{"gene":"TRA2B","run_date":"2026-04-28T21:42:59","timeline":{"discoveries":[{"year":2000,"finding":"Htra2-beta1 (TRA2B) promotes inclusion of SMN exon 7 by binding an AG-rich exonic splicing enhancer in SMN exon 7, stimulating full-length SMN2 expression in human and mouse cells carrying an SMN2 minigene.","method":"Minigene splicing assay in human/mouse cells, RNA binding assay, transient expression","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 — direct RNA binding and functional splicing assay replicated across cell types; foundational paper with 274 citations","pmids":["10931943"],"is_preprint":false},{"year":1997,"finding":"TRA2B (htra2-beta1) is a nuclear SR-like protein that colocalizes with SC35 in nuclear speckles and interacts with multiple SR proteins; a second isoform, htra2-beta2, generated by alternative splicing lacks the SR domain.","method":"Yeast two-hybrid screen using SC35 as bait, immunofluorescence colocalization, subcellular fractionation","journal":"DNA and cell biology","confidence":"Medium","confidence_rationale":"Tier 2–3 — yeast two-hybrid interaction plus direct localization; single lab but multiple methods","pmids":["9212162"],"is_preprint":false},{"year":1998,"finding":"The TRA2B isoform htra2-beta3 lacks the first SR domain, is expressed predominantly in brain, liver, testis and kidney, localizes to the nucleus, and interacts with a subset of SR proteins, paralleling a variant found in the Drosophila male germline.","method":"RT-PCR, yeast two-hybrid, immunofluorescence, radiation hybrid mapping","journal":"Genomics","confidence":"Medium","confidence_rationale":"Tier 2–3 — localization and interaction confirmed by multiple methods in single study","pmids":["9790768"],"is_preprint":false},{"year":2002,"finding":"SRp30c stimulates SMN exon 7 inclusion through the same AG-rich enhancer as TRA2B, but does so indirectly via a direct protein–protein interaction with TRA2B; in the absence of the TRA2B binding site on the enhancer, SRp30c fails to associate with SMN exon 7.","method":"Minigene splicing assay, co-immunoprecipitation, RNA pull-down","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 — reciprocal co-IP plus functional minigene assay; replicated across studies (121 citations)","pmids":["11875052"],"is_preprint":false},{"year":2009,"finding":"Oxidative stress (arsenite) induces translocation of TRA2B from the nucleus to the cytoplasm associated with enhanced phosphorylation, and TRA2B regulates alternative splicing of CD44 (combinatorial inclusion of variable exons) and controls cell growth.","method":"Immunofluorescence, Western blot (phosphorylation), siRNA knockdown, overexpression, minigene/RT-PCR, cell growth assay","journal":"American journal of physiology. Cell physiology","confidence":"Medium","confidence_rationale":"Tier 2–3 — localization change with functional consequence shown by KD and OE with multiple orthogonal methods","pmids":["19439532"],"is_preprint":false},{"year":2010,"finding":"Homozygous deletion of Sfrs10 (TRA2B) in mice causes early embryonic lethality around E7.5, demonstrating an essential role during mouse embryogenesis; motor-neuron-specific deletion does not produce an SMA phenotype, and Sfrs10 deletion in MEFs increases SmnΔ7 levels modestly but has no impact on full-length Smn splicing.","method":"Conditional knockout (Cre/loxP), embryo phenotyping, RT-PCR, MEF-derived cells with recombinant Cre","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 — in vivo genetic loss-of-function with defined lethal phenotype; multiple conditional alleles tested","pmids":["20190275"],"is_preprint":false},{"year":2011,"finding":"SFRS10 (TRA2B) regulates alternative splicing of LPIN1 pre-mRNA; reduced SFRS10 favors the lipogenic LPIN1β isoform, and LPIN1β-specific siRNA abolishes the lipogenic effects of decreased SFRS10, placing TRA2B upstream of LPIN1β in hepatic lipogenesis.","method":"siRNA knockdown, Sfrs10 heterozygous mice, hepatic gene expression analysis, VLDL secretion assay, epistasis by rescue experiment","journal":"Cell metabolism","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis (rescue), in vivo mouse model, and cell-based assays across multiple orthogonal methods; 135 citations","pmids":["21803291"],"is_preprint":false},{"year":2012,"finding":"Digitoxin depletes TRA2B (and SRSF3) from cells; re-expression of TRA2B after digitoxin treatment restores normal splicing of TRA2B-target exons, demonstrating that TRA2B depletion directly mediates the digitoxin-induced alternative splicing changes.","method":"Transcriptome-wide splicing analysis (RNA-seq), rescue by re-expression, motif enrichment analysis","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 2 — transcriptome-wide analysis plus rescue experiment establishing direct causality","pmids":["22456266"],"is_preprint":false},{"year":2014,"finding":"TRA2B is required for survival of neural progenitor cells; cortex-specific Tra2b knockout mice display apoptosis of neural progenitor cells and disorganization of the cortical plate.","method":"Cortex-specific conditional knockout (Cre/loxP), immunohistochemistry, TUNEL apoptosis assay","journal":"The Journal of comparative neurology","confidence":"High","confidence_rationale":"Tier 2 — in vivo genetic loss-of-function with defined cellular phenotype (apoptosis of progenitors)","pmids":["23818142"],"is_preprint":false},{"year":2014,"finding":"Neuronal-specific deletion of Tra2b causes massive apoptosis in ventricular layers of the cortex and perinatal lethality; Tra2b loss leads to increased p21 (CDKN1A) expression, which is functionally linked to neuronal precursor cell death. In vivo exon array analysis identifies Tubulinδ1 and Shugoshin-like2 as splicing targets of Tra2b.","method":"Nestin-Cre conditional knockout, exon arrays, immunohistochemistry, TUNEL, siRNA in NSC34 cells, Western blot","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 — in vivo genetic model with defined molecular mechanism (p21 upregulation) and transcriptome-wide target identification","pmids":["24586484"],"is_preprint":false},{"year":2014,"finding":"TRA2B promotes inclusion of PKCδ exon 9 in the PKCδI splice variant during 3T3L1 preadipocyte cell cycle; mutagenesis of TRA2B binding sites on exon 9 and RNA-immunoprecipitation confirmed direct binding is required for this splicing event, and PKCδI is required for mitotic clonal expansion of preadipocytes.","method":"Minigene splicing assay, mutagenesis, RNA-immunoprecipitation, siRNA knockdown, cell proliferation assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 — RNA-IP plus mutagenesis of binding site plus functional minigene; direct binding-function link established","pmids":["25261467"],"is_preprint":false},{"year":2015,"finding":"Tra2b knockdown in Xenopus causes defective somitogenesis and other developmental defects; RNA-seq identified 142 Tra2b-dependent splice changes (mostly intron retention and exon skipping). A novel Wnt11b isoform retaining the last intron (Wnt11b-short) acts as a dominant-negative ligand and its retention recapitulates the failure to form somites, placing Tra2b upstream of Wnt11b isoform balance in somitogenesis.","method":"Morpholino knockdown, RNA-seq, minigene intron retention induction, dominant-negative rescue experiment in Xenopus","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 — in vivo knockdown with RNA-seq, functional epistasis by recapitulating specific splice defect","pmids":["25620705"],"is_preprint":false},{"year":2016,"finding":"A TRA2B-DNAH5 gene fusion in lung squamous cell carcinoma promotes malignant progression through a SIRT6-ERK1/2-MMP1 signaling axis; ERK1/2 inhibition with selumetinib efficiently inhibits growth of lung SCC expressing this fusion.","method":"Exon array analysis, molecular cloning of fusion, functional studies (pathway analysis, ERK1/2 inhibition), patient sample analysis","journal":"Cell research","confidence":"Medium","confidence_rationale":"Tier 2–3 — mechanistic pathway placement via functional studies but fusion-specific context; single lab","pmids":["27670699"],"is_preprint":false},{"year":2017,"finding":"ILDR1 and ILDR2 (angulin proteins) physically bind to TRA2B (as well as TRA2A and SRSF1) and translocate to the nucleus when TRA2B is present; knockdown of ILDR1/ILDR2 alters alternative splicing of TUBD1 and IQCB1, targets regulated by TRA2B.","method":"Co-immunoprecipitation, nuclear translocation assay, siRNA knockdown, minigene splicing assay","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 3 — single Co-IP and functional follow-up; interaction with functional consequence demonstrated","pmids":["28785060"],"is_preprint":false},{"year":2019,"finding":"hnRNPA1 interacts with a G-quadruplex (G4) structure in the TRA2B promoter and stimulates TRA2B transcription; G4 formation suppresses TRA2B transcription, whereas hnRNPA1 binding to G4 relieves this repression. hnRNPU also positively regulates TRA2B promoter activity but does not interact with G4.","method":"Circular dichroism, EMSA, ChIP, minigene assay, siRNA knockdown, promoter reporter assay","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 1–2 — direct G4 binding confirmed by CD and EMSA, ChIP confirms in-cell interaction, multiple orthogonal methods in single study","pmids":["31311954"],"is_preprint":false},{"year":2022,"finding":"Germline loss-of-function variants clustered in the 5′ region of TRA2B (upstream of an alternative translation