{"gene":"RPL7A","run_date":"2026-06-10T07:46:26","timeline":{"discoveries":[{"year":1989,"finding":"The Surf-3 gene product (RPL7A) was identified as a 32-kDa ribosomal protein located in the 60S ribosomal subunit, established by anti-peptide serum immunofluorescence, immunoblotting of mouse cell components, in vitro translation of Surf-3 cDNA hybrid-selected mRNA, 2D-gel analysis, and homology with rat ribosomal peptide sequence.","method":"Anti-peptide serum immunofluorescence, immunoblotting, in vitro translation, 2D-gel electrophoresis, biochemical fractionation","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (immunoblot, in vitro translation, 2D gel, fractionation) in a single study establishing 60S subunit localization","pmids":["2648130"],"is_preprint":false},{"year":1990,"finding":"RPL7A (the 30 kDa protein encoded by the trk-2h N-terminal activating sequence) was identified as ribosomal large subunit protein L7a by Western immunoblotting of 2D-electrophoretically resolved ribosomal proteins; the protein shows intense nucleolar staining by immunofluorescence and has high basic amino acid content.","method":"Western blotting of 2D-resolved ribosomal proteins, immunofluorescence with antipeptide antibodies","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — two orthogonal methods (2D Western blot and immunofluorescence) confirming identity and nucleolar localization","pmids":["2403926"],"is_preprint":false},{"year":1991,"finding":"The yeast (S. cerevisiae) L4 gene is the homolog of mammalian RPL7A (Surf-3/L7a); disruption of both L4 paralogs is lethal likely due to inability to produce functional ribosomes, while disruption of L4-1 alone results in very small colonies, establishing an essential role for this protein in ribosome function.","method":"Gene disruption (knockout), colony growth assay, in vitro translation of hybrid-selected mRNA, 2D gel analysis, direct amino acid sequencing","journal":"Molecular & general genetics : MGG","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — genetic epistasis via double gene disruption (lethal), protein identity confirmed by 2D gel and direct sequencing","pmids":["2046660"],"is_preprint":false},{"year":1993,"finding":"The minimal promoter element required for human RPL7A transcription was identified as 130 bp of the 5'-flanking region; the gene lacks a canonical TATA sequence and has a C as the major transcriptional start point in a pyrimidine-rich region, features shared with other mammalian ribosomal protein genes.","method":"Promoter deletion analysis, transcription reporter assay","journal":"Gene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional promoter deletion in vivo, single lab study","pmids":["8482538"],"is_preprint":false},{"year":1992,"finding":"Two conserved promoter elements (Box A: nts -56 to -39; Box B: nts -25 to -4) in the rpL7a 5' upstream region bind distinct nuclear factors from mouse nuclear extracts, and both elements are functionally conserved between mammals and birds; constructs containing only 56 bp of upstream DNA plus the first 25 bp exon support efficient transcription without requiring first intron sequences.","method":"Electrophoretic mobility shift assay (EMSA), competition assay with homologous sequences, in vivo transcription reporter assay","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — EMSA plus in vivo reporter, single lab, two orthogonal methods","pmids":["1630908"],"is_preprint":false},{"year":1997,"finding":"Three distinct domains of human RPL7A mediate nuclear targeting: domain I (aa 23–51), domain II (aa 52–100), and domain III (aa 101–220), each containing at least one NLS. Domain II is necessary but not sufficient for nucleolar targeting; nucleolar accumulation requires domain II plus an additional basic domain (NLS or basic stretch), indicating cooperative protein–protein or protein–nucleic acid interactions.","method":"Transient expression of L7a–beta-galactosidase fusion proteins with deletion mutants in HeLa cells, indirect immunofluorescence","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — systematic deletion mutagenesis of multiple domains with reporter localization in live cells, multiple constructs tested","pmids":["9030593"],"is_preprint":false},{"year":2005,"finding":"Human RPL7A contains two RNA-binding domains: RNAB1 (aa 52–100) and RNAB2 (aa 101–161). RNAB1 lacks known nucleic-acid-binding motifs and may represent a novel class. The topology of the L7a–RNA complex was mapped using limited proteolysis, cross-linking, and mass spectrometry of the recombinant aa 101–161 domain with a 30-mer poly(G) oligonucleotide. L7a interacts in vitro with a presumably G-rich RNA structure.","method":"In vitro RNA-binding assay, deletion mutagenesis, limited proteolysis, chemical cross-linking, mass spectrometry","journal":"The Biochemical journal","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with