{"gene":"UBL4B","run_date":"2026-04-28T21:43:00","timeline":{"discoveries":[{"year":2006,"finding":"UBL4B is a testis-specific autosomal retrogene that arose from the X-linked housekeeping gene UBL4A by retroposition during mammalian evolution; it lacks introns and its expression is restricted to post-meiotic germ cells (spermatids), whereas UBL4A is expressed throughout spermatogenesis.","method":"Expression analysis (RT-PCR, in situ hybridization), phylogenetic/genomic sequence analysis","journal":"Gene expression patterns : GEP","confidence":"Medium","confidence_rationale":"Tier 2 — direct expression profiling with genomic characterization, single lab","pmids":["16872915"],"is_preprint":false},{"year":2021,"finding":"Ubl4b knockout mice generated by CRISPR/Cas9 display normal spermatogenesis and reproductive parameters; double knockout of both Ubl4a and Ubl4b also results in normal spermatogenesis, demonstrating that UBL4B (and UBL4A) are dispensable for spermatogenesis in vivo.","method":"CRISPR/Cas9 knockout, reproductive phenotyping of single and double knockout mice","journal":"Frontiers in genetics","confidence":"High","confidence_rationale":"Tier 2 — clean in vivo KO with defined cellular phenotype, single and double KO with consistent results","pmids":["34249105"],"is_preprint":false},{"year":2023,"finding":"MAEL directly binds to UBL4B in human spermatozoa, and loss of MAEL correlates with reduced UBL4B protein levels; UBL4B was identified as a downstream target of MAEL by bioinformatics and co-expression analysis, and both are reduced in asthenozoospermic sperm.","method":"Bioinformatics target prediction, immunogold staining, siRNA knockdown of MAEL, protein correlation analysis","journal":"Andrology","confidence":"Low","confidence_rationale":"Tier 3 — binding inferred from bioinformatics and expression correlation; direct binding not biochemically reconstituted","pmids":["36779514"],"is_preprint":false}],"current_model":"UBL4B is a testis-specific, intronless retrogene derived from X-linked UBL4A by retroposition, restricted in expression to post-meiotic germ cells (round spermatids); despite encoding a ubiquitin-like protein, both UBL4B and its paralog UBL4A are dispensable for spermatogenesis in mice, and UBL4B has been identified as a putative downstream target of the MAEL–mitochondria axis in human sperm, though its precise molecular function remains uncharacterized."},"narrative":{"teleology":[{"year":2006,"claim":"Establishing UBL4B as a retrogene with germ-cell-restricted expression answered how a ubiquitin-like gene acquired testis specificity — through retroposition from the broadly expressed X-linked UBL4A, followed by transcriptional restriction to post-meiotic spermatids.","evidence":"RT-PCR, in situ hybridization, and phylogenomic analysis in mouse testis","pmids":["16872915"],"confidence":"Medium","gaps":["No biochemical activity assigned to the UBL4B protein","Whether UBL4B protein is conjugated to substrates like canonical ubiquitin-like modifiers is unknown","Expression data from a single lab; independent confirmation in additional species not provided"]},{"year":2021,"claim":"Single and double knockout experiments resolved whether UBL4B (and UBL4A) are required for spermatogenesis — neither is essential, indicating functional redundancy with other pathways or a non-essential reproductive role.","evidence":"CRISPR/Cas9-generated Ubl4b−/− and Ubl4a−/−;Ubl4b−/− mice with comprehensive reproductive phenotyping","pmids":["34249105"],"confidence":"High","gaps":["No stress or fertility-challenge conditions tested that might reveal conditional phenotypes","Molecular partners and biochemical activity of UBL4B remain unidentified","Whether UBL4B contributes to sperm function post-fertilization was not assessed"]},{"year":2023,"claim":"Correlation and knockdown data positioned UBL4B as a putative downstream target of the piRNA pathway component MAEL in human sperm, linking it to the mitochondrial sheath, though direct physical interaction was not biochemically reconstituted.","evidence":"Bioinformatics target prediction, immunogold staining, siRNA knockdown of MAEL, and protein correlation analysis in human spermatozoa","pmids":["36779514"],"confidence":"Low","gaps":["Direct MAEL–UBL4B binding has not been demonstrated by reconstituted biochemical assay (e.g., pull-down with purified proteins)","Causal role of UBL4B reduction in asthenozoospermia not established","Mechanism by which MAEL regulates UBL4B protein levels is unknown"]},{"year":null,"claim":"The molecular activity of UBL4B — whether it functions as a ubiquitin-like modifier conjugated to substrates, an adaptor, or has another role — remains entirely uncharacterized.","evidence":"","pmids":[],"confidence":"Low","gaps":["No substrate or conjugation target identified","No structural model available","No interaction partners validated by reciprocal biochemical methods"]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":[],"other_free_text":[]},"mechanistic_narrative":"UBL4B is a testis-specific, intronless autosomal retrogene that arose from the X-linked housekeeping gene UBL4A by retroposition during mammalian evolution, with expression restricted to post-meiotic germ cells (round spermatids) [PMID:16872915]. Despite encoding a ubiquitin-like domain protein, CRISPR/Cas9 knockout of Ubl4b alone or in combination with Ubl4a yields normal spermatogenesis and fertility in mice, demonstrating that both paralogs are dispensable for male germ cell development in vivo [PMID:34249105]. The precise molecular function of UBL4B remains uncharacterized."