start site) decrease canonical Tra2β-1 isoform expression while increasing the shorter Tra2β-3 isoform (lacking the N-terminal RS1 domain); increased Tra2β-3 interferes with CHEK1 exon 3 inclusion, revealing a dominant-negative mechanism underlying the associated neurodevelopmental syndrome.","method":"RNA sequencing of patient cells, Western blot of isoforms, HEK-293 transfection with Tra2β1-GFP, Tra2β3-GFP, and CHEK1 exon 3 minigene","journal":"Genetics in medicine : official journal of the American College of Medical Genetics","confidence":"High","confidence_rationale":"Tier 2 — patient-derived RNA-seq plus functional cell-based isoform experiments establishing dominant-negative mechanism","pmids":["36549593"],"is_preprint":false},{"year":2023,"finding":"Two TRA2B isoforms play distinct roles in myogenic differentiation: they differentially regulate alternative splicing of TGFBR2, thereby triggering canonical TGF-β signalling cascades differently.","method":"Iso-seq, single-cell RNA-seq, isoform-specific functional analysis in myogenesis model","journal":"Cell proliferation","confidence":"Medium","confidence_rationale":"Tier 2–3 — isoform-level transcriptomic analysis with functional splicing outcome; single study","pmids":["37705195"],"is_preprint":false},{"year":2025,"finding":"An ultra-conserved poison exon (PE) in the Tra2b gene controls Tra2β protein concentration via nonsense-mediated decay; disruption of this PE in mice causes azoospermia due to catastrophic apoptotic cell death during meiotic prophase, associated with elevated Tra2β protein levels driving aberrant hyper-responsive splicing patterns. Mitotically active germ cells are spared despite requiring Tra2b function, indicating the PE prevents toxic Tra2β accumulation incompatible with meiotic prophase.","method":"Mouse genetics (PE deletion by CRISPR/homologous recombination), histology, RNA-seq, protein expression analysis","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 — in vivo mouse genetic model with defined molecular mechanism (NMD-based autoregulation) and clear phenotypic readout","pmids":["39748121"],"is_preprint":false},{"year":2026,"finding":"TRA2B promotes synthesis of the constitutively active androgen receptor splice variant AR-V7 in prostate cancer cells at the expense of full-length AR isoforms; TRA2B and its ortholog TRA2A were identified as selective protein interactors of AR-V7 mRNA, and attenuation of TRA2-mediated splicing diminishes prostate cancer cell growth.","method":"RNA-targeting CasRx approach for mRNA interactor identification, siRNA knockdown, cell growth assay, correlation with CRPC transcriptomic data","journal":"The Journal of clinical investigation","confidence":"Medium","confidence_rationale":"Tier 2–3 — CasRx-based interactor identification plus functional KD with proliferation readout; single study","pmids":["41919500"],"is_preprint":false}],"current_model":"TRA2B (SFRS10/Htra2-β1) is an SR-like nuclear RNA-binding protein that promotes exon inclusion by binding AG/GAA-rich exonic splicing enhancers and recruiting additional SR proteins (e.g., SRp30c); its cellular concentration is homeostatically controlled by a poison-exon/NMD autoregulatory loop, and it is essential for embryogenesis, neural progenitor survival, male meiosis, and lipid metabolism by governing tissue-specific alternative splicing programs—including SMN exon 7, LPIN1, PKCδ, CD44, TGFBR2, CHEK1, and AR-V7—while its subcellular localization shifts from nuclear speckles to cytoplasm under oxidative stress."},"narrative":{"teleology":[{"year":1997,"claim":"Establishing TRA2B as a nuclear SR-like protein that localizes to speckles and interacts with classical SR proteins answered the fundamental question of where and how it fits within the splicing regulatory network.","evidence":"Yeast two-hybrid with SC35 bait, immunofluorescence colocalization, subcellular fractionation in human cells","pmids":["9212162"],"confidence":"Medium","gaps":["Interaction with SR proteins relied on yeast two-hybrid without endogenous co-IP validation","RNA targets unknown at this stage","Functional consequence of speckle localization not tested"]},{"year":2000,"claim":"Demonstrating that TRA2B directly binds an AG-rich exonic splicing enhancer in SMN exon 7 to promote its inclusion resolved the mechanism by which this SR-like protein activates a specific splice event, establishing a paradigm for its RNA-binding specificity.","evidence":"Minigene splicing assay and RNA binding assay in human/mouse cells with SMN2 constructs","pmids":["10931943"],"confidence":"High","gaps":["Structural basis of AG-rich enhancer recognition not resolved","Whether TRA2B is sufficient or requires co-factors for SMN exon 7 inclusion was unclear"]},{"year":2002,"claim":"Showing that SRp30c requires a physical interaction with TRA2B to access the SMN exon 7 enhancer established the cooperative recruitment model whereby TRA2B bridges RNA and additional splicing factors.","evidence":"Reciprocal co-immunoprecipitation and RNA pull-down combined with minigene splicing assay","pmids":["11875052"],"confidence":"High","gaps":["Full composition of the TRA2B-nucleated enhancer complex on SMN exon 7 not defined","Whether this recruitment model generalizes to all TRA2B targets was untested"]},{"year":2009,"claim":"Discovery that oxidative stress triggers TRA2B phosphorylation and nuclear-to-cytoplasmic translocation, altering CD44 splicing and cell growth, revealed that TRA2B activity is dynamically regulated by signaling inputs.","evidence":"Arsenite treatment, immunofluorescence, phospho-Western blot, siRNA/overexpression with CD44 minigene in human cells","pmids":["19439532"],"confidence":"Medium","gaps":["Kinase(s) responsible for stress-induced phosphorylation not identified","Whether cytoplasmic TRA2B has non-splicing functions remains unknown"]},{"year":2010,"claim":"Demonstrating that homozygous Tra2b knockout causes embryonic lethality at E7.5 established the gene as essential for mammalian development and showed its role is not limited to SMN exon 7 splicing.","evidence":"Conditional Cre/loxP knockout mice, embryo phenotyping, RT-PCR of Smn isoforms in MEFs","pmids":["20190275"],"confidence":"High","gaps":["Critical embryonic splicing targets causing lethality not identified","Functional redundancy with TRA2A not systematically tested"]},{"year":2011,"claim":"Identifying LPIN1 as a direct splicing target placed TRA2B upstream of hepatic lipogenesis, showing its role extends to metabolic regulation: reduced TRA2B favors the lipogenic LPIN1β isoform, and epistasis experiments confirmed a linear pathway.","evidence":"siRNA in hepatocytes, Sfrs10 heterozygous mice, VLDL secretion assay, LPIN1β-specific rescue","pmids":["21803291"],"confidence":"High","gaps":["Whether TRA2B directly binds LPIN1 pre-mRNA at the regulated exon was not shown by CLIP","Other metabolic splicing targets of TRA2B not catalogued"]},{"year":2014,"claim":"Cortex-specific and neuron-specific Tra2b knockouts revealed that TRA2B is required for neural progenitor survival, with its loss causing massive apoptosis linked to p21 upregulation, and identified endogenous brain splicing targets (Tubulin δ1, Shugoshin-like 2).","evidence":"Nestin-Cre and cortex-specific Cre conditional KO, exon arrays, TUNEL, immunohistochemistry, p21 Western blot","pmids":["23818142","24586484"],"confidence":"High","gaps":["Whether p21 upregulation is a direct or indirect consequence of mis-splicing not resolved","Specific splicing events driving apoptosis not individually validated by rescue"]},{"year":2014,"claim":"Direct RNA-immunoprecipitation and binding-site mutagenesis on PKCδ exon 9 established that TRA2B directly promotes PKCδI inclusion required for preadipocyte mitotic clonal expansion, broadening its target repertoire to adipogenesis.","evidence":"RNA-IP, site-directed mutagenesis of TRA2B binding sites, minigene, siRNA, 3T3-L1 proliferation assay","pmids":["25261467"],"confidence":"High","gaps":["Genome-wide binding map in adipocytes not available","Contribution of TRA2A to this event not assessed"]},{"year":2015,"claim":"Tra2b knockdown in Xenopus caused somitogenesis failure recapitulated by a single intron-retaining Wnt11b isoform, providing the first in vivo demonstration that a single TRA2B-regulated splice event is sufficient to account for a developmental phenotype.","evidence":"Morpholino knockdown, RNA-seq of 142 splice changes, dominant-negative intron-retaining Wnt11b construct in Xenopus embryos","pmids":["25620705"],"confidence":"High","gaps":["Whether mammalian somitogenesis similarly depends on TRA2B-Wnt11b axis is untested","Mechanism by which TRA2B suppresses intron retention in Wnt11b not detailed"]},{"year":2019,"claim":"Identification of a G-quadruplex in the TRA2B promoter and its regulation by hnRNPA1 revealed a transcriptional control layer: G4 formation suppresses TRA2B transcription, and hnRNPA1 binding relieves this repression.","evidence":"Circular dichroism, EMSA, ChIP, promoter reporter assay, siRNA knockdown of hnRNPA1/hnRNPU","pmids":["31311954"],"confidence":"High","gaps":["Physiological contexts in which G4-mediated regulation is activated not defined","Whether G4 dynamics contribute to tissue-specific TRA2B expression unknown"]},{"year":2022,"claim":"Germline loss-of-function variants in TRA2B were shown to shift isoform balance toward the dominant-negative Tra2β-3 form, which interferes with CHEK1 