mutagenesis, limited proteolysis and MS to map binding interface, single lab","pmids":["15361074"],"is_preprint":false},{"year":2011,"finding":"The N-terminal domain of human RPL7A was crystallized and X-ray diffraction data collected to 3.5 Å resolution (tetragonal space group P4(1)22 or P4(3)22; unit-cell a = b = 92.28 Å, c = 236.59 Å), providing preliminary structural characterization. The paper also notes that RPL7A interacts with thyroid hormone receptor (THR) and retinoic acid receptor (RAR) to inhibit their activities.","method":"X-ray crystallography (preliminary), recombinant protein expression in E. coli","journal":"Acta crystallographica. Section F, Structural biology and crystallization communications","confidence":"Low","confidence_rationale":"Tier 1 (method) / Weak — crystallization only reported as preliminary; functional claims about THR/RAR interaction are stated but no supporting experiment described in the abstract","pmids":["21505254"],"is_preprint":false},{"year":2018,"finding":"Under ischemic stress (oxygen-glucose deprivation or peroxynitrite treatment), FKBP25 translocates to the nucleus in endothelial cells and interacts with 60S ribosomal protein L7a, as demonstrated by co-immunoprecipitation and FRET; overexpression of FKBP25 protects endothelial cells against OGD injury.","method":"Co-immunoprecipitation, fluorescence resonance energy transfer (FRET), Western blot, immunofluorescence, overexpression","journal":"Cellular physiology and biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP confirmed by FRET (two orthogonal binding assays), single lab","pmids":["29969783"],"is_preprint":false},{"year":2017,"finding":"In S. cerevisiae, paralog-specific phenotypes of RPL7A vs RPL7B (tunicamycin sensitivity, ASH1 mRNA localization, Ty1 retrotransposon mobility) are driven primarily by differences in protein/ribosome levels rather than isoform identity; however, Ty1 cDNA accumulation is influenced by both level and isoform (or intron-encoded snoRNA) expressed. Depletion of Rpl7 strongly affects Ty1 RNA localization but minimally affects Ty1 Gag protein synthesis.","method":"Paralog swap (chimeric alleles), quantitative phenotypic assays (tunicamycin growth, mRNA localization, retrotransposition assay), Western blot, Northern blot","journal":"G3 (Bethesda, Md.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — systematic allele exchange with multiple functional readouts, single lab","pmids":["28007835"],"is_preprint":false},{"year":1998,"finding":"U24 and U36 snoRNAs are encoded within introns of the rpL7a gene in human, chicken, and mouse; these box C/D antisense snoRNAs guide site-specific ribose methylation of rRNA. In mammals, three U36 variants reside in introns 4, 5, and 6 of rpL7a, with unique structural features distinct from non-mammalian variants.","method":"Sequence analysis, comparative genomics, Northern blotting (snoRNA identification within introns)","journal":"DNA and cell biology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — snoRNA identification within introns by sequence and Northern blot, replicated across species","pmids":["9703018"],"is_preprint":false},{"year":2025,"finding":"RPL7A promotes lung adenocarcinoma progression by regulating circRANBP17, which forms a complex with UPF1 to destabilize SIRT6 mRNA, thereby reducing SIRT6 protein levels and altering lipid metabolism and AKT pathway activity; RPL7A knockdown inhibits LUAD cell migration, invasion, and proliferation.","method":"RPL7A knockdown, mRNA stability assays, RNA immunoprecipitation, fluorescence in situ hybridization, dual luciferase reporter assay, in vitro and in vivo functional assays","journal":"Cellular & molecular biology letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal mechanistic methods (RIP, mRNA stability, FISH, reporter assays) in a single study, single lab","pmids":["41372808"],"is_preprint":false}],"current_model":"RPL7A encodes a basic protein component of the 60S large ribosomal subunit with nucleolar localization mediated by cooperative action of three distinct domains (aa 23–51, 52–100, 101–220); it contains two RNA-binding domains (aa 52–100 and 101–161) that interact with G-rich RNA, and its introns encode snoRNAs (U24, U36 variants) that guide rRNA methylation; beyond its structural ribosomal role, RPL7A interacts with FKBP25 in the nucleus under ischemic stress, and in cancer contexts promotes tumor progression partly through a circRANBP17–UPF1 axis that destabilizes SIRT6 mRNA."