":"The functional consequences of ZMAT5 depletion or mutation on minor intron splicing and cell physiology remain uncharacterized.","evidence":"","pmids":[],"confidence":"Low","gaps":["No knockdown/knockout phenotype reported","No disease association established through direct genetic evidence","No biochemical reconstitution of ZMAT5's contribution to splice-site duplex stability"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0]}],"complexes":["U11 snRNP"],"partners":[],"other_free_text":[]},"mechanistic_narrative":"ZMAT5 is a structural subunit of the 13-protein human U11 snRNP, a core component of the minor (U12-dependent) spliceosome. Cryo-EM structures of the U11 snRNP in apo and substrate-bound states show that ZMAT5 is positioned near the 5′ end of U11 snRNA, where it stabilizes the binding of incoming U12-type 5′ splice sites during pre-mRNA recognition [PMID:39809272]."},"prefetch_data":{"uniprot":{"accession":"Q9UDW3","full_name":"Zinc finger matrin-type protein 5","aliases":["U11/U12 small nuclear ribonucleoprotein 20 kDa protein","U11/U12 snRNP 20 kDa protein","U11/U12-20K"],"length_aa":170,"mass_kda":20.0,"function":"","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9UDW3/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/ZMAT5","classification":"Common Essential","n_dependent_lines":1178,"n_total_lines":1208,"dependency_fraction":0.9751655629139073},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/ZMAT5","total_profiled":1310},"omim":[{"mim_id":"619741","title":"ZINC FINGER, MATRIN-TYPE 5; ZMAT5","url":"https://www.omim.org/entry/619741"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ZMAT5"},"hgnc":{"alias_symbol":["SNRNP20"],"prev_symbol":["ZC3H19"]},"alphafold":{"accession":"Q9UDW3","domains":[{"cath_id":"3.30.160","chopping":"1-41","consensus_level":"medium","plddt":92.8615,"start":1,"end":41},{"cath_id":"1.10.287","chopping":"42-102","consensus_level":"medium","plddt":91.0825,"start":42,"end":102}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UDW3","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UDW3-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UDW3-F1-predicted_aligned_error_v6.png","plddt_mean":84.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ZMAT5","jax_strain_url":"https://www.jax.org/strain/search?query=ZMAT5"},"sequence":{"accession":"Q9UDW3","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UDW3.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UDW3/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UDW3"}},"corpus_meta":[{"pmid":"32047514","id":"PMC_32047514","title":"Genome-Wide Association Analysis Reveals Key Genes Responsible for Egg Production of Lion Head Goose.","date":"2020","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/32047514","citation_count":22,"is_preprint":false},{"pmid":"36918797","id":"PMC_36918797","title":"Identification of candidate genomic regions for egg yolk moisture content based on a genome-wide association study.","date":"2023","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/36918797","citation_count":7,"is_preprint":false},{"pmid":"39809272","id":"PMC_39809272","title":"Structural basis of 5' splice site recognition by the minor spliceosome.","date":"2025","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/39809272","citation_count":6,"is_preprint":false},{"pmid":"22807096","id":"PMC_22807096","title":"Search for chromosome rearrangements: new approaches toward discovery of novel translocations in head and neck squamous cell carcinoma.","date":"2012","source":"Head & neck","url":"https://pubmed.ncbi.nlm.nih.gov/22807096","citation_count":2,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3504,"output_tokens":353,"usd":0.007904},"stage2":{"model":"claude-opus-4-6","input_tokens":3498,"output_tokens":724,"usd":0.053385},"total_usd":0.061289,"stage1_batch_id":"msgbatch_01BparvgRZ9S2LMidvaoo86K","stage2_batch_id":"msgbatch_01NkBfv9SVZWthhS7j6mU6G3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2025,\n      \"finding\": \"ZMAT5 is a component of the 13-subunit human U11 snRNP complex of the minor spliceosome. Cryo-EM structures in apo and substrate-bound forms show that ZMAT5 is positioned near the 5' end of U11 snRNA, where it stabilizes binding of the incoming U12-type 5' splice site (5'SS) during recognition by the minor spliceosome.\",\n      \"method\": \"Cryo-EM reconstruction of human U11 snRNP in apo and substrate-bound forms\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — cryo-EM structure with both apo and substrate-bound forms, revealing direct mechanistic role of ZMAT5 in 5'SS recognition\",\n      \"pmids\": [\"39809272\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ZMAT5 is a subunit of the human U11 snRNP within the minor spliceosome, positioned near the 5' end of U11 snRNA where it stabilizes binding of incoming U12-type 5' splice sites during pre-mRNA splicing, as established by cryo-EM structures of the complex in apo and substrate-bound states.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"ZMAT5 is a structural subunit of the 13-protein human U11 snRNP, a core component of the minor (U12-dependent) spliceosome. Cryo-EM structures of the U11 snRNP in apo and substrate-bound states show that ZMAT5 is positioned near the 5′ end of U11 snRNA, where it stabilizes the binding of incoming U12-type 5′ splice sites during pre-mRNA recognition [PMID:39809272].\",\n  \"teleology\": [\n    {\n      \"year\": 2025,\n      \"claim\": \"The structural basis by which the minor spliceosome recognizes U12-type 5′ splice sites was unknown; cryo-EM of the human U11 snRNP revealed that ZMAT5 sits near the 5′ end of U11 snRNA and directly stabilizes 5′SS binding, establishing its mechanistic role in minor intron recognition.\",\n      \"evidence\": \"Cryo-EM reconstruction of human U11 snRNP in apo and substrate-bound conformations\",\n      \"pmids\": [\"39809272\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No loss-of-function or mutagenesis data defining which ZMAT5 residues are essential for 5′SS stabilization\",\n        \"Contribution of ZMAT5 to minor spliceosome activity in vivo (e.g., splicing efficiency of U12-type introns) has not been tested\",\n        \"Whether ZMAT5 participates in later spliceosomal complexes beyond U11 snRNP is unresolved\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The functional consequences of ZMAT5 depletion or mutation on minor intron splicing and cell physiology remain uncharacterized.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No knockdown/knockout phenotype reported\",\n        \"No disease association established through direct genetic evidence\",\n        \"No biochemical reconstitution of ZMAT5's contribution to splice-site duplex stability\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\"U11 snRNP\"],\n    \"partners\": [],\n    \"other_free_text\": []\n  }\n}\n```"}