exon 3 inclusion, establishing the molecular basis of a neurodevelopmental syndrome.","evidence":"Patient RNA-seq, Western blot of isoform ratios, HEK-293 transfection with isoform-specific GFP constructs and CHEK1 minigene","pmids":["36549593"],"confidence":"High","gaps":["Full spectrum of mis-spliced targets in patient neurons not catalogued","Whether the neurodevelopmental phenotype is primarily driven by CHEK1 mis-splicing or broader splicing dysregulation is unclear"]},{"year":2025,"claim":"Disruption of the ultra-conserved poison exon that mediates TRA2B autoregulation via NMD caused azoospermia through meiotic prophase apoptosis driven by toxic Tra2β accumulation, demonstrating that precise dosage control is essential for spermatogenesis.","evidence":"CRISPR-mediated poison exon deletion in mice, histology, RNA-seq, Tra2β protein quantification","pmids":["39748121"],"confidence":"High","gaps":["Meiotic splicing targets dysregulated by Tra2β overaccumulation not individually validated","Whether poison-exon disruption affects other tissues at subclinical levels unknown"]},{"year":2026,"claim":"Identification of TRA2B as a selective mRNA interactor promoting AR-V7 splice variant synthesis in prostate cancer connected its splicing activity to castration-resistant prostate cancer growth.","evidence":"CasRx-based mRNA interactor screen, siRNA knockdown, cell growth assay, CRPC transcriptomic correlation","pmids":["41919500"],"confidence":"Medium","gaps":["Direct RNA binding site on AR pre-mRNA not mapped","In vivo validation in prostate cancer models lacking","Therapeutic window for TRA2B attenuation not defined"]},{"year":null,"claim":"A genome-wide direct binding map (CLIP/eCLIP) across multiple tissues, a structural understanding of TRA2B enhancer recognition, and systematic delineation of functional redundancy with TRA2A remain major unresolved questions.","evidence":"","pmids":[],"confidence":"High","gaps":["No published CLIP-seq binding atlas for TRA2B across tissues","No crystal or cryo-EM structure of TRA2B-RNA complex","Systematic TRA2A/TRA2B double-knockout studies not reported"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,3,10,18]},{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[0,6,7,10,11,15,17]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[3,15]}],"localization":[{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[1,2,4]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,2,13]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[4]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,3,6,7,10,11,15,17,18]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[5,8,9,11]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[14]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[12,18]}],"complexes":[],"partners":["SRSF1","SRSF10","SRP30C","TRA2A","HNRNPA1","ILDR1","ILDR2","SC35"],"other_free_text":[]},"mechanistic_narrative":"TRA2B (Tra2β) is an SR-like RNA-binding protein that governs alternative splicing by recognizing AG/GAA-rich exonic splicing enhancers and recruiting additional SR proteins such as SRp30c to promote exon inclusion [PMID:10931943, PMID:11875052]. Its protein concentration is homeostatically controlled by a poison-exon/nonsense-mediated decay autoregulatory loop whose disruption causes meiotic catastrophe and azoospermia, while homozygous loss results in early embryonic lethality and cortex-specific deletion triggers neural progenitor apoptosis [PMID:39748121, PMID:20190275, PMID:23818142]. TRA2B directs tissue-specific splicing programs with broad physiological impact—hepatic LPIN1 isoform balance controlling lipogenesis, PKCδ splicing during adipogenesis, Wnt11b intron retention in somitogenesis, and AR-V7 generation in prostate cancer—and germline loss-of-function variants that shift isoform ratios toward a dominant-negative Tra2β-3 form cause a neurodevelopmental syndrome linked to defective CHEK1 exon 3 inclusion [PMID:21803291, PMID:25261467, PMID:25620705, PMID:41919500, PMID:36549593]."},"prefetch_data":{"uniprot":{"accession":"P62995","full_name":"Transformer-2 protein homolog beta","aliases":["Splicing factor, arginine/serine-rich 10","Transformer-2 protein homolog B"],"length_aa":288,"mass_kda":33.7,"function":"Sequence-specific RNA-binding protein which participates in the control of pre-mRNA splicing. Can either activate or suppress exon inclusion. Acts additively with RBMX to promote exon 7 inclusion of the survival motor neuron SMN2. Activates the splicing of MAPT/Tau exon 10. Alters pre-mRNA splicing patterns by antagonizing the effects of splicing regulators, like RBMX. Binds to the AG-rich SE2 domain in the SMN exon 7 RNA. Binds to pre-mRNA","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/P62995/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/TRA2B","classification":"Common Essential","n_dependent_lines":768,"n_total_lines":1208,"dependency_fraction":0.6357615894039735},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CPSF6","stoichiometry":10.0},{"gene":"PRPF4B","stoichiometry":10.0},{"gene":"SNRPA","stoichiometry":10.0},{"gene":"SNRPC","stoichiometry":10.0},{"gene":"SNRPF","stoichiometry":10.0},{"gene":"SSRP1","stoichiometry":10.0},{"gene":"TNPO3","stoichiometry":10.0},{"gene":"TOP1","stoichiometry":10.0},{"gene":"DDX21","stoichiometry":4.0},{"gene":"RBM39","stoichiometry":4.0}],"url":"https://opencell.sf.czbiohub.org/search/TRA2B","total_profiled":1310},"omim":[{"mim_id":"621421","title":"RAMOND-ELLIOTT NEURODEVELOPMENTAL SYNDROME; RAMELN","url":"https://www.omim.org/entry/621421"},{"mim_id":"617283","title":"YTH DOMAIN-CONTAINING PROTEIN 1; YTHDC1","url":"https://www.omim.org/entry/617283"},{"mim_id":"612883","title":"MENARCHE, AGE AT, QUANTITATIVE TRAIT LOCUS 3; MENAQ3","url":"https://www.omim.org/entry/612883"},{"mim_id":"612882","title":"MENARCHE, AGE AT, QUANTITATIVE TRAIT LOCUS 2; MENAQ2","url":"https://www.omim.org/entry/612882"},{"mim_id":"606447","title":"RNA-BINDING PROTEIN S1; RNPS1","url":"https://www.omim.org/entry/606447"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoplasm","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TRA2B"},"hgnc":{"alias_symbol":["Htra2-beta","PPP1R156"],"prev_symbol":["SFRS10"]},"alphafold":{"accession":"P62995","domains":[{"cath_id":"3.30.70.330","chopping":"128-192","consensus_level":"high","plddt":89.4155,"start":128,"end":192}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P62995","model_url":"https://alphafold.ebi.ac.uk/files/AF-P62995-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P62995-F1-predicted_aligned_error_v6.png","plddt_mean":57.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TRA2B","jax_strain_url":"https://www.jax.org/strain/search?query=TRA2B"},"sequence":{"accession":"P62995","fasta_url":"https://rest.uniprot.org/uniprotkb/P62995.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P62995/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P62995"}},"corpus_meta":[{"pmid":"10931943","id":"PMC_10931943","title":"Htra2-beta 1 stimulates an exonic splicing enhancer and can restore full-length SMN expression to survival motor neuron 2 (SMN2).","date":"2000","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/10931943","citation_count":274,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"21803291","id":"PMC_21803291","title":"Expression of the splicing factor gene SFRS10 is reduced in human obesity and contributes to enhanced lipogenesis.","date":"2011","source":"Cell metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/21803291","citation_count":135,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11875052","id":"PMC_11875052","title":"SRp30c-dependent stimulation of survival motor neuron (SMN) exon 7 inclusion is facilitated by a direct interaction with hTra2 beta 1.","date":"2002","source":"Human molecular 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biology","url":"https://pubmed.ncbi.nlm.nih.gov/9212162","citation_count":72,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"22456266","id":"PMC_22456266","title":"The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B.","date":"2012","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/22456266","citation_count":55,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"20190275","id":"PMC_20190275","title":"Deficiency of the splicing factor Sfrs10 results in early embryonic lethality in mice and has no impact on full-length SMN/Smn splicing.","date":"2010","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/20190275","citation_count":52,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"31311954","id":"PMC_31311954","title":"HnRNPA1 interacts with G-quadruplex in the TRA2B promoter and stimulates its transcription in human colon cancer 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     \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"SRp30c stimulates SMN exon 7 inclusion through a direct protein-protein interaction with hTra2-beta1, not by directly binding SMN exon 7 RNA; SRp30c requires the hTra2-beta1 binding site on the AG-rich ESE to associate with the exon.\",\n      \"method\": \"Minigene splicing assay, co-immunoprecipitation, direct interaction assays between SRp30c and hTra2-beta1\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal interaction confirmed, mechanistic requirement shown by mutation of binding site, replicated across methods\",\n      \"pmids\": [\"11875052\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"Htra2-beta1 is a nuclear protein that colocalizes with SC35 in a speckled pattern and interacts with several SR proteins; a second isoform htra2-beta2 generated by alternative splicing produces a truncated protein lacking an SR domain.