},"narrative":{"mechanistic_narrative":"RPL7A (originally Surf-3/L7a) is a basic protein component of the 60S large ribosomal subunit and is essential for ribosome function and viability [PMID:2648130, PMID:2046660]. It is a nucleolar protein whose targeting is encoded by three distinct domains, each carrying an NLS, with nucleolar accumulation requiring a core domain (aa 52–100) acting cooperatively with an additional basic stretch — a feature consistent with protein–protein or protein–nucleic acid contacts [PMID:9030593]. RPL7A binds RNA through two domains, RNAB1 (aa 52–100) and RNAB2 (aa 101–161), the latter mapped in complex with a G-rich poly(G) oligonucleotide; RNAB1 lacks recognizable nucleic-acid-binding motifs [PMID:15361074]. Its introns host box C/D antisense snoRNAs (U24 and three U36 variants) that guide site-specific 2'-O-ribose methylation of rRNA, coupling RPL7A expression to ribosome biogenesis [PMID:9703018]. Beyond the core ribosomal role, RPL7A is engaged in stress and disease contexts: under ischemic stress it is bound in the nucleus by FKBP25 [PMID:29969783], and in lung adenocarcinoma it promotes proliferation, migration, and invasion by regulating a circRANBP17–UPF1 complex that destabilizes SIRT6 mRNA, lowering SIRT6 and altering lipid metabolism and AKT activity [PMID:41372808].","teleology":[{"year":1990,"claim":"Establishing that the Surf-3/trk-2h gene product is the 60S ribosomal protein L7a fixed the molecular identity and nucleolar location of an otherwise enigmatic gene product.","evidence":"Anti-peptide immunoblotting of 2D-resolved ribosomal proteins, in vitro translation, and immunofluorescence in mammalian cells","pmids":["2648130","2403926"],"confidence":"High","gaps":["Did not define the protein's position or function within the assembled 60S subunit","No structural model of L7a–rRNA contacts"]},{"year":1991,"claim":"Yeast genetics established that L7a (homolog L4) is essential, tying the protein directly to functional ribosome production.","evidence":"Double gene disruption (lethal) and single-paralog disruption (growth defect) in S. cerevisiae with identity confirmed by 2D gel and direct sequencing","pmids":["2046660"],"confidence":"High","gaps":["Did not resolve which step of ribosome assembly or translation requires the protein","Mammalian essentiality inferred only by homology"]},{"year":1992,"claim":"Mapping conserved Box A/Box B promoter elements and a TATA-less pyrimidine-rich start explained how RPL7A transcription is controlled like other ribosomal protein genes.","evidence":"EMSA with nuclear extracts plus promoter-deletion reporter assays in mammalian and avian systems","pmids":["1630908","8482538"],"confidence":"Medium","gaps":["Identity of the bound nuclear factors not determined","No link to coordinate ribosomal protein gene regulation in vivo"]},{"year":1997,"claim":"Dissecting nuclear/nucleolar targeting signals showed that localization is encoded by three cooperative domains rather than a single NLS, implying that nucleolar retention depends on macromolecular interactions.","evidence":"Deletion mutagenesis of L7a–beta-galactosidase fusions with immunofluorescence in HeLa cells","pmids":["9030593"],"confidence":"High","gaps":["The cooperating nucleolar binding partners (RNA or protein) were not identified","Did not separate import from retention mechanisms"]},{"year":1998,"claim":"Discovery of intron-encoded box C/D snoRNAs (U24, U36 variants) revealed that the RPL7A locus directly contributes guides for rRNA 2'-O-methylation, embedding it in ribosome biogenesis beyond its protein product.","evidence":"Comparative genomics and Northern blotting across human, chicken, and mouse introns","pmids":["9703018"],"confidence":"Medium","gaps":["Functional consequence of individual U36 variants on specific rRNA sites not tested","Did not establish coupling between host-gene splicing and snoRNA output"]},{"year":2005,"claim":"Mapping two RNA-binding domains and a poly(G) interaction interface defined the biochemical basis of RPL7A's RNA contacts, including a domain lacking canonical motifs.","evidence":"In vitro RNA-binding with recombinant domains, limited proteolysis, cross-linking, and mass spectrometry using a 30-mer poly(G)","pmids":["15361074"],"confidence":"High","gaps":["The physiological RNA target within rRNA was not identified","RNAB1 binding mode remains structurally undefined"]},{"year":2017,"claim":"Paralog-swap experiments in yeast distinguished dosage from isoform identity, showing most Rpl7 phenotypes track protein/ribosome level while Ty1 cDNA accumulation also depends on isoform or intron-encoded snoRNA.","evidence":"Chimeric allele exchange with retrotransposition, mRNA localization, and growth assays in S. cerevisiae","pmids":["28007835"],"confidence":"Medium","gaps":["Did not separate the isoform contribution from the intron-encoded snoRNA contribution","Relevance of Ty1/ASH1 phenotypes to mammalian RPL7A unknown"]},{"year":2018,"claim":"Identifying a stress-induced FKBP25–L7a interaction in the nucleus extended RPL7A's relevance beyond constitutive translation into endothelial ischemic-stress responses.","evidence":"Reciprocal co-immunoprecipitation and FRET in endothelial cells under oxygen-glucose deprivation, with FKBP25 overexpression protection","pmids":["29969783"],"confidence":"Medium","gaps":["Functional