},"prefetch_data":{"uniprot":{"accession":"Q8N7F7","full_name":"Ubiquitin-like protein 4B","aliases":[],"length_aa":174,"mass_kda":19.9,"function":"","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q8N7F7/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/UBL4B","classification":"Not Classified","n_dependent_lines":33,"n_total_lines":1208,"dependency_fraction":0.027317880794701987},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/UBL4B","total_profiled":1310},"omim":[{"mim_id":"611127","title":"UBIQUITIN-LIKE 4B; UBL4B","url":"https://www.omim.org/entry/611127"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"testis","ntpm":104.2}],"url":"https://www.proteinatlas.org/search/UBL4B"},"hgnc":{"alias_symbol":["FLJ25690"],"prev_symbol":[]},"alphafold":{"accession":"Q8N7F7","domains":[{"cath_id":"3.10.20.90","chopping":"3-72","consensus_level":"high","plddt":89.7869,"start":3,"end":72},{"cath_id":"-","chopping":"91-141","consensus_level":"high","plddt":82.7149,"start":91,"end":141}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N7F7","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N7F7-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N7F7-F1-predicted_aligned_error_v6.png","plddt_mean":75.38},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=UBL4B","jax_strain_url":"https://www.jax.org/strain/search?query=UBL4B"},"sequence":{"accession":"Q8N7F7","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8N7F7.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8N7F7/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N7F7"}},"corpus_meta":[{"pmid":"19333399","id":"PMC_19333399","title":"Spermatogenesis associated retrogenes are expressed in the human ovary and ovarian cancers.","date":"2009","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/19333399","citation_count":24,"is_preprint":false},{"pmid":"16872915","id":"PMC_16872915","title":"Ubl4b, an X-derived retrogene, is specifically expressed in post-meiotic germ cells in mammals.","date":"2006","source":"Gene expression patterns : GEP","url":"https://pubmed.ncbi.nlm.nih.gov/16872915","citation_count":17,"is_preprint":false},{"pmid":"29936662","id":"PMC_29936662","title":"Progression Rate Associated Peripheral Blood Biomarkers of Parkinson's Disease.","date":"2018","source":"Journal of molecular neuroscience : MN","url":"https://pubmed.ncbi.nlm.nih.gov/29936662","citation_count":11,"is_preprint":false},{"pmid":"22139977","id":"PMC_22139977","title":"Generation of mice with conditional null allele for GdX/Ubl4A.","date":"2012","source":"Genesis (New York, N.Y. : 2000)","url":"https://pubmed.ncbi.nlm.nih.gov/22139977","citation_count":7,"is_preprint":false},{"pmid":"34249105","id":"PMC_34249105","title":"The Dispensable Roles of X-Linked Ubl4a and Its Autosomal Counterpart Ubl4b in Spermatogenesis Represent a New Evolutionary Type of X-Derived Retrogenes.","date":"2021","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/34249105","citation_count":1,"is_preprint":false},{"pmid":"36779514","id":"PMC_36779514","title":"The MAEL expression in mitochondria of human spermatozoa and the association with asthenozoospermia.","date":"2023","source":"Andrology","url":"https://pubmed.ncbi.nlm.nih.gov/36779514","citation_count":1,"is_preprint":false},{"pmid":"40428403","id":"PMC_40428403","title":"Genetic Determinants of Colonic Diverticulosis-A Systematic Review.","date":"2025","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/40428403","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4891,"output_tokens":774,"usd":0.013142},"stage2":{"model":"claude-opus-4-6","input_tokens":3959,"output_tokens":1028,"usd":0.068242},"total_usd":0.081384,"stage1_batch_id":"msgbatch_01RPbVc9PDH9zQmYK5Hs6srm","stage2_batch_id":"msgbatch_01JVbVLzeKN2yVrsGp3zC8aM","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2006,\n      \"finding\": \"UBL4B is a testis-specific autosomal retrogene that arose from the X-linked housekeeping gene UBL4A by retroposition during mammalian evolution; it lacks introns and its expression is restricted to post-meiotic germ cells (spermatids), whereas UBL4A is expressed throughout spermatogenesis.\",\n      \"method\": \"Expression analysis (RT-PCR, in situ hybridization), phylogenetic/genomic sequence analysis\",\n      \"journal\": \"Gene expression patterns : GEP\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct expression profiling with genomic characterization, single lab\",\n      \"pmids\": [\"16872915\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Ubl4b knockout mice generated by CRISPR/Cas9 display normal spermatogenesis and reproductive parameters; double knockout of both Ubl4a and Ubl4b also results in normal spermatogenesis, demonstrating that UBL4B (and UBL4A) are dispensable for spermatogenesis in vivo.