\",\n      \"method\": \"Yeast two-hybrid screen using SC35 as bait, immunofluorescence colocalization with SC35, RT-PCR isoform analysis\",\n      \"journal\": \"DNA and cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — subcellular localization by direct imaging, yeast two-hybrid for interactions, but no reciprocal Co-IP\",\n      \"pmids\": [\"9212162\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"Htra2-beta3, a tissue-specific isoform lacking the first SR domain, localizes to the nucleus and interacts with a subset of SR proteins; five distinct RNA isoforms are generated from the SFRS10/TRA2B gene by alternative splicing.\",\n      \"method\": \"RT-PCR isoform analysis, yeast two-hybrid, in vivo interaction assay, nuclear localization by subcellular fractionation/imaging\",\n      \"journal\": \"Genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — nuclear localization directly shown, SR protein interactions confirmed in yeast and in vivo, single lab\",\n      \"pmids\": [\"9790768\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Oxidative stress (arsenite treatment) induces translocation of Tra2beta from the nucleus to the cytoplasm accompanied by enhanced phosphorylation; knockdown of Tra2beta facilitates skipping of the central variable region of CD44 pre-mRNA and suppresses cell growth, while overexpression stimulates combinatorial inclusion of multiple CD44 variable exons.\",\n      \"method\": \"siRNA knockdown, overexpression, immunofluorescence for subcellular localization, RT-PCR for CD44 splicing, cell growth assays\",\n      \"journal\": \"American journal of physiology. Cell physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct localization experiment tied to functional consequence, KD/OE with defined splicing and growth phenotype, single lab\",\n      \"pmids\": [\"19439532\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Ubiquitous homozygous deletion of Sfrs10 in mice causes early embryonic lethality around E7.5; conditional deletion in mouse embryonic fibroblasts increases SmnDelta7 levels without affecting full-length Smn, and motor neuron-specific deletion causes no SMA phenotype, indicating Sfrs10 is essential for embryogenesis but has limited impact on FL-SMN splicing in vivo.\",\n      \"method\": \"Conditional Cre/loxP knockout mouse, Hb9-Cre motor neuron-specific deletion, RT-PCR for Smn isoforms, MEF-based recombinant Cre deletion\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean genetic KO with defined in vivo phenotype, multiple conditional alleles tested, strong evidence\",\n      \"pmids\": [\"20190275\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"SFRS10 (TRA2B) regulates alternative splicing of LPIN1; reduced SFRS10 favors the lipogenic LPIN1β isoform, promoting hepatic lipogenesis and increased VLDL secretion; LPIN1β-specific siRNA abolishes the lipogenic effects of SFRS10 knockdown.\",\n      \"method\": \"siRNA knockdown in hepatocytes, Sfrs10 heterozygous mice, RT-PCR for LPIN1 isoforms, VLDL secretion assay, plasma triglyceride measurement\",\n      \"journal\": \"Cell metabolism\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — epistasis shown by LPIN1β rescue, confirmed in both cell and mouse models, replicated across two systems\",\n      \"pmids\": [\"21803291\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Digitoxin treatment depletes TRA2B (Tra2-β) and SRSF3 (SRp20) from cells, and re-expression of TRA2B after digitoxin treatment restores normal splicing of TRA2B target exons, directly linking TRA2B depletion to digitoxin-induced transcriptome-wide alternative splicing changes.\",\n      \"method\": \"Transcriptome-wide splicing analysis, re-expression rescue experiment, enrichment of TRA2B binding motifs at regulated exons\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — rescue experiment directly links TRA2B to splicing changes, but binding to individual exons not biochemically confirmed\",\n      \"pmids\": [\"22456266\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"TRA2B is required for neural progenitor cell survival during murine cortical neurogenesis; cortex-specific Tra2b deletion causes apoptosis of neural progenitor cells and disorganization of the cortical plate.\",\n      \"method\": \"Cortex-specific Cre/loxP knockout mouse, histology, TUNEL/apoptosis assay\",\n      \"journal\": \"The Journal of comparative neurology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean tissue-specific KO with defined cellular phenotype (apoptosis) confirmed by multiple methods\",\n      \"pmids\": [\"23818142\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Neuronal-specific Tra2b knockout mice die after birth with massive apoptosis in ventricular layers of the cortex; absence of Tra2b alters splicing of Tubulinδ1 and Shugoshin-like2, and increases p21 (cyclin-dependent kinase inhibitor 1a) expression, functionally linked to apoptosis in neuronal precursor cells.\",\n      \"method\": \"Nestin-Cre conditional knockout, exon array (whole brain RNA), immunohistochemistry, NSC34 cell siRNA knockdown, p21 functional analysis\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo KO with defined molecular targets confirmed by functional follow-up in cell lines\",\n      \"pmids\": [\"24586484\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"TRA2B promotes inclusion of PKCδ exon 9 to produce the PKCδI splice variant; RNA-immunoprecipitation confirms TRA2B binding to PKCδI exon 9, and mutagenesis of the binding site abolishes this association and splicing activity; PKCδI is required for mitotic clonal expansion of preadipocytes.\",\n      \"method\": \"Heterologous PKCδ splicing minigene, RNA-immunoprecipitation, mutagenesis of TRA2B binding site, siRNA knockdown, 3T3L1 adipogenesis assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — minigene + mutagenesis + RNA-IP with functional readout, multiple orthogonal methods\",\n      \"pmids\": [\"25261467\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Tra2b knockdown in Xenopus causes defective somitogenesis; Tra2b promotes splicing of Wnt11b such that its loss results in intron retention producing a truncated Wnt11b-short isoform that acts as a dominant-negative ligand inhibiting cardiac gene induction and pronephric tubule formation.\",\n      \"method\": \"Morpholino knockdown in Xenopus, RNA sequencing, minigene intron retention assay, functional rescue/dominant-negative assay\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — RNA-seq identifies splice targets, dominant-negative mechanism tested by recapitulating intron retention, multiple phenotypes linked\",\n      \"pmids\": [\"25620705\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"The TRA2B-DNAH5 gene fusion promotes lung squamous cell carcinoma malignant progression through a SIRT6-ERK1/2-MMP1 signaling axis, and ERK1/2 inhibition with selumetinib suppresses growth of SCC cells expressing this fusion.\",\n      \"method\": \"Exon array analysis, molecular cloning of fusion, functional studies in cancer cells, signaling pathway inhibition\",\n      \"journal\": \"Cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — mechanistic pathway placement by functional studies, single lab but multiple pathway components tested\",\n      \"pmids\": [\"27670699\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"ILDR1 and ILDR2 angulin proteins bind directly to TRA2B (as well as TRA2A and SRSF1), translocate into the nucleus when these splicing factors are present, and affect alternative splicing of TUBD1, IQCB1, and PCDH19.\",\n      \"method\": \"Co-immunoprecipitation, nuclear translocation assay, siRNA knockdown of ILDR1/ILDR2, RT-PCR for splicing targets\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — Co-IP shown, nuclear translocation linked to TRA2B presence, KD phenotype, but single lab\",\n      \"pmids\": [\"28785060\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"hnRNPA1 interacts with G-quadruplex (G4) structures in the TRA2B promoter to facilitate TRA2B transcription; G4 formation suppresses TRA2B transcription, while hnRNPA1 binding to G4 relieves this suppression; hnRNPU also positively regulates TRA2B promoter activity but does not interact with G4.\",\n      \"method\": \"Circular dichroism, EMSA, chromatin immunoprecipitation, minigene exon inclusion assay, promoter-reporter assay, siRNA knockdown\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1-2 — biochemical G4 characterization + ChIP + functional promoter assay, single lab\",\n      \"pmids\": [\"31311954\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Pathogenic variants in the 5' coding region of TRA2B (upstream of an alternative translation start site) decrease expression of the canonical Tra2β-1 isoform and increase the Tra2β-3 isoform, which lacks the N-terminal RS1 domain; increased Tra2β-3 acts as a dominant negative to interfere with CHEK1 exon 3 inclusion, a splicing event normally promoted by Tra2β-1.