consequence of the interaction for L7a or ribosome activity not defined","Single lab; mechanism of the protective effect unresolved"]},{"year":2025,"claim":"A circRANBP17–UPF1–SIRT6 axis defined a non-canonical, tumor-promoting role for RPL7A in lung adenocarcinoma, linking it to lipid metabolism and AKT signaling.","evidence":"RPL7A knockdown, RNA immunoprecipitation, mRNA stability and dual-luciferase assays, FISH, and in vitro/in vivo functional assays in LUAD models","pmids":["41372808"],"confidence":"Medium","gaps":["How RPL7A controls circRANBP17 levels mechanistically is not resolved","Whether this role is separable from its ribosomal function is unknown"]},{"year":null,"claim":"It remains unresolved how RPL7A's structural ribosomal function is integrated with its extra-ribosomal activities (FKBP25 stress complex, circRANBP17/SIRT6 oncogenic axis) and whether these reflect free versus ribosome-bound pools.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structure of full-length RPL7A in the assembled 60S subunit","No determination of which RPL7A pool mediates non-ribosomal functions","No mechanistic link between RNA-binding domains and the circRNA/mRNA-regulatory roles"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,2]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[6]}],"localization":[{"term_id":"GO:0005840","term_label":"ribosome","supporting_discovery_ids":[0,2]},{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[1,5]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[5,8]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,2]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[10]}],"complexes":["60S large ribosomal subunit"],"partners":["FKBP25","UPF1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P62424","full_name":"Large ribosomal subunit protein eL8","aliases":["60S ribosomal protein L7a","PLA-X polypeptide","Surfeit locus protein 3"],"length_aa":266,"mass_kda":30.0,"function":"Component of the large ribosomal subunit (PubMed:23636399, PubMed:32669547). The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell (PubMed:23636399, PubMed:32669547)","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/P62424/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RPL7A","classification":"Common Essential","n_dependent_lines":1208,"n_total_lines":1208,"dependency_fraction":1.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CAPRIN1","stoichiometry":10.0},{"gene":"DRG1","stoichiometry":10.0},{"gene":"EIF2S3","stoichiometry":10.0},{"gene":"ENY2","stoichiometry":10.0},{"gene":"RACK1","stoichiometry":10.0},{"gene":"RBM8A","stoichiometry":10.0},{"gene":"RPL11","stoichiometry":10.0},{"gene":"RPL4","stoichiometry":10.0},{"gene":"RPL5","stoichiometry":10.0},{"gene":"RPS16","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/search/RPL7A","total_profiled":1310},"omim":[{"mim_id":"610225","title":"RIBOSOMAL PROTEIN S19 BINDING PROTEIN 1; RPS19BP1","url":"https://www.omim.org/entry/610225"},{"mim_id":"185641","title":"MEDIATOR COMPLEX SUBUNIT 22; MED22","url":"https://www.omim.org/entry/185641"},{"mim_id":"185640","title":"RIBOSOMAL PROTEIN L7a; RPL7A","url":"https://www.omim.org/entry/185640"},{"mim_id":"180466","title":"RIBOSOMAL PROTEIN L19; RPL19","url":"https://www.omim.org/entry/180466"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoli","reliability":"Approved"},{"location":"Vesicles","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RPL7A"},"hgnc":{"alias_symbol":["SURF3","TRUP","L7A","eL8"],"prev_symbol":[]},"alphafold":{"accession":"P62424","domains":[{"cath_id":"3.30.1330.30","chopping":"77-108_132-236","consensus_level":"high","plddt":96.0188,"start":77,"end":236}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P62424","model_url":"https://alphafold.ebi.ac.uk/files/AF-P62424-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P62424-F1-predicted_aligned_error_v6.png","plddt_mean":90.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RPL7A","jax_strain_url":"https://www.jax.org/strain/search?query=RPL7A"},"sequence":{"accession":"P62424","fasta_url":"https://rest.uniprot.org/uniprotkb/P62424.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P62424/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P62424"}},"corpus_meta":[{"pmid":"9724090","id":"PMC_9724090","title":"Several genes encoding ribosomal proteins are over-expressed in prostate-cancer cell lines: confirmation of L7a and L37 over-expression in prostate-cancer tissue samples.","date":"1998","source":"International journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/9724090","citation_count":94,"is_preprint":false},{"pmid":"2403926","id":"PMC_2403926","title":"Oncogenic activation of the human trk proto-oncogene by recombination with the ribosomal large subunit protein L7a.","date":"1990","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/2403926","citation_count":80,"is_preprint":false},{"pmid":"2648130","id":"PMC_2648130","title":"Ribosomal