{"gene":"RPL7L1","run_date":"2026-06-10T07:46:26","timeline":{"discoveries":[{"year":2012,"finding":"Rpl7l1 is required for blastocyst formation in mouse preimplantation embryos; functional knockdown results in failure to form a blastocoel cavity and morphologically differentiated trophectoderm, while morula development, zygotic genome activation, and initial lineage specification proceed normally.","method":"Reverse genetic screen with functional knockdown (siRNA/morpholino) in mouse preimplantation embryos, phenotypic analysis of loss-of-function","journal":"Zygote (Cambridge, England)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean loss-of-function with specific developmental phenotype in a defined cellular context, single lab, two orthogonal characterizations (developmental staging + molecular markers)","pmids":["23211737"],"is_preprint":false}],"current_model":"RPL7L1 (60S Ribosomal Protein L7-Like 1) is required for mammalian blastocyst formation, as its knockdown in mouse preimplantation embryos specifically blocks blastocoel cavity formation and trophectoderm differentiation without disrupting earlier morula development or zygotic genome activation, placing it as an essential factor in late preimplantation development."},"narrative":{"mechanistic_narrative":"RPL7L1 is required for mammalian blastocyst formation, functioning as an essential factor in late preimplantation development [PMID:23211737]. Functional knockdown in mouse preimplantation embryos specifically blocks blastocoel cavity formation and trophectoderm differentiation, while morula development, zygotic genome activation, and initial lineage specification proceed normally [PMID:23211737]. Beyond this loss-of-function phenotype, no molecular mechanism, biochemical activity, or interaction partner for RPL7L1 has been characterized in the available corpus.","teleology":[{"year":2012,"claim":"Whether RPL7L1 has a discrete developmental role was unknown; loss-of-function in mouse embryos established it as specifically required for the morula-to-blastocyst transition rather than for general early development.","evidence":"Reverse genetic functional knockdown (siRNA/morpholino) in mouse preimplantation embryos with developmental staging and molecular marker analysis","pmids":["23211737"],"confidence":"Medium","gaps":["The molecular activity underlying the phenotype is not defined","No interaction partners, substrates, or pathway placement identified","Single-lab knockdown without genetic rescue or reciprocal validation"]},{"year":null,"claim":"The biochemical function of RPL7L1 and the mechanism by which it enables blastocoel formation and trophectoderm differentiation remain unestablished.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No molecular activity assigned in the available corpus","Subcellular localization not characterized","No mechanistic link between the protein and the developmental phenotype established"]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":[],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q6DKI1","full_name":"Ribosomal protein uL30-like","aliases":["60S ribosomal protein L7-like 1","Large ribosomal subunit protein uL30-like 1"],"length_aa":255,"mass_kda":29.7,"function":"","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q6DKI1/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RPL7L1","classification":"Common Essential","n_dependent_lines":379,"n_total_lines":381,"dependency_fraction":0.994750656167979},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"PES1","stoichiometry":10.0},{"gene":"NPM1","stoichiometry":0.2},{"gene":"NPM3","stoichiometry":0.2},{"gene":"PARP1","stoichiometry":0.2},{"gene":"WDR12","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/RPL7L1","total_profiled":1310},"omim":[{"mim_id":"617417","title":"RIBOSOMAL PROTEIN L7-LIKE 1; RPL7L1","url":"https://www.omim.org/entry/617417"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoli","reliability":"Approved"},{"location":"Mitochondria","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RPL7L1"},"hgnc":{"alias_symbol":["dJ475N16.4"],"prev_symbol":[]},"alphafold":{"accession":"Q6DKI1","domains":[{"cath_id":"3.30.1390.20","chopping":"65-153_218-243","consensus_level":"high","plddt":89.4737,"start":65,"end":243}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6DKI1","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q6DKI1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q6DKI1-F1-predicted_aligned_error_v6.png","plddt_mean":87.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RPL7L1","jax_strain_url":"https://www.jax.org/strain/search?query=RPL7L1"},"sequence":{"accession":"Q6DKI1","fasta_url":"https://rest.uniprot.org/uniprotkb/Q6DKI1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q6DKI1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6DKI1"}},"corpus_meta":[{"pmid":"24523926","id":"PMC_24523926","title":"Evidence based selection of commonly used RT-qPCR reference genes for the analysis of mouse skeletal muscle.