\",\n      \"method\": \"RNA sequencing and western blot of patient-derived cells, transfection of Tra2β1-GFP and Tra2β3-GFP into HEK-293 cells, CHEK1 exon 3 splicing assay\",\n      \"journal\": \"Genetics in medicine : official journal of the American College of Medical Genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — patient cells plus cellular reconstitution with defined isoforms and functional splicing readout, dominant-negative mechanism validated\",\n      \"pmids\": [\"36549593\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Two isoforms of TRA2B play distinct roles in myogenic differentiation by triggering alternative splicing of TGFBR2, thereby differentially regulating canonical TGF-β signaling cascades.\",\n      \"method\": \"Iso-seq, single-cell RNA-seq, gene-splicing analysis during myogenesis, isoform-specific functional assays\",\n      \"journal\": \"Cell proliferation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — RNA-seq identifies isoform-specific splicing targets with functional pathway linkage, single lab\",\n      \"pmids\": [\"37705195\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Disruption of an ultra-conserved poison exon (PE) in the Tra2b gene in mice increases Tra2b expression to toxic levels, causing catastrophic cell death during meiotic prophase and azoospermia; PE splicing thus homeostically limits Tra2β protein concentration to levels compatible with meiosis.\",\n      \"method\": \"Mouse genetics (PE deletion knock-in), spermatogenesis phenotype analysis, Tra2b mRNA/protein quantification, splicing pattern analysis\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean mouse genetic model with defined meiotic phenotype, mechanistic link between PE splicing, protein levels, and cell death established\",\n      \"pmids\": [\"39748121\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"TRA2B (and its ortholog TRA2A) are direct protein interactors of AR-V7 mRNA in prostate cancer cells; TRA2B facilitates splicing of AR transcripts to produce AR-V7 at the expense of full-length AR; attenuation of TRA2B-mediated splicing diminishes prostate cancer cell growth.\",\n      \"method\": \"RNA-targeting CasRx interactor screen, functional splicing assay, siRNA/inhibitor-mediated attenuation, cell growth assay\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — CasRx-based mRNA interactor identification plus functional splicing and growth readout, single lab\",\n      \"pmids\": [\"41919500\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TRA2B is an SR-like nuclear splicing factor that binds AG-rich/GAA-rich exonic splicing enhancers to promote exon inclusion across diverse pre-mRNA targets (including SMN2, CD44, PKCδI, LPIN1, AR-V7, and TGFBR2); it interacts directly with SR proteins (SRp30c, SC35) and angulin proteins to co-regulate splicing, and its own cellular concentration is homeostatically controlled via a poison exon mechanism that targets excess transcripts for nonsense-mediated decay, with loss of TRA2B causing embryonic lethality and neural progenitor apoptosis, while excess TRA2B protein drives aberrant splicing incompatible with meiotic progression.\"\n}\n```\n\n--- ROUND 2 (R2/R3, augmented corpus) ---\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2000,\n      \"finding\": \"Htra2-beta1 (TRA2B) promotes inclusion of SMN exon 7 by binding an AG-rich exonic splicing enhancer in SMN exon 7, stimulating full-length SMN2 expression in human and mouse cells carrying an SMN2 minigene.\",\n      \"method\": \"Minigene splicing assay in human/mouse cells, RNA binding assay, transient expression\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct RNA binding and functional splicing assay replicated across cell types; foundational paper with 274 citations\",\n      \"pmids\": [\"10931943\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"TRA2B (htra2-beta1) is a nuclear SR-like protein that colocalizes with SC35 in nuclear speckles and interacts with multiple SR proteins; a second isoform, htra2-beta2, generated by alternative splicing lacks the SR domain.\",\n      \"method\": \"Yeast two-hybrid screen using SC35 as bait, immunofluorescence colocalization, subcellular fractionation\",\n      \"journal\": \"DNA and cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — yeast two-hybrid interaction plus direct localization; single lab but multiple methods\",\n      \"pmids\": [\"9212162\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"The TRA2B isoform htra2-beta3 lacks the first SR domain, is expressed predominantly in brain, liver, testis and kidney, localizes to the nucleus, and interacts with a subset of SR proteins, paralleling a variant found in the Drosophila male germline.\",\n      \"method\": \"RT-PCR, yeast two-hybrid, immunofluorescence, radiation hybrid mapping\",\n      \"journal\": \"Genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — localization and interaction confirmed by multiple methods in single study\",\n      \"pmids\": [\"9790768\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"SRp30c stimulates SMN exon 7 inclusion through the same AG-rich enhancer as TRA2B, but does so indirectly via a direct protein–protein interaction with TRA2B; in the absence of the TRA2B binding site on the enhancer, SRp30c fails to associate with SMN exon 7.\",\n      \"method\": \"Minigene splicing assay, co-immunoprecipitation, RNA pull-down\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal co-IP plus functional minigene assay; replicated across studies (121 citations)\",\n      \"pmids\": [\"11875052\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Oxidative stress (arsenite) induces translocation of TRA2B from the nucleus to the cytoplasm associated with enhanced phosphorylation, and TRA2B regulates alternative splicing of CD44 (combinatorial inclusion of variable exons) and controls cell growth.\",\n      \"method\": \"Immunofluorescence, Western blot (phosphorylation), siRNA knockdown, overexpression, minigene/RT-PCR, cell growth assay\",\n      \"journal\": \"American journal of physiology. Cell physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — localization change with functional consequence shown by KD and OE with multiple orthogonal methods\",\n      \"pmids\": [\"19439532\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Homozygous deletion of Sfrs10 (TRA2B) in mice causes early embryonic lethality around E7.5, demonstrating an essential role during mouse embryogenesis; motor-neuron-specific deletion does not produce an SMA phenotype, and Sfrs10 deletion in MEFs increases SmnΔ7 levels modestly but has no impact on full-length Smn splicing.\",\n      \"method\": \"Conditional knockout (Cre/loxP), embryo phenotyping, RT-PCR, MEF-derived cells with recombinant Cre\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo genetic loss-of-function with defined lethal phenotype; multiple conditional alleles tested\",\n      \"pmids\": [\"20190275\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"SFRS10 (TRA2B) regulates alternative splicing of LPIN1 pre-mRNA; reduced SFRS10 favors the lipogenic LPIN1β isoform, and LPIN1β-specific siRNA abolishes the lipogenic effects of decreased SFRS10, placing TRA2B upstream of LPIN1β in hepatic lipogenesis.\",\n      \"method\": \"siRNA knockdown, Sfrs10 heterozygous mice, hepatic gene expression analysis, VLDL secretion assay, epistasis by rescue experiment\",\n      \"journal\": \"Cell metabolism\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis (rescue), in vivo mouse model, and cell-based assays across multiple orthogonal methods; 135 citations\",\n      \"pmids\": [\"21803291\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Digitoxin depletes TRA2B (and SRSF3) from cells; re-expression of TRA2B after digitoxin treatment restores normal splicing of TRA2B-target exons, demonstrating that TRA2B depletion directly mediates the digitoxin-induced alternative splicing changes.\",\n      \"method\": \"Transcriptome-wide splicing analysis (RNA-seq), rescue by re-expression, motif enrichment analysis\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — transcriptome-wide analysis plus rescue experiment establishing direct causality\",\n      \"pmids\": [\"22456266\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"TRA2B is required for survival of neural progenitor cells; cortex-specific Tra2b knockout mice display apoptosis of neural progenitor cells and disorganization of the cortical plate.\",\n      \"method\": \"Cortex-specific conditional knockout (Cre/loxP), immunohistochemistry, TUNEL apoptosis assay\",\n      \"journal\": \"The Journal of comparative neurology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo genetic loss-of-function with defined cellular phenotype (apoptosis of progenitors)\",\n      \"pmids\": [\"23818142\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Neuronal-specific deletion of Tra2b causes massive apoptosis in ventricular layers of the cortex and perinatal lethality; Tra2b loss leads to increased p21 (CDKN1A) expression, which is functionally linked to neuronal precursor cell death. In vivo exon array analysis identifies Tubulinδ1 and Shugoshin-like2 as splicing targets of Tra2b.\",\n      \"method\": \"Nestin-Cre conditional knockout, exon arrays, immunohistochemistry, TUNEL, siRNA in NSC34 cells, Western blot\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo genetic model with defined molecular mechanism (p21 upregulation) and transcriptome-wide target identification\",\n      \"pmids\": [\"24586484\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"TRA2B promotes inclusion of PKCδ exon 9 in the PKCδI splice variant during 3T3L1 preadipocyte cell cycle; mutagenesis of TRA2B binding sites on exon 9 and RNA-immunoprecipitation confirmed direct binding is required for this splicing event, and PKCδI is required for mitotic clonal expansion of preadipocytes.