protein L7a is encoded by a gene (Surf-3) within the tightly clustered mouse surfeit locus.","date":"1989","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/2648130","citation_count":48,"is_preprint":false},{"pmid":"9030593","id":"PMC_9030593","title":"Different domains cooperate to target the human ribosomal L7a protein to the nucleus and to the nucleoli.","date":"1997","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/9030593","citation_count":48,"is_preprint":false},{"pmid":"16109161","id":"PMC_16109161","title":"An ancient spliceosomal intron in the ribosomal protein L7a gene (Rpl7a) of Giardia lamblia.","date":"2005","source":"BMC evolutionary biology","url":"https://pubmed.ncbi.nlm.nih.gov/16109161","citation_count":45,"is_preprint":false},{"pmid":"1756182","id":"PMC_1756182","title":"The organization and expression of the human L7a ribosomal protein gene.","date":"1991","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/1756182","citation_count":35,"is_preprint":false},{"pmid":"1630908","id":"PMC_1630908","title":"Functional elements of the ribosomal protein L7a (rpL7a) gene promoter region and their conservation between mammals and birds.","date":"1992","source":"Nucleic acids 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Section F, Structural biology and crystallization communications","url":"https://pubmed.ncbi.nlm.nih.gov/21505254","citation_count":2,"is_preprint":false},{"pmid":"9565672","id":"PMC_9565672","title":"The gene for ribosomal protein L7a-1 in Schizosaccharomyces pombe contains an intron after the initiation codon.","date":"1998","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/9565672","citation_count":2,"is_preprint":false},{"pmid":"41372808","id":"PMC_41372808","title":"Ribosomal protein RPL7A modulates lung adenocarcinoma progression via circRANBP17-UPF1-mediated SIRT6 degradation.","date":"2025","source":"Cellular & molecular biology letters","url":"https://pubmed.ncbi.nlm.nih.gov/41372808","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13511,"output_tokens":3113,"usd":0.043614,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10572,"output_tokens":3185,"usd":0.066242,"stage2_stop_reason":"end_turn"},"total_usd":0.109856,"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\": 1989,\n      \"finding\": \"The Surf-3 gene product (RPL7A) was identified as a 32-kDa ribosomal protein located in the 60S ribosomal subunit, established by anti-peptide serum immunofluorescence, immunoblotting of mouse cell components, in vitro translation of Surf-3 cDNA hybrid-selected mRNA, 2D-gel analysis, and homology with rat ribosomal peptide sequence.\",\n      \"method\": \"Anti-peptide serum immunofluorescence, immunoblotting, in vitro translation, 2D-gel electrophoresis, biochemical fractionation\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (immunoblot, in vitro translation, 2D gel, fractionation) in a single study establishing 60S subunit localization\",\n      \"pmids\": [\"2648130\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1990,\n      \"finding\": \"RPL7A (the 30 kDa protein encoded by the trk-2h N-terminal activating sequence) was identified as ribosomal large subunit protein L7a by Western immunoblotting of 2D-electrophoretically resolved ribosomal proteins; the protein shows intense nucleolar staining by immunofluorescence and has high basic amino acid content.\",\n      \"method\": \"Western blotting of 2D-resolved ribosomal proteins, immunofluorescence with antipeptide antibodies\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — two orthogonal methods (2D Western blot and immunofluorescence) confirming identity and nucleolar localization\",\n      \"pmids\": [\"2403926\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1991,\n      \"finding\": \"The yeast (S. cerevisiae) L4 gene is the homolog of mammalian RPL7A (Surf-3/L7a); disruption of both L4 paralogs is lethal likely due to inability to produce functional ribosomes, while disruption of L4-1 alone results in very small colonies, establishing an essential role for this protein in ribosome function.\",\n      \"method\": \"Gene disruption (knockout), colony growth assay, in vitro translation of hybrid-selected mRNA, 2D gel analysis, direct amino acid sequencing\",\n      \"journal\": \"Molecular & general genetics : MGG\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — genetic epistasis via double gene disruption (lethal), protein identity confirmed by 2D gel and direct sequencing\",\n      \"pmids\": [\"2046660\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"The minimal promoter element required for human RPL7A transcription was identified as 130 bp of the 5'-flanking region; the gene lacks a canonical TATA sequence and has a C as the major transcriptional start point in a pyrimidine-rich region, features shared with other mammalian ribosomal protein genes.