\",\n      \"method\": \"CRISPR/Cas9 knockout, reproductive phenotyping of single and double knockout mice\",\n      \"journal\": \"Frontiers in genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean in vivo KO with defined cellular phenotype, single and double KO with consistent results\",\n      \"pmids\": [\"34249105\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"MAEL directly binds to UBL4B in human spermatozoa, and loss of MAEL correlates with reduced UBL4B protein levels; UBL4B was identified as a downstream target of MAEL by bioinformatics and co-expression analysis, and both are reduced in asthenozoospermic sperm.\",\n      \"method\": \"Bioinformatics target prediction, immunogold staining, siRNA knockdown of MAEL, protein correlation analysis\",\n      \"journal\": \"Andrology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — binding inferred from bioinformatics and expression correlation; direct binding not biochemically reconstituted\",\n      \"pmids\": [\"36779514\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"UBL4B is a testis-specific, intronless retrogene derived from X-linked UBL4A by retroposition, restricted in expression to post-meiotic germ cells (round spermatids); despite encoding a ubiquitin-like protein, both UBL4B and its paralog UBL4A are dispensable for spermatogenesis in mice, and UBL4B has been identified as a putative downstream target of the MAEL–mitochondria axis in human sperm, though its precise molecular function remains uncharacterized.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"UBL4B is a testis-specific, intronless autosomal retrogene that arose from the X-linked housekeeping gene UBL4A by retroposition during mammalian evolution, with expression restricted to post-meiotic germ cells (round spermatids) [PMID:16872915]. Despite encoding a ubiquitin-like domain protein, CRISPR/Cas9 knockout of Ubl4b alone or in combination with Ubl4a yields normal spermatogenesis and fertility in mice, demonstrating that both paralogs are dispensable for male germ cell development in vivo [PMID:34249105]. The precise molecular function of UBL4B remains uncharacterized.\",\n  \"teleology\": [\n    {\n      \"year\": 2006,\n      \"claim\": \"Establishing UBL4B as a retrogene with germ-cell-restricted expression answered how a ubiquitin-like gene acquired testis specificity — through retroposition from the broadly expressed X-linked UBL4A, followed by transcriptional restriction to post-meiotic spermatids.\",\n      \"evidence\": \"RT-PCR, in situ hybridization, and phylogenomic analysis in mouse testis\",\n      \"pmids\": [\"16872915\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No biochemical activity assigned to the UBL4B protein\",\n        \"Whether UBL4B protein is conjugated to substrates like canonical ubiquitin-like modifiers is unknown\",\n        \"Expression data from a single lab; independent confirmation in additional species not provided\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Single and double knockout experiments resolved whether UBL4B (and UBL4A) are required for spermatogenesis — neither is essential, indicating functional redundancy with other pathways or a non-essential reproductive role.\",\n      \"evidence\": \"CRISPR/Cas9-generated Ubl4b−/− and Ubl4a−/−;Ubl4b−/− mice with comprehensive reproductive phenotyping\",\n      \"pmids\": [\"34249105\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No stress or fertility-challenge conditions tested that might reveal conditional phenotypes\",\n        \"Molecular partners and biochemical activity of UBL4B remain unidentified\",\n        \"Whether UBL4B contributes to sperm function post-fertilization was not assessed\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Correlation and knockdown data positioned UBL4B as a putative downstream target of the piRNA pathway component MAEL in human sperm, linking it to the mitochondrial sheath, though direct physical interaction was not biochemically reconstituted.\",\n      \"evidence\": \"Bioinformatics target prediction, immunogold staining, siRNA knockdown of MAEL, and protein correlation analysis in human spermatozoa\",\n      \"pmids\": [\"36779514\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Direct MAEL–UBL4B binding has not been demonstrated by reconstituted biochemical assay (e.g., pull-down with purified proteins)\",\n        \"Causal role of UBL4B reduction in asthenozoospermia not established\",\n        \"Mechanism by which MAEL regulates UBL4B protein levels is unknown\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular activity of UBL4B — whether it functions as a ubiquitin-like modifier conjugated to substrates, an adaptor, or has another role — remains entirely uncharacterized.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No substrate or conjugation target identified\",\n        \"No structural model available\",\n        \"No interaction partners validated by reciprocal biochemical methods\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [],\n    \"complexes\": [],\n    \"partners\": [],\n    \"other_free_text\": []\n  }\n}\n```"}