\",\n      \"method\": \"Minigene splicing assay, mutagenesis, RNA-immunoprecipitation, siRNA knockdown, cell proliferation assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — RNA-IP plus mutagenesis of binding site plus functional minigene; direct binding-function link established\",\n      \"pmids\": [\"25261467\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Tra2b knockdown in Xenopus causes defective somitogenesis and other developmental defects; RNA-seq identified 142 Tra2b-dependent splice changes (mostly intron retention and exon skipping). A novel Wnt11b isoform retaining the last intron (Wnt11b-short) acts as a dominant-negative ligand and its retention recapitulates the failure to form somites, placing Tra2b upstream of Wnt11b isoform balance in somitogenesis.\",\n      \"method\": \"Morpholino knockdown, RNA-seq, minigene intron retention induction, dominant-negative rescue experiment in Xenopus\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo knockdown with RNA-seq, functional epistasis by recapitulating specific splice defect\",\n      \"pmids\": [\"25620705\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"A TRA2B-DNAH5 gene fusion in lung squamous cell carcinoma promotes malignant progression through a SIRT6-ERK1/2-MMP1 signaling axis; ERK1/2 inhibition with selumetinib efficiently inhibits growth of lung SCC expressing this fusion.\",\n      \"method\": \"Exon array analysis, molecular cloning of fusion, functional studies (pathway analysis, ERK1/2 inhibition), patient sample analysis\",\n      \"journal\": \"Cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — mechanistic pathway placement via functional studies but fusion-specific context; single lab\",\n      \"pmids\": [\"27670699\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"ILDR1 and ILDR2 (angulin proteins) physically bind to TRA2B (as well as TRA2A and SRSF1) and translocate to the nucleus when TRA2B is present; knockdown of ILDR1/ILDR2 alters alternative splicing of TUBD1 and IQCB1, targets regulated by TRA2B.\",\n      \"method\": \"Co-immunoprecipitation, nuclear translocation assay, siRNA knockdown, minigene splicing assay\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single Co-IP and functional follow-up; interaction with functional consequence demonstrated\",\n      \"pmids\": [\"28785060\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"hnRNPA1 interacts with a G-quadruplex (G4) structure in the TRA2B promoter and stimulates TRA2B transcription; G4 formation suppresses TRA2B transcription, whereas hnRNPA1 binding to G4 relieves this repression. hnRNPU also positively regulates TRA2B promoter activity but does not interact with G4.\",\n      \"method\": \"Circular dichroism, EMSA, ChIP, minigene assay, siRNA knockdown, promoter reporter assay\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — direct G4 binding confirmed by CD and EMSA, ChIP confirms in-cell interaction, multiple orthogonal methods in single study\",\n      \"pmids\": [\"31311954\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Germline loss-of-function variants clustered in the 5′ region of TRA2B (upstream of an alternative translation start site) decrease canonical Tra2β-1 isoform expression while increasing the shorter Tra2β-3 isoform (lacking the N-terminal RS1 domain); increased Tra2β-3 interferes with CHEK1 exon 3 inclusion, revealing a dominant-negative mechanism underlying the associated neurodevelopmental syndrome.\",\n      \"method\": \"RNA sequencing of patient cells, Western blot of isoforms, HEK-293 transfection with Tra2β1-GFP, Tra2β3-GFP, and CHEK1 exon 3 minigene\",\n      \"journal\": \"Genetics in medicine : official journal of the American College of Medical Genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — patient-derived RNA-seq plus functional cell-based isoform experiments establishing dominant-negative mechanism\",\n      \"pmids\": [\"36549593\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Two TRA2B isoforms play distinct roles in myogenic differentiation: they differentially regulate alternative splicing of TGFBR2, thereby triggering canonical TGF-β signalling cascades differently.\",\n      \"method\": \"Iso-seq, single-cell RNA-seq, isoform-specific functional analysis in myogenesis model\",\n      \"journal\": \"Cell proliferation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — isoform-level transcriptomic analysis with functional splicing outcome; single study\",\n      \"pmids\": [\"37705195\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"An ultra-conserved poison exon (PE) in the Tra2b gene controls Tra2β protein concentration via nonsense-mediated decay; disruption of this PE in mice causes azoospermia due to catastrophic apoptotic cell death during meiotic prophase, associated with elevated Tra2β protein levels driving aberrant hyper-responsive splicing patterns. Mitotically active germ cells are spared despite requiring Tra2b function, indicating the PE prevents toxic Tra2β accumulation incompatible with meiotic prophase.\",\n      \"method\": \"Mouse genetics (PE deletion by CRISPR/homologous recombination), histology, RNA-seq, protein expression analysis\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo mouse genetic model with defined molecular mechanism (NMD-based autoregulation) and clear phenotypic readout\",\n      \"pmids\": [\"39748121\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"TRA2B promotes synthesis of the constitutively active androgen receptor splice variant AR-V7 in prostate cancer cells at the expense of full-length AR isoforms; TRA2B and its ortholog TRA2A were identified as selective protein interactors of AR-V7 mRNA, and attenuation of TRA2-mediated splicing diminishes prostate cancer cell growth.\",\n      \"method\": \"RNA-targeting CasRx approach for mRNA interactor identification, siRNA knockdown, cell growth assay, correlation with CRPC transcriptomic data\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — CasRx-based interactor identification plus functional KD with proliferation readout; single study\",\n      \"pmids\": [\"41919500\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TRA2B (SFRS10/Htra2-β1) is an SR-like nuclear RNA-binding protein that promotes exon inclusion by binding AG/GAA-rich exonic splicing enhancers and recruiting additional SR proteins (e.g., SRp30c); its cellular concentration is homeostatically controlled by a poison-exon/NMD autoregulatory loop, and it is essential for embryogenesis, neural progenitor survival, male meiosis, and lipid metabolism by governing tissue-specific alternative splicing programs—including SMN exon 7, LPIN1, PKCδ, CD44, TGFBR2, CHEK1, and AR-V7—while its subcellular localization shifts from nuclear speckles to cytoplasm under oxidative stress.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"TRA2B is an SR-like splicing factor that binds AG-rich exonic splicing enhancers to promote exon inclusion across a broad spectrum of pre-mRNA targets, thereby controlling cell survival, differentiation, and metabolic programs. It directly binds target exons—including SMN2 exon 7, PKCδ exon 9, CD44 variable exons, LPIN1, TGFBR2, and AR-V7—and recruits SR protein co-factors such as SRp30c and SC35 through protein–protein interactions to assemble splicing-competent complexes [PMID:10931943, PMID:11875052, PMID:25261467, PMID:41919500]. Homozygous loss of Tra2b causes embryonic lethality and, in the nervous system, neural progenitor apoptosis with upregulation of p21, while an ultra-conserved poison exon homeostatically limits TRA2B protein levels via nonsense-mediated decay—disruption of this autoregulatory circuit elevates TRA2B to toxic concentrations that block meiotic progression and cause azoospermia [PMID:20190275, PMID:24586484, PMID:39748121]. Pathogenic coding variants that shift usage from the canonical Tra2β-1 isoform to the RS1-domain-lacking Tra2β-3 isoform produce a dominant-negative effect on target exon inclusion, exemplified by impaired CHEK1 exon 3 splicing [PMID:36549593].\",\n  \"teleology\": [\n    {\n      \"year\": 1997,\n      \"claim\": \"Establishing TRA2B as a nuclear SR-like protein: its subnuclear localization to SC35-positive speckles and physical interaction with SR proteins placed it within the spliceosome-associated machinery.\",\n      \"evidence\": \"Yeast two-hybrid with SC35 bait, immunofluorescence colocalization in human cells\",\n      \"pmids\": [\"9212162\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No reciprocal Co-IP to confirm SR protein interactions\", \"Functional consequence of SR protein binding not tested\", \"RNA targets unknown\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Identifying the first direct RNA target and mechanism: TRA2B was shown to bind an AG-rich ESE in SMN2 exon 7 and promote its inclusion, establishing the paradigm that TRA2B recognizes specific exonic sequences to activate splicing.\",\n      \"evidence\": \"Minigene splicing assay in human and mouse cells, RNA binding assay\",\n      \"pmids\": [\"10931943\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of ESE recognition not resolved\", \"In vivo relevance to SMA not yet tested\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Defining the co-factor recruitment mechanism: SRp30c was shown to stimulate SMN exon 7 inclusion not by binding RNA directly but through protein–protein interaction with TRA2B, requiring the TRA2B-bound ESE, establishing TRA2B as a platform for co-factor assembly.