\",\n      \"method\": \"Promoter deletion analysis, transcription reporter assay\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional promoter deletion in vivo, single lab study\",\n      \"pmids\": [\"8482538\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1992,\n      \"finding\": \"Two conserved promoter elements (Box A: nts -56 to -39; Box B: nts -25 to -4) in the rpL7a 5' upstream region bind distinct nuclear factors from mouse nuclear extracts, and both elements are functionally conserved between mammals and birds; constructs containing only 56 bp of upstream DNA plus the first 25 bp exon support efficient transcription without requiring first intron sequences.\",\n      \"method\": \"Electrophoretic mobility shift assay (EMSA), competition assay with homologous sequences, in vivo transcription reporter assay\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — EMSA plus in vivo reporter, single lab, two orthogonal methods\",\n      \"pmids\": [\"1630908\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"Three distinct domains of human RPL7A mediate nuclear targeting: domain I (aa 23–51), domain II (aa 52–100), and domain III (aa 101–220), each containing at least one NLS. Domain II is necessary but not sufficient for nucleolar targeting; nucleolar accumulation requires domain II plus an additional basic domain (NLS or basic stretch), indicating cooperative protein–protein or protein–nucleic acid interactions.\",\n      \"method\": \"Transient expression of L7a–beta-galactosidase fusion proteins with deletion mutants in HeLa cells, indirect immunofluorescence\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — systematic deletion mutagenesis of multiple domains with reporter localization in live cells, multiple constructs tested\",\n      \"pmids\": [\"9030593\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Human RPL7A contains two RNA-binding domains: RNAB1 (aa 52–100) and RNAB2 (aa 101–161). RNAB1 lacks known nucleic-acid-binding motifs and may represent a novel class. The topology of the L7a–RNA complex was mapped using limited proteolysis, cross-linking, and mass spectrometry of the recombinant aa 101–161 domain with a 30-mer poly(G) oligonucleotide. L7a interacts in vitro with a presumably G-rich RNA structure.\",\n      \"method\": \"In vitro RNA-binding assay, deletion mutagenesis, limited proteolysis, chemical cross-linking, mass spectrometry\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with mutagenesis, limited proteolysis and MS to map binding interface, single lab\",\n      \"pmids\": [\"15361074\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"The N-terminal domain of human RPL7A was crystallized and X-ray diffraction data collected to 3.5 Å resolution (tetragonal space group P4(1)22 or P4(3)22; unit-cell a = b = 92.28 Å, c = 236.59 Å), providing preliminary structural characterization. The paper also notes that RPL7A interacts with thyroid hormone receptor (THR) and retinoic acid receptor (RAR) to inhibit their activities.\",\n      \"method\": \"X-ray crystallography (preliminary), recombinant protein expression in E. coli\",\n      \"journal\": \"Acta crystallographica. Section F, Structural biology and crystallization communications\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 1 (method) / Weak — crystallization only reported as preliminary; functional claims about THR/RAR interaction are stated but no supporting experiment described in the abstract\",\n      \"pmids\": [\"21505254\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Under ischemic stress (oxygen-glucose deprivation or peroxynitrite treatment), FKBP25 translocates to the nucleus in endothelial cells and interacts with 60S ribosomal protein L7a, as demonstrated by co-immunoprecipitation and FRET; overexpression of FKBP25 protects endothelial cells against OGD injury.\",\n      \"method\": \"Co-immunoprecipitation, fluorescence resonance energy transfer (FRET), Western blot, immunofluorescence, overexpression\",\n      \"journal\": \"Cellular physiology and biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP confirmed by FRET (two orthogonal binding assays), single lab\",\n      \"pmids\": [\"29969783\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"In S. cerevisiae, paralog-specific phenotypes of RPL7A vs RPL7B (tunicamycin sensitivity, ASH1 mRNA localization, Ty1 retrotransposon mobility) are driven primarily by differences in protein/ribosome levels rather than isoform identity; however, Ty1 cDNA accumulation is influenced by both level and isoform (or intron-encoded snoRNA) expressed. Depletion of Rpl7 strongly affects Ty1 RNA localization but minimally affects Ty1 Gag protein synthesis.\",\n      \"method\": \"Paralog swap (chimeric alleles), quantitative phenotypic assays (tunicamycin growth, mRNA localization, retrotransposition assay), Western blot, Northern blot\",\n      \"journal\": \"G3 (Bethesda, Md.