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24523926","citation_count":60,"is_preprint":false},{"pmid":"32705277","id":"PMC_32705277","title":"Differentially expressed lncRNAs, miRNAs and mRNAs with associated ceRNA networks in a mouse model of myocardial ischemia/reperfusion injury.","date":"2020","source":"Molecular medicine reports","url":"https://pubmed.ncbi.nlm.nih.gov/32705277","citation_count":12,"is_preprint":false},{"pmid":"23211737","id":"PMC_23211737","title":"Identification of four genes required for mammalian blastocyst formation.","date":"2012","source":"Zygote (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/23211737","citation_count":10,"is_preprint":false},{"pmid":"36509213","id":"PMC_36509213","title":"Age, sex, and frailty modify the expression of common reference genes in skeletal muscle from ageing mice.","date":"2022","source":"Mechanisms of ageing and development","url":"https://pubmed.ncbi.nlm.nih.gov/36509213","citation_count":10,"is_preprint":false},{"pmid":"38042135","id":"PMC_38042135","title":"Pan-cancer analysis of 60S Ribosomal Protein L7-Like 1 (RPL7L1) and validation in liver hepatocellular carcinoma.","date":"2023","source":"Translational oncology","url":"https://pubmed.ncbi.nlm.nih.gov/38042135","citation_count":5,"is_preprint":false},{"pmid":"35382652","id":"PMC_35382652","title":"Epigenetic reprogramming in cloned mouse embryos following treatment with DNA methyltransferase and histone deacetylase inhibitors.","date":"2022","source":"Systems biology in reproductive medicine","url":"https://pubmed.ncbi.nlm.nih.gov/35382652","citation_count":5,"is_preprint":false},{"pmid":"40427657","id":"PMC_40427657","title":"Pathway-Specific Insights into Colorectal Cancer Through Comprehensive Multi-Omics Data Integration.","date":"2025","source":"Biology","url":"https://pubmed.ncbi.nlm.nih.gov/40427657","citation_count":2,"is_preprint":false},{"pmid":"38428846","id":"PMC_38428846","title":"Role of Flt3l and Rps15 in ketamine anesthesia.","date":"2024","source":"Medicine","url":"https://pubmed.ncbi.nlm.nih.gov/38428846","citation_count":2,"is_preprint":false},{"pmid":"40097569","id":"PMC_40097569","title":"Unraveling the intricate molecular landscape and potential biomarkers in lung adenocarcinoma through integrative epigenomic and transcriptomic profiling.","date":"2025","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/40097569","citation_count":1,"is_preprint":false},{"pmid":"38832038","id":"PMC_38832038","title":"Identification of potential obese-specific biomarkers and pathways associated with abdominal subcutaneous fat deposition in pig using a comprehensive bioinformatics strategy.","date":"2024","source":"PeerJ","url":"https://pubmed.ncbi.nlm.nih.gov/38832038","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7521,"output_tokens":348,"usd":0.013891,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6582,"output_tokens":716,"usd":0.025405,"stage2_stop_reason":"end_turn"},"total_usd":0.039296,"stage1_batch_id":"msgbatch_013LWZZT6MWaqB9qyTSeQBmU","stage2_batch_id":"msgbatch_0194ZzQaTGNpruoNJBbEMbt3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2012,\n      \"finding\": \"Rpl7l1 is required for blastocyst formation in mouse preimplantation embryos; functional knockdown results in failure to form a blastocoel cavity and morphologically differentiated trophectoderm, while morula development, zygotic genome activation, and initial lineage specification proceed normally.\",\n      \"method\": \"Reverse genetic screen with functional knockdown (siRNA/morpholino) in mouse preimplantation embryos, phenotypic analysis of loss-of-function\",\n      \"journal\": \"Zygote (Cambridge, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean loss-of-function with specific developmental phenotype in a defined cellular context, single lab, two orthogonal characterizations (developmental staging + molecular markers)\",\n      \"pmids\": [\"23211737\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RPL7L1 (60S Ribosomal Protein L7-Like 1) is required for mammalian blastocyst formation, as its knockdown in mouse preimplantation embryos specifically blocks blastocoel cavity formation and trophectoderm differentiation without disrupting earlier morula development or zygotic genome activation, placing it as an essential factor in late preimplantation development.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RPL7L1 is required for mammalian blastocyst formation, functioning as an essential factor in late preimplantation development [#0]. Functional knockdown in mouse preimplantation embryos specifically blocks blastocoel cavity formation and trophectoderm differentiation, while morula development, zygotic genome activation, and initial lineage specification proceed normally [#0]. Beyond this loss-of-function phenotype, no molecular mechanism, biochemical activity, or interaction partner for RPL7L1 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2012,\n      \"claim\": \"Whether RPL7L1 has a discrete developmental role was unknown; loss-of-function in mouse embryos established it as specifically required for the morula-to-blastocyst transition rather than for general early development.\",\n      \"evidence\": \"Reverse genetic functional knockdown (siRNA/morpholino) in mouse preimplantation embryos with developmental staging and molecular marker analysis\",\n      \"pmids\": [\"23211737\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The molecular activity underlying the phenotype is not defined\",\n        \"No interaction partners, substrates, or pathway placement identified\",\n        \"Single-lab knockdown without genetic rescue or reciprocal validation\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The biochemical function of RPL7L1 and the mechanism by which it enables blastocoel formation and trophectoderm differentiation remain unestablished.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No molecular activity assigned in the available corpus\",\n        \"Subcellular localization not characterized\",\n        \"No mechanistic link between the protein and the developmental phenotype established\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [],\n    \"complexes\": [],\n    \"partners\": [],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":2,"faith_total":2,"faith_pct":100.0}}