\",\n      \"evidence\": \"Co-immunoprecipitation, minigene mutation of TRA2B binding site abolishes SRp30c effect\",\n      \"pmids\": [\"11875052\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether other SR proteins are recruited by the same mechanism unknown\", \"Stoichiometry of the complex undefined\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Extending TRA2B's target repertoire to CD44 and linking it to stress-responsive regulation: oxidative stress caused TRA2B nuclear-to-cytoplasmic translocation with enhanced phosphorylation, while knockdown altered CD44 variable exon splicing and suppressed cell growth.\",\n      \"evidence\": \"siRNA knockdown and overexpression, immunofluorescence, CD44 RT-PCR, cell growth assay\",\n      \"pmids\": [\"19439532\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Kinase(s) responsible for stress-induced phosphorylation not identified\", \"Direct binding to CD44 exons not confirmed biochemically\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Demonstrating in vivo essentiality: ubiquitous Tra2b knockout caused embryonic lethality at ~E7.5, proving TRA2B is indispensable for early development; surprisingly, motor neuron–specific deletion did not phenocopy SMA, indicating redundancy or limited impact on endogenous full-length Smn splicing in vivo.\",\n      \"evidence\": \"Conditional Cre/loxP knockout mice (ubiquitous and Hb9-Cre motor neuron–specific), RT-PCR\",\n      \"pmids\": [\"20190275\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Compensatory role of TRA2A not tested\", \"Critical embryonic splicing targets causing lethality not identified\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Connecting TRA2B to metabolic regulation: reduced TRA2B shifted LPIN1 splicing toward the lipogenic β isoform, increasing hepatic lipogenesis and VLDL secretion, with epistasis confirmed by LPIN1β-specific knockdown.\",\n      \"evidence\": \"siRNA in hepatocytes, Sfrs10 heterozygous mice, LPIN1 isoform RT-PCR, VLDL/triglyceride measurement\",\n      \"pmids\": [\"21803291\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether TRA2B binds LPIN1 pre-mRNA directly not shown\", \"Upstream signals regulating TRA2B in metabolic contexts unknown\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Defining neural-specific requirements: cortex- and neuron-specific Tra2b deletion caused massive apoptosis of neural progenitor cells with altered splicing of Tubulinδ1 and Shugoshin-like2 and upregulation of p21, linking TRA2B-dependent splicing to cell survival during neurogenesis.\",\n      \"evidence\": \"Cortex-specific and Nestin-Cre conditional knockout mice, TUNEL assay, exon array, p21 functional analysis\",\n      \"pmids\": [\"23818142\", \"24586484\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether p21 upregulation is a direct or indirect consequence of mis-splicing not resolved\", \"Full spectrum of neuronal splicing targets not catalogued\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Biochemical validation of direct exon binding: TRA2B was shown by RNA-immunoprecipitation to bind PKCδ exon 9, and mutagenesis of the binding site abolished both association and exon inclusion, providing the most rigorous early demonstration of direct target recognition.\",\n      \"evidence\": \"RNA-IP, PKCδ minigene, binding-site mutagenesis, 3T3-L1 adipogenesis assay\",\n      \"pmids\": [\"25261467\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Consensus binding motif across all targets not fully defined\", \"Crystal structure of TRA2B-RNA complex lacking\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Revealing a dominant-negative splice product mechanism in vivo: Tra2b loss in Xenopus caused intron retention in Wnt11b, producing a truncated dominant-negative ligand that disrupted cardiac gene induction and somitogenesis, showing that TRA2B's absence can generate gain-of-function aberrant proteins.\",\n      \"evidence\": \"Morpholino knockdown in Xenopus, RNA-seq, intron retention minigene, dominant-negative rescue\",\n      \"pmids\": [\"25620705\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Conservation of this mechanism in mammals not tested\", \"Quantitative contribution of Wnt11b-short versus other targets unclear\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Establishing human disease relevance and isoform-specific dominant-negative activity: pathogenic variants shifting expression from canonical Tra2β-1 to the RS1-lacking Tra2β-3 isoform produced dominant-negative interference with CHEK1 exon 3 inclusion, directly linking TRA2B isoform balance to human pathology.\",\n      \"evidence\": \"Patient-derived cell RNA-seq and western blot, Tra2β1-GFP/Tra2β3-GFP transfection in HEK-293, CHEK1 splicing assay\",\n      \"pmids\": [\"36549593\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full clinical phenotype spectrum of TRA2B variants not delineated\", \"Mechanism by which Tra2β-3 antagonizes Tra2β-1 at the molecular level not resolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Revealing the autoregulatory circuit: disruption of an ultra-conserved poison exon in Tra2b eliminated nonsense-mediated decay-based feedback, elevating TRA2B protein to toxic levels that caused meiotic prophase cell death and azoospermia, proving that poison-exon-mediated homeostasis is essential for germ cell viability.\",\n      \"evidence\": \"Mouse poison-exon deletion knock-in, spermatogenesis analysis, Tra2b mRNA/protein quantification\",\n      \"pmids\": [\"39748121\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the same autoregulatory circuit operates in somatic tissues with equivalent stringency unknown\", \"Identity of the sensor that triggers poison exon inclusion at high TRA2B levels not identified\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Identifying TRA2B as a direct regulator of oncogenic AR-V7 splicing: TRA2B was found to bind AR-V7 mRNA and promote its production at the expense of full-length AR in prostate cancer, with TRA2B attenuation reducing cancer cell growth.\",\n      \"evidence\": \"CasRx-based mRNA interactor screen, splicing and growth assays in prostate cancer cells\",\n      \"pmids\": [\"41919500\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct binding site on AR pre-mRNA not mapped\", \"Therapeutic window for TRA2B inhibition in prostate cancer not defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include the structural basis of TRA2B RNA recognition, the degree of functional redundancy with TRA2A across tissues, the identity of the molecular sensor that couples TRA2B protein concentration to poison exon inclusion, and a comprehensive catalog of essential splicing targets that explain embryonic lethality.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No crystal or cryo-EM structure of TRA2B-RNA complex\", \"Systematic TRA2A/TRA2B double-knockout analysis not performed\", \"Sensor mechanism for poison exon autoregulation unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 10, 18]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 6, 10, 11, 15]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [2, 3]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 1, 6, 10, 11, 15, 16, 18]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [8, 9, 17]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [5, 8, 9, 11]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"SRSF1\",\n      \"SRSF7\",\n      \"SRSF10\",\n      \"TRA2A\",\n      \"ILDR1\",\n      \"ILDR2\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```\n\n--- ROUND 2 (R2/R3, augmented corpus) ---\n\n```json\n{\n  \"mechanistic_narrative\": \"TRA2B (Tra2β) is an SR-like RNA-binding protein that governs alternative splicing by recognizing AG/GAA-rich exonic splicing enhancers and recruiting additional SR proteins such as SRp30c to promote exon inclusion [PMID:10931943, PMID:11875052]. Its protein concentration is homeostatically controlled by a poison-exon/nonsense-mediated decay autoregulatory loop whose disruption causes meiotic catastrophe and azoospermia, while homozygous loss results in early embryonic lethality and cortex-specific deletion triggers neural progenitor apoptosis [PMID:39748121, PMID:20190275, PMID:23818142]. TRA2B directs tissue-specific splicing programs with broad physiological impact—hepatic LPIN1 isoform balance controlling lipogenesis, PKCδ splicing during adipogenesis, Wnt11b intron retention in somitogenesis, and AR-V7 generation in prostate cancer—and germline loss-of-function variants that shift isoform ratios toward a dominant-negative Tra2β-3 form cause a neurodevelopmental syndrome linked to defective CHEK1 exon 3 inclusion [PMID:21803291, PMID:25261467, PMID:25620705, PMID:41919500, PMID:36549593].\",\n  \"teleology\": [\n    {\n      \"year\": 1997,\n      \"claim\": \"Establishing TRA2B as a nuclear SR-like protein that localizes to speckles and interacts with classical SR proteins answered the fundamental question of where and how it fits within the splicing regulatory network.