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — systematic allele exchange with multiple functional readouts, single lab\",\n      \"pmids\": [\"28007835\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"U24 and U36 snoRNAs are encoded within introns of the rpL7a gene in human, chicken, and mouse; these box C/D antisense snoRNAs guide site-specific ribose methylation of rRNA. In mammals, three U36 variants reside in introns 4, 5, and 6 of rpL7a, with unique structural features distinct from non-mammalian variants.\",\n      \"method\": \"Sequence analysis, comparative genomics, Northern blotting (snoRNA identification within introns)\",\n      \"journal\": \"DNA and cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — snoRNA identification within introns by sequence and Northern blot, replicated across species\",\n      \"pmids\": [\"9703018\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RPL7A promotes lung adenocarcinoma progression by regulating circRANBP17, which forms a complex with UPF1 to destabilize SIRT6 mRNA, thereby reducing SIRT6 protein levels and altering lipid metabolism and AKT pathway activity; RPL7A knockdown inhibits LUAD cell migration, invasion, and proliferation.\",\n      \"method\": \"RPL7A knockdown, mRNA stability assays, RNA immunoprecipitation, fluorescence in situ hybridization, dual luciferase reporter assay, in vitro and in vivo functional assays\",\n      \"journal\": \"Cellular & molecular biology letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal mechanistic methods (RIP, mRNA stability, FISH, reporter assays) in a single study, single lab\",\n      \"pmids\": [\"41372808\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RPL7A encodes a basic protein component of the 60S large ribosomal subunit with nucleolar localization mediated by cooperative action of three distinct domains (aa 23–51, 52–100, 101–220); it contains two RNA-binding domains (aa 52–100 and 101–161) that interact with G-rich RNA, and its introns encode snoRNAs (U24, U36 variants) that guide rRNA methylation; beyond its structural ribosomal role, RPL7A interacts with FKBP25 in the nucleus under ischemic stress, and in cancer contexts promotes tumor progression partly through a circRANBP17–UPF1 axis that destabilizes SIRT6 mRNA.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RPL7A (originally Surf-3/L7a) is a basic protein component of the 60S large ribosomal subunit and is essential for ribosome function and viability [#0, #2]. It is a nucleolar protein whose targeting is encoded by three distinct domains, each carrying an NLS, with nucleolar accumulation requiring a core domain (aa 52–100) acting cooperatively with an additional basic stretch — a feature consistent with protein–protein or protein–nucleic acid contacts [#5]. RPL7A binds RNA through two domains, RNAB1 (aa 52–100) and RNAB2 (aa 101–161), the latter mapped in complex with a G-rich poly(G) oligonucleotide; RNAB1 lacks recognizable nucleic-acid-binding motifs [#6]. Its introns host box C/D antisense snoRNAs (U24 and three U36 variants) that guide site-specific 2'-O-ribose methylation of rRNA, coupling RPL7A expression to ribosome biogenesis [#10]. Beyond the core ribosomal role, RPL7A is engaged in stress and disease contexts: under ischemic stress it is bound in the nucleus by FKBP25 [#8], and in lung adenocarcinoma it promotes proliferation, migration, and invasion by regulating a circRANBP17–UPF1 complex that destabilizes SIRT6 mRNA, lowering SIRT6 and altering lipid metabolism and AKT activity [#11].\",\n  \"teleology\": [\n    {\n      \"year\": 1990,\n      \"claim\": \"Establishing that the Surf-3/trk-2h gene product is the 60S ribosomal protein L7a fixed the molecular identity and nucleolar location of an otherwise enigmatic gene product.\",\n      \"evidence\": \"Anti-peptide immunoblotting of 2D-resolved ribosomal proteins, in vitro translation, and immunofluorescence in mammalian cells\",\n      \"pmids\": [\"2648130\", \"2403926\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the protein's position or function within the assembled 60S subunit\", \"No structural model of L7a–rRNA contacts\"]\n    },\n    {\n      \"year\": 1991,\n      \"claim\": \"Yeast genetics established that L7a (homolog L4) is essential, tying the protein directly to functional ribosome production.\",\n      \"evidence\": \"Double gene disruption (lethal) and single-paralog disruption (growth defect) in S. cerevisiae with identity confirmed by 2D gel and direct sequencing\",\n      \"pmids\": [\"2046660\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve which step of ribosome assembly or translation requires the protein\", \"Mammalian essentiality inferred only by homology\"]\n    },\n    {\n      \"year\": 1992,\n      \"claim\": \"Mapping conserved Box A/Box B promoter elements and a TATA-less pyrimidine-rich start explained how RPL7A transcription is controlled like other ribosomal protein genes.