\",\n      \"evidence\": \"Yeast two-hybrid with SC35 bait, immunofluorescence colocalization, subcellular fractionation in human cells\",\n      \"pmids\": [\"9212162\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Interaction with SR proteins relied on yeast two-hybrid without endogenous co-IP validation\", \"RNA targets unknown at this stage\", \"Functional consequence of speckle localization not tested\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Demonstrating that TRA2B directly binds an AG-rich exonic splicing enhancer in SMN exon 7 to promote its inclusion resolved the mechanism by which this SR-like protein activates a specific splice event, establishing a paradigm for its RNA-binding specificity.\",\n      \"evidence\": \"Minigene splicing assay and RNA binding assay in human/mouse cells with SMN2 constructs\",\n      \"pmids\": [\"10931943\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of AG-rich enhancer recognition not resolved\", \"Whether TRA2B is sufficient or requires co-factors for SMN exon 7 inclusion was unclear\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Showing that SRp30c requires a physical interaction with TRA2B to access the SMN exon 7 enhancer established the cooperative recruitment model whereby TRA2B bridges RNA and additional splicing factors.\",\n      \"evidence\": \"Reciprocal co-immunoprecipitation and RNA pull-down combined with minigene splicing assay\",\n      \"pmids\": [\"11875052\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full composition of the TRA2B-nucleated enhancer complex on SMN exon 7 not defined\", \"Whether this recruitment model generalizes to all TRA2B targets was untested\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Discovery that oxidative stress triggers TRA2B phosphorylation and nuclear-to-cytoplasmic translocation, altering CD44 splicing and cell growth, revealed that TRA2B activity is dynamically regulated by signaling inputs.\",\n      \"evidence\": \"Arsenite treatment, immunofluorescence, phospho-Western blot, siRNA/overexpression with CD44 minigene in human cells\",\n      \"pmids\": [\"19439532\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Kinase(s) responsible for stress-induced phosphorylation not identified\", \"Whether cytoplasmic TRA2B has non-splicing functions remains unknown\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Demonstrating that homozygous Tra2b knockout causes embryonic lethality at E7.5 established the gene as essential for mammalian development and showed its role is not limited to SMN exon 7 splicing.\",\n      \"evidence\": \"Conditional Cre/loxP knockout mice, embryo phenotyping, RT-PCR of Smn isoforms in MEFs\",\n      \"pmids\": [\"20190275\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Critical embryonic splicing targets causing lethality not identified\", \"Functional redundancy with TRA2A not systematically tested\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Identifying LPIN1 as a direct splicing target placed TRA2B upstream of hepatic lipogenesis, showing its role extends to metabolic regulation: reduced TRA2B favors the lipogenic LPIN1β isoform, and epistasis experiments confirmed a linear pathway.\",\n      \"evidence\": \"siRNA in hepatocytes, Sfrs10 heterozygous mice, VLDL secretion assay, LPIN1β-specific rescue\",\n      \"pmids\": [\"21803291\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether TRA2B directly binds LPIN1 pre-mRNA at the regulated exon was not shown by CLIP\", \"Other metabolic splicing targets of TRA2B not catalogued\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Cortex-specific and neuron-specific Tra2b knockouts revealed that TRA2B is required for neural progenitor survival, with its loss causing massive apoptosis linked to p21 upregulation, and identified endogenous brain splicing targets (Tubulin δ1, Shugoshin-like 2).\",\n      \"evidence\": \"Nestin-Cre and cortex-specific Cre conditional KO, exon arrays, TUNEL, immunohistochemistry, p21 Western blot\",\n      \"pmids\": [\"23818142\", \"24586484\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether p21 upregulation is a direct or indirect consequence of mis-splicing not resolved\", \"Specific splicing events driving apoptosis not individually validated by rescue\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Direct RNA-immunoprecipitation and binding-site mutagenesis on PKCδ exon 9 established that TRA2B directly promotes PKCδI inclusion required for preadipocyte mitotic clonal expansion, broadening its target repertoire to adipogenesis.\",\n      \"evidence\": \"RNA-IP, site-directed mutagenesis of TRA2B binding sites, minigene, siRNA, 3T3-L1 proliferation assay\",\n      \"pmids\": [\"25261467\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Genome-wide binding map in adipocytes not available\", \"Contribution of TRA2A to this event not assessed\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Tra2b knockdown in Xenopus caused somitogenesis failure recapitulated by a single intron-retaining Wnt11b isoform, providing the first in vivo demonstration that a single TRA2B-regulated splice event is sufficient to account for a developmental phenotype.\",\n      \"evidence\": \"Morpholino knockdown, RNA-seq of 142 splice changes, dominant-negative intron-retaining Wnt11b construct in Xenopus embryos\",\n      \"pmids\": [\"25620705\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether mammalian somitogenesis similarly depends on TRA2B-Wnt11b axis is untested\", \"Mechanism by which TRA2B suppresses intron retention in Wnt11b not detailed\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identification of a G-quadruplex in the TRA2B promoter and its regulation by hnRNPA1 revealed a transcriptional control layer: G4 formation suppresses TRA2B transcription, and hnRNPA1 binding relieves this repression.\",\n      \"evidence\": \"Circular dichroism, EMSA, ChIP, promoter reporter assay, siRNA knockdown of hnRNPA1/hnRNPU\",\n      \"pmids\": [\"31311954\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological contexts in which G4-mediated regulation is activated not defined\", \"Whether G4 dynamics contribute to tissue-specific TRA2B expression unknown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Germline loss-of-function variants in TRA2B were shown to shift isoform balance toward the dominant-negative Tra2β-3 form, which interferes with CHEK1 exon 3 inclusion, establishing the molecular basis of a neurodevelopmental syndrome.\",\n      \"evidence\": \"Patient RNA-seq, Western blot of isoform ratios, HEK-293 transfection with isoform-specific GFP constructs and CHEK1 minigene\",\n      \"pmids\": [\"36549593\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full spectrum of mis-spliced targets in patient neurons not catalogued\", \"Whether the neurodevelopmental phenotype is primarily driven by CHEK1 mis-splicing or broader splicing dysregulation is unclear\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Disruption of the ultra-conserved poison exon that mediates TRA2B autoregulation via NMD caused azoospermia through meiotic prophase apoptosis driven by toxic Tra2β accumulation, demonstrating that precise dosage control is essential for spermatogenesis.\",\n      \"evidence\": \"CRISPR-mediated poison exon deletion in mice, histology, RNA-seq, Tra2β protein quantification\",\n      \"pmids\": [\"39748121\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Meiotic splicing targets dysregulated by Tra2β overaccumulation not individually validated\", \"Whether poison-exon disruption affects other tissues at subclinical levels unknown\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Identification of TRA2B as a selective mRNA interactor promoting AR-V7 splice variant synthesis in prostate cancer connected its splicing activity to castration-resistant prostate cancer growth.\",\n      \"evidence\": \"CasRx-based mRNA interactor screen, siRNA knockdown, cell growth assay, CRPC transcriptomic correlation\",\n      \"pmids\": [\"41919500\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct RNA binding site on AR pre-mRNA not mapped\", \"In vivo validation in prostate cancer models lacking\", \"Therapeutic window for TRA2B attenuation not defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"A genome-wide direct binding map (CLIP/eCLIP) across multiple tissues, a structural understanding of TRA2B enhancer recognition, and systematic delineation of functional redundancy with TRA2A remain major unresolved questions.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No published CLIP-seq binding atlas for TRA2B across tissues\", \"No crystal or cryo-EM structure of TRA2B-RNA complex\", \"Systematic TRA2A/TRA2B double-knockout studies not reported\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 3, 10, 18]},\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [0, 6, 7, 10, 11, 15, 17]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [3, 15]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [1, 2, 4]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 2, 13]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 3, 6, 7, 10, 11, 15, 17, 18]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [5, 8, 9, 11]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [14]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [12, 18]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"SRSF1\",\n      \"SRSF10\",\n      \"SRp30c\",\n      \"TRA2A\",\n      \"hnRNPA1\",\n      \"ILDR1\",\n      \"ILDR2\",\n      \"SC35\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}