\",\n      \"evidence\": \"EMSA with nuclear extracts plus promoter-deletion reporter assays in mammalian and avian systems\",\n      \"pmids\": [\"1630908\", \"8482538\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Identity of the bound nuclear factors not determined\", \"No link to coordinate ribosomal protein gene regulation in vivo\"]\n    },\n    {\n      \"year\": 1997,\n      \"claim\": \"Dissecting nuclear/nucleolar targeting signals showed that localization is encoded by three cooperative domains rather than a single NLS, implying that nucleolar retention depends on macromolecular interactions.\",\n      \"evidence\": \"Deletion mutagenesis of L7a–beta-galactosidase fusions with immunofluorescence in HeLa cells\",\n      \"pmids\": [\"9030593\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The cooperating nucleolar binding partners (RNA or protein) were not identified\", \"Did not separate import from retention mechanisms\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Discovery of intron-encoded box C/D snoRNAs (U24, U36 variants) revealed that the RPL7A locus directly contributes guides for rRNA 2'-O-methylation, embedding it in ribosome biogenesis beyond its protein product.\",\n      \"evidence\": \"Comparative genomics and Northern blotting across human, chicken, and mouse introns\",\n      \"pmids\": [\"9703018\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of individual U36 variants on specific rRNA sites not tested\", \"Did not establish coupling between host-gene splicing and snoRNA output\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Mapping two RNA-binding domains and a poly(G) interaction interface defined the biochemical basis of RPL7A's RNA contacts, including a domain lacking canonical motifs.\",\n      \"evidence\": \"In vitro RNA-binding with recombinant domains, limited proteolysis, cross-linking, and mass spectrometry using a 30-mer poly(G)\",\n      \"pmids\": [\"15361074\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The physiological RNA target within rRNA was not identified\", \"RNAB1 binding mode remains structurally undefined\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Paralog-swap experiments in yeast distinguished dosage from isoform identity, showing most Rpl7 phenotypes track protein/ribosome level while Ty1 cDNA accumulation also depends on isoform or intron-encoded snoRNA.\",\n      \"evidence\": \"Chimeric allele exchange with retrotransposition, mRNA localization, and growth assays in S. cerevisiae\",\n      \"pmids\": [\"28007835\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not separate the isoform contribution from the intron-encoded snoRNA contribution\", \"Relevance of Ty1/ASH1 phenotypes to mammalian RPL7A unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Identifying a stress-induced FKBP25–L7a interaction in the nucleus extended RPL7A's relevance beyond constitutive translation into endothelial ischemic-stress responses.\",\n      \"evidence\": \"Reciprocal co-immunoprecipitation and FRET in endothelial cells under oxygen-glucose deprivation, with FKBP25 overexpression protection\",\n      \"pmids\": [\"29969783\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of the interaction for L7a or ribosome activity not defined\", \"Single lab; mechanism of the protective effect unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"A circRANBP17–UPF1–SIRT6 axis defined a non-canonical, tumor-promoting role for RPL7A in lung adenocarcinoma, linking it to lipid metabolism and AKT signaling.\",\n      \"evidence\": \"RPL7A knockdown, RNA immunoprecipitation, mRNA stability and dual-luciferase assays, FISH, and in vitro/in vivo functional assays in LUAD models\",\n      \"pmids\": [\"41372808\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How RPL7A controls circRANBP17 levels mechanistically is not resolved\", \"Whether this role is separable from its ribosomal function is unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how RPL7A's structural ribosomal function is integrated with its extra-ribosomal activities (FKBP25 stress complex, circRANBP17/SIRT6 oncogenic axis) and whether these reflect free versus ribosome-bound pools.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structure of full-length RPL7A in the assembled 60S subunit\", \"No determination of which RPL7A pool mediates non-ribosomal functions\", \"No mechanistic link between RNA-binding domains and the circRNA/mRNA-regulatory roles\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [1, 5]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [5, 8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [10]}\n    ],\n    \"complexes\": [\"60S large ribosomal subunit\"],\n    \"partners\": [\"FKBP25\", \"UPF1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}